Query psy7894
Match_columns 1006
No_of_seqs 555 out of 2070
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 21:33:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7894hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2206|consensus 100.0 3.1E-86 6.7E-91 748.3 30.8 645 20-928 4-660 (687)
2 PRK10829 ribonuclease D; Provi 100.0 4.5E-55 9.6E-60 492.5 38.3 337 248-609 2-339 (373)
3 TIGR01388 rnd ribonuclease D. 100.0 1.5E-50 3.3E-55 456.3 39.2 362 251-640 1-364 (367)
4 COG0349 Rnd Ribonuclease D [Tr 100.0 2E-49 4.4E-54 438.2 35.2 337 252-613 1-338 (361)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 2.8E-29 6.1E-34 252.7 17.2 157 258-414 2-161 (161)
6 cd06146 mut-7_like_exo DEDDy 3 100.0 4.3E-28 9.2E-33 251.8 18.4 165 249-413 1-192 (193)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.5E-26 3.3E-31 233.3 18.0 162 252-413 1-169 (170)
8 cd06148 Egl_like_exo DEDDy 3'- 99.9 1.5E-26 3.2E-31 240.8 14.6 158 261-419 3-180 (197)
9 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 7.6E-26 1.6E-30 225.9 17.4 169 249-417 1-176 (176)
10 cd06147 Rrp6p_like_exo DEDDy 3 99.8 1.4E-19 3.1E-24 186.8 20.8 189 245-433 1-190 (192)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 2.7E-19 5.8E-24 180.3 20.5 162 258-420 2-164 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.8 1.9E-18 4.1E-23 171.1 19.2 166 250-416 2-171 (172)
13 PRK05755 DNA polymerase I; Pro 99.7 9.3E-16 2E-20 191.3 27.2 171 247-419 294-472 (880)
14 PF08066 PMC2NT: PMC2NT (NUC01 99.7 6.2E-18 1.3E-22 156.6 2.4 82 33-119 1-91 (91)
15 cd00007 35EXOc 3'-5' exonuclea 99.7 1.8E-15 3.8E-20 147.2 15.4 146 270-415 2-154 (155)
16 cd09018 DEDDy_polA_RNaseD_like 99.6 1.6E-15 3.5E-20 148.3 13.9 143 270-413 1-149 (150)
17 cd06140 DNA_polA_I_Bacillus_li 99.6 1.1E-14 2.3E-19 147.7 17.6 152 268-420 3-160 (178)
18 PRK14975 bifunctional 3'-5' ex 99.6 1.3E-14 2.8E-19 172.9 18.5 142 248-419 2-147 (553)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.5 8.4E-13 1.8E-17 134.6 18.4 151 266-418 3-172 (193)
20 PF00570 HRDC: HRDC domain Blo 99.4 1.1E-12 2.4E-17 114.1 6.5 68 466-533 1-68 (68)
21 smart00341 HRDC Helicase and R 99.3 4.4E-12 9.4E-17 113.6 9.5 77 464-540 2-78 (81)
22 COG0749 PolA DNA polymerase I 99.3 6.7E-11 1.4E-15 140.0 15.8 168 250-420 4-184 (593)
23 KOG2207|consensus 99.2 1.7E-11 3.6E-16 143.0 8.9 172 246-417 389-586 (617)
24 PF00570 HRDC: HRDC domain Blo 99.2 2.5E-11 5.4E-16 105.6 6.4 68 573-640 1-68 (68)
25 KOG2206|consensus 99.2 3.7E-11 7.9E-16 139.3 8.4 83 569-651 402-484 (687)
26 TIGR00593 pola DNA polymerase 99.2 1.2E-09 2.6E-14 136.4 21.5 165 249-419 304-480 (887)
27 smart00341 HRDC Helicase and R 99.1 2E-10 4.4E-15 102.8 9.5 78 571-648 2-79 (81)
28 TIGR01388 rnd ribonuclease D. 98.9 2E-09 4.3E-14 123.0 8.9 82 568-650 204-285 (367)
29 PRK10829 ribonuclease D; Provi 98.9 2.1E-09 4.6E-14 122.8 8.9 83 567-650 207-289 (373)
30 cd06128 DNA_polA_exo DEDDy 3'- 98.9 3.4E-08 7.3E-13 98.1 14.3 140 272-413 5-150 (151)
31 COG0349 Rnd Ribonuclease D [Tr 98.4 3.7E-07 8.1E-12 103.2 8.1 81 569-650 205-285 (361)
32 TIGR01389 recQ ATP-dependent D 98.3 1.2E-06 2.6E-11 105.8 8.5 71 465-535 520-590 (591)
33 TIGR01389 recQ ATP-dependent D 97.9 2E-05 4.3E-10 95.4 8.6 70 573-642 521-590 (591)
34 KOG4373|consensus 97.8 5.4E-05 1.2E-09 84.3 8.1 127 283-409 145-281 (319)
35 cd06125 DnaQ_like_exo DnaQ-lik 97.8 0.00013 2.8E-09 68.4 8.9 73 271-353 1-83 (96)
36 PRK11057 ATP-dependent DNA hel 97.5 0.00021 4.5E-09 87.2 8.5 73 465-537 531-603 (607)
37 PLN03137 ATP-dependent DNA hel 97.2 0.0008 1.7E-08 85.9 8.1 70 467-536 1029-1100(1195)
38 PRK06063 DNA polymerase III su 97.0 0.013 2.7E-07 66.4 15.1 134 268-420 15-183 (313)
39 PRK06310 DNA polymerase III su 97.0 0.012 2.5E-07 64.6 14.3 132 265-416 4-174 (250)
40 cd06144 REX4_like DEDDh 3'-5' 96.9 0.0048 1E-07 62.3 9.9 82 309-409 67-151 (152)
41 PRK07740 hypothetical protein; 96.9 0.025 5.5E-07 61.8 15.8 92 310-420 132-230 (244)
42 PRK11057 ATP-dependent DNA hel 96.9 0.0023 4.9E-08 78.3 8.4 73 572-644 531-603 (607)
43 PRK06807 DNA polymerase III su 96.8 0.017 3.6E-07 65.5 14.2 129 268-418 8-174 (313)
44 cd06137 DEDDh_RNase DEDDh 3'-5 96.8 0.012 2.6E-07 60.0 11.4 80 312-409 76-160 (161)
45 PRK07942 DNA polymerase III su 96.7 0.036 7.9E-07 60.1 15.3 136 267-420 5-184 (232)
46 PRK08517 DNA polymerase III su 96.7 0.027 6E-07 62.1 14.3 133 265-418 65-233 (257)
47 cd06149 ISG20 DEDDh 3'-5' exon 96.7 0.013 2.8E-07 59.7 10.5 84 309-409 67-156 (157)
48 cd06131 DNA_pol_III_epsilon_Ec 96.6 0.035 7.5E-07 56.2 13.0 86 310-412 72-166 (167)
49 cd06145 REX1_like DEDDh 3'-5' 96.5 0.027 5.8E-07 56.9 11.6 82 310-409 66-149 (150)
50 PRK05711 DNA polymerase III su 96.4 0.061 1.3E-06 58.9 14.5 89 310-415 77-175 (240)
51 TIGR01298 RNaseT ribonuclease 96.4 0.064 1.4E-06 56.8 14.3 83 322-420 106-196 (200)
52 TIGR00573 dnaq exonuclease, DN 96.4 0.03 6.6E-07 59.9 12.0 135 265-419 4-180 (217)
53 TIGR01405 polC_Gram_pos DNA po 96.4 0.041 8.9E-07 72.1 14.9 134 266-420 188-359 (1213)
54 COG0514 RecQ Superfamily II DN 96.4 0.0064 1.4E-07 73.7 7.1 71 466-536 517-587 (590)
55 PRK07883 hypothetical protein; 96.3 0.033 7.2E-07 67.7 13.2 137 263-420 10-186 (557)
56 TIGR01406 dnaQ_proteo DNA poly 96.3 0.053 1.2E-06 58.6 13.4 88 310-414 73-170 (225)
57 PRK09145 DNA polymerase III su 96.3 0.087 1.9E-06 55.6 14.6 137 258-413 19-198 (202)
58 PRK05168 ribonuclease T; Provi 96.1 0.18 3.9E-06 53.9 15.7 147 258-420 7-205 (211)
59 PLN03137 ATP-dependent DNA hel 96.1 0.014 3E-07 75.2 8.2 72 573-644 1028-1101(1195)
60 smart00479 EXOIII exonuclease 95.9 0.14 3E-06 51.2 13.0 91 309-417 70-168 (169)
61 PRK05601 DNA polymerase III su 95.8 0.12 2.5E-06 59.9 13.6 136 265-412 43-245 (377)
62 PRK06309 DNA polymerase III su 95.8 0.15 3.2E-06 55.4 13.7 129 269-417 3-167 (232)
63 PRK09146 DNA polymerase III su 95.8 0.21 4.5E-06 54.7 14.9 132 267-417 46-228 (239)
64 cd05160 DEDDy_DNA_polB_exo DED 95.8 0.13 2.8E-06 53.7 12.9 99 310-409 67-198 (199)
65 PRK07246 bifunctional ATP-depe 95.8 0.13 2.9E-06 65.3 15.2 131 268-420 7-174 (820)
66 cd06127 DEDDh DEDDh 3'-5' exon 95.8 0.14 3E-06 49.8 12.2 83 309-409 69-158 (159)
67 TIGR01407 dinG_rel DnaQ family 95.6 0.22 4.8E-06 63.5 16.0 92 310-420 71-169 (850)
68 KOG2405|consensus 95.4 0.0074 1.6E-07 68.8 2.1 127 286-415 212-360 (458)
69 COG2176 PolC DNA polymerase II 95.4 0.046 1E-06 69.7 9.1 135 265-420 418-590 (1444)
70 cd06134 RNaseT DEDDh 3'-5' exo 95.4 0.34 7.3E-06 50.9 14.2 78 322-415 103-188 (189)
71 PF13482 RNase_H_2: RNase_H su 95.2 0.05 1.1E-06 54.8 7.2 141 271-412 1-163 (164)
72 cd06136 TREX1_2 DEDDh 3'-5' ex 95.2 0.25 5.5E-06 51.3 12.5 80 311-409 86-174 (177)
73 cd06130 DNA_pol_III_epsilon_li 95.1 0.52 1.1E-05 46.8 13.8 81 309-409 67-154 (156)
74 cd05780 DNA_polB_Kod1_like_exo 94.9 0.37 8E-06 50.7 12.6 103 309-412 59-195 (195)
75 PRK08074 bifunctional ATP-depe 94.8 0.45 9.8E-06 61.4 15.7 92 310-420 75-173 (928)
76 KOG2249|consensus 94.3 0.32 7E-06 53.8 10.7 131 269-419 106-269 (280)
77 PRK00448 polC DNA polymerase I 93.8 0.39 8.4E-06 64.3 12.1 92 310-420 490-588 (1437)
78 cd06143 PAN2_exo DEDDh 3'-5' e 93.7 0.21 4.6E-06 52.3 7.8 78 312-409 94-173 (174)
79 KOG2405|consensus 93.6 0.0087 1.9E-07 68.2 -2.9 120 284-404 73-215 (458)
80 PRK06195 DNA polymerase III su 93.4 1.3 2.9E-05 50.1 14.2 89 310-418 71-166 (309)
81 COG0514 RecQ Superfamily II DN 93.3 0.14 3.1E-06 62.4 6.6 71 573-643 517-587 (590)
82 PRK09182 DNA polymerase III su 92.2 2.2 4.7E-05 48.3 13.5 83 311-413 112-198 (294)
83 PRK07247 DNA polymerase III su 92.2 1.7 3.6E-05 46.3 12.0 86 309-415 74-168 (195)
84 cd05785 DNA_polB_like2_exo Unc 91.4 1.2 2.7E-05 47.6 10.1 139 268-409 9-206 (207)
85 PRK07983 exodeoxyribonuclease 90.5 4 8.7E-05 44.2 13.0 77 322-414 75-152 (219)
86 PRK11779 sbcB exonuclease I; P 87.7 7.9 0.00017 46.8 14.0 88 311-415 83-197 (476)
87 PF11408 Helicase_Sgs1: Sgs1 R 87.3 1.5 3.3E-05 40.6 6.0 56 469-524 8-63 (80)
88 COG0847 DnaQ DNA polymerase II 85.3 13 0.00027 40.2 12.9 132 268-415 13-181 (243)
89 PF09281 Taq-exonuc: Taq polym 83.6 3.2 7E-05 41.7 6.6 69 330-416 70-138 (138)
90 cd06133 ERI-1_3'hExo_like DEDD 82.9 25 0.00055 35.5 13.2 88 309-412 78-175 (176)
91 cd05784 DNA_polB_II_exo DEDDy 82.9 7.7 0.00017 41.3 9.7 98 310-410 55-193 (193)
92 cd05781 DNA_polB_B3_exo DEDDy 81.5 25 0.00055 37.1 12.9 141 269-411 4-187 (188)
93 KOG1275|consensus 78.9 1.2 2.7E-05 56.1 2.4 86 316-420 1009-1095(1118)
94 cd05782 DNA_polB_like1_exo Unc 78.4 17 0.00037 39.0 10.6 129 279-410 45-207 (208)
95 cd05779 DNA_polB_epsilon_exo D 77.9 32 0.00069 37.1 12.4 98 310-410 77-204 (204)
96 PF11408 Helicase_Sgs1: Sgs1 R 74.7 9.4 0.0002 35.6 6.3 69 574-642 6-76 (80)
97 cd05783 DNA_polB_B1_exo DEDDy 73.6 82 0.0018 33.9 14.2 97 309-410 76-202 (204)
98 PRK06722 exonuclease; Provisio 72.4 42 0.00092 38.0 12.1 87 309-413 80-178 (281)
99 COG3359 Predicted exonuclease 70.2 84 0.0018 35.2 13.2 149 269-418 99-271 (278)
100 PRK07748 sporulation inhibitor 66.3 31 0.00068 36.7 9.1 91 309-416 82-180 (207)
101 KOG3657|consensus 66.3 15 0.00033 46.5 7.5 98 322-420 242-387 (1075)
102 cd06135 Orn DEDDh 3'-5' exonuc 65.0 96 0.0021 32.1 12.2 40 311-350 80-127 (173)
103 KOG2248|consensus 64.1 28 0.00061 41.1 8.8 84 311-412 285-371 (380)
104 PRK05762 DNA polymerase II; Re 61.6 90 0.002 40.2 13.4 100 310-412 207-348 (786)
105 cd06138 ExoI_N N-terminal DEDD 61.5 30 0.00064 36.1 7.7 81 311-408 74-181 (183)
106 PF00929 RNase_T: Exonuclease; 56.1 7.3 0.00016 37.8 2.0 82 311-409 74-164 (164)
107 PRK00247 putative inner membra 48.0 31 0.00068 41.3 5.8 30 786-815 319-348 (429)
108 PRK05359 oligoribonuclease; Pr 45.1 3.9E+02 0.0084 28.1 12.9 36 324-359 101-143 (181)
109 PRK00247 putative inner membra 36.6 77 0.0017 38.1 6.7 23 804-826 348-370 (429)
110 KOG2002|consensus 36.0 56 0.0012 42.5 5.7 12 888-899 947-958 (1018)
111 KOG2002|consensus 34.8 56 0.0012 42.4 5.4 11 495-505 517-527 (1018)
112 cd05777 DNA_polB_delta_exo DED 24.9 89 0.0019 33.9 4.3 67 347-413 153-224 (230)
113 KOG4364|consensus 23.1 60 0.0013 40.6 2.7 8 892-899 396-403 (811)
114 PF04857 CAF1: CAF1 family rib 22.4 1.8E+02 0.0038 32.3 6.1 53 319-371 147-214 (262)
115 PF03293 Pox_RNA_pol: Poxvirus 21.8 88 0.0019 32.1 3.2 50 953-1002 68-124 (160)
116 cd05778 DNA_polB_zeta_exo inac 20.0 1E+02 0.0022 33.7 3.5 64 346-409 161-230 (231)
No 1
>KOG2206|consensus
Probab=100.00 E-value=3.1e-86 Score=748.28 Aligned_cols=645 Identities=33% Similarity=0.504 Sum_probs=519.8
Q ss_pred ccHHHHHHHHHHHHHHHHhhhcCCCCCcccccccccCCCCCCc---cchHHHHHHHHHHHHHhcccCCCCC--ccccccc
Q psy7894 20 KTFDVLVQNAYKSIVKCTKTAQSFPSTHENSLLIASPNYISGV---AGTSDKVMTLVDSLLKTQNISKSMS--KLYLEGQ 94 (1006)
Q Consensus 20 ~~~~~~~~~~~~~~v~~~r~s~~lp~~~~d~~f~~s~~~~~~f---~~~~~rll~~~~~ll~~~~~~~~~~--~~d~~~~ 94 (1006)
...+.|++.+..+++.+|+. ||+||++ ||+| +..++|++.+|+.+..++|+.++.- .+|+++.
T Consensus 4 ~~~ds~~k~~~~s~~~~t~~---------D~~fY~s---f~~F~~~~~~~~rl~~~mn~v~~s~~~~~~~~d~~~~~~~~ 71 (687)
T KOG2206|consen 4 ENPDSLVKRVINSVRAATSL---------DYDFYYS---FPGFSKLKSKADRLADMMNEVILSIGCHSESFDRPEDIEDL 71 (687)
T ss_pred ccHHHHHHHHhhccccceec---------cceeecc---CchhhhcchhHHHHHHHHHHHHHhhhccccccCCchhHHHH
Confidence 34556666665555543332 9999999 9999 8999999999999999999988762 2899999
Q ss_pred chhhhhhhHHHHhhhchhhhhhcCCCCCCCCCCCCcccccccccccccccchhhhcccccccccccccccCCCCCCCccc
Q psy7894 95 KDILTEANDKLLESINTRIDVMAGTKTPSVLPSQPKIVKESWNKNAKASNVWQEVHDNKKKSANWFMLNKGAVEIERPQL 174 (1006)
Q Consensus 95 ~~~v~~~~D~llE~~d~~lDe~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~kPQ~ 174 (1006)
|+++++++|.|+|++|++|||+++.++..... ..++|++... + +..+ +..+|.|||+
T Consensus 72 ~d~l~~~~D~i~Er~d~~lDe~k~~~k~e~~~-----~~s~~~r~fs---------G-Ka~s--------p~~~l~kpq~ 128 (687)
T KOG2206|consen 72 WDNLGNANDNILERFDHLLDELKRARKSESRG-----SPSEYDREFS---------G-KAKS--------PTMNLLKPQV 128 (687)
T ss_pred HHHHHhhhhHHHHHhcchHHHHHhhhhccccC-----Chhhhhhhcc---------c-cccC--------ccccccchHH
Confidence 99999999999999999999999998863211 1144553321 1 1111 1578999999
Q ss_pred ccCccCCCCCCCCCcccCCCCCCCCChhhhhhhccc-cccccCCCcHhhhccCCCCccccccCCCCcCCCCCCCCcEEeC
Q psy7894 175 QFKVKVDNSYEQLFEPKLKEKPNALKPLAILLEKYD-AIESFCHPYEYELDLYVPKEDFLKCEEPKQALPLSDTPLMMIT 253 (1006)
Q Consensus 175 ~F~~~vDNs~~~pf~p~l~~Kpna~~pl~~~~~~~~-~~~~~~HPYe~Ei~~~~~p~~~~~~~~p~~~~p~~~t~~~lId 253 (1006)
+|...|||++ +||-|++.+ ...... ....+.|||++|+.+|.+++.+++..+|..+.+++.+++.||+
T Consensus 129 ~f~~~idn~~-~pf~~~~~~----------~vEr~e~~~~~~~hpye~e~~~f~~~~~~le~~~~~~~~~le~T~~~~I~ 197 (687)
T KOG2206|consen 129 RFVEGIDNLH-HPFCSMLAS----------EVERLEDRPREVQHPYEDEERHFRQIDKQLEEGEPRKSSPLEITPKVWIC 197 (687)
T ss_pred HHhhcccccc-CCchhhhhh----------hhhchhhcchhccCcchhhhhhhcccchhhhcccccCCCcccccCceeee
Confidence 9999999996 999999864 111122 3456999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHH
Q psy7894 254 EPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDI 333 (1006)
Q Consensus 254 T~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl 333 (1006)
+..+|.++.+.|....++|+|+|+|++|+|.|.+|||||+|++++||||++.+++.++.|+++|+||+|+||+||+..|+
T Consensus 198 t~~el~~l~~~l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l~~~i~~l~e~fsdp~ivkvfhgaD~di 277 (687)
T KOG2206|consen 198 TLGELEALPEILDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKLRDHIGILNEVFSDPGIVKVFHGADTDI 277 (687)
T ss_pred chHHHHHHHHHHhhhhhhhhhccccchhhhcCceeEEEeeccchhheehhHHHHHHHHHhhhhccCCCeEEEEecCccch
Confidence 99999999999999999999999999999999999999999999999999999989999999999999999999999999
Q ss_pred HHHHHHhCCccCeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 334 KWLQKDFGLYVVGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 334 ~~L~rd~GI~~~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
.|||++|||+++|+|||..|+++||.+++||++|++.|||+..+|.+|++||++|||+.+|+.||+.|+|||++||+.|+
T Consensus 278 iwlqrdfgiyvvnLfdt~~a~r~L~~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr 357 (687)
T KOG2206|consen 278 IWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLR 357 (687)
T ss_pred hhhhccceEEEEechhhHHHHHHhCCCcccHHHHHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCchhHHHHHHHhhHHHHhhhcCCCCCChhhhHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCCCCCcccC
Q psy7894 414 LDLSAAAHGKQNLVLSTFTNSRNICKLKYEKPVFNEEGYMNIFRSHALLNNQQKYALRELYKWRDRIARDKDESTGYVLP 493 (1006)
Q Consensus 414 ~eL~e~g~~~~~~l~~v~~es~~l~l~~ye~~~~~~~~~~~l~~k~~~L~~~qlavlr~L~~WRD~~AR~~Dep~~~VL~ 493 (1006)
.+|.+.++++. -++.++..+|...|.++.+...+|+.++.....+++.|+.+|++|++|||.+||.+|||++||||
T Consensus 358 ~el~~~a~~~~----~~~~~~~d~c~~~~~k~~~~~~sy~~v~~~q~~ln~~q~~~l~~L~~wRd~iARaeDES~~yVlp 433 (687)
T KOG2206|consen 358 KELKRLAKGRA----VTYSESRDMCTNGYKKKTFCTKSYLEVEDIQSRLNSSQLDVLRALLRWRDFIARAEDESVHYVLP 433 (687)
T ss_pred HHHHHHhcccc----cccchhhhhhhcceecccCCCcchHhHHHHHhccchhHHHHHHHHHHHHHHHHhhccCCCceecc
Confidence 99998887654 34558889999999999999999999988777899999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHhhcCCCCCccccCCccchhhhhhcccCCCCCCCChhH
Q psy7894 494 NHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQSLTKPVEKLQPSLDGMKKKQQQQVSPPHDSNNQQ 573 (1006)
Q Consensus 494 d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar~~p~~~~i~~~~ps~~gir~~q~q~~~pP~ll~~~Q 573 (1006)
|++|+.||+.+|.+..+|++||++.+++|++|..+++.+|..|+.....
T Consensus 434 N~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~~ii~~a~~~~l~------------------------------- 482 (687)
T KOG2206|consen 434 NDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFLYIIRSAGRGFLL------------------------------- 482 (687)
T ss_pred cHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHHHHHHHHhhhhhh-------------------------------
Confidence 9999999999999999999999999999999999999999887643211
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcCCCCCCcc
Q psy7894 574 KYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQPLTKPVE 653 (1006)
Q Consensus 574 lavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~~~~~~~~ 653 (1006)
+ ... |.-.+ ..|..
T Consensus 483 ----~-----------------------------------------------------------~~~--a~g~~-~sp~~ 496 (687)
T KOG2206|consen 483 ----Q-----------------------------------------------------------NLT--ASGRK-SSPTK 496 (687)
T ss_pred ----h-----------------------------------------------------------chh--hccCC-CCCcc
Confidence 0 000 00001 11110
Q ss_pred ccCCccccccccccccccCCCCCcccccccCCCCCCCCCCcccCCCCCccCCcCccccceeEEeeecccccccc-chhhH
Q psy7894 654 KLQPSLDGMKKKKQQQQVSPPHDSMDCLNYKGLPPVFPNNIICAPSNTHLSSYDPQDKKIAQIGLFFEDKMKIG-SNKYQ 732 (1006)
Q Consensus 654 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~i~~~~~~~~~~~-~~~~~ 732 (1006)
..++ -.+..+.|||.+.-- . ..+.+ -++|++++.... --.+.
T Consensus 497 -----v~~~----l~e~i~~~~d~~e~~--s---------s~sl~-----------------~~~~~~~~k~ss~~g~l~ 539 (687)
T KOG2206|consen 497 -----VDEI----LIEPISEPHDTGERA--S---------SSSLE-----------------KSLVNESKKSSSGLGKLL 539 (687)
T ss_pred -----hhhh----hhccccccccccccc--c---------ccccc-----------------hhhhcccccccccccccc
Confidence 0001 012344566621111 0 00001 034444443332 12233
Q ss_pred hhhhhhhhccCcccccccchhhhhhhhhhhhhhhHHhhhhcccCCCcccccCCCcccchhHHHHHhhhHHHHHHHHHHHH
Q psy7894 733 KIKLKTSRFETPYQRFLKSKEYAKAIQEKVDKENAEQKKIDALTPQVKTEPEENVKITQEPVVLKQIKSEEKEKVEMEKE 812 (1006)
Q Consensus 733 k~~~~~~~~~~p~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 812 (1006)
|.+..++.+|+++++ | +++| .+..+++...+|+..+++
T Consensus 540 K~~~d~~~~ed~~~k----------i-------------------------~~~~-------~~~ra~~~~skk~~~~~~ 577 (687)
T KOG2206|consen 540 KEEHDEEVSEDLPNK----------I-------------------------ETED-------PRIRAQEFKSKKANVDTI 577 (687)
T ss_pred hhhhhHHhhhhhhhh----------h-------------------------cccC-------ccccchhhhccccccchh
Confidence 888888888887766 2 5666 445567788888889999
Q ss_pred HHHHHHHHHHHHhhcCcchhhhhccCcccchhhhhcccccCCCCCCCCCCCCCccchhhhhccccCCCCCCCCCCCCCCC
Q psy7894 813 KRKKILREREEEKEEQPATKKIKVEKPEESNEKTKQHKIKSEPKENDSSKEKPEESNEKTKRHKIKSEPKENDSSKGKSG 892 (1006)
Q Consensus 813 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 (1006)
+++.. + ..|+++.+ ++++.+ |+++.++++++| |+.....+++++.-+
T Consensus 578 ~~~~~-~----------~~~~~~~e---e~~~v~------~~~r~t~~e~~~--------~~~lv~~k~k~~~d~----- 624 (687)
T KOG2206|consen 578 KFESE-K----------LVVKVKLE---EESTVK------SESRVTSSEIDK--------KILLVVKKDKDKKDE----- 624 (687)
T ss_pred hhccc-c----------cccccchh---hhhccc------cCCCcCcccccc--------hhhhccccccccccc-----
Confidence 98885 2 77888887 555544 999999999999 888888777643222
Q ss_pred CCcccccccccccccccc--CCCCCcc---cccCCCCcccc
Q psy7894 893 GTISTVDFSKVNYNKYMA--KPGKSNQ---KKKGKGGKQNK 928 (1006)
Q Consensus 893 ~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~~~~~~ 928 (1006)
+|+||.+++|+|.+ +++ |+| |.|.+.+|++.
T Consensus 625 ----s~e~sts~~ka~~~~~~s~-s~~~~~~~~~p~~~~~~ 660 (687)
T KOG2206|consen 625 ----SKEKSTSDKKAFDSSSKSP-SKQPEQNNQQPKKKEVD 660 (687)
T ss_pred ----chhhccchHhHhhccccCc-ccCCccccccccccccc
Confidence 45999999999999 444 444 77777766543
No 2
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=4.5e-55 Score=492.50 Aligned_cols=337 Identities=22% Similarity=0.317 Sum_probs=302.6
Q ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeec
Q psy7894 248 PLMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFH 327 (1006)
Q Consensus 248 ~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~H 327 (1006)
.|.+|+|+++|.++|+.+..++.+||||||++.++|++.+|||||++++++||||++++. ++..|+++|+|++|+||+|
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~-d~~~L~~ll~~~~ivKV~H 80 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGIT-DWSPFKALLRDPQVTKFLH 80 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCcc-chHHHHHHHcCCCeEEEEe
Confidence 478999999999999999999999999999999999999999999999999999999884 6899999999999999999
Q ss_pred chhhHHHHHHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHH
Q psy7894 328 GADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLL 406 (1006)
Q Consensus 328 gak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL 406 (1006)
++++|+.+|++.+|+.+.++|||++|+++||.+ ++||+.|+++|||+.++|+++++||+.||||++|+.||+.||+||+
T Consensus 81 ~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~ 160 (373)
T PRK10829 81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160 (373)
T ss_pred ChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 999999999899999999999999999999987 6999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCchhHHHHHHHhhHHHHhhhcCCCCCChhhhHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCC
Q psy7894 407 YVYDCMKLDLSAAAHGKQNLVLSTFTNSRNICKLKYEKPVFNEEGYMNIFRSHALLNNQQKYALRELYKWRDRIARDKDE 486 (1006)
Q Consensus 407 ~Lyd~L~~eL~e~g~~~~~~l~~v~~es~~l~l~~ye~~~~~~~~~~~l~~k~~~L~~~qlavlr~L~~WRD~~AR~~De 486 (1006)
.||+.|..+|.+.| ++.|+.++|+.+|..+.. ...++..|.++.+ ...|+++|++++++|++|||++||+.|+
T Consensus 161 ~l~~~L~~~L~~~g-----~~~w~~ee~~~l~~~~~~-~~~~~~~~~~ik~-~~~L~~~~lavl~~L~~WRe~~Ar~~d~ 233 (373)
T PRK10829 161 PIAAKLMAETEAAG-----WLPAALDECRLLCQRRQE-VLAPEEAYRDITN-AWQLRTRQLACLQLLADWRLRKARERDL 233 (373)
T ss_pred HHHHHHHHHHHHcC-----cHHHHHHHHHHHHhcccc-CCChHHHHHHhcc-ccCCCHHHHHHHHHHHHHHHHHHHHhCC
Confidence 99999999999765 567888899888865432 1223456777633 2378999999999999999999999999
Q ss_pred CCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHhhcCCCCCccccCCccchhhhhhcccCCCC
Q psy7894 487 STGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQSLTKPVEKLQPSLDGMKKKQQQQVSPP 566 (1006)
Q Consensus 487 p~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar~~p~~~~i~~~~ps~~gir~~q~q~~~pP 566 (1006)
|++|||+|+.|++||+++|++.++|.++ +..+..+|+||.+|+++|++|.+.|....+... ++
T Consensus 234 p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r~~g~~ll~~i~~a~~~~~~~~P~~~----------------~~ 296 (373)
T PRK10829 234 AVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEALPPPV----------------LN 296 (373)
T ss_pred CcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHHhhHHHHHHHHHHHhcCCHhhCCCCC----------------CC
Confidence 9999999999999999999999999998 888899999999999999999988765331111 01
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHH
Q psy7894 567 HDSNNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQ 609 (1006)
Q Consensus 567 ~ll~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~ 609 (1006)
+...+....+++.|+.....+|++.+++++.|+++..|.+++.
T Consensus 297 ~~~~~~~~~~~~~l~~~v~~~a~~~~i~~ellas~~~l~~l~~ 339 (373)
T PRK10829 297 LIDMPGYRKAFKAIKALIQEVSETHGLSAELLASRRQINQLLN 339 (373)
T ss_pred cccChhHHHHHHHHHHHHHHHHHHhCCCHHHhCCHHHHHHHHH
Confidence 1123456889999999999999999999999999999999996
No 3
>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=100.00 E-value=1.5e-50 Score=456.27 Aligned_cols=362 Identities=21% Similarity=0.255 Sum_probs=308.4
Q ss_pred EeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchh
Q psy7894 251 MITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGAD 330 (1006)
Q Consensus 251 lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak 330 (1006)
||+|.++|.++++.|..++.|||||||++.++|++.+|||||++++.+||||++.+ .++..|.++|+|++|.||+|+++
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~-~~~~~L~~lL~d~~i~KV~h~~k 79 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVI-IDWSPLKELLRDESVVKVLHAAS 79 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCc-ccHHHHHHHHCCCCceEEEeecH
Confidence 58999999999999999999999999999999999999999999999999999887 47889999999999999999999
Q ss_pred hHHHHHHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 331 SDIKWLQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 331 ~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
+|+.+|++.+|+.+.++|||++|+|+||++ ++||+.|+++|||+.++|+++.+||..|||+.+|+.||+.||+||+.||
T Consensus 80 ~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~ 159 (367)
T TIGR01388 80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLY 159 (367)
T ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999877888888999999999999986 5899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCchhHHHHHHHhhHHHHhhhcCCCCCChhhhHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy7894 410 DCMKLDLSAAAHGKQNLVLSTFTNSRNICKLKYEKPVFNEEGYMNIFRSHALLNNQQKYALRELYKWRDRIARDKDESTG 489 (1006)
Q Consensus 410 d~L~~eL~e~g~~~~~~l~~v~~es~~l~l~~ye~~~~~~~~~~~l~~k~~~L~~~qlavlr~L~~WRD~~AR~~Dep~~ 489 (1006)
+.|..+|.+.| ++.|+.++|..++..... ...++..|.++.+ ...|++++++++++|++|||.+||+.|+|++
T Consensus 160 ~~L~~~L~~~g-----~~~w~~ee~~~l~~~~~~-~~~~~~~~~~i~~-~~~l~~~~l~~l~~L~~wRe~~A~~~d~p~~ 232 (367)
T TIGR01388 160 AKLMERLEESG-----RLAWLEEECTLLTDRRTY-VVNPEDAWRDIKN-AWQLRPQQLAVLQALAAWREREARERDLPRN 232 (367)
T ss_pred HHHHHHHHHcC-----cHHHHHHHHHHHhccccC-CCChHHHHHHhcc-cccCCHHHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 99999999775 456778888888765322 1234556877643 2378999999999999999999999999999
Q ss_pred cccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHhhcCCCCCccccCCccchhhhhhcccCCCCCCC
Q psy7894 490 YVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQSLTKPVEKLQPSLDGMKKKQQQQVSPPHDS 569 (1006)
Q Consensus 490 ~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar~~p~~~~i~~~~ps~~gir~~q~q~~~pP~ll 569 (1006)
|||+|+.|++||++.|+|.++|.++ ++.+..+|+||++|+++|++|.+.|.+.. |...+ +...
T Consensus 233 ~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r~~~~~l~~~i~~a~~~~~~~~-P~~~~---------------~~~~ 295 (367)
T TIGR01388 233 FVLKEEALWELARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALPEDAL-PQAPL---------------NLMP 295 (367)
T ss_pred eeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHHhhHHHHHHHHHHHhhCCHhhC-CCCCC---------------CCCC
Confidence 9999999999999999999999998 99999999999999999999998876532 11100 0112
Q ss_pred ChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhC-CCChhhhhhcCCCChHHHHhhHHHHHHHH
Q psy7894 570 NNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSI-PRDIQGIFACCNPVPQTVKEHVLDIHAII 640 (1006)
Q Consensus 570 ~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~-P~~l~~L~~~~~~~p~~VR~~g~eLl~lI 640 (1006)
+.....+++.|+.+...+|.+.+++++.|+++..|.+++... +.+.. .......++-+.-|.+++.++
T Consensus 296 ~~~~~~~~~~l~~~~~~~a~~~~i~~~~l~~~~~l~~l~~~~~~~~~~---~~~~~~~gWR~~~~~~~~~~~ 364 (367)
T TIGR01388 296 PPGYKALFKLLKVLVKDVSETLGLASELLASRRQLEQLLAWGWKLKPN---ALPPLLQGWRRELGEEALKNL 364 (367)
T ss_pred ChhHHHHHHHHHHHHHHHHHHhCCCHHHcCCHHHHHHHHHhhcccccc---cccHHHHhhHHHHHHHHHHHh
Confidence 345688999999999999999999999999999999999742 21111 111223455555566666654
No 4
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-49 Score=438.18 Aligned_cols=337 Identities=27% Similarity=0.358 Sum_probs=297.9
Q ss_pred eCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchhh
Q psy7894 252 ITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADS 331 (1006)
Q Consensus 252 IdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~ 331 (1006)
|++.+.++.++..+.+++.||||||++++++|++.+|||||+.++++++||++....++..|..+|.|++|+||||++.+
T Consensus 1 i~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfHaa~~ 80 (361)
T COG0349 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFHAARF 80 (361)
T ss_pred CCchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeeccccc
Confidence 45677899999999999999999999999999999999999999999999998855678899999999999999999999
Q ss_pred HHHHHHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHH
Q psy7894 332 DIKWLQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYD 410 (1006)
Q Consensus 332 Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd 410 (1006)
|+.+|++.||+.+.++|||++|+.++|++ ++||+.||++++|++++|++|.+||+.||||++|++||+.||.||+.||+
T Consensus 81 DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~ 160 (361)
T COG0349 81 DLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYD 160 (361)
T ss_pred cHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999997 89999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCchhHHHHHHHhhHHHHhhhcCCCCCChhhhHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCCCCCc
Q psy7894 411 CMKLDLSAAAHGKQNLVLSTFTNSRNICKLKYEKPVFNEEGYMNIFRSHALLNNQQKYALRELYKWRDRIARDKDESTGY 490 (1006)
Q Consensus 411 ~L~~eL~e~g~~~~~~l~~v~~es~~l~l~~ye~~~~~~~~~~~l~~k~~~L~~~qlavlr~L~~WRD~~AR~~Dep~~~ 490 (1006)
.|.++|.+.| ++.|+.++++.+..+++. ...++.+|.++.. ...+++.++++++.|++|||+.||.+|+|++|
T Consensus 161 ~L~~~L~~~~-----r~~~a~~ef~~l~~r~~~-~~~~~~~w~~i~~-a~~~~p~~la~l~~La~wRe~~Ar~rd~~~~~ 233 (361)
T COG0349 161 KLTEELAREG-----RLEWAEDEFRLLPTRRTY-KVLPEDAWREIKI-AHSLDPRELAVLRELAAWREREARERDLARNF 233 (361)
T ss_pred HHHHHHHHcC-----chHHHHHHHHHhhhcccc-ccChHhHHHHhhh-hhcCChHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 9999999875 455666667666655332 2356778987743 34789999999999999999999999999999
Q ss_pred ccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHhhcCCCCCccccCCccchhhhhhcccCCCCCCCC
Q psy7894 491 VLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQSLTKPVEKLQPSLDGMKKKQQQQVSPPHDSN 570 (1006)
Q Consensus 491 VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar~~p~~~~i~~~~ps~~gir~~q~q~~~pP~ll~ 570 (1006)
||+|+.|+++|+.+|++..+|.++.+... ..|.++..|+.+|.+|+..|....++...+ . .+|
T Consensus 234 vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~~~~~~l~~~~~~a~~~p~~~~p~~~~~-----------~-~~~---- 296 (361)
T COG0349 234 VLKDEALWELARYTPKNLKELDALGLIPK-ERRRHGKLLLALLANALASPESDLPPPPGR-----------L-APP---- 296 (361)
T ss_pred ccchhHHHHHHHhCCCCHHHHHhccCCcc-cchhhhHHHHHHHHHHHhCchhhCCCCCcc-----------c-CCC----
Confidence 99999999999999999999998755444 889999999999999999887543211111 0 111
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCC
Q psy7894 571 NQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPR 613 (1006)
Q Consensus 571 ~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~ 613 (1006)
+...++++.|+.--..+|...++++..+++. .|..|+...+.
T Consensus 297 p~~~~~~~~lk~l~~~~s~~~gv~~e~las~-~l~~l~~~~~~ 338 (361)
T COG0349 297 PGYKAALKALKALLKSVSEKHGVAAELLASR-DLERLLAWGDD 338 (361)
T ss_pred hhHHHHHHHHHHHHHHhhhhcCCcHHHhccH-HHHHHHHccCC
Confidence 4689999999999999999999999999999 99999997733
No 5
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.96 E-value=2.8e-29 Score=252.69 Aligned_cols=157 Identities=34% Similarity=0.545 Sum_probs=147.6
Q ss_pred HHHHHHHHh-cCCeEEEEeeeccCCccCCcEEEEEEEeC-CceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHH
Q psy7894 258 VTQLVSELK-QQQEIAIDLEYHNYRSYQGYTCLMQISTR-DKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKW 335 (1006)
Q Consensus 258 L~~lle~L~-~a~~IAVDtE~~~~rty~g~lcLIQISt~-~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~ 335 (1006)
|.++++.|. ..+.||||+||.+..++.+.+|+|||+++ +.+||||+..++.....|+++|+|++|.||+|+++.|+..
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k~D~~~ 81 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWK 81 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccHHHHHH
Confidence 678999999 99999999999988888899999999999 8999999988765678899999999999999999999999
Q ss_pred HHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHHH
Q psy7894 336 LQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKL 414 (1006)
Q Consensus 336 L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~ 414 (1006)
|++.+|+.+.++|||++|+|++|++ +.||+.|+++|+|+.++|..+++||..|||+++|+.||+.||++++.||+.|++
T Consensus 82 L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 82 LLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred HHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9878999999999999999999985 689999999999999999999999999999999999999999999999999863
No 6
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.96 E-value=4.3e-28 Score=251.80 Aligned_cols=165 Identities=26% Similarity=0.378 Sum_probs=148.9
Q ss_pred cEEeCCHHHHHHHHHH--HhcCCeEEEEeeeccCCcc--CCcEEEEEEEeCCceEEEeCcchh----h-hHHHHHHHHcC
Q psy7894 249 LMMITEPEQVTQLVSE--LKQQQEIAIDLEYHNYRSY--QGYTCLMQISTRDKDYIVDTLKLR----E-DLEVLNEVLTD 319 (1006)
Q Consensus 249 ~~lIdT~e~L~~lle~--L~~a~~IAVDtE~~~~rty--~g~lcLIQISt~~~~yIID~laL~----~-~L~~L~elLed 319 (1006)
+.+|+|++++.+++.. +.....||||+||.+...+ .+.+|+|||++.+.+||||+..++ . ....|+++|+|
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~d 80 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFED 80 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhCC
Confidence 4689999999999999 8899999999999876654 689999999999999999998764 1 24579999999
Q ss_pred CCceeeecchhhHHHHHHHHhCCc------cCeeechHhHHHhCCC------------CCccHHHHHHHHcCCCCCcccc
Q psy7894 320 KNIVKVFHGADSDIKWLQKDFGLY------VVGMFDTHQACKFLPM------------PRQSLAYLLKHYCDVDSDKTFQ 381 (1006)
Q Consensus 320 p~IvKV~Hgak~Dl~~L~rd~GI~------~~nlFDTqlAAyLLg~------------~~~SLa~Lve~yLgv~LdK~~q 381 (1006)
|+|+|||||+++|+.+|+++||+. +.++|||+.+++.++. ..+||+.|++++||+.++|..+
T Consensus 81 ~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q 160 (193)
T cd06146 81 PDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQ 160 (193)
T ss_pred CCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccc
Confidence 999999999999999999999974 5799999998887652 3579999999999999999999
Q ss_pred cccCCCCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 382 LFDWRHRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 382 ~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
++||+.|||+.+|+.|||.||++++.||+.|.
T Consensus 161 ~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 161 CSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999985
No 7
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.94 E-value=1.5e-26 Score=233.27 Aligned_cols=162 Identities=25% Similarity=0.346 Sum_probs=149.4
Q ss_pred eCCHHHHHHHHHHHh-cCCeEEEEeeeccCCc--cCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecc
Q psy7894 252 ITEPEQVTQLVSELK-QQQEIAIDLEYHNYRS--YQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHG 328 (1006)
Q Consensus 252 IdT~e~L~~lle~L~-~a~~IAVDtE~~~~rt--y~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hg 328 (1006)
+++..++..+++.+. ....||||+||.+..+ +.+.+|+|||++++.+||||+..+......|.++|++++|.||+|+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~kv~~~ 80 (170)
T cd06141 1 TDSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80 (170)
T ss_pred CCCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCeeEEEee
Confidence 357788999999998 9999999999988765 7789999999999999999998765556789999999999999999
Q ss_pred hhhHHHHHHHHhCCccCeeechHhHHHhCCCC--CccHHHHHHHHcCCCCC--cccccccCCCCCCChHHHHHHHhchhH
Q psy7894 329 ADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP--RQSLAYLLKHYCDVDSD--KTFQLFDWRHRPLPEPAIQYARTDTHY 404 (1006)
Q Consensus 329 ak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~Ld--K~~q~sDW~~RPLs~eql~YAA~DA~y 404 (1006)
++.|+..|.+.+|+.+.++|||++|+|++++. ..||+.|+.+|+|..++ |..+++||..|||+++|+.|||.||++
T Consensus 81 ~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~ 160 (170)
T cd06141 81 IKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYA 160 (170)
T ss_pred eHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHH
Confidence 99999999879999999999999999999985 47999999999999998 788999999999999999999999999
Q ss_pred HHHHHHHHH
Q psy7894 405 LLYVYDCMK 413 (1006)
Q Consensus 405 LL~Lyd~L~ 413 (1006)
++.||+.|+
T Consensus 161 ~~~l~~~l~ 169 (170)
T cd06141 161 SLELYRKLL 169 (170)
T ss_pred HHHHHHHHh
Confidence 999999985
No 8
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.94 E-value=1.5e-26 Score=240.76 Aligned_cols=158 Identities=34% Similarity=0.439 Sum_probs=142.8
Q ss_pred HHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeC-CceEEEeCcchh--hhHHHHHHHHcCCCceeeecchhhHHHHHH
Q psy7894 261 LVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTR-DKDYIVDTLKLR--EDLEVLNEVLTDKNIVKVFHGADSDIKWLQ 337 (1006)
Q Consensus 261 lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~-~~~yIID~laL~--~~L~~L~elLedp~IvKV~Hgak~Dl~~L~ 337 (1006)
+++.|..+..||||+|+.+.+. .|.+|+|||++. +.+||||+..+. .....|+++|++++|.||+||++.|+.+|+
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~-~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~ 81 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR-KGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALY 81 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC-CCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHH
Confidence 5677888999999999987765 689999999999 899999998774 246789999999999999999999999998
Q ss_pred HHhCCccCeeechHhHHHhCCCC---------CccHHHHHHHHcCCCCCc--------ccccccCCCCCCChHHHHHHHh
Q psy7894 338 KDFGLYVVGMFDTHQACKFLPMP---------RQSLAYLLKHYCDVDSDK--------TFQLFDWRHRPLPEPAIQYART 400 (1006)
Q Consensus 338 rd~GI~~~nlFDTqlAAyLLg~~---------~~SLa~Lve~yLgv~LdK--------~~q~sDW~~RPLs~eql~YAA~ 400 (1006)
+.+|+.+.++|||++|+|+|++. ..||+.|+++|+|+.++| ..+.+||..|||+++|+.|||.
T Consensus 82 ~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~ 161 (197)
T cd06148 82 HQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAAL 161 (197)
T ss_pred HhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHH
Confidence 89999999999999999999763 269999999999998864 4577999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHh
Q psy7894 401 DTHYLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 401 DA~yLL~Lyd~L~~eL~e~ 419 (1006)
||+||+.||+.|...|.+.
T Consensus 162 Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 162 DVLCLLPLYYAMLDALISK 180 (197)
T ss_pred HHHhHHHHHHHHHHHhhhh
Confidence 9999999999999999875
No 9
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.94 E-value=7.6e-26 Score=225.87 Aligned_cols=169 Identities=35% Similarity=0.582 Sum_probs=153.5
Q ss_pred cEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCc--cCCcEEEEEEEeCCceEEEeCcchhhh--HHHHHHHHcCCCcee
Q psy7894 249 LMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRS--YQGYTCLMQISTRDKDYIVDTLKLRED--LEVLNEVLTDKNIVK 324 (1006)
Q Consensus 249 ~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rt--y~g~lcLIQISt~~~~yIID~laL~~~--L~~L~elLedp~IvK 324 (1006)
|++|+|.+++.+++..+...+.+|+|+|+.+... ..+.+++||+++++.+|++|+...... +..|+++|+|++|.|
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i~k 80 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNIIK 80 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTSEE
T ss_pred CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCccE
Confidence 6789999999999999999999999999998776 677899999999999999998776543 789999999999999
Q ss_pred eecchhhHHHHHHHHhCCccCeeechHhHHHhCCCCC-ccHHHHHHHHcC-CCCCcccccccCC-CCCCChHHHHHHHhc
Q psy7894 325 VFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMPR-QSLAYLLKHYCD-VDSDKTFQLFDWR-HRPLPEPAIQYARTD 401 (1006)
Q Consensus 325 V~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~~-~SLa~Lve~yLg-v~LdK~~q~sDW~-~RPLs~eql~YAA~D 401 (1006)
|+||+++|+.+|.+.+|+.+.++|||++|++++++.. +||..|+.+|+| ..++++.+.++|. .+||+++|+.||+.|
T Consensus 81 v~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D 160 (176)
T PF01612_consen 81 VGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQD 160 (176)
T ss_dssp EESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHH
T ss_pred EEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHH
Confidence 9999999999998779999999999999999999976 999999999999 7778889999999 999999999999999
Q ss_pred hhHHHHHHHHHHHHHH
Q psy7894 402 THYLLYVYDCMKLDLS 417 (1006)
Q Consensus 402 A~yLL~Lyd~L~~eL~ 417 (1006)
|++++.||+.|.++|+
T Consensus 161 ~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 161 AVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHhhC
Confidence 9999999999998873
No 10
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.84 E-value=1.4e-19 Score=186.83 Aligned_cols=189 Identities=61% Similarity=1.055 Sum_probs=154.5
Q ss_pred CCCCcEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCcee
Q psy7894 245 SDTPLMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVK 324 (1006)
Q Consensus 245 ~~t~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvK 324 (1006)
+++++.||++.+++..+++.+...+.+++|+|+..+.++.+.++++|+++++++|+||.+........|.++|+++++.|
T Consensus 1 ~~~~~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~k 80 (192)
T cd06147 1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80 (192)
T ss_pred CCCCcEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceE
Confidence 35789999777888887777765668999998777667778999999998877787774333334566899999999999
Q ss_pred eecchhhHHHHHHHHhCCccCeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhH
Q psy7894 325 VFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHY 404 (1006)
Q Consensus 325 V~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~y 404 (1006)
|+|+++.|+.+|.+.+|+.+.++|||++|+|+|++.+++|..|+++|+|..+.|..+.++|..+||+.++..||+.++.+
T Consensus 81 v~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~~~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~ 160 (192)
T cd06147 81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160 (192)
T ss_pred EEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCCcccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHH
Confidence 99999999999944789988777999999999998546999999999998744544566798888899999999999999
Q ss_pred HHHHHHHHHHHHHHhcCC-chhHHHHHHHh
Q psy7894 405 LLYVYDCMKLDLSAAAHG-KQNLVLSTFTN 433 (1006)
Q Consensus 405 LL~Lyd~L~~eL~e~g~~-~~~~l~~v~~e 433 (1006)
++.|++.|..+|+++.+. ..++++.|+..
T Consensus 161 l~~L~~~L~~~L~e~~~~~~~~~~~~~~~~ 190 (192)
T cd06147 161 LLYIYDRLRNELLERANALAPNLLESVLNC 190 (192)
T ss_pred HHHHHHHHHHHHHHhccccchhhhhhhhhh
Confidence 999999999999887542 23566666653
No 11
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.83 E-value=2.7e-19 Score=180.25 Aligned_cols=162 Identities=38% Similarity=0.630 Sum_probs=138.2
Q ss_pred HHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHH
Q psy7894 258 VTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQ 337 (1006)
Q Consensus 258 L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~ 337 (1006)
|.++++.+...+.+++|+|+.+..++.+.++++||++.+.+|+||+... .....|.++|+|+++.||+||++.|+..|+
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~ 80 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELLK 80 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccHHHHHHHH
Confidence 3455555655669999999877666678999999999855888885433 345668899999999999999999999997
Q ss_pred HHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHH
Q psy7894 338 KDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDL 416 (1006)
Q Consensus 338 rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL 416 (1006)
+.+|+...++|||++|+|+|++. +++|..|+++|+|..+.+....++|..+||+..++.||+.|+.+++.|++.|.++|
T Consensus 81 ~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L 160 (178)
T cd06142 81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160 (178)
T ss_pred HHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 77799866789999999999995 47999999999998866655778999999999999999999999999999999999
Q ss_pred HHhc
Q psy7894 417 SAAA 420 (1006)
Q Consensus 417 ~e~g 420 (1006)
.+.+
T Consensus 161 ~e~~ 164 (178)
T cd06142 161 EEEG 164 (178)
T ss_pred HHcC
Confidence 9875
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.80 E-value=1.9e-18 Score=171.08 Aligned_cols=166 Identities=38% Similarity=0.584 Sum_probs=139.0
Q ss_pred EEeCCHHHHHHHHHHHh-cCCeEEEEeeeccCCccCCcEEEEEEEeCC-ceEEEeCcchhhhHHHHHHHHcCCCceeeec
Q psy7894 250 MMITEPEQVTQLVSELK-QQQEIAIDLEYHNYRSYQGYTCLMQISTRD-KDYIVDTLKLREDLEVLNEVLTDKNIVKVFH 327 (1006)
Q Consensus 250 ~lIdT~e~L~~lle~L~-~a~~IAVDtE~~~~rty~g~lcLIQISt~~-~~yIID~laL~~~L~~L~elLedp~IvKV~H 327 (1006)
.+|++.+++..+++.+. ....+++|+|+....++.+.++++|+++.+ .+||++.......+..|.++|+++.+.||+|
T Consensus 2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~kv~~ 81 (172)
T smart00474 2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGH 81 (172)
T ss_pred EEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCceEEEe
Confidence 57888888888777776 566999999987776667899999999644 5676654333223566899999999999999
Q ss_pred chhhHHHHHHHHhCCccCeeechHhHHHhCCCC-C-ccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHH
Q psy7894 328 GADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP-R-QSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYL 405 (1006)
Q Consensus 328 gak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~-~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yL 405 (1006)
|++.|+.+|. .+|+.+.++|||++|+|+|++. . ++|+.++..|+|..+++..+..+|..+|+...++.||+.||+++
T Consensus 82 d~k~~~~~L~-~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~ 160 (172)
T smart00474 82 NAKFDLHVLA-RFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADAL 160 (172)
T ss_pred chHHHHHHHH-HCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHH
Confidence 9999999996 4999988889999999999884 2 79999999999988655445568988899999999999999999
Q ss_pred HHHHHHHHHHH
Q psy7894 406 LYVYDCMKLDL 416 (1006)
Q Consensus 406 L~Lyd~L~~eL 416 (1006)
+.|++.|.++|
T Consensus 161 ~~L~~~l~~~l 171 (172)
T smart00474 161 LRLYEKLEKEL 171 (172)
T ss_pred HHHHHHHHHHh
Confidence 99999998876
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=99.71 E-value=9.3e-16 Score=191.27 Aligned_cols=171 Identities=22% Similarity=0.230 Sum_probs=144.7
Q ss_pred CCcEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCc-eEEEeCcchh-hhHHHHHHHHcCCCcee
Q psy7894 247 TPLMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDK-DYIVDTLKLR-EDLEVLNEVLTDKNIVK 324 (1006)
Q Consensus 247 t~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~-~yIID~laL~-~~L~~L~elLedp~IvK 324 (1006)
..|.+|++.++|..+++.+..+..+++|+|+.+.+++.+.+|+||+++.++ .|+|++..+. ..+..|.++|+++.+.|
T Consensus 294 ~~~~~I~~~~~L~~~l~~l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~k 373 (880)
T PRK05755 294 EDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAIKK 373 (880)
T ss_pred CceEEeCCHHHHHHHHHHhhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCCcE
Confidence 457889999999999999998999999999999999999999999999876 7888763332 46778999999999999
Q ss_pred eecchhhHHHHHHHHhCCcc-CeeechHhHHHhCCCCC-ccHHHHHHHHcCCCCCccc----ccccCCCCCCChHHHHHH
Q psy7894 325 VFHGADSDIKWLQKDFGLYV-VGMFDTHQACKFLPMPR-QSLAYLLKHYCDVDSDKTF----QLFDWRHRPLPEPAIQYA 398 (1006)
Q Consensus 325 V~Hgak~Dl~~L~rd~GI~~-~nlFDTqlAAyLLg~~~-~SLa~Lve~yLgv~LdK~~----q~sDW~~RPLs~eql~YA 398 (1006)
|+||+++|+.+|. .+|+.+ .++|||++|+|+|++.. +||+.|+++|+|+.+.... ...+|..+|+ +.+..||
T Consensus 374 V~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YA 451 (880)
T PRK05755 374 VGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYA 451 (880)
T ss_pred EEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCH-HHHHHHH
Confidence 9999999999996 579876 57999999999999864 8999999999998742110 1234445577 5799999
Q ss_pred HhchhHHHHHHHHHHHHHHHh
Q psy7894 399 RTDTHYLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 399 A~DA~yLL~Lyd~L~~eL~e~ 419 (1006)
+.||.+++.||..|..+|.+.
T Consensus 452 a~Dv~~~~~L~~~L~~~L~~~ 472 (880)
T PRK05755 452 AEDADVTLRLHEVLKPKLLEE 472 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999875
No 14
>PF08066 PMC2NT: PMC2NT (NUC016) domain; InterPro: IPR012588 Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [, ]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; 2.7.7.8 from EC) [], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0006396 RNA processing, 0000176 nuclear exosome (RNase complex)
Probab=99.69 E-value=6.2e-18 Score=156.62 Aligned_cols=82 Identities=24% Similarity=0.437 Sum_probs=75.5
Q ss_pred HHHHHhhhcCCCCCcccccccccCCCC-CCc----cchHHHHHHHHHHHHHhcccCCCCCc----ccccccchhhhhhhH
Q psy7894 33 IVKCTKTAQSFPSTHENSLLIASPNYI-SGV----AGTSDKVMTLVDSLLKTQNISKSMSK----LYLEGQKDILTEAND 103 (1006)
Q Consensus 33 ~v~~~r~s~~lp~~~~d~~f~~s~~~~-~~f----~~~~~rll~~~~~ll~~~~~~~~~~~----~d~~~~~~~v~~~~D 103 (1006)
||++||+||+|| + +||+||+| | |+| +++++|||+++|+||++++..+++.. +++++.|+.|+|+||
T Consensus 1 lv~~~raa~~Lp-~-~D~~Fy~s---~dp~f~~~ld~~s~rll~l~n~ll~~~~~~~~~~~~~~~~d~d~~~~~vvd~~D 75 (91)
T PF08066_consen 1 LVQTTRAANALP-A-QDYDFYRS---FDPEFAESLDEQSQRLLSLINSLLKSAGSKSNISSPDDVDDVDERWDSVVDVND 75 (91)
T ss_pred CHHHHHHHHHcc-H-HHHHHHHH---hhHHHHHHHHHHHHHHHHHHHHHHHhccccccccCCCccccHHHHHHHHHHHHH
Confidence 689999999999 4 99999999 5 888 89999999999999999999887733 679999999999999
Q ss_pred HHHhhhchhhhhhcCC
Q psy7894 104 KLLESINTRIDVMAGT 119 (1006)
Q Consensus 104 ~llE~~d~~lDe~~g~ 119 (1006)
.||||||++|||++|.
T Consensus 76 ~LlEk~D~~LDe~~g~ 91 (91)
T PF08066_consen 76 SLLEKADISLDELTGK 91 (91)
T ss_pred HHHHHHhHHHHhHcCC
Confidence 9999999999999983
No 15
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.66 E-value=1.8e-15 Score=147.19 Aligned_cols=146 Identities=34% Similarity=0.422 Sum_probs=114.6
Q ss_pred eEEEEeeeccCCccCCcEEEEEEEeCCceEEE-eCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeee
Q psy7894 270 EIAIDLEYHNYRSYQGYTCLMQISTRDKDYIV-DTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMF 348 (1006)
Q Consensus 270 ~IAVDtE~~~~rty~g~lcLIQISt~~~~yII-D~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlF 348 (1006)
.+++|+|+.+...+.+.++++|+++.+..++| +.......+..|.++|+++.+.||+||+++|+.+|.+.++....++|
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~ 81 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIF 81 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcc
Confidence 57999998776666789999999986434444 33222234566889999999999999999999999654434445789
Q ss_pred chHhHHHhCCCC--CccHHHHHHHHcCCCCCcccccccCC----CCCCChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 349 DTHQACKFLPMP--RQSLAYLLKHYCDVDSDKTFQLFDWR----HRPLPEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 349 DTqlAAyLLg~~--~~SLa~Lve~yLgv~LdK~~q~sDW~----~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
||++|+|+|++. +++|+.|+++|++..+.+..+..+|. .+|++..+..||+.|+.+++.|++.|..+
T Consensus 82 D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 82 DTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cHHHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 999999999984 47999999999998754423334442 57889999999999999999999999765
No 16
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.65 E-value=1.6e-15 Score=148.30 Aligned_cols=143 Identities=20% Similarity=0.189 Sum_probs=114.5
Q ss_pred eEEEEeeeccCCccCCcEEEEEEEeCCc-eEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccC-ee
Q psy7894 270 EIAIDLEYHNYRSYQGYTCLMQISTRDK-DYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVV-GM 347 (1006)
Q Consensus 270 ~IAVDtE~~~~rty~g~lcLIQISt~~~-~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~-nl 347 (1006)
.+++|+|+.++.++.+.++++||+++++ +|+|+..........|.++|+|+++.||+||++.|+.+|. ..|+... ++
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~~ 79 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGIA 79 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCcc
Confidence 3789998877766678999999998754 7888743211135568899999999999999999999994 5666554 68
Q ss_pred echHhHHHhCCCC--CccHHHHHHHHcCCCCCccccc--ccCCCCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 348 FDTHQACKFLPMP--RQSLAYLLKHYCDVDSDKTFQL--FDWRHRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 348 FDTqlAAyLLg~~--~~SLa~Lve~yLgv~LdK~~q~--sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
|||++|+|+|++. +++|..|+.+||+..+.+..+. .+|..++++.+|+.||+.|+.+++.|++.|.
T Consensus 80 ~D~~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 80 FDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred hhHHHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999984 4799999999999885441212 2386688899999999999999999999874
No 17
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.62 E-value=1.1e-14 Score=147.72 Aligned_cols=152 Identities=21% Similarity=0.169 Sum_probs=123.0
Q ss_pred CCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccC-e
Q psy7894 268 QQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVV-G 346 (1006)
Q Consensus 268 a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~-n 346 (1006)
.+.++||+|..+..++.+.+++++|++++..|+|+..........|.++|+|+++.||+||+|.|++.| ..+|+.+. .
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~~ 81 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAGV 81 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCCc
Confidence 356899999988877889999999998777777774221013456889999999999999999999999 46899875 5
Q ss_pred eechHhHHHhCCCCC--ccHHHHHHHHcCCCCCcccccccCC---CCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 347 MFDTHQACKFLPMPR--QSLAYLLKHYCDVDSDKTFQLFDWR---HRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 347 lFDTqlAAyLLg~~~--~SLa~Lve~yLgv~LdK~~q~sDW~---~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
+|||++|+|+|++.. ++|..|+.+|++..+.+..+..+|. .++....+..|++.|+.+++.|++.|..+|.+.+
T Consensus 82 ~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~ 160 (178)
T cd06140 82 AFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENE 160 (178)
T ss_pred chhHHHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 799999999999963 7999999999998865433344442 2444666889999999999999999999998764
No 18
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.60 E-value=1.3e-14 Score=172.87 Aligned_cols=142 Identities=20% Similarity=0.174 Sum_probs=126.9
Q ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeec
Q psy7894 248 PLMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFH 327 (1006)
Q Consensus 248 ~~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~H 327 (1006)
.+.+|++.++|..+|..+..++.+++|+|+.+.++ .+|++|++.++..|+||++.. +. ++
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~~~~~liDpl~~---l~---~~----------- 61 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEEEPRWVWASTAA---LY---PR----------- 61 (553)
T ss_pred CceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCCCceEEECchHH---hH---HH-----------
Confidence 35789999999999999999999999999998776 899999999999999998642 22 11
Q ss_pred chhhHHHHHHHHhCCccCeeechHhHHHhCCCC----CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchh
Q psy7894 328 GADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP----RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTH 403 (1006)
Q Consensus 328 gak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~----~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~ 403 (1006)
| ..+|+.+.++|||++|+|+||++ ++||+.|+.+|+++.++|..+.+||. |||++.|+.||+.||.
T Consensus 62 --------L-~~~Gv~~~~~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~ 131 (553)
T PRK14975 62 --------L-LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADAD 131 (553)
T ss_pred --------H-HHCCCccCCCchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccchHHHHHHHHHHhH
Confidence 4 35699888899999999999984 58999999999999999988899996 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHh
Q psy7894 404 YLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 404 yLL~Lyd~L~~eL~e~ 419 (1006)
|++.||..|..+|.+.
T Consensus 132 ~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 132 VLLELYAVLADQLNRI 147 (553)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999999876
No 19
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.50 E-value=8.4e-13 Score=134.64 Aligned_cols=151 Identities=25% Similarity=0.297 Sum_probs=119.9
Q ss_pred hcCCeEEEEeeeccCCccCCcEEEEEEEeCCc-eEEEeCc--------chhhhHHHHHHHHcCCCceeeecchhhHHHHH
Q psy7894 266 KQQQEIAIDLEYHNYRSYQGYTCLMQISTRDK-DYIVDTL--------KLREDLEVLNEVLTDKNIVKVFHGADSDIKWL 336 (1006)
Q Consensus 266 ~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~-~yIID~l--------aL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L 336 (1006)
.+...+++|+|..+++++.+.++.++++..++ .|+|+.. .....+..|..+|++..+.+|+||+++|+.+|
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 34578999999988888888999999998754 5555421 12234556889999988899999999999999
Q ss_pred HHHhCCccC-eeechHhHHHhCCCC--CccHHHHHHHHcCCCC-------CcccccccCCCCCCChHHHHHHHhchhHHH
Q psy7894 337 QKDFGLYVV-GMFDTHQACKFLPMP--RQSLAYLLKHYCDVDS-------DKTFQLFDWRHRPLPEPAIQYARTDTHYLL 406 (1006)
Q Consensus 337 ~rd~GI~~~-nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~L-------dK~~q~sDW~~RPLs~eql~YAA~DA~yLL 406 (1006)
+.+|+.+. .+|||++++|+|++. .++|..|+++|+|... .|+.+..+|...|+ ..+..||+.|+.+++
T Consensus 83 -~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~ 160 (193)
T cd06139 83 -ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADITL 160 (193)
T ss_pred -HHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHHH
Confidence 56888865 579999999999984 5799999999998762 12233445654455 668899999999999
Q ss_pred HHHHHHHHHHHH
Q psy7894 407 YVYDCMKLDLSA 418 (1006)
Q Consensus 407 ~Lyd~L~~eL~e 418 (1006)
+|+..|..+|.+
T Consensus 161 ~l~~~l~~~l~~ 172 (193)
T cd06139 161 RLYELLKPKLKE 172 (193)
T ss_pred HHHHHHHHHHhh
Confidence 999999999976
No 20
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.36 E-value=1.1e-12 Score=114.14 Aligned_cols=68 Identities=26% Similarity=0.432 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHH
Q psy7894 466 QKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAII 533 (1006)
Q Consensus 466 qlavlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI 533 (1006)
|++++++|+.||+++|++.|+|+++||+|.+|.+||..+|+|.++|.++.|+.+..+++||++|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 68899999999999999999999999999999999999999999999999999999999999999987
No 21
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.34 E-value=4.4e-12 Score=113.61 Aligned_cols=77 Identities=30% Similarity=0.475 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHhhcC
Q psy7894 464 NQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQS 540 (1006)
Q Consensus 464 ~~qlavlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar~~p 540 (1006)
+.+++++++|+.||+.+|++.|+|+++||+|.+|++||+.+|+|..+|.++.|+....+++||..|+++|+.+...+
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~ 78 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSP 78 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999987654
No 22
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.25 E-value=6.7e-11 Score=139.99 Aligned_cols=168 Identities=23% Similarity=0.256 Sum_probs=130.9
Q ss_pred EEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCCce-EEEeCc---chhhhHHHHHHHHcCCCceee
Q psy7894 250 MMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRDKD-YIVDTL---KLREDLEVLNEVLTDKNIVKV 325 (1006)
Q Consensus 250 ~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~~~-yIID~l---aL~~~L~~L~elLedp~IvKV 325 (1006)
..+.+.+.+..++..+...+.+++|+|+.+.+++.+.++++.++..+.. ||.... .+ .....|++||+++.+.||
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~-~~~~~l~~~l~~~~~~kv 82 (593)
T COG0749 4 GTITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPEQL-NVLAALKPLLEDEGIKKV 82 (593)
T ss_pred hhhhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccccceeEeeccchhhh-hhHHHHHHHhhCcccchh
Confidence 3455667778888887776669999999999888888888888777644 443332 22 367899999999999999
Q ss_pred ecchhhHHHHHHHHhCCccCeeechHhHHHhCCCC--CccHHHHHHHHcCCCCC-------cccccccCCCCCCChHHHH
Q psy7894 326 FHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP--RQSLAYLLKHYCDVDSD-------KTFQLFDWRHRPLPEPAIQ 396 (1006)
Q Consensus 326 ~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~Ld-------K~~q~sDW~~RPLs~eql~ 396 (1006)
+||+|+|.+.|+ .+|+..+..||||+|+|+|+++ .+++..|+++|++.+.. |+.+..+...-++ .....
T Consensus 83 ~~~~K~d~~~l~-~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~-~~~~~ 160 (593)
T COG0749 83 GQNLKYDYKVLA-NLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKL-EKATE 160 (593)
T ss_pred ccccchhHHHHH-HcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchH-HHHHH
Confidence 999999999994 7886545789999999999985 58999999999987652 3333222222222 45789
Q ss_pred HHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 397 YARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 397 YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
|++.|+..+++|+..|..+|.+..
T Consensus 161 y~a~~a~~~~~L~~~l~~~l~~~~ 184 (593)
T COG0749 161 YAAEDADATLRLESILEPELLKTP 184 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhh
Confidence 999999999999999998887653
No 23
>KOG2207|consensus
Probab=99.23 E-value=1.7e-11 Score=142.96 Aligned_cols=172 Identities=22% Similarity=0.313 Sum_probs=135.6
Q ss_pred CCCcEEeCCHHHHHHHH-HHHhcC-CeEEEEeeeccC-CccCCcEEEEEEEeCCceEEEeCcchhh----hH-HHHHHHH
Q psy7894 246 DTPLMMITEPEQVTQLV-SELKQQ-QEIAIDLEYHNY-RSYQGYTCLMQISTRDKDYIVDTLKLRE----DL-EVLNEVL 317 (1006)
Q Consensus 246 ~t~~~lIdT~e~L~~ll-e~L~~a-~~IAVDtE~~~~-rty~g~lcLIQISt~~~~yIID~laL~~----~L-~~L~elL 317 (1006)
...+.+|+++.+|..++ +.+... -.||+|.||..+ .....++|+|||++.+.+||||..++.. .+ ..+..+|
T Consensus 389 ~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if 468 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIF 468 (617)
T ss_pred ccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHc
Confidence 45678999999999887 455554 789999999765 3346789999999999999999987631 12 2566799
Q ss_pred cCCCceeeecchhhHHHHHHHH-----hCCcc---Cee-echHhHHHhCCC---------CCccHHHHHHHHcCCCCCcc
Q psy7894 318 TDKNIVKVFHGADSDIKWLQKD-----FGLYV---VGM-FDTHQACKFLPM---------PRQSLAYLLKHYCDVDSDKT 379 (1006)
Q Consensus 318 edp~IvKV~Hgak~Dl~~L~rd-----~GI~~---~nl-FDTqlAAyLLg~---------~~~SLa~Lve~yLgv~LdK~ 379 (1006)
++++|.|||++..+|++.|++. +.+.+ .++ .++-++..+.+. ...+|+.|....+|..++|.
T Consensus 469 ~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKt 548 (617)
T KOG2207|consen 469 ESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKT 548 (617)
T ss_pred cCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccc
Confidence 9999999999999999999742 22222 122 233444444331 24689999999999999999
Q ss_pred cccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHH
Q psy7894 380 FQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLS 417 (1006)
Q Consensus 380 ~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~ 417 (1006)
.|.+||--|||...|+.||+.|++.+..+|..+...-.
T Consensus 549 eqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 549 EQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 99999999999999999999999999999999876554
No 24
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.20 E-value=2.5e-11 Score=105.62 Aligned_cols=68 Identities=26% Similarity=0.432 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHH
Q psy7894 573 QKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAII 640 (1006)
Q Consensus 573 Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI 640 (1006)
|+++++.|+.||+++|++.|+++++|+++.+|.+||+..|.+.++|.++.|+.+..+++||.+|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 68899999999999999999999999999999999999999999999999999999999999999987
No 25
>KOG2206|consensus
Probab=99.18 E-value=3.7e-11 Score=139.29 Aligned_cols=83 Identities=40% Similarity=0.571 Sum_probs=79.4
Q ss_pred CChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcCCC
Q psy7894 569 SNNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQPL 648 (1006)
Q Consensus 569 l~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~~~ 648 (1006)
++++|+.+|+.|++|||.+||++|++++|||||++|.+||+.+|+++++|.+||++.++.|+||+.+++.||.+|+....
T Consensus 402 ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~~ii~~a~~~~l 481 (687)
T KOG2206|consen 402 LNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFLYIIRSAGRGFL 481 (687)
T ss_pred cchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHHHHHHHHhhhhh
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999998777
Q ss_pred CCC
Q psy7894 649 TKP 651 (1006)
Q Consensus 649 ~~~ 651 (1006)
...
T Consensus 482 ~~~ 484 (687)
T KOG2206|consen 482 LQN 484 (687)
T ss_pred hhc
Confidence 653
No 26
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.17 E-value=1.2e-09 Score=136.44 Aligned_cols=165 Identities=14% Similarity=0.051 Sum_probs=121.4
Q ss_pred cEEeCCHHHHHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEEEeCC-c-eEEEeCc-----chhhhHHHHHHHHcCCC
Q psy7894 249 LMMITEPEQVTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQISTRD-K-DYIVDTL-----KLREDLEVLNEVLTDKN 321 (1006)
Q Consensus 249 ~~lIdT~e~L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~-~-~yIID~l-----aL~~~L~~L~elLedp~ 321 (1006)
+..|.+.+++..+++. ...+.+++ .++.++...+.++.+++.+ + .|+++.. .....+..|.++|+|+.
T Consensus 304 ~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 378 (887)
T TIGR00593 304 AKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQ 378 (887)
T ss_pred ceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCC
Confidence 4567677888887765 44456777 3444556778889999865 3 5555321 12233566899999999
Q ss_pred ceeeecchhhHHHHHHHHhCCccC-eeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCC--CCCCC-hHHHH
Q psy7894 322 IVKVFHGADSDIKWLQKDFGLYVV-GMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWR--HRPLP-EPAIQ 396 (1006)
Q Consensus 322 IvKV~Hgak~Dl~~L~rd~GI~~~-nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~--~RPLs-~eql~ 396 (1006)
+.||+||+++|+.+| ..+|+.+. .+||||+|+|+|++. .++|+.|+.+|++..+........|. ...++ +.+..
T Consensus 379 ~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 457 (887)
T TIGR00593 379 IKKIGHDAKFLMHLL-KREGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATE 457 (887)
T ss_pred CcEEEeeHHHHHHHH-HhCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHH
Confidence 999999999999999 57899885 579999999999984 47999999999997653311111111 11232 45779
Q ss_pred HHHhchhHHHHHHHHHHHHHHHh
Q psy7894 397 YARTDTHYLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 397 YAA~DA~yLL~Lyd~L~~eL~e~ 419 (1006)
||+.|+.++++||..|..+|.+.
T Consensus 458 ya~~d~~~~~~L~~~l~~~l~~~ 480 (887)
T TIGR00593 458 YLARRAAATKRLAEELLKELDEN 480 (887)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999864
No 27
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.14 E-value=2e-10 Score=102.83 Aligned_cols=78 Identities=31% Similarity=0.491 Sum_probs=74.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcCCC
Q psy7894 571 NQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQPL 648 (1006)
Q Consensus 571 ~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~~~ 648 (1006)
+.++++++.|+.||+.+|++.|+|+++|+++.+|.+||+..|++..+|.++.|+....++.||..++.+|+.+...+.
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~~ 79 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPS 79 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 358999999999999999999999999999999999999999999999999999999999999999999999876554
No 28
>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=98.93 E-value=2e-09 Score=122.96 Aligned_cols=82 Identities=24% Similarity=0.403 Sum_probs=78.1
Q ss_pred CCChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcCC
Q psy7894 568 DSNNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQP 647 (1006)
Q Consensus 568 ll~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~~ 647 (1006)
.++++|+++++.|+.||+.+||++|+|+++|++++.|++||+..|++.++|.++ ++.+..+|+||++|+++|+.|...|
T Consensus 204 ~l~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r~~~~~l~~~i~~a~~~~ 282 (367)
T TIGR01388 204 QLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALP 282 (367)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHHhhHHHHHHHHHHHhhCC
Confidence 468899999999999999999999999999999999999999999999999999 9999999999999999999999877
Q ss_pred CCC
Q psy7894 648 LTK 650 (1006)
Q Consensus 648 ~~~ 650 (1006)
.+.
T Consensus 283 ~~~ 285 (367)
T TIGR01388 283 EDA 285 (367)
T ss_pred Hhh
Confidence 655
No 29
>PRK10829 ribonuclease D; Provisional
Probab=98.93 E-value=2.1e-09 Score=122.85 Aligned_cols=83 Identities=23% Similarity=0.322 Sum_probs=78.3
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcC
Q psy7894 567 HDSNNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQ 646 (1006)
Q Consensus 567 ~ll~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~ 646 (1006)
..++++|+++++.|+.||+++||++|+|+++|++++.|.+||+.+|++..+|.++ ++.+..+|+||.+|+++|+.|...
T Consensus 207 ~~L~~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r~~g~~ll~~i~~a~~~ 285 (373)
T PRK10829 207 WQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQAL 285 (373)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHHhhHHHHHHHHHHHhcC
Confidence 3467899999999999999999999999999999999999999999999999999 999999999999999999999987
Q ss_pred CCCC
Q psy7894 647 PLTK 650 (1006)
Q Consensus 647 ~~~~ 650 (1006)
|.+.
T Consensus 286 ~~~~ 289 (373)
T PRK10829 286 PEEA 289 (373)
T ss_pred CHhh
Confidence 7664
No 30
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.87 E-value=3.4e-08 Score=98.09 Aligned_cols=140 Identities=18% Similarity=0.146 Sum_probs=93.2
Q ss_pred EEEeeeccCCccCCcEEEEEEEeCCceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCe-eech
Q psy7894 272 AIDLEYHNYRSYQGYTCLMQISTRDKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVG-MFDT 350 (1006)
Q Consensus 272 AVDtE~~~~rty~g~lcLIQISt~~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~n-lFDT 350 (1006)
++.++...+.++.+.+..+.+++.++.|+|+...-. ....|.++|++..+.|++||+|.++.+| +.+|+.+.+ +|||
T Consensus 5 ~~~~~~~~~~~~~~~~~glal~~~~~~~yi~~~~~~-~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~ 82 (151)
T cd06128 5 AFGTETDSLDNISANLVGLAFAIEGVAAYIPVAHDY-ALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDT 82 (151)
T ss_pred EEEecCCCCCcccCcEEEEEEEcCCCeEEEeCCCCc-CHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhH
Confidence 344433333333466777888877666666521100 2455889999999999999999999999 578998764 6999
Q ss_pred HhHHHhCCCC-C-ccHHHHHHHHcCCCCCcccccccCCC--CCC-ChHHHHHHHhchhHHHHHHHHHH
Q psy7894 351 HQACKFLPMP-R-QSLAYLLKHYCDVDSDKTFQLFDWRH--RPL-PEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 351 qlAAyLLg~~-~-~SLa~Lve~yLgv~LdK~~q~sDW~~--RPL-s~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
++|+|||++. + .+|..|+.+|++..+..-.....+.. ..+ ......|++..+.+++.|++.|.
T Consensus 83 ~LAaYLL~p~~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 83 MLEAYLLDPVAGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999995 2 69999999999876211000111100 011 11223478888888888888774
No 31
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=98.44 E-value=3.7e-07 Score=103.16 Aligned_cols=81 Identities=25% Similarity=0.378 Sum_probs=74.6
Q ss_pred CChhHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhhcCCC
Q psy7894 569 SNNQQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKARLQPL 648 (1006)
Q Consensus 569 l~~~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar~~~~ 648 (1006)
..+.++++++.|++||++.||.+|+++++|+++..|..+|+.+|++..+|..+.+... .+|.++..|+.+|..|+..|.
T Consensus 205 ~~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~~~~~~l~~~~~~a~~~p~ 283 (361)
T COG0349 205 LDPRELAVLRELAAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPK-ERRRHGKLLLALLANALASPE 283 (361)
T ss_pred CChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcc-cchhhhHHHHHHHHHHHhCch
Confidence 4567999999999999999999999999999999999999999999999999855544 999999999999999999887
Q ss_pred CC
Q psy7894 649 TK 650 (1006)
Q Consensus 649 ~~ 650 (1006)
+.
T Consensus 284 ~~ 285 (361)
T COG0349 284 SD 285 (361)
T ss_pred hh
Confidence 54
No 32
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=98.31 E-value=1.2e-06 Score=105.83 Aligned_cols=71 Identities=11% Similarity=0.147 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHH
Q psy7894 465 QQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILK 535 (1006)
Q Consensus 465 ~qlavlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~ 535 (1006)
.+.++|++|.+||+++|++.|+|+++||+|..|++||+.+|+|.++|..+.|+....+++||.+|+++|+.
T Consensus 520 ~~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~l~~i~~ 590 (591)
T TIGR01389 520 VDNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEAFLEVIRE 590 (591)
T ss_pred cHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHHHHHHHh
Confidence 34499999999999999999999999999999999999999999999999999999999999999999964
No 33
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=97.93 E-value=2e-05 Score=95.43 Aligned_cols=70 Identities=11% Similarity=0.156 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHH
Q psy7894 573 QKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILK 642 (1006)
Q Consensus 573 Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~ 642 (1006)
+.++|++|..||+++|++.|+|+.+|+++..|.+||+..|++..+|.++.|+.+..++.||.+++++|+.
T Consensus 521 ~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~l~~i~~ 590 (591)
T TIGR01389 521 DNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEAFLEVIRE 590 (591)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHHHHHHHh
Confidence 4499999999999999999999999999999999999999999999999999999999999999999974
No 34
>KOG4373|consensus
Probab=97.79 E-value=5.4e-05 Score=84.33 Aligned_cols=127 Identities=19% Similarity=0.192 Sum_probs=97.7
Q ss_pred cCCcEEEEEEEeC-CceEEEeCcchhhhHHHHHHHHcCCCceeeecchhhHHHHHHH-HhCCccCeeechHh-HHHhCCC
Q psy7894 283 YQGYTCLMQISTR-DKDYIVDTLKLREDLEVLNEVLTDKNIVKVFHGADSDIKWLQK-DFGLYVVGMFDTHQ-ACKFLPM 359 (1006)
Q Consensus 283 y~g~lcLIQISt~-~~~yIID~laL~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~r-d~GI~~~nlFDTql-AAyLLg~ 359 (1006)
+.+....+||+.+ ..++||..+.-......|+.+|+|++.+.|+-+.+.|...|.| .+++.+..+.|+.. +.-.+|.
T Consensus 145 ~~P~~~~lqlcV~en~C~I~ql~~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~ 224 (319)
T KOG4373|consen 145 SDPPPDTLQLCVGENRCLIIQLIHCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG 224 (319)
T ss_pred cCCCcchhhhhhcccceeeEEeeccccchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc
Confidence 3445778999999 5788876544333456788889999999999999999999877 88998887777764 3334554
Q ss_pred --CCccHHHHHHH---HcC--CCCCcccccccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 360 --PRQSLAYLLKH---YCD--VDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 360 --~~~SLa~Lve~---yLg--v~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
+.-+...|+.. |.| +.+++.-+++||...||+.+|+.||+.||+....|+
T Consensus 225 ~~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 225 SMPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred CccCccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 12344444444 445 556778899999999999999999999999999998
No 35
>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=97.75 E-value=0.00013 Score=68.40 Aligned_cols=73 Identities=23% Similarity=0.291 Sum_probs=56.3
Q ss_pred EEEEeeeccCCccCCcEEEEEEEeC--CceEEEeCcchhhhHHHHHHHHcCCC-ceeeecchhhHHHHHHHHhC---Cc-
Q psy7894 271 IAIDLEYHNYRSYQGYTCLMQISTR--DKDYIVDTLKLREDLEVLNEVLTDKN-IVKVFHGADSDIKWLQKDFG---LY- 343 (1006)
Q Consensus 271 IAVDtE~~~~rty~g~lcLIQISt~--~~~yIID~laL~~~L~~L~elLedp~-IvKV~Hgak~Dl~~L~rd~G---I~- 343 (1006)
+++|+|+.+.+++...+|++|++.. +..|++| |.+++.+.. ...|+||+.+|+..|.+.+. +.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~ 70 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKY 70 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCC
Confidence 5799999999999999999999877 4667777 667777766 67899999999988765443 21
Q ss_pred ---cCeeechHhH
Q psy7894 344 ---VVGMFDTHQA 353 (1006)
Q Consensus 344 ---~~nlFDTqlA 353 (1006)
...++||+.+
T Consensus 71 p~~~~~~lDT~~l 83 (96)
T cd06125 71 PLLAGSWIDTIKL 83 (96)
T ss_pred CCcCCcEEEehHH
Confidence 2357788755
No 36
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=97.51 E-value=0.00021 Score=87.16 Aligned_cols=73 Identities=16% Similarity=0.210 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHHh
Q psy7894 465 QQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKAR 537 (1006)
Q Consensus 465 ~qlavlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~Ar 537 (1006)
....++.+|-.||.++|++.++|++.|++|.+|.+||+.+|+|.++|.++.|+....+.+||.+++++|....
T Consensus 531 ~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~l~~i~~~~ 603 (607)
T PRK11057 531 YDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPFMALIRAHV 603 (607)
T ss_pred chHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999999999999999999999999999999999999999999999998764
No 37
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=97.16 E-value=0.0008 Score=85.93 Aligned_cols=70 Identities=16% Similarity=0.147 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHHHH--hCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHH
Q psy7894 467 KYALRELYKWRDRIARD--KDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKA 536 (1006)
Q Consensus 467 lavlr~L~~WRD~~AR~--~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~A 536 (1006)
..+|.+|-.||.++|++ +++|++.|++|.+|.+||+.+|++..+|+.+.|+....+.+||.+++++|+.-
T Consensus 1029 ~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~ 1100 (1195)
T PLN03137 1029 AILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDRLLETIEST 1100 (1195)
T ss_pred HHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999 69999999999999999999999999999999999999999999999999764
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.02 E-value=0.013 Score=66.45 Aligned_cols=134 Identities=17% Similarity=0.154 Sum_probs=88.6
Q ss_pred CCeEEEEeeeccCCccCCcEEEEEEEe--CCc------eEEEeCc----c-----h-----------hhhHHHHHHHHcC
Q psy7894 268 QQEIAIDLEYHNYRSYQGYTCLMQIST--RDK------DYIVDTL----K-----L-----------REDLEVLNEVLTD 319 (1006)
Q Consensus 268 a~~IAVDtE~~~~rty~g~lcLIQISt--~~~------~yIID~l----a-----L-----------~~~L~~L~elLed 319 (1006)
...++||+|+.+.++....+|-|.+.. .++ ..+|.+- . + .+.+..|.+++.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 467899999998876655544333221 111 1244331 0 1 1234566677765
Q ss_pred CCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCCCCCCh
Q psy7894 320 KNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPE 392 (1006)
Q Consensus 320 p~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~ 392 (1006)
. +-|+||+.+|+.+|.+. +|+.. ...+||+..++.+.+ .+++|..|+++ +|+.....
T Consensus 95 ~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~~~------------- 158 (313)
T PRK06063 95 R--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQRP------------- 158 (313)
T ss_pred C--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCCCC-------------
Confidence 3 45999999999998654 35443 358999988887754 46899999976 57654221
Q ss_pred HHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 393 PAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 393 eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
+-|..||..+..|+..+..++.+.+
T Consensus 159 ---H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 159 ---HDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred ---CCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 2278899999999999988887664
No 39
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.00 E-value=0.012 Score=64.58 Aligned_cols=132 Identities=18% Similarity=0.255 Sum_probs=84.9
Q ss_pred HhcCCeEEEEeeeccCCccCCcEEEEEEEe----CC-----ceEEEeCc-c----------h-----------hhhHHHH
Q psy7894 265 LKQQQEIAIDLEYHNYRSYQGYTCLMQIST----RD-----KDYIVDTL-K----------L-----------REDLEVL 313 (1006)
Q Consensus 265 L~~a~~IAVDtE~~~~rty~g~lcLIQISt----~~-----~~yIID~l-a----------L-----------~~~L~~L 313 (1006)
|.....+.||+|+++.......+ |+|+. .+ -..+|.|- . + .+.+..+
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~I--IEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDRI--IEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 34567899999999976544433 33332 11 12234431 0 0 1123456
Q ss_pred HHHHcCCCceeeecchhhHHHHHHHH---hCCcc----CeeechHhHHHhCCC-CCccHHHHHHHHcCCCCCcccccccC
Q psy7894 314 NEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV----VGMFDTHQACKFLPM-PRQSLAYLLKHYCDVDSDKTFQLFDW 385 (1006)
Q Consensus 314 ~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~----~nlFDTqlAAyLLg~-~~~SLa~Lve~yLgv~LdK~~q~sDW 385 (1006)
.+++.+.. .-|+||+.+|+.+|.+. .|+.. ..++||+-.++.++. ++++|+.|++.| |+.....
T Consensus 82 ~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~a------ 153 (250)
T PRK06310 82 KGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDGN------ 153 (250)
T ss_pred HHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCCC------
Confidence 66665534 45999999999998643 35543 358999988888764 468999998775 6654321
Q ss_pred CCCCCChHHHHHHHhchhHHHHHHHHHHHHH
Q psy7894 386 RHRPLPEPAIQYARTDTHYLLYVYDCMKLDL 416 (1006)
Q Consensus 386 ~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL 416 (1006)
+=|..||..+..|+..|..++
T Consensus 154 ----------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 154 ----------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ----------cChHHHHHHHHHHHHHHHHhc
Confidence 228899999999998887554
No 40
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=96.95 E-value=0.0048 Score=62.29 Aligned_cols=82 Identities=21% Similarity=0.163 Sum_probs=56.8
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCC---CCccHHHHHHHHcCCCCCcccccccC
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPM---PRQSLAYLLKHYCDVDSDKTFQLFDW 385 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~---~~~SLa~Lve~yLgv~LdK~~q~sDW 385 (1006)
.+..|..++.+ .+ -|+||+.+|+.+|. .+.....++||.....+... .+++|+.|+++|+|+.+... .
T Consensus 67 ~~~~l~~~l~~-~v-lVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~--~--- 137 (152)
T cd06144 67 VQKKVAELLKG-RI-LVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG--E--- 137 (152)
T ss_pred HHHHHHHHhCC-CE-EEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC--C---
Confidence 34567778876 44 49999999999994 33333467888765444432 46899999999999865321 1
Q ss_pred CCCCCChHHHHHHHhchhHHHHHH
Q psy7894 386 RHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 386 ~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
.=|..||..+..||
T Consensus 138 ----------H~Al~DA~at~~l~ 151 (152)
T cd06144 138 ----------HSSVEDARAAMRLY 151 (152)
T ss_pred ----------cCcHHHHHHHHHHh
Confidence 12678888888776
No 41
>PRK07740 hypothetical protein; Provisional
Probab=96.90 E-value=0.025 Score=61.77 Aligned_cols=92 Identities=16% Similarity=0.143 Sum_probs=66.7
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH----hCCcc-CeeechHhHHHhCCCC--CccHHHHHHHHcCCCCCccccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD----FGLYV-VGMFDTHQACKFLPMP--RQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd----~GI~~-~nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
+..|..++.+. .-|+||+.+|..+|.+. ++... ..++||+..++.+.+. .++|.+|+.. +|+.....+
T Consensus 132 l~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~~H-- 206 (244)
T PRK07740 132 LHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPRRH-- 206 (244)
T ss_pred HHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCCCC--
Confidence 44555566553 45899999999887532 33333 3689999988877653 6899999865 677654221
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
-|..||..+..|+..+..++.+.|
T Consensus 207 --------------~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 207 --------------HALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred --------------CcHHHHHHHHHHHHHHHHHHHHcC
Confidence 278899999999999999988765
No 42
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=96.89 E-value=0.0023 Score=78.29 Aligned_cols=73 Identities=16% Similarity=0.210 Sum_probs=69.5
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhh
Q psy7894 572 QQKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKAR 644 (1006)
Q Consensus 572 ~Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar 644 (1006)
....+|.+|..||.++|++.++++..|+++..|.+||+..|.+..+|.++.|+...-+..||.+++++|....
T Consensus 531 ~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~l~~i~~~~ 603 (607)
T PRK11057 531 YDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPFMALIRAHV 603 (607)
T ss_pred chHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999999999999999999999999999999999999999999999999999998764
No 43
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.84 E-value=0.017 Score=65.52 Aligned_cols=129 Identities=22% Similarity=0.255 Sum_probs=83.1
Q ss_pred CCeEEEEeeeccCCccCCcEEEEEEEe---CCc------eEEEeCc----------------------chhhhHHHHHHH
Q psy7894 268 QQEIAIDLEYHNYRSYQGYTCLMQIST---RDK------DYIVDTL----------------------KLREDLEVLNEV 316 (1006)
Q Consensus 268 a~~IAVDtE~~~~rty~g~lcLIQISt---~~~------~yIID~l----------------------aL~~~L~~L~el 316 (1006)
...++||+|+.++++..+. +|||+. .++ ..+|.|- .+.+.+..|.++
T Consensus 8 ~~~Vv~DlETTGl~p~~~e--IIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~f 85 (313)
T PRK06807 8 LDYVVIDFETTGFNPYNDK--IIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85 (313)
T ss_pred CCEEEEEEECCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 3678999999988765444 344442 111 1233221 011234556666
Q ss_pred HcCCCceeeecchhhHHHHHHHHh---CCc-c-CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCCCC
Q psy7894 317 LTDKNIVKVFHGADSDIKWLQKDF---GLY-V-VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRHRP 389 (1006)
Q Consensus 317 Ledp~IvKV~Hgak~Dl~~L~rd~---GI~-~-~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~RP 389 (1006)
+.+..+ |+|++.+|+..|.+.+ |+. + ..++||+..++.+.+ +.++|..|++. +|+.. ..
T Consensus 86 l~~~~l--VaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~~---------- 151 (313)
T PRK06807 86 LHTNVI--VAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-SS---------- 151 (313)
T ss_pred HcCCeE--EEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-CC----------
Confidence 665433 9999999999997653 553 2 358899987765543 46899999865 56554 21
Q ss_pred CChHHHHHHHhchhHHHHHHHHHHHHHHH
Q psy7894 390 LPEPAIQYARTDTHYLLYVYDCMKLDLSA 418 (1006)
Q Consensus 390 Ls~eql~YAA~DA~yLL~Lyd~L~~eL~e 418 (1006)
+=|..||.++..||..+...+..
T Consensus 152 ------H~Al~DA~~ta~l~~~l~~~~~~ 174 (313)
T PRK06807 152 ------HNAFDDCITCAAVYQKCASIEEE 174 (313)
T ss_pred ------cChHHHHHHHHHHHHHHHHhhhh
Confidence 22788999999999999887743
No 44
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=96.78 E-value=0.012 Score=60.01 Aligned_cols=80 Identities=16% Similarity=0.076 Sum_probs=55.4
Q ss_pred HHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCC-----CCccHHHHHHHHcCCCCCcccccccCC
Q psy7894 312 VLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPM-----PRQSLAYLLKHYCDVDSDKTFQLFDWR 386 (1006)
Q Consensus 312 ~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~-----~~~SLa~Lve~yLgv~LdK~~q~sDW~ 386 (1006)
.|.+++.+.. +-|+||+.+|+.+|.. ....+.||...++.+.+ .+++|..|+.+|+|..+..++...+
T Consensus 76 ~~~~~i~~~~-vlVgHn~~fD~~fL~~----~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~-- 148 (161)
T cd06137 76 ALWKFIDPDT-ILVGHSLQNDLDALRM----IHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHD-- 148 (161)
T ss_pred HHHHhcCCCc-EEEeccHHHHHHHHhC----cCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCC--
Confidence 4556665433 4599999999999942 23457899988877654 3689999999999976643122121
Q ss_pred CCCCChHHHHHHHhchhHHHHHH
Q psy7894 387 HRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 387 ~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
|..||..+..||
T Consensus 149 -----------A~~DA~at~~l~ 160 (161)
T cd06137 149 -----------SLEDALAAREVV 160 (161)
T ss_pred -----------cHHHHHHHHHHh
Confidence 667887777765
No 45
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.74 E-value=0.036 Score=60.06 Aligned_cols=136 Identities=18% Similarity=0.182 Sum_probs=84.4
Q ss_pred cCCeEEEEeeeccCCccCCcEEE---EEEEe-CC----ceEEEeCcc-h----------h-h-----------hHHHHHH
Q psy7894 267 QQQEIAIDLEYHNYRSYQGYTCL---MQIST-RD----KDYIVDTLK-L----------R-E-----------DLEVLNE 315 (1006)
Q Consensus 267 ~a~~IAVDtE~~~~rty~g~lcL---IQISt-~~----~~yIID~la-L----------~-~-----------~L~~L~e 315 (1006)
....++||+|+.+.++..+.++- +-+.. +. ..++|++-. + . + .+..+..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 45778999999998876655432 22221 11 134666521 1 0 0 1122222
Q ss_pred HH----cCCCceeeecchhhHHHHHHHH---hCCc---cCeeechHhHHHhCCC---CCccHHHHHHHHcCCCCCccccc
Q psy7894 316 VL----TDKNIVKVFHGADSDIKWLQKD---FGLY---VVGMFDTHQACKFLPM---PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 316 lL----edp~IvKV~Hgak~Dl~~L~rd---~GI~---~~nlFDTqlAAyLLg~---~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
.| .+ ...-|+||+.+|+.+|.+. +|+. ...++||+..++.+.. ++++|..|+++ +|+.....+
T Consensus 85 ~l~~~~~~-~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~aH-- 160 (232)
T PRK07942 85 ALREAWAR-GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDNAH-- 160 (232)
T ss_pred HHHHHhhc-CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCCCC--
Confidence 22 23 3345999999999888643 3543 2358899988776543 35899999977 476554222
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
=|..||..+..|+..|..++.+.+
T Consensus 161 --------------~Al~Da~ata~l~~~l~~~~~~l~ 184 (232)
T PRK07942 161 --------------EATADALAAARVAWALARRFPELA 184 (232)
T ss_pred --------------ChHHHHHHHHHHHHHHHHHHHHhh
Confidence 278899999999999987766443
No 46
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.71 E-value=0.027 Score=62.10 Aligned_cols=133 Identities=21% Similarity=0.298 Sum_probs=84.9
Q ss_pred HhcCCeEEEEeeeccCCccCCcEEEEEEEe----CCc-----eEEEeCcc---------------------hhhhHHHHH
Q psy7894 265 LKQQQEIAIDLEYHNYRSYQGYTCLMQIST----RDK-----DYIVDTLK---------------------LREDLEVLN 314 (1006)
Q Consensus 265 L~~a~~IAVDtE~~~~rty~g~lcLIQISt----~~~-----~yIID~la---------------------L~~~L~~L~ 314 (1006)
+.....+.+|+|+.+..+..+. +|+|+. .+. ..+|.+-. +.+.+..|.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~--IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQ--IIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCe--EEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 4556889999999987765544 333332 111 12233211 113455677
Q ss_pred HHHcCCCceeeecchhhHHHHHHH---HhCCcc--CeeechHhHHH-hCCCCCccHHHHHHHHcCCCCCcccccccCCCC
Q psy7894 315 EVLTDKNIVKVFHGADSDIKWLQK---DFGLYV--VGMFDTHQACK-FLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHR 388 (1006)
Q Consensus 315 elLedp~IvKV~Hgak~Dl~~L~r---d~GI~~--~nlFDTqlAAy-LLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~R 388 (1006)
+++.+. +-|+||+.+|..+|.+ .+|+.. ...+||+-.++ ++..++++|++|++ ++|+.....+
T Consensus 143 ~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~-~lgi~~~~~H-------- 211 (257)
T PRK08517 143 LFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKE-LLGIEIEVHH-------- 211 (257)
T ss_pred HHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHH-HcCcCCCCCC--------
Confidence 777653 3589999999999854 345543 34678875554 44455789999987 4676643222
Q ss_pred CCChHHHHHHHhchhHHHHHHHHHHHHHHH
Q psy7894 389 PLPEPAIQYARTDTHYLLYVYDCMKLDLSA 418 (1006)
Q Consensus 389 PLs~eql~YAA~DA~yLL~Lyd~L~~eL~e 418 (1006)
=|..||.++..|+..+..++..
T Consensus 212 --------rAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 212 --------RAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred --------ChHHHHHHHHHHHHHHHHHhHH
Confidence 2778999999999998877753
No 47
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.66 E-value=0.013 Score=59.72 Aligned_cols=84 Identities=21% Similarity=0.057 Sum_probs=54.1
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHh---HHHhCCC---CCccHHHHHHHHcCCCCCccccc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQ---ACKFLPM---PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTql---AAyLLg~---~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
.+..|.+++.+ -+-|+||+.+|+.+|.. ......+.||.. +.+..+. .+++|..|+++|++..+...++.
T Consensus 67 v~~~l~~~l~~--~vlV~Hn~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~ 142 (157)
T cd06149 67 AQKEILKILKG--KVVVGHAIHNDFKALKY--FHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQG 142 (157)
T ss_pred HHHHHHHHcCC--CEEEEeCcHHHHHHhcc--cCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCC
Confidence 34566777764 34699999999999842 222235778864 2333222 35899999999987655432222
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
. =|..||.++..||
T Consensus 143 H-------------~Al~DA~at~~l~ 156 (157)
T cd06149 143 H-------------SSVEDARATMELY 156 (157)
T ss_pred c-------------CcHHHHHHHHHHh
Confidence 2 1667888888776
No 48
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.58 E-value=0.035 Score=56.19 Aligned_cols=86 Identities=22% Similarity=0.284 Sum_probs=58.3
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHHh---CCc-----cCeeechHhHHHhCCC-CCccHHHHHHHHcCCCCCccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKDF---GLY-----VVGMFDTHQACKFLPM-PRQSLAYLLKHYCDVDSDKTF 380 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~---GI~-----~~nlFDTqlAAyLLg~-~~~SLa~Lve~yLgv~LdK~~ 380 (1006)
+..|.+++.+.- -|+||+.+|+.+|.+.+ |+. ...++||+..++.+.+ ..++|+.|+++| |+..+..
T Consensus 72 ~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~- 147 (167)
T cd06131 72 ADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSHR- 147 (167)
T ss_pred HHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC-
Confidence 456667776633 48999999999886432 332 2357999977766554 357999999886 5543211
Q ss_pred ccccCCCCCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 381 QLFDWRHRPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 381 q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
..+-|..||.++..|+..|
T Consensus 148 -------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 -------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -------------CCCChHHHHHHHHHHHHHh
Confidence 1133888999998888665
No 49
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=96.50 E-value=0.027 Score=56.95 Aligned_cols=82 Identities=20% Similarity=0.111 Sum_probs=55.1
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCC
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRH 387 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~ 387 (1006)
+..+.+++.+ .-+-|+||+.+|+.+|. .. ...++||...++.+.. .+++|..|+++|++..+.......
T Consensus 66 ~~~~~~fl~~-~~vlVgHn~~fD~~fL~-~~---~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H---- 136 (150)
T cd06145 66 QKKLLSLISP-DTILVGHSLENDLKALK-LI---HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGH---- 136 (150)
T ss_pred HHHHHHHhCC-CCEEEEcChHHHHHHhh-cc---CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCC----
Confidence 3456667752 23459999999999994 22 2458999977765433 358999999999986542111111
Q ss_pred CCCChHHHHHHHhchhHHHHHH
Q psy7894 388 RPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 388 RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
=|..||..+..||
T Consensus 137 ---------~Al~DA~~t~~l~ 149 (150)
T cd06145 137 ---------DSVEDARAALELV 149 (150)
T ss_pred ---------CcHHHHHHHHHHh
Confidence 1667888887776
No 50
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.42 E-value=0.061 Score=58.86 Aligned_cols=89 Identities=24% Similarity=0.296 Sum_probs=60.0
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCc------cCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLY------VVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKT 379 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~------~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~ 379 (1006)
+..|.+++.+.. .|+||+.+|+..|.+. +|.. ...++||...++.+-++ +++|..|+++| |+....
T Consensus 77 ~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~~- 152 (240)
T PRK05711 77 ADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNSH- 152 (240)
T ss_pred HHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCCC-
Confidence 345666666543 4899999999888643 3422 13589999888766543 57999999876 653211
Q ss_pred cccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 380 FQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 380 ~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
|. .+=|..||..+..||..|...
T Consensus 153 --------r~-----~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 153 --------RT-----LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred --------CC-----CCCHHHHHHHHHHHHHHHHCc
Confidence 11 122888999999999887643
No 51
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=96.42 E-value=0.064 Score=56.85 Aligned_cols=83 Identities=19% Similarity=0.104 Sum_probs=59.4
Q ss_pred ceeeecchhhHHHHHHHH---hCCcc-----CeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCChH
Q psy7894 322 IVKVFHGADSDIKWLQKD---FGLYV-----VGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEP 393 (1006)
Q Consensus 322 IvKV~Hgak~Dl~~L~rd---~GI~~-----~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~e 393 (1006)
-+-|+||+.+|+.+|.+. +|... ..++||+..++.+.+ ..+|..|+++| |+... ..
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-~~~L~~l~~~~-gi~~~--------------~~ 169 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQAA-GXDFD--------------ST 169 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-cccHHHHHHHc-CCCcc--------------cc
Confidence 346999999999998643 34421 237899988876643 46899988864 65432 01
Q ss_pred HHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 394 AIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 394 ql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
..+=|..||..+..|+..|..++.+.+
T Consensus 170 ~~H~Al~Da~ata~lf~~l~~~~~~~~ 196 (200)
T TIGR01298 170 QAHSALYDTEKTAELFCEIVNRWKRLG 196 (200)
T ss_pred chhhhHHhHHHHHHHHHHHHHHHHHcc
Confidence 234488999999999999999988664
No 52
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.41 E-value=0.03 Score=59.86 Aligned_cols=135 Identities=19% Similarity=0.242 Sum_probs=82.2
Q ss_pred HhcCCeEEEEeeeccCCccCCcEEEEEEEe----CC----c--eEEEeCcc-----------h-----------hhhHHH
Q psy7894 265 LKQQQEIAIDLEYHNYRSYQGYTCLMQIST----RD----K--DYIVDTLK-----------L-----------REDLEV 312 (1006)
Q Consensus 265 L~~a~~IAVDtE~~~~rty~g~lcLIQISt----~~----~--~yIID~la-----------L-----------~~~L~~ 312 (1006)
|.....++||+|+.+..+... +|+|+. .. . ..+|.|.. + .+.+..
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~---IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHD---IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred EEecCEEEEEecCCCCCCCCC---EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 345678999999999876444 333321 11 1 12343320 0 122345
Q ss_pred HHHHHcCCCceeeecchhhHHHHHHHHhC---Cc-c--CeeechHhHHHhCC---C-CCccHHHHHHHHcCCCCCccccc
Q psy7894 313 LNEVLTDKNIVKVFHGADSDIKWLQKDFG---LY-V--VGMFDTHQACKFLP---M-PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 313 L~elLedp~IvKV~Hgak~Dl~~L~rd~G---I~-~--~nlFDTqlAAyLLg---~-~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
|..++.+. .-|+||+.+|+.+|.+.+. .. . ..++||+..++.+. + .+++|..|+++| |+..... .
T Consensus 81 ~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~~-~- 155 (217)
T TIGR00573 81 FADYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSHR-A- 155 (217)
T ss_pred HHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCCc-c-
Confidence 66666553 3489999999999976542 21 1 35789886555432 1 357899998775 6542200 1
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHh
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~ 419 (1006)
..=|..||.++..|+..|..+....
T Consensus 156 ------------~H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 156 ------------LHGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred ------------cCCHHHHHHHHHHHHHHHHhcchhh
Confidence 1228899999999999998776543
No 53
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.37 E-value=0.041 Score=72.08 Aligned_cols=134 Identities=21% Similarity=0.295 Sum_probs=92.9
Q ss_pred hcCCeEEEEeeeccCCccCCcEEEEEEEe---CCc------eEEEeCc----------------------chhhhHHHHH
Q psy7894 266 KQQQEIAIDLEYHNYRSYQGYTCLMQIST---RDK------DYIVDTL----------------------KLREDLEVLN 314 (1006)
Q Consensus 266 ~~a~~IAVDtE~~~~rty~g~lcLIQISt---~~~------~yIID~l----------------------aL~~~L~~L~ 314 (1006)
.....++||+|+++..+....+ |+|+. .++ ..+|.|. .+.+.+..|.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~I--IEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEI--IEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 5678999999999987655543 33332 111 1223331 0113456677
Q ss_pred HHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCC
Q psy7894 315 EVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRH 387 (1006)
Q Consensus 315 elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~ 387 (1006)
+++.+. +-|+||+.+|+..|.+. +|+.. ..++||+..++.+.+ ..++|+.|+++| |+.+..
T Consensus 266 ~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~~~~--------- 333 (1213)
T TIGR01405 266 EFFKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKL-GVDLDD--------- 333 (1213)
T ss_pred HHhCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCCCCC---------
Confidence 777653 45899999999988643 46542 468999998888764 468999999884 776532
Q ss_pred CCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 388 RPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 388 RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
.+-|..||..+..|+..|..++.+.+
T Consensus 334 -------~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 334 -------HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred -------CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 14488999999999999999998765
No 54
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=96.37 E-value=0.0064 Score=73.70 Aligned_cols=71 Identities=15% Similarity=0.190 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHhhHHHHHHHHHHH
Q psy7894 466 QKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKA 536 (1006)
Q Consensus 466 qlavlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~~~~eil~iI~~A 536 (1006)
....|.+|..||-++|.+.|+||+-|++|.+|.++|+.+|.+..++..+.|+....+.+||..++++|.+.
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~gvg~~k~~~yg~~fl~~i~~~ 587 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSINGVGEAKLERYGQAFLAVIQAH 587 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcCCcccchhhccHHHHHHHHHh
Confidence 45589999999999999999999999999999999999999999999999999999999999999999764
No 55
>PRK07883 hypothetical protein; Validated
Probab=96.35 E-value=0.033 Score=67.71 Aligned_cols=137 Identities=19% Similarity=0.175 Sum_probs=89.5
Q ss_pred HHHhcCCeEEEEeeeccCCccCCcEEEEEEEe----CCc-----eEEEeCcc-----------h-----------hhhHH
Q psy7894 263 SELKQQQEIAIDLEYHNYRSYQGYTCLMQIST----RDK-----DYIVDTLK-----------L-----------REDLE 311 (1006)
Q Consensus 263 e~L~~a~~IAVDtE~~~~rty~g~lcLIQISt----~~~-----~yIID~la-----------L-----------~~~L~ 311 (1006)
..+.....++||+|+++.++....+ ++|+. .+. ..+|+|-. + .+.+.
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p~~~~I--IEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~ 87 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSPAGDAI--TEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLP 87 (557)
T ss_pred CCCcCCCEEEEEEecCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 3455678899999999887654443 33332 111 22343310 1 12234
Q ss_pred HHHHHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCC----CCCccHHHHHHHHcCCCCCccccc
Q psy7894 312 VLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLP----MPRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 312 ~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg----~~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
.|..++.+ .+-|+||+.+|+.+|.+. +|+.. ...+||+..++-+- ..+++|..|++ ++|+.....
T Consensus 88 ~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~~--- 161 (557)
T PRK07883 88 AFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTPT--- 161 (557)
T ss_pred HHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCCC---
Confidence 56667765 345899999999998643 46654 35789987665432 34689999987 567765321
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
+-|..||.++..|+..|..++.+.|
T Consensus 162 -------------H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 162 -------------HRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred -------------CCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 2388999999999999999987655
No 56
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.34 E-value=0.053 Score=58.61 Aligned_cols=88 Identities=25% Similarity=0.317 Sum_probs=60.7
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH---hCC--c-c---CeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGL--Y-V---VGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKT 379 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI--~-~---~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~ 379 (1006)
+..|.+++.+.. -|+||+.+|+.+|.+. +|. . + ..++||+..++.+-++ +++|..|+++| |+....
T Consensus 73 ~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~~- 148 (225)
T TIGR01406 73 ADEFLDFIGGSE--LVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNSH- 148 (225)
T ss_pred HHHHHHHhCCCE--EEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCCC-
Confidence 455666776533 3899999999998643 452 2 1 4689999888765543 58999999986 543321
Q ss_pred cccccCCCCCCChHHHHHHHhchhHHHHHHHHHHH
Q psy7894 380 FQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKL 414 (1006)
Q Consensus 380 ~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~ 414 (1006)
| ..+=|..||..+..||..|..
T Consensus 149 --------r-----~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 149 --------R-----TLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred --------C-----CCcCHHHHHHHHHHHHHHHHc
Confidence 1 112288999999999988754
No 57
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.32 E-value=0.087 Score=55.62 Aligned_cols=137 Identities=14% Similarity=0.123 Sum_probs=80.6
Q ss_pred HHHHHHHHhcCCeEEEEeeeccCCccCCcEEEEEE-EeC-Cc-------eEEEeCcc----------------------h
Q psy7894 258 VTQLVSELKQQQEIAIDLEYHNYRSYQGYTCLMQI-STR-DK-------DYIVDTLK----------------------L 306 (1006)
Q Consensus 258 L~~lle~L~~a~~IAVDtE~~~~rty~g~lcLIQI-St~-~~-------~yIID~la----------------------L 306 (1006)
+..+.+.......++||+|+.+.++..+.++-|.. .+. +. .++|.+.. +
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~ 98 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSE 98 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCH
Confidence 33444444456889999999988765554322221 111 11 12344320 0
Q ss_pred hhhHHHHHHHHcCCCceeeecchhhHHHHHHHH----hCCccC-eeechHhHHH--hC-C----CCCccHHHHHHHHcCC
Q psy7894 307 REDLEVLNEVLTDKNIVKVFHGADSDIKWLQKD----FGLYVV-GMFDTHQACK--FL-P----MPRQSLAYLLKHYCDV 374 (1006)
Q Consensus 307 ~~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd----~GI~~~-nlFDTqlAAy--LL-g----~~~~SLa~Lve~yLgv 374 (1006)
.+.+..|..++.+. .-|+||+.+|+..|.+. +|..+. ..+||.-..+ .. . ..+++|+.|+++| |+
T Consensus 99 ~~vl~~~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~-gi 175 (202)
T PRK09145 99 EEALRQLLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL-DL 175 (202)
T ss_pred HHHHHHHHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-CC
Confidence 12345666677653 35999999999988643 344443 5788864321 11 1 1258999999764 66
Q ss_pred CCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 375 DSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 375 ~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
..... . =|..||.++..||..|.
T Consensus 176 ~~~~~---H-------------~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 176 PVLGR---H-------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCCC---C-------------CcHHHHHHHHHHHHHHH
Confidence 54321 1 27789999999998774
No 58
>PRK05168 ribonuclease T; Provisional
Probab=96.10 E-value=0.18 Score=53.94 Aligned_cols=147 Identities=16% Similarity=0.204 Sum_probs=89.2
Q ss_pred HHHHHHHHhcCCeEEEEeeeccCCccCCcE---EEEEEEeC--C-----c--eEEEeCc---ch----------h-h---
Q psy7894 258 VTQLVSELKQQQEIAIDLEYHNYRSYQGYT---CLMQISTR--D-----K--DYIVDTL---KL----------R-E--- 308 (1006)
Q Consensus 258 L~~lle~L~~a~~IAVDtE~~~~rty~g~l---cLIQISt~--~-----~--~yIID~l---aL----------~-~--- 308 (1006)
+.-+-..+.....++||+|+++..+....+ +.+.+... + . ..+|.|. .+ . +
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~ 86 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPL 86 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhh
Confidence 445556777888999999999887655543 22322211 1 1 1245441 01 0 1
Q ss_pred --------hHHHHHHHHcC-------CCceeeecchhhHHHHHHH---HhCCc---c--CeeechHhHHHhCCCCCccHH
Q psy7894 309 --------DLEVLNEVLTD-------KNIVKVFHGADSDIKWLQK---DFGLY---V--VGMFDTHQACKFLPMPRQSLA 365 (1006)
Q Consensus 309 --------~L~~L~elLed-------p~IvKV~Hgak~Dl~~L~r---d~GI~---~--~nlFDTqlAAyLLg~~~~SLa 365 (1006)
.+..+.+++.+ .+.+-|+||+.+|+..|.+ .+|+. . ..++||...++.+.. ..+|.
T Consensus 87 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-~~~L~ 165 (211)
T PRK05168 87 RGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-QTVLA 165 (211)
T ss_pred hcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-CCCHH
Confidence 11222233321 2345699999999988754 34542 1 247999887776543 36899
Q ss_pred HHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 366 YLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 366 ~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
.++.+| |+.++.. . .+=|..||..+..|+..|..++.+.|
T Consensus 166 ~l~~~~-gl~~~~~-~-------------~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 166 KACQAA-GIEFDNK-E-------------AHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred HHHHHC-CCCCCCC-C-------------CCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 988874 6554211 1 12278899999999999998887665
No 59
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=96.07 E-value=0.014 Score=75.20 Aligned_cols=72 Identities=15% Similarity=0.133 Sum_probs=67.6
Q ss_pred HHHHHHHHHHHHHHHHHh--cCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHhh
Q psy7894 573 QKYALRELYKWRDRIARD--KDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKAR 644 (1006)
Q Consensus 573 Qlavlk~L~~WRd~~ARe--~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~Ar 644 (1006)
...+|.+|..||..+|++ +++++..|+++..|.+||+..|++..+|..+.|+-..-+.+||.+++++|..--
T Consensus 1028 d~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eIA~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~~ 1101 (1195)
T PLN03137 1028 SAILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDRLLETIESTI 1101 (1195)
T ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999 699999999999999999999999999999999999999999999999998643
No 60
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.89 E-value=0.14 Score=51.23 Aligned_cols=91 Identities=23% Similarity=0.223 Sum_probs=62.1
Q ss_pred hHHHHHHHHcCCCceeeecch-hhHHHHHHHH---hCCcc---CeeechHhHHHhCCC-CCccHHHHHHHHcCCCCCccc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGA-DSDIKWLQKD---FGLYV---VGMFDTHQACKFLPM-PRQSLAYLLKHYCDVDSDKTF 380 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hga-k~Dl~~L~rd---~GI~~---~nlFDTqlAAyLLg~-~~~SLa~Lve~yLgv~LdK~~ 380 (1006)
.+..|..++.+. + .|+|++ .+|+.+|.+. +|+.. ..++||+..++.+.. ..++|..|++.| |+.....
T Consensus 70 ~~~~~~~~l~~~-~-~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~-~~~~~~~- 145 (169)
T smart00479 70 VLEELLEFLKGK-I-LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERL-GLEVIGR- 145 (169)
T ss_pred HHHHHHHHhcCC-E-EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHC-CCCCCCC-
Confidence 346677788664 3 366777 9999998643 44432 247999887776543 368999999876 3332110
Q ss_pred ccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHH
Q psy7894 381 QLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLS 417 (1006)
Q Consensus 381 q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~ 417 (1006)
.+.|..||..+..||..+..++.
T Consensus 146 --------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 146 --------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred --------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 24588999999999999876653
No 61
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=95.83 E-value=0.12 Score=59.91 Aligned_cols=136 Identities=12% Similarity=0.194 Sum_probs=84.1
Q ss_pred HhcCCeEEEEeeeccCCccCCcEEEEEEE---e--CC---c--eEEEeCcc--------------------hhhhHHHHH
Q psy7894 265 LKQQQEIAIDLEYHNYRSYQGYTCLMQIS---T--RD---K--DYIVDTLK--------------------LREDLEVLN 314 (1006)
Q Consensus 265 L~~a~~IAVDtE~~~~rty~g~lcLIQIS---t--~~---~--~yIID~la--------------------L~~~L~~L~ 314 (1006)
+.....++||+|+.++++.... +|+|+ . .. . ..+|.+-. +.+.+..|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~dr--IIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSR--LITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCe--EEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 4446889999999998876553 34432 1 11 1 12343311 123456677
Q ss_pred HHHcCCCceeeecchhhHHHHHHHHh-------------------------------CCcc-CeeechHhHHHhCCC--C
Q psy7894 315 EVLTDKNIVKVFHGADSDIKWLQKDF-------------------------------GLYV-VGMFDTHQACKFLPM--P 360 (1006)
Q Consensus 315 elLedp~IvKV~Hgak~Dl~~L~rd~-------------------------------GI~~-~nlFDTqlAAyLLg~--~ 360 (1006)
+++.+. +-|+||+.+|+..|...+ ++.. ..++||+-.++.+.+ .
T Consensus 121 ~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 121 RLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 788754 459999999999886532 1222 258999999988875 4
Q ss_pred CccHHHHHHHHcCCCCCccc---ccccCCCCCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 361 RQSLAYLLKHYCDVDSDKTF---QLFDWRHRPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 361 ~~SLa~Lve~yLgv~LdK~~---q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
++.|..|+.+ +|+..+-.. ++++ .+.. ..+..|+..|..||..+
T Consensus 199 ~~rL~~La~~-lGi~~p~~~A~~~Ra~-----~p~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 DIRIRGVAHT-LGLDAPAAEASVERAQ-----VPHR--QLCREETLLVARLYFAL 245 (377)
T ss_pred CCCHHHHHHH-hCCCCCchhhhhhhhc-----CChh--hhhhHHHHHHHHHHHHh
Confidence 7999999987 466543110 1111 1111 12457998888888765
No 62
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=95.82 E-value=0.15 Score=55.35 Aligned_cols=129 Identities=21% Similarity=0.248 Sum_probs=81.6
Q ss_pred CeEEEEeeeccCCccCCcEEEEEEEeC----Cc--eEEEeCcc-----------h-----------hhhHHHHHHHHcCC
Q psy7894 269 QEIAIDLEYHNYRSYQGYTCLMQISTR----DK--DYIVDTLK-----------L-----------REDLEVLNEVLTDK 320 (1006)
Q Consensus 269 ~~IAVDtE~~~~rty~g~lcLIQISt~----~~--~yIID~la-----------L-----------~~~L~~L~elLedp 320 (1006)
..+.||+|+++.+.-...+ |+|+.- .. ..+|.|-. + .+.+..+.+++.+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~I--Ieig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRI--IEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD 80 (232)
T ss_pred cEEEEEeeCCCCCCCCCEE--EEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC
Confidence 3688999999887544443 444321 11 22444321 1 01233555566543
Q ss_pred Cceeeecc-hhhHHHHHHHH---hCCcc--CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCCCCCCh
Q psy7894 321 NIVKVFHG-ADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPE 392 (1006)
Q Consensus 321 ~IvKV~Hg-ak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~ 392 (1006)
-.-|+|| +.+|+..|.+. +|+.. ...+||+-.++.+.+ +.++|..|+..| |+.....+
T Consensus 81 -~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~aH------------ 146 (232)
T PRK06309 81 -NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQAH------------ 146 (232)
T ss_pred -CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCCCC------------
Confidence 3459999 58999998643 45542 368999888876644 468999998776 65433222
Q ss_pred HHHHHHHhchhHHHHHHHHHHHHHH
Q psy7894 393 PAIQYARTDTHYLLYVYDCMKLDLS 417 (1006)
Q Consensus 393 eql~YAA~DA~yLL~Lyd~L~~eL~ 417 (1006)
=|..||.++..|+..|..++.
T Consensus 147 ----~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 147 ----RALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred ----CcHHHHHHHHHHHHHHHHHHH
Confidence 278899999999999876664
No 63
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.82 E-value=0.21 Score=54.70 Aligned_cols=132 Identities=16% Similarity=0.123 Sum_probs=79.6
Q ss_pred cCCeEEEEeeeccCCccCCcEEEEEEEe--CCc-------eEEEeCcc-----------h-----------hhhHHHHHH
Q psy7894 267 QQQEIAIDLEYHNYRSYQGYTCLMQIST--RDK-------DYIVDTLK-----------L-----------REDLEVLNE 315 (1006)
Q Consensus 267 ~a~~IAVDtE~~~~rty~g~lcLIQISt--~~~-------~yIID~la-----------L-----------~~~L~~L~e 315 (1006)
....++||+|+.+.++..+.++-|.+-. .+. .++|.+-. + .+.+..|.+
T Consensus 46 ~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~~ 125 (239)
T PRK09146 46 EVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLE 125 (239)
T ss_pred cCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHHH
Confidence 4567899999998876555543222211 111 23454310 1 122344555
Q ss_pred HHcCCCceeeecchhhHHHHHHHH----hCCcc-CeeechHhHHHhCCC---------------CCccHHHHHHHHcCCC
Q psy7894 316 VLTDKNIVKVFHGADSDIKWLQKD----FGLYV-VGMFDTHQACKFLPM---------------PRQSLAYLLKHYCDVD 375 (1006)
Q Consensus 316 lLedp~IvKV~Hgak~Dl~~L~rd----~GI~~-~nlFDTqlAAyLLg~---------------~~~SLa~Lve~yLgv~ 375 (1006)
++.+ . +-|+||+.+|+.+|.+. +|..+ ..++||+..++.+-+ ..++|.+|+.+ +|+.
T Consensus 126 ~~~~-~-~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gl~ 202 (239)
T PRK09146 126 ALAG-K-VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR-YGLP 202 (239)
T ss_pred HhCC-C-EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH-cCCC
Confidence 5544 2 45899999999998654 23333 358899987765411 34678888886 4554
Q ss_pred CCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHH
Q psy7894 376 SDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLS 417 (1006)
Q Consensus 376 LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~ 417 (1006)
.... +=|..||..+..|+..+..++-
T Consensus 203 ~~~~----------------H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 203 AYSP----------------HHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CCCC----------------CCcHHHHHHHHHHHHHHHHHHc
Confidence 3211 2278899999999888776664
No 64
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=95.81 E-value=0.13 Score=53.67 Aligned_cols=99 Identities=21% Similarity=0.219 Sum_probs=64.7
Q ss_pred HHHHHHHHc--CCCceeeecch-hhHHHHHHH---HhCCcc-----------------------C-eeechHhHHHhCC-
Q psy7894 310 LEVLNEVLT--DKNIVKVFHGA-DSDIKWLQK---DFGLYV-----------------------V-GMFDTHQACKFLP- 358 (1006)
Q Consensus 310 L~~L~elLe--dp~IvKV~Hga-k~Dl~~L~r---d~GI~~-----------------------~-nlFDTqlAAyLLg- 358 (1006)
+..|..++. ||.+ -|+||. .+|+..|.. .+|+.. + .++|++..++-..
T Consensus 67 L~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~ 145 (199)
T cd05160 67 LKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK 145 (199)
T ss_pred HHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC
Confidence 455556655 3665 499999 789988753 355544 1 3689987776543
Q ss_pred CCCccHHHHHHHHcCCCCCc--ccccccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 359 MPRQSLAYLLKHYCDVDSDK--TFQLFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 359 ~~~~SLa~Lve~yLgv~LdK--~~q~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
.++++|..++++++|..-.. .....+|....-....++|...||..++.|+
T Consensus 146 l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 146 LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 45799999999999864221 1122222111223568999999999998876
No 65
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.80 E-value=0.13 Score=65.35 Aligned_cols=131 Identities=15% Similarity=0.162 Sum_probs=87.2
Q ss_pred CCeEEEEeeeccCCccCCcEEEEEEEe----CCc-----eEEEeCcc-----------h-----------hhhHHHHHHH
Q psy7894 268 QQEIAIDLEYHNYRSYQGYTCLMQIST----RDK-----DYIVDTLK-----------L-----------REDLEVLNEV 316 (1006)
Q Consensus 268 a~~IAVDtE~~~~rty~g~lcLIQISt----~~~-----~yIID~la-----------L-----------~~~L~~L~el 316 (1006)
...++||+|+.+..+. + .+|||+. ++. ..+|.|.. + .+.+..|.++
T Consensus 7 ~~~vvvD~ETTGl~~~-d--~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 7 RKYAVVDLEATGAGPN-A--SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCEEEEEEecCCcCCC-C--eEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 4689999999987642 3 3455543 111 12343310 1 1234556667
Q ss_pred HcCCCceeeecchhhHHHHHHHH---hCCcc-CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccccccCCCCCC
Q psy7894 317 LTDKNIVKVFHGADSDIKWLQKD---FGLYV-VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQLFDWRHRPL 390 (1006)
Q Consensus 317 Ledp~IvKV~Hgak~Dl~~L~rd---~GI~~-~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPL 390 (1006)
+.+. +-|+||+.+|+..|.+. .|+.+ ...+||+..++.+-+ .+++|..|++. +|+.....+
T Consensus 84 l~~~--~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~~H---------- 150 (820)
T PRK07246 84 IEDC--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLADAH---------- 150 (820)
T ss_pred hCCC--EEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCCCC----------
Confidence 7653 35999999999998654 35544 357899988876654 46899999976 676643222
Q ss_pred ChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 391 PEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 391 s~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
=|..||..+..|+..|..++...+
T Consensus 151 ------~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 151 ------TAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred ------CHHHHHHHHHHHHHHHHHHHhhcC
Confidence 278899999999999998887543
No 66
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=95.78 E-value=0.14 Score=49.82 Aligned_cols=83 Identities=20% Similarity=0.167 Sum_probs=55.5
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHHhC-----CccCeeechHhHHHhCC-C-CCccHHHHHHHHcCCCCCcccc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFG-----LYVVGMFDTHQACKFLP-M-PRQSLAYLLKHYCDVDSDKTFQ 381 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~G-----I~~~nlFDTqlAAyLLg-~-~~~SLa~Lve~yLgv~LdK~~q 381 (1006)
.+..|..++.+ ...|+||+.+|..+|.+.+. ......+||+..++.+. . ..+++..+...++|.....
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~--- 143 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEG--- 143 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCCC---
Confidence 34667778876 45699999999999865543 22346899997665543 3 3477888755556653321
Q ss_pred cccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 382 LFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 382 ~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
.+-|..||.++..||
T Consensus 144 -------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 144 -------------AHRALADALATAELL 158 (159)
T ss_pred -------------CCCcHHHHHHHHHHh
Confidence 233788998888776
No 67
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=95.55 E-value=0.22 Score=63.54 Aligned_cols=92 Identities=15% Similarity=0.151 Sum_probs=66.9
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCc--cCeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCccccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLY--VVGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~--~~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
+..|.+++.+ . .-|+||+.+|+.+|.+. .|+. ....+||+..++.+.+ .+++|.+|+++ +|+..+..+
T Consensus 71 ~~~l~~~l~~-~-~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~~~H-- 145 (850)
T TIGR01407 71 AQEIYDLLED-G-IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHENPH-- 145 (850)
T ss_pred HHHHHHHhCC-C-EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCCCCC--
Confidence 3456667755 3 35999999999998643 4554 2468999988877654 36899999887 576554222
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
=|..||..+..|+..|..++.+..
T Consensus 146 --------------~Al~DA~ata~l~~~l~~~~~~l~ 169 (850)
T TIGR01407 146 --------------RADSDAQATAELLLLLFEKMEKLP 169 (850)
T ss_pred --------------ChHHHHHHHHHHHHHHHHHHHhcC
Confidence 278899999999999988887543
No 68
>KOG2405|consensus
Probab=95.44 E-value=0.0074 Score=68.78 Aligned_cols=127 Identities=19% Similarity=0.187 Sum_probs=85.6
Q ss_pred cEEEEEEEeCCceEEEeCcchh--hhHHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCCC---
Q psy7894 286 YTCLMQISTRDKDYIVDTLKLR--EDLEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP--- 360 (1006)
Q Consensus 286 ~lcLIQISt~~~~yIID~laL~--~~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~--- 360 (1006)
.+.+|+|+++...|++|.+.-+ ...+.....|+...+ |. |+..++..|...|++.+.+++||++|..++.+.
T Consensus 212 e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve~~e~g 288 (458)
T KOG2405|consen 212 EATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVEPSEYG 288 (458)
T ss_pred hhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhhhHHhc
Confidence 3445899999999999875421 112224445655444 44 999999999889999999999999999998642
Q ss_pred -CccHHHHH------H--HHcCCCCC------cc-c-ccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 361 -RQSLAYLL------K--HYCDVDSD------KT-F-QLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 361 -~~SLa~Lv------e--~yLgv~Ld------K~-~-q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
++....++ . .|++.... +. . ..-.|..||.++.+..-++.||+.|+..++.|.+.
T Consensus 289 rr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~ 360 (458)
T KOG2405|consen 289 RRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAV 360 (458)
T ss_pred ccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhh
Confidence 12222111 1 22222211 11 1 22369999999999999999999999977666544
No 69
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.44 E-value=0.046 Score=69.74 Aligned_cols=135 Identities=21% Similarity=0.287 Sum_probs=97.3
Q ss_pred HhcCCeEEEEeeeccCCccCCcEEEEEEEeCC--c-------eEEEeCcc----------------------hhhhHHHH
Q psy7894 265 LKQQQEIAIDLEYHNYRSYQGYTCLMQISTRD--K-------DYIVDTLK----------------------LREDLEVL 313 (1006)
Q Consensus 265 L~~a~~IAVDtE~~~~rty~g~lcLIQISt~~--~-------~yIID~la----------------------L~~~L~~L 313 (1006)
|..+..+.+|+|+.++.+.+.. +|+|+... . .+.|+|.. +...+..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 4557889999999998776654 45554321 1 12233210 11346778
Q ss_pred HHHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCCC--CccHHHHHHHHcCCCCCcccccccCC
Q psy7894 314 NEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPMP--RQSLAYLLKHYCDVDSDKTFQLFDWR 386 (1006)
Q Consensus 314 ~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~LdK~~q~sDW~ 386 (1006)
.+++.|. +-|.||+.+|+..|... +|+.+ .++.||.-.|+.|+|. +|+|..|+++| |+.+
T Consensus 496 ~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~l---------- 562 (1444)
T COG2176 496 REFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVEL---------- 562 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-CccH----------
Confidence 8888774 34999999999888644 56655 4699999999999974 79999999885 5444
Q ss_pred CCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 387 HRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 387 ~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
+..+-|-.|+.++-+|+-.+.+.|.+.|
T Consensus 563 ------e~hHRA~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 563 ------ERHHRADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred ------HHhhhhhhhHHHHHHHHHHHHHHHHHhc
Confidence 2344567799999999999999999986
No 70
>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=95.39 E-value=0.34 Score=50.91 Aligned_cols=78 Identities=18% Similarity=0.111 Sum_probs=53.7
Q ss_pred ceeeecchhhHHHHHHH---HhCCc-----cCeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCChH
Q psy7894 322 IVKVFHGADSDIKWLQK---DFGLY-----VVGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEP 393 (1006)
Q Consensus 322 IvKV~Hgak~Dl~~L~r---d~GI~-----~~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~e 393 (1006)
.+-|+||+.+|+..|.+ .+|+. ...++||+..++.+.+ ..+|+.++++| |+..+. ..
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-~~~L~~l~~~~-gi~~~~-~~------------ 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-QTVLAKACQAA-GIEFDN-KE------------ 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-CCcHHHHHHHC-CCCCCC-CC------------
Confidence 35699999999988864 35551 1247999988877643 46899988864 665321 11
Q ss_pred HHHHHHhchhHHHHHHHHHHHH
Q psy7894 394 AIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 394 ql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
.+=|..||..+..|+..|.++
T Consensus 168 -~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 -AHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -CcChHHHHHHHHHHHHHHHHh
Confidence 122778999998888887643
No 71
>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=95.24 E-value=0.05 Score=54.81 Aligned_cols=141 Identities=16% Similarity=0.236 Sum_probs=73.6
Q ss_pred EEEEeeeccCCccCCcEEEEEEEe--CCc-eEEEeCcchh-hhHHHHH---HHHcCCCceeeecchhhHHHHHHHHh---
Q psy7894 271 IAIDLEYHNYRSYQGYTCLMQIST--RDK-DYIVDTLKLR-EDLEVLN---EVLTDKNIVKVFHGADSDIKWLQKDF--- 340 (1006)
Q Consensus 271 IAVDtE~~~~rty~g~lcLIQISt--~~~-~yIID~laL~-~~L~~L~---elLedp~IvKV~Hgak~Dl~~L~rd~--- 340 (1006)
+.+|+|+.++.+..+.+.++.+.. ++. .++.....-. ..-..+. ..+.+...+.++|+..+|+..|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~~iv~yng~~FD~p~L~~~~~~~ 80 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEADNIVTYNGKNFDIPFLKRRAKRY 80 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT--EEESSTTTTHHHHHHHHH-HH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCCeEEEEeCcccCHHHHHHHHHHc
Confidence 468999998876667777787775 232 2232221111 1111222 45666666666677788999987655
Q ss_pred CCc-cCeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcc----ccc----ccCC---CCCCChHHHHHHHhchhHHHHH
Q psy7894 341 GLY-VVGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKT----FQL----FDWR---HRPLPEPAIQYARTDTHYLLYV 408 (1006)
Q Consensus 341 GI~-~~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~----~q~----sDW~---~RPLs~eql~YAA~DA~yLL~L 408 (1006)
++. ..+.+|++..++-...+++||..+... +|+.-... ... ..|. .+..-..++.|...|+..+.+|
T Consensus 81 ~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L 159 (164)
T PF13482_consen 81 GLPPPFNHIDLLKIIKKHFLESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRL 159 (164)
T ss_dssp HH--GGGEEEHHHHHT-TTSCCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHH
T ss_pred CCCcccchhhHHHHHHhccCCCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 333 457899998887555566788887666 67654311 100 1121 1234578999999999999999
Q ss_pred HHHH
Q psy7894 409 YDCM 412 (1006)
Q Consensus 409 yd~L 412 (1006)
++.|
T Consensus 160 ~~~l 163 (164)
T PF13482_consen 160 YEWL 163 (164)
T ss_dssp HHHH
T ss_pred HHHh
Confidence 9887
No 72
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=95.22 E-value=0.25 Score=51.25 Aligned_cols=80 Identities=24% Similarity=0.256 Sum_probs=55.1
Q ss_pred HHHHHHHcC--CCceeeecch-hhHHHHHHHH---hCCcc---CeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccc
Q psy7894 311 EVLNEVLTD--KNIVKVFHGA-DSDIKWLQKD---FGLYV---VGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQ 381 (1006)
Q Consensus 311 ~~L~elLed--p~IvKV~Hga-k~Dl~~L~rd---~GI~~---~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q 381 (1006)
..|.+++.. ...+-|+||+ .+|+..|.+. +|+.+ ..++||+..++.+.+ +|+.|+++++|+.....
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~---~L~~l~~~~~~~~~~~~-- 160 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ---SLGSLYKRLFGQEPKNS-- 160 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh---hHHHHHHHHhCCCcccc--
Confidence 345555542 2346799998 8999988543 45543 235799988887665 89999999888765432
Q ss_pred cccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 382 LFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 382 ~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
+-|..||..+..++
T Consensus 161 --------------H~A~~Da~at~~v~ 174 (177)
T cd06136 161 --------------HTAEGDVLALLKCA 174 (177)
T ss_pred --------------cchHHHHHHHHHHH
Confidence 22778888887765
No 73
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=95.06 E-value=0.52 Score=46.80 Aligned_cols=81 Identities=17% Similarity=0.153 Sum_probs=55.8
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQ 381 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q 381 (1006)
.+..|..++.+. .-|+||+.+|..+|.+. +|+.. ...+||+..+..+-+ +.++|..|++. +|+..+ .+
T Consensus 67 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~-~H- 141 (156)
T cd06130 67 VWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-HH- 141 (156)
T ss_pred HHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc-Cc-
Confidence 345677777763 45999999999998643 35543 358999877665433 46899999886 566543 22
Q ss_pred cccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 382 LFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 382 ~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
=|..||..+.+|+
T Consensus 142 ---------------~Al~Da~~ta~l~ 154 (156)
T cd06130 142 ---------------DALEDARACAEIL 154 (156)
T ss_pred ---------------CchHHHHHHHHHH
Confidence 2667888887775
No 74
>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=94.86 E-value=0.37 Score=50.75 Aligned_cols=103 Identities=14% Similarity=0.260 Sum_probs=68.2
Q ss_pred hHHHHHHHHcC--CCceeeecch-hhHHHHHHHH---hCCccC------------------------eeechHhHHHh-C
Q psy7894 309 DLEVLNEVLTD--KNIVKVFHGA-DSDIKWLQKD---FGLYVV------------------------GMFDTHQACKF-L 357 (1006)
Q Consensus 309 ~L~~L~elLed--p~IvKV~Hga-k~Dl~~L~rd---~GI~~~------------------------nlFDTqlAAyL-L 357 (1006)
.+..+..++.. |.++ |+||. .+|+..|..+ +|+... .++|++..++- +
T Consensus 59 lL~~F~~~i~~~dpdii-vgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~ 137 (195)
T cd05780 59 MIKRFIEIVKEKDPDVI-YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL 137 (195)
T ss_pred HHHHHHHHHHHcCCCEE-EecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC
Confidence 35566666654 8764 89997 5799887643 455411 27888876654 4
Q ss_pred CCCCccHHHHHHHHcCCCCCc--ccccc-cCCCCCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 358 PMPRQSLAYLLKHYCDVDSDK--TFQLF-DWRHRPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 358 g~~~~SLa~Lve~yLgv~LdK--~~q~s-DW~~RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
+..+++|..+++++||..... ..+.. -|...+--...++|+..||..+++|...|
T Consensus 138 ~l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 138 NLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 556899999999999975321 11112 23333334668999999999999987653
No 75
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.83 E-value=0.45 Score=61.44 Aligned_cols=92 Identities=17% Similarity=0.181 Sum_probs=67.4
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCccccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
+..|..++.+. .-|+||+.+|+.+|.+. .|+.. ..++||+-.++.+-+ .+++|..|++. +|+..+..+
T Consensus 75 ~~~l~~~l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~~~H-- 149 (928)
T PRK08074 75 APEIVELLEGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHDQPH-- 149 (928)
T ss_pred HHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCCCCC--
Confidence 45666777653 44999999999998643 45543 368999988777654 46899999887 466543222
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
=|..||.++..|+..|..++.+.+
T Consensus 150 --------------~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 150 --------------RADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred --------------ChHHHHHHHHHHHHHHHHHHHhcC
Confidence 278899999999999998887654
No 76
>KOG2249|consensus
Probab=94.27 E-value=0.32 Score=53.76 Aligned_cols=131 Identities=16% Similarity=0.164 Sum_probs=82.1
Q ss_pred CeEEEEeeeccCCcc--CCcEEEEEEEeCCceEEEeCc---------------chh-h------hH----HHHHHHHcCC
Q psy7894 269 QEIAIDLEYHNYRSY--QGYTCLMQISTRDKDYIVDTL---------------KLR-E------DL----EVLNEVLTDK 320 (1006)
Q Consensus 269 ~~IAVDtE~~~~rty--~g~lcLIQISt~~~~yIID~l---------------aL~-~------~L----~~L~elLedp 320 (1006)
..||+|+|..+..+- ...++-+.|-..-+..++|.. .++ . .+ ....++|.+
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g- 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG- 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC-
Confidence 689999999876532 222333444333344444421 111 0 11 234567765
Q ss_pred CceeeecchhhHHHHHHHHhCCccC-eeechHhHHHhC---CC-CCccHHHHHHHHcCCCCCcccccccCCCCCCChHHH
Q psy7894 321 NIVKVFHGADSDIKWLQKDFGLYVV-GMFDTHQACKFL---PM-PRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAI 395 (1006)
Q Consensus 321 ~IvKV~Hgak~Dl~~L~rd~GI~~~-nlFDTqlAAyLL---g~-~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql 395 (1006)
. +.|||+...|+..|+-.+ +. -+-||...--|. .. ...||..|.+.+||.++--++..
T Consensus 185 R-IlVGHaLhnDl~~L~l~h---p~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHs------------- 247 (280)
T KOG2249|consen 185 R-ILVGHALHNDLQALKLEH---PRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHS------------- 247 (280)
T ss_pred C-EEeccccccHHHHHhhhC---chhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccC-------------
Confidence 3 459999999999996332 32 466887543332 22 35899999999999887544422
Q ss_pred HHHHhchhHHHHHHHHHHHHHHHh
Q psy7894 396 QYARTDTHYLLYVYDCMKLDLSAA 419 (1006)
Q Consensus 396 ~YAA~DA~yLL~Lyd~L~~eL~e~ 419 (1006)
..+||....+||..++.+-++.
T Consensus 248 --SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 248 --SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred --cHHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999999998666543
No 77
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.76 E-value=0.39 Score=64.25 Aligned_cols=92 Identities=24% Similarity=0.304 Sum_probs=67.6
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHH---HHhCCc-c-CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCccccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQ---KDFGLY-V-VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~---rd~GI~-~-~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
+..+..++.+ ...|.|++.+|+..|. +.+|+. + ...+||+-.++.+.+ ..++|..|+++ +|+.....
T Consensus 490 L~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~~--- 563 (1437)
T PRK00448 490 LPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEHH--- 563 (1437)
T ss_pred HHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCCC---
Confidence 3445555544 4569999999997763 345663 2 358899988887765 36899999987 57655422
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
+-|..||.++..|+..|..++.+.|
T Consensus 564 -------------HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 564 -------------HRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred -------------cChHHHHHHHHHHHHHHHHHHHHcC
Confidence 3488999999999999999998765
No 78
>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=93.72 E-value=0.21 Score=52.31 Aligned_cols=78 Identities=18% Similarity=0.162 Sum_probs=53.9
Q ss_pred HHHHHHcCCCceeeecchhhHHHHHHHHhCCc-c-CeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCC
Q psy7894 312 VLNEVLTDKNIVKVFHGADSDIKWLQKDFGLY-V-VGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRP 389 (1006)
Q Consensus 312 ~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~-~-~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RP 389 (1006)
.|..++ ++..+-|||+...|+.+|. +. + ..+.||.+....-+..+.||..|+.+|||..+..+. .
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~----l~hp~~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~--H------ 160 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVIN----IQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET--H------ 160 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhc----CcCCCcceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCC--c------
Confidence 455555 4455669999999999993 33 2 368999754332222358999999999998774321 1
Q ss_pred CChHHHHHHHhchhHHHHHH
Q psy7894 390 LPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 390 Ls~eql~YAA~DA~yLL~Ly 409 (1006)
=..+||.+.+.||
T Consensus 161 -------dSvEDArAam~Ly 173 (174)
T cd06143 161 -------DSIEDARTALKLY 173 (174)
T ss_pred -------CcHHHHHHHHHHh
Confidence 1457888888887
No 79
>KOG2405|consensus
Probab=93.57 E-value=0.0087 Score=68.24 Aligned_cols=120 Identities=26% Similarity=0.398 Sum_probs=84.9
Q ss_pred CCcEEEEEEEeCCceEEEeCcchhhh--HHHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCC--
Q psy7894 284 QGYTCLMQISTRDKDYIVDTLKLRED--LEVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPM-- 359 (1006)
Q Consensus 284 ~g~lcLIQISt~~~~yIID~laL~~~--L~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~-- 359 (1006)
.|.+|++|.++.-..|++|.+.++.. -..|..+++|..|.|+.|+|..-..++.+.|||...++|||++|.-+-..
T Consensus 73 ~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~d~~q~~~e 152 (458)
T KOG2405|consen 73 HGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSME 152 (458)
T ss_pred cCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhhhhhhhccc
Confidence 46899999999888899998766422 24677799999999999999999999988999999999999997654221
Q ss_pred -----CC--ccHH-HHHHHHcCCCC------Cc-----ccccccCCCCCCChHHHHHHHhchhH
Q psy7894 360 -----PR--QSLA-YLLKHYCDVDS------DK-----TFQLFDWRHRPLPEPAIQYARTDTHY 404 (1006)
Q Consensus 360 -----~~--~SLa-~Lve~yLgv~L------dK-----~~q~sDW~~RPLs~eql~YAA~DA~y 404 (1006)
+. ..+. .|.. .|.+.+ .| .+...-|-+||.++..+.-.+..+.|
T Consensus 153 ~g~~~~n~~~~~q~sl~k-h~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 153 TGGYLPNCITTLQESLIK-HLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred ccccCCccccchHHHHHH-HHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 11 2333 3444 333322 11 12345699999988777665555544
No 80
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.44 E-value=1.3 Score=50.06 Aligned_cols=89 Identities=15% Similarity=0.136 Sum_probs=61.2
Q ss_pred HHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCC--CCCccHHHHHHHHcCCCCCccccc
Q psy7894 310 LEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLP--MPRQSLAYLLKHYCDVDSDKTFQL 382 (1006)
Q Consensus 310 L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg--~~~~SLa~Lve~yLgv~LdK~~q~ 382 (1006)
+..|.+++.+ -.-|+||+.+|+..|.+. +|+.. ...+||+..++-+- ...++|..|+.+| |+..+
T Consensus 71 ~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~----- 142 (309)
T PRK06195 71 WEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK----- 142 (309)
T ss_pred HHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc-----
Confidence 4456667754 345999999999888543 45443 35889987665443 3468999998885 54321
Q ss_pred ccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHHHH
Q psy7894 383 FDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDLSA 418 (1006)
Q Consensus 383 sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL~e 418 (1006)
.+-|..||..+..|+..|..++..
T Consensus 143 ------------~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 ------------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ------------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 133788999999998888776643
No 81
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=93.33 E-value=0.14 Score=62.37 Aligned_cols=71 Identities=15% Similarity=0.190 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhhHHHHHHHHHHh
Q psy7894 573 QKYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEHVLDIHAIILKA 643 (1006)
Q Consensus 573 Qlavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~g~eLl~lI~~A 643 (1006)
....|.+|..||-++|.+.++|+..|.++..|.++|+.+|.+.+++..+.|.-..-+.++|...++.|.+.
T Consensus 517 ~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~gvg~~k~~~yg~~fl~~i~~~ 587 (590)
T COG0514 517 DRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSINGVGEAKLERYGQAFLAVIQAH 587 (590)
T ss_pred cHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcCCcccchhhccHHHHHHHHHh
Confidence 45589999999999999999999999999999999999999999999999999999999999999999864
No 82
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=92.17 E-value=2.2 Score=48.33 Aligned_cols=83 Identities=13% Similarity=0.078 Sum_probs=52.3
Q ss_pred HHHHHHHcCCCceeeecchhhHHHHHHHHhCCcc--CeeechHhHHHh--CCCCCccHHHHHHHHcCCCCCcccccccCC
Q psy7894 311 EVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYV--VGMFDTHQACKF--LPMPRQSLAYLLKHYCDVDSDKTFQLFDWR 386 (1006)
Q Consensus 311 ~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~--~nlFDTqlAAyL--Lg~~~~SLa~Lve~yLgv~LdK~~q~sDW~ 386 (1006)
..|..++.+.. +-|+||+.+|+.+|.+.+ ... ....+|+..... .+..+++|.+|+.+| |.. . .
T Consensus 112 ~~l~~fl~~~~-vlVAHNA~FD~~fL~~~~-~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~-g~~-~---~----- 179 (294)
T PRK09182 112 AAVDALIAPAD-LIIAHNAGFDRPFLERFS-PVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA-GFF-H---E----- 179 (294)
T ss_pred HHHHHHhcCCC-EEEEeCHHHHHHHHHHHH-HhccCCcccccHHHHhhccccCCCCCHHHHHHHc-CCC-C---C-----
Confidence 45666776643 459999999999996533 222 234556543322 234578999999875 421 1 1
Q ss_pred CCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 387 HRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 387 ~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
.+=|..|+.++..|+..+.
T Consensus 180 --------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 180 --------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred --------CcChHHHHHHHHHHHHHHH
Confidence 1238889999988777543
No 83
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=92.16 E-value=1.7 Score=46.32 Aligned_cols=86 Identities=15% Similarity=0.132 Sum_probs=55.7
Q ss_pred hHHHHHHHHcCCCceeeecchh-hHHHHHHHHhCCccCe--eechH---hHHHhC---CCCCccHHHHHHHHcCCCCCcc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGAD-SDIKWLQKDFGLYVVG--MFDTH---QACKFL---PMPRQSLAYLLKHYCDVDSDKT 379 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak-~Dl~~L~rd~GI~~~n--lFDTq---lAAyLL---g~~~~SLa~Lve~yLgv~LdK~ 379 (1006)
.+..|..++.+.. -|+||+. +|+.+|. ..|+.+.+ ..||. .+.+.. +..+++|..|+++ +|+... .
T Consensus 74 vl~~f~~f~~~~~--lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~-~ 148 (195)
T PRK07247 74 VLAAFKEFVGELP--LIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR-G 148 (195)
T ss_pred HHHHHHHHHCCCe--EEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC-C
Confidence 3566777776543 5899995 8999994 56766532 34554 222221 2246899999886 566421 1
Q ss_pred cccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 380 FQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 380 ~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
+=|..||..+..||..|...
T Consensus 149 ----------------HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 149 ----------------HNSLEDARMTARVYESFLES 168 (195)
T ss_pred ----------------cCCHHHHHHHHHHHHHHHhh
Confidence 22778999999998877544
No 84
>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=91.38 E-value=1.2 Score=47.60 Aligned_cols=139 Identities=20% Similarity=0.323 Sum_probs=79.2
Q ss_pred CCeEEEEeeeccCCc------cCCcEEEEEEEeCC--c-eEEEeC--cchhhhHHHHHHHHc--CCCceeeecch-hhHH
Q psy7894 268 QQEIAIDLEYHNYRS------YQGYTCLMQISTRD--K-DYIVDT--LKLREDLEVLNEVLT--DKNIVKVFHGA-DSDI 333 (1006)
Q Consensus 268 a~~IAVDtE~~~~rt------y~g~lcLIQISt~~--~-~yIID~--laL~~~L~~L~elLe--dp~IvKV~Hga-k~Dl 333 (1006)
-..++||+|..+... ..+.-+.+||+... + ..++.. ..-++.+..+..++. ||.|+ |+||. .+|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdii-~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDVI-EGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCEE-eccCCcccCH
Confidence 367899999865332 12334678887642 1 112211 111233455555554 47764 78888 7898
Q ss_pred HHHHH---HhCCcc--------------------------------CeeechHhHHHhC-----CCCCccHHHHHHHH--
Q psy7894 334 KWLQK---DFGLYV--------------------------------VGMFDTHQACKFL-----PMPRQSLAYLLKHY-- 371 (1006)
Q Consensus 334 ~~L~r---d~GI~~--------------------------------~nlFDTqlAAyLL-----g~~~~SLa~Lve~y-- 371 (1006)
..|.. .+|+.. ..++|++.+..-. ...+++|..+++.+
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~ 167 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGL 167 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcc
Confidence 77643 245433 1237998766532 23468999999986
Q ss_pred cCCC-C--CcccccccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 372 CDVD-S--DKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 372 Lgv~-L--dK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
++.. . +-..-..-|...+ ...++|+..||..++.|+
T Consensus 168 ~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 168 ASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred cCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 2321 1 1111112244332 678999999999888775
No 85
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=90.51 E-value=4 Score=44.23 Aligned_cols=77 Identities=16% Similarity=-0.076 Sum_probs=52.2
Q ss_pred ceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHh
Q psy7894 322 IVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYART 400 (1006)
Q Consensus 322 IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~ 400 (1006)
-.-|+||+.+|...|. .+ ....+||+-.++.+-+. .+++..|+.. +|+..+.... ...+=|..
T Consensus 75 ~~lVaHNa~FD~~~L~-~~---~~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~~~-----------~~aHrAl~ 138 (219)
T PRK07983 75 EWYVAHNASFDRRVLP-EM---PGEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTPPG-----------LHHHRALY 138 (219)
T ss_pred CEEEEeCcHhhHHHHh-Cc---CCCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCCCC-----------CCCCcHHH
Confidence 3459999999999984 32 24678999988766553 5889888865 4544311000 01234888
Q ss_pred chhHHHHHHHHHHH
Q psy7894 401 DTHYLLYVYDCMKL 414 (1006)
Q Consensus 401 DA~yLL~Lyd~L~~ 414 (1006)
||..+..|+..|..
T Consensus 139 Da~ata~ll~~l~~ 152 (219)
T PRK07983 139 DCYITAALLIDIMN 152 (219)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999998888753
No 86
>PRK11779 sbcB exonuclease I; Provisional
Probab=87.72 E-value=7.9 Score=46.76 Aligned_cols=88 Identities=15% Similarity=0.109 Sum_probs=55.5
Q ss_pred HHHHHHHcCCCceeeecc-hhhHHHHHHHHhCCc--------------cCeeechHhHHHhC------------CCCCcc
Q psy7894 311 EVLNEVLTDKNIVKVFHG-ADSDIKWLQKDFGLY--------------VVGMFDTHQACKFL------------PMPRQS 363 (1006)
Q Consensus 311 ~~L~elLedp~IvKV~Hg-ak~Dl~~L~rd~GI~--------------~~nlFDTqlAAyLL------------g~~~~S 363 (1006)
..+..+|..+...-|+|| +.+|...|...+... ...++||.-+++.+ |.+++.
T Consensus 83 ~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~r 162 (476)
T PRK11779 83 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFK 162 (476)
T ss_pred HHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCc
Confidence 355566754455569997 689998875433111 01234666666554 224588
Q ss_pred HHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 364 LAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 364 La~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
|+.|+..| |+..... +=|..||..+..|+..|..+
T Consensus 163 Le~L~~~~-gI~~~~A----------------HdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 163 LEHLTKAN-GIEHENA----------------HDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHHc-CCCCCCC----------------CCcHHHHHHHHHHHHHHHHh
Confidence 99999875 5543211 22778999999999888865
No 87
>PF11408 Helicase_Sgs1: Sgs1 RecQ helicase; InterPro: IPR022758 RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA []. The proteins matching this entry are restricted to fungi (Saccharomycetaceae). ; PDB: 1D8B_A.
Probab=87.32 E-value=1.5 Score=40.62 Aligned_cols=56 Identities=14% Similarity=0.172 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHhCCCCCcccCHHHHHHHHHhCCCCHHHHhhccCCCchhHHh
Q psy7894 469 ALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKE 524 (1006)
Q Consensus 469 vlr~L~~WRD~~AR~~Dep~~~VL~d~~L~~LA~~~P~s~~~L~~~~g~~~~~vR~ 524 (1006)
.+..|-.-|-.++.+.+-|..-.|||..|..||..+|+|..+...+.|......++
T Consensus 8 aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~k 63 (80)
T PF11408_consen 8 AYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKK 63 (80)
T ss_dssp HHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHH
T ss_pred HHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHH
Confidence 46778888999999999999989999999999999999999999999888777553
No 88
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=85.29 E-value=13 Score=40.19 Aligned_cols=132 Identities=18% Similarity=0.212 Sum_probs=82.2
Q ss_pred CCeEEEEeeeccCCccCCcE---EEEEEEeCC---c--eEEEeCcc--------h--------------hhhHHHHHHHH
Q psy7894 268 QQEIAIDLEYHNYRSYQGYT---CLMQISTRD---K--DYIVDTLK--------L--------------REDLEVLNEVL 317 (1006)
Q Consensus 268 a~~IAVDtE~~~~rty~g~l---cLIQISt~~---~--~yIID~la--------L--------------~~~L~~L~elL 317 (1006)
...+.||+|+.+.+.....+ +.+.+..+. . ..++.|-. + ...+..+..++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 46799999999987644433 333333331 1 12344311 0 01233444566
Q ss_pred cCCCceeeecchhhHHHHHHHH---hCCcc--CeeechHhHHHhCCCC--CccHHHHHHHHcCCCCCcccccccCCCCCC
Q psy7894 318 TDKNIVKVFHGADSDIKWLQKD---FGLYV--VGMFDTHQACKFLPMP--RQSLAYLLKHYCDVDSDKTFQLFDWRHRPL 390 (1006)
Q Consensus 318 edp~IvKV~Hgak~Dl~~L~rd---~GI~~--~nlFDTqlAAyLLg~~--~~SLa~Lve~yLgv~LdK~~q~sDW~~RPL 390 (1006)
.+. -.-|.||+.+|+..|... ++..+ ..+.||.-.++...++ .++|..|+. ++|+... ....
T Consensus 93 ~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~~-------- 161 (243)
T COG0847 93 GGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFHP-------- 161 (243)
T ss_pred CCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcCC--------
Confidence 553 345999999999998543 34443 3577999888776654 689999999 6677633 1111
Q ss_pred ChHHHHHHHhchhHHHHHHHHHHHH
Q psy7894 391 PEPAIQYARTDTHYLLYVYDCMKLD 415 (1006)
Q Consensus 391 s~eql~YAA~DA~yLL~Lyd~L~~e 415 (1006)
.=|..|+..+..+|..+...
T Consensus 162 -----H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 -----HRALFDALALAELFLLLQTG 181 (243)
T ss_pred -----cchHHHHHHHHHHHHHHHhc
Confidence 22778999999888888764
No 89
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=83.56 E-value=3.2 Score=41.71 Aligned_cols=69 Identities=14% Similarity=0.083 Sum_probs=41.8
Q ss_pred hhHHHHHHHHhCCccCeeechHhHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 330 DSDIKWLQKDFGLYVVGMFDTHQACKFLPMPRQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 330 k~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
..|+..+...-|+.+.+--|-++.+|||++.+.....++.+|+|- +|... |+..+....+|+
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsNt~p~~varRY~~~---------~W~~d---------A~~RA~~t~~L~ 131 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSNTNPEGVARRYLGG---------EWPED---------AATRALATARLL 131 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT--SHHHHHHHH-TS------------SS---------HHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccCCChHHHHHHhcCC---------CCCcc---------HHHHHHHHHHHH
Confidence 455555546789988888899999999999888899999999873 55322 666777777788
Q ss_pred HHHHHHH
Q psy7894 410 DCMKLDL 416 (1006)
Q Consensus 410 d~L~~eL 416 (1006)
..|..+|
T Consensus 132 ~~L~prL 138 (138)
T PF09281_consen 132 RALPPRL 138 (138)
T ss_dssp HHHHHHT
T ss_pred HHhhhcC
Confidence 7777654
No 90
>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=82.92 E-value=25 Score=35.47 Aligned_cols=88 Identities=14% Similarity=0.134 Sum_probs=53.3
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHH---HhCC-----ccCeeechHhHHHh-CCC-CCccHHHHHHHHcCCCCCc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQK---DFGL-----YVVGMFDTHQACKF-LPM-PRQSLAYLLKHYCDVDSDK 378 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~r---d~GI-----~~~nlFDTqlAAyL-Lg~-~~~SLa~Lve~yLgv~LdK 378 (1006)
.+..|.+++.+..-..+.|++.+|...|.+ .++. .....+|++..+.. .+. ..++|..|+.. +|+....
T Consensus 78 vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~ 156 (176)
T cd06133 78 VLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFEG 156 (176)
T ss_pred HHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCCC
Confidence 345677788774112345556888665432 2333 22468899866554 443 36899999866 4765541
Q ss_pred ccccccCCCCCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 379 TFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 379 ~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
..+-|..||..+..|+..|
T Consensus 157 ---------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 ---------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred ---------------CCcCcHHHHHHHHHHHHHh
Confidence 1123778998888887765
No 91
>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=82.89 E-value=7.7 Score=41.28 Aligned_cols=98 Identities=17% Similarity=0.190 Sum_probs=61.1
Q ss_pred HHHHHHHHc--CCCceeeecch-hhHHHHHHHH---hCCcc------------------------C--eeechHhHHH--
Q psy7894 310 LEVLNEVLT--DKNIVKVFHGA-DSDIKWLQKD---FGLYV------------------------V--GMFDTHQACK-- 355 (1006)
Q Consensus 310 L~~L~elLe--dp~IvKV~Hga-k~Dl~~L~rd---~GI~~------------------------~--nlFDTqlAAy-- 355 (1006)
+..+..++. ||.|+ ++||. .+|+..|..+ +|+.+ . -++|++...+
T Consensus 55 L~~f~~~i~~~dPDvi-~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~ 133 (193)
T cd05784 55 LLALIAWFAQYDPDII-IGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTA 133 (193)
T ss_pred HHHHHHHHHhhCCCEE-EECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHc
Confidence 444444443 56664 88887 5588776432 34432 1 1678876554
Q ss_pred hCCCCCccHHHHHHHHcCCCCCc-cc-----c-cccCCCCCCChHHHHHHHhchhHHHHHHH
Q psy7894 356 FLPMPRQSLAYLLKHYCDVDSDK-TF-----Q-LFDWRHRPLPEPAIQYARTDTHYLLYVYD 410 (1006)
Q Consensus 356 LLg~~~~SLa~Lve~yLgv~LdK-~~-----q-~sDW~~RPLs~eql~YAA~DA~yLL~Lyd 410 (1006)
.+...+++|.++++++||..-.. .. . ..-|...+ ...++|+..||..+++|++
T Consensus 134 ~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 134 TYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 34556899999999999964221 10 0 11233333 5689999999999998873
No 92
>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=81.51 E-value=25 Score=37.11 Aligned_cols=141 Identities=15% Similarity=0.196 Sum_probs=80.7
Q ss_pred CeEEEEeeeccCCcc----CCcEEEEEEEeCCc-eEEE-eC-cchhhhHHHHHHHHc--CCCceeeecch-hhHHHHHHH
Q psy7894 269 QEIAIDLEYHNYRSY----QGYTCLMQISTRDK-DYIV-DT-LKLREDLEVLNEVLT--DKNIVKVFHGA-DSDIKWLQK 338 (1006)
Q Consensus 269 ~~IAVDtE~~~~rty----~g~lcLIQISt~~~-~yII-D~-laL~~~L~~L~elLe--dp~IvKV~Hga-k~Dl~~L~r 338 (1006)
..+++|+|+.+...+ ...+..|.++..++ ..++ .. ..-.+.+..+..++. ||.++ ++||. .+|+..|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-EecCCCcCcHHHHHH
Confidence 468999999743222 23445555555332 2333 21 111233555555554 56654 68885 678877643
Q ss_pred ---HhCCccC----------------------eeechHhHHHh-CCCCCccHHHHHHHHcCCC--CCcc----ccc-ccC
Q psy7894 339 ---DFGLYVV----------------------GMFDTHQACKF-LPMPRQSLAYLLKHYCDVD--SDKT----FQL-FDW 385 (1006)
Q Consensus 339 ---d~GI~~~----------------------nlFDTqlAAyL-Lg~~~~SLa~Lve~yLgv~--LdK~----~q~-sDW 385 (1006)
.+|+.+. ..+|++...+- ...++++|..+++ +||.. .+|. .+. .-|
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i~~~~ 161 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAE-YLGVMKKSERVLIEWYRIYEYW 161 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHH-HHCCCccccccCCCHHHHHHHH
Confidence 3554321 16787765443 3446799999987 58863 1211 111 124
Q ss_pred CCCCCChHHHHHHHhchhHHHHHHHH
Q psy7894 386 RHRPLPEPAIQYARTDTHYLLYVYDC 411 (1006)
Q Consensus 386 ~~RPLs~eql~YAA~DA~yLL~Lyd~ 411 (1006)
...--....+.|+..|+..++.|+..
T Consensus 162 ~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 162 DDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 43213367899999999999999875
No 93
>KOG1275|consensus
Probab=78.93 E-value=1.2 Score=56.07 Aligned_cols=86 Identities=20% Similarity=0.215 Sum_probs=61.5
Q ss_pred HHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCChHH
Q psy7894 316 VLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQACKFLPMP-RQSLAYLLKHYCDVDSDKTFQLFDWRHRPLPEPA 394 (1006)
Q Consensus 316 lLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAAyLLg~~-~~SLa~Lve~yLgv~LdK~~q~sDW~~RPLs~eq 394 (1006)
+|-+-.++-||||...|..++ ..-+....++||.+.- +++.. ..||.+|+-++||.++--.. .|
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf-~~~s~R~LSLrfLa~~lLg~~IQ~~~--HD---------- 1073 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLF-RLGSQRMLSLRFLAWELLGETIQMEA--HD---------- 1073 (1118)
T ss_pred HHHHcCcEEEcccccccceEE--EEecChhhheeeeEEE-ecccccEEEHHHHHHHHhcchhhccc--cc----------
Confidence 677889999999999998876 2222223489987543 33443 47999999999997763211 11
Q ss_pred HHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 395 IQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 395 l~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
..+||++.|.||+.. -+|+++|
T Consensus 1074 ---SIeDA~taLkLYk~Y-l~lkeq~ 1095 (1118)
T KOG1275|consen 1074 ---SIEDARTALKLYKKY-LKLKEQG 1095 (1118)
T ss_pred ---cHHHHHHHHHHHHHH-HHHHHhh
Confidence 468999999999987 4677765
No 94
>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=78.44 E-value=17 Score=39.02 Aligned_cols=129 Identities=18% Similarity=0.065 Sum_probs=76.0
Q ss_pred cCCccCCcEEEEEEEe---CCceEEE-eCc-c-hhhhHHHHHHHHcCCCceeeecch-hhHHHHHHHH---hCCccC---
Q psy7894 279 NYRSYQGYTCLMQIST---RDKDYIV-DTL-K-LREDLEVLNEVLTDKNIVKVFHGA-DSDIKWLQKD---FGLYVV--- 345 (1006)
Q Consensus 279 ~~rty~g~lcLIQISt---~~~~yII-D~l-a-L~~~L~~L~elLedp~IvKV~Hga-k~Dl~~L~rd---~GI~~~--- 345 (1006)
......+.++.|.+.. .+..+.+ ... . -.+.+..+..++.+-.-.-|+||. .+|+..|..+ +|+.+.
T Consensus 45 ~l~~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~ 124 (208)
T cd05782 45 FLPLPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYF 124 (208)
T ss_pred CCccccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCcccc
Confidence 3444556777777766 3343333 111 1 113355666666541223489997 7899888643 566321
Q ss_pred ---------------eeechHhHHHhCCC-CCccHHHHHHHHcCCCCCccc----c-cccCCCCCCChHHHHHHHhchhH
Q psy7894 346 ---------------GMFDTHQACKFLPM-PRQSLAYLLKHYCDVDSDKTF----Q-LFDWRHRPLPEPAIQYARTDTHY 404 (1006)
Q Consensus 346 ---------------nlFDTqlAAyLLg~-~~~SLa~Lve~yLgv~LdK~~----q-~sDW~~RPLs~eql~YAA~DA~y 404 (1006)
..+|++....-.+. .+.+|..+++ +||+. .|.. + ..-|.... -....+|+..||..
T Consensus 125 ~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~ 201 (208)
T cd05782 125 DLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLN 201 (208)
T ss_pred CcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHH
Confidence 16788877655443 4689998875 67773 2211 1 12244434 35688999999999
Q ss_pred HHHHHH
Q psy7894 405 LLYVYD 410 (1006)
Q Consensus 405 LL~Lyd 410 (1006)
+..||-
T Consensus 202 t~~l~l 207 (208)
T cd05782 202 TYLLYL 207 (208)
T ss_pred HHHHHh
Confidence 888874
No 95
>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=77.87 E-value=32 Score=37.06 Aligned_cols=98 Identities=21% Similarity=0.217 Sum_probs=61.6
Q ss_pred HHHHHHHHc--CCCceeeecch-hhHHHHHHH---HhCCccC------------------eeechHhHHH---hCCCCCc
Q psy7894 310 LEVLNEVLT--DKNIVKVFHGA-DSDIKWLQK---DFGLYVV------------------GMFDTHQACK---FLPMPRQ 362 (1006)
Q Consensus 310 L~~L~elLe--dp~IvKV~Hga-k~Dl~~L~r---d~GI~~~------------------nlFDTqlAAy---LLg~~~~ 362 (1006)
+..+..++. +|.++ +++|. .+|+..|.. .+|+.+. ..+|++-... .+..+.+
T Consensus 77 L~~f~~~i~~~~Pd~i-~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sy 155 (204)
T cd05779 77 LQRFFEHIREVKPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQ 155 (204)
T ss_pred HHHHHHHHHHhCCCEE-EecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCc
Confidence 455555554 46664 67775 678877643 3454321 1467776544 3444578
Q ss_pred cHHHHHHHHcCCCCCcc-c-c-cccCCCCCCChHHHHHHHhchhHHHHHHH
Q psy7894 363 SLAYLLKHYCDVDSDKT-F-Q-LFDWRHRPLPEPAIQYARTDTHYLLYVYD 410 (1006)
Q Consensus 363 SLa~Lve~yLgv~LdK~-~-q-~sDW~~RPLs~eql~YAA~DA~yLL~Lyd 410 (1006)
+|..+++++||..-..- . . ..-|...+ ...++|...||..++.||.
T Consensus 156 sLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 156 GLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred cHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 99999999999742110 0 0 01354444 5789999999999999984
No 96
>PF11408 Helicase_Sgs1: Sgs1 RecQ helicase; InterPro: IPR022758 RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA []. The proteins matching this entry are restricted to fungi (Saccharomycetaceae). ; PDB: 1D8B_A.
Probab=74.75 E-value=9.4 Score=35.55 Aligned_cols=69 Identities=13% Similarity=0.133 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCcccCHHHHHHHHHhCCCChhhhhhcCCCChHHHHhh--HHHHHHHHHH
Q psy7894 574 KYALRELYKWRDRIARDKDESTGYVLPNHMLLQMAQSIPRDIQGIFACCNPVPQTVKEH--VLDIHAIILK 642 (1006)
Q Consensus 574 lavlk~L~~WRd~~ARe~D~s~~~VL~n~~L~~IA~~~P~~l~~L~~~~~~~p~~VR~~--g~eLl~lI~~ 642 (1006)
-.++..|..-+-..+.+.+-|..-.|++..|.++|..+|.+-.+-..++|......+.. -+..+..+.+
T Consensus 6 ~~aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~kFkyFK~tl~~Lrr 76 (80)
T PF11408_consen 6 TSAYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKKFKYFKDTLMRLRR 76 (80)
T ss_dssp HHHHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGGGTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999988888999999999999999999999999998886644 3444444333
No 97
>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=73.56 E-value=82 Score=33.86 Aligned_cols=97 Identities=10% Similarity=0.027 Sum_probs=60.0
Q ss_pred hHHHHHHHHcCCCceeeecch-hhHHHHHHH---HhCCc----------------cCeeechHhHHH--h-----C--CC
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGA-DSDIKWLQK---DFGLY----------------VVGMFDTHQACK--F-----L--PM 359 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hga-k~Dl~~L~r---d~GI~----------------~~nlFDTqlAAy--L-----L--g~ 359 (1006)
.+..+..++.+..+ -|++|. .+|+..|.. .+|+. -...+|++.... . . ..
T Consensus 76 lL~~F~~~i~~~~~-iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~ 154 (204)
T cd05783 76 LIREAFKIISEYPI-VLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKY 154 (204)
T ss_pred HHHHHHHHHhcCCE-EEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcccc
Confidence 35666667766544 467776 678877653 35665 123578765432 1 2 22
Q ss_pred CCccHHHHHHHHcCCCC-CcccccccCCCCCCChHHHHHHHhchhHHHHHHH
Q psy7894 360 PRQSLAYLLKHYCDVDS-DKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYD 410 (1006)
Q Consensus 360 ~~~SLa~Lve~yLgv~L-dK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd 410 (1006)
.+++|..+++.+||..- +-..+ -|.. =....+.|+..||..++.|..
T Consensus 155 ~~~~L~~Va~~~lg~~K~~~~~~--i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEGKVELEKN--ISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCCcccCCch--hhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 57899999999999631 11111 1211 125678999999998888753
No 98
>PRK06722 exonuclease; Provisional
Probab=72.39 E-value=42 Score=38.01 Aligned_cols=87 Identities=11% Similarity=0.063 Sum_probs=52.6
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCccC-----eeechHhHHH-hCC---CCCccHHHHHHHHcCCCC
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYVV-----GMFDTHQACK-FLP---MPRQSLAYLLKHYCDVDS 376 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~~-----nlFDTqlAAy-LLg---~~~~SLa~Lve~yLgv~L 376 (1006)
.+..|..++.+..+ |+|++.+|+..|.+. +|+... ..+|++-.++ +.. ...++|..|++.| |+..
T Consensus 80 Vl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~ 156 (281)
T PRK06722 80 IIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIW 156 (281)
T ss_pred HHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCC
Confidence 34566777765433 677789999988654 454332 1357764332 221 2346899998875 6543
Q ss_pred CcccccccCCCCCCChHHHHHHHhchhHHHHHHHHHH
Q psy7894 377 DKTFQLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 377 dK~~q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
.. + .+=|..||..+..|+..|.
T Consensus 157 ~g--~-------------~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 157 EG--K-------------QHRALADAENTANILLKAY 178 (281)
T ss_pred CC--C-------------CcCcHHHHHHHHHHHHHHh
Confidence 21 1 1226788888888887776
No 99
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=70.20 E-value=84 Score=35.25 Aligned_cols=149 Identities=18% Similarity=0.229 Sum_probs=88.8
Q ss_pred CeEEEEeeeccCCccCCcEEEEEEEeCC-ceEEEe---CcchhhhHHHHHHHHcCCC--ceeeecchhhHHHHHHH---H
Q psy7894 269 QEIAIDLEYHNYRSYQGYTCLMQISTRD-KDYIVD---TLKLREDLEVLNEVLTDKN--IVKVFHGADSDIKWLQK---D 339 (1006)
Q Consensus 269 ~~IAVDtE~~~~rty~g~lcLIQISt~~-~~yIID---~laL~~~L~~L~elLedp~--IvKV~Hgak~Dl~~L~r---d 339 (1006)
...-||+|+.++......+.++..+... ..+.|- .-+.+.....|..++.++. +..-+-|..+|+..++| +
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~~ 178 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVRD 178 (278)
T ss_pred ceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHHHhc
Confidence 4778999999988744445555555543 333332 1122223445666676663 44345667889988862 1
Q ss_pred -hCCccC-eeechHhHHHhCCC---CCccHHHHHHHHcCCCCCc---cc----ccccCCCCC---CChHHHHHHHhchhH
Q psy7894 340 -FGLYVV-GMFDTHQACKFLPM---PRQSLAYLLKHYCDVDSDK---TF----QLFDWRHRP---LPEPAIQYARTDTHY 404 (1006)
Q Consensus 340 -~GI~~~-nlFDTqlAAyLLg~---~~~SLa~Lve~yLgv~LdK---~~----q~sDW~~RP---Ls~eql~YAA~DA~y 404 (1006)
+...+. .-||++..++-|.. ++.+|..+ +++||+.-.- ++ -.-.|+.-+ |-...+.|-..|+.-
T Consensus 179 ~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~V-Er~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvln 257 (278)
T COG3359 179 RLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTV-ERILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVLN 257 (278)
T ss_pred ccccCccccchhhhhhhhhhhhccCCCCChhhH-HHHhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHHHHHh
Confidence 233333 57999999998873 35677764 5599975321 11 001233221 223456777888888
Q ss_pred HHHHHHHHHHHHHH
Q psy7894 405 LLYVYDCMKLDLSA 418 (1006)
Q Consensus 405 LL~Lyd~L~~eL~e 418 (1006)
|..|+..+...+.+
T Consensus 258 L~~i~~h~~~~i~~ 271 (278)
T COG3359 258 LPTIIKHVSKKILE 271 (278)
T ss_pred HHHHHHHHHHHHHH
Confidence 88888888777654
No 100
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=66.32 E-value=31 Score=36.69 Aligned_cols=91 Identities=14% Similarity=0.076 Sum_probs=57.8
Q ss_pred hHHHHHHHHcCCCceeeecchhhHHHHHHHH---hCCcc---CeeechHhHHHhC-CC-CCccHHHHHHHHcCCCCCccc
Q psy7894 309 DLEVLNEVLTDKNIVKVFHGADSDIKWLQKD---FGLYV---VGMFDTHQACKFL-PM-PRQSLAYLLKHYCDVDSDKTF 380 (1006)
Q Consensus 309 ~L~~L~elLedp~IvKV~Hgak~Dl~~L~rd---~GI~~---~nlFDTqlAAyLL-g~-~~~SLa~Lve~yLgv~LdK~~ 380 (1006)
.+..|..++.+.... |+|++.+|+..|.+. +|+.. ....|++...+.+ +. ..++|..++++ +|+....
T Consensus 82 vl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~-~gi~~~~-- 157 (207)
T PRK07748 82 LVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEE-YGKEGTG-- 157 (207)
T ss_pred HHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHH-cCCCCCC--
Confidence 356677788763333 446678999888654 45542 2467777655433 32 35899998877 4554211
Q ss_pred ccccCCCCCCChHHHHHHHhchhHHHHHHHHHHHHH
Q psy7894 381 QLFDWRHRPLPEPAIQYARTDTHYLLYVYDCMKLDL 416 (1006)
Q Consensus 381 q~sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L~~eL 416 (1006)
+ .+-|..||..+..|+..|....
T Consensus 158 ~-------------~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 158 K-------------HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred C-------------CcChHHHHHHHHHHHHHHHhCc
Confidence 0 1237889999999999887653
No 101
>KOG3657|consensus
Probab=66.25 E-value=15 Score=46.50 Aligned_cols=98 Identities=18% Similarity=0.143 Sum_probs=67.8
Q ss_pred ceeeecchhhHHHHHHHHhCCccC--eeechHhHHHh--------------------------------------CCCC-
Q psy7894 322 IVKVFHGADSDIKWLQKDFGLYVV--GMFDTHQACKF--------------------------------------LPMP- 360 (1006)
Q Consensus 322 IvKV~Hgak~Dl~~L~rd~GI~~~--nlFDTqlAAyL--------------------------------------Lg~~- 360 (1006)
-+-||||..+|-..+...|.|.-. ...|||-.... |+..
T Consensus 242 ~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~SS 321 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGRSS 321 (1075)
T ss_pred ceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhhhh
Confidence 455999999999998778877653 35699843211 1111
Q ss_pred CccHHHHHHHHcCCC-CCcccccccCCCCCCC------hHHHHHHHhchhHHHHHHHHHHHHHHHhc
Q psy7894 361 RQSLAYLLKHYCDVD-SDKTFQLFDWRHRPLP------EPAIQYARTDTHYLLYVYDCMKLDLSAAA 420 (1006)
Q Consensus 361 ~~SLa~Lve~yLgv~-LdK~~q~sDW~~RPLs------~eql~YAA~DA~yLL~Lyd~L~~eL~e~g 420 (1006)
-.||.++...|||.. ++|.. +.++-.-++. .+.+.|+|.|+..+.++|..+-....++.
T Consensus 322 ~NSL~dVhk~~c~~~~LdKt~-Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Flerc 387 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDKTP-RDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLERC 387 (1075)
T ss_pred hHHHHHHHHhhCCCCccccch-HHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHhC
Confidence 146778888999988 77643 2233222222 34689999999999999999998877763
No 102
>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=64.99 E-value=96 Score=32.14 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=24.9
Q ss_pred HHHHHHHcC----CCceeeecchhhHHHHHHHHh---CCccC-eeech
Q psy7894 311 EVLNEVLTD----KNIVKVFHGADSDIKWLQKDF---GLYVV-GMFDT 350 (1006)
Q Consensus 311 ~~L~elLed----p~IvKV~Hgak~Dl~~L~rd~---GI~~~-nlFDT 350 (1006)
..|..++.+ ....-++|++.+|+.+|.+.+ |.... ...||
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~ 127 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDV 127 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhH
Confidence 445556653 245668999999999986543 43332 34665
No 103
>KOG2248|consensus
Probab=64.09 E-value=28 Score=41.05 Aligned_cols=84 Identities=24% Similarity=0.207 Sum_probs=53.2
Q ss_pred HHHHHHHcCCCceeeecchhhHHHHHHHHhCCccCeeechHhHH-HhCCC-C-CccHHHHHHHHcCCCCCcccccccCCC
Q psy7894 311 EVLNEVLTDKNIVKVFHGADSDIKWLQKDFGLYVVGMFDTHQAC-KFLPM-P-RQSLAYLLKHYCDVDSDKTFQLFDWRH 387 (1006)
Q Consensus 311 ~~L~elLedp~IvKV~Hgak~Dl~~L~rd~GI~~~nlFDTqlAA-yLLg~-~-~~SLa~Lve~yLgv~LdK~~q~sDW~~ 387 (1006)
..|..++ +++-+-|||+...|+..|...| ..+.||.+.- +-.|+ + ..+|..|++.|+|..+.-+....|
T Consensus 285 ~~l~~~~-~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~Hd--- 356 (380)
T KOG2248|consen 285 KELLELI-SKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHD--- 356 (380)
T ss_pred HHHHhhc-CcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCc---
Confidence 3566655 4555569999999999995433 3467888332 23442 3 468999999999976641111111
Q ss_pred CCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 388 RPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 388 RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
..+||...+.|....
T Consensus 357 ----------S~eDA~acm~Lv~~k 371 (380)
T KOG2248|consen 357 ----------SVEDALACMKLVKLK 371 (380)
T ss_pred ----------cHHHHHHHHHHHHHH
Confidence 457777777765443
No 104
>PRK05762 DNA polymerase II; Reviewed
Probab=61.60 E-value=90 Score=40.20 Aligned_cols=100 Identities=16% Similarity=0.239 Sum_probs=62.9
Q ss_pred HHHHHHHHc--CCCceeeecch-hhHHHHHHHH---hCCcc-------------------------C--eeechHhHHHh
Q psy7894 310 LEVLNEVLT--DKNIVKVFHGA-DSDIKWLQKD---FGLYV-------------------------V--GMFDTHQACKF 356 (1006)
Q Consensus 310 L~~L~elLe--dp~IvKV~Hga-k~Dl~~L~rd---~GI~~-------------------------~--nlFDTqlAAyL 356 (1006)
+..|..++. ||+|+ ++||. .+|+..|.++ +|+.. . .++|++....-
T Consensus 207 L~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~ 285 (786)
T PRK05762 207 LEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKS 285 (786)
T ss_pred HHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHH
Confidence 444555543 58865 88986 5788777532 44421 0 25688776554
Q ss_pred C--CCCCccHHHHHHHHcCCCCCc--c----ccc-ccCCCCCCChHHHHHHHhchhHHHHHHHHH
Q psy7894 357 L--PMPRQSLAYLLKHYCDVDSDK--T----FQL-FDWRHRPLPEPAIQYARTDTHYLLYVYDCM 412 (1006)
Q Consensus 357 L--g~~~~SLa~Lve~yLgv~LdK--~----~q~-sDW~~RPLs~eql~YAA~DA~yLL~Lyd~L 412 (1006)
. ..++++|..+++++||..-.. . .+. .-|... ....+.|...|+..++.|+..+
T Consensus 286 ~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 286 ATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred hhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 3 346799999999999854211 0 000 123211 2567899999999999999844
No 105
>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=61.52 E-value=30 Score=36.11 Aligned_cols=81 Identities=14% Similarity=0.105 Sum_probs=46.9
Q ss_pred HHHHHHHcCCCceeeecc-hhhHHHHHHHHh---CCcc--------CeeechHhHHHh---CC------------CCCcc
Q psy7894 311 EVLNEVLTDKNIVKVFHG-ADSDIKWLQKDF---GLYV--------VGMFDTHQACKF---LP------------MPRQS 363 (1006)
Q Consensus 311 ~~L~elLedp~IvKV~Hg-ak~Dl~~L~rd~---GI~~--------~nlFDTqlAAyL---Lg------------~~~~S 363 (1006)
..+..++..+...-|+|| +.+|+..|.+.+ |+.. ...+||.-.+++ +. ..+++
T Consensus 74 ~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~ 153 (183)
T cd06138 74 AKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFK 153 (183)
T ss_pred HHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchh
Confidence 455566654443458886 799999986543 3311 123577744443 21 23578
Q ss_pred HHHHHHHHcCCCCCcccccccCCCCCCChHHHHHHHhchhHHHHH
Q psy7894 364 LAYLLKHYCDVDSDKTFQLFDWRHRPLPEPAIQYARTDTHYLLYV 408 (1006)
Q Consensus 364 La~Lve~yLgv~LdK~~q~sDW~~RPLs~eql~YAA~DA~yLL~L 408 (1006)
|+.|+++ +|+.... .+-|..||..+..|
T Consensus 154 L~~l~~~-~gi~~~~----------------~H~Al~Da~~ta~l 181 (183)
T cd06138 154 LEDLAQA-NGIEHSN----------------AHDALSDVEATIAL 181 (183)
T ss_pred HHHHHHH-CCCCccc----------------cccHHHHHHHHHHH
Confidence 9999986 4655421 13367777766554
No 106
>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=56.09 E-value=7.3 Score=37.76 Aligned_cols=82 Identities=24% Similarity=0.224 Sum_probs=47.2
Q ss_pred HHHHHHHcCCCceeeecchhhHHHHHHH---Hh-CCcc---CeeechHhHHHhCCC--CCccHHHHHHHHcCCCCCcccc
Q psy7894 311 EVLNEVLTDKNIVKVFHGADSDIKWLQK---DF-GLYV---VGMFDTHQACKFLPM--PRQSLAYLLKHYCDVDSDKTFQ 381 (1006)
Q Consensus 311 ~~L~elLedp~IvKV~Hgak~Dl~~L~r---d~-GI~~---~nlFDTqlAAyLLg~--~~~SLa~Lve~yLgv~LdK~~q 381 (1006)
..|.+++.. ...-|+||+.+|+.++.+ .+ +... ..++|++...+.+.. ...+|..|++.|..-.. ..
T Consensus 74 ~~~~~~~~~-~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~-~~-- 149 (164)
T PF00929_consen 74 DEFEEFLKK-NDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFD-GT-- 149 (164)
T ss_dssp HHHHHHHHH-HTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSST-ST--
T ss_pred Hhhhhhhhc-ccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCC-CC--
Confidence 446666752 244589998887744322 12 2221 246777765554322 23689999888754222 11
Q ss_pred cccCCCCCCChHHHHHHHhchhHHHHHH
Q psy7894 382 LFDWRHRPLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 382 ~sDW~~RPLs~eql~YAA~DA~yLL~Ly 409 (1006)
. +=|..||..+.+||
T Consensus 150 ~-------------H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 150 A-------------HDALDDARATAELF 164 (164)
T ss_dssp T-------------TSHHHHHHHHHHHH
T ss_pred C-------------cChHHHHHHHhCcC
Confidence 1 12788999988875
No 107
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=47.97 E-value=31 Score=41.28 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=12.6
Q ss_pred CcccchhHHHHHhhhHHHHHHHHHHHHHHH
Q psy7894 786 NVKITQEPVVLKQIKSEEKEKVEMEKEKRK 815 (1006)
Q Consensus 786 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 (1006)
=|++..--..-++.|.+.++..+++++.++
T Consensus 319 p~~~~~~~~~~~~~~~~~~~~~~~~k~~~k 348 (429)
T PRK00247 319 PWRAPELHAENAEIKKTRTAEKNEAKARKK 348 (429)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366555333334444433333333333333
No 108
>PRK05359 oligoribonuclease; Provisional
Probab=45.12 E-value=3.9e+02 Score=28.13 Aligned_cols=36 Identities=14% Similarity=0.118 Sum_probs=22.4
Q ss_pred eeecchhhHHHHHHHHh---CCccC-eeec--hH-hHHHhCCC
Q psy7894 324 KVFHGADSDIKWLQKDF---GLYVV-GMFD--TH-QACKFLPM 359 (1006)
Q Consensus 324 KV~Hgak~Dl~~L~rd~---GI~~~-nlFD--Tq-lAAyLLg~ 359 (1006)
-|+|++.+|..+|.+.+ |..+. .+.| |. ..++.+.+
T Consensus 101 l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P 143 (181)
T PRK05359 101 LCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKP 143 (181)
T ss_pred eeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhCh
Confidence 38999999999887654 44443 3456 44 34444444
No 109
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=36.60 E-value=77 Score=38.11 Aligned_cols=23 Identities=26% Similarity=0.424 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q psy7894 804 KEKVEMEKEKRKKILREREEEKE 826 (1006)
Q Consensus 804 ~~~~~~~~~~~~~~~~~~~~~~~ 826 (1006)
|+.+++..|++.++.+|+.+|..
T Consensus 348 k~~~~~~~~~~~~~~~~~~~~~~ 370 (429)
T PRK00247 348 KEIAQKRRAAEREINREARQERA 370 (429)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHH
Confidence 33333333333333333333333
No 110
>KOG2002|consensus
Probab=36.03 E-value=56 Score=42.46 Aligned_cols=12 Identities=50% Similarity=0.407 Sum_probs=7.0
Q ss_pred CCCCCCCccccc
Q psy7894 888 KGKSGGTISTVD 899 (1006)
Q Consensus 888 ~~~~~~~~~~~~ 899 (1006)
|.+|....++++
T Consensus 947 k~~sk~~~~t~e 958 (1018)
T KOG2002|consen 947 KPKSKAFISTSE 958 (1018)
T ss_pred chhhhhhhcccc
Confidence 445555666666
No 111
>KOG2002|consensus
Probab=34.79 E-value=56 Score=42.44 Aligned_cols=11 Identities=18% Similarity=0.341 Sum_probs=3.9
Q ss_pred HHHHHHHHhCC
Q psy7894 495 HMLLQMAQSIP 505 (1006)
Q Consensus 495 ~~L~~LA~~~P 505 (1006)
.+-.+|.+..|
T Consensus 517 e~Yk~Ilkehp 527 (1018)
T KOG2002|consen 517 EMYKSILKEHP 527 (1018)
T ss_pred HHHHHHHHHCc
Confidence 33333333333
No 112
>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=24.92 E-value=89 Score=33.89 Aligned_cols=67 Identities=18% Similarity=0.172 Sum_probs=45.3
Q ss_pred eechHhHHHh-CCCCCccHHHHHHHHcCCCCCc-c-ccccc-CCCCCCC-hHHHHHHHhchhHHHHHHHHHH
Q psy7894 347 MFDTHQACKF-LPMPRQSLAYLLKHYCDVDSDK-T-FQLFD-WRHRPLP-EPAIQYARTDTHYLLYVYDCMK 413 (1006)
Q Consensus 347 lFDTqlAAyL-Lg~~~~SLa~Lve~yLgv~LdK-~-~q~sD-W~~RPLs-~eql~YAA~DA~yLL~Lyd~L~ 413 (1006)
++|++....- ....+++|.++++++||..-.. . ..... |...|-. ...++|...||.+.++|+..|.
T Consensus 153 ~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 153 QFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred eeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 5687766543 3456799999999999964321 1 12222 3323321 4689999999999999999874
No 113
>KOG4364|consensus
Probab=23.08 E-value=60 Score=40.59 Aligned_cols=8 Identities=0% Similarity=-0.018 Sum_probs=4.6
Q ss_pred CCCccccc
Q psy7894 892 GGTISTVD 899 (1006)
Q Consensus 892 ~~~~~~~~ 899 (1006)
-.-|-||-
T Consensus 396 ~~~f~pFe 403 (811)
T KOG4364|consen 396 DIRFEPFE 403 (811)
T ss_pred ccccccch
Confidence 45566664
No 114
>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=22.39 E-value=1.8e+02 Score=32.33 Aligned_cols=53 Identities=25% Similarity=0.248 Sum_probs=38.4
Q ss_pred CCCceeeecchhhHHHHHHHHh-CC--------------ccCeeechHhHHHhCCCCCccHHHHHHHH
Q psy7894 319 DKNIVKVFHGADSDIKWLQKDF-GL--------------YVVGMFDTHQACKFLPMPRQSLAYLLKHY 371 (1006)
Q Consensus 319 dp~IvKV~Hgak~Dl~~L~rd~-GI--------------~~~nlFDTqlAAyLLg~~~~SLa~Lve~y 371 (1006)
+.++..|+||+-.|+-.|++.| |- ....++||-+.+..+.....+|+.|.+.+
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l 214 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECPGKSTSLQELAEEL 214 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhccccccCHHHHHHHh
Confidence 3447789999999998776543 21 12458999999998876567899988774
No 115
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=21.79 E-value=88 Score=32.11 Aligned_cols=50 Identities=36% Similarity=0.527 Sum_probs=35.0
Q ss_pred hhhceeeecceeEE-------EecccccCCCcccCCCcccccCCCccceeccceEEE
Q psy7894 953 WELPILVKGKYFQV-------VNIESAHNLPQFCGGGGTYCPRAHGQVHFNQSTILF 1002 (1006)
Q Consensus 953 ~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1002 (1006)
-..|.+|.=||+.| .|||.-.|+-..||.=-.---|.-|.|.||.|-.-|
T Consensus 68 v~VPC~vtykyYk~GDvV~GtLnIedESni~V~CgDLiCkl~rdsGtVSf~dsKYCf 124 (160)
T PF03293_consen 68 VKVPCNVTYKYYKVGDVVRGTLNIEDESNITVQCGDLICKLSRDSGTVSFNDSKYCF 124 (160)
T ss_pred EEeeeEEEEEEEeeCCEEEEEEEecccCceEEEcCcEEEEeeccCCeEEecCceEEE
Confidence 45788899999986 689999999999985322224555555555555444
No 116
>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=20.03 E-value=1e+02 Score=33.75 Aligned_cols=64 Identities=11% Similarity=0.163 Sum_probs=42.9
Q ss_pred eeechHhHHH-hCCCCCccHHHHHHHHcCCCCCc--ccccccC-CC-C-CCChHHHHHHHhchhHHHHHH
Q psy7894 346 GMFDTHQACK-FLPMPRQSLAYLLKHYCDVDSDK--TFQLFDW-RH-R-PLPEPAIQYARTDTHYLLYVY 409 (1006)
Q Consensus 346 nlFDTqlAAy-LLg~~~~SLa~Lve~yLgv~LdK--~~q~sDW-~~-R-PLs~eql~YAA~DA~yLL~Ly 409 (1006)
-++|++...+ .+...+++|..++.++||...+. ....++| .. . .--...+.|...||...++|.
T Consensus 161 i~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 161 HILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 3788886554 35667899999999999986432 1234455 21 1 122457889999988888774
Done!