Query psy2882
Match_columns 1428
No_of_seqs 1059 out of 5540
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 19:18:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2882hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2925 SbcB Exonuclease I [DN 100.0 6E-133 1E-137 1107.9 42.2 460 310-779 8-473 (475)
2 PRK11779 sbcB exonuclease I; P 100.0 6E-107 1E-111 975.3 50.1 462 310-780 5-472 (476)
3 PF08411 Exonuc_X-T_C: Exonucl 100.0 2.4E-67 5.3E-72 595.7 22.5 262 514-779 1-268 (269)
4 PRK14976 5'-3' exonuclease; Pr 100.0 2.9E-62 6.3E-67 557.5 27.1 267 777-1048 6-281 (281)
5 PRK09482 flap endonuclease-lik 100.0 2E-61 4.4E-66 538.8 23.5 239 777-1020 6-248 (256)
6 smart00475 53EXOc 5'-3' exonuc 100.0 1.3E-60 2.8E-65 538.1 24.6 243 777-1020 4-252 (259)
7 TIGR00593 pola DNA polymerase 100.0 1.2E-58 2.6E-63 594.1 25.6 266 778-1048 3-276 (887)
8 cd00008 53EXOc 5'-3' exonuclea 100.0 2.4E-55 5.1E-60 492.5 24.6 234 777-1011 4-240 (240)
9 PRK05755 DNA polymerase I; Pro 100.0 4.4E-54 9.5E-59 560.9 26.7 267 777-1048 5-277 (880)
10 COG0258 Exo 5'-3' exonuclease 100.0 1E-48 2.2E-53 455.6 21.2 271 776-1048 13-291 (310)
11 COG1678 Putative transcription 100.0 1.1E-46 2.5E-51 394.4 16.8 182 1072-1266 11-193 (194)
12 PHA00439 exonuclease 100.0 1.3E-46 2.9E-51 421.7 18.3 196 778-984 10-220 (286)
13 PRK00228 hypothetical protein; 100.0 1.5E-45 3.2E-50 397.9 16.8 184 1071-1266 7-190 (191)
14 PHA02567 rnh RnaseH; Provision 100.0 4.3E-39 9.3E-44 362.1 17.8 181 776-963 16-209 (304)
15 PF02622 DUF179: Uncharacteriz 100.0 3.1E-39 6.7E-44 341.6 11.6 160 1082-1254 1-161 (161)
16 PTZ00217 flap endonuclease-1; 100.0 1.1E-37 2.4E-42 370.0 18.0 257 770-1048 23-319 (393)
17 TIGR00158 L9 ribosomal protein 100.0 1.3E-37 2.9E-42 321.3 14.5 138 174-311 1-138 (148)
18 TIGR03674 fen_arch flap struct 100.0 1.7E-37 3.7E-42 363.6 16.4 243 776-1048 23-312 (338)
19 CHL00160 rpl9 ribosomal protei 100.0 7.8E-37 1.7E-41 316.1 14.1 138 172-311 4-143 (153)
20 PF02739 5_3_exonuc_N: 5'-3' e 100.0 4E-37 8.6E-42 327.0 10.4 158 777-935 4-169 (169)
21 PRK00137 rplI 50S ribosomal pr 100.0 3.4E-36 7.4E-41 311.4 15.3 137 174-311 1-137 (147)
22 COG0359 RplI Ribosomal protein 100.0 5.4E-36 1.2E-40 304.4 13.7 136 174-310 1-136 (148)
23 PRK03980 flap endonuclease-1; 100.0 8.4E-35 1.8E-39 333.4 18.1 223 796-1048 1-265 (292)
24 cd06138 ExoI_N N-terminal DEDD 100.0 7.8E-33 1.7E-37 299.3 18.5 183 314-497 1-183 (183)
25 COG3737 Uncharacterized conser 100.0 3.4E-33 7.3E-38 267.0 7.7 123 1303-1427 3-127 (127)
26 cd00128 XPG Xeroderma pigmento 100.0 4.1E-32 8.9E-37 317.7 15.6 250 777-1048 27-306 (316)
27 cd05560 Xcc1710_like Xcc1710_l 100.0 3.3E-31 7E-36 261.6 13.6 109 1317-1426 1-109 (109)
28 cd00248 Mth938-like Mth938-lik 100.0 7.4E-31 1.6E-35 259.4 13.0 108 1317-1426 1-109 (109)
29 cd05125 Mth938_2P1-like Mth938 100.0 2.4E-30 5.2E-35 256.1 13.6 111 1316-1428 1-113 (114)
30 PF04430 DUF498: Protein of un 100.0 2.1E-29 4.6E-34 250.0 10.5 108 1318-1426 1-110 (110)
31 PRK14538 putative bifunctional 100.0 3.5E-29 7.7E-34 319.0 13.9 138 172-311 687-825 (838)
32 cd05126 Mth938 Mth938 domain. 100.0 2.4E-28 5.3E-33 243.4 13.0 106 1318-1425 2-115 (117)
33 PRK07942 DNA polymerase III su 99.9 1.3E-26 2.9E-31 259.5 18.3 175 311-506 6-183 (232)
34 PRK06310 DNA polymerase III su 99.9 3.8E-25 8.3E-30 250.1 20.4 201 311-550 7-207 (250)
35 PRK09146 DNA polymerase III su 99.9 7.7E-25 1.7E-29 245.7 19.9 177 311-502 47-226 (239)
36 PRK06309 DNA polymerase III su 99.9 6E-25 1.3E-29 246.3 18.6 195 311-546 2-196 (232)
37 KOG3363|consensus 99.9 1.7E-25 3.8E-30 224.1 11.1 124 1304-1428 45-172 (196)
38 PRK09145 DNA polymerase III su 99.9 5.2E-24 1.1E-28 234.1 19.3 173 311-503 29-201 (202)
39 PF01367 5_3_exonuc: 5'-3' exo 99.9 6.9E-27 1.5E-31 226.0 -3.0 100 937-1040 1-101 (101)
40 cd06134 RNaseT DEDDh 3'-5' exo 99.9 4.3E-24 9.3E-29 232.3 18.5 171 312-502 6-188 (189)
41 TIGR00573 dnaq exonuclease, DN 99.9 7.5E-24 1.6E-28 235.3 20.1 173 311-507 7-181 (217)
42 PRK07740 hypothetical protein; 99.9 7.6E-24 1.6E-28 238.8 18.1 166 311-502 59-225 (244)
43 PRK05168 ribonuclease T; Provi 99.9 1.1E-23 2.3E-28 232.9 18.6 174 311-504 17-202 (211)
44 TIGR01298 RNaseT ribonuclease 99.9 9.4E-24 2E-28 231.5 17.9 174 311-504 8-193 (200)
45 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 5.7E-24 1.2E-28 229.0 15.1 160 313-498 1-176 (177)
46 PRK06063 DNA polymerase III su 99.9 9.9E-24 2.1E-28 245.6 18.0 164 311-502 15-178 (313)
47 PRK08517 DNA polymerase III su 99.9 1.9E-23 4.2E-28 236.4 19.7 166 311-505 68-233 (257)
48 TIGR01406 dnaQ_proteo DNA poly 99.9 3E-23 6.6E-28 231.2 18.9 173 312-507 1-176 (225)
49 PRK05711 DNA polymerase III su 99.9 3.7E-23 8.1E-28 231.7 19.6 174 310-506 3-179 (240)
50 cd06131 DNA_pol_III_epsilon_Ec 99.9 8.1E-23 1.8E-27 217.6 18.5 163 313-499 1-166 (167)
51 smart00479 EXOIII exonuclease 99.9 1.3E-22 2.8E-27 215.4 19.5 165 312-502 1-166 (169)
52 PRK06807 DNA polymerase III su 99.9 1.4E-22 3E-27 235.5 19.1 165 311-503 8-172 (313)
53 PRK07883 hypothetical protein; 99.9 2.9E-22 6.3E-27 249.3 21.2 182 297-505 3-184 (557)
54 COG0238 RpsR Ribosomal protein 99.9 1.5E-23 3.3E-28 186.4 4.1 70 110-179 5-74 (75)
55 PRK06195 DNA polymerase III su 99.9 6.1E-22 1.3E-26 231.0 18.5 163 311-502 1-163 (309)
56 PRK07247 DNA polymerase III su 99.9 1.2E-21 2.5E-26 213.5 18.2 191 310-538 4-194 (195)
57 PRK05601 DNA polymerase III su 99.9 2.4E-21 5.3E-26 223.9 20.0 173 311-502 46-248 (377)
58 PRK05359 oligoribonuclease; Pr 99.9 1.3E-21 2.8E-26 211.2 16.3 163 311-502 3-174 (181)
59 cd06130 DNA_pol_III_epsilon_li 99.9 2.8E-21 6E-26 203.1 17.2 154 313-496 1-154 (156)
60 PRK07748 sporulation inhibitor 99.9 3.9E-21 8.5E-26 212.2 18.4 168 311-502 4-179 (207)
61 PRK08074 bifunctional ATP-depe 99.9 2.9E-21 6.4E-26 254.1 19.1 166 311-503 3-169 (928)
62 PRK09182 DNA polymerase III su 99.9 4.9E-21 1.1E-25 220.6 18.3 171 311-514 37-213 (294)
63 TIGR01407 dinG_rel DnaQ family 99.9 3.8E-21 8.3E-26 251.9 18.7 166 312-504 1-166 (850)
64 cd06133 ERI-1_3'hExo_like DEDD 99.9 8.6E-21 1.9E-25 203.2 17.6 168 313-499 1-175 (176)
65 cd06127 DEDDh DEDDh 3'-5' exon 99.9 5.5E-21 1.2E-25 199.1 15.5 157 314-496 1-158 (159)
66 COG2176 PolC DNA polymerase II 99.9 9.3E-22 2E-26 244.7 11.2 165 311-502 421-585 (1444)
67 cd06135 Orn DEDDh 3'-5' exonuc 99.9 4.2E-21 9.1E-26 206.1 14.8 161 313-501 1-170 (173)
68 TIGR01405 polC_Gram_pos DNA po 99.9 7.7E-21 1.7E-25 250.5 19.5 165 311-502 190-354 (1213)
69 KOG2519|consensus 99.9 2.8E-21 6E-26 224.9 13.5 254 775-1048 29-315 (449)
70 PRK07246 bifunctional ATP-depe 99.8 1.2E-20 2.6E-25 244.4 19.0 165 310-503 6-170 (820)
71 PRK07983 exodeoxyribonuclease 99.8 5.7E-20 1.2E-24 203.7 18.0 177 313-545 2-183 (219)
72 cd06137 DEDDh_RNase DEDDh 3'-5 99.8 2.1E-20 4.5E-25 198.4 10.1 150 314-496 1-160 (161)
73 PRK06722 exonuclease; Provisio 99.8 5.6E-19 1.2E-23 201.1 19.2 169 310-500 4-178 (281)
74 TIGR00165 S18 ribosomal protei 99.8 1.3E-20 2.8E-25 168.9 4.4 63 117-179 2-64 (70)
75 PRK00391 rpsR 30S ribosomal pr 99.8 1.6E-20 3.5E-25 172.1 4.8 69 111-179 5-73 (79)
76 PRK13401 30S ribosomal protein 99.8 2.4E-20 5.2E-25 170.6 4.8 65 115-179 8-72 (82)
77 COG0360 RpsF Ribosomal protein 99.8 6.3E-20 1.4E-24 180.0 7.1 86 1-86 21-106 (112)
78 PRK13400 30S ribosomal protein 99.8 4.3E-20 9.3E-25 182.4 5.7 89 109-197 11-101 (147)
79 cd06149 ISG20 DEDDh 3'-5' exon 99.8 4.9E-19 1.1E-23 187.1 10.4 149 314-497 1-157 (157)
80 PF00929 RNase_T: Exonuclease; 99.8 1.2E-19 2.7E-24 189.4 4.5 162 314-496 1-164 (164)
81 COG0847 DnaQ DNA polymerase II 99.8 7.8E-18 1.7E-22 190.3 19.0 167 311-502 13-181 (243)
82 cd06144 REX4_like DEDDh 3'-5' 99.8 1.8E-18 3.8E-23 182.0 11.4 149 314-497 1-152 (152)
83 KOG4607|consensus 99.8 1.4E-18 3.1E-23 183.0 9.0 134 169-308 44-182 (222)
84 cd06145 REX1_like DEDDh 3'-5' 99.8 3.4E-18 7.4E-23 179.4 11.5 146 314-497 1-150 (150)
85 PRK00448 polC DNA polymerase I 99.8 8E-18 1.7E-22 224.5 17.6 165 311-502 419-583 (1437)
86 PF01281 Ribosomal_L9_N: Ribos 99.7 3.7E-19 8E-24 148.2 2.8 48 174-221 1-48 (48)
87 CHL00123 rps6 ribosomal protei 99.7 2.1E-18 4.5E-23 167.2 8.3 72 1-72 26-97 (97)
88 TIGR00166 S6 ribosomal protein 99.7 4.1E-18 8.9E-23 164.3 8.3 73 1-73 20-92 (93)
89 PTZ00315 2'-phosphotransferase 99.7 1.4E-16 3.1E-21 194.0 19.7 180 311-503 56-255 (582)
90 PRK00453 rpsF 30S ribosomal pr 99.7 1.6E-17 3.4E-22 164.7 8.9 84 1-84 22-105 (108)
91 CHL00077 rps18 ribosomal prote 99.7 4.4E-18 9.5E-23 157.0 3.9 63 115-179 12-74 (86)
92 PRK14074 rpsF 30S ribosomal pr 99.7 1.5E-17 3.3E-22 177.7 7.2 85 1-87 168-252 (257)
93 cd00080 HhH2_motif Helix-hairp 99.7 1.3E-17 2.7E-22 154.3 5.4 73 934-1008 2-74 (75)
94 TIGR00600 rad2 DNA excision re 99.7 1.6E-16 3.5E-21 204.3 16.3 180 857-1048 772-974 (1034)
95 PF01250 Ribosomal_S6: Ribosom 99.7 1.3E-16 2.8E-21 153.7 7.5 71 2-72 22-92 (92)
96 PF03948 Ribosomal_L9_C: Ribos 99.7 3.7E-16 7.9E-21 148.5 9.8 76 235-311 1-77 (87)
97 COG1949 Orn Oligoribonuclease 99.6 2.9E-15 6.3E-20 152.4 10.9 165 310-502 5-177 (184)
98 PF01084 Ribosomal_S18: Riboso 99.5 5.1E-15 1.1E-19 127.1 2.9 50 130-179 4-53 (54)
99 KOG2518|consensus 99.4 6.5E-13 1.4E-17 156.8 12.7 200 774-983 24-254 (556)
100 KOG3242|consensus 99.4 5.1E-13 1.1E-17 137.1 8.9 164 311-501 26-197 (208)
101 smart00279 HhH2 Helix-hairpin- 99.4 1.6E-13 3.6E-18 108.2 3.3 36 939-974 1-36 (36)
102 COG1504 Uncharacterized conser 99.3 3.1E-12 6.8E-17 122.0 9.5 106 1318-1425 4-117 (121)
103 KOG4708|consensus 99.2 1E-11 2.2E-16 123.7 5.3 104 2-106 24-134 (141)
104 KOG2520|consensus 99.0 2.2E-09 4.7E-14 135.1 13.8 196 839-1048 448-666 (815)
105 KOG3162|consensus 99.0 3E-10 6.6E-15 117.7 3.3 72 114-185 60-132 (159)
106 cd05160 DEDDy_DNA_polB_exo DED 98.8 3.3E-08 7.2E-13 108.7 13.7 145 314-484 2-167 (199)
107 KOG2249|consensus 98.4 2E-06 4.3E-11 95.4 12.2 155 312-501 106-264 (280)
108 cd05781 DNA_polB_B3_exo DEDDy 98.3 2.3E-06 4.9E-11 93.6 9.9 122 312-478 4-144 (188)
109 cd06143 PAN2_exo DEDDh 3'-5' e 98.2 4.2E-06 9.1E-11 89.4 9.3 133 329-497 32-174 (174)
110 KOG0542|consensus 98.2 1.7E-05 3.7E-10 87.4 13.2 170 311-502 56-241 (280)
111 PF13482 RNase_H_2: RNase_H su 98.1 9.5E-06 2.1E-10 86.3 9.4 147 314-513 1-148 (164)
112 cd06125 DnaQ_like_exo DnaQ-lik 98.1 1E-05 2.3E-10 78.9 8.8 68 314-424 1-69 (96)
113 cd05780 DNA_polB_Kod1_like_exo 98.1 3E-05 6.5E-10 85.4 13.5 131 312-480 4-157 (195)
114 PF00867 XPG_I: XPG I-region; 98.1 2.6E-06 5.7E-11 82.7 4.1 80 867-954 1-94 (94)
115 cd05779 DNA_polB_epsilon_exo D 98.0 7.1E-05 1.5E-09 82.9 13.7 145 312-480 3-170 (204)
116 cd05785 DNA_polB_like2_exo Unc 97.8 0.00011 2.4E-09 81.6 11.4 129 312-479 10-169 (207)
117 cd06139 DNA_polA_I_Ecoli_like_ 97.8 0.00039 8.5E-09 75.6 14.5 142 311-502 5-169 (193)
118 COG5018 KapD Inhibitor of the 97.6 0.0002 4.4E-09 74.5 7.8 168 311-500 4-182 (210)
119 KOG4793|consensus 97.6 0.00015 3.3E-09 80.6 7.2 211 311-550 13-247 (318)
120 KOG4021|consensus 97.5 4.1E-05 8.8E-10 80.6 2.4 63 121-183 109-174 (239)
121 PRK05755 DNA polymerase I; Pro 97.5 0.00065 1.4E-08 90.9 13.9 134 311-502 315-468 (880)
122 COG3359 Predicted exonuclease 97.4 0.0019 4.1E-08 71.5 13.3 160 310-522 97-258 (278)
123 cd05782 DNA_polB_like1_exo Unc 97.4 0.0016 3.4E-08 72.6 12.4 118 318-479 41-170 (208)
124 COG0816 Predicted endonuclease 97.2 5.2E-05 1.1E-09 78.6 -0.9 52 1251-1302 3-57 (141)
125 cd05783 DNA_polB_B1_exo DEDDy 97.0 0.0038 8.2E-08 69.4 10.8 150 312-480 6-172 (204)
126 cd05777 DNA_polB_delta_exo DED 97.0 0.0046 1E-07 70.0 11.7 100 311-424 7-113 (230)
127 PF10108 DNA_pol_B_exo2: Predi 96.9 0.02 4.3E-07 63.5 14.7 143 325-506 6-176 (209)
128 PF04857 CAF1: CAF1 family rib 96.9 0.0025 5.4E-08 73.6 8.0 173 311-497 22-261 (262)
129 KOG2248|consensus 96.7 0.015 3.3E-07 69.9 13.5 152 311-501 216-373 (380)
130 smart00484 XPGI Xeroderma pigm 96.4 0.0064 1.4E-07 56.4 5.7 63 868-936 2-72 (73)
131 PF01612 DNA_pol_A_exo1: 3'-5' 96.3 0.085 1.8E-06 56.2 15.1 136 311-502 20-174 (176)
132 KOG0304|consensus 96.3 0.043 9.2E-07 60.2 12.1 168 320-502 54-238 (239)
133 cd05784 DNA_polB_II_exo DEDDy 96.3 0.033 7.1E-07 61.5 11.7 90 312-425 4-94 (193)
134 PRK05762 DNA polymerase II; Re 96.1 0.099 2.1E-06 69.5 16.6 172 270-478 92-305 (786)
135 smart00485 XPGN Xeroderma pigm 95.9 0.0037 8E-08 61.3 1.9 71 777-850 27-98 (99)
136 PF03652 UPF0081: Uncharacteri 95.8 0.0012 2.6E-08 68.5 -2.1 53 1250-1302 1-55 (135)
137 smart00486 POLBc DNA polymeras 95.6 0.22 4.9E-06 61.7 16.5 102 311-425 3-112 (471)
138 PTZ00166 DNA polymerase delta 95.6 0.11 2.4E-06 70.7 14.6 95 312-421 265-369 (1054)
139 PHA02528 43 DNA polymerase; Pr 95.6 0.1 2.2E-06 69.4 13.6 179 298-499 93-324 (881)
140 PF00752 XPG_N: XPG N-terminal 95.3 0.0055 1.2E-07 60.3 0.6 67 777-846 29-96 (101)
141 PF12826 HHH_2: Helix-hairpin- 95.2 0.012 2.6E-07 53.2 2.2 26 958-983 7-32 (64)
142 PHA02570 dexA exonuclease; Pro 95.1 0.22 4.8E-06 55.4 12.3 101 314-421 4-130 (220)
143 cd05778 DNA_polB_zeta_exo inac 95.1 0.19 4.2E-06 57.1 12.1 104 311-420 4-119 (231)
144 cd00007 35EXOc 3'-5' exonuclea 94.8 0.5 1.1E-05 48.9 13.6 67 385-476 41-107 (155)
145 PHA02524 43A DNA polymerase su 94.7 0.32 6.9E-06 60.7 13.4 115 300-418 95-216 (498)
146 PRK00109 Holliday junction res 94.4 0.0096 2.1E-07 62.1 -0.4 53 1250-1302 4-58 (138)
147 TIGR00250 RNAse_H_YqgF RNAse H 94.2 0.016 3.6E-07 59.8 0.7 50 1253-1302 1-52 (130)
148 PF03104 DNA_pol_B_exo1: DNA p 93.8 0.28 6E-06 58.0 10.1 97 311-421 157-261 (325)
149 PF12813 XPG_I_2: XPG domain c 93.3 0.081 1.8E-06 60.6 4.4 73 859-938 6-100 (246)
150 TIGR03491 RecB family nuclease 93.1 1.1 2.3E-05 56.2 14.2 156 311-513 284-442 (457)
151 PF05991 NYN_YacP: YacP-like N 92.7 0.16 3.5E-06 54.7 5.3 106 779-914 3-111 (166)
152 cd06146 mut-7_like_exo DEDDy 3 92.1 1.2 2.6E-05 49.2 11.3 150 311-500 22-192 (193)
153 TIGR00600 rad2 DNA excision re 91.9 0.068 1.5E-06 71.3 1.5 73 777-853 27-100 (1034)
154 cd05776 DNA_polB_alpha_exo ina 91.3 1.5 3.3E-05 49.9 11.4 42 382-424 81-124 (234)
155 KOG1798|consensus 90.7 1.2 2.6E-05 60.1 10.7 100 311-424 246-359 (2173)
156 cd06141 WRN_exo DEDDy 3'-5' ex 90.5 1.5 3.2E-05 47.1 9.8 130 310-500 17-169 (170)
157 cd06129 RNaseD_like DEDDy 3'-5 90.3 6.4 0.00014 42.0 14.4 129 311-500 13-160 (161)
158 PRK00116 ruvA Holliday junctio 89.8 0.68 1.5E-05 51.2 6.6 24 959-982 78-104 (192)
159 TIGR00592 pol2 DNA polymerase 89.5 7.7 0.00017 54.2 17.7 165 296-477 481-681 (1172)
160 COG0749 PolA DNA polymerase I 88.8 3.1 6.8E-05 52.9 12.0 105 314-475 25-129 (593)
161 PF11074 DUF2779: Domain of un 87.5 1.1 2.4E-05 46.5 5.9 107 314-445 1-117 (130)
162 PF14520 HHH_5: Helix-hairpin- 86.6 0.81 1.8E-05 40.7 3.8 27 957-983 8-35 (60)
163 PF00633 HHH: Helix-hairpin-he 85.5 0.53 1.1E-05 36.2 1.7 17 956-972 13-29 (30)
164 PRK14669 uvrC excinuclease ABC 85.3 0.65 1.4E-05 59.8 3.5 33 956-988 554-587 (624)
165 COG0349 Rnd Ribonuclease D [Tr 85.3 11 0.00023 45.5 13.2 129 311-502 17-165 (361)
166 PRK14670 uvrC excinuclease ABC 84.6 0.78 1.7E-05 58.6 3.7 30 954-983 514-543 (574)
167 TIGR00084 ruvA Holliday juncti 84.2 0.66 1.4E-05 51.2 2.5 70 905-985 31-102 (191)
168 PRK14667 uvrC excinuclease ABC 84.2 0.8 1.7E-05 58.4 3.6 34 955-988 515-549 (567)
169 PRK14605 ruvA Holliday junctio 83.2 0.88 1.9E-05 50.4 3.0 70 904-984 30-102 (194)
170 cd06140 DNA_polA_I_Bacillus_li 82.8 19 0.00042 38.6 13.2 105 312-475 4-108 (178)
171 TIGR01388 rnd ribonuclease D. 82.4 22 0.00047 43.4 14.7 128 311-501 18-164 (367)
172 PF10391 DNA_pol_lambd_f: Fing 82.4 2.1 4.5E-05 37.3 4.3 33 957-989 5-38 (52)
173 PRK14671 uvrC excinuclease ABC 81.8 1.2 2.5E-05 57.8 3.7 27 957-983 572-598 (621)
174 PRK14602 ruvA Holliday junctio 81.6 1 2.2E-05 50.2 2.8 69 906-985 33-104 (203)
175 TIGR00194 uvrC excinuclease AB 81.6 0.98 2.1E-05 57.8 2.9 28 956-983 543-570 (574)
176 PRK14666 uvrC excinuclease ABC 80.1 1.6 3.5E-05 56.4 4.1 29 955-983 638-666 (694)
177 PRK12766 50S ribosomal protein 79.0 2.3 5.1E-05 47.8 4.4 29 955-983 4-33 (232)
178 PRK14601 ruvA Holliday junctio 78.5 1.4 3E-05 48.4 2.4 66 909-985 36-103 (183)
179 PRK10829 ribonuclease D; Provi 78.5 36 0.00079 41.6 14.7 128 311-502 22-169 (373)
180 PRK02515 psbU photosystem II c 78.2 2.1 4.6E-05 44.0 3.5 41 959-1000 66-108 (132)
181 smart00278 HhH1 Helix-hairpin- 77.2 1.5 3.2E-05 32.5 1.5 18 956-973 3-20 (26)
182 cd06142 RNaseD_exo DEDDy 3'-5' 77.1 48 0.001 35.3 13.9 85 390-501 56-158 (178)
183 PRK14600 ruvA Holliday junctio 76.4 2.4 5.2E-05 46.7 3.6 46 931-985 57-103 (186)
184 PRK13901 ruvA Holliday junctio 75.5 1.9 4.2E-05 47.7 2.5 45 932-985 57-102 (196)
185 COG5228 POP2 mRNA deadenylase 74.9 6.6 0.00014 43.4 6.3 185 294-502 56-252 (299)
186 PRK05761 DNA polymerase I; Rev 74.6 16 0.00034 49.0 11.1 111 381-496 208-334 (787)
187 PRK14604 ruvA Holliday junctio 74.5 2.9 6.2E-05 46.4 3.6 70 905-985 31-103 (195)
188 KOG0969|consensus 73.7 2.1 4.5E-05 54.7 2.4 88 312-414 275-370 (1066)
189 PRK14672 uvrC excinuclease ABC 73.0 2.5 5.5E-05 54.5 3.0 33 956-988 610-643 (691)
190 PRK14668 uvrC excinuclease ABC 72.9 2.3 4.9E-05 54.7 2.6 32 953-984 524-555 (577)
191 PRK00558 uvrC excinuclease ABC 72.9 2.4 5.2E-05 54.8 2.9 28 956-983 545-572 (598)
192 TIGR00575 dnlj DNA ligase, NAD 71.9 3.7 8E-05 53.6 4.2 26 958-983 502-527 (652)
193 COG0417 PolB DNA polymerase el 70.2 20 0.00044 48.1 10.7 135 311-478 154-307 (792)
194 smart00474 35EXOc 3'-5' exonuc 69.4 40 0.00087 35.3 10.9 66 387-478 64-130 (172)
195 PRK14606 ruvA Holliday junctio 67.7 5.1 0.00011 44.2 3.6 61 914-985 42-103 (188)
196 PRK14351 ligA NAD-dependent DN 67.1 5.5 0.00012 52.2 4.4 27 957-983 531-557 (689)
197 TIGR00596 rad1 DNA repair prot 64.5 52 0.0011 44.3 12.5 136 809-983 646-786 (814)
198 PRK07956 ligA NAD-dependent DN 64.5 6.1 0.00013 51.7 4.0 26 958-983 515-540 (665)
199 TIGR01259 comE comEA protein. 63.3 7.6 0.00016 39.8 3.7 38 957-995 71-114 (120)
200 PRK14603 ruvA Holliday junctio 63.0 5.2 0.00011 44.5 2.6 69 906-985 32-102 (197)
201 cd00141 NT_POLXc Nucleotidyltr 63.0 7.8 0.00017 46.1 4.2 26 958-984 89-116 (307)
202 PRK14601 ruvA Holliday junctio 62.8 4.2 9.1E-05 44.7 1.8 47 926-974 81-128 (183)
203 PF04599 Pox_G5: Poxvirus G5 p 62.0 17 0.00037 44.5 6.8 117 862-985 148-273 (425)
204 PRK13766 Hef nuclease; Provisi 60.7 9.7 0.00021 51.0 5.0 28 956-983 717-744 (773)
205 PHA03065 Hypothetical protein; 59.7 17 0.00036 44.3 6.1 117 862-985 150-275 (438)
206 TIGR01448 recD_rel helicase, p 59.1 9.7 0.00021 50.5 4.5 39 939-985 77-117 (720)
207 PHA03036 DNA polymerase; Provi 58.5 57 0.0012 44.5 11.3 99 311-416 160-274 (1004)
208 COG0322 UvrC Nuclease subunit 58.5 6.8 0.00015 50.2 2.8 149 825-984 398-560 (581)
209 cd06148 Egl_like_exo DEDDy 3'- 58.1 68 0.0015 35.5 10.3 97 388-502 55-176 (197)
210 PRK13901 ruvA Holliday junctio 58.1 5.6 0.00012 44.1 1.8 36 937-974 92-127 (196)
211 PF02371 Transposase_20: Trans 56.8 7 0.00015 37.5 2.0 25 956-980 4-28 (87)
212 COG1948 MUS81 ERCC4-type nucle 55.7 8.7 0.00019 44.1 2.8 133 801-984 78-212 (254)
213 TIGR00426 competence protein C 54.7 15 0.00033 33.5 3.7 36 959-995 22-63 (69)
214 PRK14600 ruvA Holliday junctio 54.1 8.8 0.00019 42.3 2.5 46 926-974 81-127 (186)
215 PF11798 IMS_HHH: IMS family H 53.9 7.6 0.00017 30.3 1.4 19 956-975 13-31 (32)
216 PRK14606 ruvA Holliday junctio 53.4 6.7 0.00015 43.3 1.4 47 926-974 81-128 (188)
217 TIGR00593 pola DNA polymerase 50.6 40 0.00087 45.9 8.2 66 384-475 364-429 (887)
218 PRK14604 ruvA Holliday junctio 50.3 9.1 0.0002 42.5 1.8 47 926-974 81-128 (195)
219 smart00483 POLXc DNA polymeras 49.2 12 0.00026 45.1 2.8 28 957-985 92-121 (334)
220 COG0632 RuvA Holliday junction 47.7 35 0.00076 38.2 5.8 49 928-985 54-103 (201)
221 PRK14603 ruvA Holliday junctio 47.2 9.4 0.0002 42.5 1.3 47 926-974 80-127 (197)
222 KOG4793|consensus 45.7 28 0.00061 40.1 4.7 106 384-502 179-290 (318)
223 PRK14602 ruvA Holliday junctio 42.3 11 0.00024 42.1 1.0 36 937-974 94-129 (203)
224 PRK08609 hypothetical protein; 41.2 22 0.00047 46.0 3.5 28 958-985 92-121 (570)
225 KOG1602|consensus 39.8 1.3E+02 0.0028 34.8 8.7 66 819-889 34-109 (271)
226 PF01927 Mut7-C: Mut7-C RNAse 39.2 46 0.00099 35.3 5.0 85 859-950 9-98 (147)
227 cd06167 LabA_like LabA_like pr 38.7 53 0.0012 34.2 5.4 55 860-914 55-117 (149)
228 PF01936 NYN: NYN domain; Int 38.0 51 0.0011 33.9 5.1 55 860-914 50-113 (146)
229 COG0272 Lig NAD-dependent DNA 37.6 21 0.00045 46.2 2.4 28 957-984 514-541 (667)
230 COG1555 ComEA DNA uptake prote 37.4 32 0.00069 36.7 3.4 23 959-981 102-130 (149)
231 PF11977 RNase_Zc3h12a: Zc3h12 36.2 79 0.0017 33.7 6.2 99 776-907 4-110 (155)
232 cd07357 HN_L-whirlin_R2_like S 35.3 89 0.0019 29.8 5.4 53 720-778 14-66 (81)
233 COG4081 Uncharacterized protei 34.1 44 0.00096 34.5 3.6 42 1372-1413 6-49 (148)
234 PF14520 HHH_5: Helix-hairpin- 33.7 29 0.00064 30.8 2.1 23 952-974 36-58 (60)
235 cd06147 Rrp6p_like_exo DEDDy 3 32.7 4.9E+02 0.011 28.4 11.9 59 390-475 69-127 (192)
236 PF12826 HHH_2: Helix-hairpin- 32.4 13 0.00028 33.7 -0.4 33 947-979 28-60 (64)
237 KOG1275|consensus 31.4 61 0.0013 43.0 5.0 156 311-500 910-1089(1118)
238 PF05499 DMAP1: DNA methyltran 31.3 31 0.00068 37.5 2.2 30 1388-1417 110-139 (176)
239 PRK13482 DNA integrity scannin 31.2 34 0.00073 41.3 2.7 27 957-983 290-316 (352)
240 PF11731 Cdd1: Pathogenicity l 30.8 49 0.0011 32.5 3.2 24 957-980 15-39 (93)
241 cd09018 DEDDy_polA_RNaseD_like 30.0 2.6E+02 0.0057 28.6 8.9 64 390-478 45-109 (150)
242 PF13052 DUF3913: Protein of u 29.1 29 0.00062 29.3 1.1 23 940-966 9-31 (57)
243 TIGR00084 ruvA Holliday juncti 28.1 46 0.001 36.9 2.9 44 926-971 80-124 (191)
244 PRK14605 ruvA Holliday junctio 28.1 34 0.00074 38.0 1.9 34 938-973 94-127 (194)
245 PF02084 Bindin: Bindin; Inte 27.2 67 0.0015 36.1 3.8 32 627-658 129-163 (238)
246 PRK14350 ligA NAD-dependent DN 26.9 60 0.0013 42.8 4.0 25 958-982 506-531 (669)
247 COG4408 Uncharacterized protei 26.2 57 0.0012 38.8 3.2 42 1373-1414 172-213 (431)
248 PF14579 HHH_6: Helix-hairpin- 24.7 87 0.0019 30.2 3.8 33 956-988 29-66 (90)
249 PRK14837 undecaprenyl pyrophos 23.8 1.4E+02 0.003 34.3 5.7 82 821-909 6-104 (230)
250 PF11097 DUF2883: Protein of u 23.5 43 0.00092 30.3 1.2 20 1205-1224 6-25 (75)
251 PRK00254 ski2-like helicase; P 23.5 63 0.0014 43.1 3.4 27 957-983 648-675 (720)
252 PRK14841 undecaprenyl pyrophos 23.4 1.4E+02 0.0029 34.4 5.5 67 821-892 3-79 (233)
253 TIGR03252 uncharacterized HhH- 22.5 42 0.0009 36.8 1.2 21 956-976 117-137 (177)
254 COG0632 RuvA Holliday junction 22.3 51 0.0011 36.9 1.9 35 938-974 94-128 (201)
255 KOG2841|consensus 21.8 77 0.0017 36.0 3.1 128 838-974 104-247 (254)
256 cd00475 CIS_IPPS Cis (Z)-Isopr 21.6 1.4E+02 0.0031 33.9 5.3 66 822-892 1-76 (221)
257 PF14229 DUF4332: Domain of un 20.6 93 0.002 32.0 3.2 54 960-1014 1-58 (122)
258 KOG0038|consensus 20.4 6.6E+02 0.014 26.9 9.1 136 585-756 30-176 (189)
259 cd01141 TroA_d Periplasmic bin 20.3 1.2E+02 0.0026 32.7 4.3 40 1360-1403 60-99 (186)
No 1
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.2e-133 Score=1107.92 Aligned_cols=460 Identities=40% Similarity=0.726 Sum_probs=451.5
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
..+|+|||+||+|.+|+.||+.|||+||||.++|+|++|.++||+|+.|++|+|+|++|||||||++.++|++|++|+.+
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~~ 87 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAAR 87 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
|+..|++|+||++||||++||+||+|+.|||||+|||.++|+|||||||++|++|+||+|||+||+||.+++|.+|||||
T Consensus 88 I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkLE 167 (475)
T COG2925 88 IHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLE 167 (475)
T ss_pred HHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeeccCcCCCCceEEE
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMW 549 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~~~~~ 549 (1428)
+|+++|||+|.+|||||+||+|||++|++++++||+||+|+|.+|+|+++.++||+.+++|+||||||||+.+||++||+
T Consensus 168 hLt~ANgieH~nAHdAmsDVyATIamAklvk~~QPrLfdy~f~~R~K~~~~~lid~~~~~PlvHVSgm~ga~r~~~s~V~ 247 (475)
T COG2925 168 HLTKANGIEHSNAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQLRKKHKLLALIDIPNMQPLVHVSGMFGAERGNTSWVL 247 (475)
T ss_pred HHhhccccccchhhHHHHHHHHHHHHHHHHHhhCcHHHHHHHHhccHHHHHHHhcccccCceEEeecccchhhCCceEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccCCCCceEEEEeCCCCchhhhcCCHHHHHHHhcccccCCCCC---CCeeEEEecCCccccccccCCChhhhhhhCC
Q psy2882 550 PICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKF 626 (1428)
Q Consensus 550 p~~~~p~~~n~~i~~dL~~d~~~l~~~~~~~l~~~l~~~~~~~~~~---~plk~i~~Nk~P~~~~p~~~l~~~~~~rl~i 626 (1428)
||+|||+|+|++|||||..||++|++|++++|++||||++.+|+|| +|+|.|||||||+ |+|+++|++++++||||
T Consensus 248 PLaWHP~N~NalIv~DL~~Di~~Ll~l~a~~lr~rLyT~~~dL~eg~~~vP~KlvHiNkcPi-lap~ktL~~eda~RlGi 326 (475)
T COG2925 248 PLAWHPTNRNAVIVCDLAGDISPLLELDADTLRERLYTRKADLGEGELAVPVKLVHINKCPI-LAPAKTLRPEDADRLGI 326 (475)
T ss_pred eecccCCCCceEEEEEccCChHHHHhhCHHHHHHHhccccccccCCcccCceEEEEecCCCe-ecchhhcChhhhhhcCC
Confidence 9999999999999999999999999999999999999999999999 8999999999999 99999999999999999
Q ss_pred CHHHHHHHHHhHHhHhhChHHHHHHHHHhhccC-CCCCCChhhhhhcCCCChhHHHHHHHHHcCChhcccccCCCCCccc
Q psy2882 627 DLNCAFKNIKCASSILNNTYIWKKIFLDYKINN-SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKK 705 (1428)
Q Consensus 627 d~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~-~~~~~d~d~~lY~gF~s~~D~~~~~~~~~~~~~~l~~~~~~f~D~R 705 (1428)
|.+.|++|++. |+.+|++++|+.++|++.. |+++.|||++||+||||++||+.|+++|.++|++|+++...|.|+|
T Consensus 327 dr~~c~~~~~~---l~~~p~~rekv~~if~~e~~f~~~~dvd~~LY~GFf~~~Dr~~~~ilR~~~pe~La~~~~~f~D~R 403 (475)
T COG2925 327 DRQHCLDNLEL---LRENPDVREKVVAIFAEEEPFNPSDDVDAQLYNGFFSDADRAAMKILRETEPENLAALDITFVDKR 403 (475)
T ss_pred cHHHHHHHHHH---HhhCchHHHHHHHHHhccccCCCccchhHHHHccccCHHHHHHHHHHHhCChhhhhhccCCccchh
Confidence 99999999999 9999999999999999765 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhcCcc--hHHHHHHHHhhhhh
Q psy2882 706 LEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEH--DTKILNALLMYGKI 779 (1428)
Q Consensus 706 l~~l~fr~~arn~p~~L~~~e~~~w~~~~~~rl~~~~~~~~~~~~~~~~i~~L~~~~~~~--~~~lL~~L~~Y~~i 779 (1428)
|.+|||||||||||+|||.+||++|.+||++||.. ....|...++.+.++++.+ |+.+|++|++|++.
T Consensus 404 l~~LlFrYRARnfp~tLt~~Eq~rW~~~rr~~l~~------~~~~~~~tl~~~~~~~~~d~~k~~lL~~l~~y~~~ 473 (475)
T COG2925 404 LEELLFRYRARNFPETLTDAEQQRWLEHRRQRLTP------ELQGYELTLQALVQEHSDDKEKLALLKALYEYAAE 473 (475)
T ss_pred HHHHHHHHHhhcCccccCHHHHHHHHHHHHHhcCh------hhhhhHHHHHHHHHHhhcchHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999987 3677888888889888888 99999999999975
No 2
>PRK11779 sbcB exonuclease I; Provisional
Probab=100.00 E-value=5.8e-107 Score=975.27 Aligned_cols=462 Identities=40% Similarity=0.742 Sum_probs=447.0
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
..+|||||+||||+||.+|+|||||||+++.++++++++++++|+|..+.+|+|+|+.|||||++++..+|.++.+++.+
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~ 84 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAAR 84 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHH
Confidence 46899999999999999999999999999998888888899999999988889999999999999998899999999999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+++++..+++|+||||+++||++|++++|||+++++|..+|++||++||++|++++++.++|+++.||.+++|.+||||+
T Consensus 85 i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe 164 (476)
T PRK11779 85 IHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLE 164 (476)
T ss_pred HHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHH
Confidence 99999888899999999999999999999999999999999999999999999999999999999999988899999999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeeccCcCCCCceEEE
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMW 549 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~~~~~ 549 (1428)
+||++|||++.+||||++||+||++|+++|+++||+||+|++++|+|+.|++++++.+++|++|+|++||+.+||+++|+
T Consensus 165 ~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~qP~l~~~~~~~~~k~~v~~l~~~~~~~p~~~~s~~fg~~~g~~~~v~ 244 (476)
T PRK11779 165 HLTKANGIEHENAHDAMSDVYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSGMFGAERGCTSWVA 244 (476)
T ss_pred HHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHhChHHHHHHHHhcchHHHHHHhhhhccCCceEEeeecccccCceeEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccCCCCceEEEEeCCCCchhhhcCCHHHHHHHhcccccCCCCC---CCeeEEEecCCccccccccCCChhhhhhhCC
Q psy2882 550 PICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKF 626 (1428)
Q Consensus 550 p~~~~p~~~n~~i~~dL~~d~~~l~~~~~~~l~~~l~~~~~~~~~~---~plk~i~~Nk~P~~~~p~~~l~~~~~~rl~i 626 (1428)
||||||+|+|++|||||+.||++|++|++++|++||||++++|||| +|||.|||||||| |+|+++|++++++||||
T Consensus 245 pl~~hp~n~n~~i~~DL~~d~~~l~~l~~~~l~~~l~~~~~~l~~~~~~~plk~i~~Nk~P~-l~p~~~l~~~~~~rl~~ 323 (476)
T PRK11779 245 PLAWHPTNKNAVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHLNKCPV-LAPAKTLRPEDAERLGI 323 (476)
T ss_pred ccccCCCCCCcEEEEECcCChHHHhcCCHHHHHHHhccChhhccccCCCCCceEEEeCCCCE-ecchhhCCHHHHHHhCC
Confidence 9999999999999999999999999999999999999999999998 8999999999999 99999999999999999
Q ss_pred CHHHHHHHHHhHHhHhhChHHHHHHHHHhhccC-CCCCCChhhhhhcCCCChhHHHHHHHHHcCChhcccccCCCCCccc
Q psy2882 627 DLNCAFKNIKCASSILNNTYIWKKIFLDYKINN-SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKK 705 (1428)
Q Consensus 627 d~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~-~~~~~d~d~~lY~gF~s~~D~~~~~~~~~~~~~~l~~~~~~f~D~R 705 (1428)
|.++|++|+++ |++||+|++|+.++|++.. +.++.|||+|||+||||++||++|++||.++|++|+.+...|+|+|
T Consensus 324 d~~~~~~~~~~---l~~~~~~~~~~~~~~~~~~~~~~~~d~d~~lY~gF~~~~D~~~~~~~~~~~~~~l~~~~~~f~D~R 400 (476)
T PRK11779 324 DRQQCLDNLAL---LRQNPDLREKVVAVFAEAEPFAPSDDVDAQLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPR 400 (476)
T ss_pred cHHHHHHHHHH---HHhCHHHHHHHHHHHhccccCCCCCCHHHHHhCCCCCHHHHHHHHHHHcCCHHHHHhccccCCChh
Confidence 99999999999 9999999999999997533 6777899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhcCcc--hHHHHHHHHhhhhhc
Q psy2882 706 LEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEH--DTKILNALLMYGKID 780 (1428)
Q Consensus 706 l~~l~fr~~arn~p~~L~~~e~~~w~~~~~~rl~~~~~~~~~~~~~~~~i~~L~~~~~~~--~~~lL~~L~~Y~~i~ 780 (1428)
|++|+|||||||||+||+++|+++|++||++||..+ .+++|.++|++|+++++.+ |.+||++|++|++..
T Consensus 401 l~~l~~ry~arn~p~~L~~~e~~~w~~~~~~rl~~~-----~~~~~~~~~~~l~~~~~~~~~~~~~L~~l~~y~~~~ 472 (476)
T PRK11779 401 LEELLFRYRARNFPETLDDEEQQRWLEHRRQRLTPE-----RLQQYAAELEQLAQEYEDDEEKQALLKALYDYAEEL 472 (476)
T ss_pred HHHHHHHHHHccChhhCCHHHHHHHHHHHHHHhccc-----hHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999772 2899999999999999877 889999999999865
No 3
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=100.00 E-value=2.4e-67 Score=595.70 Aligned_cols=262 Identities=31% Similarity=0.505 Sum_probs=205.6
Q ss_pred cCHHHHHHHhCCCCCcceEEEeeccCcCCCCceEEEeeeccCCCCceEEEEeCCCCchhhhcCCHHHHHHHhcccccCCC
Q psy2882 514 RKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFK 593 (1428)
Q Consensus 514 ~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~~~~~p~~~~p~~~n~~i~~dL~~d~~~l~~~~~~~l~~~l~~~~~~~~ 593 (1428)
|+|++|+++|++.+++||+|||+|||+.+||+++|+|||+||+|+|+||||||+.||++|++|++++|++||||+.++||
T Consensus 1 R~K~~v~~lid~~~~~P~lhvS~~~~a~~~~~~~v~Pla~hp~nkN~vI~~DL~~Dp~~l~~l~~eei~~~lft~~~~l~ 80 (269)
T PF08411_consen 1 RDKKAVAKLIDLNSMKPLLHVSGMFGAERGCTSLVLPLAQHPTNKNAVICFDLSSDPEPLLDLSAEEIRERLFTKREDLP 80 (269)
T ss_dssp TSHHHHHHT--TTTT--EEEE-GGG-GGGTTEEEEEEEEE-SS-TTEEEEEETTS--HHHHHS-HHHHHHHHHHTTS---
T ss_pred CCHHHHHHHhCccCCCcEEEecccchhhcCCceEEEeeeeCCCCCCeEEEEECCCCHHHHHcCCHHHHHHHhccChhhhc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC---CCeeEEEecCCccccccccCCChhhhhhhCCCHHHHHHHHHhHHhHhhChHHHHHHHHHhh-ccCCCCCCChhhh
Q psy2882 594 ED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFLDYK-INNSDLELNIDEE 669 (1428)
Q Consensus 594 ~~---~plk~i~~Nk~P~~~~p~~~l~~~~~~rl~id~~~~~~~~~~~~~l~~~~~l~~~~~~~~~-~~~~~~~~d~d~~ 669 (1428)
|| +|||+|||||||| |+|+++|++++++|||||.+.|++|+++ |++|++|++||.++|+ +..+.++.|||++
T Consensus 81 eg~~r~plk~i~iNk~Pv-l~p~~~l~~~~a~rL~iD~~~~~~~~~~---l~~~~~l~~kl~~v~~~~~~~~~~~D~D~~ 156 (269)
T PF08411_consen 81 EGVERLPLKTIHINKCPV-LAPAKVLRPEDAERLGIDRDLCRKNAEL---LRANPDLQEKLQEVFAEERPFPPPTDPDQQ 156 (269)
T ss_dssp -------EEEEETTS--E-EEEGGGS-HHHHHHHT--HHHHHHHHHH---HHH-THHHHHHHHHHC--------S-GGG-
T ss_pred ccccCCCceEEeeCCCCc-cCccccCCHhHHHHcCCcHHHHHHHHHH---HHhCHHHHHHHHHHHhccccCCCCCChhHH
Confidence 99 8999999999999 9999999999999999999999999999 9999999999999999 4447888999999
Q ss_pred hhcCCCChhHHHHHHHHHcCChhcccccCCCCCcccHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcccCCCccccHH
Q psy2882 670 LYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNIN 749 (1428)
Q Consensus 670 lY~gF~s~~D~~~~~~~~~~~~~~l~~~~~~f~D~Rl~~l~fr~~arn~p~~L~~~e~~~w~~~~~~rl~~~~~~~~~~~ 749 (1428)
||+||||++||++|++||+++|++|+++.+.|+|+||++|+|||||||||+|||++|+++|++||++||.++.++++|++
T Consensus 157 LY~GF~s~~Dk~~m~~ir~~~p~~l~~~~~~F~D~RL~eLlfRyraRN~P~tL~~~E~~~W~~~~~~rL~~~~~~~~tl~ 236 (269)
T PF08411_consen 157 LYSGFFSDADKRLMDQIRQASPEQLAELAFNFEDPRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLTDPDGGWLTLE 236 (269)
T ss_dssp GGG----HHHHHHHHHHHHS-GGGSTT-----SSTHHHHHHHHHHHHH-GGG--HHHHHHHHHHHHHHS-HHH-----HH
T ss_pred HHccCCCHHHHHHHHHHHcCCHHHHHhccCCCCChhHHHHHHHHHHhcChhhCCHHHHHHHHHHHHHHccCCccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988777889999
Q ss_pred HHHHHHHHHHhhcCcc--hHHHHHHHHhhhhh
Q psy2882 750 MFYLEIESLLKKANEH--DTKILNALLMYGKI 779 (1428)
Q Consensus 750 ~~~~~i~~L~~~~~~~--~~~lL~~L~~Y~~i 779 (1428)
+|+++|++|++++..+ |++||++|++|++.
T Consensus 237 ~~~~~i~~L~~~~~~~~~~~~lL~~L~~Y~~~ 268 (269)
T PF08411_consen 237 EYFQEIEELRAEYDDDEEKQALLEALEDYAES 268 (269)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHHHHHhc
Confidence 9999999999999887 89999999999974
No 4
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=2.9e-62 Score=557.51 Aligned_cols=267 Identities=40% Similarity=0.604 Sum_probs=253.4
Q ss_pred hhhccchhhhhhhccC----CcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCC
Q psy2882 777 GKIDGSSCIYRAFYAL----PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP 852 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~----~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p 852 (1428)
+-+||++++||+|||. +.++|++|.+|+|++||++++.++++.++|+|++||||+++++||+++||+||+||+++|
T Consensus 6 lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p 85 (281)
T PRK14976 6 LLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKKTP 85 (281)
T ss_pred EEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCCCC
Confidence 4689999999999996 568899999999999999999999999999999999999889999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeC--C---eecc
Q psy2882 853 YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINN--N---KIHD 927 (1428)
Q Consensus 853 ~~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~--~---~~~~ 927 (1428)
++|..|++.++++++++|||++..||+||||+|||+|+++. ..|..|+|+|+||||+||++++|.++.+ . ..++
T Consensus 86 ~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~-~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~ 164 (281)
T PRK14976 86 ESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLS-KQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILN 164 (281)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHH-HCCCeEEEEeCCCCcCccCCCCeEEEEecCCCCcEEEc
Confidence 99999999999999999999999999999999999999874 4578899999999999999999998863 2 4688
Q ss_pred HHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhh
Q psy2882 928 RTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 1007 (1428)
Q Consensus 928 ~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~ 1007 (1428)
.+.|.++||++|+||+||++|+||+|||||||||||||||.+||++|||+|+||+|+++++++++++|+++++.+++|++
T Consensus 165 ~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~~~s~~ 244 (281)
T PRK14976 165 TNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKALLSKK 244 (281)
T ss_pred HHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999998999999999999999999
Q ss_pred hhhccccCCCCCCcCCCccccccCCCCHHHHHHHHHHccCC
Q psy2882 1008 ILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNIP 1048 (1428)
Q Consensus 1008 L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~~~~f~ 1048 (1428)
|+||++|+|++.+ ++++.+.++|.+++.++|+++||+
T Consensus 245 L~~l~~d~~l~~~----l~~~~~~~~~~~~l~~~~~~~e~~ 281 (281)
T PRK14976 245 LATIKTDVPLDFQ----IEDIKLKKLDQPELKKIFEELELK 281 (281)
T ss_pred hhEEeecCCCCCC----HHHhccCCCCHHHHHHHHHHcCCC
Confidence 9999999999987 578888899999999999999985
No 5
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=2e-61 Score=538.84 Aligned_cols=239 Identities=31% Similarity=0.438 Sum_probs=226.9
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCC--cccCCChhhhcCCCCCChH
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKN--FRNILYPSYKATRKKMPYN 854 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~--fR~~l~p~YKa~R~~~p~~ 854 (1428)
+-+||++++||+|||.|+ ++|. |||++||+++|.+++++++|+|++||||+++++ |||++||+||+||+++|++
T Consensus 6 lLiDg~~l~~R~~~a~~~---~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe~ 81 (256)
T PRK09482 6 LIIDALNLIRRIHAVQPS---PNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEA 81 (256)
T ss_pred EEEeCcHHHHHHHhCCCC---CCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcHH
Confidence 458999999999999863 6788 999999999999999999999999999998777 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCC--eeccHHHHH
Q psy2882 855 LILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNN--KIHDRTTII 932 (1428)
Q Consensus 855 l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~--~~~~~~~v~ 932 (1428)
|..|++.|+++++++|||++..|||||||+|||+|+++. +.+.+|+|+|+||||+||++++|+++++. ..++.+.+.
T Consensus 82 l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~-~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~~~~~~~~~~v~ 160 (256)
T PRK09482 82 LQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVA-QAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDAPFIE 160 (256)
T ss_pred HHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHH-HCCCeEEEEECCCCccccCCCCeEEEeccccccCCHHHHH
Confidence 999999999999999999999999999999999999874 45789999999999999999999998743 368999999
Q ss_pred HHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhhcc
Q psy2882 933 SRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIK 1012 (1428)
Q Consensus 933 ~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~i~ 1012 (1428)
++||++|+|++||++|+||+|||||||||||||||.+||++|||+|+||+|+++++++++++|+++++.+++||+|+||+
T Consensus 161 ~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~a~lsr~L~~l~ 240 (256)
T PRK09482 161 QEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLEEHKEMARLCRKLAQLQ 240 (256)
T ss_pred HHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHHHhHHHHHHHHhhheEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCC
Q psy2882 1013 TDCDLTKN 1020 (1428)
Q Consensus 1013 ~d~~l~~~ 1020 (1428)
+|+|++.+
T Consensus 241 ~dv~l~~~ 248 (256)
T PRK09482 241 TDLPLGGN 248 (256)
T ss_pred eCCCCCCC
Confidence 99999876
No 6
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.3e-60 Score=538.10 Aligned_cols=243 Identities=44% Similarity=0.729 Sum_probs=232.3
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHH
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLI 856 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~ 856 (1428)
+-+||++++||+|||.+.++|++|.||||++||++++.++++.++|+|+++|||+++++||+++||+||+||+++|++|.
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe~L~ 83 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPDELL 83 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHHHHhCCCCCCHHHH
Confidence 46899999999999999899999999999999999999999999999999999998899999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCC------eeccHHH
Q psy2882 857 LQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNN------KIHDRTT 930 (1428)
Q Consensus 857 ~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~------~~~~~~~ 930 (1428)
.|++.++++|+++|||++..|||||||+|||||+++.. .|..++|+|+||||+||++++|.++.+. ..++.+.
T Consensus 84 ~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~-~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~ 162 (259)
T smart00475 84 EQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA-EGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPEN 162 (259)
T ss_pred HHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHh-CCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHH
Confidence 99999999999999999999999999999999998643 5789999999999999999999887642 4689999
Q ss_pred HHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhh
Q psy2882 931 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILT 1010 (1428)
Q Consensus 931 v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~ 1010 (1428)
|.++||++|+||+||++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|+++++.+++||+|+|
T Consensus 163 v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~~~~~~~~l~~~~~~~~ls~~L~~ 242 (259)
T smart00475 163 VIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKKLREKLLAHKEDAKLSRKLAT 242 (259)
T ss_pred HHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcHHHHHHhhhhhe
Confidence 99999999999999999999999999999999999999999999999999999999998999999999999999999999
Q ss_pred ccccCCCCCC
Q psy2882 1011 IKTDCDLTKN 1020 (1428)
Q Consensus 1011 i~~d~~l~~~ 1020 (1428)
|++|+|++.+
T Consensus 243 l~~d~~l~~~ 252 (259)
T smart00475 243 IETDVPLEVD 252 (259)
T ss_pred eeeCCCCCCC
Confidence 9999999876
No 7
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.2e-58 Score=594.14 Aligned_cols=266 Identities=41% Similarity=0.603 Sum_probs=253.7
Q ss_pred hhccchhhhhhhccCC--cCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHH
Q psy2882 778 KIDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNL 855 (1428)
Q Consensus 778 ~i~g~~~~~Ra~~a~~--~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l 855 (1428)
-+||++++||+|||+| +++|++|.||||++||++|+.++++.++|+|++||||++++||||++||+||+||+++|++|
T Consensus 3 lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~Pe~l 82 (887)
T TIGR00593 3 LIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPEEL 82 (887)
T ss_pred EEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHHHHHHHHhCCCCChHHH
Confidence 4799999999999997 48899999999999999999999999999999999999989999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCC-----eeccHHH
Q psy2882 856 ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNN-----KIHDRTT 930 (1428)
Q Consensus 856 ~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~-----~~~~~~~ 930 (1428)
..|++.|+++|++||||++..|||||||+|||||+++. +.|.+|+|+|+||||+||++++|.++++. ..++.+.
T Consensus 83 ~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~-~~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~~~~~~~~~~ 161 (887)
T TIGR00593 83 IEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAE-KEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEY 161 (887)
T ss_pred HHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHH-hCCCcEEEEECCCChhhcCCCCEEEEeccCCCCceEEcHHH
Confidence 99999999999999999999999999999999999874 46889999999999999999999998743 3689999
Q ss_pred HHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcch-hhhhhHHHhhhhchhhhhhh
Q psy2882 931 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKKIL 1009 (1428)
Q Consensus 931 v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~-k~~~~l~~~~~~~~~~~~L~ 1009 (1428)
|.++||++|+||+||++|+||+|||||||||||||||.+||++|||+|+||+|++++++ +++++|+++++.+++||+|+
T Consensus 162 v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~a~ls~~L~ 241 (887)
T TIGR00593 162 VVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDAFLSKELA 241 (887)
T ss_pred HHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999976 68999999999999999999
Q ss_pred hccccCCCCCCcCCCccccccCCCCHHHHHHHHHHccCC
Q psy2882 1010 TIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNIP 1048 (1428)
Q Consensus 1010 ~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~~~~f~ 1048 (1428)
||++|+|++.+ ++++.+.++|.+++.++|++|||+
T Consensus 242 ti~~d~~l~~~----~~~~~~~~~~~~~l~~~~~~lef~ 276 (887)
T TIGR00593 242 TIVTDVPLEVD----LEDLRLSEPDRERLYALLQELEFK 276 (887)
T ss_pred eeecCCCCCCC----HHHhccCCCCHHHHHHHHHHhCCc
Confidence 99999999987 477888899999999999999999
No 8
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=100.00 E-value=2.4e-55 Score=492.54 Aligned_cols=234 Identities=49% Similarity=0.792 Sum_probs=223.4
Q ss_pred hhhccchhhhhhhccCCcCcCC-CCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHH
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNI-DNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNL 855 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~-~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l 855 (1428)
+-+||++++||+|||.+.+.++ +|.||+|++||++++.++++.++|+|+++|||+++++||+++||+||+||+++|++|
T Consensus 4 llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p~~l 83 (240)
T cd00008 4 LLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMPEEL 83 (240)
T ss_pred EEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCCHHH
Confidence 4589999999999999877777 899999999999999999999999999999999889999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCC--eeccHHHHHH
Q psy2882 856 ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNN--KIHDRTTIIS 933 (1428)
Q Consensus 856 ~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~--~~~~~~~v~~ 933 (1428)
..|++.++++|+.+|||++..||+||||+|||||+++. ..|..++|+|+||||+||++++|.|+++. +.++.+.+.+
T Consensus 84 ~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~-~~g~~~~I~S~DkD~~ql~~~~v~~~~~~~~~~i~~~~v~~ 162 (240)
T cd00008 84 REQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAE-AEGYKVVIVSGDKDLLQLVSDNVKVVSPMKKKLVTEENVIE 162 (240)
T ss_pred HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHH-HcCCeEEEEeCCCChhhhCCCCEEEEeCCCceEEeHHHHHH
Confidence 99999999999999999999999999999999999874 45789999999999999999999998753 5789999999
Q ss_pred HhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhhc
Q psy2882 934 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTI 1011 (1428)
Q Consensus 934 ~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~i 1011 (1428)
++|++|+|++||++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|+++++.+++|++|+||
T Consensus 163 ~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~~s~~L~~l 240 (240)
T cd00008 163 KYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKGKLREKLEEGKEMAFLSKRLATI 240 (240)
T ss_pred HhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhHHHHHHHHHhHHHHHHHHHhhcC
Confidence 999999999999999999999999999999999999999999999999999999889999999999999999999986
No 9
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=4.4e-54 Score=560.86 Aligned_cols=267 Identities=48% Similarity=0.760 Sum_probs=254.1
Q ss_pred hhhccchhhhhhhccC-CcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHH
Q psy2882 777 GKIDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNL 855 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~-~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l 855 (1428)
+-+||++++||+|||. +.+++++|.||||++||++++.++++.++|+|++||||+++++||+++||+||+||+++|++|
T Consensus 5 ~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~p~~l 84 (880)
T PRK05755 5 LLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMPEDL 84 (880)
T ss_pred EEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCCccccccCHHHhCCCCCCcHHH
Confidence 4689999999999998 678899999999999999999999999999999999999889999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeC-----CeeccHHH
Q psy2882 856 ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINN-----NKIHDRTT 930 (1428)
Q Consensus 856 ~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~-----~~~~~~~~ 930 (1428)
..|++.++++|+.+|||++..|||||||+|||||+++. ..|..|+|+|+||||+||++++|+++.+ ...++.+.
T Consensus 85 ~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~-~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~~~~~~~~~~~ 163 (880)
T PRK05755 85 REQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAE-AAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEE 163 (880)
T ss_pred HHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHH-hCCCcEEEEcCCCChhhhCCCCEEEeeccCCCCCeEEcHHH
Confidence 99999999999999999999999999999999999874 4578999999999999999999998874 34688999
Q ss_pred HHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhh
Q psy2882 931 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILT 1010 (1428)
Q Consensus 931 v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~ 1010 (1428)
|.++||++|+||+||++|+||+|||||||||||||||.+||++|||+|+||+++++++++++++|+++++.+++|++|++
T Consensus 164 v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~ls~~l~~ 243 (880)
T PRK05755 164 VVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAFLSRKLAT 243 (880)
T ss_pred HHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhchHHHHHHHHhHHHHHhhhhhhe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCcCCCccccccCCCCHHHHHHHHHHccCC
Q psy2882 1011 IKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNIP 1048 (1428)
Q Consensus 1011 i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~~~~f~ 1048 (1428)
|++|+|++.+ ++++.+.++|.++|.++|+++||+
T Consensus 244 l~~d~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~ 277 (880)
T PRK05755 244 IKTDVPLEVD----LEDLELQPPDREKLIALFKELEFK 277 (880)
T ss_pred eeeCCCCCCC----HHHhccCCCCHHHHHHHHHHhCcH
Confidence 9999999876 477888899999999999999999
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-48 Score=455.63 Aligned_cols=271 Identities=39% Similarity=0.552 Sum_probs=249.8
Q ss_pred hhhhccchhhhhhhccCCc-CcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCC-CCh
Q psy2882 776 YGKIDGSSCIYRAFYALPD-IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK-MPY 853 (1428)
Q Consensus 776 Y~~i~g~~~~~Ra~~a~~~-l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~-~p~ 853 (1428)
.+.+||++++||+|||++. +.++.|.+||+++||..++.++++..+|+|+++|||+++++||+++|++||++|.+ +|+
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~ 92 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMPD 92 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCHH
Confidence 3568999999999999975 78899999999999999999999999999999999999999999999999999999 999
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCCe-----eccH
Q psy2882 854 NLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNK-----IHDR 928 (1428)
Q Consensus 854 ~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~~-----~~~~ 928 (1428)
+|..|++.+++++.++|++++..+|+||||+|||+|+++. +.|..+.|+|+|||++||+++++.+++..+ .++.
T Consensus 93 ~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~-~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~~~~ 171 (310)
T COG0258 93 ELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY-KKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDL 171 (310)
T ss_pred HHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH-hcCCeEEEEeCCcchhhhcCCCcEEEeccCCCCcccCCH
Confidence 9999999999999999999999999999999999999875 678999999999999999999988887433 2588
Q ss_pred HHHHHHh-CCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhh
Q psy2882 929 TTIISRF-GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 1007 (1428)
Q Consensus 929 ~~v~~~~-Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~ 1007 (1428)
..+.++| |++|.|++|+++|+||+|||||||||||||||.+||++|||+|.++++++.++++.++++.++++.+++++.
T Consensus 172 ~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l~~~~~~afl~~~ 251 (310)
T COG0258 172 EEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLSKP 251 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHHHHHHHHHhcCcc
Confidence 8999999 999999999999999999999999999999999999999999999999998888999999999999999999
Q ss_pred hhhccccCCCCCCcCCCccccccCCCCHHHHHHHHHHccCC
Q psy2882 1008 ILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNIP 1048 (1428)
Q Consensus 1008 L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~~~~f~ 1048 (1428)
|+|+++|++++.+..+. ..+.....|.+++..++.+++|+
T Consensus 252 l~t~~~d~~l~~~~~~~-~~~~~~~~d~~~~~~~~~~~~~~ 291 (310)
T COG0258 252 LATIKTDVPLEFDLEDI-LELLVPEHDFSKLLEERVELGFK 291 (310)
T ss_pred cccccccccCCcCccch-hhhccCcccHHHHHHHHHHHhHH
Confidence 99999999999763110 12444555888888999999988
No 11
>COG1678 Putative transcriptional regulator [Transcription]
Probab=100.00 E-value=1.1e-46 Score=394.37 Aligned_cols=182 Identities=46% Similarity=0.880 Sum_probs=164.9
Q ss_pred ccccCceEeecCCCCCCCccceEEEEEEeCCCceEEEEEcCCCC-ccHHHHhhcccccccccCCCchhhhhcccccceec
Q psy2882 1072 FNLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTD-MTINILLDNDSNLKLKLVPNTKEFILEKTTKTIMF 1150 (1428)
Q Consensus 1072 ~~~~G~lLIA~P~l~d~~F~rSVVll~eH~~~Ga~GlILNrP~~-~~l~~l~~~~~~l~~~~~~~~~~~~~~~~~~~v~~ 1150 (1428)
+.++|+||||+|+|.|++|+||||||||||++||||||||||++ .++++++.. +++...+ ...+.+||.
T Consensus 11 ~~l~g~fLiAmP~m~d~~F~RSVvyiceH~e~GamGliiNrp~~~~~~~~l~~~---~~~~~~~-------~~~~~~v~~ 80 (194)
T COG1678 11 MNLQGHFLVAMPDMQDPIFARSVVYICEHNENGAMGLIINRPSETLTLAELLEK---LKLEIKI-------LRLPKPVYL 80 (194)
T ss_pred cccCCcEEEecCCCCCCccceeEEEEEEeCCCCcEEEEecCCccccCHHHHHHH---hcccccc-------cccCceEEe
Confidence 45799999999999999999999999999999999999999999 999999876 2332110 024789999
Q ss_pred CCccccCeEEEEEecCCCCCCCccccceecCCEeecccHHHHHHhhcCCCCccEEEEEeccCCCCCCcHHHHhcCCeEEe
Q psy2882 1151 GGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDILESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIV 1230 (1428)
Q Consensus 1151 GGPV~~~~~~~LH~~~~~~~~~~~~~~~i~~gl~l~~~~d~l~~~~~g~~~~~~r~f~GYsGW~pGQLe~Ei~~g~W~v~ 1230 (1428)
||||+++++||||+.+.. .+.+++++++|++++++.|++++++.|.+|+++++++|||||++||||+||++|.|+++
T Consensus 81 GGPv~~~rgfvLh~~~~~---~~~ssl~v~~~~~lt~s~Dvl~~i~~~~~p~~~l~~lGYagW~~GQLE~Ei~~n~WL~~ 157 (194)
T COG1678 81 GGPVQRDRGFVLHSSDYG---AFQSSLRVSDGLALTTSLDVLEAIAAGKGPEKALVALGYAGWAAGQLEEEIEDNDWLTV 157 (194)
T ss_pred CCcccccceEEEEeCCCC---CCcccceecCCEEEEecHhHHHHHhccCCCCceEEEEEecccccchhHHHHhhCCEEEe
Confidence 999999999999996432 34678999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccccCCCcHHHHHHHHHhcCCCcchhhhhhcc
Q psy2882 1231 DANSEVIFNVPCEQRFFAAVKLLGVNPLIIGIAFGN 1266 (1428)
Q Consensus 1231 ~a~~~~if~~~~~~~W~~~l~~~~~d~~~i~~~~G~ 1266 (1428)
||++++||+.+++++|.++++++|+++.+++..+|.
T Consensus 158 pA~~~~lF~~~~edrw~~al~~lGi~~~~lst~agh 193 (194)
T COG1678 158 PADPEILFDTPPEDRWARALRRLGIDLALLSTPAGH 193 (194)
T ss_pred cCCHHHhcCCCHHHHHHHHHHHcCCCHHHcCCCcCC
Confidence 999999999999999999999999999998887764
No 12
>PHA00439 exonuclease
Probab=100.00 E-value=1.3e-46 Score=421.68 Aligned_cols=196 Identities=19% Similarity=0.344 Sum_probs=172.7
Q ss_pred hhccchhhhhhhccC-------CcCcCCCCccchHHHHHHHHHHHHHHh---cCCCEEEEEEeCCCCCcccCCChhhhcC
Q psy2882 778 KIDGSSCIYRAFYAL-------PDIRNIDNFPVGALYGTIKMLRKLYKN---YRATYIACIFDAKGKNFRNILYPSYKAT 847 (1428)
Q Consensus 778 ~i~g~~~~~Ra~~a~-------~~l~~~~G~~t~av~gf~~~l~~l~~~---~~p~~~v~~fD~~~~~fR~~l~p~YKa~ 847 (1428)
-+||++++||+|||+ +++++++|.||||++||+++|.+++++ ++|+|++|||| +++||||++||+||+|
T Consensus 10 LIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~~tfR~elyp~YKan 88 (286)
T PHA00439 10 VMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DSVNWRKEVVPTYKAN 88 (286)
T ss_pred EEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CCCChHhhhhhHhcCC
Confidence 489999999999999 468899999999999999999999999 99999999999 6799999999999999
Q ss_pred CCCCChHHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCC-EEEEEeCCCCccccccCcEEEEeCCee-
Q psy2882 848 RKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL-KVIISTNDKDMAQLVSNKIALINNNKI- 925 (1428)
Q Consensus 848 R~~~p~~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~-~v~IvS~DkDl~QLv~~~v~~~~~~~~- 925 (1428)
|+++|++ ..|++.++++++++|||++..+||||||+|||||+++.. .|. +|+|+|+||||+||++..+ ++.+.+.
T Consensus 89 R~~~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~-~g~~~vvIvS~DKDl~QLv~~~~-~~~~~~~~ 165 (286)
T PHA00439 89 RKAKRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSL-FGFKKAVLVSCDKDFKTIPNCDF-LWCTTGNI 165 (286)
T ss_pred CCCCCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHH-CCCCeEEEEeCCCCHhhcCcceE-EEccCCce
Confidence 9999999 789999999999999999999999999999999998743 566 8999999999999997643 3332211
Q ss_pred ccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHH---hCCHHHHHHHh
Q psy2882 926 HDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQ---YNSLENIINNA 984 (1428)
Q Consensus 926 ~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~---~gsle~i~~~~ 984 (1428)
+. +.. -.|+||+||++|+||+||||||||||| |||.+||++ |-.++..+.+.
T Consensus 166 ~~---~~~---~~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~sg 220 (286)
T PHA00439 166 LT---QTP---ETADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKSG 220 (286)
T ss_pred EE---cCc---ccHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhcc
Confidence 10 111 149999999999999999999999999 999999999 66777777764
No 13
>PRK00228 hypothetical protein; Validated
Probab=100.00 E-value=1.5e-45 Score=397.86 Aligned_cols=184 Identities=41% Similarity=0.821 Sum_probs=164.2
Q ss_pred cccccCceEeecCCCCCCCccceEEEEEEeCCCceEEEEEcCCCCccHHHHhhcccccccccCCCchhhhhcccccceec
Q psy2882 1071 LFNLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKLVPNTKEFILEKTTKTIMF 1150 (1428)
Q Consensus 1071 ~~~~~G~lLIA~P~l~d~~F~rSVVll~eH~~~Ga~GlILNrP~~~~l~~l~~~~~~l~~~~~~~~~~~~~~~~~~~v~~ 1150 (1428)
..+++|+||||+|.|.|++|+|||||||+|+++||||||||||++.+++++++++ .+.... + ..+.+.|||+
T Consensus 7 ~~~~~G~lLiA~P~l~d~~F~rSVIll~eH~~~Ga~GlIlNrp~~~~l~~ll~~~---~~~~~~--~---~~~~~~~v~~ 78 (191)
T PRK00228 7 PMNLQGQLLIAMPDLQDPNFARSVIYICEHNENGAMGLVINRPSELDVAEVLPQL---DILATP--P---EIRLDQPVFL 78 (191)
T ss_pred CccCCCeEEEeCCCCCCCCcCccEEEEEEeCCCCceEEEEcCCCCCCHHHHHHHh---cccccC--c---ccccCCeEEe
Confidence 3578999999999999999999999999999999999999999999999999764 221000 0 0134689999
Q ss_pred CCccccCeEEEEEecCCCCCCCccccceecCCEeecccHHHHHHhhcCCCCccEEEEEeccCCCCCCcHHHHhcCCeEEe
Q psy2882 1151 GGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDILESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIV 1230 (1428)
Q Consensus 1151 GGPV~~~~~~~LH~~~~~~~~~~~~~~~i~~gl~l~~~~d~l~~~~~g~~~~~~r~f~GYsGW~pGQLe~Ei~~g~W~v~ 1230 (1428)
||||+++++|+||+... .+.++.+|.+|||++++.+++++++.+.+|+++|||+|||||+|||||+||++|+|+++
T Consensus 79 GGPV~~~~~~~Lh~~~~----~~~~s~~v~~gl~l~~s~d~l~~l~~~~~~~~~~~flGyaGW~~gQLe~Ei~~g~W~v~ 154 (191)
T PRK00228 79 GGPVQTDRGFVLHSPRD----GFDSSIRVSDGLVLTTSRDVLEALATGPGPEGVLVALGYAGWGAGQLEQEIEENAWLTA 154 (191)
T ss_pred CCCccCCcEEEEEECCC----cCCCceeecCCeEEeCCHHHHHHHhcCCCCCcEEEEEEECCCCHHHHHHHHHcCCeEEc
Confidence 99999999999998632 36688999999999999999999998888999999999999999999999999999999
Q ss_pred cCCCccccCCCcHHHHHHHHHhcCCCcchhhhhhcc
Q psy2882 1231 DANSEVIFNVPCEQRFFAAVKLLGVNPLIIGIAFGN 1266 (1428)
Q Consensus 1231 ~a~~~~if~~~~~~~W~~~l~~~~~d~~~i~~~~G~ 1266 (1428)
+|++++||+++++++|++++++||+++..++...|.
T Consensus 155 ~a~~~~lf~~~~~~~W~~~l~~~G~~~~~ls~~~g~ 190 (191)
T PRK00228 155 PADPEILFDTPPEDRWRAALRRLGIDLALLSTQAGH 190 (191)
T ss_pred cCCHHHhcCCCHHHHHHHHHHHhCCCHHHhcCCccC
Confidence 999999999999999999999999999998886654
No 14
>PHA02567 rnh RnaseH; Provisional
Probab=100.00 E-value=4.3e-39 Score=362.15 Aligned_cols=181 Identities=22% Similarity=0.277 Sum_probs=162.5
Q ss_pred hhhhccchhhhhhhccCCcCcCCCCccchHHHH-HHHHHHHHHHhcCC--CEEEEEEeCCC-CCcccCCChhhhcCCCCC
Q psy2882 776 YGKIDGSSCIYRAFYALPDIRNIDNFPVGALYG-TIKMLRKLYKNYRA--TYIACIFDAKG-KNFRNILYPSYKATRKKM 851 (1428)
Q Consensus 776 Y~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~g-f~~~l~~l~~~~~p--~~~v~~fD~~~-~~fR~~l~p~YKa~R~~~ 851 (1428)
+.-+|||+++||+|||. +++++|.+|+++++ |+++|+++++.+++ +|++||||+++ ++|||++||+||+||+++
T Consensus 16 ~~LiDgs~i~~~~~~a~--l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~~ 93 (304)
T PHA02567 16 VNLIDFSQIIIATIMAN--FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKD 93 (304)
T ss_pred EEEEehHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCCC
Confidence 45689999999999994 88999999999955 99999999998655 45999999965 799999999999999999
Q ss_pred ChHHHHHH--------HHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCcccccc-CcEEEEeC
Q psy2882 852 PYNLILQI--------NLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS-NKIALINN 922 (1428)
Q Consensus 852 p~~l~~q~--------~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~-~~v~~~~~ 922 (1428)
|+++..|+ +.+++++++|||+++..+||||||+|||||+++.. .|.+|+|+|+||||+||+. ++|.++.+
T Consensus 94 Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~-~g~~VvIvS~DKDl~QLv~~~~v~~~~~ 172 (304)
T PHA02567 94 REESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSA-EGRPVLIVSSDGDFTQLHKYPGVKQWSP 172 (304)
T ss_pred ChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHh-CCCcEEEEeCCCChhhccCCCCeEEeec
Confidence 99988777 77888999999999999999999999999999744 5789999999999999995 88998875
Q ss_pred CeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccc
Q psy2882 923 NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIG 963 (1428)
Q Consensus 923 ~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG 963 (1428)
. +..+|.++||. |+|++||++|+||+||||||||-=|
T Consensus 173 ~---~~~~V~~k~G~-P~q~iD~kaL~GDsSDNIPGVp~~~ 209 (304)
T PHA02567 173 M---QKKWVKPKYGS-PEKDLMTKIIKGDKKDGVASIKVRS 209 (304)
T ss_pred C---CHHHHHHHhCC-HHHHHHHHHhCCcccCCcCCCCCCC
Confidence 3 46889999994 9999999999999999999997543
No 15
>PF02622 DUF179: Uncharacterized ACR, COG1678; InterPro: IPR003774 This entry describes proteins of unknown function.; PDB: 2DO8_A 2EW0_A 2GS5_A 2HRX_A 2AJ2_A 2HAF_A 2GZO_A.
Probab=100.00 E-value=3.1e-39 Score=341.64 Aligned_cols=160 Identities=38% Similarity=0.762 Sum_probs=139.4
Q ss_pred cCCCCCCCccceEEEEEEeCCCceEEEEEcCCCCccHHHHhhcccccccccCCCchhhhhcccccceecCCccccCeEEE
Q psy2882 1082 MPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKLVPNTKEFILEKTTKTIMFGGPIQIDRGFV 1161 (1428)
Q Consensus 1082 ~P~l~d~~F~rSVVll~eH~~~Ga~GlILNrP~~~~l~~l~~~~~~l~~~~~~~~~~~~~~~~~~~v~~GGPV~~~~~~~ 1161 (1428)
||.|.|++|+|||||||+||++||+|||||||++.++.++++++....+ ..+.+.|||+||||+++++|+
T Consensus 1 ~P~l~d~~F~~sVVli~~h~~~Ga~GlILNrp~~~~l~~~~~~~~~~~~----------~~~~~~~v~~GGPV~~~~~~~ 70 (161)
T PF02622_consen 1 MPSLNDPNFHRSVVLICEHDEEGAMGLILNRPTNITLSELLEELELLPI----------SAFSDQPVYFGGPVEPDRGFV 70 (161)
T ss_dssp -TTSTSTTTTTEEEEEEEEETTEEEEEESSSEEEEEHHHHHHHTTCCSS----------TTCCCSEEEES-SEEEEEEEE
T ss_pred CCCCCCCCcCceEEEEEEECCCCcEEEEecCCCCCCHHHHHHhhccccc----------cccccCeEEECCCcccCeEEE
Confidence 7999999999999999999999999999999999999999876321110 124688999999999999999
Q ss_pred EEecCCCCCCCccccceecCCEeecccHHHHHH-hhcCCCCccEEEEEeccCCCCCCcHHHHhcCCeEEecCCCccccCC
Q psy2882 1162 LHNITNEKSPIFNSTLNIASDISLTTSRDILES-FSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNV 1240 (1428)
Q Consensus 1162 LH~~~~~~~~~~~~~~~i~~gl~l~~~~d~l~~-~~~g~~~~~~r~f~GYsGW~pGQLe~Ei~~g~W~v~~a~~~~if~~ 1240 (1428)
||+.++. ...++.+|.+|+|++++.+++++ +.+|.++.+||||+|||||+|||||+||++|+|++++|++++||++
T Consensus 71 Lh~~~~~---~~~~s~~v~~gl~~~~~~~~~~~~i~~~~~~~~~~~f~GysgW~~gQLe~Ei~~g~W~~~~a~~~~vf~~ 147 (161)
T PF02622_consen 71 LHSIPDL---EGPGSIEVSPGLYLGGSLDALEALIAEGAGPEDFRFFLGYSGWGPGQLEDEIARGSWLVAPASPDIVFET 147 (161)
T ss_dssp EEEC-TT---GCSSEEECSSSEEEEESTHHHHHHHTSTTSCSSEEEEEEEEEECTTHHHHHHHTTTEEEEE--HHHHCTS
T ss_pred EEECCCC---CCCCceEEeCCeEEeccHHHHHHHHhCCCCCceEEEEEEECCCCHHHHHHHHHcCCEEEeeCCHHHhhCC
Confidence 9997642 13568999999999999999999 6666789999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHHHhcC
Q psy2882 1241 PCEQRFFAAVKLLG 1254 (1428)
Q Consensus 1241 ~~~~~W~~~l~~~~ 1254 (1428)
+++++|+++|++||
T Consensus 148 ~~~~~W~~~l~~~G 161 (161)
T PF02622_consen 148 PPEELWREALRRLG 161 (161)
T ss_dssp TSSHHHHHHHHCTT
T ss_pred CHHHHHHHHHHHCc
Confidence 99999999999998
No 16
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.1e-37 Score=370.01 Aligned_cols=257 Identities=21% Similarity=0.275 Sum_probs=216.6
Q ss_pred HHHHHh-hhhhccchhhhhhhccCC------cCcCCCCccchHHHHHHHHHHHHHHh-cCCCEEEEEEeCCCCCcccCCC
Q psy2882 770 LNALLM-YGKIDGSSCIYRAFYALP------DIRNIDNFPVGALYGTIKMLRKLYKN-YRATYIACIFDAKGKNFRNILY 841 (1428)
Q Consensus 770 L~~L~~-Y~~i~g~~~~~Ra~~a~~------~l~~~~G~~t~av~gf~~~l~~l~~~-~~p~~~v~~fD~~~~~fR~~l~ 841 (1428)
|+.|.- -+.+||++++||+|||++ ++.|++|++|++++||++++.++++. .+| ++||||.++++|++.+
T Consensus 23 l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~gikP---v~VFDG~~p~~K~~~~ 99 (393)
T PTZ00217 23 LKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAGIKP---VYVFDGKPPELKSGEL 99 (393)
T ss_pred HHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCCCCE---EEEEcCCCchhhHHHH
Confidence 445544 368999999999999986 37899999999999999999999985 777 7899999999999999
Q ss_pred hhhhcCCCCCChHH-----------------------HHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCC
Q psy2882 842 PSYKATRKKMPYNL-----------------------ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL 898 (1428)
Q Consensus 842 p~YKa~R~~~p~~l-----------------------~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~ 898 (1428)
+.||++|+++++++ ..|++.++++|+.||||++.+|+ ||||+||+|++. |.
T Consensus 100 ~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~-EAdaq~A~L~~~-----g~ 173 (393)
T PTZ00217 100 EKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPC-EAEAQCAELVKK-----GK 173 (393)
T ss_pred HHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCc-CHHHHHHHHHHC-----CC
Confidence 99999999999888 67889999999999999999997 999999999863 67
Q ss_pred EEEEEeCCCCccccccCcEEE-Ee-------CCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHH
Q psy2882 899 KVIISTNDKDMAQLVSNKIAL-IN-------NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKL 970 (1428)
Q Consensus 899 ~v~IvS~DkDl~QLv~~~v~~-~~-------~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kL 970 (1428)
.+.|+|.|+|++|+.++.+.. ++ +...++.+.+.+.+|++|+||+|+++|+| |||+|||||||||||.+|
T Consensus 174 v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G--~Dy~pgi~GIG~ktA~~L 251 (393)
T PTZ00217 174 VYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKL 251 (393)
T ss_pred eEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHH
Confidence 788999999999998875421 22 12357889999999999999999999999 999999999999999999
Q ss_pred HHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHH-HHccCC
Q psy2882 971 LNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYNIP 1048 (1428)
Q Consensus 971 L~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~-~~~~f~ 1048 (1428)
|++|||+|+|++++++.+..+. .-+...+...++.+.++... . ..++.|.+||.++|.+|| ++++|+
T Consensus 252 i~~~gsle~il~~~~~~k~~~p--------~~~~~~~~~~~f~~p~V~~~-~--~~~l~w~~pD~~~l~~fl~~e~~f~ 319 (393)
T PTZ00217 252 IKKYKSIEEILEHLDKTKYPVP--------ENFDYKEARELFLNPEVTPA-E--EIDLKWNEPDEEGLKKFLVKEKNFN 319 (393)
T ss_pred HHHcCCHHHHHHHHHhcCCCCC--------CCCChHHHHHHhcCCCcCCC-C--CCCCCCCCCCHHHHHHHHHhccCCC
Confidence 9999999999999986542221 12224566666666666542 0 126889999999999977 789998
No 17
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=100.00 E-value=1.3e-37 Score=321.27 Aligned_cols=138 Identities=44% Similarity=0.657 Sum_probs=133.4
Q ss_pred ccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccceEEEE
Q psy2882 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKLNINII 253 (1428)
Q Consensus 174 ~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 253 (1428)
|+|||++||+|||++||+|+|++|||||||||+|+|++||++|++.++.+++..++++++.+++|++++++|+++.++|.
T Consensus 1 MkVIL~~dV~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~~~~i~ 80 (148)
T TIGR00158 1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARRKKLEEKLAANKAAAARLKEVLELGTLTIS 80 (148)
T ss_pred CeEEEcccccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCceeecccHHHHHHHHHHCCceecCcceecCCcccccccceeeeeeeccCCc
Q psy2882 254 KKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311 (1428)
Q Consensus 254 ~~~~~~gklfgsVt~~~I~~~l~~~gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~~ 311 (1428)
+++|++|+||||||++||+++|+++|++||+++|.||+.|||++|+|+|+|+||+++.
T Consensus 81 ~k~ge~gklfGSVt~~~I~~~l~~~g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V~ 138 (148)
T TIGR00158 81 KKVGDEGKLFGSITTKQIADALKAAGLDLDKKKIELPDGVIRTTGEHEVTIKLHEEVF 138 (148)
T ss_pred EEeCCCCeEEEeECHHHHHHHHHHcCCcccHhhEECCCCceeceEEEEEEEEEcCCcE
Confidence 9999999999999999999999888999999999999645999999999999999764
No 18
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.7e-37 Score=363.61 Aligned_cols=243 Identities=17% Similarity=0.288 Sum_probs=211.6
Q ss_pred hhhhccchhhhhhhccCC-----cCcCCCCccchHHHHHHHHHHHHHHh-cCCCEEEEEEeCCCCCcccCCChhhhcCCC
Q psy2882 776 YGKIDGSSCIYRAFYALP-----DIRNIDNFPVGALYGTIKMLRKLYKN-YRATYIACIFDAKGKNFRNILYPSYKATRK 849 (1428)
Q Consensus 776 Y~~i~g~~~~~Ra~~a~~-----~l~~~~G~~t~av~gf~~~l~~l~~~-~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~ 849 (1428)
-+.+|||+++||+|||++ +++|++|.||++++||++++.++++. .+| ++|||++++++|++.+++||+.|+
T Consensus 23 ~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P---v~VFDG~~p~~K~~~~~~R~~~r~ 99 (338)
T TIGR03674 23 VVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP---VYVFDGKPPELKAETLEERREIRE 99 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE---EEEECCCChhhhHhhHHHHHHHHH
Confidence 457999999999999974 47899999999999999999999976 666 899999999999999999999999
Q ss_pred CCChHHHHH-----------------------HHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCC
Q psy2882 850 KMPYNLILQ-----------------------INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTND 906 (1428)
Q Consensus 850 ~~p~~l~~q-----------------------~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~D 906 (1428)
++++.+..+ ++.++++|+.||||++.+|| |||++||+|++. |....|+|.|
T Consensus 100 ~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~-EAeaq~a~L~~~-----g~vd~v~S~D 173 (338)
T TIGR03674 100 EAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQAAYMAKK-----GDVDYVGSQD 173 (338)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCc-cHHHHHHHHHHC-----CCeeEEecCC
Confidence 877776533 88999999999999999999 999999999963 5566899999
Q ss_pred CCccccccCcEEE-Ee-C---------------CeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHH
Q psy2882 907 KDMAQLVSNKIAL-IN-N---------------NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVK 969 (1428)
Q Consensus 907 kDl~QLv~~~v~~-~~-~---------------~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~k 969 (1428)
+|++|+.++++.. +. . ...++.+.+.+++|++|+||+|+++|+|| +|| |||||||||||.+
T Consensus 174 ~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~-dyn-~Gv~GIG~ktA~k 251 (338)
T TIGR03674 174 YDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGT-DYN-EGVKGIGPKTALK 251 (338)
T ss_pred cCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCC-CCC-CCCCCccHHHHHH
Confidence 9999999988622 11 1 12378888999999999999999999999 677 9999999999999
Q ss_pred HHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHH-HHHHccCC
Q psy2882 970 LLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQ-LFNKYNIP 1048 (1428)
Q Consensus 970 LL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~-l~~~~~f~ 1048 (1428)
||++|||+|+|+++++.. + +. .+++++|++++++..+ .++.|..||.++|.+ ++++++|+
T Consensus 252 li~~~gsie~il~~~~~~-------~----~~---~~~~~~~f~~~~v~~~-----~~~~~~~pd~e~l~~fl~~e~~~~ 312 (338)
T TIGR03674 252 LIKEHGDLEKVLKARGED-------I----EN---YDEIREFFLNPPVTDD-----YELKWRKPDKEGIIEFLCDEHDFS 312 (338)
T ss_pred HHHHcCCHHHHHHhhcCC-------C----CC---HHHHHHHhCCCCCCCC-----CCccCCCCCHHHHHHHHhhcCCCC
Confidence 999999999999997532 1 11 2699999999998865 578899999999999 77999998
No 19
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=7.8e-37 Score=316.13 Aligned_cols=138 Identities=37% Similarity=0.573 Sum_probs=133.2
Q ss_pred ccccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccc-eE
Q psy2882 172 KNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKL-NI 250 (1428)
Q Consensus 172 k~~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~-~l 250 (1428)
|.|+|||++||++||+.||+|+|+||||||||||+|+|++||++|++.++.+++..++++++.+++|++++++|+++ .+
T Consensus 4 kkmkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~~~~~~~~~~~a~~la~~l~~~~~~ 83 (153)
T CHL00160 4 KKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDLKLKEAKEKCLKVKQLLEEIQKF 83 (153)
T ss_pred ceEEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCceE
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999998 69
Q ss_pred EEEEecCCCCceeecccHHHHHHHHHHC-CceecCcceecCCcccccccceeeeeeeccCCc
Q psy2882 251 NIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311 (1428)
Q Consensus 251 ~i~~~~~~~gklfgsVt~~~I~~~l~~~-gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~~ 311 (1428)
+|.+++|++|+||||||++||+++|+++ |++||+++|.|| + ||++|+|+|+|+||+++.
T Consensus 84 ~i~~k~ge~gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~-~-Ik~~G~~~v~v~L~~~V~ 143 (153)
T CHL00160 84 SVKKKVGENNQIFGSVTEKEISQIIKNKTNIDLEKQNIELP-E-IKTIGIYNIEIKLTSDVK 143 (153)
T ss_pred EEEEEeCCCCeEEcccCHHHHHHHHHHhhCCccccceeehh-h-ccccEeEEEEEEecCCcE
Confidence 9999999999999999999999999877 999999999998 4 999999999999999764
No 20
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=100.00 E-value=4e-37 Score=327.02 Aligned_cols=158 Identities=45% Similarity=0.778 Sum_probs=143.4
Q ss_pred hhhccchhhhhhhccCC--cCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChH
Q psy2882 777 GKIDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYN 854 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~--~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~ 854 (1428)
+-+||++++||+|||.+ ++.+++|+||+|++||++++.++++..+|+|+++|||+++++||+++||+||+||+++|++
T Consensus 4 lLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~~p~~ 83 (169)
T PF02739_consen 4 LLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRKPMPEE 83 (169)
T ss_dssp EEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHHHHHHH
T ss_pred EEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCCCCCHH
Confidence 34799999999999998 7999999999999999999999999999999999999988899999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccC--cEEEEeC----CeeccH
Q psy2882 855 LILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSN--KIALINN----NKIHDR 928 (1428)
Q Consensus 855 l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~--~v~~~~~----~~~~~~ 928 (1428)
|..|++.++++++.+||+++..||+||||+|||+|+++.. .|.+|+|+|+||||+||+++ +|.++++ .+.++.
T Consensus 84 l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~-~~~~v~IvS~DkD~~QLv~~~~~V~~~~~~~~~~~~~~~ 162 (169)
T PF02739_consen 84 LIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASE-EGFEVIIVSGDKDLLQLVDENVNVYLLDPGKKKFKVYDP 162 (169)
T ss_dssp HHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHH-TTCEEEEE-SSGGGGGGTCS-TSEEEEETTTTCS-EB-H
T ss_pred HHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhcc-CCCEEEEEcCCCCHHHhcCCCceEEEeecCCCCCEEEcH
Confidence 9999999999999999999999999999999999999754 57899999999999999999 7888875 457899
Q ss_pred HHHHHHh
Q psy2882 929 TTIISRF 935 (1428)
Q Consensus 929 ~~v~~~~ 935 (1428)
+.|.|+|
T Consensus 163 ~~v~eky 169 (169)
T PF02739_consen 163 EEVEEKY 169 (169)
T ss_dssp HHHHHHT
T ss_pred HHHhhcC
Confidence 9999886
No 21
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=3.4e-36 Score=311.39 Aligned_cols=137 Identities=47% Similarity=0.782 Sum_probs=133.1
Q ss_pred ccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccceEEEE
Q psy2882 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKLNINII 253 (1428)
Q Consensus 174 ~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 253 (1428)
|+|||++||+|||++||+|+|++|||||||||+|+|+|||++|++.++.+++..++++++.+++|++++++|++.+++|.
T Consensus 1 mkVIL~~dv~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~l~i~ 80 (147)
T PRK00137 1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAELEAKAAEELAEAEALAEKLEGLTVTIK 80 (147)
T ss_pred CeEEEcccccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCceeecccHHHHHHHHHHCCceecCcceecCCcccccccceeeeeeeccCCc
Q psy2882 254 KKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311 (1428)
Q Consensus 254 ~~~~~~gklfgsVt~~~I~~~l~~~gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~~ 311 (1428)
+++|++|+||||||++||+++|+++|++||+++|.|| +|||++|+|+|+|+||++..
T Consensus 81 ~k~g~~gklfGsVt~~~I~~~l~~~g~~idk~~I~l~-~~Ik~~G~y~v~i~L~~~v~ 137 (147)
T PRK00137 81 AKAGEDGKLFGSVTTKDIAEALKKQGIEIDKRKIELP-GPIKTLGEYEVPVKLHPEVT 137 (147)
T ss_pred EEcCCCCeEEeeeCHHHHHHHHHHcCCccCHHHeECC-CcccccEEEEEEEEECCCcE
Confidence 9999999999999999999999888999999999998 59999999999999999653
No 22
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.4e-36 Score=304.41 Aligned_cols=136 Identities=48% Similarity=0.738 Sum_probs=132.8
Q ss_pred ccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccceEEEE
Q psy2882 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKLNINII 253 (1428)
Q Consensus 174 ~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~ 253 (1428)
|+|||++||.|||+.||+|+|++|||||||||+|+|+.||+.|++.++.++++.+++.++.+++|+.++++|++.+++|.
T Consensus 1 MkVILl~dV~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r~~~e~~~~~~~~~a~~lk~~Le~~~~~i~ 80 (148)
T COG0359 1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKLEKKAAEELAEAEALKEKLEGKTVEIA 80 (148)
T ss_pred CeEEEecchhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCceEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999889999
Q ss_pred EecCCCCceeecccHHHHHHHHHHCCceecCcceecCCcccccccceeeeeeeccCC
Q psy2882 254 KKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDILLHNGN 310 (1428)
Q Consensus 254 ~~~~~~gklfgsVt~~~I~~~l~~~gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~ 310 (1428)
+++|++|+||||||++||+++|+++|++|||++|.||+ +||++|.|+|+|+||+++
T Consensus 81 ~kag~~GklfGSVt~~dIa~~l~~~g~~idk~~i~l~~-~ik~~G~~~V~vkLh~eV 136 (148)
T COG0359 81 VKAGEDGKLFGSVTSKDIAEALKAAGFKLDKRKIRLPN-GIKTLGEHEVEVKLHEEV 136 (148)
T ss_pred EEcCCCCceeccccHHHHHHHHHHcCCCcchheeEcCc-hhhhcceeEEEEEecCce
Confidence 99999999999999999999999999999999999996 599999999999999964
No 23
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=8.4e-35 Score=333.36 Aligned_cols=223 Identities=17% Similarity=0.296 Sum_probs=194.5
Q ss_pred cCCCCccchHHHHHHHHHHHHHHh-cCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHHH-----------------
Q psy2882 796 RNIDNFPVGALYGTIKMLRKLYKN-YRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLIL----------------- 857 (1428)
Q Consensus 796 ~~~~G~~t~av~gf~~~l~~l~~~-~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~----------------- 857 (1428)
+|++|++|+|++||++++.++++. .+| ++||||.++++|++.+++||++|.++++.+..
T Consensus 1 ~~~~G~~Ts~l~g~~~r~~~ll~~gi~P---vfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~ 77 (292)
T PRK03980 1 MDSKGRITSHLSGIFYRTINLLENGIKP---VYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRS 77 (292)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHCCCEE---EEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhcc
Confidence 478999999999999999999987 777 89999999999999999999999999998876
Q ss_pred ------HHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEE-Ee-C-------
Q psy2882 858 ------QINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIAL-IN-N------- 922 (1428)
Q Consensus 858 ------q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~-~~-~------- 922 (1428)
|++.++++|+.||||++.+|| |||..||+|++. |..+.|+|.|+|++|+..+++.. +. .
T Consensus 78 ~~vt~~~~~~~k~lL~~~GIp~i~AP~-EAEAq~A~L~~~-----g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~ 151 (292)
T PRK03980 78 SRLTDEIVEDSKKLLDLMGIPYVQAPS-EGEAQAAYMAKK-----GDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPG 151 (292)
T ss_pred ccCCHHHHHHHHHHHHHCCCCEEecCc-hHHHHHHHHHHC-----CCeEEEecCCcCeeeecCCEEEEeecccccccCcc
Confidence 999999999999999999998 888889999953 66778999999999999987522 11 1
Q ss_pred --------CeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhh
Q psy2882 923 --------NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKN 994 (1428)
Q Consensus 923 --------~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~ 994 (1428)
...++.+.+.+++|++|+||+|+++|+| |||+|||||||||||.+||++|||+|+|+++.+.-
T Consensus 152 ~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~iL~G--~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~~~------- 222 (292)
T PRK03980 152 KNVYVEVKPELIELEEVLKELGITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFE------- 222 (292)
T ss_pred ccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHCCCHHHHHHhccCC-------
Confidence 1257888999999999999999999999 99999999999999999999999999999965310
Q ss_pred HHHhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHH-HHccCC
Q psy2882 995 LRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYNIP 1048 (1428)
Q Consensus 995 l~~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~-~~~~f~ 1048 (1428)
..-..+...++.++++..+ .++.|..||.++|++|| ++.+|+
T Consensus 223 -------~~~~~~~r~~f~~p~v~~~-----~~~~~~~pd~~~l~~fl~~e~~f~ 265 (292)
T PRK03980 223 -------IENYDEIREFFLNPPVTDD-----YELKWKEPDKEGIIEFLVEEHDFS 265 (292)
T ss_pred -------CCCHHHHHHHhcCCCCCCC-----CCccCCCCCHHHHHHHHhccCCCC
Confidence 1122466677888888754 67899999999999966 789998
No 24
>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=100.00 E-value=7.8e-33 Score=299.29 Aligned_cols=183 Identities=55% Similarity=0.998 Sum_probs=169.3
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
+|||+||||++|.+|+|||||+|+++.++++++. ++++|+|.++..+.|+++.|||||++++...|.+..+++.++.++
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~-~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEP-FNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccc-eeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHH
Confidence 5899999999999999999999999988777755 999999998777788999999999999966588899999999999
Q ss_pred HcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHH
Q psy2882 394 FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSF 473 (1428)
Q Consensus 394 ~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~ 473 (1428)
+.+++.++|||||+.||..||+++|+|++++++...|.++|.++|+++++++++.+.|..+.||..+.+.++|+|++||+
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~ 159 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQ 159 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHHH
Confidence 98766789999999999999999999999999988888889999999999999999999999998777788999999999
Q ss_pred HcCCCCCCCCChHHHHHHHHHHHH
Q psy2882 474 VNNLSHKKAHDALSDVRATLGLAR 497 (1428)
Q Consensus 474 ~~gi~~~~AHdAlaDv~AT~~l~~ 497 (1428)
+||++..++|||++||++|++|++
T Consensus 160 ~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 160 ANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred HCCCCccccccHHHHHHHHHHHhC
Confidence 999999999999999999999863
No 25
>COG3737 Uncharacterized conserved protein [Function unknown]
Probab=99.98 E-value=3.4e-33 Score=266.96 Aligned_cols=123 Identities=32% Similarity=0.442 Sum_probs=119.3
Q ss_pred cceeEeeccCCCCceEEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhhhccCC--cEEEEeeCCC
Q psy2882 1303 KKMELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKFNP--SVVILGTGNI 1380 (1428)
Q Consensus 1303 ~~M~~~~~~~~~~~~I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~ll~~~p--evliiGTG~~ 1380 (1428)
++|.|.+..+|+...|++|++|||++ +++.+.||++|+|++ +..|.+..+++||+|+|+.++++.| ||||||||.+
T Consensus 3 k~m~~~e~~~Pg~~~~~ayG~Gg~R~-a~~sh~~SlL~lpdg-v~~W~v~~~~~Lt~e~f~~vl~~a~~~EilliGTG~~ 80 (127)
T COG3737 3 KGMLFREAHFPGRAPIDAYGAGGFRF-ADMSHRGSLLVLPDG-VCDWEVATLSDLTPEDFERVLAEAPDVEILLIGTGAR 80 (127)
T ss_pred CcceeecCCCCCcchhhhhcCCceEe-ccccccccEEEecCc-cccccccChhhCCHHHHHHHHhcCCCceEEEEecCcc
Confidence 68999999999999999999999998 999999999999999 9999999999999999999987665 9999999999
Q ss_pred CCCCCHHHHHHHHHcCCeEEEcChhhHHHHHHhhhhccceeeeeccc
Q psy2882 1381 QHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALIL 1427 (1428)
Q Consensus 1381 ~~~~~~~~~~~l~~~GI~vE~M~T~aAcrTyNiL~sEgR~VaaaLi~ 1427 (1428)
++|+|+.+++.|+++||++|+|+|++||||||+|+||||+||||||+
T Consensus 81 ~rf~p~~l~aal~~~gIsve~Mst~AA~RTYNvL~sEgRrvAAALi~ 127 (127)
T COG3737 81 LRFPPPKLRAALKAAGISVEPMSTGAAVRTYNVLLSEGRRVAAALIA 127 (127)
T ss_pred ccCCCHHHHHHHHHcCCccccccchhhHHHHHHHHhccHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999985
No 26
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=99.97 E-value=4.1e-32 Score=317.69 Aligned_cols=250 Identities=21% Similarity=0.220 Sum_probs=202.4
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCc-------ccCCChhhhcCCC
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF-------RNILYPSYKATRK 849 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~f-------R~~l~p~YKa~R~ 849 (1428)
+.+||++++||+||+.+....++|.++++++||++++.++++. + .+.++||||..+++ |++..++||++|.
T Consensus 27 laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~-~-i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~ 104 (316)
T cd00128 27 VAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLEL-G-IKPVFVFDGKPPPLKAETLAKRRERREEAEEEAK 104 (316)
T ss_pred EEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHC-C-CEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999998754457899999999999999998864 3 47899999987777 8888899999988
Q ss_pred CCCh----------------HHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccc
Q psy2882 850 KMPY----------------NLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLV 913 (1428)
Q Consensus 850 ~~p~----------------~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv 913 (1428)
++++ ....|++.++++|+.+|||++.+| +||||+||+|++. |....|+|.|+|++|+.
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap-~EAdaq~a~l~~~-----g~v~~i~S~DsD~l~fg 178 (316)
T cd00128 105 EALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAP-YEAEAQCAYLAKK-----GLVDAIITEDSDLLLFG 178 (316)
T ss_pred HHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECC-cCHHHHHHHHHhC-----CCeeEEEecCCCeeeec
Confidence 7776 236788999999999999999999 5999999999875 55678999999999998
Q ss_pred cCcEEE-Ee-----CCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhc
Q psy2882 914 SNKIAL-IN-----NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNI 987 (1428)
Q Consensus 914 ~~~v~~-~~-----~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i 987 (1428)
.+++.. ++ ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||||||.+||++|||++++++++..-
T Consensus 179 ~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G--~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~ 256 (316)
T cd00128 179 APRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDIERLKKK 256 (316)
T ss_pred CceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHcCChHHHHHHHHHh
Confidence 876543 22 22358899999999999999999999999 99999999999999999999999999999887532
Q ss_pred chhhhhhHHHhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHH-HHccCC
Q psy2882 988 KGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYNIP 1048 (1428)
Q Consensus 988 ~~k~~~~l~~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~-~~~~f~ 1048 (1428)
... ...-+.......++.++++..+ ...+.|..|+.++|+.|+ .+.+|+
T Consensus 257 ~~~--------~~~~~~~~~~~~~f~~p~~~~~----~~~~~~~~p~~~~l~~~~~~~~~~~ 306 (316)
T cd00128 257 LYR--------SPEDFPLKEAREFFLNPEVTDD----FIDLRWRDPDEEGIIEFLCKEHGFN 306 (316)
T ss_pred Ccc--------CCCcCChHHHHHHHcCCCCCCC----CCceeecCCCHHHHHHHccCCCCCC
Confidence 110 0012334455555555555443 246788999999999987 556655
No 27
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=99.97 E-value=3.3e-31 Score=261.57 Aligned_cols=109 Identities=38% Similarity=0.618 Sum_probs=105.5
Q ss_pred eEEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhhhccCCcEEEEeeCCCCCCCCHHHHHHHHHcC
Q psy2882 1317 TIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKFNPSVVILGTGNIQHFIHPKLTYILTQKN 1396 (1428)
Q Consensus 1317 ~I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~ll~~~pevliiGTG~~~~~~~~~~~~~l~~~G 1396 (1428)
.|++|++|+|+| ||++|+|||+|+|++++.+|.+++.++++++||+.++..+||+||||||.++.+++|+++++|+++|
T Consensus 1 ~I~~y~~g~~~i-~g~~y~~sviv~p~~~~~~w~~~~~~~l~~e~l~~l~~~~peiliiGTG~~~~~~~~~~~~~l~~~g 79 (109)
T cd05560 1 TITAYGDGYVEI-NDQRYEHSLIVTPDELITDWPVARFEDLTAAHFEALLALQPEVILLGTGERQRFPPPALLAPLLARG 79 (109)
T ss_pred CeEeecCCEEEE-CCEEEecCEEEECCceeeccccCCcccCCHHHHHHHHhcCCCEEEEecCCCCCcCCHHHHHHHHHcC
Confidence 489999999997 9999999999999996666999999999999999999999999999999999999999999999999
Q ss_pred CeEEEcChhhHHHHHHhhhhccceeeeecc
Q psy2882 1397 IGIECMNNQAACRTYNILVSDDIKAMLALI 1426 (1428)
Q Consensus 1397 I~vE~M~T~aAcrTyNiL~sEgR~VaaaLi 1426 (1428)
|++|+|+|++||||||+|++|||+||||||
T Consensus 80 i~vE~m~T~~AcrTyN~L~~EgR~V~Aali 109 (109)
T cd05560 80 IGVEVMDTQAACRTYNILMGEGRRVVAALL 109 (109)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCcEEEEeC
Confidence 999999999999999999999999999997
No 28
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=99.97 E-value=7.4e-31 Score=259.38 Aligned_cols=108 Identities=31% Similarity=0.525 Sum_probs=104.9
Q ss_pred eEEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhhhccC-CcEEEEeeCCCCCCCCHHHHHHHHHc
Q psy2882 1317 TIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKFN-PSVVILGTGNIQHFIHPKLTYILTQK 1395 (1428)
Q Consensus 1317 ~I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~ll~~~-pevliiGTG~~~~~~~~~~~~~l~~~ 1395 (1428)
.|++|++|+|+| ||+.|.|||+|+|++ +.+|+++++++++++||+.++... ||+||||||.+++|++|+++++|+++
T Consensus 1 ~i~~y~~g~~~i-~g~~y~~~viv~p~~-~~~w~~~~~~~l~~~~l~~~~~~~~peiliiGTG~~~~~~~~~~~~~l~~~ 78 (109)
T cd00248 1 PIDGYGPGGFRI-AGQVYRGPLLVLPDG-VVPWDGTSLSDLDPEALLPLLAEDRPDILLIGTGAEIAFLPRALRAALRAA 78 (109)
T ss_pred CeeeecCCEEEE-CCEEEeeCEEEeCCc-eeecCCcCcccCCHHHHHHHHhhCCCCEEEEcCCCCCCcCCHHHHHHHHHc
Confidence 489999999997 999999999999997 799999999999999999998887 99999999999999999999999999
Q ss_pred CCeEEEcChhhHHHHHHhhhhccceeeeecc
Q psy2882 1396 NIGIECMNNQAACRTYNILVSDDIKAMLALI 1426 (1428)
Q Consensus 1396 GI~vE~M~T~aAcrTyNiL~sEgR~VaaaLi 1426 (1428)
||++|+|+|++||||||+|++|||+||||||
T Consensus 79 gI~vE~m~T~aAcrTyNiL~~EgR~Vaaali 109 (109)
T cd00248 79 GIGVEVMSTGAACRTYNVLLSEGRRVAAALI 109 (109)
T ss_pred CCeEEEeCcHHHHHHHHHHHhCCcceEEEeC
Confidence 9999999999999999999999999999997
No 29
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=99.97 E-value=2.4e-30 Score=256.12 Aligned_cols=111 Identities=23% Similarity=0.429 Sum_probs=106.6
Q ss_pred ceEEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhhh--ccCCcEEEEeeCCCCCCCCHHHHHHHH
Q psy2882 1316 QTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHIS--KFNPSVVILGTGNIQHFIHPKLTYILT 1393 (1428)
Q Consensus 1316 ~~I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~ll--~~~pevliiGTG~~~~~~~~~~~~~l~ 1393 (1428)
+.|+||++|+|+| ||+.|.||++|+|+. +++|+++++++++++||+.++ .++||+||||||.++.+++|++++.|+
T Consensus 1 ~~I~~y~~~~f~i-n~~~~~gs~iv~p~~-~~~W~~~~~~~l~~~~l~~l~~~~~~peiliiGtG~~~~~~~~~~~~~l~ 78 (114)
T cd05125 1 NYIDAYSENGFRL-NNNKVIGSGAILPKE-VFSWNVSSFEDITEESLSLFELLEPRPEILVIGTGRKSRPLSPELRKYFK 78 (114)
T ss_pred CeEEeECCCeEEE-CCEEEEEeEEEccCc-eeccCCCChhhCCHHHHHHHHhccCCCCEEEEccCCCCCcCCHHHHHHHH
Confidence 4699999999997 999999999999997 999999999999999999985 568999999999999999999999999
Q ss_pred HcCCeEEEcChhhHHHHHHhhhhccceeeeecccC
Q psy2882 1394 QKNIGIECMNNQAACRTYNILVSDDIKAMLALILD 1428 (1428)
Q Consensus 1394 ~~GI~vE~M~T~aAcrTyNiL~sEgR~VaaaLi~~ 1428 (1428)
++||++|+|+|++||||||+|++|||+||||||||
T Consensus 79 ~~gi~vevm~T~~AcrtyN~L~~EgR~VaaaLip~ 113 (114)
T cd05125 79 KLGIAVEVVDTRNACATFNFLAEEGRRVAAALIPP 113 (114)
T ss_pred HcCCEEEEECHHHHHHHHHHHHhCCCeEEEEEecC
Confidence 99999999999999999999999999999999986
No 30
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=99.96 E-value=2.1e-29 Score=250.01 Aligned_cols=108 Identities=38% Similarity=0.592 Sum_probs=99.2
Q ss_pred EEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhhhcc--CCcEEEEeeCCCCCCCCHHHHHHHHHc
Q psy2882 1318 IVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKF--NPSVVILGTGNIQHFIHPKLTYILTQK 1395 (1428)
Q Consensus 1318 I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~ll~~--~pevliiGTG~~~~~~~~~~~~~l~~~ 1395 (1428)
|++|++|+|+| ||++|.||++|+|++++..|++++++++++++|+.++.. +||+||||||.++.+++|+++++|+++
T Consensus 1 I~~y~~g~~~i-~g~~~~~~iii~p~~~~~~w~~~~~~~l~~~~l~~l~~~~p~pe~liiGtG~~~~~~~~~~~~~l~~~ 79 (110)
T PF04430_consen 1 ITGYGFGGFVI-NGKEYEGSIIIFPDGVIRDWKVKSPHDLTPEDLEELLELEPKPEVLIIGTGKRQLFLPPELREYLRKK 79 (110)
T ss_dssp EEEEETTEEEE-TTEEESSEEEEETTSEEEEEHHSSTTCEETHHHHHHHCTCCS-SEEEEEETTS-SECTHHHHHHHHTT
T ss_pred CceEeCCEEEE-CCEEEccCEEEECCCcccCcCCCCcccCCHHHHHHHHhccCCCcEEEEccCCccccCCHHHHHHHHHc
Confidence 79999999997 999999999999999658999999999999999999765 999999999999999999999999999
Q ss_pred CCeEEEcChhhHHHHHHhhhhccceeeeecc
Q psy2882 1396 NIGIECMNNQAACRTYNILVSDDIKAMLALI 1426 (1428)
Q Consensus 1396 GI~vE~M~T~aAcrTyNiL~sEgR~VaaaLi 1426 (1428)
||+||+|+|++||||||+|++|||+|||||+
T Consensus 80 GI~ve~m~T~~Ac~tyN~L~~EgR~V~aal~ 110 (110)
T PF04430_consen 80 GIGVEVMDTPAACRTYNILASEGRRVAAALI 110 (110)
T ss_dssp T-EEEEE-HHHHHHHHHHHHHTTC-EEEEEE
T ss_pred CCeEEEECHHHHHHHHHHHHhCCccEEEEeC
Confidence 9999999999999999999999999999986
No 31
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=99.96 E-value=3.5e-29 Score=319.04 Aligned_cols=138 Identities=39% Similarity=0.561 Sum_probs=133.6
Q ss_pred ccccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccceEE
Q psy2882 172 KNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKLNIN 251 (1428)
Q Consensus 172 k~~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~ 251 (1428)
..|+|||++||+|||++||||+|||||| |||||+|+|++||++|++.+++++++.++++++++++|++++++|++++++
T Consensus 687 ~~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~~~~ 765 (838)
T PRK14538 687 KNMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILEQEKKRNHELLMKKLKSEIDNKKIT 765 (838)
T ss_pred hhhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcEEE
Confidence 4799999999999999999999999999 999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCCceeecccHHHHHHHHHHC-CceecCcceecCCcccccccceeeeeeeccCCc
Q psy2882 252 IIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311 (1428)
Q Consensus 252 i~~~~~~~gklfgsVt~~~I~~~l~~~-gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~~ 311 (1428)
|.+++|++|+||||||++||+++|+++ |++|||++|.||+ |||++|+|+|+|+||+++.
T Consensus 766 i~~k~ge~gklfGSVt~~~I~~~l~~~~g~~idk~~I~l~~-~Ik~~G~~~v~i~L~~~V~ 825 (838)
T PRK14538 766 LDIQLGPKGKIYGKITLKQIVEEFHKIHNITIDRKKISLEN-EIISVGIYPVDVFLTDQIK 825 (838)
T ss_pred EEEEeCCCCeeeeccCHHHHHHHHHHhhCCccccceeeCCC-cccccEEEEEEEEEcCCeE
Confidence 999999999999999999999999887 9999999999985 9999999999999999764
No 32
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=99.95 E-value=2.4e-28 Score=243.40 Aligned_cols=106 Identities=15% Similarity=0.244 Sum_probs=101.3
Q ss_pred EEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCC-------CCCCCCHhHHHhhhccCCcEEEEeeCCCCC-CCCHHHH
Q psy2882 1318 IVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSIN-------KYNFLTKKDFIHISKFNPSVVILGTGNIQH-FIHPKLT 1389 (1428)
Q Consensus 1318 I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~-------~~~~l~~e~l~~ll~~~pevliiGTG~~~~-~~~~~~~ 1389 (1428)
|++|++|+|+| ||++|++||+|.|++ +..|+.+ ++++|+++||+.+++.+||+||||||.+++ ++||+++
T Consensus 2 i~~y~~G~i~i-~g~~y~~~viv~p~~-~~~w~~~~~s~~~~~~~~l~~~~l~~ll~~~peivliGTG~~~~~~~~~~~~ 79 (117)
T cd05126 2 IESTSFGSITV-GGETYEHDIVVYPDG-SRARRWKELSKKTGTSHGLQPEELEELLEEGVEVIVIGTGQSGALKVPPETV 79 (117)
T ss_pred cceecCCEEEE-CCEEEcCCEEEeCCc-cccccccccccccCCcccCCHHHHHHHHhcCCCEEEEcCCCCccccCCHHHH
Confidence 79999999997 999999999999997 7788766 888999999999999999999999999988 6899999
Q ss_pred HHHHHcCCeEEEcChhhHHHHHHhhhhccceeeeec
Q psy2882 1390 YILTQKNIGIECMNNQAACRTYNILVSDDIKAMLAL 1425 (1428)
Q Consensus 1390 ~~l~~~GI~vE~M~T~aAcrTyNiL~sEgR~VaaaL 1425 (1428)
+.|+++||++|+|+|++||||||+|++|||+|+|||
T Consensus 80 ~~l~~~Gi~ve~m~T~aAcrTYN~L~~EgRrV~Aa~ 115 (117)
T cd05126 80 EKLEKRGVEVLVLPTEEAVKRYNELAGKGRRVLAVI 115 (117)
T ss_pred HHHHhcCCEEEEcChHHHHHHHHHHHhCCCeEEEEE
Confidence 999999999999999999999999999999999997
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.3e-26 Score=259.49 Aligned_cols=175 Identities=18% Similarity=0.194 Sum_probs=146.0
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|++||+||||++|..|+|||||+|+++.++.++++ ++++++|...+ +|++..|||||++++..+|.+..+++.++
T Consensus 6 ~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~-~~~lv~P~~~i--~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 6 GPLAAFDLETTGVDPETARIVTAALVVVDADGEVVES-REWLADPGVEI--PEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred CcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccc-eEEEECCCCCC--CHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 5899999999999999999999999999876777776 88999997643 46999999999999987899988888888
Q ss_pred HHHHcC---CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCC
Q psy2882 391 EKIFLK---PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFK 467 (1428)
Q Consensus 391 ~~~~~~---~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~k 467 (1428)
..++.. .+.++|||| ++||..||++++.|++..++. .+.++|++.+++.+.+. ...+++
T Consensus 83 ~~~l~~~~~~~~~lVahN-a~FD~~fL~~~~~r~~~~~~~--------~~~~iDt~~l~~~~~~~---------~~~~~~ 144 (232)
T PRK07942 83 ADALREAWARGVPVVVFN-APYDLTVLDRELRRHGLPSLV--------PGPVIDPYVIDKAVDRY---------RKGKRT 144 (232)
T ss_pred HHHHHHHhhcCCEEEEeC-cHhhHHHHHHHHHHcCCCCcc--------CCcEeeHHHHHhhhhcc---------cCCCCC
Confidence 887743 467899999 699999999999998765431 11236666666665432 124689
Q ss_pred hHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchh
Q psy2882 468 LEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRL 506 (1428)
Q Consensus 468 Le~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l 506 (1428)
|++||++||++..++|+|++||.||++|+..+.++.|+|
T Consensus 145 L~~l~~~~gi~~~~aH~Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 145 LTALCEHYGVRLDNAHEATADALAAARVAWALARRFPEL 183 (232)
T ss_pred HHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999888855
No 34
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=3.8e-25 Score=250.12 Aligned_cols=201 Identities=20% Similarity=0.235 Sum_probs=157.1
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
++|||+|+||||++|.+|+|||||+|+++.+ .+++. ++.+|+|... ++++++.|||||++++. ...+..+++.++
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~-~~~~~-~~~li~P~~~--I~~~a~~ihgIt~e~v~-~~p~~~ev~~~~ 81 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFD-EVIDS-VEFLINPERV--VSAESQRIHHISDAMLR-DKPKIAEVFPQI 81 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEECC-eEEEE-EEEEECcCCC--CCHhhhhccCcCHHHHh-CCCCHHHHHHHH
Confidence 6899999999999999999999999999865 44554 8999998764 34699999999999994 444668999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++.+ +.++|||| ++||..||+++|.|++.+.... .+.++|++++++.+ | +.++++|+.
T Consensus 82 ~~fl~~-~~~lvghn-~~FD~~~L~~~~~r~g~~~~~~-------~~~~iDtl~lar~~-------~----~~~~~~L~~ 141 (250)
T PRK06310 82 KGFFKE-GDYIVGHS-VGFDLQVLSQESERIGETFLSK-------HYYIIDTLRLAKEY-------G----DSPNNSLEA 141 (250)
T ss_pred HHHhCC-CCEEEEEC-HHHHHHHHHHHHHHcCCCcccc-------CCcEEehHHHHHhc-------c----cCCCCCHHH
Confidence 998864 36899997 8999999999999987653211 13458888887753 2 246799999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeeccCcCCCCceEEEe
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWP 550 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~~~~~p 550 (1428)
|+++||++..+||+|++||+||++|++.+.++.+.+ .++.+++. +|.+.-.-.||+.+|....-+|
T Consensus 142 l~~~~g~~~~~aH~Al~Da~at~~vl~~l~~~~~~~----------~~l~~~~~----~~~~~~~~~fGK~kG~~~~~~~ 207 (250)
T PRK06310 142 LAVHFNVPYDGNHRAMKDVEINIKVFKHLCKRFRTL----------EQLKQILS----KPIKMKYMPLGKHKGRLFSEIP 207 (250)
T ss_pred HHHHCCCCCCCCcChHHHHHHHHHHHHHHHHhcccH----------HHHHHHhh----cCcccccccCcccCCCCcccCC
Confidence 999999999999999999999999999988765432 22223332 5655545689999988544333
No 35
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=7.7e-25 Score=245.66 Aligned_cols=177 Identities=15% Similarity=0.127 Sum_probs=146.2
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|+++|+||||++|.+|+|||||+|+++.+.....+.++.+++|...+ +++++.|||||++++ ..+.+..+++.++
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i--~~~~~~IhGIt~e~l-~~ap~~~evl~~l 123 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPL--EEESVVIHGITHSEL-QDAPDLERILDEL 123 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCC--ChhhhhhcCCCHHHH-hCCCCHHHHHHHH
Confidence 5899999999999999999999999999876544455588999998653 369999999999999 4577778999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCC--cCCCCC-CCCCCCCC
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYG--ITWPYK-NNGKPSFK 467 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~--~~~p~~-~~g~~s~k 467 (1428)
.+++.+ .++|||| ++||..||++++.|....+.... .+|++++++.+.|.. -.||.. ..+.++++
T Consensus 124 ~~~~~~--~~lVaHn-a~FD~~fL~~~l~~~~~~~~~~~---------~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~ 191 (239)
T PRK09146 124 LEALAG--KVVVVHY-RRIERDFLDQALRNRIGEGIEFP---------VIDTMEIEARIQRKQAGGLWNRLKGKKPESIR 191 (239)
T ss_pred HHHhCC--CEEEEEC-HHHHHHHHHHHHHHhcCCCCCCc---------eechHHHHHHHcccccccccchhccCCCCCCC
Confidence 999863 5899999 79999999999988654443333 389999998887753 234432 23348899
Q ss_pred hHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 468 LEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 468 Le~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
|++++++||++..++|+|++||.||++|+..+.++
T Consensus 192 L~~l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 192 LADSRLRYGLPAYSPHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999987765
No 36
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=6e-25 Score=246.35 Aligned_cols=195 Identities=20% Similarity=0.170 Sum_probs=150.2
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
++|+|||+||||+++.+|+|||||+|.. ... +.++.+++|...+ +|+++.|||||++++. .+.+..+++.++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~~----~~~-~~f~~lv~P~~~I--~~~a~~IhGIt~e~v~-~~p~f~ev~~~~ 73 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYNG----VTS-ESFQTLVNPEIPI--PAEASKIHGITTDEVA-DAPKFPEAYQKF 73 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEcC----ccc-cEEEEEeCCCCCC--ChhHHhhcCCCHHHHh-CCCCHHHHHHHH
Confidence 5799999999999999999999999732 223 3488899987643 5699999999999994 455678999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++++ +.++||||+.+||..||+.++.|++.+...+. .+|++++++.++|+ .++++|+.
T Consensus 74 ~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~---------~iDt~~l~~~~~~~----------~~~~~L~~ 133 (232)
T PRK06309 74 IEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLR---------TIDSLKWAQKYRPD----------LPKHNLQY 133 (232)
T ss_pred HHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCc---------EEeHHHHHHHHcCC----------CCCCCHHH
Confidence 998864 36899999779999999999999887643322 38888888887553 34689999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeeccCcCCCCce
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYIS 546 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~~ 546 (1428)
|+..||++..++|||++||.+|++|+..+.++.+ ...+..+.+.+ ..|- ...-.||+.+|...
T Consensus 134 l~~~~~~~~~~aH~Al~Da~~t~~vl~~l~~~~~-----------~~~l~~l~~~~-~~~~-~~~~~fgk~kg~~~ 196 (232)
T PRK06309 134 LRQVYGFEENQAHRALDDVITLHRVFSALVGDLS-----------PQQVYDLLNES-CHPR-IFKMPFGKYKGKPL 196 (232)
T ss_pred HHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHH-----------HhhHHHHHHhh-ccCc-cceecccccCCEEH
Confidence 9999999999999999999999999998876532 12233333321 1121 12447888888743
No 37
>KOG3363|consensus
Probab=99.92 E-value=1.7e-25 Score=224.13 Aligned_cols=124 Identities=19% Similarity=0.397 Sum_probs=116.6
Q ss_pred ceeEeeccCCCCceEEEEcCCeEEEeCCeEEeccEEEeCCCcccccCCCCCCCCCHhHHHhh--hccCCcEEEEeeCCCC
Q psy2882 1304 KMELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHI--SKFNPSVVILGTGNIQ 1381 (1428)
Q Consensus 1304 ~M~~~~~~~~~~~~I~~y~~g~f~i~ng~~~~gsviv~p~~~~~~W~~~~~~~l~~e~l~~l--l~~~pevliiGTG~~~ 1381 (1428)
...+.......+..++||+.+||+++||+.|.||+.|+|+. +++|++.+++|+|++||+.+ ++|+||+||||+|...
T Consensus 45 qI~l~~te~~~ql~v~gys~ygfrl~ng~~l~Gpi~~fp~~-~lSW~v~~fedIt~dSLslF~tlePkidlLIvG~Gd~~ 123 (196)
T KOG3363|consen 45 QINLIDTEPEDQLRVQGYSCYGFRLVNGVKLEGPILCFPNL-LLSWSVRTFEDITTDSLSLFQTLEPKIDLLIVGCGDKK 123 (196)
T ss_pred eeeeecCCchhhheeeeecccceEeecCeEEEecceecccc-eeeccCCChhhcCcchHhHhhhcCCCccEEEEecCCcC
Confidence 34666666777889999999999999999999999999998 99999999999999999998 8899999999999988
Q ss_pred CC--CCHHHHHHHHHcCCeEEEcChhhHHHHHHhhhhccceeeeecccC
Q psy2882 1382 HF--IHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALILD 1428 (1428)
Q Consensus 1382 ~~--~~~~~~~~l~~~GI~vE~M~T~aAcrTyNiL~sEgR~VaaaLi~~ 1428 (1428)
++ +.+++++++++.||++|+|+|++||.|||+|++|||-|||||+||
T Consensus 124 ~p~~v~~~V~~F~k~~ki~lEi~dte~A~aTfNfLNaEgR~VaaAL~Pp 172 (196)
T KOG3363|consen 124 HPDKVRPSVRQFVKSHKIKLEIVDTENAAATFNFLNAEGRYVAAALLPP 172 (196)
T ss_pred CchhcCHHHHHHHHHhCcceEEecchhhhhHhhhccccccEEEEEecCC
Confidence 77 999999999999999999999999999999999999999999987
No 38
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=5.2e-24 Score=234.14 Aligned_cols=173 Identities=20% Similarity=0.215 Sum_probs=140.6
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
..|||+|+||||++|..|+|||||+|+++.+.++..+.|+++|+|... .++++..|||||++++ ..|.+..+++.++
T Consensus 29 ~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~--i~~~~~~ihGIt~~~l-~~~~~~~~vl~~~ 105 (202)
T PRK09145 29 DEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQS--LSAESIKIHRLRHQDL-EDGLSEEEALRQL 105 (202)
T ss_pred CCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCC--CCHhHhhhcCcCHHHH-hcCCCHHHHHHHH
Confidence 589999999999999999999999999998766665669999999853 3479999999999999 5788889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++.+ .++|||| +.||..||..++.|....++... .+|+..++...... .+| .+.++++|++
T Consensus 106 ~~~i~~--~~lv~hn-~~fD~~fL~~~~~~~~~~~~~~~---------~id~~~l~~~~~~~--~~~---~~~~~~~L~~ 168 (202)
T PRK09145 106 LAFIGN--RPLVGYY-LEFDVAMLNRYVRPLLGIPLPNP---------LIEVSALYYDKKER--HLP---DAYIDLRFDA 168 (202)
T ss_pred HHHHcC--CeEEEeC-HHHHHHHHHHHHHHhcCCCCCCC---------eeeHHHHHHHHhhc--cCC---CcccCCCHHH
Confidence 999974 5799998 79999999999988643333222 25565555433221 123 2456899999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhC
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 503 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~ 503 (1428)
+++.||++..++|+|++||++|++|+..|.+.|
T Consensus 169 l~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (202)
T PRK09145 169 ILKHLDLPVLGRHDALNDAIMAALIFLRLRKGD 201 (202)
T ss_pred HHHHcCCCCCCCCCcHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999887654
No 39
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=99.92 E-value=6.9e-27 Score=226.03 Aligned_cols=100 Identities=50% Similarity=0.717 Sum_probs=69.5
Q ss_pred CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcch-hhhhhHHHhhhhchhhhhhhhccccC
Q psy2882 937 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKKILTIKTDC 1015 (1428)
Q Consensus 937 v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~-k~~~~l~~~~~~~~~~~~L~~i~~d~ 1015 (1428)
|+|+||+||++|+||+|||||||||||||||.+||++|||+|+||+|++++++ +++++|+++++.+++||+|+||++|+
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~dv 80 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTDV 80 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S--
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcCC
Confidence 68999999999999999999999999999999999999999999999999998 88999999999999999999999999
Q ss_pred CCCCCcCCCccccccCCCCHHHHHH
Q psy2882 1016 DLTKNIVSIPESLILQPKDEKLLMQ 1040 (1428)
Q Consensus 1016 ~l~~~~~~~~~~~~~~~~d~~~l~~ 1040 (1428)
|++.+ ++++.++++|.+++.+
T Consensus 81 ~l~~~----l~~l~~~~~d~~~l~~ 101 (101)
T PF01367_consen 81 PLPFS----LEDLRLQPPDREKLIE 101 (101)
T ss_dssp -------------------HHHH--
T ss_pred CCCCC----cchhccCCCCHHHhcC
Confidence 99998 5889999999988753
No 40
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.92 E-value=4.3e-24 Score=232.27 Aligned_cols=171 Identities=22% Similarity=0.150 Sum_probs=133.7
Q ss_pred eEEEEeeccccCccCCCcceeEEEEEEeC--Ccee-eccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDI--MLNT-IDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~DrIiqiaaIr~~~--~~~~-i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
-+|++|+||||++|..|+|||||+|++.. ++.+ +.+.|+++++|.+....+|+++.|||||++++.+.|++..+.+.
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~~ 85 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEALK 85 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHHH
Confidence 47999999999999999999999999964 2332 33449999999755444579999999999986678887777777
Q ss_pred HHHHHHc----C---CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCC
Q psy2882 389 IIEKIFL----K---PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNN 461 (1428)
Q Consensus 389 ~i~~~~~----~---~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~ 461 (1428)
++.+++. + .+.++|||| ++||..||++++.|+++.. ..| .++..+|++++++.+.|
T Consensus 86 ~~~~~l~~~~~~~~~~~~~lVaHn-a~FD~~fL~~~~~~~~~~~--~~~----~~~~~lDt~~la~~~~~---------- 148 (189)
T cd06134 86 EIFKPIRKALKAQGCTRAILVGHN-AHFDLGFLNAAVARCKIKR--NPF----HPFSTFDTATLAGLAYG---------- 148 (189)
T ss_pred HHHHHHHHHHhhcccCCCeEEEec-chhhHHHHHHHHHHhCCCC--CCC----CCCcEEEHHHHHHHHhC----------
Confidence 6666653 2 246899999 7999999999999987630 011 11234778888776643
Q ss_pred CCCCCChHhHHHHcCCCC--CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 462 GKPSFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 462 g~~s~kLe~L~~~~gi~~--~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
+++|+++|+++||+. .++|+|++||+||++|+.+|.++
T Consensus 149 ---~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 149 ---QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred ---CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 368999999999984 57999999999999999988764
No 41
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.91 E-value=7.5e-24 Score=235.30 Aligned_cols=173 Identities=19% Similarity=0.087 Sum_probs=137.1
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+||++|+||||++|..| |||||+|++..+..++++ |..+++|... .+|+++.|||||++++. .+.+..+++.++
T Consensus 7 ~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~~~~~-f~~li~P~~~--i~~~a~~ihGIt~e~l~-~~p~~~ev~~~~ 81 (217)
T TIGR00573 7 DTETTGDNETTGLYAGHD-IIEIGAVEIINRRITGNK-FHTYIKPDRP--IDPDAIKIHGITDDMLK-DKPDFKEIAEDF 81 (217)
T ss_pred cCEEEEEecCCCCCCCCC-EEEEEEEEEECCCEeeeE-EEEEECcCCC--CCHHHHhhcCCCHHHHc-CCCCHHHHHHHH
Confidence 589999999999999999 999999997665555555 8889988753 45799999999999994 455678999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
..++.+ .++|||| ++||..||+++|.|....+.. .+..+|++++.+.++... | ..+++|++
T Consensus 82 ~~~~~~--~~lVaHN-a~FD~~fL~~~~~r~~~~~~~-----~~~~~dtl~l~~~~~~~~------~-----~~~~~L~~ 142 (217)
T TIGR00573 82 ADYIRG--AELVIHN-ASFDVGFLNYEFSKLYKVEPK-----TNDVIDTTDTLQYARPEF------P-----GKRNTLDA 142 (217)
T ss_pred HHHhCC--CEEEEec-cHHHHHHHHHHHHHhcCCCCC-----ccceecHHHHHHHHHHhC------C-----CCCCCHHH
Confidence 998864 5899999 799999999999986433111 112345555555443322 1 23589999
Q ss_pred HHHHcCCCCC--CCCChHHHHHHHHHHHHHHHhhCchhH
Q psy2882 471 LSFVNNLSHK--KAHDALSDVRATLGLARLIRNNNPRLF 507 (1428)
Q Consensus 471 L~~~~gi~~~--~AHdAlaDv~AT~~l~~~l~~~~p~l~ 507 (1428)
++.++|++.. .+|||++||++|++|++.+.+++|++.
T Consensus 143 l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 143 LCKRYEITNSHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 9999999876 799999999999999999999988766
No 42
>PRK07740 hypothetical protein; Provisional
Probab=99.91 E-value=7.6e-24 Score=238.77 Aligned_cols=166 Identities=19% Similarity=0.191 Sum_probs=139.7
Q ss_pred ceEEEEeeccccCccCC-CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRR-DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~-DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
.+|||||+||||++|.+ |+|||||+|+++.+..+.++ |..+++|.. .+++.+..+||||++++ ..+.+..+++.+
T Consensus 59 ~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~-f~~lv~P~~--~i~~~~~~ltGIt~e~l-~~ap~~~evl~~ 134 (244)
T PRK07740 59 LPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDT-FYSLVKPKR--PIPEHILELTGITAEDV-AFAPPLAEVLHR 134 (244)
T ss_pred CCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEE-EEEEeCcCC--CCChhheeccCCCHHHH-hCCCCHHHHHHH
Confidence 58999999999999987 99999999999866443555 888888865 34579999999999999 567788999999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.+++.+ .++|||| +.||..|++.+++|++..++... ++|+..+++.+.|. .++++|+
T Consensus 135 f~~fi~~--~~lVahn-a~fD~~fL~~~~~~~~~~~~~~~---------~iDt~~l~r~l~~~----------~~~~sL~ 192 (244)
T PRK07740 135 FYAFIGA--GVLVAHH-AGHDKAFLRHALWRTYRQPFTHR---------LIDTMFLTKLLAHE----------RDFPTLD 192 (244)
T ss_pred HHHHhCC--CEEEEeC-HHHHHHHHHHHHHHhcCCCcCCC---------eechHHHHHHHcCC----------CCCCCHH
Confidence 9998864 5899998 79999999999999876665433 37888887777552 3578999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
+++.++|++...+|+|++||+||++|+.++...
T Consensus 193 ~l~~~~gi~~~~~H~Al~Da~ata~l~~~ll~~ 225 (244)
T PRK07740 193 DALAYYGIPIPRRHHALGDALMTAKLWAILLVE 225 (244)
T ss_pred HHHHHCCcCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999998877654
No 43
>PRK05168 ribonuclease T; Provisional
Probab=99.91 E-value=1.1e-23 Score=232.92 Aligned_cols=174 Identities=21% Similarity=0.139 Sum_probs=137.5
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeC--Ccee-eccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDI--MLNT-IDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFA 387 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~--~~~~-i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~ 387 (1428)
.+|+++|+||||++|..|+|||||+|++.. ++.+ +.+.|+.+++|.+....+++++.|||||++++.+.|.+..+++
T Consensus 17 ~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~~l 96 (211)
T PRK05168 17 FLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKEAL 96 (211)
T ss_pred CceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChHHHH
Confidence 589999999999999999999999999863 3333 3445999999965444457999999999998557888888888
Q ss_pred HHHHHHHcC-------CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCC
Q psy2882 388 SIIEKIFLK-------PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKN 460 (1428)
Q Consensus 388 ~~i~~~~~~-------~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~ 460 (1428)
.++.+++.+ .+.++|||| ++||..||++++.|+.+.. ..| ..|.++|++++++.+.|
T Consensus 97 ~~~~~~l~~~~~~~~~~~~~lVaHN-a~FD~~fL~~~~~r~~~~~--~~~----~~~~~iDt~~lar~~~~--------- 160 (211)
T PRK05168 97 HEIFKMVRKGIKASGCNRAILVAHN-AHFDLSFLMAAAERAGLKR--NPF----HPFSTFDTATLSGLALG--------- 160 (211)
T ss_pred HHHHHHHHHHHHhcccCCceEEEec-cHHhHHHHHHHHHHhCCCC--CCC----CCCcEeeHHHHHHHHcC---------
Confidence 888877652 357899999 7999999999999986531 111 12335788888776633
Q ss_pred CCCCCCChHhHHHHcCCCC--CCCCChHHHHHHHHHHHHHHHhhCc
Q psy2882 461 NGKPSFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNNNP 504 (1428)
Q Consensus 461 ~g~~s~kLe~L~~~~gi~~--~~AHdAlaDv~AT~~l~~~l~~~~p 504 (1428)
.++|+++|.++|++. ..+|+|++||+||++|+..+.++.+
T Consensus 161 ----~~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 161 ----QTVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred ----CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 258999999999985 4699999999999999998887643
No 44
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.91 E-value=9.4e-24 Score=231.50 Aligned_cols=174 Identities=21% Similarity=0.142 Sum_probs=135.2
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeC--Ccee-eccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDI--MLNT-IDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFA 387 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~--~~~~-i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~ 387 (1428)
-.++++|+||||++|..|+|||||+|++.. ++.+ .++.|+.+++|.+....++++..|||||+++....+.+..+++
T Consensus 8 ~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~~~ 87 (200)
T TIGR01298 8 YLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYEAL 87 (200)
T ss_pred CeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHHHH
Confidence 379999999999999999999999999853 3333 2344899999976655568999999999876446777777877
Q ss_pred HHHHHHHc----C---CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCC
Q psy2882 388 SIIEKIFL----K---PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKN 460 (1428)
Q Consensus 388 ~~i~~~~~----~---~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~ 460 (1428)
.++.+++. + .+.++|||| ++||..||++++.|+...+. .+ .....+|++++++.+.|
T Consensus 88 ~~~~~~l~~~~~~~~~~~~~lVaHN-a~FD~~fL~~~~~r~~~~~~--~~----~~~~~lDTl~lar~~~~--------- 151 (200)
T TIGR01298 88 HEIFKVVRKAMKASGCQRAILVGHN-ANFDLGFLNAAVERTSLKRN--PF----HPFSTFDTATLAGLAYG--------- 151 (200)
T ss_pred HHHHHHHHHHHHhcccCCCEEEEEC-chhhHHHHHHHHHHhCCCCC--CC----CCCcEEEHHHHHHHHcC---------
Confidence 77777762 1 346899999 79999999999999875421 11 11124777777766533
Q ss_pred CCCCCCChHhHHHHcCCCC--CCCCChHHHHHHHHHHHHHHHhhCc
Q psy2882 461 NGKPSFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNNNP 504 (1428)
Q Consensus 461 ~g~~s~kLe~L~~~~gi~~--~~AHdAlaDv~AT~~l~~~l~~~~p 504 (1428)
+++|+.+|+.+|++. .++|+|++||.+|++|+..+.++.+
T Consensus 152 ----~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 152 ----QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred ----cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 368999999999985 5899999999999999998876643
No 45
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.91 E-value=5.7e-24 Score=228.99 Aligned_cols=160 Identities=23% Similarity=0.183 Sum_probs=124.7
Q ss_pred EEEEeeccccCc-cCCCcceeEEEEEEeCCce------------eeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcC
Q psy2882 313 FLWYDYETFGLN-VRRDRPFQFAAIRTDIMLN------------TIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNN 379 (1428)
Q Consensus 313 ~v~~D~ETTGld-p~~DrIiqiaaIr~~~~~~------------~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~ 379 (1428)
|++||+|||||+ +.+|+|||||+|+++.+.. ++++ ++++++|...+ +++++.|||||++++...
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~-~~~lv~P~~~I--~~~a~~IhGIt~e~l~~~ 77 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDK-LSLCFNPGRAI--SPGASEITGLSNDLLEHK 77 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeee-eeEEeCCCCcC--ChhHHHHhCcCHHHHhcC
Confidence 799999999999 6899999999999987643 3444 88999998543 469999999999999776
Q ss_pred CCChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCC
Q psy2882 380 GIPEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWP 457 (1428)
Q Consensus 380 g~~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p 457 (1428)
+..+.++.+.+.+++.. .+.++||||..+||..||++++.|.+..... . ...+|++++++.+.|
T Consensus 78 ~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~-~-------~~~iDtl~l~r~~~~------ 143 (177)
T cd06136 78 APFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPD-D-------ILCVDSLPAFRELDQ------ 143 (177)
T ss_pred CCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCC-C-------CEEEEeHHHHhhhHh------
Confidence 64334455666666543 2368999995489999999999998754311 1 122567777766532
Q ss_pred CCCCCCCCCChHhHHHH-cCCCCCCCCChHHHHHHHHHHHHH
Q psy2882 458 YKNNGKPSFKLEHLSFV-NNLSHKKAHDALSDVRATLGLARL 498 (1428)
Q Consensus 458 ~~~~g~~s~kLe~L~~~-~gi~~~~AHdAlaDv~AT~~l~~~ 498 (1428)
+|++|+++ ||++..++|+|++||.||+++++.
T Consensus 144 ---------~L~~l~~~~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 144 ---------SLGSLYKRLFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred ---------hHHHHHHHHhCCCcccccchHHHHHHHHHHHhh
Confidence 89999985 999999999999999999998763
No 46
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=9.9e-24 Score=245.57 Aligned_cols=164 Identities=20% Similarity=0.225 Sum_probs=136.7
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|+++|+||||++|.+|+|||||+|+++.+++++++ ++.+++|..+ |.++.|||||++++. ...+..+++.++
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~-~~~lv~P~~~----~~~~~IhGIt~e~l~-~ap~f~ev~~~l 88 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQS-VVTLLNPGVD----PGPTHVHGLTAEMLE-GQPQFADIAGEV 88 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeE-EEEEECcCCC----CCCeecCCCCHHHHh-CCCCHHHHHHHH
Confidence 4799999999999999999999999999888887777 8889988642 467889999999994 333457899999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++. +.++|||| +.||..||+++|.|......... .+|++++++.+.| +.+++||++
T Consensus 89 ~~~l~--~~~lVaHN-a~FD~~fL~~~~~r~g~~~~~~~---------~ldTl~lar~~~~----------~~~~~kL~~ 146 (313)
T PRK06063 89 AELLR--GRTLVAHN-VAFDYSFLAAEAERAGAELPVDQ---------VMCTVELARRLGL----------GLPNLRLET 146 (313)
T ss_pred HHHcC--CCEEEEeC-HHHHHHHHHHHHHHcCCCCCCCC---------EEehHHHHHHhcc----------CCCCCCHHH
Confidence 99986 45899999 79999999999999875422212 3777888777643 246899999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
||++|||+..++|||++||+||++|+..+.++
T Consensus 147 l~~~~gi~~~~~H~Al~DA~ata~l~~~ll~~ 178 (313)
T PRK06063 147 LAAHWGVPQQRPHDALDDARVLAGILRPSLER 178 (313)
T ss_pred HHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998877654
No 47
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=1.9e-23 Score=236.43 Aligned_cols=166 Identities=17% Similarity=0.174 Sum_probs=138.7
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
..|+++|+||||++|..|+|||||||+++. +.++++ |+.+++|. .+| +.+..+||||++++ ..+.+..+++.++
T Consensus 68 ~~~vv~DiETTG~~~~~~~IIEIGAv~v~~-g~i~~~-f~~~v~p~--~ip-~~~~~itGIt~e~l-~~ap~~~evl~~f 141 (257)
T PRK08517 68 QVFCFVDIETNGSKPKKHQIIEIGAVKVKN-GEIIDR-FESFVKAK--EVP-EYITELTGITYEDL-ENAPSLKEVLEEF 141 (257)
T ss_pred CCEEEEEEeCCCCCCCCCeEEEEEEEEEEC-CEEEEE-EEEEECCC--CCC-hhhhhhcCcCHHHH-cCCCCHHHHHHHH
Confidence 589999999999999999999999999974 567776 89999985 333 58899999999999 4677889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++++ .++|||| ++||..||++++.|.+..+..+. . +|++.+++.+.| .++++|++
T Consensus 142 ~~fl~~--~v~VaHN-a~FD~~fL~~~l~r~g~~~~~~~------~---ldtl~la~~~~~-----------~~~~~L~~ 198 (257)
T PRK08517 142 RLFLGD--SVFVAHN-VNFDYNFISRSLEEIGLGPLLNR------K---LCTIDLAKRTIE-----------SPRYGLSF 198 (257)
T ss_pred HHHHCC--CeEEEEC-HHHHHHHHHHHHHHcCCCCCCCC------c---EehHHHHHHHcc-----------CCCCCHHH
Confidence 999864 5899999 79999999999999887654433 2 445555544432 23589999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCch
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPR 505 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~ 505 (1428)
|++.+|++...+|+|++||.||++|+..+.++.|.
T Consensus 199 L~~~lgi~~~~~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 199 LKELLGIEIEVHHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred HHHHcCcCCCCCCChHHHHHHHHHHHHHHHHHhHH
Confidence 99999999989999999999999999999887764
No 48
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.90 E-value=3e-23 Score=231.22 Aligned_cols=173 Identities=17% Similarity=0.114 Sum_probs=136.7
Q ss_pred eEEEEeeccccCccCC-CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 312 TFLWYDYETFGLNVRR-DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~-DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+||+|+||||++|.. |+|||||+|++... .+.++.|+.|++|..++ +|++..|||||++++. .+.+..+++.++
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~-~~~~~~f~~~i~P~~~i--~~~a~~vhGIt~e~l~-~~p~f~ev~~~f 76 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNR-MLTGDNFHVYVNPERDM--PAEAAKVHGITDEFLA-DKPKFKEIADEF 76 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECC-cEecceEEEEECcCCCC--CHHHHhccCCCHHHHh-CCCCHHHHHHHH
Confidence 4899999999999987 99999999998754 34555599999998654 4699999999999994 455668999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++.+ ..+|||| +.||..||+++|.|.... +. .+ ...+.++|++.+++.+.|. .+++|++
T Consensus 77 ~~fi~~--~~lVaHN-a~FD~~fL~~el~r~g~~-~~-~~---~~~~~~iDTl~lar~~~p~-----------~~~~L~~ 137 (225)
T TIGR01406 77 LDFIGG--SELVIHN-AAFDVGFLNYELERLGPT-IK-KI---GEFCRVIDTLAMARERFPG-----------QRNSLDA 137 (225)
T ss_pred HHHhCC--CEEEEEe-cHHHHHHHHHHHHHhCCC-Cc-cc---ccCCCEEEHHHHHHHHcCC-----------CCCCHHH
Confidence 999874 4789999 699999999999987621 11 00 1112347888888877552 2589999
Q ss_pred HHHHcCCCCC--CCCChHHHHHHHHHHHHHHHhhCchhH
Q psy2882 471 LSFVNNLSHK--KAHDALSDVRATLGLARLIRNNNPRLF 507 (1428)
Q Consensus 471 L~~~~gi~~~--~AHdAlaDv~AT~~l~~~l~~~~p~l~ 507 (1428)
||++|||+.. .+|+|+.||++|++|+..|...+-.+.
T Consensus 138 L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~~~~~ 176 (225)
T TIGR01406 138 LCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQESLL 176 (225)
T ss_pred HHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCCcchh
Confidence 9999999864 479999999999999998877654444
No 49
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.90 E-value=3.7e-23 Score=231.69 Aligned_cols=174 Identities=18% Similarity=0.121 Sum_probs=138.6
Q ss_pred CceEEEEeeccccCccC-CCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVR-RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~-~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
.+.|+|+|+||||++|. .|+|||||+|.+..+ .++++.|+.|++|..++ +|++..|||||++++. .+.+..+++.
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~-~~~~~~f~~~i~P~~~i--~~~a~~VHGIT~e~l~-~~p~f~ev~~ 78 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINR-RLTGRNFHVYIKPDRLV--DPEALAVHGITDEFLA-DKPTFAEVAD 78 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECC-EEeccEEEEEECcCCcC--CHHHhhhcCCCHHHHc-CCCCHHHHHH
Confidence 36899999999999998 899999999998754 45666699999997653 4699999999999994 4556689999
Q ss_pred HHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 389 IIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 389 ~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
++.+++.+ ..+|||| +.||..||+++|.|.... +. .+. ..+.++|++.+++.+.|. .+++|
T Consensus 79 ~f~~fi~~--~~lVaHN-a~FD~~fL~~el~r~g~~-~~-~~~---~~~~~iDTl~lar~~~p~-----------~~~~L 139 (240)
T PRK05711 79 EFLDFIRG--AELIIHN-APFDIGFMDYEFALLGRD-IP-KTN---TFCKVTDTLAMARRMFPG-----------KRNSL 139 (240)
T ss_pred HHHHHhCC--CEEEEEc-cHHhHHHHHHHHHHhCCC-CC-ccc---ccCceeeHHHHHHHHcCC-----------CCCCH
Confidence 99999864 4689999 699999999999987521 11 111 112358888888887552 24799
Q ss_pred HhHHHHcCCCCC--CCCChHHHHHHHHHHHHHHHhhCchh
Q psy2882 469 EHLSFVNNLSHK--KAHDALSDVRATLGLARLIRNNNPRL 506 (1428)
Q Consensus 469 e~L~~~~gi~~~--~AHdAlaDv~AT~~l~~~l~~~~p~l 506 (1428)
+.||++|||+.. .+|+|+.||++|++|+..|...|..|
T Consensus 140 ~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~~~l 179 (240)
T PRK05711 140 DALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGGQTSL 179 (240)
T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCccccc
Confidence 999999999864 47999999999999998887665444
No 50
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.90 E-value=8.1e-23 Score=217.64 Aligned_cols=163 Identities=17% Similarity=0.064 Sum_probs=130.9
Q ss_pred EEEEeeccccCcc-CCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 313 FLWYDYETFGLNV-RRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 313 ~v~~D~ETTGldp-~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
|||+|+||||++| ..|+|||||+|+++.+ .+.++.++.+|+|... .+|++..|||||++++. .+.+..+++.++.
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~-~~~~~~~~~~v~P~~~--i~~~~~~ihGIt~e~l~-~~~~~~~v~~~l~ 76 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINR-RLTGNTFHVYINPERD--IPEEAFKVHGITDEFLA-DKPKFAEIADEFL 76 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECC-cEeccEEEEEECCCCC--CCHHHHHHhCCCHHHHh-cCCCHHHHHHHHH
Confidence 6999999999999 7899999999999764 3445458899999864 34799999999999994 5667789999999
Q ss_pred HHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhH
Q psy2882 392 KIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL 471 (1428)
Q Consensus 392 ~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L 471 (1428)
+++.+ .++|||| +.||..||++++.|++..+-.. ..+..+|++++++.+.|. .+++|+++
T Consensus 77 ~~l~~--~~lv~hn-~~fD~~~l~~~~~~~~~~~~~~------~~~~~idt~~~~~~~~~~-----------~~~~L~~l 136 (167)
T cd06131 77 DFIRG--AELVIHN-ASFDVGFLNAELSLLGLGKKII------DFCRVIDTLALARKKFPG-----------KPNSLDAL 136 (167)
T ss_pred HHHCC--CeEEEeC-hHHhHHHHHHHHHHhCCCcccc------cCCCceEhHHHHHHHcCC-----------CCCCHHHH
Confidence 98864 4689999 6999999999999975432110 112338888888776442 24799999
Q ss_pred HHHcCCCCC--CCCChHHHHHHHHHHHHHH
Q psy2882 472 SFVNNLSHK--KAHDALSDVRATLGLARLI 499 (1428)
Q Consensus 472 ~~~~gi~~~--~AHdAlaDv~AT~~l~~~l 499 (1428)
++++|++.. ++|+|++||++|++|+..|
T Consensus 137 ~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 137 CKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred HHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 999999864 5899999999999999775
No 51
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.90 E-value=1.3e-22 Score=215.36 Aligned_cols=165 Identities=25% Similarity=0.207 Sum_probs=137.0
Q ss_pred eEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
.||++|+||||+++..++|+|||+|+++.+. +.+. |+.+|+|.. .++|.+..+||||++++. .|.+..+++.++.
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~-~~~~-f~~~v~p~~--~i~~~~~~~~Git~~~l~-~~~~~~~~~~~~~ 75 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGR-IIVV-FDTYVKPDR--PITDYATEIHGITPEMLD-DAPTFEEVLEELL 75 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCE-eEEE-EEEEECCCC--CCCHHHHHHhCCCHHHHh-CCCCHHHHHHHHH
Confidence 4899999999999999999999999998874 4454 999999954 346799999999999994 5889999999999
Q ss_pred HHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhH
Q psy2882 392 KIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL 471 (1428)
Q Consensus 392 ~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L 471 (1428)
+++.+ .++|+||+.+||..||+..+.|++...-. .+ + .+|++.+++.+.|. .+++|+++
T Consensus 76 ~~l~~--~~~v~~n~~~fD~~~L~~~~~~~~~~~~~-----~~-~--~iD~~~~~~~~~~~-----------~~~~L~~l 134 (169)
T smart00479 76 EFLKG--KILVAGNALNFDLRFLKLEHPRLGIKDPP-----KN-P--VIDTLKLARALNPG-----------RKYSLKKL 134 (169)
T ss_pred HHhcC--CEEEEeCCHHHhHHHHHHHHHHhCCCCCc-----CC-C--eeEHHHHHHHHCCC-----------CCCCHHHH
Confidence 99964 47899998899999999999998754210 11 1 36777777766431 27999999
Q ss_pred HHHcCCCCCCC-CChHHHHHHHHHHHHHHHhh
Q psy2882 472 SFVNNLSHKKA-HDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 472 ~~~~gi~~~~A-HdAlaDv~AT~~l~~~l~~~ 502 (1428)
++.+|++..++ |+|++||++|++|++.+.++
T Consensus 135 ~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 166 (169)
T smart00479 135 AERLGLEVIGRAHRALDDARATAKLFKKLVER 166 (169)
T ss_pred HHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHH
Confidence 99999998876 99999999999999988754
No 52
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=1.4e-22 Score=235.46 Aligned_cols=165 Identities=18% Similarity=0.182 Sum_probs=140.0
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
++||++|+||||++|..|+|||||||+++ ++.++++ |+.+++|...+ +|.+..+||||++++ ..+.+..+++..+
T Consensus 8 ~~~Vv~DlETTGl~p~~~eIIEIgaV~v~-~g~i~~~-f~~lVkP~~~I--~~~a~~ihGIT~e~l-~~~~~~~evl~~f 82 (313)
T PRK06807 8 LDYVVIDFETTGFNPYNDKIIQVAAVKYR-NHELVDQ-FVSYVNPERPI--PDRITSLTGITNYRV-SDAPTIEEVLPLF 82 (313)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEE-CCEEEEE-EEEEECcCCCC--CHhhhccCCCCHHHH-hCCCCHHHHHHHH
Confidence 58999999999999999999999999997 5577777 99999998654 469999999999999 4566788999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++++ .++|||| +.||..||++.+.|++++.. ....+|++.+++.+.| +.++++|++
T Consensus 83 ~~fl~~--~~lVaHN-a~FD~~fL~~~~~~~gl~~~---------~~~~iDtl~la~~~~~----------~~~~~kL~~ 140 (313)
T PRK06807 83 LAFLHT--NVIVAHN-ASFDMRFLKSNVNMLGLPEP---------KNKVIDTVFLAKKYMK----------HAPNHKLET 140 (313)
T ss_pred HHHHcC--CeEEEEc-HHHHHHHHHHHHHHcCCCCC---------CCCEeeHHHHHHHHhC----------CCCCCCHHH
Confidence 999864 4799998 69999999999998876422 1234788888887755 245789999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhC
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 503 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~ 503 (1428)
|++++|++. ++|||++||++|++|+..+....
T Consensus 141 L~~~lgi~~-~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 141 LKRMLGIRL-SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred HHHHcCCCC-CCcChHHHHHHHHHHHHHHHHhh
Confidence 999999998 99999999999999998877554
No 53
>PRK07883 hypothetical protein; Validated
Probab=99.89 E-value=2.9e-22 Score=249.30 Aligned_cols=182 Identities=18% Similarity=0.165 Sum_probs=149.9
Q ss_pred ccceeeeeeeccCCceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHH
Q psy2882 297 IGNYYIDILLHNGNSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFC 376 (1428)
Q Consensus 297 ~G~~~V~v~l~~~~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~ 376 (1428)
.|...+...+.. .+|||+|+||||++|..|+|+|||+|+++. +.++++ |+.+|+|...+ +|.++.|||||++++
T Consensus 3 ~~~~~~~~~~~~--~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~-g~iv~~-f~~lV~P~~~i--~~~~~~itGIt~e~l 76 (557)
T PRK07883 3 LSFDDLGTPLRD--VTFVVVDLETTGGSPAGDAITEIGAVKVRG-GEVLGE-FATLVNPGRPI--PPFITVLTGITTAMV 76 (557)
T ss_pred CChhhhCCCCcC--CCEEEEEEecCCCCCCCCeEEEEEEEEEEC-CEEEEE-EEEEECCCCCC--ChhHHhhcCCCHHHH
Confidence 455555555555 699999999999999999999999999974 467777 99999997654 469999999999999
Q ss_pred hcCCCChHHHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCC
Q psy2882 377 LNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITW 456 (1428)
Q Consensus 377 ~~~g~~e~e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~ 456 (1428)
..+.+..+++.++.+++. +.++|||| ++||..||+.+|.|++++..... .+|++++++.+.|.
T Consensus 77 -~~ap~~~evl~~f~~fl~--~~~lVaHN-a~FD~~fL~~~~~r~g~~~~~~~---------~iDTl~lar~l~~~---- 139 (557)
T PRK07883 77 -AGAPPIEEVLPAFLEFAR--GAVLVAHN-APFDIGFLRAAAARCGYPWPGPP---------VLCTVRLARRVLPR---- 139 (557)
T ss_pred -hCCCCHHHHHHHHHHHhc--CCEEEEeC-cHHHHHHHHHHHHHcCCCCCCCC---------cEecHHHHHHhccc----
Confidence 567788999999999886 46899998 69999999999999987632222 37777877776442
Q ss_pred CCCCCCCCCCChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCch
Q psy2882 457 PYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPR 505 (1428)
Q Consensus 457 p~~~~g~~s~kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~ 505 (1428)
.+..+++|++|++++|++..++|+|++||.||++|+..+.++.+.
T Consensus 140 ----~~~~~~~L~~L~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 140 ----DEAPNVRLSTLARLFGATTTPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred ----CCCCCCCHHHHHHHCCcccCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 245789999999999999999999999999999999988766543
No 54
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.5e-23 Score=186.38 Aligned_cols=70 Identities=44% Similarity=0.767 Sum_probs=65.1
Q ss_pred cccCCccccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 110 RQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 110 ~~~~~~~~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
.+.++++++++|+|+||..+++.|||||+++|++||||+|||+|||+||+|+|+||+|++||||||.+.|
T Consensus 5 ~~~r~~~~rrrk~c~~~~~~~~~iDYKd~~~L~rfise~GKI~prRiTG~sak~QR~la~AIKRAR~laL 74 (75)
T COG0238 5 FGRRAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQRRLARAIKRARYLAL 74 (75)
T ss_pred ccccccccccccccccccccCCccCccCHHHHHHHhcccCcccccccccccHHHHHHHHHHHHHHHHHhc
Confidence 3445568889999999999999999999999999999999999999999999999999999999998865
No 55
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=6.1e-22 Score=231.00 Aligned_cols=163 Identities=19% Similarity=0.166 Sum_probs=134.8
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
+.||++|+|||| +.+|+|||||+|+++. +.++++ |+.+|+|.... .+|.++.|||||++++. .+.+..+++.++
T Consensus 1 ~~~vviD~ETTg--~~~d~IieIgav~v~~-g~i~~~-f~~lv~P~~~~-~~~~~~~IhGIT~e~v~-~ap~f~ev~~~~ 74 (309)
T PRK06195 1 MNFVAIDFETAN--EKRNSPCSIGIVVVKD-GEIVEK-VHYLIKPKEMR-FMPINIGIHGIRPHMVE-DELEFDKIWEKI 74 (309)
T ss_pred CcEEEEEEeCCC--CCCCceEEEEEEEEEC-CEEEEE-EEEEECCCCCC-CChhheeccCcCHHHHh-CCCCHHHHHHHH
Confidence 479999999997 4689999999999974 567776 99999997533 34688899999999994 455778999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++. +.++|||| ++||..||++++.|+....... +.+|++++++.+.| +.++++|++
T Consensus 75 ~~fl~--~~~lVaHN-a~FD~~fL~~~~~r~~~~~~~~---------~~idT~~lar~l~~----------~~~~~~L~~ 132 (309)
T PRK06195 75 KHYFN--NNLVIAHN-ASFDISVLRKTLELYNIPMPSF---------EYICTMKLAKNFYS----------NIDNARLNT 132 (309)
T ss_pred HHHhC--CCEEEEEC-cHHHHHHHHHHHHHhCCCCCCC---------CEEEHHHHHHHHcC----------CCCcCCHHH
Confidence 99996 46899999 7999999999999976543222 33888888888755 346799999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
|+.++|++. .+|+|++||+||++|+..+.++
T Consensus 133 L~~~~gi~~-~~H~Al~DA~ata~l~~~l~~~ 163 (309)
T PRK06195 133 VNNFLGYEF-KHHDALADAMACSNILLNISKE 163 (309)
T ss_pred HHHHcCCCC-cccCCHHHHHHHHHHHHHHHHH
Confidence 999999995 6999999999999998877654
No 56
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=1.2e-21 Score=213.50 Aligned_cols=191 Identities=17% Similarity=0.186 Sum_probs=137.3
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
..+||++|+||||+++ .|+|||||||+++.+ .++++ |..+++|...+ ++.+..|||||++++ ..+.+..+++.+
T Consensus 4 ~~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g-~~~~~-f~~lv~P~~~i--~~~~~~lhGIt~~~v-~~ap~~~evl~~ 77 (195)
T PRK07247 4 LETYIAFDLEFNTVNG-VSHIIQVSAVKYDDH-KEVDS-FDSYVYTDVPL--QSFINGLTGITADKI-ADAPKVEEVLAA 77 (195)
T ss_pred CCeEEEEEeeCCCCCC-CCeEEEEEEEEEECC-EEEEE-EEEEECCCCCC--CccceecCCCCHHHH-hCCCCHHHHHHH
Confidence 4689999999999985 799999999999854 56666 99999997643 458889999999999 456678999999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.++++ +.++||||...||..||+. ++++. ... -.+|+++ .++..+. ..+| +.+++||+
T Consensus 78 f~~f~~--~~~lVaHNa~~fD~~fL~~----~g~~~-~~~-----~~idt~~---~~~~~~~--~~~~----~~~~~~L~ 136 (195)
T PRK07247 78 FKEFVG--ELPLIGYNAQKSDLPILAE----NGLDL-SDQ-----YQVDLYD---EAFERRS--SDLN----GIANLKLQ 136 (195)
T ss_pred HHHHHC--CCeEEEEeCcHhHHHHHHH----cCCCc-CCC-----ceeehHH---HHHHhhc--cccC----CCCCCCHH
Confidence 999996 4579999954599999864 33331 111 1234443 3322211 1122 46789999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeecc
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMF 538 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~ 538 (1428)
+||++||++. .+|||++||++|+.|+..+.+.. .+|....+.=+..+..||..+.|.|
T Consensus 137 ~La~~~gi~~-~~HrAl~DA~~ta~v~~~ll~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (195)
T PRK07247 137 TVADFLGIKG-RGHNSLEDARMTARVYESFLESD----------QNKEYLEQQEEVTSDNPFAALGGLF 194 (195)
T ss_pred HHHHhcCCCC-CCcCCHHHHHHHHHHHHHHHhhc----------cchhhhhcchhhccCCchhhhhccc
Confidence 9999999995 68999999999999999887652 2333333333334556765555443
No 57
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=2.4e-21 Score=223.88 Aligned_cols=173 Identities=10% Similarity=0.051 Sum_probs=137.9
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+||++|+|||||+|..|+||+||||++..++.+.++ |+.+++|..+..| ..|||||++++ ..+.+..+++.++
T Consensus 46 ~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~-f~tLVnP~~~~~p----~~LHGIT~e~L-a~AP~f~eVl~el 119 (377)
T PRK05601 46 APFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEH-FHAVLNPGEDPGP----FHLHGLSAEEF-AQGKRFSQILKPL 119 (377)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEE-EEEEECcCCCCCC----ccccCCCHHHH-hcCCCHHHHHHHH
Confidence 4799999999999999999999999999878777777 9999999865332 36999999999 4587889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccch-hhh----h-------------hcCCCCCchhhHHHHHHHhCCC
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPY-ERE----W-------------KNNCSRWDLINVIKAFYVLSPY 452 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y-~~~----~-------------~~g~sr~D~ld~~rl~~~l~p~ 452 (1428)
.+++. +.++|+|| +.||..||.++|.|.+.... .+. + ........++|++.+++.+.|
T Consensus 120 ~~fL~--g~vLVaHN-A~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p- 195 (377)
T PRK05601 120 DRLID--GRTLILHN-APRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGV- 195 (377)
T ss_pred HHHhC--CCEEEEEC-cHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcC-
Confidence 99997 45899999 79999999999988643210 000 0 000111246888999888865
Q ss_pred CcCCCCCCCCCCCCChHhHHHHcCCCC----------CCCCChHH--HHHHHHHHHHHHHhh
Q psy2882 453 GITWPYKNNGKPSFKLEHLSFVNNLSH----------KKAHDALS--DVRATLGLARLIRNN 502 (1428)
Q Consensus 453 ~~~~p~~~~g~~s~kLe~L~~~~gi~~----------~~AHdAla--Dv~AT~~l~~~l~~~ 502 (1428)
..++|||++||++|||+. ...|+|++ |++.+++|+..++++
T Consensus 196 ---------~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 196 ---------ALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred ---------CCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 356899999999999998 77899995 999999999876443
No 58
>PRK05359 oligoribonuclease; Provisional
Probab=99.87 E-value=1.3e-21 Score=211.19 Aligned_cols=163 Identities=18% Similarity=0.228 Sum_probs=130.0
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCC--CChhhHhhc---CCCHHHHhcCCCChHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFL--PDPRACLIT---KITPQFCLNNGIPEYK 385 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~--p~pea~~it---GITpe~~~~~g~~e~e 385 (1428)
.+|||+|+|||||||.+|+|+|||||+++.+++++++.++++|+|+...+ .++.+..+| |||++++ +.+.+..+
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l-~~~~~~~e 81 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVR-ASTVSEAE 81 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHH-hcCCCHHH
Confidence 58999999999999999999999999999988889888999999987643 245777887 8999887 67788899
Q ss_pred HHHHHHHHHcC----CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCC
Q psy2882 386 FASIIEKIFLK----PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNN 461 (1428)
Q Consensus 386 ~~~~i~~~~~~----~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~ 461 (1428)
++.++.+++.+ .+.+++| ||++||..||++.+.+.. .++. +..+|+..+..+++.+.|+.
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g-~~v~FD~~FL~~~~~~~~-~~l~------~~~~Dv~tl~~l~r~~~P~~-------- 145 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCG-NSIGQDRRFLARYMPELE-AYFH------YRNLDVSTLKELARRWKPEI-------- 145 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceee-cchhhCHHHHHHHHHHhc-ccCC------CcccchhHHHHHHHHhChhh--------
Confidence 99999999964 2345666 559999999999886532 2221 23456433337888886641
Q ss_pred CCCCCChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 462 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 462 g~~s~kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
.+++++.++|+|++||++|+++++.+++.
T Consensus 146 ------------~~~~~~~~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 146 ------------LNGFKKQGTHRALADIRESIAELKYYREH 174 (181)
T ss_pred ------------hhCCCCcCCcccHHHHHHHHHHHHHHHHH
Confidence 25888889999999999999999988864
No 59
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.87 E-value=2.8e-21 Score=203.08 Aligned_cols=154 Identities=21% Similarity=0.256 Sum_probs=128.6
Q ss_pred EEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHH
Q psy2882 313 FLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEK 392 (1428)
Q Consensus 313 ~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~ 392 (1428)
||++|+||||.+ .|+|||||+|+++. ++++++ ++.+++|...+ +|++..+||||++++. .+.+..+++.++.+
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~-~~~~~~-~~~~i~p~~~~--~~~~~~i~GIt~e~l~-~~~~~~~v~~~l~~ 73 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRD-GQIVDT-FYTLIRPPTRF--DPFNIAIHGITPEDVA-DAPTFPEVWPEIKP 73 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEEC-CEEEEE-EEEEeCcCCCC--ChhhccccCcCHHHHh-cCCCHHHHHHHHHH
Confidence 799999999965 68999999999984 466666 89999998733 4699999999999995 56667899999999
Q ss_pred HHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHH
Q psy2882 393 IFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLS 472 (1428)
Q Consensus 393 ~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~ 472 (1428)
++.+ .++|||| ++||..||+..+.|.+.++.. ...+|+..++..+.| +.++++|++++
T Consensus 74 ~l~~--~~lv~hn-~~fD~~~l~~~~~~~g~~~~~---------~~~idt~~~~~~~~~----------~~~~~~L~~l~ 131 (156)
T cd06130 74 FLGG--SLVVAHN-ASFDRSVLRAALEAYGLPPPP---------YQYLCTVRLARRVWP----------LLPNHKLNTVA 131 (156)
T ss_pred HhCC--CEEEEeC-hHHhHHHHHHHHHHcCCCCCC---------CCEEEHHHHHHHHhc----------cCCCCCHHHHH
Confidence 9975 4899998 799999999999998765322 234777777777644 24579999999
Q ss_pred HHcCCCCCCCCChHHHHHHHHHHH
Q psy2882 473 FVNNLSHKKAHDALSDVRATLGLA 496 (1428)
Q Consensus 473 ~~~gi~~~~AHdAlaDv~AT~~l~ 496 (1428)
+.+|++.. +|+|++||++|++|+
T Consensus 132 ~~~g~~~~-~H~Al~Da~~ta~l~ 154 (156)
T cd06130 132 EHLGIELN-HHDALEDARACAEIL 154 (156)
T ss_pred HHcCCCcc-CcCchHHHHHHHHHH
Confidence 99999988 999999999999886
No 60
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.86 E-value=3.9e-21 Score=212.15 Aligned_cols=168 Identities=14% Similarity=0.073 Sum_probs=132.5
Q ss_pred ceEEEEeeccccCccC------CCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChH
Q psy2882 311 STFLWYDYETFGLNVR------RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEY 384 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~------~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~ 384 (1428)
++|+++|+||||+++. .|+|||||||+++.+ +++++ |+.||+|......++.++.|||||++++ ..|.+..
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~-~i~~~-f~~lV~P~~~~~i~~~~~~ltGIt~~~l-~~ap~~~ 80 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGC-EVEDT-FSSYVKPKTFPSLTERCKSFLGITQEDV-DKGISFE 80 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecC-cChhh-hcceECCCccCccChhhhhhcCcCHHHH-ccCCCHH
Confidence 5899999999997764 489999999999855 66666 9999999763223468999999999999 5788889
Q ss_pred HHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHcccc-chhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCC
Q psy2882 385 KFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLIN-PYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463 (1428)
Q Consensus 385 e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~-~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~ 463 (1428)
+++.++.++++... .++.+| .+||..||+.++.++.++ |+...| +|+..+++.+.+. .
T Consensus 81 evl~~f~~~~~~~~-~~iv~~-~~fD~~fL~~~~~~~~~~~~~~~~~---------~dl~~~~~~~~~~----------~ 139 (207)
T PRK07748 81 ELVEKLAEYDKRCK-PTIVTW-GNMDMKVLKHNCEKAGVPFPFKGQC---------RDLSLEYKKFFGE----------R 139 (207)
T ss_pred HHHHHHHHHhCcCC-eEEEEE-CHHHHHHHHHHHHHcCCCCcccccc---------eeHHHHHHHHhCc----------C
Confidence 99999999997522 344456 489999999999998765 333332 5566665555331 2
Q ss_pred CCCChHhHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHhh
Q psy2882 464 PSFKLEHLSFVNNLSHK-KAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 464 ~s~kLe~L~~~~gi~~~-~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
.+++|+++++.+|++.. ++|+|++||++|++|+..+.+.
T Consensus 140 ~~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 140 NQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred CCCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhC
Confidence 35899999999999964 5899999999999999988754
No 61
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=2.9e-21 Score=254.06 Aligned_cols=166 Identities=22% Similarity=0.228 Sum_probs=142.8
Q ss_pred ceEEEEeeccccCccCC-CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRR-DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~-DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
++||++|+||||++|.. |+|||||+|+++ ++.++++ |+.+|+|...+ +|++..+||||++++ ..+.+..+++..
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~-~~~i~~~-f~~~v~P~~~i--~~~~~~ltGIt~~~l-~~ap~f~ev~~~ 77 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVE-DGEILER-FSSFVNPERPI--PPFITELTGISEEMV-KQAPLFEDVAPE 77 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEE-CCEEEEE-EEEEECcCCCC--CHHHhhcCCCCHHHH-hcCCCHHHHHHH
Confidence 57999999999999885 999999999996 4577777 99999998654 368999999999999 466677899999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.+++. ++++|||| +.||..||+++|.|++++++...| +|++.+++.+.|. .++|+|+
T Consensus 78 l~~~l~--~~~~VaHN-~~FD~~fL~~~~~~~g~~~~~~~~---------iDt~~la~~~~p~----------~~~~~L~ 135 (928)
T PRK08074 78 IVELLE--GAYFVAHN-VHFDLNFLNEELERAGYTEIHCPK---------LDTVELARILLPT----------AESYKLR 135 (928)
T ss_pred HHHHhC--CCeEEEEC-hHHHHHHHHHHHHHcCCCCCCCCe---------eeHHHHHHHhcCC----------CCCCCHH
Confidence 999996 56899999 799999999999999887654333 7888888777552 4579999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhC
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 503 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~ 503 (1428)
+||+++|+++.++|+|++||+||++|+..+.++.
T Consensus 136 ~l~~~l~i~~~~~H~Al~DA~ata~l~~~l~~~~ 169 (928)
T PRK08074 136 DLSEELGLEHDQPHRADSDAEVTAELFLQLLNKL 169 (928)
T ss_pred HHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999887653
No 62
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=4.9e-21 Score=220.56 Aligned_cols=171 Identities=19% Similarity=0.205 Sum_probs=122.1
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeC--Cce--eeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDI--MLN--TIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKF 386 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~--~~~--~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~ 386 (1428)
.+++|+|+||||+||..|+|||||+|+++. ++. .+.+.++.+++|...+ +++++.|||||++++...+.+..
T Consensus 37 ~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I--~~~~t~IhGIt~e~v~~~~~~~~-- 112 (294)
T PRK09182 37 RLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPI--PPEITRLTGITDEMVAGQTIDPA-- 112 (294)
T ss_pred CeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCC--CHHHHHhcCCCHHHHhcCCCcHH--
Confidence 589999999999999999999999999974 232 2334489999998643 46999999999999966665433
Q ss_pred HHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCC
Q psy2882 387 ASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSF 466 (1428)
Q Consensus 387 ~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~ 466 (1428)
.+..++.. ..++|||| +.||..||+..+.+.. ...| .+++. .+.|+. .+..++
T Consensus 113 --~l~~fl~~-~~vlVAHN-A~FD~~fL~~~~~~~~----~~~~---------~ct~~--------~i~~~~--~~~~~~ 165 (294)
T PRK09182 113 --AVDALIAP-ADLIIAHN-AGFDRPFLERFSPVFA----TKPW---------ACSVS--------EIDWSA--RGFEGT 165 (294)
T ss_pred --HHHHHhcC-CCEEEEeC-HHHHHHHHHHHHHhcc----CCcc---------cccHH--------HHhhcc--ccCCCC
Confidence 34444443 46899999 6999999987654321 1122 11221 123542 245789
Q ss_pred ChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHh-hC-chhHHHHHhhc
Q psy2882 467 KLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN-NN-PRLFNFILSLR 514 (1428)
Q Consensus 467 kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~-~~-p~l~~~~~~~~ 514 (1428)
||++||.+|| ...++|+|++||+||++|+..+.. .. +.| +.++..+
T Consensus 166 kL~~La~~~g-~~~~aHrAl~Da~Ata~ll~~~l~~~~~~~l-~~Ll~~~ 213 (294)
T PRK09182 166 KLGYLAGQAG-FFHEGHRAVDDCQALLELLARPLPETGQPPL-AELLEAS 213 (294)
T ss_pred CHHHHHHHcC-CCCCCcChHHHHHHHHHHHHHHHhhcCCcCH-HHHHHHh
Confidence 9999999999 456899999999999999885442 22 333 5554443
No 63
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.86 E-value=3.8e-21 Score=251.89 Aligned_cols=166 Identities=21% Similarity=0.208 Sum_probs=140.3
Q ss_pred eEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
+||++|+||||++|..|+|||||+|+++ ++.++++ ++.+++|...+ ++.+..+||||++++. .+.+..+++.++.
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~-~~~i~~~-f~~~v~P~~~i--~~~~~~ltGIt~e~l~-~ap~~~ev~~~l~ 75 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVE-DGEIVDT-FHTDVNPNEPI--PPFIQELTGISDNMLQ-QAPYFSQVAQEIY 75 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEE-CCEEEEE-EEEEeCCCCCC--ChhhhhhcCcCHHHHh-CCCCHHHHHHHHH
Confidence 4999999999999999999999999996 4567776 99999998654 3589999999999994 5556789999999
Q ss_pred HHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhH
Q psy2882 392 KIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL 471 (1428)
Q Consensus 392 ~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L 471 (1428)
+++. +.++|||| +.||..||+++|.|++++++...| +|++.+++.+.| ..++++|++|
T Consensus 76 ~~l~--~~~~VahN-~~fD~~fL~~~~~~~g~~~~~~~~---------iDt~~l~~~~~p----------~~~~~~L~~l 133 (850)
T TIGR01407 76 DLLE--DGIFVAHN-VHFDLNFLAKALKDCGYEPLPKPR---------IDTVELAQIFFP----------TEESYQLSEL 133 (850)
T ss_pred HHhC--CCEEEEeC-cHHHHHHHHHHHHHcCCCCCCCCe---------EeHHHHHHHhcC----------CCCCCCHHHH
Confidence 9986 46899999 799999999999999877654332 666666666644 2457999999
Q ss_pred HHHcCCCCCCCCChHHHHHHHHHHHHHHHhhCc
Q psy2882 472 SFVNNLSHKKAHDALSDVRATLGLARLIRNNNP 504 (1428)
Q Consensus 472 ~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~p 504 (1428)
++++|+++.++|+|++||.||++|+..+.++.+
T Consensus 134 ~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 134 SEALGLTHENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred HHHCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999998877644
No 64
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.85 E-value=8.6e-21 Score=203.22 Aligned_cols=168 Identities=17% Similarity=0.083 Sum_probs=133.9
Q ss_pred EEEEeeccccCccCC-----CcceeEEEEEEeCCce-eeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHH
Q psy2882 313 FLWYDYETFGLNVRR-----DRPFQFAAIRTDIMLN-TIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKF 386 (1428)
Q Consensus 313 ~v~~D~ETTGldp~~-----DrIiqiaaIr~~~~~~-~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~ 386 (1428)
||++|+||||+++.. |+|||||+|+++.+.+ ++++ |+.+++|......++.+..+||||++++ ..+.+..++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~-f~~~i~P~~~~~i~~~~~~i~gIt~e~l-~~~~~~~~v 78 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDT-FSSYVKPVINPKLSDFCTELTGITQEDV-DNAPSFPEV 78 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEee-eeeeECCCcCCchhHHHHHhcCcCHHHH-hcCCCHHHH
Confidence 799999999999986 9999999999998876 5555 9999999874344679999999999999 567788999
Q ss_pred HHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCC
Q psy2882 387 ASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSF 466 (1428)
Q Consensus 387 ~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~ 466 (1428)
+.++.+++......++++|+ .||..++...+.+....+.. ...++.+|+.+++..+.|. .+++
T Consensus 79 l~~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~------~~~~~~~D~~~~~~~~~~~----------~~~~ 141 (176)
T cd06133 79 LKEFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLP------PFFRQWIDLKKEFAKFYGL----------KKRT 141 (176)
T ss_pred HHHHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCc------ccccceEEHHHHHHHHhCC----------CCCC
Confidence 99999999753113445553 89999988888877653211 1123447787777776542 2578
Q ss_pred ChHhHHHHcCCCCC-CCCChHHHHHHHHHHHHHH
Q psy2882 467 KLEHLSFVNNLSHK-KAHDALSDVRATLGLARLI 499 (1428)
Q Consensus 467 kLe~L~~~~gi~~~-~AHdAlaDv~AT~~l~~~l 499 (1428)
+|++++.++|++.. ++|+|++||++|++|+++|
T Consensus 142 ~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 142 GLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 99999999999988 7999999999999999876
No 65
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.85 E-value=5.5e-21 Score=199.12 Aligned_cols=157 Identities=23% Similarity=0.243 Sum_probs=132.2
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
|++|+||||++|..++|+|||+|.++.++.+++. ++.+|+|..++ ++.+..+||||++++ ..|.+..+++..+.++
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~-~~~~i~p~~~~--~~~~~~~~gi~~~~~-~~~~~~~~~~~~~~~~ 76 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVER-FETLVNPGRPI--PPEATAIHGITDEML-ADAPPFEEVLPEFLEF 76 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhh-hheeeCcCCcC--CHhheeccCCCHHHH-hcCCCHHHHHHHHHHH
Confidence 5899999999999999999999999988666666 99999998764 457778899999998 5788889999999999
Q ss_pred HcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhH-H
Q psy2882 394 FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL-S 472 (1428)
Q Consensus 394 ~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L-~ 472 (1428)
+.. .++|||| +.||..||++.|.+++..++... .+|++++++.+.+. ..+++|..+ +
T Consensus 77 l~~--~~~v~~n-~~fD~~~l~~~~~~~~~~~~~~~---------~iDt~~~~~~~~~~----------~~~~~l~~~~~ 134 (159)
T cd06127 77 LGG--RVLVAHN-ASFDLRFLNRELRRLGGPPLPNP---------WIDTLRLARRLLPG----------LRSHRLGLLLA 134 (159)
T ss_pred HCC--CEEEEeC-cHhhHHHHHHHHHHhCCCCCCCC---------eeEHHHHHHHHcCC----------CCcCchHHHHH
Confidence 976 5899999 59999999999998874333333 37777777776553 345788888 8
Q ss_pred HHcCCCCCCCCChHHHHHHHHHHH
Q psy2882 473 FVNNLSHKKAHDALSDVRATLGLA 496 (1428)
Q Consensus 473 ~~~gi~~~~AHdAlaDv~AT~~l~ 496 (1428)
+.+|++..++|||++||++|++|+
T Consensus 135 ~~~~~~~~~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 135 ERYGIPLEGAHRALADALATAELL 158 (159)
T ss_pred HHcCCCCCCCCCcHHHHHHHHHHh
Confidence 999999999999999999999986
No 66
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.85 E-value=9.3e-22 Score=244.66 Aligned_cols=165 Identities=21% Similarity=0.235 Sum_probs=147.9
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|||||+|||||+|..|.||||||+++. +++++++ |+++++|.... +...+.+||||.+++ ..+.+..+++..+
T Consensus 421 atyVVfDiETTGLs~~~d~iIE~aAvKik-ng~iId~-f~~Fi~P~~pl--~~~~telTgITdeml-~~a~~i~~vL~kf 495 (1444)
T COG2176 421 ATYVVFDIETTGLSPVYDEIIEIAAVKIK-NGRIIDK-FQFFIKPGRPL--SATITELTGITDEML-ENAPEIEEVLEKF 495 (1444)
T ss_pred ccEEEEEeecCCcCcccchhhhheeeeee-CCcchHH-HHHhcCCCCcC--chhhhhccccCHHHH-cCCccHHHHHHHH
Confidence 58999999999999999999999999995 5688888 99999998643 358889999999999 5777889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++. ++++|+|| ++||..||+..+.|+++.++.+. ++|++.+++++.|. ..||+|..
T Consensus 496 ~~~~~--d~IlVAHN-asFD~gFl~~~~~k~~~~~~~~p---------vIDTL~lar~L~P~----------~ksh~Lg~ 553 (1444)
T COG2176 496 REFIG--DSILVAHN-ASFDMGFLNTNYEKYGLEPLTNP---------VIDTLELARALNPE----------FKSHRLGT 553 (1444)
T ss_pred HHHhc--CcEEEecc-CccchhHHHHHHHHhCCccccCc---------hhhHHHHHHHhChh----------hhhcchHH
Confidence 99997 46999999 89999999999999998887655 49999999999874 67899999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
||+.+|+...++|+|..|+.||+.|+..+.+.
T Consensus 554 l~kk~~v~le~hHRA~yDaeat~~vf~~f~~~ 585 (1444)
T COG2176 554 LCKKLGVELERHHRADYDAEATAKVFFVFLKD 585 (1444)
T ss_pred HHHHhCccHHHhhhhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999998887654
No 67
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.85 E-value=4.2e-21 Score=206.06 Aligned_cols=161 Identities=20% Similarity=0.212 Sum_probs=126.8
Q ss_pred EEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCC--ChhhHhhc---CCCHHHHhcCCCChHHHH
Q psy2882 313 FLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLP--DPRACLIT---KITPQFCLNNGIPEYKFA 387 (1428)
Q Consensus 313 ~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p--~pea~~it---GITpe~~~~~g~~e~e~~ 387 (1428)
++|+|+||||++|..|+|||||||+++.+...+.+.|+.+|+|.....+ ++.+..+| |||++++ ..+.+..+++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l-~~~~~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVR-ASTVTLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHH-hCCCCHHHHH
Confidence 6899999999999999999999999988766665669999999875432 34666775 9999998 5677889999
Q ss_pred HHHHHHHcC----CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCC
Q psy2882 388 SIIEKIFLK----PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463 (1428)
Q Consensus 388 ~~i~~~~~~----~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~ 463 (1428)
.++.+++.+ ...+++| ||++||..||+.++.|.. ++ | .+...|+..++.+++.+.|+.
T Consensus 80 ~~~~~f~~~~~~~~~~~lvg-h~~~FD~~fL~~~~~~~~--~~---~--~~~~~D~~~l~~l~~~l~p~~---------- 141 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAG-NSVHQDRRFLDKYMPELE--EY---L--HYRILDVSSIKELARRWYPEI---------- 141 (173)
T ss_pred HHHHHHHHHhcCCCCCceee-cchhhCHHHHHHHHHHHh--cc---C--CcchhhHHHHHHHHHHhCcHh----------
Confidence 999999974 2244555 558999999999998854 11 2 122357766688888887641
Q ss_pred CCCChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHh
Q psy2882 464 PSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 501 (1428)
Q Consensus 464 ~s~kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~ 501 (1428)
++ +++++..+|+||+||.||+.+++.+++
T Consensus 142 ~~---------~~~~~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 142 YR---------KAPKKKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred hh---------cCCCCCCCcchHHHHHHHHHHHHHHHH
Confidence 11 578888999999999999999998875
No 68
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.85 E-value=7.7e-21 Score=250.47 Aligned_cols=165 Identities=22% Similarity=0.284 Sum_probs=143.6
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|||||+||||++|..|+|||||||+++. +.++++ |+++|+|...+ ++.+..+||||++++ ..+.+..+++.++
T Consensus 190 ~~~VVfDiETTGL~~~~d~IIEIGAVkv~~-g~iid~-f~~~V~P~~~I--~~~~~~ltGIT~e~L-~~ap~~~evl~~f 264 (1213)
T TIGR01405 190 ATYVVFDIETTGLSPQYDEIIEFGAVKVKN-GRIIDK-FQFFIKPHEPL--SAFVTELTGITQDML-ENAPEIEEVLEKF 264 (1213)
T ss_pred CcEEEEEeEecCCCCCCCeEEEEEEEEEEC-CeEEEE-EEEEECCCCCC--CHHHHHHhCCCHHHH-hCCCCHHHHHHHH
Confidence 489999999999999999999999999985 477777 99999998643 469999999999999 5688889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++. ++++|||| +.||..||+..+.|++.+++... .+|++.+++.+.| +..+++|++
T Consensus 265 ~~fl~--~~iLVaHN-a~FD~~fL~~~~~r~g~~~~~~~---------~IDTl~lar~l~p----------~~k~~kL~~ 322 (1213)
T TIGR01405 265 KEFFK--DSILVAHN-ASFDIGFLNTNFEKVGLEPLENP---------VIDTLELARALNP----------EYKSHRLGN 322 (1213)
T ss_pred HHHhC--CCeEEEEC-hHHHHHHHHHHHHHcCCCccCCC---------EeEHHHHHHHHhc----------cCCCCCHHH
Confidence 99996 46899999 89999999999999887765433 3777788877755 346799999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
||+++|++..++|+|++||.||++|+..+.+.
T Consensus 323 Lak~lgi~~~~~HrAl~DA~aTa~I~~~ll~~ 354 (1213)
T TIGR01405 323 ICKKLGVDLDDHHRADYDAEATAKVFKVMVEQ 354 (1213)
T ss_pred HHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999888754
No 69
>KOG2519|consensus
Probab=99.85 E-value=2.8e-21 Score=224.92 Aligned_cols=254 Identities=22% Similarity=0.272 Sum_probs=193.8
Q ss_pred hhhhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChH
Q psy2882 775 MYGKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYN 854 (1428)
Q Consensus 775 ~Y~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~ 854 (1428)
.++++|||.++||++-+...-+|..|.+|+++.|++..++++++. + ...|+||||.+|.++.+.+......|......
T Consensus 29 kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~~~-g-i~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~ 106 (449)
T KOG2519|consen 29 KKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLIEN-G-IKPVYVFDGKPPDLKSQELAKRSERRSEADKE 106 (449)
T ss_pred ceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHHHc-C-CcEEEEECCCCCCcchHHHHHHHHHhhhhhhh
Confidence 468999999999999997655678999999999999999999954 2 23489999998999888888777767432211
Q ss_pred H-----------------------HHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccc
Q psy2882 855 L-----------------------ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQ 911 (1428)
Q Consensus 855 l-----------------------~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~Q 911 (1428)
+ ..+-+.|+++|..||||++.+|+ ||+..||.|++. |....++|.|.|-+.
T Consensus 107 ~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~-EAEAqCA~Lnk~-----g~V~~~at~DsD~l~ 180 (449)
T KOG2519|consen 107 LKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPG-EAEAQCAALNKA-----GKVYAVATEDSDALT 180 (449)
T ss_pred hhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCc-hHHHHHHHHhhc-----Cceeeeeccccchhh
Confidence 1 22335799999999999999997 999999999975 556779999999777
Q ss_pred cccCcE---EEEe-----CCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHH-
Q psy2882 912 LVSNKI---ALIN-----NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN- 982 (1428)
Q Consensus 912 Lv~~~v---~~~~-----~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~- 982 (1428)
+..+.+ .+.. |...++...+.+.+|+...+|+|+++|+| ||++|+|.||||++|.+||++|+++++|++
T Consensus 181 fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlG--CDYc~~I~Gig~~~al~lir~~~~i~~ile~ 258 (449)
T KOG2519|consen 181 FGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLG--CDYCPTIRGIGPKKALKLIRQHGDIENILEI 258 (449)
T ss_pred ccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhc--CcccccccccChHHHHHHHHHhcCHHHHhhh
Confidence 665421 1111 44568889999999999999999999999 999999999999999999999999999999
Q ss_pred HhhhcchhhhhhHHHhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHHH-HccCC
Q psy2882 983 NANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFN-KYNIP 1048 (1428)
Q Consensus 983 ~~~~i~~k~~~~l~~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~-~~~f~ 1048 (1428)
+.+.-.-.+... +-.+....+..+..+.... ..-++.|..||.+++.+|+. +.+|.
T Consensus 259 ~~~~~~~~ip~~--------w~~~~~r~~f~~p~~~~~~--~~~~i~w~~pd~~~li~fl~~~~~f~ 315 (449)
T KOG2519|consen 259 NSDLKEYPIPED--------WSYKLARKLFLEPEFPNPE--SILDLKWKTPDTEGLIQFLVGEKQFN 315 (449)
T ss_pred ccchhhcCCCCC--------ccHHHHHHHhcCcccCCcc--ceeecccCCCChHHHHHHHHhhhccC
Confidence 543211111111 1111233344444444331 01368899999999999887 88887
No 70
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.85 E-value=1.2e-20 Score=244.39 Aligned_cols=165 Identities=21% Similarity=0.169 Sum_probs=138.1
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
..+||++|+||||+++ .|+|||||+|+++. +.++++ |..+++|...+ ++.+..|||||++++. .+.+..+++.+
T Consensus 6 ~~~~vvvD~ETTGl~~-~d~IIeIgaV~v~~-g~i~~~-f~~lv~P~~~i--~~~~~~ltGIt~e~l~-~ap~~~ev~~~ 79 (820)
T PRK07246 6 LRKYAVVDLEATGAGP-NASIIQVGIVIIEG-GEIIDS-YTTDVNPHEPL--DEHIKHLTGITDQQLA-QAPDFSQVARH 79 (820)
T ss_pred CCCEEEEEEecCCcCC-CCeEEEEEEEEEEC-CEEEEE-EEEEeCcCCCC--CHhHhhcCCCCHHHHh-cCCCHHHHHHH
Confidence 3589999999999998 59999999999974 567777 99999998644 3699999999999994 56677899999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.+++. ++++|||| +.||..||+.++.|.+++. ... .+|++.+++.+.|. .++|+|+
T Consensus 80 ~~~~l~--~~~lVaHN-~~FD~~fL~~~~~~~g~~~-~~~---------~iDT~~la~~~~p~----------~~~~~L~ 136 (820)
T PRK07246 80 IYDLIE--DCIFVAHN-VKFDANLLAEALFLEGYEL-RTP---------RVDTVELAQVFFPT----------LEKYSLS 136 (820)
T ss_pred HHHHhC--CCEEEEEC-cHHHHHHHHHHHHHcCCCC-CCC---------ceeHHHHHHHHhCC----------CCCCCHH
Confidence 999986 46899998 7999999999998866542 122 26777777777552 4579999
Q ss_pred hHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhhC
Q psy2882 470 HLSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 503 (1428)
Q Consensus 470 ~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~~ 503 (1428)
+||.++|+++.++|+|++||+||++|+..+.++.
T Consensus 137 ~L~~~lgl~~~~~H~Al~DA~ata~L~~~l~~~l 170 (820)
T PRK07246 137 HLSRELNIDLADAHTAIADARATAELFLKLLQKI 170 (820)
T ss_pred HHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999998887654
No 71
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.83 E-value=5.7e-20 Score=203.74 Aligned_cols=177 Identities=20% Similarity=0.157 Sum_probs=131.0
Q ss_pred EEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHH
Q psy2882 313 FLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEK 392 (1428)
Q Consensus 313 ~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~ 392 (1428)
|+++|+||||+++. |||||+|++. ++.++++ ++.+++|...+ +++++.|||||++++. ...+..+++..
T Consensus 2 ~~vlD~ETTGl~~~---IieIg~v~v~-~~~i~~~-~~~lv~P~~~i--~~~~~~ihgIt~e~v~-~ap~~~ev~~~--- 70 (219)
T PRK07983 2 LRVIDTETCGLQGG---IVEIASVDVI-DGKIVNP-MSHLVRPDRPI--SPQAMAIHRITEAMVA-DKPWIEDVIPH--- 70 (219)
T ss_pred eEEEEEECCCCCCC---CEEEEEEEEE-CCEEEEE-EEEEECcCCCC--CHHHhhcCCCCHHHHc-CCCCHHHHHHH---
Confidence 78999999999864 9999999986 5566665 89999998653 5699999999999993 33344555554
Q ss_pred HHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHH
Q psy2882 393 IFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLS 472 (1428)
Q Consensus 393 ~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~ 472 (1428)
|.+ +.++|||| +.||..||.. ....| +|++++++.+.|+ . +++|+.|+
T Consensus 71 -~~~-~~~lVaHN-a~FD~~~L~~---------~~~~~---------idTl~lar~l~p~----------~-~~~l~~L~ 118 (219)
T PRK07983 71 -YYG-SEWYVAHN-ASFDRRVLPE---------MPGEW---------ICTMKLARRLWPG----------I-KYSNMALY 118 (219)
T ss_pred -HcC-CCEEEEeC-cHhhHHHHhC---------cCCCc---------EeHHHHHHHHccC----------C-CCCHHHHH
Confidence 433 46899999 7999998742 12223 8999999888553 2 38999999
Q ss_pred HHcCCCC-----CCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCCCCcceEEEeeccCcCCCCc
Q psy2882 473 FVNNLSH-----KKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYI 545 (1428)
Q Consensus 473 ~~~gi~~-----~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~~~~p~~~vs~~~~~~~~~~ 545 (1428)
..+|++. .++|+|++||++|++|+..+.+...- . +.+++++ +.+|-+.-.-.||+.+|-.
T Consensus 119 ~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~~~---------~---~~~l~~~-~~~~~~~~~~~fGk~kg~~ 183 (219)
T PRK07983 119 KSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTSGW---------T---AEEMADI-TGRPSLLTTFTFGKYRGKA 183 (219)
T ss_pred HHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC---------C---HHHHHHH-hcCCccCCCccccCccCcc
Confidence 9999863 57999999999999999988754321 1 1333333 2356665566899988873
No 72
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.82 E-value=2.1e-20 Score=198.45 Aligned_cols=150 Identities=17% Similarity=0.107 Sum_probs=114.5
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCC------hHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIP------EYKFA 387 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~------e~e~~ 387 (1428)
|++|+||||++|..|+|+|||+|++. +++++ +..+++|...+ | +.++.+||||++++...... ..++.
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~-~g~i~---~~~~v~P~~~i-~-~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~ 74 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVL-TGEVL---IDSLVRPSVRV-T-DWRTRFSGVTPADLEEAAKAGKTIFGWEAAR 74 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcC-CCeEE---EeccccCCCCC-C-ccceeccCCCHHHHhhhhhcCCccccHHHHH
Confidence 58999999999999999999999994 34443 55799997654 3 48999999999998432111 13788
Q ss_pred HHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCC
Q psy2882 388 SIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFK 467 (1428)
Q Consensus 388 ~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~k 467 (1428)
.++.+++.+ ++++|||| +.||..||+.. .. .++|++++++.+.|.. ...++++
T Consensus 75 ~~~~~~i~~-~~vlVgHn-~~fD~~fL~~~---------~~---------~~iDT~~l~~~~~~~~-------~~~~~~~ 127 (161)
T cd06137 75 AALWKFIDP-DTILVGHS-LQNDLDALRMI---------HT---------RVVDTAILTREAVKGP-------LAKRQWS 127 (161)
T ss_pred HHHHHhcCC-CcEEEecc-HHHHHHHHhCc---------CC---------CeeEehhhhhhccCCC-------cCCCCcc
Confidence 888888863 26899998 79999999742 11 2378888887765531 0126799
Q ss_pred hHhHHHH-cCCCC---CCCCChHHHHHHHHHHH
Q psy2882 468 LEHLSFV-NNLSH---KKAHDALSDVRATLGLA 496 (1428)
Q Consensus 468 Le~L~~~-~gi~~---~~AHdAlaDv~AT~~l~ 496 (1428)
|.+||+. +|++. ..+|||++||+||++|+
T Consensus 128 L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 128 LRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred HHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 9999997 68775 56999999999999886
No 73
>PRK06722 exonuclease; Provisional
Probab=99.81 E-value=5.6e-19 Score=201.09 Aligned_cols=169 Identities=13% Similarity=-0.002 Sum_probs=130.5
Q ss_pred CceEEEEeeccccCccC----CCcceeEEEEEEeCC-ceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChH
Q psy2882 310 NSTFLWYDYETFGLNVR----RDRPFQFAAIRTDIM-LNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEY 384 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~----~DrIiqiaaIr~~~~-~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~ 384 (1428)
..+|+|+|+|||| +|. .|+|||||||+++.+ +.++++ |..+++|...+ ++.+..+||||++++ ..+.+..
T Consensus 4 ~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~-F~sLV~P~~~I--~~~i~~LTGIT~emV-~~AP~f~ 78 (281)
T PRK06722 4 ATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGE-FSELVKPGARL--TRHTTKLTGITKKDL-IGVEKFP 78 (281)
T ss_pred CCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEee-EEEEECCCCcC--CHhHhhhcCCCHHHH-cCCCCHH
Confidence 3689999999995 443 399999999999864 356676 99999998643 469999999999999 5677789
Q ss_pred HHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCC
Q psy2882 385 KFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKP 464 (1428)
Q Consensus 385 e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~ 464 (1428)
+++.++.+++++ ..+|+||+ .||..||.+++.++.++..... ..+.+|+.++++.+.|... ..
T Consensus 79 eVl~ef~~fig~--~~lvahna-~FD~~FL~~~l~~~gi~~p~~~------~~~~idl~~la~~~~~~l~--------~~ 141 (281)
T PRK06722 79 QIIEKFIQFIGE--DSIFVTWG-KEDYRFLSHDCTLHSVECPCME------KERRIDLQKFVFQAYEELF--------EH 141 (281)
T ss_pred HHHHHHHHHHCC--CcEEEEEe-HHHHHHHHHHHHHcCCCCCccc------ccchhHHHHHHHHHhhhhc--------cC
Confidence 999999999964 35777774 8999999999998775421100 1124777777665544311 12
Q ss_pred CCChHhHHHHcCCCC-CCCCChHHHHHHHHHHHHHHH
Q psy2882 465 SFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 465 s~kLe~L~~~~gi~~-~~AHdAlaDv~AT~~l~~~l~ 500 (1428)
+++|+++++.+||+. +++|+|++||++|++|+..+.
T Consensus 142 ~~sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 142 TPSLQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred CCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 357999999999996 469999999999999988765
No 74
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=99.81 E-value=1.3e-20 Score=168.86 Aligned_cols=63 Identities=49% Similarity=0.868 Sum_probs=60.1
Q ss_pred ccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 117 FKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 117 ~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
++|++.||||.++++.|||||+++|++|||++|||+|||+||+|+||||+|++|||+||.+.+
T Consensus 2 ~~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRriTgl~~k~Qr~l~~aIKrAR~~~L 64 (70)
T TIGR00165 2 FRRKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRRLARAIKRARYLAL 64 (70)
T ss_pred CCCCCCCCccCCCCCcCCccCHHHHHHhcCCCCeEcCCccCCcCHHHHHHHHHHHHHHHHHhc
Confidence 567899999999999999999999999999999999999999999999999999999998865
No 75
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=99.81 E-value=1.6e-20 Score=172.14 Aligned_cols=69 Identities=45% Similarity=0.753 Sum_probs=63.8
Q ss_pred ccCCccccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 111 QQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 111 ~~~~~~~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
..++++++|++.||||..+++.|||||+++|++|||++|||+|||+||+|+|+||+|++|||+||.+.+
T Consensus 5 ~~~~~~~~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~~GkIlprriTG~~~k~Qr~l~~aIkrAR~~~L 73 (79)
T PRK00391 5 KARRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLATAIKRARFLAL 73 (79)
T ss_pred ccccccCCCCCCCcccCCCCCcCCccCHHHHHHhcCCCceEcCcccCCcCHHHHHHHHHHHHHHHHhhC
Confidence 345566778999999999999999999999999999999999999999999999999999999999865
No 76
>PRK13401 30S ribosomal protein S18; Provisional
Probab=99.80 E-value=2.4e-20 Score=170.63 Aligned_cols=65 Identities=32% Similarity=0.443 Sum_probs=61.1
Q ss_pred ccccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 115 PLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 115 ~~~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
..++|+|.|+||..+++.|||||+++|++|||++|||+|||+||+|+|+||+|++|||+||.+.+
T Consensus 8 ~~~~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRR~TGl~~k~QR~l~~AIKrAR~laL 72 (82)
T PRK13401 8 KGPTKAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQVATAIKNAREMAL 72 (82)
T ss_pred ccCCCCCCCCcccCCCCcCCccCHHHHHHhcCCCccCcCcccCCcCHHHHHHHHHHHHHHHHHhc
Confidence 33567899999999999999999999999999999999999999999999999999999999865
No 77
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=6.3e-20 Score=180.00 Aligned_cols=86 Identities=40% Similarity=0.745 Sum_probs=81.4
Q ss_pred CHHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeeccCcccccc
Q psy2882 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTKKVETEES 80 (1428)
Q Consensus 1 ~i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~~~~~~~~~ 80 (1428)
++++++++|+++||+|.++++||+|+|||||+|+++|||++++|+++|++++||||.+|+|++||||||+|+++.....+
T Consensus 21 ~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~l~~f~~~~~~i~Eler~~rin~~VlR~liik~~~~~~~~~ 100 (112)
T COG0360 21 LVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRINEDVLRHLIIKVEKAKEELS 100 (112)
T ss_pred HHHHHHHHHHHCCCEEEEehhhhhhhhcceecccceEEEEEEEEEcCHHHHHHHHHHhccchhhheeeEEEechhhcccc
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999888888
Q ss_pred hhhHHH
Q psy2882 81 SFLRFI 86 (1428)
Q Consensus 81 ~~~e~~ 86 (1428)
++....
T Consensus 101 ~~~~~~ 106 (112)
T COG0360 101 PMLKKK 106 (112)
T ss_pred hhhhhh
Confidence 876543
No 78
>PRK13400 30S ribosomal protein S18; Provisional
Probab=99.79 E-value=4.3e-20 Score=182.44 Aligned_cols=89 Identities=28% Similarity=0.489 Sum_probs=75.5
Q ss_pred ccccCCccccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhccc-c-cCcc
Q psy2882 109 KRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILLKD-I-PNLG 186 (1428)
Q Consensus 109 ~~~~~~~~~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~~d-V-~~lG 186 (1428)
...+++++++|+|.|+||.+++..|||||+++|++|||++|||+|||+||+|+||||+|++||||||.+.|=- | +.+-
T Consensus 11 ~~~gr~~~~~RrK~C~~c~~~~~~IDYKNv~lL~~FISe~GKIlPRRiTGlcaK~QRkLakAIKRAR~laLLPfv~~~ir 90 (147)
T PRK13400 11 ARGGRGRYTPKRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRALANAIKRARFIALMPFVSEHVR 90 (147)
T ss_pred CcCCCCccCCCCCCCCccCCCCCccCCcCHHHHHHhcCcCccCcCcccCCcCHHHHHHHHHHHHHHHHHhcccccccccc
Confidence 3445667778899999999999999999999999999999999999999999999999999999999996633 2 4555
Q ss_pred CCCCEEEeccc
Q psy2882 187 KLGEIIKVKNG 197 (1428)
Q Consensus 187 ~~GdvV~Vk~G 197 (1428)
..|.+-++++|
T Consensus 91 ~~g~~~~~s~~ 101 (147)
T PRK13400 91 RQGNVATFSPI 101 (147)
T ss_pred ccCCCCccCCc
Confidence 66666666665
No 79
>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=99.78 E-value=4.9e-19 Score=187.12 Aligned_cols=149 Identities=17% Similarity=0.163 Sum_probs=113.7
Q ss_pred EEEeeccccCccC--CCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 314 LWYDYETFGLNVR--RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 314 v~~D~ETTGldp~--~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
|++|+||||++|. .++|++|++|..+ +.++ +..+++|...+ | +.+..+||||++++ +.+.+..+++.++.
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~--g~~~---~~~lv~P~~~i-~-~~~~~i~GIt~~~l-~~a~~~~~v~~~l~ 72 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYH--GDVL---YDKYIRPEGPV-T-DYRTRWSGIRRQHL-VNATPFAVAQKEIL 72 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCC--CCEE---EEEeECCCCcc-C-ccceECCCCCHHHH-hcCCCHHHHHHHHH
Confidence 5899999999997 6899999999763 3444 67899998654 3 48999999999999 56778899999999
Q ss_pred HHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHH--HHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 392 KIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKA--FYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 392 ~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl--~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+++. ++++|||| +.||..||+.. ..+ .+++|++.+ ++.. ..+| ..++++|+
T Consensus 73 ~~l~--~~vlV~Hn-~~~D~~~l~~~-----~~~-----------~~~~Dt~~l~~~~~~----~~~p----~~~~~~L~ 125 (157)
T cd06149 73 KILK--GKVVVGHA-IHNDFKALKYF-----HPK-----------HMTRDTSTIPLLNRK----AGFP----ENCRVSLK 125 (157)
T ss_pred HHcC--CCEEEEeC-cHHHHHHhccc-----CCC-----------cCEEECcccccchhh----cCCc----ccCChhHH
Confidence 9995 57999999 89999998743 110 112333332 2111 1123 24679999
Q ss_pred hHHHHc---CCCC-CCCCChHHHHHHHHHHHH
Q psy2882 470 HLSFVN---NLSH-KKAHDALSDVRATLGLAR 497 (1428)
Q Consensus 470 ~L~~~~---gi~~-~~AHdAlaDv~AT~~l~~ 497 (1428)
+||+++ +++. .++|||++||+||++|+|
T Consensus 126 ~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 126 VLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred HHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 999999 7876 678999999999999875
No 80
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.77 E-value=1.2e-19 Score=189.40 Aligned_cols=162 Identities=25% Similarity=0.258 Sum_probs=129.0
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCce-eeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLN-TIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEK 392 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~-~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~ 392 (1428)
||+|+||||+++..++|+|||+|+++.+.. +... ++.+++|......++.+..+||||.+++.. +.+..+++..+.+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~-~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~-~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVES-FNSLIRPEEPPKISPWATKVHGITQEDLED-APSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEE-EEEEBEHSSHCSSEHHHHHHHHHCHHHHHC-HCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCcccccee-eeecccccccccCCHHHeeecCCccccccc-CCcHHHHHHhhhh
Confidence 799999999999999999999999998876 4444 899999998744568999999999999854 4466778898999
Q ss_pred HHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHH
Q psy2882 393 IFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLS 472 (1428)
Q Consensus 393 ~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~ 472 (1428)
++... .++|||| ++||..+++..+.+.+..++... +.-+|.+.+.+..+..++ .++|++|+
T Consensus 79 ~~~~~-~~~v~~n-~~fd~~~l~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~-------------~~~l~~l~ 139 (164)
T PF00929_consen 79 FLKKN-DILVGHN-ASFDIGFLRREDKRFLGKPIPKP----NPFIDTLELARALFPNRK-------------KYSLDDLA 139 (164)
T ss_dssp HHHHH-TEEEETT-CCHEEESSHHHHHHHHHHHHHHH----HHECEEEEEHHHHHHHHH-------------HHSHHHHH
T ss_pred hhhcc-ccccccc-ccchhhHHHHhhhhccccccccc----chhhhhhHHHHHHhhccc-------------cCCHHHHH
Confidence 88632 6899999 89999999999988764443311 112455555555444322 27999999
Q ss_pred HHcCCCCCC-CCChHHHHHHHHHHH
Q psy2882 473 FVNNLSHKK-AHDALSDVRATLGLA 496 (1428)
Q Consensus 473 ~~~gi~~~~-AHdAlaDv~AT~~l~ 496 (1428)
+.+|++... +|||++||++|++|+
T Consensus 140 ~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 140 EYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp HHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred HHcCCCCCCCCcChHHHHHHHhCcC
Confidence 999999877 799999999999885
No 81
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.77 E-value=7.8e-18 Score=190.33 Aligned_cols=167 Identities=20% Similarity=0.156 Sum_probs=138.1
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+|+++|+||||+++..|+|||||+|.+..+ .++++.+..+++|... ..+++..+||||++++..+ ....+++.++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~-~i~~~~~~~~v~P~~~--i~~~~~~i~git~e~l~~~-p~~~~v~~~~ 88 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDG-RIVERSFHTLVNPERP--IPPEIFKIHGITDEMLADA-PKFAEVLPEF 88 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECC-eeecceeEEEECCCCC--CChhhhhhcCCCHHHHhcC-CCHHHHHHHH
Confidence 5899999999999999999999999999765 5555558899999433 3469999999999999543 4447999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++... ..+|+|| +.||..|++..+.+...+..... ++|++.+++...| +..+++|+.
T Consensus 89 ~~~i~~~-~~~Vahn-a~fD~~fl~~~~~~~~~~~~~~~---------~~~t~~~~r~~~~----------~~~~~~L~~ 147 (243)
T COG0847 89 LDFIGGL-RLLVAHN-AAFDVGFLRVESERLGIEIPGDP---------VLDTLALARRHFP----------GFDRSSLDA 147 (243)
T ss_pred HHHHCCC-CeEEEEc-hhhcHHHHHHHHHHcCCCcccCc---------eehHHHHHHHHcC----------CCccchHHH
Confidence 9999864 6899999 89999999999999887654222 2677777777654 356799999
Q ss_pred HHHHcCCC--CCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLS--HKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~--~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
||.++||+ +.+.|+|+.|+++|++++..+...
T Consensus 148 l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 148 LAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred HHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 99999999 678899999999999998888764
No 82
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.76 E-value=1.8e-18 Score=181.98 Aligned_cols=149 Identities=17% Similarity=0.169 Sum_probs=108.4
Q ss_pred EEEeeccccCccCCCcceeEEEEEE-eCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRT-DIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEK 392 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~-~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~ 392 (1428)
|++|+||||++|. ++++|++.|.+ +.++.++ |+.|++|... + ++.++.|||||++++ +.+.+..+++.++.+
T Consensus 1 v~lD~EttGl~~~-~~~~~i~~v~~v~~~~~~~---~~~~v~P~~~-i-~~~~~~ihGIt~~~v-~~a~~~~~~~~~l~~ 73 (152)
T cd06144 1 VALDCEMVGVGPD-GSESALARVSIVNEDGNVV---YDTYVKPQEP-V-TDYRTAVSGIRPEHL-KDAPDFEEVQKKVAE 73 (152)
T ss_pred CEEEEEeecccCC-CCEEEEEEEEEEeCCCCEE---EEEEECCCCC-C-CcccccCCCCCHHHH-cCCCCHHHHHHHHHH
Confidence 5899999999986 46667665543 3333333 6889999754 3 358999999999999 467788999999999
Q ss_pred HHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHH
Q psy2882 393 IFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLS 472 (1428)
Q Consensus 393 ~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~ 472 (1428)
+++ ++++|||| +.||..||+... + +..++|+.++.....+ |+ .++++|++||
T Consensus 74 ~l~--~~vlVgHn-~~fD~~~L~~~~-----~-----------~~~~~dt~~l~~~~~~----~~-----~~~~sL~~l~ 125 (152)
T cd06144 74 LLK--GRILVGHA-LKNDLKVLKLDH-----P-----------KKLIRDTSKYKPLRKT----AK-----GKSPSLKKLA 125 (152)
T ss_pred HhC--CCEEEEcC-cHHHHHHhcCcC-----C-----------CccEEEeEEeeccccc----cC-----CCChhHHHHH
Confidence 997 36899998 699999986210 0 1112444443222211 22 4689999999
Q ss_pred HH-cCCCC-CCCCChHHHHHHHHHHHH
Q psy2882 473 FV-NNLSH-KKAHDALSDVRATLGLAR 497 (1428)
Q Consensus 473 ~~-~gi~~-~~AHdAlaDv~AT~~l~~ 497 (1428)
++ +|++. .++|||++||++|++|++
T Consensus 126 ~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 126 KQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred HHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 97 59985 479999999999999874
No 83
>KOG4607|consensus
Probab=99.75 E-value=1.4e-18 Score=182.98 Aligned_cols=134 Identities=26% Similarity=0.424 Sum_probs=108.2
Q ss_pred hhcccccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhccc
Q psy2882 169 FIRKNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIFLNAKKIGEEIKKL 248 (1428)
Q Consensus 169 ~aik~~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~ 248 (1428)
++.+...|||++||+|||++||+|+|++||+||+|+|+|+|+|+||.|.+++...+++....+.+...+++.++ .|..+
T Consensus 44 k~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~~k~~~~e~~~~k~~vk~e~k~V~-~lqt~ 122 (222)
T KOG4607|consen 44 KPKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKKYKLREQEEEAEKIRVKEEAKVVA-VLQTV 122 (222)
T ss_pred cCCcceeeeeehhhhhhcccCcEEEeecchhhhhcccccccccCChhhHHHHHHHHHHHHhhhhccHHHHHHHH-HHHhh
Confidence 35668899999999999999999999999999999999999999999999888877777766666666666666 89999
Q ss_pred eEEEEEecCCCCceeecccHHHHHHHHHHCCceecCcceecCCc----c-cccccceeeeeeecc
Q psy2882 249 NINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNN----S-IKKIGNYYIDILLHN 308 (1428)
Q Consensus 249 ~l~i~~~~~~~gklfgsVt~~~I~~~l~~~gi~v~~~~I~l~~~----p-Ik~~G~~~V~v~l~~ 308 (1428)
.+.+.++.++.| .+.+..|...|.+ |+.+..++|.||.+ | +|.-|+|.+.|+++.
T Consensus 123 v~~~~~~k~~kw----~l~~~~V~~~l~~-gv~~~~~t~~l~k~~vs~P~~k~e~~~~~~V~in~ 182 (222)
T KOG4607|consen 123 VLFKVMNKGGKW----KLNPNLVKASLRK-GVIVAELTIKLDKELVSGPITKEEGEYICEVKINP 182 (222)
T ss_pred hhhheeccCCce----eecHHHHHHHHhc-ceEeccccccCcccccCCCcccccceEEEEEEECC
Confidence 999999999884 5556666666665 66555555555443 3 556669999999999
No 84
>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=99.75 E-value=3.4e-18 Score=179.42 Aligned_cols=146 Identities=16% Similarity=0.114 Sum_probs=113.0
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
|++|+||||++.. |+|++|+++..+ +++ .|+.|++|...+ .+.++.+||||++++...+.+..++..++.++
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~--~~~---~f~~lv~P~~~i--~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~f 72 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDEN--GKV---VLDELVKPDGEI--VDYNTRFSGITEEMLENVTTTLEDVQKKLLSL 72 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCC--CCE---EEEEeECCCCcc--chhccCcCCCCHHHhccCCCCHHHHHHHHHHH
Confidence 5799999999987 999999999763 333 278899998543 35899999999999955445789999999999
Q ss_pred HcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHH
Q psy2882 394 FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSF 473 (1428)
Q Consensus 394 ~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~ 473 (1428)
+. +++++|||| ++||..||+.. .. .++|++.+++.+.| . ..+++|++||+
T Consensus 73 l~-~~~vlVgHn-~~fD~~fL~~~---------~~---------~~iDT~~l~r~~~~------~----~~~~~L~~L~~ 122 (150)
T cd06145 73 IS-PDTILVGHS-LENDLKALKLI---------HP---------RVIDTAILFPHPRG------P----PYKPSLKNLAK 122 (150)
T ss_pred hC-CCCEEEEcC-hHHHHHHhhcc---------CC---------CEEEcHHhccccCC------C----CCChhHHHHHH
Confidence 95 346899999 79999998641 01 13777776554432 1 23799999999
Q ss_pred Hc-CC--CC-CCCCChHHHHHHHHHHHH
Q psy2882 474 VN-NL--SH-KKAHDALSDVRATLGLAR 497 (1428)
Q Consensus 474 ~~-gi--~~-~~AHdAlaDv~AT~~l~~ 497 (1428)
+| |+ .+ ..+|||++||++|++|++
T Consensus 123 ~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 123 KYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred HHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 87 53 33 578999999999999873
No 85
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.75 E-value=8e-18 Score=224.51 Aligned_cols=165 Identities=19% Similarity=0.199 Sum_probs=141.5
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+||++|+||||+++..|+|+|||+++++. +.+++. |..+|+|...+ ++.++.+||||++++. .+.+..+++..+
T Consensus 419 ~~~VVfDLETTGL~~~~deIIEIgAV~V~~-G~iie~-F~~~V~P~~~I--~~~~~~LTGIT~e~L~-~aps~~EaL~~f 493 (1437)
T PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKN-GEIIDK-FEFFIKPGHPL--SAFTTELTGITDDMVK-DAPSIEEVLPKF 493 (1437)
T ss_pred CcEEEEEhhhcCCCCchhhhheeeeEEEeC-CeEeee-EEEEECCCCCC--CHHHHHHhCCCHHHHc-CCCCHHHHHHHH
Confidence 479999999999999999999999999974 566766 99999997643 4699999999999995 788889999999
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
+++++ +.++|||| ..||..||+..+.|.+++++... .+|++.+++.+.| ...+++|++
T Consensus 494 ~~fig--g~vLVAHN-a~FD~~fL~~~l~rlgl~~l~~~---------~IDTLelar~l~p----------~~k~~kL~~ 551 (1437)
T PRK00448 494 KEFCG--DSILVAHN-ASFDVGFINTNYEKLGLEKIKNP---------VIDTLELSRFLYP----------ELKSHRLNT 551 (1437)
T ss_pred HHHhC--CCEEEEeC-ccccHHHHHHHHHHcCCcccccc---------ceeHHHHHHHHcC----------ccccccHHH
Confidence 99886 46899999 59999999999999877655433 2777778777755 246799999
Q ss_pred HHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
||+++|++..++|||++||+||++|+..+.+.
T Consensus 552 LAk~lGL~~~~~HrAl~DA~aTa~lf~~ll~~ 583 (1437)
T PRK00448 552 LAKKFGVELEHHHRADYDAEATAYLLIKFLKD 583 (1437)
T ss_pred HHHHcCCCCCCCcChHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999888754
No 86
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.75 E-value=3.7e-19 Score=148.24 Aligned_cols=48 Identities=60% Similarity=0.920 Sum_probs=44.9
Q ss_pred ccchhcccccCccCCCCEEEecccccccccccCCcEeccCHHHHHHHH
Q psy2882 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFE 221 (1428)
Q Consensus 174 ~~vil~~dV~~lG~~GdvV~Vk~GyaRN~Lip~~lA~~at~~n~~~~~ 221 (1428)
|+|||++||+|||++||||+|++|||||||+|+|+|+|||++|++++|
T Consensus 1 m~ViL~~dv~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~e 48 (48)
T PF01281_consen 1 MKVILLKDVPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQLE 48 (48)
T ss_dssp -EEEESSCCTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHHH
T ss_pred CEEEEcccccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhcC
Confidence 789999999999999999999999999999999999999999999875
No 87
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=99.75 E-value=2.1e-18 Score=167.15 Aligned_cols=72 Identities=33% Similarity=0.552 Sum_probs=69.7
Q ss_pred CHHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeec
Q psy2882 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKT 72 (1428)
Q Consensus 1 ~i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~ 72 (1428)
++++++++|+++||+|.++++||+|+|||||+|+++|||++++|+++|++++||||.||+||+|||||++|.
T Consensus 26 ~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~~~G~Yv~~~f~~~~~~i~eler~lri~e~VlR~m~vk~ 97 (97)
T CHL00123 26 WIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQMNYSGNGKLVNSLEKALKLDENVLRYLTFKK 97 (97)
T ss_pred HHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCCCEEEEEEEEEEECHHHHHHHHHHhCCCCCeEEEEEEeC
Confidence 378999999999999999999999999999999999999999999999999999999999999999999973
No 88
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=99.74 E-value=4.1e-18 Score=164.35 Aligned_cols=73 Identities=45% Similarity=0.745 Sum_probs=70.7
Q ss_pred CHHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeecc
Q psy2882 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTK 73 (1428)
Q Consensus 1 ~i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~~ 73 (1428)
+++++.++|+++||+|.++++||+|+|||||+|+++|+|++|.|+++|++++||++.||+|++|||||++|++
T Consensus 20 ~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lr~~~~VlR~~~vk~~ 92 (93)
T TIGR00166 20 QIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVLMNFSGEAQVIKEFERTARINDNVIRSLIIKLE 92 (93)
T ss_pred HHHHHHHHHHhCCCEEEEEEeecceecceEcCCCceEEEEEEEEEeCHHHHHHHHHHhcCCcCeEEEEEEEec
Confidence 3688999999999999999999999999999999999999999999999999999999999999999999975
No 89
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.72 E-value=1.4e-16 Score=194.03 Aligned_cols=180 Identities=12% Similarity=0.071 Sum_probs=135.7
Q ss_pred ceEEEEeeccccCccC---CCcceeEEEEEEe-CCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHH
Q psy2882 311 STFLWYDYETFGLNVR---RDRPFQFAAIRTD-IMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKF 386 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~---~DrIiqiaaIr~~-~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~ 386 (1428)
..|+++|+||||+++. .|+|||||+|+++ .++.++++ |..|++|......++....+||||.+++ +.+.+..++
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~-F~~yVkP~~~p~Ls~fct~LTGITqe~V-~~Ap~F~eV 133 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAE-FQRYVRPVKNPVLSRFCTELTGITQSMV-SRADPFPVV 133 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEE-EEEEECCCCCCCCChhHhhhcCcCHHHH-hcCCCHHHH
Confidence 6899999999999975 4999999999997 46777877 9999999764233568999999999999 567788999
Q ss_pred HHHHHHHHcCCC--------ceEEEEcchhhhH-HHHHHHHH---HccccchhhhhhcCCCCCchhhHHHHHHHhCCCCc
Q psy2882 387 ASIIEKIFLKPG--------TISVGYNTILFDD-EITRFMFW---RNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGI 454 (1428)
Q Consensus 387 ~~~i~~~~~~~~--------~~~VGyN~i~FD~-~flr~~f~---Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~ 454 (1428)
+.++.+++.+.. .+++++| ..||. .||..++. ++.++.+.. +|+-+. ..++..+.|+.-
T Consensus 134 l~ef~~fL~~~~~~e~~~~~~~~vah~-g~fDl~~fL~~e~~~~~~~g~p~~f~-------~widLk-~~lar~l~p~~~ 204 (582)
T PTZ00315 134 YCEALQFLAEAGLGDAPPLRSYCVVTC-GDWDLKTMLPSQMRVSGQQGTPLSFQ-------RWCNLK-KYMSQLGFGNGS 204 (582)
T ss_pred HHHHHHHHhccccccccccCceEEEec-cHHHHHHHHHHHHHHhhhcCCCcccc-------eEEEhH-HHHHHHhCcccc
Confidence 999999997532 3688888 69998 59988876 334443222 343332 133344444210
Q ss_pred C---CCCCCCCCCCCChHhHHHHcCCCCC-CCCChHHHHHHHHHHHHHHHhhC
Q psy2882 455 T---WPYKNNGKPSFKLEHLSFVNNLSHK-KAHDALSDVRATLGLARLIRNNN 503 (1428)
Q Consensus 455 ~---~p~~~~g~~s~kLe~L~~~~gi~~~-~AHdAlaDv~AT~~l~~~l~~~~ 503 (1428)
. -+ -.+..+++|+++++.+||+.. .+|+|++||++|++|+..|.++.
T Consensus 205 ~~~~~~--~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g 255 (582)
T PTZ00315 205 GCGGGA--TPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRG 255 (582)
T ss_pred cccccc--ccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcC
Confidence 0 00 124567999999999999965 58999999999999999887653
No 90
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=99.71 E-value=1.6e-17 Score=164.73 Aligned_cols=84 Identities=43% Similarity=0.843 Sum_probs=78.8
Q ss_pred CHHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeeccCcccccc
Q psy2882 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTKKVETEES 80 (1428)
Q Consensus 1 ~i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~~~~~~~~~ 80 (1428)
++++++++|.++||+|.++++||+|+|||+|+|+++|+|++++|+++|+++++|++.|++|++||||+++|+++......
T Consensus 22 ~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~~~~~VlR~~~vk~~~~~~~~~ 101 (108)
T PRK00453 22 LVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYVLLNFEAPPAAIAELERLFRINEDVLRFLTVKVEEAEEEPS 101 (108)
T ss_pred HHHHHHHHHHHCCCEEEEEecccccccceEcCCCcEEEEEEEEEEeCHHHHHHHHHHhCCCCCeEEEEEEEecccccccC
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999998877776
Q ss_pred hhhH
Q psy2882 81 SFLR 84 (1428)
Q Consensus 81 ~~~e 84 (1428)
+...
T Consensus 102 ~~~~ 105 (108)
T PRK00453 102 PMMK 105 (108)
T ss_pred hhhh
Confidence 6543
No 91
>CHL00077 rps18 ribosomal protein S18
Probab=99.71 E-value=4.4e-18 Score=157.01 Aligned_cols=63 Identities=32% Similarity=0.426 Sum_probs=58.1
Q ss_pred ccccCCcccccccCCCCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 115 PLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 115 ~~~~~~k~c~~~~~~~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
+.++|+|.||||... .|||||+++|++|||++|||+|||+||+|+|+||+|++|||+||.+.+
T Consensus 12 ~~~~rrk~~~~~~~~--~iDYKnv~lL~~Fis~~GkIlpRriTGl~~K~QR~l~~aIKrAR~~gL 74 (86)
T CHL00077 12 KRSFRRRLPPIQSGD--RIDYKNMSLLSRFISEQGKILSRRVTRLTLKQQRLITKAIKQARILSL 74 (86)
T ss_pred hhhcccCCCCCCCCC--cCCccCHHHHHHhcCCCCeEcCcccCCcCHHHHHHHHHHHHHHHHHhc
Confidence 345578999999985 599999999999999999999999999999999999999999999865
No 92
>PRK14074 rpsF 30S ribosomal protein S6; Provisional
Probab=99.70 E-value=1.5e-17 Score=177.74 Aligned_cols=85 Identities=24% Similarity=0.355 Sum_probs=79.8
Q ss_pred CHHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeeccCcccccc
Q psy2882 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTKKVETEES 80 (1428)
Q Consensus 1 ~i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~~~~~~~~~ 80 (1428)
+++++.++|+++| +.++++||+|+|||||+|+++|||++++|+++|++++||||.+|+||+|||||+||++++...++
T Consensus 168 vvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~~eGyYvL~nFeAep~aIaELER~lRInE~VIRfLtVKlDe~~~~pS 245 (257)
T PRK14074 168 TLEMLLKNIEASG--LIKYEYWGLLDFAYPINKMKSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDKFFEGKS 245 (257)
T ss_pred HHHHHHHHHHhcC--eeehHhhcchhhccccCCCCeEEEEEEEEEcCHHHHHHHHHHhcCccceeeEEEEeeccccccCC
Confidence 3789999999995 56999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHH
Q psy2882 81 SFLRFIQ 87 (1428)
Q Consensus 81 ~~~e~~~ 87 (1428)
|++...-
T Consensus 246 pimkk~~ 252 (257)
T PRK14074 246 YMMNKQI 252 (257)
T ss_pred hhhhhhh
Confidence 9987543
No 93
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.70 E-value=1.3e-17 Score=154.25 Aligned_cols=73 Identities=44% Similarity=0.722 Sum_probs=67.6
Q ss_pred HhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhhhcchhhhhhHHHhhhhchhhhhh
Q psy2882 934 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKI 1008 (1428)
Q Consensus 934 ~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~~i~~k~~~~l~~~~~~~~~~~~L 1008 (1428)
++|++|+||+||++|+||+|||+|||||||+|||.+||++||+++++++++++++ .++++..+.+.+.+++.|
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l 74 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKIK--LREKLLEHKELAKLSKLL 74 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHHHh--HHHhhhccHHHHHHHHhh
Confidence 6899999999999999999999999999999999999999999999999999885 777888888888887765
No 94
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.69 E-value=1.6e-16 Score=204.28 Aligned_cols=180 Identities=16% Similarity=0.212 Sum_probs=137.0
Q ss_pred HHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEE--EeC---CeeccHHHH
Q psy2882 857 LQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIAL--INN---NKIHDRTTI 931 (1428)
Q Consensus 857 ~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~--~~~---~~~~~~~~v 931 (1428)
..+..|+++|+.||||+|.+| +|||+.||+|++. |....|+|.|.|++-+.+.+|.- .+. ...++...+
T Consensus 772 ~m~~~~~~LL~~~GIP~i~AP-~EAEAqcA~L~~~-----G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~~~i 845 (1034)
T TIGR00600 772 QMILESQELLRLFGIPYIVAP-MEAEAQCAILDLL-----DQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDI 845 (1034)
T ss_pred HHHHHHHHHHHHCCCCeeeCC-ccHHHHHHHHHhC-----CCeEEEEccccceeccCCceeeecccCCCCceEEeeHHHH
Confidence 347789999999999999999 5999999999864 77889999999999555554321 111 234778889
Q ss_pred HHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhC--CHHHHHH---Hhhhcch---------hhhhhHH-
Q psy2882 932 ISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYN--SLENIIN---NANNIKG---------VIGKNLR- 996 (1428)
Q Consensus 932 ~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~g--sle~i~~---~~~~i~~---------k~~~~l~- 996 (1428)
.+.+|++++||+++++|+| |||.+||||||||||.+||++|| +++++++ .+.++.. ...++.+
T Consensus 846 ~~~lglt~~qli~laiL~G--~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~~~~~~~~~~~~~~~~ 923 (1034)
T TIGR00600 846 HNQLGLDRNKLINLAYLLG--SDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKL 923 (1034)
T ss_pred HHHhCCCHHHHHHHHHeeC--CCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhccccccccchhhhhhcc
Confidence 9999999999999999999 99999999999999999999999 4777774 2222110 0000000
Q ss_pred --HhhhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHH-HHccCC
Q psy2882 997 --FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYNIP 1048 (1428)
Q Consensus 997 --~~~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~-~~~~f~ 1048 (1428)
.....-+-+..+..++.+++++.+ ...+.|..||.++|++|| ++++|.
T Consensus 924 ~~~~lp~~FP~~~V~~~yl~P~V~~~----~~~f~W~~PD~e~L~~Fl~~~~gws 974 (1034)
T TIGR00600 924 RLLQLTPGFPNPAVADAYLRPVVDDS----KGSFLWGKPDLDKIREFCQRYFGWN 974 (1034)
T ss_pred cccccCCCCCcHHHHHHhcCCCCCCC----cCCCCCCCCCHHHHHHHHHHccCCC
Confidence 123344556677888888888764 367899999999999966 556676
No 95
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=99.66 E-value=1.3e-16 Score=153.74 Aligned_cols=71 Identities=42% Similarity=0.798 Sum_probs=68.9
Q ss_pred HHHHHHHHhcCCcEEEEEeeccccccccccCCcceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeec
Q psy2882 2 IERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKT 72 (1428)
Q Consensus 2 i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~ 72 (1428)
++++.++|.++||+|.++++||.|+|||||+|+.+|+|++++|+++|+++++|++.|++|++|||||++|.
T Consensus 22 ~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~~~~f~~~~~~i~el~~~l~~~~~VlR~~~vK~ 92 (92)
T PF01250_consen 22 IERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQKEGHYFLFNFDASPSAIKELERKLRLDEDVLRYLIVKK 92 (92)
T ss_dssp HHHHHHHHHHTTEEEEEEEEEEEEEESSEETTECEEEEEEEEEEESTTHHHHHHHHHHTSTTEEEEEEEE-
T ss_pred HHHHHHHHHHCCCEEEEEEEEeecccccCCCCCCEEEEEEEEEEeCHHHHHHHHHHhcCCCCeEEEEEEeC
Confidence 68899999999999999999999999999999999999999999999999999999999999999999984
No 96
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.65 E-value=3.7e-16 Score=148.45 Aligned_cols=76 Identities=41% Similarity=0.736 Sum_probs=72.5
Q ss_pred HHHHHHHHHHhccceEEEEEecCCCCceeecccHHHHHHHHHHC-CceecCcceecCCcccccccceeeeeeeccCCc
Q psy2882 235 FLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311 (1428)
Q Consensus 235 ~~~a~~~~~~L~~~~l~i~~~~~~~gklfgsVt~~~I~~~l~~~-gi~v~~~~I~l~~~pIk~~G~~~V~v~l~~~~~ 311 (1428)
+++|++++++|+++.|+|.+++|++|+||||||++||+++|+++ |++|||++|.||+ |||++|+|+|+|+||+++.
T Consensus 1 k~~A~~l~~~l~~~~l~i~~k~g~~gklfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~-~IK~~G~~~v~v~L~~~V~ 77 (87)
T PF03948_consen 1 KAEAQALAEKLEGITLTIKRKAGENGKLFGSVTSKDIAKALKEQTGIEIDKKKIELPE-PIKSLGEYEVKVKLHPEVS 77 (87)
T ss_dssp HHHHHHHHHHHCSSEEEEEECBSSCSSBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSS-TBESSEEEEEEEEEETTEE
T ss_pred CHHHHHHHHHhcCCEEEEEEEecCCcceecCcCHHHHHHHHHHhhCCeEeccEEECCC-chhccEEEEEEEEeCCCeE
Confidence 36899999999999999999999999999999999999999999 9999999999996 9999999999999999753
No 97
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.60 E-value=2.9e-15 Score=152.39 Aligned_cols=165 Identities=19% Similarity=0.246 Sum_probs=125.1
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHh--h---cCCCHHHHhcCCCChH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACL--I---TKITPQFCLNNGIPEY 384 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~--i---tGITpe~~~~~g~~e~ 384 (1428)
..++||+|+|+|||||.+|+||+||+|.||.++|+++++.++.+..+...+....... . +|+| +.+.+..+.+.
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~-~rV~~S~~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLT-ERVKASTVTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHH-HHHHHhhccHH
Confidence 3589999999999999999999999999999999999988888887765554333222 2 3777 45667788889
Q ss_pred HHHHHHHHHHcC---CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCC
Q psy2882 385 KFASIIEKIFLK---PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNN 461 (1428)
Q Consensus 385 e~~~~i~~~~~~---~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~ 461 (1428)
++..+++.++.+ .+...++.||+.-|..||...+=+ +..|.+. ...|+-.+-.+|+.+.|+.+
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~--Le~yfHY-----R~lDVSTlKELa~RW~P~i~------- 149 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPK--LEAYFHY-----RYLDVSTLKELARRWNPEIL------- 149 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhh--HHHHhhh-----HhhhHHHHHHHHHhhCcHhh-------
Confidence 999999998877 456677889999999998543221 1112211 12477788889999888633
Q ss_pred CCCCCChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 462 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 462 g~~s~kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
.|+...++|.||+|++-.++-++..++.
T Consensus 150 -------------~~~~K~~~H~Al~DI~ESI~EL~~YR~~ 177 (184)
T COG1949 150 -------------AGFKKGGTHRALDDIRESIAELRYYREH 177 (184)
T ss_pred -------------hccccccchhHHHHHHHHHHHHHHHHHH
Confidence 2345678999999999999887777754
No 98
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=99.51 E-value=5.1e-15 Score=127.05 Aligned_cols=50 Identities=38% Similarity=0.629 Sum_probs=47.0
Q ss_pred CCccccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhc
Q psy2882 130 IKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILL 179 (1428)
Q Consensus 130 ~~~~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~ 179 (1428)
...|||||+.+|++|||++|||+|||+||+|+++||++++|||+||.+.+
T Consensus 4 ~~~idykn~~lL~~Fi~~~GkIl~rr~Tgl~~k~Qr~l~~aIkrAR~~gL 53 (54)
T PF01084_consen 4 NEYIDYKNVELLSQFISPTGKILPRRITGLCAKQQRKLAKAIKRARQLGL 53 (54)
T ss_dssp SSSSSSSSHHHHGCGBTTSSSBSTHHHHTSTHHHHHHHHHHHHHHHHTTS
T ss_pred CCcCCcCCHHHHHHHcCcccceehhhhccccHHHHHHHHHHHHHHHHhhC
Confidence 35699999999999999999999999999999999999999999998754
No 99
>KOG2518|consensus
Probab=99.42 E-value=6.5e-13 Score=156.80 Aligned_cols=200 Identities=21% Similarity=0.199 Sum_probs=145.3
Q ss_pred HhhhhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCC--
Q psy2882 774 LMYGKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKM-- 851 (1428)
Q Consensus 774 ~~Y~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~-- 851 (1428)
..=+.+||++++||+-++... .-..|.||.--..|+-.-.+++..++- +.++||||+.-.-+...-+.....|++.
T Consensus 24 g~tvavD~y~WLhrg~~~Ca~-el~~~~pT~ryi~y~ik~v~lL~~~gi-kPilVFDG~~LP~K~~te~~Rr~~R~~n~~ 101 (556)
T KOG2518|consen 24 GKTVAVDGYCWLHRGALACAE-KLAKGKPTDRYIQFFIKRVKLLLSYGI-KPILVFDGDPLPSKKETERKRRERRKKNLD 101 (556)
T ss_pred CceEEEehhhHHhhhHHhHHH-HHhcCCChHHHHHHHHHHHHHHHhcCC-eEEEEecCCCcccccccchHHHHHHHHhHH
Confidence 344689999999999999762 234689998888888888888887654 4589999864333444433333333321
Q ss_pred ----------ChHHHHH-----------HHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCcc
Q psy2882 852 ----------PYNLILQ-----------INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMA 910 (1428)
Q Consensus 852 ----------p~~l~~q-----------~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~ 910 (1428)
+.+-... .-.+.+.|+..|+.+|.+| ||||..+++|.+. |.--.|+|.|.||+
T Consensus 102 ~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAP-yEADAQlayL~~~-----~~i~~IITEDSDLl 175 (556)
T KOG2518|consen 102 AAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAP-YEADAQLAYLERE-----GIVDAIITEDSDLL 175 (556)
T ss_pred HHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecC-ccccchhHHHHhc-----CcceEEEecccccc
Confidence 1111111 2225567788899999999 8999999999954 44556889999999
Q ss_pred ccccCcEEEE-e---CCeeccHHHHHHHhC----CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHH
Q psy2882 911 QLVSNKIALI-N---NNKIHDRTTIISRFG----VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 982 (1428)
Q Consensus 911 QLv~~~v~~~-~---~~~~~~~~~v~~~~G----v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~ 982 (1428)
++....|... + ....++....-+.++ ++-++|..+|+|.| ||+.+||||||-+||.++|.+|.+.|-++.
T Consensus 176 ~fGc~~vifK~d~~G~~le~~~~~l~~~~~l~~~~~~ekfr~mciLSG--CDYl~slpGvGl~tA~k~l~k~~~~d~vi~ 253 (556)
T KOG2518|consen 176 VFGCKKVIFKMDSFGNGLEINRSKLPECKPLGDKFTEEKFRRMCILSG--CDYLSSLPGVGLATAHKLLSKYNTPDRVII 253 (556)
T ss_pred ccCchhheeeccCCCCcccccHhhhhhccccccccCHHHHHHHHHhcC--CcccccCccccHHHHHHHHHhcCcHHHHHH
Confidence 9998876542 2 122344444444444 45788999999999 999999999999999999999999999985
Q ss_pred H
Q psy2882 983 N 983 (1428)
Q Consensus 983 ~ 983 (1428)
.
T Consensus 254 ~ 254 (556)
T KOG2518|consen 254 S 254 (556)
T ss_pred H
Confidence 3
No 100
>KOG3242|consensus
Probab=99.41 E-value=5.1e-13 Score=137.06 Aligned_cols=164 Identities=21% Similarity=0.209 Sum_probs=122.8
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhh-----cCCCHHHHhcCCCChHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLI-----TKITPQFCLNNGIPEYK 385 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~i-----tGITpe~~~~~g~~e~e 385 (1428)
..+||+|+|+||||...|+|++||+|.||.+++++.+.+++.++.+++.+....-.-+ .|+|. .+....++.++
T Consensus 26 q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~-kv~~S~~tl~~ 104 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTE-KVLASKITLAD 104 (208)
T ss_pred CceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHH-HHHHhhccHHH
Confidence 4799999999999999999999999999999999999888888887766654333222 36774 44467777888
Q ss_pred HHHHHHHHHcC---CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCC
Q psy2882 386 FASIIEKIFLK---PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNG 462 (1428)
Q Consensus 386 ~~~~i~~~~~~---~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g 462 (1428)
+-.++++++.+ +|.|+++.||+.-|.-||...+=. + ..+.+. .-.|+-.+-.+|++++|+.....
T Consensus 105 aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk-~-~~~lhy-----rivDVStIkeL~~Rw~P~~~~~a----- 172 (208)
T KOG3242|consen 105 AENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPK-L-IKHLHY-----RIVDVSTIKELARRWYPDIKARA----- 172 (208)
T ss_pred HHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHH-H-HHhcce-----eeeeHHHHHHHHHHhCchhhccC-----
Confidence 88888888765 778899999999998888754322 1 111111 23588888899999988743321
Q ss_pred CCCCChHhHHHHcCCCCCCCCChHHHHHHHHHHHHHHHh
Q psy2882 463 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 501 (1428)
Q Consensus 463 ~~s~kLe~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l~~ 501 (1428)
=.....|+|++|++..++-++..++
T Consensus 173 --------------PkK~~~HrAldDI~ESI~ELq~Yr~ 197 (208)
T KOG3242|consen 173 --------------PKKKATHRALDDIRESIKELQYYRE 197 (208)
T ss_pred --------------cccccccchHHHHHHHHHHHHHHHH
Confidence 0124689999999999877776654
No 101
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.39 E-value=1.6e-13 Score=108.17 Aligned_cols=36 Identities=64% Similarity=1.154 Sum_probs=35.1
Q ss_pred hhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 939 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 939 p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
|+||+|+++|+||++||||||||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 789999999999999999999999999999999987
No 102
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=99.35 E-value=3.1e-12 Score=122.00 Aligned_cols=106 Identities=14% Similarity=0.198 Sum_probs=95.8
Q ss_pred EEEEcCCeEEEeCCeEEeccEEEeCCCccc-----ccC--CCCCCCCCHhHHHhhhccCCcEEEEeeCCCCC-CCCHHHH
Q psy2882 1318 IVAYTNYGVKFRNGIFYTKSFLVSPEIDPI-----FWS--INKYNFLTKKDFIHISKFNPSVVILGTGNIQH-FIHPKLT 1389 (1428)
Q Consensus 1318 I~~y~~g~f~i~ng~~~~gsviv~p~~~~~-----~W~--~~~~~~l~~e~l~~ll~~~pevliiGTG~~~~-~~~~~~~ 1389 (1428)
|++|++|.++| +|..|+++|+|.|++-+. .|+ ..+.|.+.+|++..+++..||+||+|||.... -++++.+
T Consensus 4 ie~~~FG~v~i-~Gk~f~~DIvi~~dG~v~rr~K~lskrK~GTSHkl~~eEle~~lee~~E~ivvGTG~~G~l~l~~ea~ 82 (121)
T COG1504 4 IESTSFGSVTI-GGKDFEHDIVIRPDGKVERREKELSKRKYGTSHKLALEELEELLEEGPEVIVVGTGQSGMLELSEEAR 82 (121)
T ss_pred ccccceeeEEE-CCEeccccEEEecCCceehhhhhhhhhhcCcccccCHHHHHHHHhcCCcEEEEecCceeEEEeCHHHH
Confidence 78999999997 999999999999995432 344 46679999999999999999999999997555 8999999
Q ss_pred HHHHHcCCeEEEcChhhHHHHHHhhhhccceeeeec
Q psy2882 1390 YILTQKNIGIECMNNQAACRTYNILVSDDIKAMLAL 1425 (1428)
Q Consensus 1390 ~~l~~~GI~vE~M~T~aAcrTyNiL~sEgR~VaaaL 1425 (1428)
++|+++|++|...+|+.|...||-|.+. |+|+|++
T Consensus 83 e~~r~k~~~vi~~pT~EAikr~nel~~~-krV~aii 117 (121)
T COG1504 83 EFFRKKGCEVIELPTPEAIKRYNELRGK-KRVAAII 117 (121)
T ss_pred HHHHhcCCeEEEeCCHHHHHHHHHHhcc-ceEEEEE
Confidence 9999999999999999999999999999 9999875
No 103
>KOG4708|consensus
Probab=99.21 E-value=1e-11 Score=123.71 Aligned_cols=104 Identities=21% Similarity=0.328 Sum_probs=88.1
Q ss_pred HHHHHHHHhcCCcEEEEEeeccccccccccCC----cceEEEEEEEEEeCcccHHHHHHHcCCCcceeeeeEeeccC--c
Q psy2882 2 IERYKKIIISGKGKIHRLEDWGRRSLAYQIKK----VIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTKK--V 75 (1428)
Q Consensus 2 i~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k----~~~G~Y~~~~f~~~~~~v~eler~lrl~e~VlR~l~vk~~~--~ 75 (1428)
+.|..+.+-..||.|++++++|.|.|+|+|+| |.+|+||+|.|.+++++..|+.+.|+.|.+|||+++||++. .
T Consensus 24 l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~~~l~~D~dviR~~IVKv~~~~~ 103 (141)
T KOG4708|consen 24 LARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIKRILKRDPDVIRWLIVKVDDIKQ 103 (141)
T ss_pred HHHHhhHHhhcCCeEeechhcchhhhcchHHHhcCccccceEEEEeecCCHHHHHHHHHHHhcChhhHHhhheecccccc
Confidence 45667777788899999999999999999985 77999999999999999999999999999999999999997 6
Q ss_pred ccccchhhHHHHH-HHHHhhhhhccccCcccc
Q psy2882 76 ETEESSFLRFIQK-KEKVLKMIFGKKNNKNRF 106 (1428)
Q Consensus 76 ~~~~~~~~e~~~~-r~k~qk~~~~kk~~k~k~ 106 (1428)
...+|. ++++.| ++-+.....+++.++.++
T Consensus 104 ~~~ec~-~e~~~p~r~~~e~l~e~~k~~~~~~ 134 (141)
T KOG4708|consen 104 EQKECE-HEEILPNRLTSESLYEGQKSKKDDN 134 (141)
T ss_pred cccccc-HhhhcCchhHHHHHHHHHhhcccch
Confidence 888999 888888 555544446665544433
No 104
>KOG2520|consensus
Probab=99.00 E-value=2.2e-09 Score=135.09 Aligned_cols=196 Identities=19% Similarity=0.269 Sum_probs=137.8
Q ss_pred CCCh-hhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcE
Q psy2882 839 ILYP-SYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKI 917 (1428)
Q Consensus 839 ~l~p-~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v 917 (1428)
+++. .|+.-|-... .-...+..|+++|..+|||+|.+|+ ||+..||-|... +..--|+|.|.|.+-+.+-+|
T Consensus 448 el~~ek~~~~r~~~e-vt~~m~~e~QElL~~fGIPyI~APm-EAEAQCa~Le~~-----~LvdGiITDDSDV~LFGg~~V 520 (815)
T KOG2520|consen 448 ELLSEKYIQSRGADE-VTSDMFKELQELLRLFGIPYIIAPM-EAEAQCAFLEQL-----NLVDGIITDDSDVFLFGGTRV 520 (815)
T ss_pred HHHHHHHHHhccCch-hHHHHHHHHHHHHHHcCCceecccc-cHHHHHHHHHHc-----CCcceeecccccceeeccchh
Confidence 3343 6777777665 4445688899999999999999997 999999998764 445568999999887766554
Q ss_pred E--EEeCC---eeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHH---HHhhhcch
Q psy2882 918 A--LINNN---KIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII---NNANNIKG 989 (1428)
Q Consensus 918 ~--~~~~~---~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~---~~~~~i~~ 989 (1428)
+ +++.. ..|....+...||+...-++-+-.|.| ||+..|++||||.+|..+|.+|+.-++++ +.+.+..+
T Consensus 521 Yrn~F~knk~ve~y~~~di~kel~l~R~~lI~lA~LlG--sDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~ 598 (815)
T KOG2520|consen 521 YRNFFNKNKYVEKYQLDDIEKELGLDRPNLISLAQLLG--SDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGP 598 (815)
T ss_pred hHHHhhcCccceeeehHHHHHHHccCchhhHHHHHhcc--cccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCc
Confidence 3 22222 347788899999999999999999999 99999999999999999999999444433 22221100
Q ss_pred -------h----hhhhHHHh---hhhchhhhhhhhccccCCCCCCcCCCccccccCCCCHHHHHHHHHHccCC
Q psy2882 990 -------V----IGKNLRFA---LNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNIP 1048 (1428)
Q Consensus 990 -------k----~~~~l~~~---~~~~~~~~~L~~i~~d~~l~~~~~~~~~~~~~~~~d~~~l~~l~~~~~f~ 1048 (1428)
+ +++++.+. ...-+-+...+.-...+.++.. -+.+.|..||.+.|++|+.++ |.
T Consensus 599 ~~~~~~s~~~~~lrkkl~n~~~~l~~~fP~~~v~~AYLrP~VD~s----k~~f~WG~pdl~~lRef~~~~-fg 666 (815)
T KOG2520|consen 599 ADKEVGSTQQKMLRKKLKNPKIILPSDFPNPNVIEAYLRPEVDDS----KEKFRWGKPDLDILREFMKRL-FG 666 (815)
T ss_pred cccccccHHHHHHHHHhcCcccccCcCCCchhHHHHhhCCccCCC----cccccCCCCCHHHHHHHHHHH-cC
Confidence 1 12222221 1111223333333334444433 477999999999999999765 66
No 105
>KOG3162|consensus
Probab=98.96 E-value=3e-10 Score=117.66 Aligned_cols=72 Identities=28% Similarity=0.485 Sum_probs=60.8
Q ss_pred CccccCCcccccccCCCCc-cccCCHHHHHhccccCCccccccccCcCHHHhhhHhhhcccccchhcccccCc
Q psy2882 114 NPLFKRKKFCRFTVMNIKQ-IDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKNMQVILLKDIPNL 185 (1428)
Q Consensus 114 ~~~~~~~k~c~~~~~~~~~-~dyk~~~~l~~fi~~~gki~prr~tg~~~~~qr~~~~aik~~~vil~~dV~~l 185 (1428)
+++.+..+.|+.|..+++. .+||||.+|++||++.|.|+||++||+|+|+||++++||++|+...+=.|-+.
T Consensus 60 n~~~~~~~~c~~c~~~Vd~~~~yknv~iLsqFv~~~G~il~RkiTGLc~k~Qrki~~aI~~A~~~GlmP~~~~ 132 (159)
T KOG3162|consen 60 NPEKKSEPQCILCTKGVDIKLSYKNVLLLSQFVSEDGGILPRKITGLCAKNQRKIERAIKRARAAGLMPVTNT 132 (159)
T ss_pred CCcccCcccCcccccCCCcccccCccchhhhhcccccceecchhhhhhHHHHHHHHHHHHHHHHhcccccccc
Confidence 3444445899999999762 25999999999999999999999999999999999999999998877653333
No 106
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=98.83 E-value=3.3e-08 Score=108.69 Aligned_cols=145 Identities=16% Similarity=-0.038 Sum_probs=95.3
Q ss_pred EEEeeccccC----ccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 314 LWYDYETFGL----NVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 314 v~~D~ETTGl----dp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
++||+||||. +|..|+|++||++....+... . +.....+.+... . ||+..++ ..-.+|.+++..
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~--~-~~~~~~~~~~~~---~-----~i~~~~v-~~~~~E~~lL~~ 69 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADSFDGVKV--V-FLLKTSTVGDDI---E-----FIDGIEV-EYFADEKELLKR 69 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCcee--e-EEEeecccCCcC---C-----CCCCceE-EEeCCHHHHHHH
Confidence 6899999999 999999999999886222211 1 111111211111 1 6776666 345578999999
Q ss_pred HHHHHcCC-CceEEEEcchhhhHHHHHHHHHHccccch-hhh--hh-------------cCCCCCchhhHHHHHHHhCCC
Q psy2882 390 IEKIFLKP-GTISVGYNTILFDDEITRFMFWRNLINPY-ERE--WK-------------NNCSRWDLINVIKAFYVLSPY 452 (1428)
Q Consensus 390 i~~~~~~~-~~~~VGyN~i~FD~~flr~~f~Rn~~~~y-~~~--~~-------------~g~sr~D~ld~~rl~~~l~p~ 452 (1428)
+.+++.+- -.++||||..+||..||..-+.++.++.. ... +. .|. ..+|+..+++...+
T Consensus 70 f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr---~~~D~~~~~r~~~~- 145 (199)
T cd05160 70 FFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGR---VVFDLLAAYKRDFK- 145 (199)
T ss_pred HHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeecc---EeeehHHHHHHhcC-
Confidence 99999762 26899999889999999988887776541 111 10 122 24555555554421
Q ss_pred CcCCCCCCCCCCCCChHhHHHHcCCCCCCCCC
Q psy2882 453 GITWPYKNNGKPSFKLEHLSFVNNLSHKKAHD 484 (1428)
Q Consensus 453 ~~~~p~~~~g~~s~kLe~L~~~~gi~~~~AHd 484 (1428)
.+||+|+++|+.++.....-|+
T Consensus 146 ----------l~sy~L~~v~~~~l~~~k~~~~ 167 (199)
T cd05160 146 ----------LKSYTLDAVAEELLGEGKEKVD 167 (199)
T ss_pred ----------cccCCHHHHHHHHhCCCCCcCC
Confidence 5689999999988766444444
No 107
>KOG2249|consensus
Probab=98.40 E-value=2e-06 Score=95.39 Aligned_cols=155 Identities=17% Similarity=0.167 Sum_probs=107.1
Q ss_pred eEEEEeeccccCccC--CCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 312 TFLWYDYETFGLNVR--RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~--~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
.+|..|||+-|.-|+ .|-...++.|-. .+.++= .-|++|...+.. --+.++||+||.+ ..+.|...+-.+
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~--~G~Vvy---DkyVkP~~~VtD--yRT~vSGIrpehm-~~A~pf~~aQ~e 177 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNY--HGHVVY---DKYVKPTEPVTD--YRTRVSGIRPEHM-RDAMPFKVAQKE 177 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeec--cCcEee---eeecCCCccccc--ceeeecccCHHHh-ccCccHHHHHHH
Confidence 599999999999986 677777877754 444443 359999876654 5677999999998 688899999999
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
|.+++. |.++|||- +.-|...|....=+. .+-|+.+. ..|... . ....+-+|-
T Consensus 178 v~klL~--gRIlVGHa-LhnDl~~L~l~hp~s----------------~iRDTs~~-~pl~k~---~----~~~~tpSLK 230 (280)
T KOG2249|consen 178 VLKLLK--GRILVGHA-LHNDLQALKLEHPRS----------------MIRDTSKY-PPLMKL---L----SKKATPSLK 230 (280)
T ss_pred HHHHHh--CCEEeccc-cccHHHHHhhhCchh----------------hhcccccC-chHHHH---h----hccCCccHH
Confidence 999998 46999976 777877664322111 11222211 000000 0 112235677
Q ss_pred hHHHH-cCCCC-CCCCChHHHHHHHHHHHHHHHh
Q psy2882 470 HLSFV-NNLSH-KKAHDALSDVRATLGLARLIRN 501 (1428)
Q Consensus 470 ~L~~~-~gi~~-~~AHdAlaDv~AT~~l~~~l~~ 501 (1428)
.|+++ +|++. ..-|+...||+||++|+++++.
T Consensus 231 ~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~ 264 (280)
T KOG2249|consen 231 KLTEALLGKDIQVGEHSSVEDARATMELYKRVKV 264 (280)
T ss_pred HHHHHHhchhhhccccCcHHHHHHHHHHHHHHHH
Confidence 88886 56653 3359999999999999999974
No 108
>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=98.30 E-value=2.3e-06 Score=93.64 Aligned_cols=122 Identities=19% Similarity=0.121 Sum_probs=83.0
Q ss_pred eEEEEeeccc---cC-ccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHH
Q psy2882 312 TFLWYDYETF---GL-NVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFA 387 (1428)
Q Consensus 312 ~~v~~D~ETT---Gl-dp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~ 387 (1428)
..++||+||| |+ ++..|+|++||....++.. .++. ..+.+|.+++
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~-------~~~~------------------------~~~~~E~~lL 52 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDV-------EFIL------------------------AEGLDDRKII 52 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCE-------EEEE------------------------ecCCCHHHHH
Confidence 4689999999 65 8999999999987643321 1111 1245788999
Q ss_pred HHHHHHHcCCC-ceEEEEcchhhhHHHHHHHHHHccccch-hhhhh-------------cCCCCCchhhHHHHHHHhCCC
Q psy2882 388 SIIEKIFLKPG-TISVGYNTILFDDEITRFMFWRNLINPY-EREWK-------------NNCSRWDLINVIKAFYVLSPY 452 (1428)
Q Consensus 388 ~~i~~~~~~~~-~~~VGyN~i~FD~~flr~~f~Rn~~~~y-~~~~~-------------~g~sr~D~ld~~rl~~~l~p~ 452 (1428)
..+.+++..-+ .+++|||...||..+|..=..++.++.- .+... .|.-.+|++++++ ...
T Consensus 53 ~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~---~~~-- 127 (188)
T cd05781 53 REFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAE---EIP-- 127 (188)
T ss_pred HHHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHH---hhC--
Confidence 99999997732 6799999999999999876666665421 11110 0111345555544 221
Q ss_pred CcCCCCCCCCCCCCChHhHHHHcCCC
Q psy2882 453 GITWPYKNNGKPSFKLEHLSFVNNLS 478 (1428)
Q Consensus 453 ~~~~p~~~~g~~s~kLe~L~~~~gi~ 478 (1428)
..+||+|+++|..+|+.
T Consensus 128 ---------~l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 128 ---------EVKVKTLENVAEYLGVM 144 (188)
T ss_pred ---------CCCCCCHHHHHHHHCCC
Confidence 25689999999999885
No 109
>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=98.22 E-value=4.2e-06 Score=89.40 Aligned_cols=133 Identities=16% Similarity=0.157 Sum_probs=85.4
Q ss_pred cceeEEEEEEe--CCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCC------ChHHHHHHHHHHHcCCCce
Q psy2882 329 RPFQFAAIRTD--IMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGI------PEYKFASIIEKIFLKPGTI 400 (1428)
Q Consensus 329 rIiqiaaIr~~--~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~------~e~e~~~~i~~~~~~~~~~ 400 (1428)
....+++|..+ ..++++= ..|++|...+.- --+.++|||++++. .+. +..++..++.+++ .++++
T Consensus 32 ~LaRVsiVd~~~~~~g~vll---D~~VkP~~~V~D--YrT~~SGIt~~~L~-~a~~~~~~~t~~~v~~~l~~li-~~~tI 104 (174)
T cd06143 32 SLARVSVVRGEGELEGVPFI---DDYISTTEPVVD--YLTRFSGIKPGDLD-PKTSSKNLTTLKSAYLKLRLLV-DLGCI 104 (174)
T ss_pred eeEEEEEEcCCCCcCCCEEE---eeeECCCCCccC--cCccccccCHHHcC-ccccccccCCHHHHHHHHHHHc-CCCCE
Confidence 46667777521 2334332 359999865543 56779999999984 332 2345566666655 46689
Q ss_pred EEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHHH-cCCCC
Q psy2882 401 SVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFV-NNLSH 479 (1428)
Q Consensus 401 ~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~~-~gi~~ 479 (1428)
+|||. +..|...|+-. ++ .-.++|+..++ |. |. ...++|..||+. +|..-
T Consensus 105 LVGHs-L~nDL~aL~l~----------hp------~~~viDTa~l~----~~----~~----~r~~sLk~La~~~L~~~I 155 (174)
T cd06143 105 FVGHG-LAKDFRVINIQ----------VP------KEQVIDTVELF----HL----PG----QRKLSLRFLAWYLLGEKI 155 (174)
T ss_pred EEecc-chhHHHHhcCc----------CC------CcceEEcHHhc----cC----CC----CCChhHHHHHHHHcCCcc
Confidence 99976 89998877411 11 11347776542 11 11 125899999996 46553
Q ss_pred C-CCCChHHHHHHHHHHHH
Q psy2882 480 K-KAHDALSDVRATLGLAR 497 (1428)
Q Consensus 480 ~-~AHdAlaDv~AT~~l~~ 497 (1428)
. ..||.+.||+||++|++
T Consensus 156 Q~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 156 QSETHDSIEDARTALKLYR 174 (174)
T ss_pred cCCCcCcHHHHHHHHHHhC
Confidence 3 48999999999999984
No 110
>KOG0542|consensus
Probab=98.19 E-value=1.7e-05 Score=87.41 Aligned_cols=170 Identities=16% Similarity=0.194 Sum_probs=121.9
Q ss_pred ceEEEEeeccccCccCC----CcceeEEEEEEeC-CceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHH
Q psy2882 311 STFLWYDYETFGLNVRR----DRPFQFAAIRTDI-MLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYK 385 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~----DrIiqiaaIr~~~-~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e 385 (1428)
..++++|+|+|--+-.. .+||||.+|..+. +-.+|+..|+-|++|.....-+..-+.+|||.-+++ +.+.+-.+
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tV-D~a~~f~~ 134 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETV-DEAPTFPQ 134 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhh-ccCCCHHH
Confidence 47899999999544332 7899999996554 445666349999999876555666778999998888 77888889
Q ss_pred HHHHHHHHHcCC------C-ceEEEEcchhhhH-HHHHHHHHHcc--ccchhhhhhcCCCCCchhhHHHHHHHhCCCCcC
Q psy2882 386 FASIIEKIFLKP------G-TISVGYNTILFDD-EITRFMFWRNL--INPYEREWKNNCSRWDLINVIKAFYVLSPYGIT 455 (1428)
Q Consensus 386 ~~~~i~~~~~~~------~-~~~VGyN~i~FD~-~flr~~f~Rn~--~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~ 455 (1428)
++.++..++... + ..+|.-- +-|. .||.+++.+.. .++|.++| ||+-..+...+.
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvtdg--~wDl~~~l~~qck~~~i~~P~~f~qw---------Inirk~yk~~y~---- 199 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVTDG--DWDLWVFLQYQCKLKNIRIPAFFNQW---------INIRKIYKNFYN---- 199 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEeCc--hhhHHHHHHHHHHHhcCCCcHHHHHH---------hHHHHHHHHHhc----
Confidence 999998888541 2 2344322 4454 46677776543 45788888 666655544321
Q ss_pred CCCCCCCCCCCChHhHHHHcCCCC-CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 456 WPYKNNGKPSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 456 ~p~~~~g~~s~kLe~L~~~~gi~~-~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
-| ..-.+..+-+++|+++ +.+|+++.||+-+++++++|.+.
T Consensus 200 ~~------~~t~it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~d 241 (280)
T KOG0542|consen 200 RP------APTNITGMLEHYGLQFEGRAHSGIDDARNIARIAQKMIRD 241 (280)
T ss_pred Cc------cccCHHHHHHHhCCcccCCcccCchhHHHHHHHHHHHHhC
Confidence 11 1236888999999986 45899999999999999988654
No 111
>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=98.11 E-value=9.5e-06 Score=86.34 Aligned_cols=147 Identities=17% Similarity=0.148 Sum_probs=68.3
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
++||+|||||+|..+.|.-||.+..+.+.. ..+..-. ... ..+.+.+.+....
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~------~~~~~~~---~~~------------------~~ee~~~~~~~~~ 53 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEI------ITFIQWF---AED------------------PDEEEIILEFFEL 53 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTT------E-EEEE----GGG------------------HHHHHHHHH--HH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCce------EEeeHhh---ccC------------------cHHHHHHHHHHHH
Confidence 589999999999999999999998765421 1111100 000 0122333333355
Q ss_pred HcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHH
Q psy2882 394 FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSF 473 (1428)
Q Consensus 394 ~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~ 473 (1428)
+.+. ..+|+||..+||..+|+..+.+...++ ... . +|+...++.. ..+|++|.++++
T Consensus 54 l~~~-~~iv~yng~~FD~p~L~~~~~~~~~~~-~~~------~---iDl~~~~~~~------------~~~~~~Lk~ve~ 110 (164)
T PF13482_consen 54 LDEA-DNIVTYNGKNFDIPFLKRRAKRYGLPP-PFN------H---IDLLKIIKKH------------FLESYSLKNVEK 110 (164)
T ss_dssp HHTT---EEESSTTTTHHHHHHHHH-HHHH---GGG------E---EEHHHHHT-T------------TSCCTT--SHHH
T ss_pred HhcC-CeEEEEeCcccCHHHHHHHHHHcCCCc-ccc------h---hhHHHHHHhc------------cCCCCCHHHHhh
Confidence 5554 579999999999999998885544443 111 2 5555544322 226899999999
Q ss_pred HcCCCCCCCCChHHHHHHHHHHHHH-HHhhCchhHHHHHhh
Q psy2882 474 VNNLSHKKAHDALSDVRATLGLARL-IRNNNPRLFNFILSL 513 (1428)
Q Consensus 474 ~~gi~~~~AHdAlaDv~AT~~l~~~-l~~~~p~l~~~~~~~ 513 (1428)
.+|++...- -.|-...+.+++. +....+..++.++.+
T Consensus 111 ~lg~~~~~~---~~~G~~~~~~~~~~~~~~~~~~~~~i~~y 148 (164)
T PF13482_consen 111 FLGIERRDD---DISGSESVKLYKEYLETGDPEALEEILEY 148 (164)
T ss_dssp --------------HHHHHHHHHH---TTGGTS--HHHHHH
T ss_pred hcccccccC---CCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 999986311 1233444555554 445556666655543
No 112
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.11 E-value=1e-05 Score=78.85 Aligned_cols=68 Identities=18% Similarity=0.097 Sum_probs=50.2
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
+++|+||||+++..++|+.|+...-+.+ . .++. . +.++
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~-----~--~~~~-~----------------------------------f~~~ 38 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPE-----D--TAVI-D----------------------------------LKDI 38 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCC-----C--EEEe-h----------------------------------HHHH
Confidence 4799999999999999999988753211 1 1221 1 4455
Q ss_pred HcCCC-ceEEEEcchhhhHHHHHHHHHHcccc
Q psy2882 394 FLKPG-TISVGYNTILFDDEITRFMFWRNLIN 424 (1428)
Q Consensus 394 ~~~~~-~~~VGyN~i~FD~~flr~~f~Rn~~~ 424 (1428)
+.... .++||||. +||..||++.+.|++..
T Consensus 39 l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 39 LRDKPLAILVGHNG-SFDLPFLNNRCAELGLK 69 (96)
T ss_pred HhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCC
Confidence 55543 68999995 99999999999987654
No 113
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.11 E-value=3e-05 Score=85.38 Aligned_cols=131 Identities=17% Similarity=0.102 Sum_probs=83.3
Q ss_pred eEEEEeeccc---cC-ccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHH
Q psy2882 312 TFLWYDYETF---GL-NVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFA 387 (1428)
Q Consensus 312 ~~v~~D~ETT---Gl-dp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~ 387 (1428)
..++||+||| |+ ++..|.|++||.+.. +.+ . .+..++ .+ + . .+. .-.+|.+++
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~---~--~~~~~~-~~--~--~--~v~---------~~~~E~~lL 60 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGN---K--VITWKK-FD--L--P--FVE---------VVKTEKEMI 60 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCc---e--EEEecC-CC--C--C--eEE---------EeCCHHHHH
Confidence 4689999998 76 889999999998652 221 1 111111 11 1 0 111 123678899
Q ss_pred HHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHcccc-chhhh-----h----------hcCCCCCchhhHHHHHHHh
Q psy2882 388 SIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLIN-PYERE-----W----------KNNCSRWDLINVIKAFYVL 449 (1428)
Q Consensus 388 ~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~-~y~~~-----~----------~~g~sr~D~ld~~rl~~~l 449 (1428)
..+...+.. | .+++|||..+||..+|..-+.++.++ ++.+. | ..|...+|++. .++..
T Consensus 61 ~~F~~~i~~~dp-diivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~---~~~~~ 136 (195)
T cd05780 61 KRFIEIVKEKDP-DVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYP---VARRT 136 (195)
T ss_pred HHHHHHHHHcCC-CEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHH---HHHhh
Confidence 999999987 5 68999999999999998777776655 22110 0 01223334444 44332
Q ss_pred CCCCcCCCCCCCCCCCCChHhHHH-HcCCCCC
Q psy2882 450 SPYGITWPYKNNGKPSFKLEHLSF-VNNLSHK 480 (1428)
Q Consensus 450 ~p~~~~~p~~~~g~~s~kLe~L~~-~~gi~~~ 480 (1428)
| ..+||+|+++|+ .+|.+..
T Consensus 137 ------~-----~l~sy~L~~v~~~~Lg~~k~ 157 (195)
T cd05780 137 ------L-----NLTRYTLERVYEELFGIEKE 157 (195)
T ss_pred ------C-----CCCcCcHHHHHHHHhCCCCC
Confidence 1 367899999988 5687643
No 114
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=98.09 E-value=2.6e-06 Score=82.71 Aligned_cols=80 Identities=23% Similarity=0.402 Sum_probs=58.8
Q ss_pred HHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEE-Ee-C------------CeeccHHHHH
Q psy2882 867 KAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIAL-IN-N------------NKIHDRTTII 932 (1428)
Q Consensus 867 ~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~-~~-~------------~~~~~~~~v~ 932 (1428)
+.+|||++.+| ||||..||.|.+. |....|+|.|.|++-+-.+.|.. +. . ...++...+.
T Consensus 1 ~~~gv~~i~AP-~EAeAq~A~L~~~-----g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 74 (94)
T PF00867_consen 1 RLMGVPYIVAP-YEAEAQCAYLERN-----GLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDIL 74 (94)
T ss_dssp HHHT-EEEE-S-S-HHHHHHHHHHT-----TSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHH
T ss_pred CCCCCeEEEcC-chHHHHHHHHHHh-----cceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHH
Confidence 46899999999 5999999999974 55567889999999775443322 11 0 1247778899
Q ss_pred HHhCCChhhHHhhhhccccccC
Q psy2882 933 SRFGVSPEKIVDYFSLIGDMSD 954 (1428)
Q Consensus 933 ~~~Gv~p~q~~d~~aL~GD~sD 954 (1428)
+.+|++.+||+++++|+| +|
T Consensus 75 ~~l~l~~~~fi~~~iL~G--~D 94 (94)
T PF00867_consen 75 KELGLTREQFIDLCILCG--CD 94 (94)
T ss_dssp HHHTTSHHHHHHHHHHHH--ET
T ss_pred HHcCCCHHHHHHHheecC--CC
Confidence 999999999999999999 55
No 115
>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=98.00 E-value=7.1e-05 Score=82.95 Aligned_cols=145 Identities=15% Similarity=0.018 Sum_probs=87.0
Q ss_pred eEEEEeeccccC-----ccCCCcceeEEEEEEeCCceeeccce------EEEEecCCCCCCChhhHhhcCCCHHHHhcCC
Q psy2882 312 TFLWYDYETFGL-----NVRRDRPFQFAAIRTDIMLNTIDNPI------MLYCKPAPDFLPDPRACLITKITPQFCLNNG 380 (1428)
Q Consensus 312 ~~v~~D~ETTGl-----dp~~DrIiqiaaIr~~~~~~~i~~~~------~~~~~p~~~~~p~pea~~itGITpe~~~~~g 380 (1428)
..+.||+||++. +|..|.|+|||.+-...+..+..+.. .+...|.+ + +.|.+ .+ ..-
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~------~---~~~~~--~v-~~~ 70 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKP------E---YEGPF--KV-FNE 70 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCC------C---CCCce--EE-ecC
Confidence 568999999863 78999999999774322211111100 01111111 1 11110 00 012
Q ss_pred CChHHHHHHHHHHHcCCC-ceEEEEcchhhhHHHHHHHHHHccccch---hhhhh-------cCCCCCchhhHHHHHHHh
Q psy2882 381 IPEYKFASIIEKIFLKPG-TISVGYNTILFDDEITRFMFWRNLINPY---EREWK-------NNCSRWDLINVIKAFYVL 449 (1428)
Q Consensus 381 ~~e~e~~~~i~~~~~~~~-~~~VGyN~i~FD~~flr~~f~Rn~~~~y---~~~~~-------~g~sr~D~ld~~rl~~~l 449 (1428)
.+|.+++..+.+++..-+ .+++|||..+||..+|..-..++.+... .+.+. .|...+|++++++....+
T Consensus 71 ~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l 150 (204)
T cd05779 71 PDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYL 150 (204)
T ss_pred CCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcC
Confidence 368899999999997732 6899999999999999766666554422 11111 123356777777753321
Q ss_pred CCCCcCCCCCCCCCCCCChHhHHHH-cCCCCC
Q psy2882 450 SPYGITWPYKNNGKPSFKLEHLSFV-NNLSHK 480 (1428)
Q Consensus 450 ~p~~~~~p~~~~g~~s~kLe~L~~~-~gi~~~ 480 (1428)
..+||+|+++|++ +|....
T Consensus 151 ------------~~~sysLd~Va~~~Lg~~K~ 170 (204)
T cd05779 151 ------------PQGSQGLKAVTKAKLGYDPV 170 (204)
T ss_pred ------------CCCCccHHHHHHHHhCCCcC
Confidence 2358999999996 788644
No 116
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.82 E-value=0.00011 Score=81.63 Aligned_cols=129 Identities=19% Similarity=0.170 Sum_probs=81.0
Q ss_pred eEEEEeeccccC--------ccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCCh
Q psy2882 312 TFLWYDYETFGL--------NVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPE 383 (1428)
Q Consensus 312 ~~v~~D~ETTGl--------dp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e 383 (1428)
..+.||+||++. ++..|.|++||... .++ +...+. ....+|
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~--~~~------~~~~~~-----------------------~~~~~E 58 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD--NRG------WEEVLH-----------------------AEDAAE 58 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc--CCC------ceeeec-----------------------cCCCCH
Confidence 578999999763 45679999999752 221 111110 014578
Q ss_pred HHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHccccc-hhhh-----h-----hc-----CCCCCch-----h
Q psy2882 384 YKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLINP-YERE-----W-----KN-----NCSRWDL-----I 440 (1428)
Q Consensus 384 ~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~~-y~~~-----~-----~~-----g~sr~D~-----l 440 (1428)
.+++..+.+++.. | .+++|||...||..+|..-..++.++. +.+. | .. +...+++ +
T Consensus 59 ~~lL~~f~~~i~~~dP-dii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~i 137 (207)
T cd05785 59 KELLEELVAIIRERDP-DVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVI 137 (207)
T ss_pred HHHHHHHHHHHHHhCC-CEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEE
Confidence 8999999999977 4 688999988999999998888876653 1110 0 00 0012221 3
Q ss_pred hHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHHHcCCCC
Q psy2882 441 NVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSH 479 (1428)
Q Consensus 441 d~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~~~gi~~ 479 (1428)
|+..++..+... ....+||+|+++|..+|+..
T Consensus 138 Dl~~~~~~~~~~-------~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 138 DTYFLVQLFDVS-------SRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred EcHHHHHhhccc-------ccCCCCCCHHHHHHHhcccC
Confidence 444443332111 11357899999999998754
No 117
>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=97.77 E-value=0.00039 Score=75.61 Aligned_cols=142 Identities=18% Similarity=0.215 Sum_probs=92.3
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
..++++|+||||++|..++|+.++.. .+ + ++ .+++-... +. . ..+.+..+.+..+
T Consensus 5 ~~~~a~d~e~~~~~~~~~~i~~l~~~-~~-~----~~--~~~~~~~~------~~--~---------~~~~~~~~~~~~l 59 (193)
T cd06139 5 AKVFAFDTETTSLDPMQAELVGISFA-VE-P----GE--AYYIPLGH------DY--G---------GEQLPREEVLAAL 59 (193)
T ss_pred CCeEEEEeecCCCCcCCCeEEEEEEE-cC-C----CC--EEEEecCC------Cc--c---------ccCCCHHHHHHHH
Confidence 57899999999999999999988754 21 1 11 23331111 00 0 1344556778888
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
..++...+..+|||| ++||..+++. +++.. . .+ +.|+..++|.+.|. ..+++|++
T Consensus 60 ~~~l~~~~~~~v~hn-~k~d~~~l~~----~gi~~-~-------~~--~~Dt~l~a~ll~p~----------~~~~~l~~ 114 (193)
T cd06139 60 KPLLEDPSIKKVGQN-LKFDLHVLAN----HGIEL-R-------GP--AFDTMLASYLLNPG----------RRRHGLDD 114 (193)
T ss_pred HHHHhCCCCcEEeec-cHHHHHHHHH----CCCCC-C-------CC--cccHHHHHHHhCCC----------CCCCCHHH
Confidence 888877656789999 6999999853 33331 1 11 27788888888663 22468888
Q ss_pred HHHHc-CCCC------------------C----CCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVN-NLSH------------------K----KAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~-gi~~------------------~----~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
+++.| |... . ..|.|..|+.+|.+|+..+.++
T Consensus 115 l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~ 169 (193)
T cd06139 115 LAERYLGHKTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPK 169 (193)
T ss_pred HHHHHhCCCCccHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88875 3220 0 1235888899999888888754
No 118
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=97.56 E-value=0.0002 Score=74.49 Aligned_cols=168 Identities=16% Similarity=0.118 Sum_probs=111.4
Q ss_pred ceEEEEeeccc----cCccCCCcceeEEEEEEeC-CceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCCh-H
Q psy2882 311 STFLWYDYETF----GLNVRRDRPFQFAAIRTDI-MLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPE-Y 384 (1428)
Q Consensus 311 ~~~v~~D~ETT----Gldp~~DrIiqiaaIr~~~-~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e-~ 384 (1428)
+.++++|+|.| |-.+..-+||+|.|..++. +-.++++ |+.|++|.....-+-.--.+||||-..+ .+.|. .
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~-F~syVRP~~~P~Lt~~Ckslt~I~Q~~V--D~apifs 80 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDT-FSSYVRPKKFPKLTKRCKSLTKITQKQV--DEAPIFS 80 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHH-HHHhcCcccCchHHHHHHHhhhhhhhhc--cccchHH
Confidence 57899999998 4567778999999887765 5567788 9999999875444434446899995555 33333 3
Q ss_pred HHHHHHHHHHcC----CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCC
Q psy2882 385 KFASIIEKIFLK----PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKN 460 (1428)
Q Consensus 385 e~~~~i~~~~~~----~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~ 460 (1428)
.+...+..++.+ .+..++... ..|...|.+.+..|.+.|+..+ | ...|+-.-+..++. -|.-
T Consensus 81 ~v~E~f~r~L~~h~Pr~~~~wa~wG--~~Dm~~l~q~~~~~~~~p~~~k---g----p~vdl~~~yk~v~~----~pr~- 146 (210)
T COG5018 81 MVFEDFIRKLNEHDPRKNSTWATWG--NMDMKVLKQNCMFNHIPPFPFK---G----PMVDLSLEYKNVFG----DPRL- 146 (210)
T ss_pred HHHHHHHHHHHhcCcccCCcccccc--chhHHHHHHHHHhcCCCCcccc---C----ccchHHHHHHHHhc----CCcc-
Confidence 556666666655 222344433 4899999999998888754322 1 12343333322221 1110
Q ss_pred CCCCCCChHhHHHHcCCCC-CCCCChHHHHHHHHHHHHHHH
Q psy2882 461 NGKPSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 461 ~g~~s~kLe~L~~~~gi~~-~~AHdAlaDv~AT~~l~~~l~ 500 (1428)
--|-...+.+|... +..|+|+.||+-|..|++++-
T Consensus 147 -----tgln~ale~~G~sf~G~~HraldDArn~~rl~klv~ 182 (210)
T COG5018 147 -----TGLNKALEEYGDSFTGTHHRALDDARNAYRLFKLVE 182 (210)
T ss_pred -----ccHHHHHHHhccccCCchhhhHHHHHHHHHHHHHHc
Confidence 23556677888875 457999999999999998875
No 119
>KOG4793|consensus
Probab=97.55 E-value=0.00015 Score=80.57 Aligned_cols=211 Identities=17% Similarity=0.169 Sum_probs=126.6
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeC---Cce--eeccc-------------eEEEEecCCCCCCChhhHhhcCCC
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDI---MLN--TIDNP-------------IMLYCKPAPDFLPDPRACLITKIT 372 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~---~~~--~i~~~-------------~~~~~~p~~~~~p~pea~~itGIT 372 (1428)
.+|+|+|.|||||......|.+.....+.. ++. .+++. .+....|.+ +-.|.|-.|||++
T Consensus 13 ~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aeeitgls 90 (318)
T KOG4793|consen 13 RTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEEITGLS 90 (318)
T ss_pred eEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhhhcccc
Confidence 589999999999998888776654322111 111 11110 223333333 3367999999999
Q ss_pred HHHHhcCCCCh--HHHHHHHHHHHcC-CC-ceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHH
Q psy2882 373 PQFCLNNGIPE--YKFASIIEKIFLK-PG-TISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYV 448 (1428)
Q Consensus 373 pe~~~~~g~~e--~e~~~~i~~~~~~-~~-~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~ 448 (1428)
..-...++... ..+.+-+..|++. +. .|+|.||.-+||.++++++|.+-++.....-. . +|.+++..+
T Consensus 91 ~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lv-----c---vdslpa~~a 162 (318)
T KOG4793|consen 91 QPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLV-----C---VDSLPALNA 162 (318)
T ss_pred cHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhc-----C---cchhHHHHH
Confidence 75543333222 3566666666655 22 68999999999999999999987766333221 2 344444444
Q ss_pred hCCCCcCCCCCCCCCCCCChHhHHHHc-CC-CCCCCCChHHHHHHHHHHHHHHHhhCchhHHHHHhhcCHHHHHHHhCCC
Q psy2882 449 LSPYGITWPYKNNGKPSFKLEHLSFVN-NL-SHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWP 526 (1428)
Q Consensus 449 l~p~~~~~p~~~~g~~s~kLe~L~~~~-gi-~~~~AHdAlaDv~AT~~l~~~l~~~~p~l~~~~~~~~~k~~v~~~~~~~ 526 (1428)
+.... ..-....+.+++.|..+-..| +- +....|.|..|+..-.-.+.-..++ |..+ .| .
T Consensus 163 ld~a~-s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~e---llR~-------------~d-e 224 (318)
T KOG4793|consen 163 LDRAN-SMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINE---LLRW-------------SD-E 224 (318)
T ss_pred Hhhhc-CcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHH---HHhh-------------Hh-h
Confidence 43211 111123457789999987654 44 5677899999987644333332222 1111 11 2
Q ss_pred CCcceEEEeeccCcCCCCceEEEe
Q psy2882 527 IARPFFYITHMFSSKHSYISLMWP 550 (1428)
Q Consensus 527 ~~~p~~~vs~~~~~~~~~~~~~~p 550 (1428)
..+|+.++-.+|++. -|+.-+.|
T Consensus 225 qa~pw~~ir~l~~~~-~~a~~~~P 247 (318)
T KOG4793|consen 225 QARPWLLIRPLYLAR-ENAKSVEP 247 (318)
T ss_pred cCCCcccccchhhhh-hhccccCC
Confidence 468899999999865 44433444
No 120
>KOG4021|consensus
Probab=97.54 E-value=4.1e-05 Score=80.60 Aligned_cols=63 Identities=17% Similarity=0.330 Sum_probs=55.3
Q ss_pred cccccccCCCCccccCCHHHHHhcccc-CCccccccccCcCHHHhhhHhhhcccccc--hhccccc
Q psy2882 121 KFCRFTVMNIKQIDYKDIETLKDFIQE-NGKIMAARLTGTCSHYQRQITFIRKNMQV--ILLKDIP 183 (1428)
Q Consensus 121 k~c~~~~~~~~~~dyk~~~~l~~fi~~-~gki~prr~tg~~~~~qr~~~~aik~~~v--il~~dV~ 183 (1428)
-.||+|.+...++||.|+.||.+||++ +|.++.--.||+|.|+...|..|+-+||= .|+=+||
T Consensus 109 npCPICRDeyL~~DyRN~~LlEQF~~~htg~~i~y~ktGlC~kqh~rL~~a~qkArdhG~lty~Vp 174 (239)
T KOG4021|consen 109 NPCPICRDEYLYFDYRNPGLLEQFLADHTGQPIDYLKTGLCRKQHTRLRAALQKARDHGTLTYGVP 174 (239)
T ss_pred CCCCccccceEEEeccCHHHHHHHhccCCCCchhhhhcchHHHHHHHHHHHHHHhhhcCeEEecCC
Confidence 469999999999999999999999999 89999999999999999999999888863 3444444
No 121
>PRK05755 DNA polymerase I; Provisional
Probab=97.51 E-value=0.00065 Score=90.86 Aligned_cols=134 Identities=17% Similarity=0.213 Sum_probs=93.0
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
..++++|+||||++|..++|+.|+. .++ ++ ..+++.+ +++. . +....+
T Consensus 315 ~~~~a~DtEt~~l~~~~~~i~~i~l-s~~-~g------~~~~ip~-------------~~i~----------~-~~l~~l 362 (880)
T PRK05755 315 AGLFAFDTETTSLDPMQAELVGLSF-AVE-PG------EAAYIPL-------------DQLD----------R-EVLAAL 362 (880)
T ss_pred cCeEEEEeccCCCCcccccEEEEEE-EeC-CC------cEEEEec-------------cccc----------H-HHHHHH
Confidence 4699999999999999999999885 332 21 1344421 1111 1 456667
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.+++..+....|+|| +.||..||+. +++. +... +.|+.-+++.+.|. . +++|++
T Consensus 363 ~~~L~d~~v~kV~HN-akfDl~~L~~----~gi~-~~~~---------~~DT~iAa~Ll~~~----------~-~~~L~~ 416 (880)
T PRK05755 363 KPLLEDPAIKKVGQN-LKYDLHVLAR----YGIE-LRGI---------AFDTMLASYLLDPG----------R-RHGLDS 416 (880)
T ss_pred HHHHhCCCCcEEEec-cHhHHHHHHh----CCCC-cCCC---------cccHHHHHHHcCCC----------C-CCCHHH
Confidence 788887766789998 7999999873 2322 1111 37778888888663 1 289999
Q ss_pred HHHHc-CCCC-------------------CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVN-NLSH-------------------KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~-gi~~-------------------~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
|++.| |++. ...|-|..||.+|.+|+..+.+.
T Consensus 417 L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 417 LAERYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99987 5541 12377999999999999888764
No 122
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.41 E-value=0.0019 Score=71.55 Aligned_cols=160 Identities=18% Similarity=0.237 Sum_probs=90.6
Q ss_pred CceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHH
Q psy2882 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASI 389 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~ 389 (1428)
...++|||+|||||++..+.|+-.|.-+...+ .++++.. .+|.|+ .|-.+.+
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~--------~~~Vrq~--~lp~p~-----------------~E~avle- 148 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDD--------TMHVRQH--FLPAPE-----------------EEVAVLE- 148 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCc--------eEEEEee--cCCCcc-----------------hhhHHHH-
Confidence 35799999999999997777777666665332 2455443 233211 0111222
Q ss_pred HHHHHcC-CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 390 IEKIFLK-PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 390 i~~~~~~-~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
.++.. +-+.+|.||..+||..|++. +.|..++ +..+ +.. +|++..++.+ |.. -.++=+|
T Consensus 149 --~fl~~~~~~~lvsfNGkaFD~PfikR-~v~~~~e-l~l~----~~H---~DL~h~~RRl------wk~---~l~~c~L 208 (278)
T COG3359 149 --NFLHDPDFNMLVSFNGKAFDIPFIKR-MVRDRLE-LSLE----FGH---FDLYHPSRRL------WKH---LLPRCGL 208 (278)
T ss_pred --HHhcCCCcceEEEecCcccCcHHHHH-HHhcccc-cCcc----ccc---hhhhhhhhhh------hhc---cCCCCCh
Confidence 22222 34689999999999999995 6665443 2222 223 5666666666 321 2455688
Q ss_pred HhHHHHcCCCCCCCCChHHHHHHHHHHHH-HHHhhCchhHHHHHhhcCHHHHHHH
Q psy2882 469 EHLSFVNNLSHKKAHDALSDVRATLGLAR-LIRNNNPRLFNFILSLRKKKYVLAE 522 (1428)
Q Consensus 469 e~L~~~~gi~~~~AHdAlaDv~AT~~l~~-~l~~~~p~l~~~~~~~~~k~~v~~~ 522 (1428)
.++-+.+||....--+- .-.-++++ .++...|.+..-++.+ +...|.++
T Consensus 209 k~VEr~LGi~R~edtdG----~~~p~lyr~~~~~~dp~ll~~l~~h-N~eDvlnL 258 (278)
T COG3359 209 KTVERILGIRREEDTDG----YDGPELYRLYRRYGDPGLLDGLVLH-NREDVLNL 258 (278)
T ss_pred hhHHHHhCccccccCCC----cchHHHHHHHHHcCCHHHHHHHHHc-cHHHHHhH
Confidence 89888888764322111 11223333 3445667766555543 33334333
No 123
>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=97.36 E-value=0.0016 Score=72.63 Aligned_cols=118 Identities=14% Similarity=0.122 Sum_probs=78.5
Q ss_pred eccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHHHcCC
Q psy2882 318 YETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKIFLKP 397 (1428)
Q Consensus 318 ~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~~~~~ 397 (1428)
++++|+.+.+++|+-||++..+.+. . .+.+. . ..+.+|.+++..+.+.+.+-
T Consensus 41 ~~~~~l~~~~~~Iv~Is~~~~~~~~----~--~~~~~-~---------------------~~~~~E~elL~~F~~~i~~~ 92 (208)
T cd05782 41 SGSDFLPLPFHKVVSISALYRDDDG----G--FLKVR-T---------------------LDGADEKELLEDFFQLIEKK 92 (208)
T ss_pred cCCCCCccccCceEEEEEEEEecCC----C--eEEEe-e---------------------cCCCCHHHHHHHHHHHHHHh
Confidence 4688999999999999998764322 1 11111 0 12335678888888888763
Q ss_pred CceEEEEcchhhhHHHHHHHHHHcccc-chhh-----------hhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCC
Q psy2882 398 GTISVGYNTILFDDEITRFMFWRNLIN-PYER-----------EWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPS 465 (1428)
Q Consensus 398 ~~~~VGyN~i~FD~~flr~~f~Rn~~~-~y~~-----------~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s 465 (1428)
+.++||||..+||..+|..-..++.++ |... .| .+ ..+|++++++ .. ....+
T Consensus 93 ~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~-~~-~h~DL~~~~~---~~-----------~~~~~ 156 (208)
T cd05782 93 NPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRY-SE-RHLDLMDLLA---FY-----------GARAR 156 (208)
T ss_pred CCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcC-CC-CcccHHHHHh---cc-----------CccCC
Confidence 348999999999999998877777664 2111 12 11 1455555443 11 12468
Q ss_pred CChHhHHHHcCCCC
Q psy2882 466 FKLEHLSFVNNLSH 479 (1428)
Q Consensus 466 ~kLe~L~~~~gi~~ 479 (1428)
++|+++|+.+|++.
T Consensus 157 ~~L~~va~~lG~~~ 170 (208)
T cd05782 157 ASLDLLAKLLGIPG 170 (208)
T ss_pred CCHHHHHHHhCCCC
Confidence 99999999999964
No 124
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=97.24 E-value=5.2e-05 Score=78.58 Aligned_cols=52 Identities=33% Similarity=0.523 Sum_probs=49.3
Q ss_pred HhcCCCcch--hhhhhccccccccCcceeeccccccc-ccccchhhhhhcCCCcc
Q psy2882 1251 KLLGVNPLI--IGIAFGNTLIKHAKPLKIIHSITNKA-KFNEISKLVEKWKPNTV 1302 (1428)
Q Consensus 1251 ~~~~~d~~~--i~~~~G~~~~~~a~p~~~~~~~~~~~-~~~~~~~~~~~~~p~~v 1302 (1428)
..+|+|+|+ ||.|+|+..+.+|+|+.+|++..+.+ +|++|..++++|+|+.|
T Consensus 3 ~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~~~~~~l~~li~~~~~~~v 57 (141)
T COG0816 3 RILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTV 57 (141)
T ss_pred eEEEEecCCceEEEEEecCCCccccchhhheeccccHhhHHHHHHHHHHhCCCEE
Confidence 458999988 99999999999999999999999997 99999999999999887
No 125
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=97.01 E-value=0.0038 Score=69.40 Aligned_cols=150 Identities=13% Similarity=-0.048 Sum_probs=81.0
Q ss_pred eEEEEeecccc------CccCC--CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCCh
Q psy2882 312 TFLWYDYETFG------LNVRR--DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPE 383 (1428)
Q Consensus 312 ~~v~~D~ETTG------ldp~~--DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e 383 (1428)
..+.||+||++ -+|+. |.|++||... .++ ... .+.+..........+. .-+.. + ..=.+|
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~--~~~--~~~--v~~~~~~~~~~~~~~~--~~~~~---v-~~~~~E 73 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAG--SDG--LKR--VLVLKREGVEGLEGLL--PEGAE---V-EFFDSE 73 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcC--CCC--CcE--EEEEecCCcccccccC--CCCCe---E-EecCCH
Confidence 57899999984 23444 7899999852 121 112 2222211100000000 00110 1 011368
Q ss_pred HHHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchh--hhhh------cCCCCCchhhHHHHHHHhCCCCcC
Q psy2882 384 YKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYE--REWK------NNCSRWDLINVIKAFYVLSPYGIT 455 (1428)
Q Consensus 384 ~e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~--~~~~------~g~sr~D~ld~~rl~~~l~p~~~~ 455 (1428)
.+++..+.+++.+. .++||||..+||..+|..=..++++.... ..|. .|.-.+|+.++++. ..+ . .+.
T Consensus 74 ~~lL~~F~~~i~~~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~-~~~-~-~~~ 149 (204)
T cd05783 74 KELIREAFKIISEY-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSN-RAI-Q-VYA 149 (204)
T ss_pred HHHHHHHHHHHhcC-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhc-cch-h-hhh
Confidence 89999999999865 58999999999999998777666654111 1111 12223455554331 000 0 011
Q ss_pred CCCCCCCCCCCChHhHHHHc-CCCCC
Q psy2882 456 WPYKNNGKPSFKLEHLSFVN-NLSHK 480 (1428)
Q Consensus 456 ~p~~~~g~~s~kLe~L~~~~-gi~~~ 480 (1428)
|- ...+|++|+++|+++ |....
T Consensus 150 ~~---~~~~~~~L~~Va~~~lg~~K~ 172 (204)
T cd05783 150 FG---NKYREYTLDAVAKALLGEGKV 172 (204)
T ss_pred hc---cccccCcHHHHHHHhcCCCcc
Confidence 11 135789999999976 55433
No 126
>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=97.01 E-value=0.0046 Score=70.01 Aligned_cols=100 Identities=17% Similarity=0.062 Sum_probs=65.2
Q ss_pred ceEEEEeeccccC-----ccCCCcceeEEEEEE-eCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChH
Q psy2882 311 STFLWYDYETFGL-----NVRRDRPFQFAAIRT-DIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEY 384 (1428)
Q Consensus 311 ~~~v~~D~ETTGl-----dp~~DrIiqiaaIr~-~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~ 384 (1428)
-+.+.||+||+.- +|+.|.|++||..-. +.+.....+ .+++.-... +.+ |.. +. .=.+|.
T Consensus 7 l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~--~~~~l~~~~--~~~------~~~---v~-~~~~E~ 72 (230)
T cd05777 7 LRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIR--NIFTLKTCA--PIV------GAQ---VF-SFETEE 72 (230)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCcee--EEEEeCCCC--CCC------CCE---EE-EECCHH
Confidence 3578999999853 889999999998854 222222233 333422211 111 111 10 113688
Q ss_pred HHHHHHHHHHcCCC-ceEEEEcchhhhHHHHHHHHHHcccc
Q psy2882 385 KFASIIEKIFLKPG-TISVGYNTILFDDEITRFMFWRNLIN 424 (1428)
Q Consensus 385 e~~~~i~~~~~~~~-~~~VGyN~i~FD~~flr~~f~Rn~~~ 424 (1428)
+++..+.+++..-+ .+++|||...||..+|..=..+..++
T Consensus 73 eLL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~ 113 (230)
T cd05777 73 ELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLN 113 (230)
T ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCc
Confidence 99999999997722 68999999999999997666665444
No 127
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=96.87 E-value=0.02 Score=63.51 Aligned_cols=143 Identities=14% Similarity=0.057 Sum_probs=89.9
Q ss_pred cCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHHHcCCCceEEEE
Q psy2882 325 VRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGY 404 (1428)
Q Consensus 325 p~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~~~~~~~~~VGy 404 (1428)
....+||.||++..+.+.. + .+ +.++ ...-+|.+++..+.+.+.+-+..+|+|
T Consensus 6 ~~f~kIV~Is~~~~~~~~~-----~--~v---------------~s~~-----~~~~~E~~lL~~F~~~~~~~~p~LVs~ 58 (209)
T PF10108_consen 6 LPFHKIVCISVVYADDDGQ-----F--KV---------------KSLG-----GPDDDEKELLQDFFDLVEKYNPQLVSF 58 (209)
T ss_pred ccCCCeEEEEEEEEecCCc-----E--EE---------------Eecc-----CCCCCHHHHHHHHHHHHHhCCCeEEec
Confidence 4568999999997764321 1 11 1111 122358899999999998755589999
Q ss_pred cchhhhHHHHHHHHHHccccchhhhhhcCCCCCc---------hhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHHHc
Q psy2882 405 NTILFDDEITRFMFWRNLINPYEREWKNNCSRWD---------LINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVN 475 (1428)
Q Consensus 405 N~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D---------~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~~~ 475 (1428)
|...||..||..-..++++.. ...|..++.+|+ -+|++.+...+ ++..+.+|+.||..+
T Consensus 59 NG~~FDlP~L~~Ral~~gi~~-p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~-----------g~~~~~sLd~la~~l 126 (209)
T PF10108_consen 59 NGRGFDLPVLCRRALIHGISA-PRYLDIGNKPWENYRNRYSERHLDLMDLLSFY-----------GAKARTSLDELAALL 126 (209)
T ss_pred CCccCCHHHHHHHHHHhCCCC-chhhhcCCCCccccccccCcccccHHHHHhcc-----------CccccCCHHHHHHHc
Confidence 999999999987777777652 122222222222 24444431111 134568999999999
Q ss_pred CCCCCCC-------------------CChHHHHHHHHHHHHHHHhhCchh
Q psy2882 476 NLSHKKA-------------------HDALSDVRATLGLARLIRNNNPRL 506 (1428)
Q Consensus 476 gi~~~~A-------------------HdAlaDv~AT~~l~~~l~~~~p~l 506 (1428)
|||...- .=-..||.+|..|+.++.--...|
T Consensus 127 giPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~~G~l 176 (209)
T PF10108_consen 127 GIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELLRGRL 176 (209)
T ss_pred CCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 9984221 112578999999988876544333
No 128
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=96.86 E-value=0.0025 Score=73.57 Aligned_cols=173 Identities=21% Similarity=0.131 Sum_probs=100.8
Q ss_pred ceEEEEeeccccCccCCC---------------------cceeEEEEEE-eCCceee----ccceEEEEecCCCCCCChh
Q psy2882 311 STFLWYDYETFGLNVRRD---------------------RPFQFAAIRT-DIMLNTI----DNPIMLYCKPAPDFLPDPR 364 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~D---------------------rIiqiaaIr~-~~~~~~i----~~~~~~~~~p~~~~~p~pe 364 (1428)
..||.+|+|-||+..... .|+|+|.--. +.+.+.- -.+++++..|.....-+++
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~ 101 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQAS 101 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecch
Confidence 469999999999977543 3699998777 5555543 2234555444333322455
Q ss_pred hHh---hcCCCHHHHhcCCCChHHHHHH-----------HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhh
Q psy2882 365 ACL---ITKITPQFCLNNGIPEYKFASI-----------IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREW 430 (1428)
Q Consensus 365 a~~---itGITpe~~~~~g~~e~e~~~~-----------i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~ 430 (1428)
++. -||+.=+.+...|++-..+..+ +...+......+||||. -+|..+|-..|+. ++...
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~-~~Dl~~l~~~f~~----~LP~t- 175 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNG-LYDLMYLYKKFIG----PLPET- 175 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESST-HHHHHHHHHHHTT----S--SS-
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeCh-HhHHHHHHHHhcC----CCCCC-
Confidence 543 4899999998999987444421 11111123368999994 7999887655554 33222
Q ss_pred hcCCCCCchhhHHHHHHHhCCCCcCCCC--CCCCCCCCChHhHHHHcCCCC------------------------CC-CC
Q psy2882 431 KNNCSRWDLINVIKAFYVLSPYGITWPY--KNNGKPSFKLEHLSFVNNLSH------------------------KK-AH 483 (1428)
Q Consensus 431 ~~g~sr~D~ld~~rl~~~l~p~~~~~p~--~~~g~~s~kLe~L~~~~gi~~------------------------~~-AH 483 (1428)
+-+..+..+.+.|..+..-. ......+-.|+.|+..++... .. +|
T Consensus 176 --------~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H 247 (262)
T PF04857_consen 176 --------LEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAH 247 (262)
T ss_dssp --------HHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TT
T ss_pred --------HHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCC
Confidence 24445555566664332110 011134578999999888653 33 99
Q ss_pred ChHHHHHHHHHHHH
Q psy2882 484 DALSDVRATLGLAR 497 (1428)
Q Consensus 484 dAlaDv~AT~~l~~ 497 (1428)
.|=.|++.|..++-
T Consensus 248 eAGyDA~mTg~~F~ 261 (262)
T PF04857_consen 248 EAGYDAYMTGCVFI 261 (262)
T ss_dssp SHHHHHHHHHHHHH
T ss_pred CcchHHHHHHHHHc
Confidence 99999999998764
No 129
>KOG2248|consensus
Probab=96.73 E-value=0.015 Score=69.86 Aligned_cols=152 Identities=18% Similarity=0.152 Sum_probs=104.9
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
++.+++|+|+....-. =.+..+++|-.+... +.+ .+|+|...++- -.+..+|||.+++...++...++-.++
T Consensus 216 ~~i~AlDCEm~~te~g-~el~RVt~VD~~~~v-i~D----~fVkP~~~VvD--y~T~~SGIT~~~~e~~t~tl~dvq~~l 287 (380)
T KOG2248|consen 216 PNIFALDCEMVVTENG-LELTRVTAVDRDGKV-ILD----TFVKPNKPVVD--YNTRYSGITEEDLENSTITLEDVQKEL 287 (380)
T ss_pred CCeEEEEeeeeeeccc-eeeEEeeeeeccCcE-EeE----EeecCCCcccc--cccccccccHHHHhcCccCHHHHHHHH
Confidence 5799999999988877 778888888654332 333 59999987765 667899999999977787878888888
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCC-CCC-CCh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNG-KPS-FKL 468 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g-~~s-~kL 468 (1428)
.+ |-..+|++|| |++.=|...|+-.+- . ++|+.-+ ++. ..| .+. .+|
T Consensus 288 ~~-~~~~~TILVG-HSLenDL~aLKl~H~-~-----------------ViDTa~l----------f~~-~~g~~~~k~sL 336 (380)
T KOG2248|consen 288 LE-LISKNTILVG-HSLENDLKALKLDHP-S-----------------VIDTAVL----------FKH-PTGPYPFKSSL 336 (380)
T ss_pred Hh-hcCcCcEEEe-echhhHHHHHhhhCC-c-----------------eeeeeEE----------Eec-CCCCccchHHH
Confidence 88 4456699999 458889887764211 0 1333311 111 112 111 347
Q ss_pred HhHHHHc-CCCC---CCCCChHHHHHHHHHHHHHHHh
Q psy2882 469 EHLSFVN-NLSH---KKAHDALSDVRATLGLARLIRN 501 (1428)
Q Consensus 469 e~L~~~~-gi~~---~~AHdAlaDv~AT~~l~~~l~~ 501 (1428)
..||+.| |... ..-||+..|+.||++|++....
T Consensus 337 k~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 337 KNLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIK 373 (380)
T ss_pred HHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHh
Confidence 7887754 3322 2459999999999999876543
No 130
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=96.38 E-value=0.0064 Score=56.41 Aligned_cols=63 Identities=24% Similarity=0.333 Sum_probs=47.0
Q ss_pred HcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEE-Ee-C------CeeccHHHHHHHhC
Q psy2882 868 AIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIAL-IN-N------NKIHDRTTIISRFG 936 (1428)
Q Consensus 868 ~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~-~~-~------~~~~~~~~v~~~~G 936 (1428)
.+|||++.+|+ |||..||.|.+. |....|+|.|.|++-+..+++.. ++ + ...++...+.+++|
T Consensus 2 ~~gi~~i~AP~-eAeAq~A~L~~~-----g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~ 72 (73)
T smart00484 2 LMGIPYIVAPY-EAEAQCAYLAKS-----GLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELG 72 (73)
T ss_pred cCCCeEEEcCC-cHHHHHHHHHhC-----CCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcC
Confidence 58999999997 999999999974 56668999999999886665433 11 1 22456666776665
No 131
>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=96.34 E-value=0.085 Score=56.23 Aligned_cols=136 Identities=21% Similarity=0.214 Sum_probs=82.2
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
.+.+.+|+||+|+++... -..++.|.+... + ..+++.+... .. . .+...+
T Consensus 20 ~~~~a~D~E~~~~~~~~~-~~~~~~iq~~~~-----~-~~~i~~~~~~--~~-----------------~----~~~~~l 69 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSY-NPKIALIQLATG-----E-GCYIIDPIDL--GD-----------------N----WILDAL 69 (176)
T ss_dssp TSEEEEEEEEETSTSTTS-SEEEEEEEEEES-----C-EEEEECGTTS--TT-----------------T----THHHHH
T ss_pred CCeEEEEEEECCCCcccc-CCeEEEEEEecC-----C-Cceeeeeccc--cc-----------------c----chHHHH
Confidence 359999999999998433 334444444222 2 2333333221 10 0 066777
Q ss_pred HHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHh
Q psy2882 391 EKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEH 470 (1428)
Q Consensus 391 ~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~ 470 (1428)
.++|..++.+.|||| ++||..+|.+. ....+ . .+.|+.-+++.+.|. .++.|.+
T Consensus 70 ~~ll~~~~i~kv~~n-~~~D~~~L~~~---~~i~~--------~---~~~D~~l~~~~l~~~-----------~~~~L~~ 123 (176)
T PF01612_consen 70 KELLEDPNIIKVGHN-AKFDLKWLYRS---FGIDL--------K---NVFDTMLAAYLLDPT-----------RSYSLKD 123 (176)
T ss_dssp HHHHTTTTSEEEESS-HHHHHHHHHHH---HTS----------S---SEEEHHHHHHHTTTS-----------TTSSHHH
T ss_pred HHHHhCCCccEEEEE-EechHHHHHHH---hcccc--------C---Cccchhhhhhccccc-----------ccccHHH
Confidence 788888888999988 89999998764 12111 1 125555555666443 1289999
Q ss_pred HHHHc-C-CCC------CC-C-CC---------hHHHHHHHHHHHHHHHhh
Q psy2882 471 LSFVN-N-LSH------KK-A-HD---------ALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 471 L~~~~-g-i~~------~~-A-Hd---------AlaDv~AT~~l~~~l~~~ 502 (1428)
|+..+ | ++. .. . -+ |..||.+|.+|+..|..+
T Consensus 124 L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~ 174 (176)
T PF01612_consen 124 LAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQ 174 (176)
T ss_dssp HHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 98865 5 221 11 1 12 667999999998888753
No 132
>KOG0304|consensus
Probab=96.29 E-value=0.043 Score=60.15 Aligned_cols=168 Identities=18% Similarity=0.067 Sum_probs=110.1
Q ss_pred cccCccCCCcceeEEEEEEeCCceeec----c-ceEEE-EecCCCCCCChhhH---hhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 320 TFGLNVRRDRPFQFAAIRTDIMLNTID----N-PIMLY-CKPAPDFLPDPRAC---LITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 320 TTGldp~~DrIiqiaaIr~~~~~~~i~----~-~~~~~-~~p~~~~~p~pea~---~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
|-=.|...=.+||+|---.|.+++.-+ . .|+|. ..+..+.. +++++ +-+||.-+..++.|+...+|.+.+
T Consensus 54 ~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~-a~~SIElLr~~Gidf~K~~e~GI~~~~F~ell 132 (239)
T KOG0304|consen 54 TLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMY-AQDSIELLRRSGIDFEKHREEGIDIEEFAELL 132 (239)
T ss_pred HHHhchhhhhhhheeeeeeccCCCCCCCCCceeEEecccCCchhhcc-chhhHHHHHHcCcCHHHHHHcCCCHHHHHHHH
Confidence 333455566799999999998777654 1 13444 44444443 34554 458999999999999999888887
Q ss_pred HHHHc--CCCceEEEEcchhhhHHHHHHHHHHccccchhhhh-----hcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCC
Q psy2882 391 EKIFL--KPGTISVGYNTILFDDEITRFMFWRNLINPYEREW-----KNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463 (1428)
Q Consensus 391 ~~~~~--~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~-----~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~ 463 (1428)
..... .++-..|-||+ .+|...|=..+-+.-++--..++ +-...-+|+--+++.|.-+ .
T Consensus 133 m~sg~v~~~~V~WvTFhs-~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~-------------~ 198 (239)
T KOG0304|consen 133 MTSGLVLDENVTWVTFHS-GYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGL-------------S 198 (239)
T ss_pred HHhhhhccCceEEEEeec-cchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhh-------------h
Confidence 77653 25678999995 89998886554443222100000 0001123444444443221 1
Q ss_pred CCCChHhHHHHcCCCC-CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 464 PSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 464 ~s~kLe~L~~~~gi~~-~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
-.+-|+.||..+|++. +.+|.|=+|...|+..+.++++.
T Consensus 199 l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 199 LKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred hhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 2367999999999985 55999999999999999999863
No 133
>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=96.29 E-value=0.033 Score=61.51 Aligned_cols=90 Identities=13% Similarity=0.007 Sum_probs=57.6
Q ss_pred eEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
..++||+||+|.. .|..||..-. . .++ ++|....+... |.+ + ..=.+|.+++..+.
T Consensus 4 ~~~~fDIE~~~~~----~i~~i~~~~~--~----~~~--i~~~~~~~~~~--------~~~---v-~~~~~E~~lL~~f~ 59 (193)
T cd05784 4 KVVSLDIETSMDG----ELYSIGLYGE--G----QER--VLMVGDPEDDA--------PDN---I-EWFADEKSLLLALI 59 (193)
T ss_pred cEEEEEeecCCCC----CEEEEEeecC--C----CCE--EEEECCCCCCC--------CCE---E-EEECCHHHHHHHHH
Confidence 4689999999865 7777776421 1 221 22222211111 211 1 11136888999999
Q ss_pred HHHcCCC-ceEEEEcchhhhHHHHHHHHHHccccc
Q psy2882 392 KIFLKPG-TISVGYNTILFDDEITRFMFWRNLINP 425 (1428)
Q Consensus 392 ~~~~~~~-~~~VGyN~i~FD~~flr~~f~Rn~~~~ 425 (1428)
+.+..-+ .+++|||...||..+|..-+.+..+++
T Consensus 60 ~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~ 94 (193)
T cd05784 60 AWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL 94 (193)
T ss_pred HHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCc
Confidence 9997633 689999999999999987777766553
No 134
>PRK05762 DNA polymerase II; Reviewed
Probab=96.07 E-value=0.099 Score=69.48 Aligned_cols=172 Identities=16% Similarity=0.113 Sum_probs=96.2
Q ss_pred HHHHHHHHCCceecCcceec-----CCcccccccceeeeeee--------------cc---CCceEEEEeeccccCccCC
Q psy2882 270 DIVKELEKKGLKIEKNKIKL-----PNNSIKKIGNYYIDILL--------------HN---GNSTFLWYDYETFGLNVRR 327 (1428)
Q Consensus 270 ~I~~~l~~~gi~v~~~~I~l-----~~~pIk~~G~~~V~v~l--------------~~---~~~~~v~~D~ETTGldp~~ 327 (1428)
.+.+.|++.|+++=...|.. -+.-|...|.|.+...- .+ ..-..+.||+||+.-
T Consensus 92 ~~~~~~~~~~~~i~EaDI~~~~R~lid~~i~~~~w~~~~~~~~~~~~~~~~~~i~~~~~~~p~lrvlsfDIE~~~~---- 167 (786)
T PRK05762 92 RLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEQYTTDGVLRNARLKPAPDYRPPLKVVSLDIETSNK---- 167 (786)
T ss_pred HHHHHHHHcCCeEEECCCChhHhheeeCCCCCcEEEEEEeeccccceeEEecceeeCCCCCCCCeEEEEEEEEcCC----
Confidence 45555665566333222221 12347777776654321 11 123689999999874
Q ss_pred CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHHHcCCC-ceEEEEcc
Q psy2882 328 DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKIFLKPG-TISVGYNT 406 (1428)
Q Consensus 328 DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~~~~~~-~~~VGyN~ 406 (1428)
+.|.+|+..-.. ++..+.+-+..+. + +. .+ ..-.+|.+++..+..++.+-+ .+++|||.
T Consensus 168 ~~i~sI~~~~~~-------~~~vi~ig~~~~~-~--~~---------~v-~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi 227 (786)
T PRK05762 168 GELYSIGLEGCG-------QRPVIMLGPPNGE-A--LD---------FL-EYVADEKALLEKFNAWFAEHDPDVIIGWNV 227 (786)
T ss_pred CceEEeeecCCC-------CCeEEEEECCCCC-C--cc---------eE-EEcCCHHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 357777764211 1123333322111 0 10 02 123478899999999997722 68999999
Q ss_pred hhhhHHHHHHHHHHccccch-h-----hhhh-------------cCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCC
Q psy2882 407 ILFDDEITRFMFWRNLINPY-E-----REWK-------------NNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFK 467 (1428)
Q Consensus 407 i~FD~~flr~~f~Rn~~~~y-~-----~~~~-------------~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~k 467 (1428)
.+||..+|..-+.++.+..- . ..|. .|...+|++++++. .. ...+||+
T Consensus 228 ~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~---~~----------~~l~sys 294 (786)
T PRK05762 228 VQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKS---AT----------WVFDSFS 294 (786)
T ss_pred CCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHH---hh----------ccCCCCC
Confidence 99999999776666655421 1 0121 11223355555443 21 1357899
Q ss_pred hHhHHHHcCCC
Q psy2882 468 LEHLSFVNNLS 478 (1428)
Q Consensus 468 Le~L~~~~gi~ 478 (1428)
|+++|+++.-+
T Consensus 295 L~~Va~~~Lg~ 305 (786)
T PRK05762 295 LEYVSQRLLGE 305 (786)
T ss_pred HHHHHHHHhCC
Confidence 99999986554
No 135
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=95.93 E-value=0.0037 Score=61.31 Aligned_cols=71 Identities=18% Similarity=0.202 Sum_probs=50.9
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccch-HHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCC
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVG-ALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK 850 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~-av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~ 850 (1428)
+.+|++.++||++++... ....+.++. ++.++++.+..+++. + -..++||||..+..+.+.....+..|++
T Consensus 27 vaIDa~~wl~~~~~~~~~-~~~~~~~~~~~l~~~~~rl~~L~~~-~-I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 27 LAIDASIWLYQFLTACRE-KLGTPLPNSKHLMGLFYRTCRLLEF-G-IKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred EeccHHHHHHHHHHHHhh-hhcCCCCchHHHHHHHHHHHHHHHC-C-CeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 368999999999999742 111223344 899999999988753 2 2358999998777777777777776653
No 136
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=95.82 E-value=0.0012 Score=68.51 Aligned_cols=53 Identities=28% Similarity=0.481 Sum_probs=49.4
Q ss_pred HHhcCCCcch--hhhhhccccccccCcceeecccccccccccchhhhhhcCCCcc
Q psy2882 1250 VKLLGVNPLI--IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302 (1428)
Q Consensus 1250 l~~~~~d~~~--i~~~~G~~~~~~a~p~~~~~~~~~~~~~~~~~~~~~~~~p~~v 1302 (1428)
|+.||+|||+ ||.|+++..+..|.|+++|++......|+.|..++++|+|+.+
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~i 55 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGI 55 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEE
T ss_pred CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEE
Confidence 3568999998 9999999999999999999999899999999999999999887
No 137
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=95.65 E-value=0.22 Score=61.68 Aligned_cols=102 Identities=18% Similarity=0.076 Sum_probs=66.3
Q ss_pred ceEEEEeeccccCc-----cC--CCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCCh
Q psy2882 311 STFLWYDYETFGLN-----VR--RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPE 383 (1428)
Q Consensus 311 ~~~v~~D~ETTGld-----p~--~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e 383 (1428)
...+.||+||+.-. +. .|.|++|+.+..+.+.........+...+.. + ++|+.-... -.|
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~---~------~~~~~~~~~----~~E 69 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK---E------IDGVEVYEF----NNE 69 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC---C------CCCCeEEec----CCH
Confidence 35789999998642 33 6899999999877654322221222222211 1 223222111 267
Q ss_pred HHHHHHHHHHHcC-CCceEEEEcchhhhHHHHHHHHHHccccc
Q psy2882 384 YKFASIIEKIFLK-PGTISVGYNTILFDDEITRFMFWRNLINP 425 (1428)
Q Consensus 384 ~e~~~~i~~~~~~-~~~~~VGyN~i~FD~~flr~~f~Rn~~~~ 425 (1428)
.+++..+.+.+.+ ...+++|||..+||..+|..-+.+...+.
T Consensus 70 ~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~ 112 (471)
T smart00486 70 KELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKP 112 (471)
T ss_pred HHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCC
Confidence 8999999998876 22789999998999999987776655543
No 138
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.63 E-value=0.11 Score=70.67 Aligned_cols=95 Identities=19% Similarity=0.225 Sum_probs=61.2
Q ss_pred eEEEEeeccccC------ccCCCcceeEEEEEEeCCceeeccce--EEEEecCCCCCCChhhHhhcCCCHHHHhcCCCCh
Q psy2882 312 TFLWYDYETFGL------NVRRDRPFQFAAIRTDIMLNTIDNPI--MLYCKPAPDFLPDPRACLITKITPQFCLNNGIPE 383 (1428)
Q Consensus 312 ~~v~~D~ETTGl------dp~~DrIiqiaaIr~~~~~~~i~~~~--~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e 383 (1428)
+.+.||+||++. +|..|.|||||.+....+ ...+ ++ ..++.-. ..+ +.|.. +. .=.+|
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g-~~~~-~~~r~vftl~~--c~~------i~g~~---V~-~f~sE 330 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQG-DEEE-PLTKFIFTLKE--CAS------IAGAN---VL-SFETE 330 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCC-CccC-CcceEEEecCc--ccc------CCCce---EE-EeCCH
Confidence 588999999864 356899999999865432 2111 12 2333221 111 12221 11 11368
Q ss_pred HHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHc
Q psy2882 384 YKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRN 421 (1428)
Q Consensus 384 ~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn 421 (1428)
.+++..+.+++.. | .+++|||..+||..+|..=..+.
T Consensus 331 ~eLL~~f~~~I~~~DP-DII~GYNi~~FDlpYL~~Ra~~l 369 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDP-DFLTGYNIINFDLPYLLNRAKAL 369 (1054)
T ss_pred HHHHHHHHHHHHhcCC-CEEEecCCcCCcHHHHHHHHHHh
Confidence 8999999998876 4 78999999999999996554443
No 139
>PHA02528 43 DNA polymerase; Provisional
Probab=95.55 E-value=0.1 Score=69.45 Aligned_cols=179 Identities=15% Similarity=0.125 Sum_probs=98.0
Q ss_pred cceeeeeeeccCCceEEEEeecccc----CccC--CCcceeEEEEEEeCCceeeccceEEEEecCCC-----CCCChhhH
Q psy2882 298 GNYYIDILLHNGNSTFLWYDYETFG----LNVR--RDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPD-----FLPDPRAC 366 (1428)
Q Consensus 298 G~~~V~v~l~~~~~~~v~~D~ETTG----ldp~--~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~-----~~p~pea~ 366 (1428)
|+|.=+++.....-..+.||+||+. -+|+ .|.|++||.- +.+.. . +.++...... -.+.|..
T Consensus 93 ~~~~~~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~~---~-~~v~~~~~~~~~~~~~~~~~~~- 165 (881)
T PHA02528 93 DTYPGEIKYDRSKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSIDD---R-FYVFDLGSVEEWDAKGDEVPQE- 165 (881)
T ss_pred hhcCCCCCCCCCCccEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCCC---E-EEEEEecCcccccccCCccccc-
Confidence 5554344444234578999999986 4566 7899999973 22221 2 2233221100 0000000
Q ss_pred hhcCCCHHHHhcCCCChHHHHHHHHHHHcC-CCceEEEEcchhhhHHHHHHHHHHccc-------cchhhh--------h
Q psy2882 367 LITKITPQFCLNNGIPEYKFASIIEKIFLK-PGTISVGYNTILFDDEITRFMFWRNLI-------NPYERE--------W 430 (1428)
Q Consensus 367 ~itGITpe~~~~~g~~e~e~~~~i~~~~~~-~~~~~VGyN~i~FD~~flr~~f~Rn~~-------~~y~~~--------~ 430 (1428)
...++. . ..-.+|.+++..+.+++.. .-.+++|||...||..+|..=..+.+. .++... +
T Consensus 166 ~~~~v~---~-~~~~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~ 241 (881)
T PHA02528 166 ILDKVV---Y-MPFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMY 241 (881)
T ss_pred ccCCee---E-EEcCCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccc
Confidence 011111 0 0123789999999999966 227899999999999999655443211 111110 0
Q ss_pred --------hcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHHH-cCCCCCCC-----------------CC
Q psy2882 431 --------KNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFV-NNLSHKKA-----------------HD 484 (1428)
Q Consensus 431 --------~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~~-~gi~~~~A-----------------Hd 484 (1428)
-.|...+|.+++++.+. | ...+||+|+++|.+ +|.....- +=
T Consensus 242 g~~~~~~~i~GRv~lD~~dl~k~~~--------~----~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Y 309 (881)
T PHA02528 242 GREEIAYDISGISILDYLDLYKKFT--------F----TNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEY 309 (881)
T ss_pred cccceeEEEcceEEEeHHHHHHHhh--------h----cccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHH
Confidence 01222345555555421 1 13678999999996 77653221 12
Q ss_pred hHHHHHHHHHHHHHH
Q psy2882 485 ALSDVRATLGLARLI 499 (1428)
Q Consensus 485 AlaDv~AT~~l~~~l 499 (1428)
.+.||..|.+|+.++
T Consensus 310 nl~Da~Lv~~L~~kl 324 (881)
T PHA02528 310 NIIDVELVDRLDDKR 324 (881)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345777777776663
No 140
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=95.32 E-value=0.0055 Score=60.25 Aligned_cols=67 Identities=15% Similarity=0.165 Sum_probs=44.4
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHh-cCCCEEEEEEeCCCCCcccCCChhhhc
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKN-YRATYIACIFDAKGKNFRNILYPSYKA 846 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~-~~p~~~v~~fD~~~~~fR~~l~p~YKa 846 (1428)
+.+||+.++||++++........+..+..+.++++.+..++.. ..| +|||||..+..+.+.....+.
T Consensus 29 vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~P---ifVFDG~~~~~K~~~~~~R~~ 96 (101)
T PF00752_consen 29 VAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKP---IFVFDGKPPPLKRETIQKRRK 96 (101)
T ss_dssp EEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEE---EEEE--STTGGCHHHHHHHHH
T ss_pred EEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEE---EEEECCCCchhhHHHHHHHHH
Confidence 6799999999999997532222222268899999999987664 455 899999866665554444433
No 141
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.17 E-value=0.012 Score=53.24 Aligned_cols=26 Identities=38% Similarity=0.643 Sum_probs=21.8
Q ss_pred CCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 958 GVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 958 GvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
||||||+++|..|+++|||++++.+.
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 89999999999999999999998754
No 142
>PHA02570 dexA exonuclease; Provisional
Probab=95.14 E-value=0.22 Score=55.36 Aligned_cols=101 Identities=16% Similarity=0.076 Sum_probs=64.5
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEe------cC----CC-CCC-----------ChhhHhhcCC
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCK------PA----PD-FLP-----------DPRACLITKI 371 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~------p~----~~-~~p-----------~pea~~itGI 371 (1428)
+.+|+||.|..|. .-|++||||-.+.+.....+ |+-++. .. .. ..+ ++||-.+ |
T Consensus 4 lMIDlETmG~~p~-AaIisIgAV~Fdp~~~~g~t-F~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~--L 79 (220)
T PHA02570 4 FIIDFETFGNTPD-GAVIDLAVIAFEHDPHNPPT-FEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKN--L 79 (220)
T ss_pred EEEEeeccCCCCC-ceEEEEEEEEecCCCCcccc-HHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHh--c
Confidence 6799999999965 78999999999876443333 432222 21 11 122 2333332 1
Q ss_pred CHHHHhcCCCChHHHHHHHHHHHcCCC----ceEEEEcchhhhHHHHHHHHHHc
Q psy2882 372 TPQFCLNNGIPEYKFASIIEKIFLKPG----TISVGYNTILFDDEITRFMFWRN 421 (1428)
Q Consensus 372 Tpe~~~~~g~~e~e~~~~i~~~~~~~~----~~~VGyN~i~FD~~flr~~f~Rn 421 (1428)
.|. ...++..+++.++.+++...+ ...|=.|..+||..+|+.+|.|.
T Consensus 80 ~~s---~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~ 130 (220)
T PHA02570 80 KPS---DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDI 130 (220)
T ss_pred cCC---CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHH
Confidence 110 012456788888888887532 34555588899999999998887
No 143
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=95.07 E-value=0.19 Score=57.07 Aligned_cols=104 Identities=10% Similarity=-0.089 Sum_probs=63.2
Q ss_pred ceEEEEeecccc-----CccCCCcceeEEEEEEeCCceeecc----ceEEEEecCCCCCCCh-hhHhhcCCCHHHHhcCC
Q psy2882 311 STFLWYDYETFG-----LNVRRDRPFQFAAIRTDIMLNTIDN----PIMLYCKPAPDFLPDP-RACLITKITPQFCLNNG 380 (1428)
Q Consensus 311 ~~~v~~D~ETTG-----ldp~~DrIiqiaaIr~~~~~~~i~~----~~~~~~~p~~~~~p~p-ea~~itGITpe~~~~~g 380 (1428)
-+.+.||+||.+ -||..|.|++|+.+.-+ +...... ...+++.......... ....+.|.+ + ..=
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---v-~~~ 78 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDD-DVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIP---V-EVV 78 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEec-CCCcccccccceeEEEEcCccchhhhhccccCCCCCe---E-EEe
Confidence 467889999874 38899999999988543 3222221 1234444332100000 000122222 1 122
Q ss_pred CChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHH
Q psy2882 381 IPEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWR 420 (1428)
Q Consensus 381 ~~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~R 420 (1428)
.+|.+++..+..++.. | .+++|||..+||..+|-.=...
T Consensus 79 ~~E~~LL~~f~~~i~~~DP-Dii~GyNi~~fd~~YL~~Ra~~ 119 (231)
T cd05778 79 ESELELFEELIDLVRRFDP-DILSGYEIQRSSWGYLIERAAA 119 (231)
T ss_pred CCHHHHHHHHHHHHHHhCC-CEEEEeccccCcHHHHHHHHHH
Confidence 3678999999999976 4 7899999999999998644433
No 144
>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=94.82 E-value=0.5 Score=48.87 Aligned_cols=67 Identities=18% Similarity=0.192 Sum_probs=45.1
Q ss_pred HHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCC
Q psy2882 385 KFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKP 464 (1428)
Q Consensus 385 e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~ 464 (1428)
++...+.+++..++...|||| +.||..+|+.. +.. .. + .+.|+.-++|.+.|. ..
T Consensus 41 ~~~~~l~~~l~~~~~~~v~~~-~k~d~~~L~~~----~~~-~~------~---~~~D~~~~ayll~~~----------~~ 95 (155)
T cd00007 41 EDLEALKELLEDEDITKVGHD-AKFDLVVLARD----GIE-LP------G---NIFDTMLAAYLLNPG----------EG 95 (155)
T ss_pred HHHHHHHHHHcCCCCcEEecc-HHHHHHHHHHC----CCC-CC------C---CcccHHHHHHHhCCC----------CC
Confidence 455566777877767799998 79999987532 211 01 1 136778888888764 11
Q ss_pred CCChHhHHHHcC
Q psy2882 465 SFKLEHLSFVNN 476 (1428)
Q Consensus 465 s~kLe~L~~~~g 476 (1428)
++.|+.+++.+.
T Consensus 96 ~~~l~~l~~~~l 107 (155)
T cd00007 96 SHSLDDLAKEYL 107 (155)
T ss_pred cCCHHHHHHHHc
Confidence 358999999873
No 145
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=94.70 E-value=0.32 Score=60.69 Aligned_cols=115 Identities=13% Similarity=0.066 Sum_probs=60.1
Q ss_pred eeeeeeeccCCceEEEEeeccccCccCCCcc----eeEEEEEEeCCceeeccceEEEEecC-CCCCCChhhHhhcCCCHH
Q psy2882 300 YYIDILLHNGNSTFLWYDYETFGLNVRRDRP----FQFAAIRTDIMLNTIDNPIMLYCKPA-PDFLPDPRACLITKITPQ 374 (1428)
Q Consensus 300 ~~V~v~l~~~~~~~v~~D~ETTGldp~~DrI----iqiaaIr~~~~~~~i~~~~~~~~~p~-~~~~p~pea~~itGITpe 374 (1428)
|.-.|+.+...-...++|+|+|+ +.+-.+ -+|-+|-.. +.......+.++..+. ....-...+...-++.+.
T Consensus 95 y~~~~~~d~~~i~~~~~DIEv~~--~~fp~~~~a~~~i~~i~~~-d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (498)
T PHA02524 95 YRGVIDFDRDDVVIDVVDIEVTA--PEFPEPKYAKYEIDMISHV-RLHNGKKTYYIFDLVKDVGHWDPKKSVLEKYILDN 171 (498)
T ss_pred cCCccccchhhceEEEEEEEecC--CCCCChhhcCCceEEEEee-ecccCCccEEEEeccccccCCCcccccccccccCC
Confidence 44456666666678889999987 234333 233344332 1111122143443221 111111112111111110
Q ss_pred HHhcCCCChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHH
Q psy2882 375 FCLNNGIPEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMF 418 (1428)
Q Consensus 375 ~~~~~g~~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f 418 (1428)
-.--.=.+|.+++.++.+++.+ | .+++|||..+||..+|..=.
T Consensus 172 v~v~~f~sE~eLL~~F~~~i~~~DP-DIItGYNi~nFDlPYL~~Ra 216 (498)
T PHA02524 172 VVYMPFEDEVDLLLNYIQLWKANTP-DLVFGWNSEGFDIPYIITRI 216 (498)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhCC-CEEEeCCCcccCHHHHHHHH
Confidence 0001113678999999999977 4 68999999999999985443
No 146
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=94.43 E-value=0.0096 Score=62.14 Aligned_cols=53 Identities=26% Similarity=0.595 Sum_probs=48.7
Q ss_pred HHhcCCCcch--hhhhhccccccccCcceeecccccccccccchhhhhhcCCCcc
Q psy2882 1250 VKLLGVNPLI--IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302 (1428)
Q Consensus 1250 l~~~~~d~~~--i~~~~G~~~~~~a~p~~~~~~~~~~~~~~~~~~~~~~~~p~~v 1302 (1428)
++.||+|||+ ||.|+++.....|+|+.+++......+|..|..++++|+|+.+
T Consensus 4 ~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~i 58 (138)
T PRK00109 4 GRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGL 58 (138)
T ss_pred CcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEE
Confidence 3578999998 9999999999999999999998888899999999999998777
No 147
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=94.20 E-value=0.016 Score=59.81 Aligned_cols=50 Identities=22% Similarity=0.425 Sum_probs=46.6
Q ss_pred cCCCcch--hhhhhccccccccCcceeecccccccccccchhhhhhcCCCcc
Q psy2882 1253 LGVNPLI--IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302 (1428)
Q Consensus 1253 ~~~d~~~--i~~~~G~~~~~~a~p~~~~~~~~~~~~~~~~~~~~~~~~p~~v 1302 (1428)
||+|||+ ||.|+++.....|+|+.++.......+|..|..++++|+|+.+
T Consensus 1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~i 52 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKI 52 (130)
T ss_pred CeEccCCCeEEEEEECCCCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEE
Confidence 6899988 9999999988999999999998888999999999999999777
No 148
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=93.77 E-value=0.28 Score=58.02 Aligned_cols=97 Identities=15% Similarity=0.086 Sum_probs=62.3
Q ss_pred ceEEEEeeccccCc-----cCCCcceeEEEEEEeCCc-eeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChH
Q psy2882 311 STFLWYDYETFGLN-----VRRDRPFQFAAIRTDIML-NTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEY 384 (1428)
Q Consensus 311 ~~~v~~D~ETTGld-----p~~DrIiqiaaIr~~~~~-~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~ 384 (1428)
-+.+.||+||..-+ +..|.|++|+.+-.+... ..... ..++.-..+..+ .-..|+- - -+|.
T Consensus 157 l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~--~~~~~~~~~~~~--~~~~v~~--------~-~~E~ 223 (325)
T PF03104_consen 157 LRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRR--KVFTLGSCDSIE--DNVEVIY--------F-DSEK 223 (325)
T ss_dssp SEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEE--EEEECSCSCCTT--CTTEEEE--------E-SSHH
T ss_pred cceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCce--EEEEecCCCCCC--CCcEEEE--------E-CCHH
Confidence 57899999999775 788999999987654321 11112 233322222211 1111111 1 3678
Q ss_pred HHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHc
Q psy2882 385 KFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRN 421 (1428)
Q Consensus 385 e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn 421 (1428)
+++..+...+.+ | .+++|||...||..+|..=..+.
T Consensus 224 ~lL~~f~~~i~~~dP-Dii~GyN~~~fD~~yl~~R~~~l 261 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDP-DIITGYNIDGFDLPYLIERAKKL 261 (325)
T ss_dssp HHHHHHHHHHHHHS--SEEEESSTTTTHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcCC-cEEEEecccCCCHHHHHHHHHHh
Confidence 888888888866 4 68999999999999997655555
No 149
>PF12813 XPG_I_2: XPG domain containing
Probab=93.33 E-value=0.081 Score=60.59 Aligned_cols=73 Identities=22% Similarity=0.312 Sum_probs=52.0
Q ss_pred HHHHHHHHHHc---CCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCcccccc---CcEEEEe-----C-----
Q psy2882 859 INLIHQMVKAI---GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS---NKIALIN-----N----- 922 (1428)
Q Consensus 859 ~~~i~~~l~~~---gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~---~~v~~~~-----~----- 922 (1428)
.+.+.+.|+.+ |++++..+| |||.-||.+|++. | ..|+|.|.||+=.-- ..+.-++ .
T Consensus 6 ~~~~~e~L~~~~~~~~~~~~~~~-EAD~~~A~~A~~~----~--~~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~ 78 (246)
T PF12813_consen 6 VPAFIEALRESWRYGVPVVQCPG-EADRECAALARKW----G--CPVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTG 78 (246)
T ss_pred HHHHHHHHHHHhhcCCcEEEcCc-cchHHHHHHHHHc----C--CeEEccCCCEEEeccCCCceEEEeeeeEeecccccC
Confidence 35567777777 999999998 9999999999874 3 378999999875422 1222222 1
Q ss_pred ------CeeccHHHHHHHhCCC
Q psy2882 923 ------NKIHDRTTIISRFGVS 938 (1428)
Q Consensus 923 ------~~~~~~~~v~~~~Gv~ 938 (1428)
.+.+.++.+..++|+.
T Consensus 79 ~~~~i~~~~y~~~~i~~~l~l~ 100 (246)
T PF12813_consen 79 SGSYISAKVYSPDKICKRLGLP 100 (246)
T ss_pred CCCeeEEEEEcHHHHHHHcCCc
Confidence 1236777788888876
No 150
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=93.12 E-value=1.1 Score=56.16 Aligned_cols=156 Identities=13% Similarity=0.104 Sum_probs=90.5
Q ss_pred ceEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASII 390 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i 390 (1428)
...++||+||+ |...-+.++|.+..+.+. ..+. +.-+.- ..+..|.+...++
T Consensus 284 ~~~~ffDiEt~---P~~~~~yL~G~~~~~~~~-~~~~-~~~fla-----------------------~~~~~E~~~~~~f 335 (457)
T TIGR03491 284 PGELIFDIESD---PDENLDYLHGFLVVDKGQ-ENEK-YRPFLA-----------------------EDPNTEELAWQQF 335 (457)
T ss_pred CccEEEEecCC---CCCCCceEEEEEEecCCC-CCcc-eeeeec-----------------------CCchHHHHHHHHH
Confidence 57899999999 677788999997764331 1111 111111 1112344455555
Q ss_pred HHHHcC-CCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCC-CCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 391 EKIFLK-PGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNC-SRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 391 ~~~~~~-~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~-sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
.+++.. ++..++.|| .|-...|+....++... ..++..-. .-+|+..+++-.+. .| .+||+|
T Consensus 336 ~~~l~~~~~~~i~hY~--~~e~~~l~rla~~~~~~--~~~~~~l~~~~vDL~~~vr~~~~-------~p-----~~sysL 399 (457)
T TIGR03491 336 LQLLQSYPDAPIYHYG--ETEKDSLRRLAKRYGTP--EAEIEELLKRFVDIHTIVRRSWI-------LP-----IESYSL 399 (457)
T ss_pred HHHHHHCCCCeEEeeC--HHHHHHHHHHHHHcCCC--HHHHHHHHHHheehHHHHHhhEE-------CC-----CCCCCH
Confidence 555543 667899999 58888888887776543 11111111 12466666665322 23 468999
Q ss_pred HhHHHHcCCCCCCCCChHHHHHHHHHHHHHH-HhhCchhHHHHHhh
Q psy2882 469 EHLSFVNNLSHKKAHDALSDVRATLGLARLI-RNNNPRLFNFILSL 513 (1428)
Q Consensus 469 e~L~~~~gi~~~~AHdAlaDv~AT~~l~~~l-~~~~p~l~~~~~~~ 513 (1428)
..++..+|++... ...|-..++..+... ....+.+.+.++.+
T Consensus 400 K~v~~~lg~~~~~---~~~~G~~ai~~y~~~~~~~~~~~l~~l~~Y 442 (457)
T TIGR03491 400 KSIARWLGFEWRQ---KEASGAKSLLWYRQWKKTGDRRLLERILRY 442 (457)
T ss_pred HHHHHHhCcccCC---CCCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 9999999998652 233444555555543 33445555554443
No 151
>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=92.68 E-value=0.16 Score=54.72 Aligned_cols=106 Identities=23% Similarity=0.291 Sum_probs=65.1
Q ss_pred hccchhhhhhhccCCcCcCC--CCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHH
Q psy2882 779 IDGSSCIYRAFYALPDIRNI--DNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLI 856 (1428)
Q Consensus 779 i~g~~~~~Ra~~a~~~l~~~--~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~ 856 (1428)
+||+|+||. .|.+... .+.--.|=--++.+|..... .....++||||+.....-. ...+
T Consensus 3 IDGYNli~~----~~~l~~~~~~~~l~~aR~~Li~~L~~y~~-~~~~~v~VVFDa~~~~~~~-----------~~~~--- 63 (166)
T PF05991_consen 3 IDGYNLIHA----WPELRSLAERGDLEAARERLIEMLSEYAQ-FSGYEVIVVFDAYKVPGGS-----------EERE--- 63 (166)
T ss_pred EcchhhhCC----CHHHHhhcCcCCHHHHHHHHHHHHHHHhc-ccCCEEEEEEeCCcCCCCC-----------ceee---
Confidence 799999975 4433221 22323343445555544333 4556799999984211100 0000
Q ss_pred HHHHHHHHHHHHcCCcEEEec-chhhHHHHHHHHHHHhhhCCCEEEEEeCCCCcccccc
Q psy2882 857 LQINLIHQMVKAIGWPILIIK-GVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS 914 (1428)
Q Consensus 857 ~q~~~i~~~l~~~gi~~i~~~-g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~ 914 (1428)
..-|+.++..+ |-.||++|--++..... .+..|+|||+|....+.+.
T Consensus 64 ----------~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~-~~~~v~VVTSD~~iq~~~~ 111 (166)
T PF05991_consen 64 ----------EYGGIEVVFTKEGETADDYIERLVRELKN-RPRQVTVVTSDREIQRAAR 111 (166)
T ss_pred ----------eeCceEEEECCCCCCHHHHHHHHHHHhcc-CCCeEEEEeCCHHHHHHHh
Confidence 01266666655 68999999999988632 3579999999999888774
No 152
>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=92.06 E-value=1.2 Score=49.19 Aligned_cols=150 Identities=11% Similarity=-0.001 Sum_probs=83.0
Q ss_pred ceEEEEeeccccCccC--C--CcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHH
Q psy2882 311 STFLWYDYETFGLNVR--R--DRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKF 386 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~--~--DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~ 386 (1428)
...+.+|+|+++.... . =.++|||. .+ -.+.+.+.. ++. .+...+
T Consensus 22 ~~vig~D~Ew~~~~~~~~~~~v~LiQiat----~~-------~~~lid~~~--~~~------------------~~~~~~ 70 (193)
T cd06146 22 GRVVGIDSEWKPSFLGDSDPRVAILQLAT----ED-------EVFLLDLLA--LEN------------------LESEDW 70 (193)
T ss_pred CCEEEEECccCCCccCCCCCCceEEEEec----CC-------CEEEEEchh--ccc------------------cchHHH
Confidence 4789999999877543 2 34577772 11 134443322 110 012234
Q ss_pred HHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCC
Q psy2882 387 ASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSF 466 (1428)
Q Consensus 387 ~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~ 466 (1428)
...+.++|..++.+-|||+ +++|..+|+..|-... .| +...--++|+..+++.+......-+........+
T Consensus 71 ~~~L~~ll~d~~i~KVg~~-~~~D~~~L~~~~~~~~------~~--~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 71 DRLLKRLFEDPDVLKLGFG-FKQDLKALSASYPALK------CM--FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred HHHHHHHhCCCCeeEEEec-hHHHHHHHHHhcCccc------cc--cccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 5557777888877789998 8999999865332100 00 0001123555555554432110000001123467
Q ss_pred ChHhHHHHc-CCCC----------------CCCCChHHHHHHHHHHHHHHH
Q psy2882 467 KLEHLSFVN-NLSH----------------KKAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 467 kLe~L~~~~-gi~~----------------~~AHdAlaDv~AT~~l~~~l~ 500 (1428)
.|..|++.+ |.+. .+-+=|..||++++.|+.+|.
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 999999865 4321 223568999999999998875
No 153
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.92 E-value=0.068 Score=71.31 Aligned_cols=73 Identities=16% Similarity=0.114 Sum_probs=57.9
Q ss_pred hhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHh-cCCCEEEEEEeCCCCCcccCCChhhhcCCCCCCh
Q psy2882 777 GKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKN-YRATYIACIFDAKGKNFRNILYPSYKATRKKMPY 853 (1428)
Q Consensus 777 ~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~-~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~ 853 (1428)
+++|+|.+|||+.+++... ...+....++.||++.+.+|+.. .+| |+||||+.+..+++....++..|.+.-+
T Consensus 27 vAIDasiWL~q~l~~vr~~-~g~~l~n~hl~g~f~Ri~~Ll~~gI~P---VfVFDG~~p~lK~~t~~~R~~rR~~a~~ 100 (1034)
T TIGR00600 27 LAVDISIWLNQALKGVRDR-EGNAIKNSHLLTLFHRLCKLLFFRIRP---IFVFDGGAPLLKRQTLAKRRQRRDGASE 100 (1034)
T ss_pred EEechHHHHHHHHHHHHhc-cCCccCCHHHHHHHHHHHHHHHCCCeE---EEEECCCCchHhHHHHHHHHHHHHHHHH
Confidence 5799999999999987521 11223568999999999999884 455 9999999899999999999988876533
No 154
>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=91.27 E-value=1.5 Score=49.89 Aligned_cols=42 Identities=17% Similarity=0.113 Sum_probs=33.8
Q ss_pred ChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHcccc
Q psy2882 382 PEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLIN 424 (1428)
Q Consensus 382 ~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~ 424 (1428)
+|.+.+..+...+.+ | .+++|||...||.++|-.=......+
T Consensus 81 ~E~~LL~~f~~~i~~~DP-DiivG~Ni~~fdl~~L~~R~~~l~i~ 124 (234)
T cd05776 81 NERALLNFFLAKLQKIDP-DVLVGHDLEGFDLDVLLSRIQELKVP 124 (234)
T ss_pred CHHHHHHHHHHHHhhcCC-CEEEeeccCCCCHHHHHHHHHHhCCC
Confidence 678999999999977 4 78999998899999997655554444
No 155
>KOG1798|consensus
Probab=90.69 E-value=1.2 Score=60.07 Aligned_cols=100 Identities=20% Similarity=0.167 Sum_probs=64.2
Q ss_pred ceEEEEeeccccC-----ccCCCcceeEEEEEEeCCce-eeccc-----e-EEEEecCCCCCCChhhHhhcCCCHHHHhc
Q psy2882 311 STFLWYDYETFGL-----NVRRDRPFQFAAIRTDIMLN-TIDNP-----I-MLYCKPAPDFLPDPRACLITKITPQFCLN 378 (1428)
Q Consensus 311 ~~~v~~D~ETTGl-----dp~~DrIiqiaaIr~~~~~~-~i~~~-----~-~~~~~p~~~~~p~pea~~itGITpe~~~~ 378 (1428)
+....||+|||-+ |.+.|+|.=|+.. +|+.+- |+.+. . .|.--|.+++. .-..|+.-+
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYM-iDGqGfLItNREiVs~DIedfEYTPKpE~e---G~F~v~Ne~------ 315 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYM-IDGQGFLITNREIVSEDIEDFEYTPKPEYE---GPFCVFNEP------ 315 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEE-ecCceEEEechhhhccchhhcccCCccccc---cceEEecCC------
Confidence 6799999999998 6678999999765 455332 22220 0 12222222221 111222222
Q ss_pred CCCChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHcccc
Q psy2882 379 NGIPEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLIN 424 (1428)
Q Consensus 379 ~g~~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~ 424 (1428)
+|.+.+.+..+.+.+ | +++|-||.-=||..|+.+-...+++.
T Consensus 316 ---dEv~Ll~RfFeHiq~~kP-~iivTyNGDFFDWPFve~Ra~~hGi~ 359 (2173)
T KOG1798|consen 316 ---DEVGLLQRFFEHIQEVKP-TIIVTYNGDFFDWPFVEARAKIHGIS 359 (2173)
T ss_pred ---cHHHHHHHHHHHHHhcCC-cEEEEecCccccchhhHHHHHhcCCC
Confidence 466788888888865 5 89999999999999998766665554
No 156
>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=90.52 E-value=1.5 Score=47.06 Aligned_cols=130 Identities=18% Similarity=0.132 Sum_probs=79.6
Q ss_pred CceEEEEeeccccCcc--CCC--cceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHH
Q psy2882 310 NSTFLWYDYETFGLNV--RRD--RPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYK 385 (1428)
Q Consensus 310 ~~~~v~~D~ETTGldp--~~D--rIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e 385 (1428)
....+.||+|+++..+ ..+ .++||| +. + ..+.+.+... ..
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~---~~-~-------~~~l~~~~~~--------------------~~----- 60 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLA---TE-S-------RCLLFQLAHM--------------------DK----- 60 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEe---cC-C-------cEEEEEhhhh--------------------hc-----
Confidence 3578999999999876 333 357777 21 1 2344433321 01
Q ss_pred HHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCC
Q psy2882 386 FASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPS 465 (1428)
Q Consensus 386 ~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s 465 (1428)
+...+.++|..++...|||+ +++|..+|... .... . ++ ++|+..+++.+.|. ..+
T Consensus 61 ~~~~l~~ll~~~~i~kv~~~-~k~D~~~L~~~---~g~~-----~---~~---~~Dl~~aa~ll~~~----------~~~ 115 (170)
T cd06141 61 LPPSLKQLLEDPSILKVGVG-IKGDARKLARD---FGIE-----V---RG---VVDLSHLAKRVGPR----------RKL 115 (170)
T ss_pred ccHHHHHHhcCCCeeEEEee-eHHHHHHHHhH---cCCC-----C---CC---eeeHHHHHHHhCCC----------cCC
Confidence 11345566777777789998 79998887432 1111 1 11 26777777777653 122
Q ss_pred CChHhHHHHc-CCCCC------------------CCCChHHHHHHHHHHHHHHH
Q psy2882 466 FKLEHLSFVN-NLSHK------------------KAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 466 ~kLe~L~~~~-gi~~~------------------~AHdAlaDv~AT~~l~~~l~ 500 (1428)
..|++++..+ |+... +-|=|..||+.+..|+..|.
T Consensus 116 ~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 116 VSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred ccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4788888775 54322 23558899999999988875
No 157
>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=90.31 E-value=6.4 Score=42.04 Aligned_cols=129 Identities=13% Similarity=-0.072 Sum_probs=77.7
Q ss_pred ceEEEEeeccccCccCCCc--ceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDR--PFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~Dr--IiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
...+.||+|+........+ ++|||. ..+ ..+.+.+... . . ...
T Consensus 13 ~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~-------~~~l~d~~~~--~--~---------------------~~~ 57 (161)
T cd06129 13 GDVIAFDMEWPPGRRYYGEVALIQLCV---SEE-------KCYLFDPLSL--S--V---------------------DWQ 57 (161)
T ss_pred CCEEEEECCccCCCCCCCceEEEEEEE---CCC-------CEEEEecccC--c--c---------------------CHH
Confidence 4789999999988764443 466653 111 2344443321 1 0 112
Q ss_pred HHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 389 IIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 389 ~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
.+.++|..++.+.|||+ +++|...+... .... .. -++|+..+++.+.|. .+..|
T Consensus 58 ~L~~lL~d~~i~Kvg~~-~k~D~~~L~~~---~gi~-~~----------~~~D~~~aa~ll~~~-----------~~~~L 111 (161)
T cd06129 58 GLKMLLENPSIVKALHG-IEGDLWKLLRD---FGEK-LQ----------RLFDTTIAANLKGLP-----------ERWSL 111 (161)
T ss_pred HHHHHhCCCCEEEEEec-cHHHHHHHHHH---cCCC-cc----------cHhHHHHHHHHhCCC-----------CCchH
Confidence 23455666767779988 78998876421 1111 00 136777777776542 13578
Q ss_pred HhHHHHc-CCCC----------------CCCCChHHHHHHHHHHHHHHH
Q psy2882 469 EHLSFVN-NLSH----------------KKAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 469 e~L~~~~-gi~~----------------~~AHdAlaDv~AT~~l~~~l~ 500 (1428)
+.+++.+ |+.. .+-|=|..||+++..|++.|+
T Consensus 112 ~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 112 ASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 8888875 6532 223568899999999998875
No 158
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=89.78 E-value=0.68 Score=51.19 Aligned_cols=24 Identities=33% Similarity=0.606 Sum_probs=20.2
Q ss_pred CCccchhhHHHHHHHhCC---HHHHHH
Q psy2882 959 VKKIGPKTAVKLLNQYNS---LENIIN 982 (1428)
Q Consensus 959 vpGIG~KtA~kLL~~~gs---le~i~~ 982 (1428)
|||||||||.++|+.||+ .+.|.+
T Consensus 78 i~GIGpk~A~~il~~fg~~~l~~~i~~ 104 (192)
T PRK00116 78 VSGVGPKLALAILSGLSPEELVQAIAN 104 (192)
T ss_pred CCCCCHHHHHHHHHhCCHHHHHHHHHh
Confidence 899999999999999997 444544
No 159
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.49 E-value=7.7 Score=54.18 Aligned_cols=165 Identities=12% Similarity=0.007 Sum_probs=94.4
Q ss_pred cccceeeeeeecc--------CCceEEEEeeccccCccC--CCcceeEEEEEEeCCce-----e---eccceEEEEecCC
Q psy2882 296 KIGNYYIDILLHN--------GNSTFLWYDYETFGLNVR--RDRPFQFAAIRTDIMLN-----T---IDNPIMLYCKPAP 357 (1428)
Q Consensus 296 ~~G~~~V~v~l~~--------~~~~~v~~D~ETTGldp~--~DrIiqiaaIr~~~~~~-----~---i~~~~~~~~~p~~ 357 (1428)
+...|++.+-+.+ ..++++++|+-.-.+.|. .+.+++|+.+.... .. . ....+...++|..
T Consensus 481 S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~-~~~d~~~~~~~~~~~~~~~~~~~~ 559 (1172)
T TIGR00592 481 SWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHRE-FALDKPPPEPPYDVHPCVGTRPKD 559 (1172)
T ss_pred cccceEEEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeec-ccccCCCCCCccceEEEEEEccCC
Confidence 4567888777666 123577766551135554 58899998886543 11 0 0011122233422
Q ss_pred CCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHHHcC--CCceEEEEcchhhhHHHHHHHHHHccccchhhh------
Q psy2882 358 DFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKIFLK--PGTISVGYNTILFDDEITRFMFWRNLINPYERE------ 429 (1428)
Q Consensus 358 ~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~~~~--~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~------ 429 (1428)
...|........|+.+..+ ..=.+|.+.+......+.+ | .+++|||...||..+|-+-+.+...+.+..-
T Consensus 560 ~~~p~~~~~~~~~~~~~~L-~~~~sEr~lL~~fl~~~~~~DP-Dii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~ 637 (1172)
T TIGR00592 560 CSFPLDLKGEFPGKKPSLV-EDLATERALIKKFMAKVKKIDP-DEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRS 637 (1172)
T ss_pred CCCCchhhhhhhccCCcEE-EEecCHHHHHHHHHHHHHhcCC-CEEEEEcccCccHHHHHHHHHHcCCCcccccCccccC
Confidence 2334333334556666555 2334677888888888874 5 7899999999999999776655444321100
Q ss_pred ---------hhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHHH-cCC
Q psy2882 430 ---------WKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFV-NNL 477 (1428)
Q Consensus 430 ---------~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~~-~gi 477 (1428)
...|...+|+...++-.+ ...||+|++++.+ +|.
T Consensus 638 ~~~~~~~~~~~~Grl~~D~~~~~k~~~--------------~~~sy~L~~v~~~~L~~ 681 (1172)
T TIGR00592 638 PKFGRRFGERTCGRMICDVEISAKELI--------------RCKSYDLSELVQQILKT 681 (1172)
T ss_pred CCccccccceECCEEEEEHHHHHHHHh--------------CcCCCCHHHHHHHHhCC
Confidence 012333345555543322 2568999999985 444
No 160
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=88.78 E-value=3.1 Score=52.91 Aligned_cols=105 Identities=19% Similarity=0.270 Sum_probs=70.3
Q ss_pred EEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHHHH
Q psy2882 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIEKI 393 (1428)
Q Consensus 314 v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~~~ 393 (1428)
+.+|+||+|+++....++-++..--+ + .+|+-... + ++.+ +....+..+
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-------~--~~yi~~~~------------~--~~~~--------~~~~~l~~~ 73 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-------E--AAYIPLLH------------G--PEQL--------NVLAALKPL 73 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-------c--ceeEeecc------------c--hhhh--------hhHHHHHHH
Confidence 89999999999977777766654321 2 23331111 1 2222 277778888
Q ss_pred HcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhHHH
Q psy2882 394 FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSF 473 (1428)
Q Consensus 394 ~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L~~ 473 (1428)
+..++...+||| ..||..++. ++++. .+ -..|++-++|.+.| +..++.+++|+.
T Consensus 74 l~~~~~~kv~~~-~K~d~~~l~----~~Gi~--------~~---~~~DtmlasYll~~----------~~~~~~~~~l~~ 127 (593)
T COG0749 74 LEDEGIKKVGQN-LKYDYKVLA----NLGIE--------PG---VAFDTMLASYLLNP----------GAGAHNLDDLAK 127 (593)
T ss_pred hhCcccchhccc-cchhHHHHH----HcCCc--------cc---chHHHHHHHhccCc----------CcCcCCHHHHHH
Confidence 888877799999 799988764 33311 01 23788888898876 345588899988
Q ss_pred Hc
Q psy2882 474 VN 475 (1428)
Q Consensus 474 ~~ 475 (1428)
.+
T Consensus 128 r~ 129 (593)
T COG0749 128 RY 129 (593)
T ss_pred Hh
Confidence 87
No 161
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=87.52 E-value=1.1 Score=46.50 Aligned_cols=107 Identities=21% Similarity=0.252 Sum_probs=63.0
Q ss_pred EEEeecccc--------CccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCC-ChH
Q psy2882 314 LWYDYETFG--------LNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGI-PEY 384 (1428)
Q Consensus 314 v~~D~ETTG--------ldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~-~e~ 384 (1428)
+|+|+||.. +.|-.-=+.|++...+..++...++ + .+. +.+...|. |-.
T Consensus 1 y~lDFEt~~~aiP~~~g~~PyqqipfQ~Slhi~~~~g~~~~~-~-------------------~h~--efL~~~~~DPr~ 58 (130)
T PF11074_consen 1 YFLDFETFSSAIPPFDGTRPYQQIPFQFSLHITDNDGIIYKE-L-------------------EHV--EFLADPGEDPRR 58 (130)
T ss_pred CeEecccccccCCCCCCCccccccceEEEEEEEcCCCcccCc-h-------------------hhH--HHhccCCCCchH
Confidence 589999974 4665666789988888776522111 0 000 11111222 446
Q ss_pred HHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCC-CchhhHHHH
Q psy2882 385 KFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSR-WDLINVIKA 445 (1428)
Q Consensus 385 e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr-~D~ld~~rl 445 (1428)
+++..+.+.+.....++|.|| .+|-...|+..... .+.|....+.-++| +|+.+.++.
T Consensus 59 ~~~~~L~~~i~~~~g~ivvyN-~sfE~~rL~ela~~--~p~~~~~l~~I~~r~vDL~~~f~~ 117 (130)
T PF11074_consen 59 ELIEALIKAIGSIYGSIVVYN-KSFEKTRLKELAEL--FPDYAEKLNSIIERTVDLLDPFKN 117 (130)
T ss_pred HHHHHHHHHhhhhcCeEEEec-hHHHHHHHHHHHHH--hHHHHHHHHHHHHHHHHHHHHHhh
Confidence 788888888876635688899 57998888875543 34444333332332 355555554
No 162
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=86.59 E-value=0.81 Score=40.74 Aligned_cols=27 Identities=37% Similarity=0.568 Sum_probs=23.9
Q ss_pred CCCCccchhhHHHHHHH-hCCHHHHHHH
Q psy2882 957 PGVKKIGPKTAVKLLNQ-YNSLENIINN 983 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~-~gsle~i~~~ 983 (1428)
-.||||||++|.+|.+. |+|+++++..
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~~l~~a 35 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLEDLANA 35 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred ccCCCCCHHHHHHHHhcCCCcHHHHHcC
Confidence 35899999999999999 9999999863
No 163
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=85.52 E-value=0.53 Score=36.23 Aligned_cols=17 Identities=47% Similarity=0.628 Sum_probs=12.8
Q ss_pred CCCCCccchhhHHHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLN 972 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~ 972 (1428)
+-.+||||||||..++.
T Consensus 13 L~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 13 LMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHTSTT-SHHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHHh
Confidence 34579999999998874
No 164
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=85.34 E-value=0.65 Score=59.80 Aligned_cols=33 Identities=27% Similarity=0.498 Sum_probs=27.7
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHHHHHh-hhcc
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENIINNA-NNIK 988 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i~~~~-~~i~ 988 (1428)
+.+|||||||++.+||+.|||+++|.++- +++.
T Consensus 554 L~~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~ 587 (624)
T PRK14669 554 LLEIPGVGAKTVQRLLKHFGSLERVRAATETQLA 587 (624)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHH
Confidence 45889999999999999999999998753 4443
No 165
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=85.30 E-value=11 Score=45.48 Aligned_cols=129 Identities=19% Similarity=0.133 Sum_probs=78.6
Q ss_pred ceEEEEeeccccCccCCCcc--eeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRP--FQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrI--iqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
..++++||||.|+.+.+|+. |||+. ++ ....+.|.... +.. +
T Consensus 17 ~~~iAiDTEf~r~~t~~p~LcLIQi~~----~e-------~~~lIdpl~~~---------~d~----------~------ 60 (361)
T COG0349 17 SKAIAIDTEFMRLRTYYPRLCLIQISD----GE-------GASLIDPLAGI---------LDL----------P------ 60 (361)
T ss_pred CCceEEecccccccccCCceEEEEEec----CC-------CceEecccccc---------ccc----------c------
Confidence 46999999999999999995 45432 11 12455444311 001 1
Q ss_pred HHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCC-CCC
Q psy2882 389 IIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKP-SFK 467 (1428)
Q Consensus 389 ~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~-s~k 467 (1428)
-+...+..++ ++=-+|+.+||.+++.+.|-.+ .-.++||--++... |.+ ++.
T Consensus 61 ~l~~Ll~d~~-v~KIfHaa~~DL~~l~~~~g~~--------------p~plfdTqiAa~l~------------g~~~~~g 113 (361)
T COG0349 61 PLVALLADPN-VVKIFHAARFDLEVLLNLFGLL--------------PTPLFDTQIAAKLA------------GFGTSHG 113 (361)
T ss_pred hHHHHhcCCc-eeeeeccccccHHHHHHhcCCC--------------CCchhHHHHHHHHh------------CCccccc
Confidence 1122334443 3335566899999976554211 12357777766665 223 899
Q ss_pred hHhHHHH-cCCCCCCCCC----------------hHHHHHHHHHHHHHHHhh
Q psy2882 468 LEHLSFV-NNLSHKKAHD----------------ALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 468 Le~L~~~-~gi~~~~AHd----------------AlaDv~AT~~l~~~l~~~ 502 (1428)
|.+|++. .|++.+..|. |.+||..-+.|+.+|.+.
T Consensus 114 l~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~ 165 (361)
T COG0349 114 LADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEE 165 (361)
T ss_pred HHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999986 5776555543 677888777777776653
No 166
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=84.63 E-value=0.78 Score=58.58 Aligned_cols=30 Identities=30% Similarity=0.392 Sum_probs=27.1
Q ss_pred CCCCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 954 DNLPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 954 DnipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
--+.+|||||||+..+||+.|||+++|.++
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 356789999999999999999999999876
No 167
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=84.22 E-value=0.66 Score=51.23 Aligned_cols=70 Identities=23% Similarity=0.239 Sum_probs=44.7
Q ss_pred CCCCccccc-cCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHH
Q psy2882 905 NDKDMAQLV-SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 982 (1428)
Q Consensus 905 ~DkDl~QLv-~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~ 982 (1428)
+...+.++. ++.+.+|.... -.++-..-||+ +.+.-.-|..|++ |+|||||+|..+|..+ +.+++.+
T Consensus 31 ~~~~~~~l~~g~~v~l~t~~~--vred~~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~Al~iL~~~-~~~el~~ 99 (191)
T TIGR00084 31 PMTCAYELNLEQKAQVFTHLV--VREDAELLFGFNTLEERELFKELIK--------VNGVGPKLALAILSNM-SPEEFVY 99 (191)
T ss_pred cHHHHHhcCCCCeEEEEEEEE--EecCCceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHhcC-CHHHHHH
Confidence 455566653 45566664221 12233346886 4555555666754 9999999999999877 5777776
Q ss_pred Hhh
Q psy2882 983 NAN 985 (1428)
Q Consensus 983 ~~~ 985 (1428)
.+.
T Consensus 100 aI~ 102 (191)
T TIGR00084 100 AIE 102 (191)
T ss_pred HHH
Confidence 654
No 168
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=84.19 E-value=0.8 Score=58.45 Aligned_cols=34 Identities=18% Similarity=0.346 Sum_probs=27.7
Q ss_pred CCCCCCccchhhHHHHHHHhCCHHHHHHHh-hhcc
Q psy2882 955 NLPGVKKIGPKTAVKLLNQYNSLENIINNA-NNIK 988 (1428)
Q Consensus 955 nipGvpGIG~KtA~kLL~~~gsle~i~~~~-~~i~ 988 (1428)
-+.+|||||||+..+||+.|||+++|.++- +++.
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~ 549 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELK 549 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHH
Confidence 345788899999999999999999998763 4443
No 169
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.24 E-value=0.88 Score=50.37 Aligned_cols=70 Identities=23% Similarity=0.367 Sum_probs=44.4
Q ss_pred eCCCCccccc--cCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHH
Q psy2882 904 TNDKDMAQLV--SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENI 980 (1428)
Q Consensus 904 S~DkDl~QLv--~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i 980 (1428)
.+...+.+|. ++.+.+|.... -.++-..-||+ +.++---|..|.+ |+|||||+|..+|..|+ .+++
T Consensus 30 ~s~~~~~~l~~~g~~~~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~ILs~~~-~~~l 98 (194)
T PRK14605 30 MPATSPALIGGLGQRVRVFTHLH--VREDALSLFGFATTEELSLFETLID--------VSGIGPKLGLAMLSAMN-AEAL 98 (194)
T ss_pred eCHHHHHhcccCCCeEEEEEEEE--EecCCceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHHhCC-HHHH
Confidence 3455555553 45566664211 12333345786 4555556677754 89999999999999986 6666
Q ss_pred HHHh
Q psy2882 981 INNA 984 (1428)
Q Consensus 981 ~~~~ 984 (1428)
++.+
T Consensus 99 ~~aI 102 (194)
T PRK14605 99 ASAI 102 (194)
T ss_pred HHHH
Confidence 5554
No 170
>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=82.81 E-value=19 Score=38.60 Aligned_cols=105 Identities=16% Similarity=0.085 Sum_probs=65.1
Q ss_pred eEEEEeeccccCccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHHHHH
Q psy2882 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFASIIE 391 (1428)
Q Consensus 312 ~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~~i~ 391 (1428)
+.+.+|+|++|.+|-+++++-++.- . .+ . .+|+.+. + . + .....+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~-~-~~-----~--~~~i~~~-~------~--~----------------~~~~~l~ 49 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALA-N-GG-----G--AYYIPLE-L------A--L----------------LDLAALK 49 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEE-e-CC-----c--EEEEecc-c------h--H----------------HHHHHHH
Confidence 5678999999999878877655433 1 11 2 3443211 1 0 0 1233355
Q ss_pred HHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChHhH
Q psy2882 392 KIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHL 471 (1428)
Q Consensus 392 ~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe~L 471 (1428)
+++..++...++|| +.+|..++. +++++. . + -..|+.-++|.+.|. ..++.|+++
T Consensus 50 ~~l~~~~~~ki~~d-~K~~~~~l~----~~gi~~-~-----~----~~fDt~laaYLL~p~----------~~~~~l~~l 104 (178)
T cd06140 50 EWLEDEKIPKVGHD-AKRAYVALK----RHGIEL-A-----G----VAFDTMLAAYLLDPT----------RSSYDLADL 104 (178)
T ss_pred HHHhCCCCceeccc-hhHHHHHHH----HCCCcC-C-----C----cchhHHHHHHHcCCC----------CCCCCHHHH
Confidence 56666666789988 789887764 333321 1 1 137899999999773 334688999
Q ss_pred HHHc
Q psy2882 472 SFVN 475 (1428)
Q Consensus 472 ~~~~ 475 (1428)
+..|
T Consensus 105 ~~~y 108 (178)
T cd06140 105 AKRY 108 (178)
T ss_pred HHHH
Confidence 8875
No 171
>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=82.35 E-value=22 Score=43.43 Aligned_cols=128 Identities=16% Similarity=-0.019 Sum_probs=76.8
Q ss_pred ceEEEEeeccccCccCCCcc--eeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDRP--FQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrI--iqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
.+++.+|||+++.+..++++ ||||. ++ ..+++.|... . .+.
T Consensus 18 ~~~ia~DtE~~~~~~y~~~l~LiQia~----~~-------~~~liD~~~~--~------------------------~~~ 60 (367)
T TIGR01388 18 FPFVALDTEFVRERTFWPQLGLIQVAD----GE-------QLALIDPLVI--I------------------------DWS 60 (367)
T ss_pred CCEEEEeccccCCCCCCCcceEEEEee----CC-------eEEEEeCCCc--c------------------------cHH
Confidence 47899999999988766654 66662 21 1344433210 0 012
Q ss_pred HHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 389 IIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 389 ~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
.+.+.|..++...|+|+ .++|..+++.. +.. +.. -++|+.-+++.+.|. .++.|
T Consensus 61 ~L~~lL~d~~i~KV~h~-~k~Dl~~L~~~----~~~-~~~---------~~fDtqlAa~lL~~~-----------~~~~l 114 (367)
T TIGR01388 61 PLKELLRDESVVKVLHA-ASEDLEVFLNL----FGE-LPQ---------PLFDTQIAAAFCGFG-----------MSMGY 114 (367)
T ss_pred HHHHHHCCCCceEEEee-cHHHHHHHHHH----hCC-CCC---------CcccHHHHHHHhCCC-----------CCccH
Confidence 34456666666678988 79999887532 211 111 237778888887552 13578
Q ss_pred HhHHHHc-CCCCCCC-------CC---------hHHHHHHHHHHHHHHHh
Q psy2882 469 EHLSFVN-NLSHKKA-------HD---------ALSDVRATLGLARLIRN 501 (1428)
Q Consensus 469 e~L~~~~-gi~~~~A-------Hd---------AlaDv~AT~~l~~~l~~ 501 (1428)
+.|++.| |+..... .+ |..||.+...|+..|.+
T Consensus 115 ~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 115 AKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888865 6543221 22 67788877777776654
No 172
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=82.35 E-value=2.1 Score=37.33 Aligned_cols=33 Identities=27% Similarity=0.461 Sum_probs=21.2
Q ss_pred CCCCccchhhHHHHHHH-hCCHHHHHHHhhhcch
Q psy2882 957 PGVKKIGPKTAVKLLNQ-YNSLENIINNANNIKG 989 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~-~gsle~i~~~~~~i~~ 989 (1428)
-+|-||||+||.++.++ +.|+|++-..-..++.
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~ 38 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTW 38 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-H
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhhhhccCCH
Confidence 36899999999999984 3599999553334444
No 173
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=81.77 E-value=1.2 Score=57.76 Aligned_cols=27 Identities=37% Similarity=0.594 Sum_probs=24.4
Q ss_pred CCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 957 PGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
.||||||||+|..||+.|||+++|..+
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~A 598 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAKA 598 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 578999999999999999999998764
No 174
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.59 E-value=1 Score=50.21 Aligned_cols=69 Identities=20% Similarity=0.404 Sum_probs=42.8
Q ss_pred CCCcccc--ccCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHH
Q psy2882 906 DKDMAQL--VSNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 982 (1428)
Q Consensus 906 DkDl~QL--v~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~ 982 (1428)
..-+.+| .++.+.+|.... -.++-..-||+ +.++-.-|..|.+ |.|||||+|..+|..+ +.+++++
T Consensus 33 ~~~~~~l~~~g~~v~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~~l~~ 101 (203)
T PRK14602 33 AHTLARLPEKGGQVSFFVHTV--VREDALELFGFATWDERQTFIVLIS--------ISKVGAKTALAILSQF-RPDDLRR 101 (203)
T ss_pred HHHHHHhccCCCeEEEEEEEE--EecCcceeeCCCCHHHHHHHHHHhC--------CCCcCHHHHHHHHhhC-CHHHHHH
Confidence 4444444 245566654211 12233345786 4455555666754 8999999999999987 5777777
Q ss_pred Hhh
Q psy2882 983 NAN 985 (1428)
Q Consensus 983 ~~~ 985 (1428)
++.
T Consensus 102 aI~ 104 (203)
T PRK14602 102 LVA 104 (203)
T ss_pred HHH
Confidence 654
No 175
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=81.55 E-value=0.98 Score=57.82 Aligned_cols=28 Identities=32% Similarity=0.463 Sum_probs=25.0
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
+-+|||||||+..+||+.|||+++|.++
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4578889999999999999999999765
No 176
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=80.12 E-value=1.6 Score=56.40 Aligned_cols=29 Identities=34% Similarity=0.526 Sum_probs=26.3
Q ss_pred CCCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 955 NLPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 955 nipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
-+-.|||||||++.+||+.|||+++|+++
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 45678999999999999999999999985
No 177
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=78.97 E-value=2.3 Score=47.83 Aligned_cols=29 Identities=24% Similarity=0.491 Sum_probs=25.7
Q ss_pred CCCCCCccchhhHHHHHHH-hCCHHHHHHH
Q psy2882 955 NLPGVKKIGPKTAVKLLNQ-YNSLENIINN 983 (1428)
Q Consensus 955 nipGvpGIG~KtA~kLL~~-~gsle~i~~~ 983 (1428)
.+..|||||+++|.+|++. |+|+++|..+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 3567899999999999999 9999999765
No 178
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.45 E-value=1.4 Score=48.39 Aligned_cols=66 Identities=15% Similarity=0.207 Sum_probs=41.4
Q ss_pred cccc-ccCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhh
Q psy2882 909 MAQL-VSNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 909 l~QL-v~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~ 985 (1428)
+.+| .++.+.+|.... -.++-..-||+ +.++---|..|.+ |.|||||+|..+|..+ +.+++...+.
T Consensus 36 ~~~l~~g~~v~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~Li~--------VsGIGpK~Al~ILs~~-~~~el~~aI~ 103 (183)
T PRK14601 36 SAKIQKGEKHELFITQI--IKEDSNKLYGFLDKDEQKMFEMLLK--------VNGIGANTAMAVCSSL-DVNSFYKALS 103 (183)
T ss_pred HHHcCCCCeEEEEEEEE--EecCCceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 3344 345565554211 12223345776 4555555666754 8999999999999887 5778877654
No 179
>PRK10829 ribonuclease D; Provisional
Probab=78.45 E-value=36 Score=41.63 Aligned_cols=128 Identities=16% Similarity=0.033 Sum_probs=79.6
Q ss_pred ceEEEEeeccccCccCCCc--ceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHHHHH
Q psy2882 311 STFLWYDYETFGLNVRRDR--PFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYKFAS 388 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~Dr--IiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e~~~ 388 (1428)
.+.+.+|||..+.+..+.+ +|||+ + + + ..+.+.|.. +. + ..
T Consensus 22 ~~~lalDtEf~~~~ty~~~l~LiQl~---~-~------~-~~~LiD~l~--~~-------------d-----------~~ 64 (373)
T PRK10829 22 FPAIALDTEFVRTRTYYPQLGLIQLY---D-G------E-QLSLIDPLG--IT-------------D-----------WS 64 (373)
T ss_pred CCeEEEecccccCccCCCceeEEEEe---c-C------C-ceEEEecCC--cc-------------c-----------hH
Confidence 4789999999998876665 46776 1 2 1 234443331 01 0 12
Q ss_pred HHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCC-CCC
Q psy2882 389 IIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKP-SFK 467 (1428)
Q Consensus 389 ~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~-s~k 467 (1428)
.+.+.|..++.+-|+|+ .++|.+++...| +..| -.++||.-++..+ |.+ ++.
T Consensus 65 ~L~~ll~~~~ivKV~H~-~~~Dl~~l~~~~---g~~p-----------~~~fDTqiaa~~l------------g~~~~~g 117 (373)
T PRK10829 65 PFKALLRDPQVTKFLHA-GSEDLEVFLNAF---GELP-----------QPLIDTQILAAFC------------GRPLSCG 117 (373)
T ss_pred HHHHHHcCCCeEEEEeC-hHhHHHHHHHHc---CCCc-----------CCeeeHHHHHHHc------------CCCcccc
Confidence 35566777766667877 799999874321 1111 1246776666655 222 578
Q ss_pred hHhHHHH-cCCCCCCC----------------CChHHHHHHHHHHHHHHHhh
Q psy2882 468 LEHLSFV-NNLSHKKA----------------HDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 468 Le~L~~~-~gi~~~~A----------------HdAlaDv~AT~~l~~~l~~~ 502 (1428)
|..|++. +|+..+.. +=|..||+....|+..|.+.
T Consensus 118 l~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~ 169 (373)
T PRK10829 118 FASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAE 169 (373)
T ss_pred HHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888875 57653322 33888999999998887754
No 180
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=78.19 E-value=2.1 Score=43.96 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=29.6
Q ss_pred CCccchhhHHHHHH--HhCCHHHHHHHhhhcchhhhhhHHHhhh
Q psy2882 959 VKKIGPKTAVKLLN--QYNSLENIINNANNIKGVIGKNLRFALN 1000 (1428)
Q Consensus 959 vpGIG~KtA~kLL~--~~gsle~i~~~~~~i~~k~~~~l~~~~~ 1000 (1428)
+|||||++|.++++ .|.|+|++++ +.-|..+..+.++.+++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~-V~GIgekqk~~l~k~~~ 108 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN-LPGLSERQKELLEANLD 108 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc-CCCCCHHHHHHHHHhhc
Confidence 49999999999997 3678999875 55566555555555433
No 181
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=77.24 E-value=1.5 Score=32.46 Aligned_cols=18 Identities=56% Similarity=0.693 Sum_probs=15.5
Q ss_pred CCCCCccchhhHHHHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLNQ 973 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~ 973 (1428)
+..|||||+|+|..+++.
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 457999999999999874
No 182
>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=77.10 E-value=48 Score=35.33 Aligned_cols=85 Identities=22% Similarity=0.154 Sum_probs=51.7
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHc-cccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCCh
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRN-LINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKL 468 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn-~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kL 468 (1428)
+.+++..++...|||| +.+|..++. ++ .+. . +. +.|+.-++|.+.|. . +..|
T Consensus 56 l~~ll~~~~i~kv~~d-~K~~~~~L~----~~~gi~--~------~~---~~D~~laayLl~p~----------~-~~~l 108 (178)
T cd06142 56 LKELLADPNIVKVFHA-AREDLELLK----RDFGIL--P------QN---LFDTQIAARLLGLG----------D-SVGL 108 (178)
T ss_pred HHHHHcCCCceEEEec-cHHHHHHHH----HHcCCC--C------CC---cccHHHHHHHhCCC----------c-cccH
Confidence 4456766777889998 689877754 33 221 1 11 25667778888763 2 2489
Q ss_pred HhHHHHc-CCCCCCC----------------CChHHHHHHHHHHHHHHHh
Q psy2882 469 EHLSFVN-NLSHKKA----------------HDALSDVRATLGLARLIRN 501 (1428)
Q Consensus 469 e~L~~~~-gi~~~~A----------------HdAlaDv~AT~~l~~~l~~ 501 (1428)
+++++.| |+..... +-|..|+.++.+|+..+.+
T Consensus 109 ~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~ 158 (178)
T cd06142 109 AALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKE 158 (178)
T ss_pred HHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Confidence 9998865 5541111 1256667777777666653
No 183
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.42 E-value=2.4 Score=46.68 Aligned_cols=46 Identities=20% Similarity=0.271 Sum_probs=33.3
Q ss_pred HHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhh
Q psy2882 931 IISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 931 v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~ 985 (1428)
-..-||+ ++++---|..|. +|.|||||+|..+|..+ +.+++...+.
T Consensus 57 ~~~LyGF~~~~Er~lF~~Li--------sV~GIGpK~Al~iLs~~-~~~~l~~aI~ 103 (186)
T PRK14600 57 VTQLYGFLNREEQDCLRMLV--------KVSGVNYKTAMSILSKL-TPEQLFSAIV 103 (186)
T ss_pred CceeeCCCCHHHHHHHHHHh--------CcCCcCHHHHHHHHccC-CHHHHHHHHH
Confidence 3345786 455555566675 48999999999999987 5777776654
No 184
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.48 E-value=1.9 Score=47.67 Aligned_cols=45 Identities=24% Similarity=0.489 Sum_probs=33.1
Q ss_pred HHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhh
Q psy2882 932 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 932 ~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~ 985 (1428)
..-||+ +.++---|..|.+ |.|||||+|..+|..+ +.+++...+.
T Consensus 57 ~~LYGF~t~~Er~lF~~Lis--------VsGIGPK~ALaILs~~-~~~el~~aI~ 102 (196)
T PRK13901 57 LKLFGFLNSSEREVFEELIG--------VDGIGPRAALRVLSGI-KYNEFRDAID 102 (196)
T ss_pred ceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHHH
Confidence 345786 4555555666754 8999999999999987 5777777654
No 185
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=74.88 E-value=6.6 Score=43.40 Aligned_cols=185 Identities=16% Similarity=0.107 Sum_probs=122.0
Q ss_pred cccccceeeeeeeccCCceEEEEeeccccCccCCCcceeEEEEEEeCCceeec----cceEEEEecCCCCCCChhhHhh-
Q psy2882 294 IKKIGNYYIDILLHNGNSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTID----NPIMLYCKPAPDFLPDPRACLI- 368 (1428)
Q Consensus 294 Ik~~G~~~V~v~l~~~~~~~v~~D~ETTGldp~~DrIiqiaaIr~~~~~~~i~----~~~~~~~~p~~~~~p~pea~~i- 368 (1428)
-|-+|+|+-.+..|- .|--.|...=.|||+|.-..|.++|--. ..|+|...|..+... +|+..+
T Consensus 56 ArPiG~FkSs~dyhY----------QtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya-~ESieLL 124 (299)
T COG5228 56 ARPIGTFKSSVDYHY----------QTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYA-TESIELL 124 (299)
T ss_pred ecccccccccchHHH----------HHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhhcc-hHHHHHH
Confidence 466788887777665 5666777888999999998888877432 235778888877654 566654
Q ss_pred --cCCCHHHHhcCCCChHHHHHHHHH--HHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHH
Q psy2882 369 --TKITPQFCLNNGIPEYKFASIIEK--IFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIK 444 (1428)
Q Consensus 369 --tGITpe~~~~~g~~e~e~~~~i~~--~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~r 444 (1428)
.||.-+.-++.|+..+||.+-+.. ...+...+.|.||+ .+|..+|-..+-.+ |...+. -|..+
T Consensus 125 ~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfHs-aYDfgyLikilt~~---plP~~~---------EdFy~ 191 (299)
T COG5228 125 RKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHS-AYDFGYLIKILTND---PLPNNK---------EDFYW 191 (299)
T ss_pred HHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEeec-chhHHHHHHHHhcC---CCCccH---------HHHHH
Confidence 699988887889988888776543 12235578999995 79999987665543 322221 45555
Q ss_pred HHHHhCCCCcCCC--CCCCCCCCCChHhHHHHcCCCC-CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 445 AFYVLSPYGITWP--YKNNGKPSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 445 l~~~l~p~~~~~p--~~~~g~~s~kLe~L~~~~gi~~-~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
..+.+.|+-+.-. .+.--..|--|.+++..+++.. ...|.|-+|+..|+..+-+.|..
T Consensus 192 ~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~ 252 (299)
T COG5228 192 WLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252 (299)
T ss_pred HHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhh
Confidence 6666766532211 0100111233555555555543 45799999999998887777654
No 186
>PRK05761 DNA polymerase I; Reviewed
Probab=74.56 E-value=16 Score=49.01 Aligned_cols=111 Identities=16% Similarity=0.034 Sum_probs=65.0
Q ss_pred CChHHHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccch--hhhhhcCCCCCchhhHHHHHHHhCCCCcCCCC
Q psy2882 381 IPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPY--EREWKNNCSRWDLINVIKAFYVLSPYGITWPY 458 (1428)
Q Consensus 381 ~~e~e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y--~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~ 458 (1428)
.+|.+++..+..++..-+ +.|+||..+||..+|..-..+.+++.. ...+..+.+..|+...++.. .+ ..+ |..
T Consensus 208 ~~E~eLL~~f~~~i~~~d-Pdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~-~~--~~y-~~~ 282 (787)
T PRK05761 208 DSEKELLAELFDIILEYP-PVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNK-AV--RSY-AFY 282 (787)
T ss_pred CCHHHHHHHHHHHHHhcC-CEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeec-ce--eee-ecc
Confidence 368899999999997742 367799999999999776666666532 22222222224444333210 00 000 111
Q ss_pred CCCCCCCCChHhHHH-HcCCCCCCCC-------------ChHHHHHHHHHHH
Q psy2882 459 KNNGKPSFKLEHLSF-VNNLSHKKAH-------------DALSDVRATLGLA 496 (1428)
Q Consensus 459 ~~~g~~s~kLe~L~~-~~gi~~~~AH-------------dAlaDv~AT~~l~ 496 (1428)
..-...+|+|+.++. .+|.....-| =.+.||..|..|.
T Consensus 283 ~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 283 GKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 112234799999999 5676543222 2467778777764
No 187
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.45 E-value=2.9 Score=46.42 Aligned_cols=70 Identities=21% Similarity=0.330 Sum_probs=44.4
Q ss_pred CCCCccccc--cCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHH
Q psy2882 905 NDKDMAQLV--SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 981 (1428)
Q Consensus 905 ~DkDl~QLv--~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~ 981 (1428)
+...+.+|. ++.+.+|.... -.++...-||+ +.++-.-|..|. +|.|||||+|..+|..+ +.+++.
T Consensus 31 s~~~~~~l~~~g~~v~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~Li--------~V~GIGpK~Al~iLs~~-~~~el~ 99 (195)
T PRK14604 31 PRSVLAAIGAIGDEVFLYTHLI--VREDALTLYGFSTPAQRQLFELLI--------GVSGVGPKAALNLLSSG-TPDELQ 99 (195)
T ss_pred CHHHHHHhccCCCeEEEEEEEE--EecCCceeeCCCCHHHHHHHHHHh--------CcCCcCHHHHHHHHcCC-CHHHHH
Confidence 466666663 45566654211 12223345786 344444556664 48999999999999976 678887
Q ss_pred HHhh
Q psy2882 982 NNAN 985 (1428)
Q Consensus 982 ~~~~ 985 (1428)
..+.
T Consensus 100 ~aI~ 103 (195)
T PRK14604 100 LAIA 103 (195)
T ss_pred HHHH
Confidence 7654
No 188
>KOG0969|consensus
Probab=73.71 E-value=2.1 Score=54.72 Aligned_cols=88 Identities=19% Similarity=0.184 Sum_probs=54.6
Q ss_pred eEEEEeeccccC-----ccCCCcceeEEEEEEeCCceeeccce--EEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChH
Q psy2882 312 TFLWYDYETFGL-----NVRRDRPFQFAAIRTDIMLNTIDNPI--MLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEY 384 (1428)
Q Consensus 312 ~~v~~D~ETTGl-----dp~~DrIiqiaaIr~~~~~~~i~~~~--~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~ 384 (1428)
...-||+|+.|- .|..|.+||||-+.+--+ ..+|| +.+|.+.. -|.+.+...... .|.
T Consensus 275 rvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~G---e~~pf~rnvf~l~~c--apI~G~~V~~~~----------~e~ 339 (1066)
T KOG0969|consen 275 RVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQG---ENEPFVRNVFTLKTC--APIVGSNVHSYE----------TEK 339 (1066)
T ss_pred cccceeEEeccCCCCCCccccChHHHHHHHHHHhc---CCchHHHhhhcccCc--CCCCCceeEEec----------cHH
Confidence 356799999985 567899999997764222 13333 34444432 232233222223 355
Q ss_pred HHHHHHHHHHcC-CCceEEEEcchhhhHHHH
Q psy2882 385 KFASIIEKIFLK-PGTISVGYNTILFDDEIT 414 (1428)
Q Consensus 385 e~~~~i~~~~~~-~~~~~VGyN~i~FD~~fl 414 (1428)
+++..-..++.+ .-.|++|||...||...+
T Consensus 340 elL~~W~~firevDPDvI~GYNi~nFDiPYl 370 (1066)
T KOG0969|consen 340 ELLESWRKFIREVDPDVIIGYNICNFDIPYL 370 (1066)
T ss_pred HHHHHHHHHHHhcCCCeEeccccccccccee
Confidence 666666666654 226899999989998766
No 189
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=73.03 E-value=2.5 Score=54.55 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=27.3
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHHHHHh-hhcc
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENIINNA-NNIK 988 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i~~~~-~~i~ 988 (1428)
+..|||||||++.+||+.|||+++|.++- ++|.
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~ 643 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIA 643 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHH
Confidence 45788899999999999999999998763 4443
No 190
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=72.94 E-value=2.3 Score=54.65 Aligned_cols=32 Identities=31% Similarity=0.544 Sum_probs=28.3
Q ss_pred cCCCCCCCccchhhHHHHHHHhCCHHHHHHHh
Q psy2882 953 SDNLPGVKKIGPKTAVKLLNQYNSLENIINNA 984 (1428)
Q Consensus 953 sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~ 984 (1428)
..-+..|||||++++.+||+.|||+++|+++-
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As 555 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRFGSVEGVREAS 555 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 45567899999999999999999999999863
No 191
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=72.87 E-value=2.4 Score=54.80 Aligned_cols=28 Identities=36% Similarity=0.577 Sum_probs=25.4
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
+.+|||||++++.+||+.|||+++|+++
T Consensus 545 L~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 545 LDDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred HhhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 3578999999999999999999999875
No 192
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=71.85 E-value=3.7 Score=53.63 Aligned_cols=26 Identities=23% Similarity=0.563 Sum_probs=23.8
Q ss_pred CCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 958 GVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 958 GvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
||||||+++|..|++.|||++++..+
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~A 527 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKAA 527 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 78999999999999999999998764
No 193
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=70.21 E-value=20 Score=48.10 Aligned_cols=135 Identities=16% Similarity=-0.051 Sum_probs=80.8
Q ss_pred ceEEEEeeccccC-----ccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChhhHhhcCCCHHHHhcCCCChHH
Q psy2882 311 STFLWYDYETFGL-----NVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFCLNNGIPEYK 385 (1428)
Q Consensus 311 ~~~v~~D~ETTGl-----dp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pea~~itGITpe~~~~~g~~e~e 385 (1428)
...+.||+||.+. ++..|-++.|+......+... +.+.....+.+. + ..-.++.+
T Consensus 154 l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~~~~~~~~-----------v-~~~~~e~e 213 (792)
T COG0417 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIYTSGEGFS-----------V-EVVISEAE 213 (792)
T ss_pred ceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------ccccccCCCCce-----------e-EEecCHHH
Confidence 4689999999975 334777888877654332211 111111101001 1 22346789
Q ss_pred HHHHHHHHHcC-CCceEEEEcchhhhHHHHHHHHHHccccch-----------hh--hhhcCCCCCchhhHHHHHHHhCC
Q psy2882 386 FASIIEKIFLK-PGTISVGYNTILFDDEITRFMFWRNLINPY-----------ER--EWKNNCSRWDLINVIKAFYVLSP 451 (1428)
Q Consensus 386 ~~~~i~~~~~~-~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y-----------~~--~~~~g~sr~D~ld~~rl~~~l~p 451 (1428)
.+..+..++.. ...+++|||...||..+|..-..+.+++.. .. .+..|...+|+...++- +.
T Consensus 214 ~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~-~~--- 289 (792)
T COG0417 214 LLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRR-RP--- 289 (792)
T ss_pred HHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhh-hh---
Confidence 99999999866 337999999999999999766555544422 00 11114455666666663 01
Q ss_pred CCcCCCCCCCCCCCCChHhHHHHcCCC
Q psy2882 452 YGITWPYKNNGKPSFKLEHLSFVNNLS 478 (1428)
Q Consensus 452 ~~~~~p~~~~g~~s~kLe~L~~~~gi~ 478 (1428)
-...+|.|+..+..+...
T Consensus 290 ---------~~~~~ysl~~v~~~~l~~ 307 (792)
T COG0417 290 ---------LNLKSYSLEAVSEALLGE 307 (792)
T ss_pred ---------cccccccHHHHHHHhccc
Confidence 135678999998776443
No 194
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=69.39 E-value=40 Score=35.31 Aligned_cols=66 Identities=20% Similarity=0.207 Sum_probs=43.0
Q ss_pred HHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCC
Q psy2882 387 ASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSF 466 (1428)
Q Consensus 387 ~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~ 466 (1428)
...+.+++..++...|||| +.||..+|+ ++++. .. . +.|+.-++|.+.|. ..++
T Consensus 64 ~~~l~~~l~~~~~~kv~~d-~k~~~~~L~----~~gi~-----~~----~--~~D~~laayll~p~----------~~~~ 117 (172)
T smart00474 64 LEILKDLLEDETITKVGHN-AKFDLHVLA----RFGIE-----LE----N--IFDTMLAAYLLLGG----------PSKH 117 (172)
T ss_pred HHHHHHHhcCCCceEEEec-hHHHHHHHH----HCCCc-----cc----c--hhHHHHHHHHHcCC----------CCcC
Confidence 3445566776667789999 799988875 22221 11 1 27888888888663 2235
Q ss_pred ChHhHHHHc-CCC
Q psy2882 467 KLEHLSFVN-NLS 478 (1428)
Q Consensus 467 kLe~L~~~~-gi~ 478 (1428)
.|++++..| |+.
T Consensus 118 ~l~~l~~~~l~~~ 130 (172)
T smart00474 118 GLATLLKEYLGVE 130 (172)
T ss_pred CHHHHHHHHhCCC
Confidence 899998876 544
No 195
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.72 E-value=5.1 Score=44.23 Aligned_cols=61 Identities=23% Similarity=0.315 Sum_probs=39.0
Q ss_pred cCcEEEEeCCeeccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhh
Q psy2882 914 SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 914 ~~~v~~~~~~~~~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~ 985 (1428)
++.+.+|.... -.++-..-||+ +.++-.-|..|. +|.|||||+|..+|..+ +.+++.+.+.
T Consensus 42 g~~v~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~Li--------~V~GIGpK~AL~iLs~~-~~~el~~aI~ 103 (188)
T PRK14606 42 GGECFLHTFLS--VSQDGITLYGFSNERKKELFLSLT--------KVSRLGPKTALKIISNE-DAETLVTMIA 103 (188)
T ss_pred CCeEEEEEEEE--EecCCceeeCCCCHHHHHHHHHHh--------ccCCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 44565554211 12233355786 445555566665 48999999999999887 5777777654
No 196
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=67.12 E-value=5.5 Score=52.22 Aligned_cols=27 Identities=30% Similarity=0.674 Sum_probs=24.2
Q ss_pred CCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 957 PGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
=||||||+++|.+|++.|+|++++..+
T Consensus 531 LgIpgIG~~~ak~L~~~F~si~~L~~A 557 (689)
T PRK14351 531 LGIPEVGPTTARNLAREFGTFEAIMDA 557 (689)
T ss_pred cCCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 378999999999999999999998754
No 197
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=64.54 E-value=52 Score=44.29 Aligned_cols=136 Identities=11% Similarity=0.140 Sum_probs=73.8
Q ss_pred HHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCC--hHHHHHHHHHHHHHHHcCCcEEEecc-hhhHHHH
Q psy2882 809 TIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP--YNLILQINLIHQMVKAIGWPILIIKG-VEADDVI 885 (1428)
Q Consensus 809 f~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p--~~l~~q~~~i~~~l~~~gi~~i~~~g-~EADD~i 885 (1428)
++..+.+|.+.|+-.-+++=||. ...|..+-+.++ .|.-.| .++...+ +.=.+..-|++++...+ +|-=+++
T Consensus 646 L~~Q~~~m~~~Y~~PvLLIE~d~-~~~f~l~~~~~~--~~~~~~~~~~i~~~L--~~L~l~fP~l~IiwS~s~~~TA~i~ 720 (814)
T TIGR00596 646 LYNQCEKMLRYYAYPVLLIEFDQ-NKSFSLEPRNDL--SQEISSVNNDIQQKL--ALLTLHFPKLRIIWSSSPYATAEIF 720 (814)
T ss_pred HHHHHHHHHHhcCCcEEEEEecC-Cccccccccccc--ccccCccHHHHHHHH--HHHHHhcCCceEEecCCHHHHHHHH
Confidence 45566677777776678888885 355555444444 233334 3442222 22133333999999876 4445577
Q ss_pred HHHHHHHhhhCCC--EEEEEeCCCCccccccCcEEEEeCCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccc
Q psy2882 886 GTLAKQAVTKHNL--KVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIG 963 (1428)
Q Consensus 886 atla~~~~~~~~~--~v~IvS~DkDl~QLv~~~v~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG 963 (1428)
..|+++..+ ++. .+.+- .|.+ .. .+ + .++ .+. ..+| | -++||||
T Consensus 721 ~~Lk~~e~e-pd~~~~v~i~-~~~~-------~~-----~k--~-----~~~--~~~-~q~~--L--------~~lPgI~ 766 (814)
T TIGR00596 721 EELKLGKEE-PDPATAAALG-SDEN-------TT-----AE--G-----LKF--NDG-PQDF--L--------LKLPGVT 766 (814)
T ss_pred HHHHhcCCC-CCcccceecC-cccc-------cc-----cc--c-----ccc--cHH-HHHH--H--------HHCCCCC
Confidence 777765321 211 11121 1110 00 00 0 000 111 1222 2 3479999
Q ss_pred hhhHHHHHHHhCCHHHHHHH
Q psy2882 964 PKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 964 ~KtA~kLL~~~gsle~i~~~ 983 (1428)
++.|..||.+|||++++...
T Consensus 767 ~~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 767 KKNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHHHHHHHcCCHHHHHhC
Confidence 99999999999999999874
No 198
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=64.50 E-value=6.1 Score=51.73 Aligned_cols=26 Identities=31% Similarity=0.583 Sum_probs=23.6
Q ss_pred CCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 958 GVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 958 GvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
||||||+++|..|++.|+|++++..+
T Consensus 515 gi~~IG~~~ak~L~~~f~sl~~l~~A 540 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSLEALRAA 540 (665)
T ss_pred hccCcCHHHHHHHHHHcCCHHHHHhC
Confidence 78999999999999999999998754
No 199
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=63.25 E-value=7.6 Score=39.75 Aligned_cols=38 Identities=18% Similarity=0.316 Sum_probs=24.5
Q ss_pred CCCCccchhhHHHHHHHh------CCHHHHHHHhhhcchhhhhhH
Q psy2882 957 PGVKKIGPKTAVKLLNQY------NSLENIINNANNIKGVIGKNL 995 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~------gsle~i~~~~~~i~~k~~~~l 995 (1428)
..+||||+++|.++|+.+ .|+|++. ++..+..+..++|
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~-~V~GIg~k~~~~i 114 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYREENGAFKSVDDLT-KVSGIGEKSLEKL 114 (120)
T ss_pred hcCCCCCHHHHHHHHHHHHhcCCcCCHHHHH-cCCCCCHHHHHHH
Confidence 457999999999999985 4566653 2333333433333
No 200
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=63.05 E-value=5.2 Score=44.49 Aligned_cols=69 Identities=22% Similarity=0.301 Sum_probs=41.0
Q ss_pred CCCcccc-ccCcEEEEeCCeeccHHHHHHHhCCC-hhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 906 DKDMAQL-VSNKIALINNNKIHDRTTIISRFGVS-PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 906 DkDl~QL-v~~~v~~~~~~~~~~~~~v~~~~Gv~-p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
+.-+.+| .++.+.+|.... -.++-..-||+. .++-.-|..|. +|.|||||+|..+|..+ +.+++.+.
T Consensus 32 ~~~~~~l~~g~~v~l~t~~~--vrEd~~~LyGF~~~~Er~lF~~L~--------~V~GIGpK~AL~iLs~~-~~~~l~~a 100 (197)
T PRK14603 32 APTLARLVEGQEAELHTRLV--VREDALSLYGFPDEDSLELFELLL--------GVSGVGPKLALALLSAL-PPALLARA 100 (197)
T ss_pred HHHHHHcCCCCeEEEEEEEE--EccCCceeeCcCCHHHHHHHHHHh--------CcCCcCHHHHHHHHcCC-CHHHHHHH
Confidence 4433444 244566554211 122233457764 33444455564 48999999999999987 57777776
Q ss_pred hh
Q psy2882 984 AN 985 (1428)
Q Consensus 984 ~~ 985 (1428)
+.
T Consensus 101 I~ 102 (197)
T PRK14603 101 LL 102 (197)
T ss_pred HH
Confidence 54
No 201
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=62.97 E-value=7.8 Score=46.09 Aligned_cols=26 Identities=42% Similarity=0.616 Sum_probs=23.1
Q ss_pred CCCccchhhHHHHHHHhC--CHHHHHHHh
Q psy2882 958 GVKKIGPKTAVKLLNQYN--SLENIINNA 984 (1428)
Q Consensus 958 GvpGIG~KtA~kLL~~~g--sle~i~~~~ 984 (1428)
+|||||||||.+|. +.| |++++..+.
T Consensus 89 ~i~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 89 RVPGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred cCCCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 68999999999999 666 999999876
No 202
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.79 E-value=4.2 Score=44.67 Aligned_cols=47 Identities=21% Similarity=0.328 Sum_probs=31.0
Q ss_pred ccHHHHHHHh-CCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 926 HDRTTIISRF-GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 926 ~~~~~v~~~~-Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+++..-..-. +++|+++.. .+..|| ..-+..|||||+|||.+++-+.
T Consensus 81 IGpK~Al~ILs~~~~~el~~-aI~~~D-~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 81 IGANTAMAVCSSLDVNSFYK-ALSLGD-ESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred ccHHHHHHHHcCCCHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 3444333444 357777753 234454 6678899999999999998663
No 203
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=61.96 E-value=17 Score=44.48 Aligned_cols=117 Identities=22% Similarity=0.338 Sum_probs=78.1
Q ss_pred HHHHHHHc--CCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCCeeccHHHHHHHhCCCh
Q psy2882 862 IHQMVKAI--GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSP 939 (1428)
Q Consensus 862 i~~~l~~~--gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~~~~~~~~v~~~~Gv~p 939 (1428)
+.+.|..+ ++.++..+|..|+=++..-|+......|.=-+++|.|.|.+-+.+.+. +.++ ...+.+-|-+-|
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~----~~Ki--I~t~~~~Y~~~P 221 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDT----PPKI--IKTMNQLYKFIP 221 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCc----hHHH--HHhHHhHeeecC
Confidence 44455554 789999999999999999998876666655578899999998876432 1111 122334455666
Q ss_pred hhHHhhhh---ccccccCCCCCCCccc--hhhH--HHHHHHhCCHHHHHHHhh
Q psy2882 940 EKIVDYFS---LIGDMSDNLPGVKKIG--PKTA--VKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 940 ~q~~d~~a---L~GD~sDnipGvpGIG--~KtA--~kLL~~~gsle~i~~~~~ 985 (1428)
....-|++ ..=-.||..||+-|+- +|+- .+|..+| |+++++..+.
T Consensus 222 ~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~ 273 (425)
T PF04599_consen 222 CSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLA 273 (425)
T ss_pred CchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHh
Confidence 55554543 2223499999999974 3332 2466666 6889888764
No 204
>PRK13766 Hef nuclease; Provisional
Probab=60.65 E-value=9.7 Score=50.97 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=25.2
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
+-++||||+++|.+|+++|||+++++..
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4568999999999999999999999864
No 205
>PHA03065 Hypothetical protein; Provisional
Probab=59.70 E-value=17 Score=44.30 Aligned_cols=117 Identities=21% Similarity=0.311 Sum_probs=80.5
Q ss_pred HHHHHHHc--CCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCCeeccHHHHHHHhCCCh
Q psy2882 862 IHQMVKAI--GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSP 939 (1428)
Q Consensus 862 i~~~l~~~--gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~~~~~~~~v~~~~Gv~p 939 (1428)
+.+.|..+ ++.++..+|..|+=++..-|+......|.=-+++|.|.|.+-+.+.+. ..++ ...+.+-|-+-|
T Consensus 150 l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~----~~Ki--I~t~~~~Y~~~P 223 (438)
T PHA03065 150 LESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDR----LPKI--IKTANQLYKFIP 223 (438)
T ss_pred HHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCc----HHHH--HHhHHHHheeCC
Confidence 44456667 799999999999999999998876666655578899999988876331 1111 223445566667
Q ss_pred hhHHhhhh---ccccccCCCCCCCccc--hhhHH--HHHHHhCCHHHHHHHhh
Q psy2882 940 EKIVDYFS---LIGDMSDNLPGVKKIG--PKTAV--KLLNQYNSLENIINNAN 985 (1428)
Q Consensus 940 ~q~~d~~a---L~GD~sDnipGvpGIG--~KtA~--kLL~~~gsle~i~~~~~ 985 (1428)
....-|++ ..=-.||..||+-|+- +|+-. +|..+| |++|+..++.
T Consensus 224 ~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~ 275 (438)
T PHA03065 224 CAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLA 275 (438)
T ss_pred ChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHH
Confidence 66555553 2223499999999974 44432 467777 6888888763
No 206
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=59.14 E-value=9.7 Score=50.52 Aligned_cols=39 Identities=23% Similarity=0.485 Sum_probs=28.0
Q ss_pred hhhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCC--HHHHHHHhh
Q psy2882 939 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS--LENIINNAN 985 (1428)
Q Consensus 939 p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gs--le~i~~~~~ 985 (1428)
.+.++.|++ .| -+||||||||.++.+.||. ++-|.++.+
T Consensus 77 ~~~i~~yL~-s~-------~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~ 117 (720)
T TIGR01448 77 KEGIVAYLS-SR-------SIKGVGKKLAQRIVKTFGEAAFDVLDDDPE 117 (720)
T ss_pred HHHHHHHHh-cC-------CCCCcCHHHHHHHHHHhCHhHHHHHHhCHH
Confidence 456777766 22 3788999999999999994 555555443
No 207
>PHA03036 DNA polymerase; Provisional
Probab=58.48 E-value=57 Score=44.52 Aligned_cols=99 Identities=15% Similarity=0.084 Sum_probs=54.2
Q ss_pred ceEEEEeecccc----CccCCCcceeEEEEEEeCCceeeccceEEEEecCCCCCCChh--hHhhcCC---CHHHHhcCC-
Q psy2882 311 STFLWYDYETFG----LNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPR--ACLITKI---TPQFCLNNG- 380 (1428)
Q Consensus 311 ~~~v~~D~ETTG----ldp~~DrIiqiaaIr~~~~~~~i~~~~~~~~~p~~~~~p~pe--a~~itGI---Tpe~~~~~g- 380 (1428)
.+|++||+|+-. -+|..|-|+||+.--++..+. + -.+.....+.++..+ -..+-|. .+ -..-.|
T Consensus 160 ~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~---~--~~~~l~n~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 233 (1004)
T PHA03036 160 RSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGK---E--KRFTLINEDMLSEDEIEEAVKRGYYEIES-LLDMDYS 233 (1004)
T ss_pred ceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCC---e--eEEEEeccccccccccccceeeeeecccc-ccccCCc
Confidence 379999999974 245679999999744555442 1 122223333322111 1111222 11 000011
Q ss_pred -----CChHHHHHHHHHHHcC-CCceEEEEcchhhhHHHHHH
Q psy2882 381 -----IPEYKFASIIEKIFLK-PGTISVGYNTILFDDEITRF 416 (1428)
Q Consensus 381 -----~~e~e~~~~i~~~~~~-~~~~~VGyN~i~FD~~flr~ 416 (1428)
.+|.+++ ++.+.+.. .-.+++|||.-.||...+..
T Consensus 234 ~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~ 274 (1004)
T PHA03036 234 KELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISN 274 (1004)
T ss_pred eeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHHH
Confidence 2445544 55666654 23689999999999988853
No 208
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=58.46 E-value=6.8 Score=50.25 Aligned_cols=149 Identities=16% Similarity=0.239 Sum_probs=73.6
Q ss_pred EEEEEeCCCCCcccCCChhhhcCCCCCChHHHHHHHHHHHH-HHHc--CCc-EEEecchhhHHHHHHHHHHHhhhCCC--
Q psy2882 825 IACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQM-VKAI--GWP-ILIIKGVEADDVIGTLAKQAVTKHNL-- 898 (1428)
Q Consensus 825 ~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~q~~~i~~~-l~~~--gi~-~i~~~g~EADD~iatla~~~~~~~~~-- 898 (1428)
..|+|..+ .+.+..|..||-. -..++++....+.+.+- .+.+ -+| ++..+| +.-.+.+.-.-. ++-|.
T Consensus 398 smvvf~~g--~~~k~~YRry~i~-~~~~dDya~m~evl~RR~~~~~~~~~Pdli~iDG--GkgQl~~a~~vl-~~l~~~~ 471 (581)
T COG0322 398 SMVVFEDG--GPSKKDYRRYNIK-ITGGDDYASMREVLTRRYSRLLKEELPDLILIDG--GKGQLNAAKEVL-KELGLDI 471 (581)
T ss_pred EEEEEcCC--CCChhhccccccc-CCCCchHHHHHHHHHHHhhhccccCCCCEEEEeC--CHHHHHHHHHHH-HHcCCCc
Confidence 35566543 4567777778876 44467765544443332 1222 245 555666 333443322222 22332
Q ss_pred EEEEEeCCCCcccccc--C-cEEEEeCCe--eccHHHHH---HHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHH
Q psy2882 899 KVIISTNDKDMAQLVS--N-KIALINNNK--IHDRTTII---SRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKL 970 (1428)
Q Consensus 899 ~v~IvS~DkDl~QLv~--~-~v~~~~~~~--~~~~~~v~---~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kL 970 (1428)
.|+-++.+.+ +++- + ....+.+.. ..-...+. ..|.++-+.=.-.+...= .-.-+|||||||+..+|
T Consensus 472 ~viglaK~~~--~~~~~~~~~~~~l~~~~p~l~~lq~irDEaHrfAi~~hR~~R~k~~~~---s~Ld~I~GiG~~r~~~L 546 (581)
T COG0322 472 PVIGLAKGEE--ELLLPGPGEEFDLPPNSPALYLLQRIRDEAHRFAITYHRKKRSKAMLQ---SSLDDIPGIGPKRRKAL 546 (581)
T ss_pred cEEEEEecCc--eeEecCCCceecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc---CccccCCCcCHHHHHHH
Confidence 2444444444 2211 1 122222111 01111121 224444333333444433 22346778999999999
Q ss_pred HHHhCCHHHHHHHh
Q psy2882 971 LNQYNSLENIINNA 984 (1428)
Q Consensus 971 L~~~gsle~i~~~~ 984 (1428)
|+.|||+++|.++-
T Consensus 547 L~~Fgs~~~i~~As 560 (581)
T COG0322 547 LKHFGSLKGIKSAS 560 (581)
T ss_pred HHHhhCHHHHHhcC
Confidence 99999999998763
No 209
>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=58.11 E-value=68 Score=35.54 Aligned_cols=97 Identities=15% Similarity=0.019 Sum_probs=51.9
Q ss_pred HHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCC
Q psy2882 388 SIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFK 467 (1428)
Q Consensus 388 ~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~k 467 (1428)
..+.+.|..++..-|||+ +++|..++.. +.++.+ .+ +.|+.-+++.+.|..-. +. .......
T Consensus 55 ~~L~~iLe~~~i~Kv~h~-~k~D~~~L~~---~~gi~~--------~~---~fDt~iA~~lL~~~~~~-~~--~~~~~~~ 116 (197)
T cd06148 55 NGLKDILESKKILKVIHD-CRRDSDALYH---QYGIKL--------NN---VFDTQVADALLQEQETG-GF--NPDRVIS 116 (197)
T ss_pred HHHHHHhcCCCccEEEEe-chhHHHHHHH---hcCccc--------cc---eeeHHHHHHHHHHHhcC-Cc--ccccccc
Confidence 445556766766678988 7999887632 112111 11 14555555555442100 00 0011235
Q ss_pred hHhHHHHc-CCCC------------------------CCCCChHHHHHHHHHHHHHHHhh
Q psy2882 468 LEHLSFVN-NLSH------------------------KKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 468 Le~L~~~~-gi~~------------------------~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
|+.+++.+ |++. .+-+=|..||..+..|+..|.+.
T Consensus 117 L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~ 176 (197)
T cd06148 117 LVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDA 176 (197)
T ss_pred HHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 66666653 4432 12244788999988888877654
No 210
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.07 E-value=5.6 Score=44.10 Aligned_cols=36 Identities=25% Similarity=0.212 Sum_probs=26.5
Q ss_pred CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 937 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 937 v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
++|+++.. .+..|| ..-+..|||||+|||.+++-+.
T Consensus 92 ~~~~el~~-aI~~~D-~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 92 IKYNEFRD-AIDRED-IELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred CCHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 46666653 234555 6678899999999999998664
No 211
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=56.75 E-value=7 Score=37.52 Aligned_cols=25 Identities=32% Similarity=0.547 Sum_probs=21.7
Q ss_pred CCCCCccchhhHHHHHHHhCCHHHH
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNSLENI 980 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gsle~i 980 (1428)
+--|||||+.||..||.+.|+++.+
T Consensus 4 l~sipGig~~~a~~llaeigd~~rF 28 (87)
T PF02371_consen 4 LTSIPGIGPITAATLLAEIGDISRF 28 (87)
T ss_pred hcCCCCccHHHHHHHHHHHcCchhc
Confidence 4568999999999999999998653
No 212
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=55.67 E-value=8.7 Score=44.10 Aligned_cols=133 Identities=20% Similarity=0.349 Sum_probs=71.0
Q ss_pred ccchHHHH-HHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEecc-
Q psy2882 801 FPVGALYG-TIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKG- 878 (1428)
Q Consensus 801 ~~t~av~g-f~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~~g- 878 (1428)
+.-+.+-| |+....+|-+.+.-.-+++-+| ...-+.. .-.|+.+...+..+ .+ .+|+|++...+
T Consensus 78 fv~Si~dgRlfeQ~~rL~~~y~rpvliVegd--~~~~~~~---------~i~~~av~~al~s~--~v-dfg~~vi~t~~~ 143 (254)
T COG1948 78 FVSSIIDGRLFEQAKRLKKSYERPVLIVEGD--DSFSRRP---------KIHPNAVRGALASL--AV-DFGLPVIWTRSP 143 (254)
T ss_pred HHHHHhcchHHHHHHHHHhcCCccEEEEEcc--ccccccc---------ccCHHHHHHHHHHH--Hh-hcCceEEEeCCH
Confidence 33334444 5666666666654444556666 1111111 13566665544333 22 27899998754
Q ss_pred hhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCcEEEEeCCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCC
Q psy2882 879 VEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPG 958 (1428)
Q Consensus 879 ~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~v~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipG 958 (1428)
.|-=.+|..|+++...+ +..-+..++. .+..+.... | .+.|. +
T Consensus 144 ~~Ta~~i~~la~req~e-~~r~v~~~~~----------------~~~~t~~e~---------q---~~il~--------s 186 (254)
T COG1948 144 EETAELIHELARREQEE-RKRSVNPHGK----------------KKAKTLKEL---------Q---LYILE--------S 186 (254)
T ss_pred HHHHHHHHHHHHHHHHh-cccccccccc----------------ccccchHHH---------H---HHHHH--------c
Confidence 44556777788775321 1111111100 011111111 1 23333 4
Q ss_pred CCccchhhHHHHHHHhCCHHHHHHHh
Q psy2882 959 VKKIGPKTAVKLLNQYNSLENIINNA 984 (1428)
Q Consensus 959 vpGIG~KtA~kLL~~~gsle~i~~~~ 984 (1428)
+||||++.|..||..|||++++..+-
T Consensus 187 ~pgig~~~a~~ll~~fgS~~~~~tas 212 (254)
T COG1948 187 IPGIGPKLAERLLKKFGSVEDVLTAS 212 (254)
T ss_pred CCCccHHHHHHHHHHhcCHHHHhhcC
Confidence 58999999999999999999998763
No 213
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=54.65 E-value=15 Score=33.54 Aligned_cols=36 Identities=17% Similarity=0.326 Sum_probs=23.1
Q ss_pred CCccchhhHHHHHHH---hC---CHHHHHHHhhhcchhhhhhH
Q psy2882 959 VKKIGPKTAVKLLNQ---YN---SLENIINNANNIKGVIGKNL 995 (1428)
Q Consensus 959 vpGIG~KtA~kLL~~---~g---sle~i~~~~~~i~~k~~~~l 995 (1428)
+||||+++|.++|+. +| +++++. .+..+..+..+++
T Consensus 22 ipgig~~~a~~Il~~R~~~g~~~s~~dL~-~v~gi~~~~~~~i 63 (69)
T TIGR00426 22 MNGVGLKKAEAIVSYREEYGPFKTVEDLK-QVPGIGNSLVEKN 63 (69)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcCCHHHHH-cCCCCCHHHHHHH
Confidence 688999999999998 66 455553 2333444443333
No 214
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.14 E-value=8.8 Score=42.34 Aligned_cols=46 Identities=22% Similarity=0.340 Sum_probs=31.1
Q ss_pred ccHHHHHHHhC-CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 926 HDRTTIISRFG-VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 926 ~~~~~v~~~~G-v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+++..-..-.. ++|+++.+. +-.||. .-+ .|||||+|||.+++-+.
T Consensus 81 IGpK~Al~iLs~~~~~~l~~a-I~~~D~-~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 81 VNYKTAMSILSKLTPEQLFSA-IVNEDK-AAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred cCHHHHHHHHccCCHHHHHHH-HHcCCH-hhe-ECCCCcHHHHHHHHHHH
Confidence 33433333333 467777643 456885 677 89999999999998663
No 215
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=53.86 E-value=7.6 Score=30.35 Aligned_cols=19 Identities=42% Similarity=0.450 Sum_probs=13.3
Q ss_pred CCCCCccchhhHHHHHHHhC
Q psy2882 956 LPGVKKIGPKTAVKLLNQYN 975 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~g 975 (1428)
|--++|||+||+.+| +++|
T Consensus 13 i~~~~GIG~kt~~kL-~~~G 31 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL-NKLG 31 (32)
T ss_dssp GGGSTTS-HHHHHHH-HCTT
T ss_pred HHhhCCccHHHHHHH-HHcc
Confidence 457899999999984 4443
No 216
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.43 E-value=6.7 Score=43.31 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=31.8
Q ss_pred ccHHHHHHHh-CCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 926 HDRTTIISRF-GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 926 ~~~~~v~~~~-Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+++..-..-. +++|+++.. .+..|| ..-+-.|||||+|||.+++-+.
T Consensus 81 IGpK~AL~iLs~~~~~el~~-aI~~~D-~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 81 LGPKTALKIISNEDAETLVT-MIASQD-VEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred ccHHHHHHHHcCCCHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 3444444444 357777763 344565 6678899999999999998664
No 217
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.58 E-value=40 Score=45.85 Aligned_cols=66 Identities=17% Similarity=0.195 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCC
Q psy2882 384 YKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGK 463 (1428)
Q Consensus 384 ~e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~ 463 (1428)
..+...+.++|..++...|||| +.||..+|+ ++++.. . | -+.|++-++|.+.|+ .
T Consensus 364 ~~~~~~l~~~l~~~~~~~v~~n-~K~d~~~l~----~~gi~~-~-----~----~~~Dt~la~yll~~~----------~ 418 (887)
T TIGR00593 364 ILTDDKFARWLLNEQIKKIGHD-AKFLMHLLK----REGIEL-G-----G----VIFDTMLAAYLLDPA----------Q 418 (887)
T ss_pred HHHHHHHHHHHhCCCCcEEEee-HHHHHHHHH----hCCCCC-C-----C----cchhHHHHHHHcCCC----------C
Confidence 3455667777877766689999 899998875 444432 1 1 137888999998763 1
Q ss_pred CCCChHhHHHHc
Q psy2882 464 PSFKLEHLSFVN 475 (1428)
Q Consensus 464 ~s~kLe~L~~~~ 475 (1428)
++.|++++..|
T Consensus 419 -~~~l~~la~~y 429 (887)
T TIGR00593 419 -VSTLDTLARRY 429 (887)
T ss_pred -CCCHHHHHHHH
Confidence 24899998876
No 218
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.26 E-value=9.1 Score=42.54 Aligned_cols=47 Identities=21% Similarity=0.255 Sum_probs=30.5
Q ss_pred ccHHHHHHHhC-CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 926 HDRTTIISRFG-VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 926 ~~~~~v~~~~G-v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+++..-..-.. .+|+++.. .+..|| ..-+..|||||+|||.+++-+.
T Consensus 81 IGpK~Al~iLs~~~~~el~~-aI~~~D-~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 81 VGPKAALNLLSSGTPDELQL-AIAGGD-VARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred cCHHHHHHHHcCCCHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 33433333333 46777663 234455 5667899999999999998764
No 219
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=49.20 E-value=12 Score=45.06 Aligned_cols=28 Identities=36% Similarity=0.500 Sum_probs=23.6
Q ss_pred CCCCccchhhHHHHHHHhC--CHHHHHHHhh
Q psy2882 957 PGVKKIGPKTAVKLLNQYN--SLENIINNAN 985 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~g--sle~i~~~~~ 985 (1428)
-.|||||||||.+|.+ .| |++++.++..
T Consensus 92 ~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~~ 121 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KGIRTLEELKKNKE 121 (334)
T ss_pred HccCCcCHHHHHHHHH-hCCCCHHHHHhccc
Confidence 3589999999999998 87 8999977654
No 220
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=47.67 E-value=35 Score=38.15 Aligned_cols=49 Identities=27% Similarity=0.350 Sum_probs=34.0
Q ss_pred HHHHHHHhCCCh-hhHHhhhhccccccCCCCCCCccchhhHHHHHHHhCCHHHHHHHhh
Q psy2882 928 RTTIISRFGVSP-EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985 (1428)
Q Consensus 928 ~~~v~~~~Gv~p-~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~i~~~~~ 985 (1428)
+++...-||+.- +.=..|.-|. .|-|||||+|..+|... +++++.+.+.
T Consensus 54 REd~~~LyGF~~~~ER~lF~~Li--------sVnGIGpK~ALaiLs~~-~~~~l~~aI~ 103 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLLI--------SVNGIGPKLALAILSNL-DPEELAQAIA 103 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHHH--------ccCCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 444567788743 3334455564 37899999999999775 5777776654
No 221
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.17 E-value=9.4 Score=42.49 Aligned_cols=47 Identities=17% Similarity=0.241 Sum_probs=31.5
Q ss_pred ccHHHHHHHhC-CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 926 HDRTTIISRFG-VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 926 ~~~~~v~~~~G-v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+++..-..-.. ++|+++... +..|| ..-+..|||||+|||.+++-+.
T Consensus 80 IGpK~AL~iLs~~~~~~l~~a-I~~~D-~~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 80 VGPKLALALLSALPPALLARA-LLEGD-ARLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred cCHHHHHHHHcCCCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 44444444444 577777632 34455 4557789999999999998764
No 222
>KOG4793|consensus
Probab=45.74 E-value=28 Score=40.06 Aligned_cols=106 Identities=23% Similarity=0.167 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHcC---CC--ceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCC
Q psy2882 384 YKFASIIEKIFLK---PG--TISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPY 458 (1428)
Q Consensus 384 ~e~~~~i~~~~~~---~~--~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~ 458 (1428)
++...-.+..+.+ ++ +....+|...|+..|.-++|.|..... .+.| -.++-+-.++.-... ..|
T Consensus 179 ~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deq-a~pw-------~~ir~l~~~~~~a~~--~~P- 247 (318)
T KOG4793|consen 179 YSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQ-ARPW-------LLIRPLYLARENAKS--VEP- 247 (318)
T ss_pred cccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhc-CCCc-------ccccchhhhhhhccc--cCC-
Confidence 3444444444444 22 344466778899999999998875431 2333 223322222111111 112
Q ss_pred CCCCCCCCChHhHHHHcC-CCCCCCCChHHHHHHHHHHHHHHHhh
Q psy2882 459 KNNGKPSFKLEHLSFVNN-LSHKKAHDALSDVRATLGLARLIRNN 502 (1428)
Q Consensus 459 ~~~g~~s~kLe~L~~~~g-i~~~~AHdAlaDv~AT~~l~~~l~~~ 502 (1428)
.-.-+..|+.|+..+. ++...||+|++||..+-.+++++...
T Consensus 248 --~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~id 290 (318)
T KOG4793|consen 248 --TPKLVSSLEALATYYSLTPELDAHRALSDVLLLSKVFQKLTID 290 (318)
T ss_pred --CCccchhHHHHHHHhhcCcccchhhhccccchhhhHHHHhhhh
Confidence 1234689999998765 57788999999999998888887653
No 223
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.28 E-value=11 Score=42.15 Aligned_cols=36 Identities=22% Similarity=0.286 Sum_probs=26.2
Q ss_pred CChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 937 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 937 v~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
++|+++. .++......-+..|||||+|||.+++-+.
T Consensus 94 ~~~~~l~--~aI~~~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 94 FRPDDLR--RLVAEEDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCHHHHH--HHHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 4666665 23444347778899999999999998763
No 224
>PRK08609 hypothetical protein; Provisional
Probab=41.23 E-value=22 Score=46.00 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=24.5
Q ss_pred CCCccchhhHHHHHHHhC--CHHHHHHHhh
Q psy2882 958 GVKKIGPKTAVKLLNQYN--SLENIINNAN 985 (1428)
Q Consensus 958 GvpGIG~KtA~kLL~~~g--sle~i~~~~~ 985 (1428)
.|||||||||.+|-++.| |++++.++..
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 589999999999998776 8999998764
No 225
>KOG1602|consensus
Probab=39.79 E-value=1.3e+02 Score=34.78 Aligned_cols=66 Identities=12% Similarity=0.138 Sum_probs=42.5
Q ss_pred hcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEe----------cchhhHHHHHHH
Q psy2882 819 NYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTL 888 (1428)
Q Consensus 819 ~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~----------~g~EADD~iatl 888 (1428)
..-|.||+++.||-+.--|+.-++.-+++++. ..++..+-++|..+||+.+.+ +-.|-|-++.-+
T Consensus 34 g~~P~HVaFIMDGNRR~AKk~~L~~~~GH~aG-----f~~l~~ile~C~~lGI~~vT~fAFSieNFkRs~eEVd~LM~L~ 108 (271)
T KOG1602|consen 34 GPMPRHVAFIMDGNRRYAKKRGLETSEGHEAG-----FEALKEILELCKELGIKEVTVFAFSIENFKRSPEEVDGLMDLA 108 (271)
T ss_pred CCCcceeEEEecCchHHHHhcCCCcccchHHH-----HHHHHHHHHHHHHcCCcEEEEEEEehhhhCCCHHHHHHHHHHH
Confidence 57899999999985443355555554444432 233445556777799999876 345777776643
Q ss_pred H
Q psy2882 889 A 889 (1428)
Q Consensus 889 a 889 (1428)
-
T Consensus 109 ~ 109 (271)
T KOG1602|consen 109 L 109 (271)
T ss_pred H
Confidence 3
No 226
>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=39.21 E-value=46 Score=35.25 Aligned_cols=85 Identities=20% Similarity=0.366 Sum_probs=54.3
Q ss_pred HHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEEEEeCCCCccccccCc--EEEEeCCe-eccHHHHHHHh
Q psy2882 859 INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNK--IALINNNK-IHDRTTIISRF 935 (1428)
Q Consensus 859 ~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~IvS~DkDl~QLv~~~--v~~~~~~~-~~~~~~v~~~~ 935 (1428)
+..+-+.|+.+|+-++..+++ .|+-|..+|+.- .=+|+|.|++|....... +....... .-....+.+.+
T Consensus 9 L~~Lar~LR~lG~Dt~~~~~~-~D~~il~~A~~e------~RillTrd~~l~~~~~~~~~~~li~~~~~~~QL~ev~~~~ 81 (147)
T PF01927_consen 9 LGRLARWLRLLGYDTLYSRDI-DDDEILELAREE------GRILLTRDRDLLKRRRVSGGVILIRSDDPEEQLREVLERF 81 (147)
T ss_pred HHHHHHHHHHCCCcEEEeCCC-ChHHHHHHhhhC------CeEEEECCHHHHHHhhccCCEEEEcCCCHHHHHHHHHHHc
Confidence 345677999999999999975 566666666541 246889999998876643 22333222 22345677888
Q ss_pred CCCh--hhHHhhhhccc
Q psy2882 936 GVSP--EKIVDYFSLIG 950 (1428)
Q Consensus 936 Gv~p--~q~~d~~aL~G 950 (1428)
|+.+ +-+..-|..++
T Consensus 82 ~l~~~~~~~~sRC~~CN 98 (147)
T PF01927_consen 82 GLKLRLDPIFSRCPKCN 98 (147)
T ss_pred CCccccCCCCCccCCCC
Confidence 8766 32334555555
No 227
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=38.73 E-value=53 Score=34.18 Aligned_cols=55 Identities=15% Similarity=0.155 Sum_probs=38.9
Q ss_pred HHHHHHHHHcCCcEEEecch-------hhHHHHHHHHHHHhhh-CCCEEEEEeCCCCcccccc
Q psy2882 860 NLIHQMVKAIGWPILIIKGV-------EADDVIGTLAKQAVTK-HNLKVIISTNDKDMAQLVS 914 (1428)
Q Consensus 860 ~~i~~~l~~~gi~~i~~~g~-------EADD~iatla~~~~~~-~~~~v~IvS~DkDl~QLv~ 914 (1428)
....+.|...|+.++..+.. .+|--|++-+...... .-..++++|+|.||..++.
T Consensus 55 ~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~ 117 (149)
T cd06167 55 RGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVE 117 (149)
T ss_pred HHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHH
Confidence 34556778899999888743 3787777654443322 3468999999999998864
No 228
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=37.97 E-value=51 Score=33.90 Aligned_cols=55 Identities=13% Similarity=0.148 Sum_probs=29.7
Q ss_pred HHHHHHHHHcCCcEEEecch--------hhHHHHHHHHHHHh-hhCCCEEEEEeCCCCcccccc
Q psy2882 860 NLIHQMVKAIGWPILIIKGV--------EADDVIGTLAKQAV-TKHNLKVIISTNDKDMAQLVS 914 (1428)
Q Consensus 860 ~~i~~~l~~~gi~~i~~~g~--------EADD~iatla~~~~-~~~~~~v~IvS~DkDl~QLv~ 914 (1428)
..+.+.|...|+++...+.. .+|-.|++=+.... +.....++|+|+|.||..++.
T Consensus 50 ~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 50 KSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVR 113 (146)
T ss_dssp HHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHH
T ss_pred hhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHH
Confidence 44556778889977655432 37777765444332 222478999999999998875
No 229
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=37.62 E-value=21 Score=46.21 Aligned_cols=28 Identities=25% Similarity=0.572 Sum_probs=25.7
Q ss_pred CCCCccchhhHHHHHHHhCCHHHHHHHh
Q psy2882 957 PGVKKIGPKTAVKLLNQYNSLENIINNA 984 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~gsle~i~~~~ 984 (1428)
=|||.||+++|..|.+.|||+++++++-
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a~ 541 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAAS 541 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhcC
Confidence 5899999999999999999999998763
No 230
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=37.36 E-value=32 Score=36.66 Aligned_cols=23 Identities=26% Similarity=0.674 Sum_probs=17.0
Q ss_pred CCccchhhHHHHHH------HhCCHHHHH
Q psy2882 959 VKKIGPKTAVKLLN------QYNSLENII 981 (1428)
Q Consensus 959 vpGIG~KtA~kLL~------~~gsle~i~ 981 (1428)
+||||||+|.++++ .|.|+|++-
T Consensus 102 lpgIG~~kA~aIi~yRe~~G~f~sv~dL~ 130 (149)
T COG1555 102 LPGIGPKKAQAIIDYREENGPFKSVDDLA 130 (149)
T ss_pred CCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence 58999999999886 245666654
No 231
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=36.17 E-value=79 Score=33.70 Aligned_cols=99 Identities=21% Similarity=0.257 Sum_probs=45.9
Q ss_pred hhhhccchhhhhhhccCCcCcCCCCccchHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHH
Q psy2882 776 YGKIDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNL 855 (1428)
Q Consensus 776 Y~~i~g~~~~~Ra~~a~~~l~~~~G~~t~av~gf~~~l~~l~~~~~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l 855 (1428)
.+-+||+++.|. |... +.... .|....+..+.+. +.+ ++++|+. ++|...+ +.+...++.|
T Consensus 4 ~VVIDG~NVA~~--~~~~-----~~f~~---~~i~~~v~~~~~r-G~~-~v~v~~~---~~~~~~~----~~~~~~~~~L 64 (155)
T PF11977_consen 4 PVVIDGSNVAYS--HGNQ-----KFFSV---RGIQIAVEYFKSR-GHE-VVVVFPP---NYRYKKL----AKKSDDQEEL 64 (155)
T ss_dssp -EEEEHHHHHHH--HTTT-----TSEEH---HHHHHHHHHHHHT-T----EEEEEE---GGGGS-T----TS-EESTCHH
T ss_pred EEEEeCHHHHhh--cCCC-----CCcCH---HHHHHHHHHHHHc-CCC-eEEEEcc---hhhhccc----cCCCChHHHH
Confidence 355899999872 2111 11222 3333344443333 221 4677873 5554441 1112223333
Q ss_pred HHHHHHHHHHHHHcCCcEEEecchh--------hHHHHHHHHHHHhhhCCCEEEEEeCCC
Q psy2882 856 ILQINLIHQMVKAIGWPILIIKGVE--------ADDVIGTLAKQAVTKHNLKVIISTNDK 907 (1428)
Q Consensus 856 ~~q~~~i~~~l~~~gi~~i~~~g~E--------ADD~iatla~~~~~~~~~~v~IvS~Dk 907 (1428)
.++ ...|+-++...|.. +|=.|-++|... ..+|||.|+
T Consensus 65 -------~~l-~~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~~------~a~IVSND~ 110 (155)
T PF11977_consen 65 -------EKL-IRKGIIYFTPSGSNYGSRSRNYDDRYILYYAEEK------DAVIVSNDR 110 (155)
T ss_dssp -------HHH-HHTTSEEEE-EEEETTEEEEB-HHHHHHHHHHHT------T-EEE-S--
T ss_pred -------HHH-HHCCeEEEcCCCCCCCCcccccchHHHHHHHHHc------CCEEEeCch
Confidence 223 33687777777766 777777777652 246889996
No 232
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=35.32 E-value=89 Score=29.77 Aligned_cols=53 Identities=13% Similarity=0.078 Sum_probs=44.2
Q ss_pred CCCCHHHHHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhcCcchHHHHHHHHhhhh
Q psy2882 720 ETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTKILNALLMYGK 778 (1428)
Q Consensus 720 ~~L~~~e~~~w~~~~~~rl~~~~~~~~~~~~~~~~i~~L~~~~~~~~~~lL~~L~~Y~~ 778 (1428)
..||++|+.--.-||++.-.+ .++.+.+...+-+|++.++ |..+|.++..++.
T Consensus 14 ~lL~e~E~~tm~yyl~eY~~~----~~tVealV~aL~elLnt~~--K~sLLsEiR~lI~ 66 (81)
T cd07357 14 HLLSENERATLSYYLDEYRSG----HISVDALVMALFELLNTHE--KFSLLSEIRELIS 66 (81)
T ss_pred HHcCHHHHHHHHHHHHHHHcC----CCCHHHHHHHHHHHhccHH--HHHHHHHHHHhcC
Confidence 368999999998899877544 5799999999999997665 9999999988763
No 233
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.08 E-value=44 Score=34.48 Aligned_cols=42 Identities=21% Similarity=0.318 Sum_probs=34.7
Q ss_pred EEEEeeCCCCCCCCHHH--HHHHHHcCCeEEEcChhhHHHHHHh
Q psy2882 1372 VVILGTGNIQHFIHPKL--TYILTQKNIGIECMNNQAACRTYNI 1413 (1428)
Q Consensus 1372 vliiGTG~~~~~~~~~~--~~~l~~~GI~vE~M~T~aAcrTyNi 1413 (1428)
+|++||-.-...+|..+ .-.|.++|..|-+-.|+||||-.-+
T Consensus 6 lv~lGCPeiP~qissaiYls~klkkkgf~v~VaateAa~kLlev 49 (148)
T COG4081 6 LVSLGCPEIPPQISSAIYLSHKLKKKGFDVTVAATEAALKLLEV 49 (148)
T ss_pred EEEecCCCCCccchHHHHHHHHhhccCccEEEecCHhhheeeee
Confidence 57789988777777777 5678999999999999999985433
No 234
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=33.71 E-value=29 Score=30.78 Aligned_cols=23 Identities=30% Similarity=0.429 Sum_probs=18.3
Q ss_pred ccCCCCCCCccchhhHHHHHHHh
Q psy2882 952 MSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 952 ~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+.|-+-.|||||+++|.+|+...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 34557778999999999998753
No 235
>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=32.69 E-value=4.9e+02 Score=28.42 Aligned_cols=59 Identities=17% Similarity=-0.002 Sum_probs=37.9
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.+++..++...|||| +..|..+++. ++++.. . + +.|+.-++|.+.| + +..|+
T Consensus 69 L~~~L~~~~i~kv~~d-~K~~~~~L~~---~~gi~~------~-~----~fD~~laaYLL~p----------~--~~~l~ 121 (192)
T cd06147 69 LNEVFTDPNILKVFHG-ADSDIIWLQR---DFGLYV------V-N----LFDTGQAARVLNL----------P--RHSLA 121 (192)
T ss_pred HHHHhcCCCceEEEec-hHHHHHHHHH---HhCCCc------C-c----hHHHHHHHHHhCC----------C--cccHH
Confidence 4456666667789988 6888777542 222221 0 1 1788889999876 2 23788
Q ss_pred hHHHHc
Q psy2882 470 HLSFVN 475 (1428)
Q Consensus 470 ~L~~~~ 475 (1428)
.|++.|
T Consensus 122 ~l~~~y 127 (192)
T cd06147 122 YLLQKY 127 (192)
T ss_pred HHHHHH
Confidence 888876
No 236
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=32.42 E-value=13 Score=33.74 Aligned_cols=33 Identities=27% Similarity=0.501 Sum_probs=20.3
Q ss_pred hccccccCCCCCCCccchhhHHHHHHHhCCHHH
Q psy2882 947 SLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLEN 979 (1428)
Q Consensus 947 aL~GD~sDnipGvpGIG~KtA~kLL~~~gsle~ 979 (1428)
.|+--+-+-+.-||||||++|..+.+-|..-++
T Consensus 28 ~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n 60 (64)
T PF12826_consen 28 ALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN 60 (64)
T ss_dssp HHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred HHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence 344445566778999999999998877765443
No 237
>KOG1275|consensus
Probab=31.41 E-value=61 Score=43.04 Aligned_cols=156 Identities=18% Similarity=0.228 Sum_probs=84.8
Q ss_pred ceEEEEeeccccCccCCCcc----------------eeEEEEEEeCCceeeccceE-EEEecCCCCCCChhhHhhcCCCH
Q psy2882 311 STFLWYDYETFGLNVRRDRP----------------FQFAAIRTDIMLNTIDNPIM-LYCKPAPDFLPDPRACLITKITP 373 (1428)
Q Consensus 311 ~~~v~~D~ETTGldp~~DrI----------------iqiaaIr~~~~~~~i~~~~~-~~~~p~~~~~p~pea~~itGITp 373 (1428)
..+|.+|-|=--|+++..+| ..|+.||-.+ ---+-||. =|+.-...+ . .--+.-.||-|
T Consensus 910 g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeG--p~eGiPFiDDYv~T~d~V-v-DYLTqySGI~P 985 (1118)
T KOG1275|consen 910 GDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEG--PNEGIPFIDDYVSTDDKV-V-DYLTQYSGIKP 985 (1118)
T ss_pred CceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccC--CCCCCccccceecchhHH-H-HHHHHhcCCCc
Confidence 46888888877776665544 3344554331 11122221 122222111 1 13345679999
Q ss_pred HHHhcCCCCh-----HHHHHHHHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHH
Q psy2882 374 QFCLNNGIPE-----YKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYV 448 (1428)
Q Consensus 374 e~~~~~g~~e-----~e~~~~i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~ 448 (1428)
-++ ....++ -.+.-.-..++.+.|.++|||- +.=|..+++ ..-| + + -++|++.+.+.
T Consensus 986 GDL-Dp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHG-L~nDFrvIN------i~Vp---~----~---QiiDTv~lf~~ 1047 (1118)
T KOG1275|consen 986 GDL-DPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHG-LQNDFRVIN------IHVP---E----E---QIIDTVTLFRL 1047 (1118)
T ss_pred ccc-CCccCcceehhHHHHHHHHHHHHHcCcEEEccc-ccccceEEE------EecC---h----h---hheeeeEEEec
Confidence 998 344444 3455555666777889999976 666644432 2111 1 1 12344333111
Q ss_pred hCCCCcCCCCCCCCCCCCChHhHHHHc-CCC-CCCCCChHHHHHHHHHHHHHHH
Q psy2882 449 LSPYGITWPYKNNGKPSFKLEHLSFVN-NLS-HKKAHDALSDVRATLGLARLIR 500 (1428)
Q Consensus 449 l~p~~~~~p~~~~g~~s~kLe~L~~~~-gi~-~~~AHdAlaDv~AT~~l~~~l~ 500 (1428)
|. ..-..|.-||-.+ |-. ...+||...||+.|+.|+++..
T Consensus 1048 --------~s----~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl 1089 (1118)
T KOG1275|consen 1048 --------GS----QRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYL 1089 (1118)
T ss_pred --------cc----ccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHH
Confidence 10 1125777777753 433 2459999999999999988654
No 238
>PF05499 DMAP1: DNA methyltransferase 1-associated protein 1 (DMAP1); InterPro: IPR008468 DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic N terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=31.34 E-value=31 Score=37.53 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=26.6
Q ss_pred HHHHHHHcCCeEEEcChhhHHHHHHhhhhc
Q psy2882 1388 LTYILTQKNIGIECMNNQAACRTYNILVSD 1417 (1428)
Q Consensus 1388 ~~~~l~~~GI~vE~M~T~aAcrTyNiL~sE 1417 (1428)
+-..|.+.||.+..|+|..-|.+||-|.++
T Consensus 110 iEq~L~elgv~~~PmPTe~Ic~~fneLRsd 139 (176)
T PF05499_consen 110 IEQFLQELGVDLNPMPTEEICQEFNELRSD 139 (176)
T ss_pred HHHHHHHcCCCCCCCChHHHHHHHHHHHHH
Confidence 344789999999999999999999999876
No 239
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=31.23 E-value=34 Score=41.30 Aligned_cols=27 Identities=11% Similarity=0.378 Sum_probs=24.4
Q ss_pred CCCCccchhhHHHHHHHhCCHHHHHHH
Q psy2882 957 PGVKKIGPKTAVKLLNQYNSLENIINN 983 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~~gsle~i~~~ 983 (1428)
-.||+||++.|..|+++|||+.+|+++
T Consensus 290 s~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 290 SKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 357999999999999999999999975
No 240
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=30.85 E-value=49 Score=32.49 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=16.7
Q ss_pred CCCCccchhhHHHHHH-HhCCHHHH
Q psy2882 957 PGVKKIGPKTAVKLLN-QYNSLENI 980 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~-~~gsle~i 980 (1428)
-.|||||+++|..|.. .|.|++++
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s~~~L 39 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRSPADL 39 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCCHHHH
Confidence 3579999999999874 23355444
No 241
>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=30.05 E-value=2.6e+02 Score=28.59 Aligned_cols=64 Identities=14% Similarity=0.235 Sum_probs=40.3
Q ss_pred HHHHHcCCCceEEEEcchhhhHHHHHHHHHHccccchhhhhhcCCCCCchhhHHHHHHHhCCCCcCCCCCCCCCCCCChH
Q psy2882 390 IEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLE 469 (1428)
Q Consensus 390 i~~~~~~~~~~~VGyN~i~FD~~flr~~f~Rn~~~~y~~~~~~g~sr~D~ld~~rl~~~l~p~~~~~p~~~~g~~s~kLe 469 (1428)
+.++|..++...+||| +.+|..+++ +++... . + -..|+.-++|.+.|. ..+..|+
T Consensus 45 l~~~l~~~~~~kv~~d-~K~~~~~L~----~~~~~~-~-----~----~~~D~~laayLl~p~----------~~~~~l~ 99 (150)
T cd09018 45 LKPLLEDEKALKVGQN-LKYDRGILL----NYFIEL-R-----G----IAFDTMLEAYILNSV----------AGRWDMD 99 (150)
T ss_pred HHHHhcCCCCceeeec-HHHHHHHHH----HcCCcc-C-----C----cchhHHHHHHHhCCC----------CCCCCHH
Confidence 4556666666789988 789987764 232221 0 1 136788888998763 1023788
Q ss_pred hHHHHc-CCC
Q psy2882 470 HLSFVN-NLS 478 (1428)
Q Consensus 470 ~L~~~~-gi~ 478 (1428)
+|+..+ |..
T Consensus 100 ~l~~~~l~~~ 109 (150)
T cd09018 100 SLVERWLGHK 109 (150)
T ss_pred HHHHHHhCCC
Confidence 898876 443
No 242
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=29.06 E-value=29 Score=29.32 Aligned_cols=23 Identities=30% Similarity=0.548 Sum_probs=17.9
Q ss_pred hhHHhhhhccccccCCCCCCCccchhh
Q psy2882 940 EKIVDYFSLIGDMSDNLPGVKKIGPKT 966 (1428)
Q Consensus 940 ~q~~d~~aL~GD~sDnipGvpGIG~Kt 966 (1428)
.|.-|++.+ .||+|-||.||+|.
T Consensus 9 aq~ddllgi----wdnvptiprigekv 31 (57)
T PF13052_consen 9 AQEDDLLGI----WDNVPTIPRIGEKV 31 (57)
T ss_pred cchhhhhhh----hccCCCccccchhh
Confidence 455566555 79999999999985
No 243
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=28.06 E-value=46 Score=36.93 Aligned_cols=44 Identities=25% Similarity=0.269 Sum_probs=27.1
Q ss_pred ccHHHHHHHhCC-ChhhHHhhhhccccccCCCCCCCccchhhHHHHH
Q psy2882 926 HDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLL 971 (1428)
Q Consensus 926 ~~~~~v~~~~Gv-~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL 971 (1428)
+++.....-.+. +|+++... +..|| ..-+-.|||||+|||.+++
T Consensus 80 IGpK~Al~iL~~~~~~el~~a-I~~~d-~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 80 VGPKLALAILSNMSPEEFVYA-IETEE-VKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCHHHHHHHHhcCCHHHHHHH-HHhCC-HHHHHhCCCCCHHHHHHHH
Confidence 344444444443 45555422 23365 3447789999999999998
No 244
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.05 E-value=34 Score=38.03 Aligned_cols=34 Identities=24% Similarity=0.415 Sum_probs=23.5
Q ss_pred ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHH
Q psy2882 938 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQ 973 (1428)
Q Consensus 938 ~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~ 973 (1428)
+|+++... +..|| ..-+-.|||||+|||.+++-+
T Consensus 94 ~~~~l~~a-I~~~D-~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 94 NAEALASA-IISGN-AELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CHHHHHHH-HHhCC-HHHHHhCCCCCHHHHHHHHHH
Confidence 45655422 22465 444778999999999998866
No 245
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=27.22 E-value=67 Score=36.12 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=27.2
Q ss_pred CHHHHHHHHHhHHhHhhC---hHHHHHHHHHhhcc
Q psy2882 627 DLNCAFKNIKCASSILNN---TYIWKKIFLDYKIN 658 (1428)
Q Consensus 627 d~~~~~~~~~~~~~l~~~---~~l~~~~~~~~~~~ 658 (1428)
|+.+++||++--|-|.+| |++|+.|..++.+.
T Consensus 129 DlGLLLRhLRHHSNLLAnIgdP~VreqVLsAMqEe 163 (238)
T PF02084_consen 129 DLGLLLRHLRHHSNLLANIGDPEVREQVLSAMQEE 163 (238)
T ss_pred hHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHhhh
Confidence 778888888887778776 99999999999864
No 246
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.93 E-value=60 Score=42.79 Aligned_cols=25 Identities=36% Similarity=0.667 Sum_probs=22.5
Q ss_pred CCCccchhhHHHHH-HHhCCHHHHHH
Q psy2882 958 GVKKIGPKTAVKLL-NQYNSLENIIN 982 (1428)
Q Consensus 958 GvpGIG~KtA~kLL-~~~gsle~i~~ 982 (1428)
|||+||+++|..|. +.|++++++.+
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 78999999999999 89999998864
No 247
>COG4408 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.21 E-value=57 Score=38.77 Aligned_cols=42 Identities=29% Similarity=0.275 Sum_probs=32.8
Q ss_pred EEEeeCCCCCCCCHHHHHHHHHcCCeEEEcChhhHHHHHHhh
Q psy2882 1373 VILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNIL 1414 (1428)
Q Consensus 1373 liiGTG~~~~~~~~~~~~~l~~~GI~vE~M~T~aAcrTyNiL 1414 (1428)
|-+|.-..-..--..+.+-|.+.||.||+|.++-|+.|+|+-
T Consensus 172 iYlgs~~~ns~~~e~l~~v~aq~~I~v~~~esp~~AEtrnit 213 (431)
T COG4408 172 IYLGSQHGNSGSAEMLTAVLAQHGIDVEPCESPLAAETRNIT 213 (431)
T ss_pred eeeccCCCCChHHHHHHHHHHhcCCceEEcCChhhhhhcccc
Confidence 556665444444455788999999999999999999999973
No 248
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=24.66 E-value=87 Score=30.24 Aligned_cols=33 Identities=30% Similarity=0.591 Sum_probs=23.6
Q ss_pred CCCCCccchhhHHHHHHH-----hCCHHHHHHHhhhcc
Q psy2882 956 LPGVKKIGPKTAVKLLNQ-----YNSLENIINNANNIK 988 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~-----~gsle~i~~~~~~i~ 988 (1428)
.-.|+|||+++|.+++++ |.|+++++..++.++
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~~i~ 66 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLPKIN 66 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS-TS-
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHhcCC
Confidence 346899999999999974 578999988875333
No 249
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.82 E-value=1.4e+02 Score=34.27 Aligned_cols=82 Identities=15% Similarity=0.252 Sum_probs=48.8
Q ss_pred CCCEEEEEEeCCCCCc-ccCCChhhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEe----------cchhhHHHHHHHH
Q psy2882 821 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 889 (1428)
Q Consensus 821 ~p~~~v~~fD~~~~~f-R~~l~p~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~----------~g~EADD~iatla 889 (1428)
-|.||+++.||- .-| |+.-.|.+.++|... ..+..+-+.+..+||++++. |--|=+.++.-+.
T Consensus 6 ~P~HVAiImDGN-rRwAk~~gl~~~~GH~~G~-----~~~~~i~~~c~~~GI~~lT~YaFS~EN~~Rp~~EV~~Lm~L~~ 79 (230)
T PRK14837 6 LPSHVGIIMDGN-RRWALKKGLSFFEGHKEGL-----KRAKEIVKHSLKLGIKYLSLYVFSTENWNRTDSEIEHLMFLIA 79 (230)
T ss_pred CCCeEEEEccCC-HHHHHHCCCchhhhHHHHH-----HHHHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHH
Confidence 489999999984 334 444456555655532 12334455666789999886 4557777776655
Q ss_pred HHHh------hhCCCEEEEEeCCCCc
Q psy2882 890 KQAV------TKHNLKVIISTNDKDM 909 (1428)
Q Consensus 890 ~~~~------~~~~~~v~IvS~DkDl 909 (1428)
.... .+.|.++.+ .+|.++
T Consensus 80 ~~l~~~~~~~~~~~irvr~-iGd~~~ 104 (230)
T PRK14837 80 DYLSSEFNFYKKNNIKIIV-SGDIES 104 (230)
T ss_pred HHHHHHHHHHHHCCcEEEE-EcChhh
Confidence 4331 123444433 466665
No 250
>PF11097 DUF2883: Protein of unknown function (DUF2883); InterPro: IPR020112 This group of proteins currently have no known function and are found primarily in the T4-like bacteriophages.
Probab=23.52 E-value=43 Score=30.29 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=16.5
Q ss_pred EEEEeccCCCCCCcHHHHhc
Q psy2882 1205 LISLGCSGWGAGQLEEEIMN 1224 (1428)
Q Consensus 1205 r~f~GYsGW~pGQLe~Ei~~ 1224 (1428)
-+++||.||.+.-||+=|.+
T Consensus 6 ~VYLg~pg~p~nKle~LMlE 25 (75)
T PF11097_consen 6 DVYLGYPGLPPNKLEGLMLE 25 (75)
T ss_pred eEEEeCCCCChHHHHHHHHH
Confidence 48999999999999975543
No 251
>PRK00254 ski2-like helicase; Provisional
Probab=23.49 E-value=63 Score=43.10 Aligned_cols=27 Identities=37% Similarity=0.538 Sum_probs=24.5
Q ss_pred CCCCccchhhHHHHHHH-hCCHHHHHHH
Q psy2882 957 PGVKKIGPKTAVKLLNQ-YNSLENIINN 983 (1428)
Q Consensus 957 pGvpGIG~KtA~kLL~~-~gsle~i~~~ 983 (1428)
..|||||+++|.+|++. |+|+++|.+.
T Consensus 648 ~~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 648 MRLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred hcCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 45899999999999999 9999999875
No 252
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.40 E-value=1.4e+02 Score=34.41 Aligned_cols=67 Identities=13% Similarity=0.141 Sum_probs=43.2
Q ss_pred CCCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEe----------cchhhHHHHHHHHH
Q psy2882 821 RATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLAK 890 (1428)
Q Consensus 821 ~p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~----------~g~EADD~iatla~ 890 (1428)
-|.||+++.||-+.-=|+.-.+.+.+++... ..+..+-+++..+||++++. |--|=+.++.-+..
T Consensus 3 ~P~HVaiImDGNrRwAk~~g~~~~~GH~~G~-----~~l~~i~~~~~~lgIk~lTvYaFS~eN~~R~~~Ev~~Lm~L~~~ 77 (233)
T PRK14841 3 IPQHVAIIMDGNGRWAKKRGLPRIKGHQRGA-----EVLHNTVKWSLELGIKYLTAFSFSTENWKRPKEEVEFLMDLFVQ 77 (233)
T ss_pred CCCEEEEEccCCHHHHHHCCCchhhhHHHHH-----HHHHHHHHHHHHcCCCEEEEEeeeHhhcCCCHHHHHHHHHHHHH
Confidence 4899999999853322555556666665532 12333445666789999887 45588888877665
Q ss_pred HH
Q psy2882 891 QA 892 (1428)
Q Consensus 891 ~~ 892 (1428)
..
T Consensus 78 ~l 79 (233)
T PRK14841 78 MI 79 (233)
T ss_pred HH
Confidence 43
No 253
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=22.47 E-value=42 Score=36.80 Aligned_cols=21 Identities=19% Similarity=0.252 Sum_probs=17.1
Q ss_pred CCCCCccchhhHHHHHHHhCC
Q psy2882 956 LPGVKKIGPKTAVKLLNQYNS 976 (1428)
Q Consensus 956 ipGvpGIG~KtA~kLL~~~gs 976 (1428)
.-.+||||+|||-=.|..+|+
T Consensus 117 Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 117 LKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHcCCCCCHHHHHHHHHHHHH
Confidence 556899999999988876664
No 254
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=22.34 E-value=51 Score=36.91 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=23.4
Q ss_pred ChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 938 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 938 ~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
+|+.+... +-.|| ...+-.+||||+|||.+++-+-
T Consensus 94 ~~~~l~~a-I~~~d-~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 94 DPEELAQA-IANED-VKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred CHHHHHHH-HHhcC-hHhhhcCCCCCHHHHHHHHHHH
Confidence 44545432 22333 4567789999999999988654
No 255
>KOG2841|consensus
Probab=21.78 E-value=77 Score=36.05 Aligned_cols=128 Identities=16% Similarity=0.214 Sum_probs=0.0
Q ss_pred cCCChhhhcCCC----------------CCChHHHHHHHHHHHHHHHcCCcEEEecchhhHHHHHHHHHHHhhhCCCEEE
Q psy2882 838 NILYPSYKATRK----------------KMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVI 901 (1428)
Q Consensus 838 ~~l~p~YKa~R~----------------~~p~~l~~q~~~i~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~~~~~v~ 901 (1428)
|.++|+|--.|- .+++......+..+ ++..-++..+.+-.+|+-.-.=-+.+.. ++....++
T Consensus 104 H~l~pdYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~el~k-~~~l~~~Tl~lA~s~EeaaryIE~~k~~-ek~p~dli 181 (254)
T KOG2841|consen 104 HKLHPDYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLELTK-TCDLNDVTLVLAWSMEEAARYIETYKEY-EKKPIDLI 181 (254)
T ss_pred hhcCcHHHHHHHHHhcccccceEEEEEecCcchHHHHHHHHH-HHHhhceeeeeeccHHHHHHHHHHHHHh-hcCCchhh
Q ss_pred EEeCCCCccccccCcEEEEeCCeeccHHHHHHHhCCChhhHHhhhhccccccCCCCCCCccchhhHHHHHHHh
Q psy2882 902 ISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974 (1428)
Q Consensus 902 IvS~DkDl~QLv~~~v~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGvpGIG~KtA~kLL~~~ 974 (1428)
.--.|.|+++=+-.-+.-+......|...+..+|| -++.+.+=|.+-+.-|||+||..|.+|.+-+
T Consensus 182 ~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~Fg-------sLq~~~~AS~~ele~~~G~G~~kak~l~~~l 247 (254)
T KOG2841|consen 182 MERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFG-------SLQQISNASEGELEQCPGLGPAKAKRLHKFL 247 (254)
T ss_pred hhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcc-------cHHHHHhcCHhHHHhCcCcCHHHHHHHHHHH
No 256
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=21.59 E-value=1.4e+02 Score=33.92 Aligned_cols=66 Identities=11% Similarity=0.068 Sum_probs=41.6
Q ss_pred CCEEEEEEeCCCCCcccCCChhhhcCCCCCChHHHHHHHHHHHHHHHcCCcEEEec----------chhhHHHHHHHHHH
Q psy2882 822 ATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIK----------GVEADDVIGTLAKQ 891 (1428)
Q Consensus 822 p~~~v~~fD~~~~~fR~~l~p~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~i~~~----------g~EADD~iatla~~ 891 (1428)
|.||+++.||-+.-=|+.-.+...++|... ..+..+-+++..+||++++.- --|=++++.-+...
T Consensus 1 P~HvaiImDGNrRwA~~~gl~~~~GH~~G~-----~~~~~i~~~~~~~gI~~lTvyaFS~eN~~R~~~EV~~Lm~l~~~~ 75 (221)
T cd00475 1 PKHVAFIMDGNRRWAKQRGMDRIEGHKAGA-----EKLRDILRWCLELGVKEVTLYAFSTENWKRPKEEVDFLMELFRDV 75 (221)
T ss_pred CCeEEEecCCCHHHHHHCCCChhHhHHHHH-----HHHHHHHHHHHHcCCCEEEEEeechhhhCcCHHHHHHHHHHHHHH
Confidence 789999999843322444456666655532 123344556677899998873 34877777766655
Q ss_pred H
Q psy2882 892 A 892 (1428)
Q Consensus 892 ~ 892 (1428)
.
T Consensus 76 l 76 (221)
T cd00475 76 L 76 (221)
T ss_pred H
Confidence 3
No 257
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=20.58 E-value=93 Score=32.00 Aligned_cols=54 Identities=22% Similarity=0.267 Sum_probs=34.4
Q ss_pred CccchhhHHHHHHHhC--CHHHHHHHhhhcchh--hhhhHHHhhhhchhhhhhhhcccc
Q psy2882 960 KKIGPKTAVKLLNQYN--SLENIINNANNIKGV--IGKNLRFALNWLPKLKKILTIKTD 1014 (1428)
Q Consensus 960 pGIG~KtA~kLL~~~g--sle~i~~~~~~i~~k--~~~~l~~~~~~~~~~~~L~~i~~d 1014 (1428)
||||++++.+| ++.| |.+++++....-.++ +..++.-....+..++.++.|.+-
T Consensus 1 pgi~~~~~~~L-~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ri 58 (122)
T PF14229_consen 1 PGIGPKEAAKL-KAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLMRI 58 (122)
T ss_pred CCCCHHHHHHH-HHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhhhc
Confidence 89999999998 6665 889999876544433 333333344445555566655533
No 258
>KOG0038|consensus
Probab=20.37 E-value=6.6e+02 Score=26.85 Aligned_cols=136 Identities=15% Similarity=0.148 Sum_probs=67.4
Q ss_pred hcccccCCCCC-CCeeEEEecCCccccccccCCChhhhhhhCCCHHHHHHHHHhHHhHhhChHHHHHHHHHhhccCCCCC
Q psy2882 585 LCFKKNSFKED-IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFLDYKINNSDLE 663 (1428)
Q Consensus 585 l~~~~~~~~~~-~plk~i~~Nk~P~~~~p~~~l~~~~~~rl~id~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~~~ 663 (1428)
|+.+-.+|.+. +|. -..-|+||+|-+|... + ...-+||.|| +++||.++|+++..
T Consensus 30 l~~Rf~~L~P~lVP~-~~~~~~~~~v~vp~e~---------------i----~kMPELkenp-fk~ri~e~FSeDG~--- 85 (189)
T KOG0038|consen 30 LHKRFYELAPHLVPT-DMTGNRPPIVKVPFEL---------------I----EKMPELKENP-FKRRICEVFSEDGR--- 85 (189)
T ss_pred HHHHHHHhCcccccc-cccCCCCCceeecHHH---------------H----hhChhhhcCh-HHHHHHHHhccCCC---
Confidence 34443355443 554 4567889984455432 2 1224588887 89999999987531
Q ss_pred CChhhhhhcCCCChhHH-HHHHHHHcCChhccccc-CC---CCC-cccH-HHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q psy2882 664 LNIDEELYNNFISKKDN-LKLAILRSMSPKKLSNV-NF---CFE-NKKL-EELIFLYRARNFIETLSYKELKRWKKYRIS 736 (1428)
Q Consensus 664 ~d~d~~lY~gF~s~~D~-~~~~~~~~~~~~~l~~~-~~---~f~-D~Rl-~~l~fr~~arn~p~~L~~~e~~~w~~~~~~ 736 (1428)
|=.|-.|- ..+.-|..+-|.+|... ++ .|+ |.=+ .+=|..-..+--.+-||++|-+.. |.+
T Consensus 86 ---------GnlsfddFlDmfSV~sE~APrdlK~~YAFkIYDfd~D~~i~~~DL~~~l~~lTr~eLs~eEv~~i---~ek 153 (189)
T KOG0038|consen 86 ---------GNLSFDDFLDMFSVFSEMAPRDLKAKYAFKIYDFDGDEFIGHDDLEKTLTSLTRDELSDEEVELI---CEK 153 (189)
T ss_pred ---------CcccHHHHHHHHHHHHhhChHHhhhhheeEEeecCCCCcccHHHHHHHHHHHhhccCCHHHHHHH---HHH
Confidence 22222221 22334555666665432 11 121 1110 011112222333456888876543 333
Q ss_pred Hc---ccCCCccccHHHHHHHHH
Q psy2882 737 RF---YNKKNNLYNINMFYLEIE 756 (1428)
Q Consensus 737 rl---~~~~~~~~~~~~~~~~i~ 756 (1428)
-+ ..++.|.+++.+|..-|.
T Consensus 154 vieEAD~DgDgkl~~~eFe~~i~ 176 (189)
T KOG0038|consen 154 VIEEADLDGDGKLSFAEFEHVIL 176 (189)
T ss_pred HHHHhcCCCCCcccHHHHHHHHH
Confidence 33 222336778888866553
No 259
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=20.27 E-value=1.2e+02 Score=32.67 Aligned_cols=40 Identities=28% Similarity=0.311 Sum_probs=29.9
Q ss_pred hHHHhhhccCCcEEEEeeCCCCCCCCHHHHHHHHHcCCeEEEcC
Q psy2882 1360 KDFIHISKFNPSVVILGTGNIQHFIHPKLTYILTQKNIGIECMN 1403 (1428)
Q Consensus 1360 e~l~~ll~~~pevliiGTG~~~~~~~~~~~~~l~~~GI~vE~M~ 1403 (1428)
-+++.++..+||++|...+ +.+.++.+.|++.||.+-+++
T Consensus 60 ~n~E~ll~l~PDlii~~~~----~~~~~~~~~l~~~gIpvv~i~ 99 (186)
T cd01141 60 LNVELIVALKPDLVILYGG----FQAQTILDKLEQLGIPVLYVN 99 (186)
T ss_pred CCHHHHhccCCCEEEEecC----CCchhHHHHHHHcCCCEEEeC
Confidence 4677778889999887433 223368899999999887775
Done!