Query 001267
Match_columns 1112
No_of_seqs 367 out of 2118
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 20:18:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001267.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001267hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0749 PolA DNA polymerase I 100.0 2E-124 5E-129 1096.9 43.5 580 344-1111 2-583 (593)
2 TIGR00593 pola DNA polymerase 100.0 5E-110 1E-114 1033.2 56.3 607 297-1111 267-877 (887)
3 PRK05755 DNA polymerase I; Pro 100.0 1E-104 3E-109 995.3 57.5 601 298-1111 269-870 (880)
4 PRK14975 bifunctional 3'-5' ex 100.0 2.2E-92 4.8E-97 845.6 45.6 529 344-1111 2-543 (553)
5 cd08637 DNA_pol_A_pol_I_C Poly 100.0 8.7E-81 1.9E-85 714.3 34.4 369 620-1111 1-370 (377)
6 cd08640 DNA_pol_A_plastid_like 100.0 1.7E-81 3.7E-86 715.5 28.3 361 728-1111 1-363 (371)
7 PF00476 DNA_pol_A: DNA polyme 100.0 7.3E-80 1.6E-84 708.9 33.1 371 619-1111 1-374 (383)
8 cd08643 DNA_pol_A_pol_I_B Poly 100.0 3.1E-78 6.8E-83 698.6 32.9 356 619-1111 1-419 (429)
9 cd08638 DNA_pol_A_theta DNA po 100.0 1.3E-75 2.7E-80 670.9 32.5 294 792-1111 46-364 (373)
10 cd08642 DNA_pol_A_pol_I_A Poly 100.0 3.2E-70 6.9E-75 620.1 29.9 325 629-1110 7-370 (378)
11 cd06444 DNA_pol_A Family A pol 100.0 1.3E-69 2.8E-74 615.8 25.5 294 789-1111 26-340 (347)
12 cd08639 DNA_pol_A_Aquificae_li 100.0 1.1E-67 2.4E-72 593.9 23.0 280 789-1111 29-317 (324)
13 cd08641 DNA_pol_gammaA Pol gam 100.0 4.1E-55 8.9E-60 490.8 19.6 238 819-1097 94-386 (425)
14 smart00482 POLAc DNA polymeras 100.0 1.3E-53 2.8E-58 453.3 20.8 206 854-1082 1-206 (206)
15 PRK10829 ribonuclease D; Provi 99.8 1.1E-18 2.4E-23 200.6 23.0 218 344-634 2-224 (373)
16 PF01612 DNA_pol_A_exo1: 3'-5' 99.8 2.1E-18 4.5E-23 175.8 17.7 173 345-578 1-176 (176)
17 COG0349 Rnd Ribonuclease D [Tr 99.8 1.5E-18 3.3E-23 195.5 18.2 217 348-637 1-223 (361)
18 cd06139 DNA_polA_I_Ecoli_like_ 99.8 5.3E-18 1.2E-22 176.0 18.6 182 368-611 6-193 (193)
19 TIGR01388 rnd ribonuclease D. 99.8 7E-18 1.5E-22 194.3 20.3 169 347-580 1-169 (367)
20 cd06140 DNA_polA_I_Bacillus_li 99.8 3.4E-18 7.4E-23 176.3 15.5 174 368-610 4-177 (178)
21 cd06129 RNaseD_like DEDDy 3'-5 99.7 4.3E-16 9.4E-21 159.7 14.3 156 354-574 2-160 (161)
22 cd06141 WRN_exo DEDDy 3'-5' ex 99.6 3.4E-15 7.4E-20 153.5 15.2 165 348-574 1-169 (170)
23 cd06146 mut-7_like_exo DEDDy 3 99.6 5.1E-15 1.1E-19 156.5 15.6 172 345-574 1-192 (193)
24 cd06148 Egl_like_exo DEDDy 3'- 99.6 2.6E-15 5.7E-20 159.1 12.8 170 358-579 4-179 (197)
25 smart00474 35EXOc 3'-5' exonuc 99.5 2E-13 4.3E-18 138.0 16.9 170 345-577 1-171 (172)
26 cd06142 RNaseD_exo DEDDy 3'-5' 99.5 6.9E-13 1.5E-17 136.3 16.6 168 354-599 2-170 (178)
27 cd06147 Rrp6p_like_exo DEDDy 3 99.4 4.1E-12 8.8E-17 133.7 16.3 173 342-580 2-175 (192)
28 cd00007 35EXOc 3'-5' exonuclea 99.3 2E-11 4.4E-16 121.1 15.8 153 369-576 2-154 (155)
29 cd09018 DEDDy_polA_RNaseD_like 99.3 2.1E-11 4.6E-16 121.5 13.3 148 370-574 2-149 (150)
30 KOG3657 Mitochondrial DNA poly 99.1 4.5E-11 9.8E-16 143.1 7.2 246 821-1101 686-1000(1075)
31 KOG2206 Exosome 3'-5' exoribon 98.9 3.6E-09 7.7E-14 124.2 7.4 175 338-580 188-363 (687)
32 cd06128 DNA_polA_exo DEDDy 3'- 98.8 4.1E-08 8.9E-13 99.1 13.9 64 425-491 42-105 (151)
33 COG2176 PolC DNA polymerase II 98.8 1.1E-08 2.3E-13 127.5 8.6 119 367-490 421-557 (1444)
34 PRK05711 DNA polymerase III su 98.6 3E-07 6.4E-12 101.0 13.7 112 368-491 5-146 (240)
35 PRK07942 DNA polymerase III su 98.6 2.3E-07 5E-12 101.3 10.9 115 368-490 7-151 (232)
36 TIGR01406 dnaQ_proteo DNA poly 98.5 9.1E-07 2E-11 96.3 14.1 111 369-491 2-142 (225)
37 PRK09146 DNA polymerase III su 98.5 1.9E-06 4.1E-11 94.7 15.0 121 368-490 48-198 (239)
38 PRK06063 DNA polymerase III su 98.5 1.1E-06 2.3E-11 100.2 13.4 112 368-490 16-150 (313)
39 PRK07740 hypothetical protein; 98.5 1.2E-06 2.6E-11 96.5 13.1 114 368-490 60-197 (244)
40 PRK06310 DNA polymerase III su 98.5 1.9E-06 4.1E-11 95.2 14.0 118 368-490 8-145 (250)
41 PRK06309 DNA polymerase III su 98.4 2.4E-06 5.1E-11 93.4 14.1 119 368-490 3-137 (232)
42 PRK05601 DNA polymerase III su 98.4 8.5E-07 1.8E-11 101.9 9.3 113 368-491 47-209 (377)
43 PRK07246 bifunctional ATP-depe 98.4 1.7E-06 3.6E-11 109.9 12.8 117 368-490 8-141 (820)
44 PRK06807 DNA polymerase III su 98.4 2.1E-06 4.6E-11 97.8 11.6 119 367-490 8-144 (313)
45 cd06131 DNA_pol_III_epsilon_Ec 98.3 8.6E-06 1.9E-10 83.7 13.9 110 369-490 1-139 (167)
46 TIGR01298 RNaseT ribonuclease 98.3 1E-05 2.2E-10 86.6 14.3 48 437-490 106-161 (200)
47 TIGR00573 dnaq exonuclease, DN 98.3 4.7E-06 1E-10 90.1 11.8 113 368-490 8-146 (217)
48 TIGR01405 polC_Gram_pos DNA po 98.2 3.3E-06 7.2E-11 110.2 10.6 118 368-490 191-326 (1213)
49 PRK05168 ribonuclease T; Provi 98.2 1.1E-05 2.4E-10 87.1 12.7 123 355-490 8-170 (211)
50 TIGR01407 dinG_rel DnaQ family 98.2 1.2E-05 2.6E-10 102.9 15.2 117 369-490 2-136 (850)
51 cd06134 RNaseT DEDDh 3'-5' exo 98.2 1.2E-05 2.7E-10 85.2 12.8 48 437-490 103-158 (189)
52 cd06137 DEDDh_RNase DEDDh 3'-5 98.2 2.4E-06 5.2E-11 88.2 7.1 111 370-490 1-134 (161)
53 PRK07883 hypothetical protein; 98.2 8.7E-06 1.9E-10 99.5 11.4 120 368-490 16-153 (557)
54 PRK08517 DNA polymerase III su 98.1 1.1E-05 2.4E-10 89.7 11.0 110 368-490 69-202 (257)
55 PRK09182 DNA polymerase III su 98.1 1.6E-05 3.5E-10 89.9 12.3 115 368-490 38-173 (294)
56 cd06136 TREX1_2 DEDDh 3'-5' ex 98.1 3.7E-06 8E-11 88.1 6.6 59 424-490 84-151 (177)
57 PRK09145 DNA polymerase III su 98.1 4.4E-05 9.5E-10 81.6 14.7 116 368-490 30-172 (202)
58 PRK08074 bifunctional ATP-depe 98.1 3.3E-05 7.2E-10 99.7 15.3 118 368-490 4-140 (928)
59 PRK07247 DNA polymerase III su 98.1 5.1E-05 1.1E-09 81.2 13.6 117 368-490 6-141 (195)
60 PRK06195 DNA polymerase III su 98.0 4.1E-05 8.9E-10 87.2 13.3 65 421-490 67-136 (309)
61 smart00479 EXOIII exonuclease 98.0 3.8E-05 8.2E-10 78.2 11.6 109 369-490 2-137 (169)
62 cd06149 ISG20 DEDDh 3'-5' exon 98.0 1.7E-05 3.7E-10 81.7 8.9 63 421-490 64-130 (157)
63 PRK07983 exodeoxyribonuclease 98.0 5.9E-05 1.3E-09 82.1 12.2 46 437-490 75-120 (219)
64 cd06144 REX4_like DEDDh 3'-5' 97.8 2E-05 4.3E-10 80.6 4.4 63 421-490 64-127 (152)
65 PRK00448 polC DNA polymerase I 97.8 0.00014 3E-09 96.6 12.9 117 368-490 420-555 (1437)
66 cd06130 DNA_pol_III_epsilon_li 97.7 0.0002 4.3E-09 72.4 10.9 64 422-490 65-133 (156)
67 PRK07748 sporulation inhibitor 97.6 0.00019 4.2E-09 77.1 8.6 66 421-490 79-150 (207)
68 cd06145 REX1_like DEDDh 3'-5' 97.6 8.5E-05 1.8E-09 76.0 5.4 62 421-490 62-123 (150)
69 cd06125 DnaQ_like_exo DnaQ-lik 97.5 0.00014 3.1E-09 69.0 5.6 75 370-468 1-83 (96)
70 PRK05359 oligoribonuclease; Pr 97.5 0.00037 8E-09 73.7 8.9 103 368-475 4-144 (181)
71 cd06127 DEDDh DEDDh 3'-5' exon 97.4 0.00056 1.2E-08 67.9 9.2 107 370-487 1-132 (159)
72 cd06138 ExoI_N N-terminal DEDD 97.4 0.00078 1.7E-08 71.0 10.5 115 370-490 1-160 (183)
73 cd06135 Orn DEDDh 3'-5' exonuc 97.4 0.00049 1.1E-08 72.0 8.5 103 369-476 1-141 (173)
74 COG0847 DnaQ DNA polymerase II 97.4 0.0011 2.4E-08 72.5 10.9 113 368-490 14-151 (243)
75 cd06133 ERI-1_3'hExo_like DEDD 97.3 0.0013 2.7E-08 67.8 10.4 67 421-490 75-149 (176)
76 PRK11779 sbcB exonuclease I; P 97.3 0.0019 4.2E-08 77.7 13.3 81 368-453 7-111 (476)
77 cd05160 DEDDy_DNA_polB_exo DED 97.3 0.0022 4.8E-08 68.0 12.2 65 421-490 63-157 (199)
78 PRK06722 exonuclease; Provisio 97.3 0.0024 5.2E-08 72.0 12.5 67 421-490 77-151 (281)
79 PF13482 RNase_H_2: RNase_H su 96.7 0.0044 9.5E-08 63.4 7.9 156 370-573 1-163 (164)
80 KOG2207 Predicted 3'-5' exonuc 96.6 0.015 3.3E-07 70.3 12.1 178 343-577 390-585 (617)
81 PF10108 DNA_pol_B_exo2: Predi 96.4 0.016 3.4E-07 62.9 9.8 111 421-574 37-170 (209)
82 cd05785 DNA_polB_like2_exo Unc 96.3 0.043 9.4E-07 59.4 12.7 112 368-491 10-165 (207)
83 PTZ00315 2'-phosphotransferase 96.3 0.015 3.3E-07 71.1 9.6 70 421-490 130-225 (582)
84 cd05780 DNA_polB_Kod1_like_exo 96.2 0.034 7.5E-07 59.3 10.7 109 422-573 57-195 (195)
85 cd05781 DNA_polB_B3_exo DEDDy 95.4 0.29 6.3E-06 52.3 14.1 108 368-489 4-139 (188)
86 cd05782 DNA_polB_like1_exo Unc 94.8 0.17 3.8E-06 54.8 10.3 66 421-490 78-165 (208)
87 COG3359 Predicted exonuclease 92.9 1.3 2.9E-05 49.1 12.4 164 368-579 99-271 (278)
88 cd05784 DNA_polB_II_exo DEDDy 92.2 1.7 3.7E-05 46.8 12.3 65 422-490 52-148 (193)
89 cd05779 DNA_polB_epsilon_exo D 90.7 2.3 5E-05 46.2 11.4 65 422-490 74-163 (204)
90 KOG0950 DNA polymerase theta/e 90.3 0.1 2.2E-06 66.3 0.8 208 822-1099 792-1000(1008)
91 PF00940 RNA_pol: DNA-dependen 90.2 3.7 8E-05 49.1 13.6 133 868-1012 87-251 (405)
92 cd05777 DNA_polB_delta_exo DED 90.1 5.4 0.00012 43.8 13.8 22 553-574 203-224 (230)
93 cd05783 DNA_polB_B1_exo DEDDy 89.9 5.4 0.00012 43.3 13.4 36 421-457 73-113 (204)
94 KOG2249 3'-5' exonuclease [Rep 87.2 1.8 3.9E-05 48.5 7.6 61 421-490 171-235 (280)
95 KOG3657 Mitochondrial DNA poly 86.9 6 0.00013 50.3 12.4 72 553-646 359-436 (1075)
96 PHA02528 43 DNA polymerase; Pr 84.6 12 0.00026 49.0 14.3 22 552-573 303-324 (881)
97 PRK05762 DNA polymerase II; Re 71.4 50 0.0011 43.0 14.2 65 422-490 204-301 (786)
98 cd05776 DNA_polB_alpha_exo ina 71.4 15 0.00033 40.5 8.4 109 422-573 83-226 (234)
99 cd06143 PAN2_exo DEDDh 3'-5' e 68.8 4 8.7E-05 43.5 3.0 59 424-490 91-149 (174)
100 PHA00452 T3/T7-like RNA polyme 61.5 39 0.00084 44.1 10.2 207 870-1098 499-762 (807)
101 PF09281 Taq-exonuc: Taq polym 59.6 22 0.00048 36.2 5.9 40 445-490 70-110 (138)
102 PTZ00166 DNA polymerase delta 59.0 1.3E+02 0.0027 40.8 14.5 22 553-574 462-483 (1054)
103 KOG0304 mRNA deadenylase subun 57.0 1.2E+02 0.0027 33.7 11.4 54 433-489 139-208 (239)
104 PF00929 RNase_T: Exonuclease; 57.0 7.4 0.00016 38.4 2.3 112 370-490 1-141 (164)
105 KOG4373 Predicted 3'-5' exonuc 46.2 50 0.0011 38.4 6.9 107 424-570 172-281 (319)
106 smart00486 POLBc DNA polymeras 42.7 3.7E+02 0.008 31.9 13.9 22 552-573 199-220 (471)
107 KOG1798 DNA polymerase epsilon 42.1 1.8E+02 0.004 40.2 11.5 24 552-575 429-452 (2173)
108 TIGR03491 RecB family nuclease 39.3 2.2E+02 0.0048 34.8 11.4 64 422-490 329-405 (457)
109 COG2925 SbcB Exonuclease I [DN 29.3 5.7E+02 0.012 31.0 11.8 104 368-475 10-150 (475)
110 PF04857 CAF1: CAF1 family rib 28.8 55 0.0012 36.8 3.7 51 434-490 147-213 (262)
111 KOG2405 Predicted 3'-5' exonuc 27.0 29 0.00064 41.1 1.1 45 428-476 241-286 (458)
112 PF04857 CAF1: CAF1 family rib 24.9 77 0.0017 35.7 3.9 30 351-383 9-38 (262)
113 PHA02524 43A DNA polymerase su 20.7 2.6E+02 0.0057 34.8 7.5 29 422-451 181-212 (498)
No 1
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.5e-124 Score=1096.93 Aligned_cols=580 Identities=32% Similarity=0.439 Sum_probs=514.5
Q ss_pred CeEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCC-Chh
Q 001267 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDG-GGR 422 (1112)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~-~~~ 422 (1112)
.|..+++.+.+..++..+..+ +.+++||||++++++...++| +++...+ ..+|++..+. ..-
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~---~~~a~~~et~~l~~~~~~lvg------~s~~~~~--------~~~yi~~~~~~~~~ 64 (593)
T COG0749 2 PYGTITDLAVLNAWLTKLNAA---ANIAFDTETDGLDPHGADLVG------LSVASEE--------EAAYIPLLHGPEQL 64 (593)
T ss_pred cchhhhHHHHHHHHHHHHhhc---ccceeeccccccCcccCCeeE------EEeeccc--------cceeEeeccchhhh
Confidence 355677888889999888886 349999999999998888776 4443322 3466666541 112
Q ss_pred hhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhc
Q 001267 423 DLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (1112)
Q Consensus 423 ~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~ 502 (1112)
.+...|++||+++...+++||+|+|+++|.++|+. .+..+|||||+|+++|+.. .|++++|+.+ +++++
T Consensus 65 ~~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~-~~~~~DtmlasYll~~~~~---~~~~~~l~~r-------~l~~~ 133 (593)
T COG0749 65 NVLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIE-PGVAFDTMLASYLLNPGAG---AHNLDDLAKR-------YLGLE 133 (593)
T ss_pred hhHHHHHHHhhCcccchhccccchhHHHHHHcCCc-ccchHHHHHHHhccCcCcC---cCCHHHHHHH-------hcCCc
Confidence 37888999999999999999999999999999966 5789999999999999875 6999999998 55553
Q ss_pred ccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 001267 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSW 582 (1112)
Q Consensus 503 ~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~ 582 (1112)
.+. +++++||+. ++.++ ...+ .+....|++.|++++++|+..|.++|.+.
T Consensus 134 -----~~~---------~~~i~~kg~--~~~~~----~~~~--------~~~~~~y~a~~a~~~~~L~~~l~~~l~~~-- 183 (593)
T COG0749 134 -----TIT---------FEDIAGKGK--KQLTF----ADVK--------LEKATEYAAEDADATLRLESILEPELLKT-- 183 (593)
T ss_pred -----cch---------hHHhhcccc--ccCcc----ccch--------HHHHHHHHHHHHHHHHHHHHHHHHHhhhh--
Confidence 222 344555543 22221 1123 36678999999999999999999998874
Q ss_pred ccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHH
Q 001267 583 KLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDT 662 (1112)
Q Consensus 583 ~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~e~L~~L~~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~k 662 (1112)
..|..+|++||||+..||+.||.+||.||.++|.++..++..++..++++|++. +|++||++|||
T Consensus 184 ---------~~L~~l~~~iE~Pl~~VLa~ME~~Gi~vD~~~L~~l~~el~~~l~~le~eiy~l------aG~~FNi~SPK 248 (593)
T COG0749 184 ---------PVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELGCELAELEEEIYEL------AGEEFNINSPK 248 (593)
T ss_pred ---------hhHHHHHHHHhccHHHHHHHhHhcCceecHHHHHHHHHHHHHHHHHHHHHHHHH------hcCcCCCCCHH
Confidence 467999999999999999999999999999999999999999999999999665 68899999999
Q ss_pred HHHHHhhCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHh
Q 001267 663 QLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLAR 742 (1112)
Q Consensus 663 QL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~ 742 (1112)
||+.+||+ +++||. ..++||||+|||+++||++|+.
T Consensus 249 QL~~ILfe--------Kl~Lp~------------------------------------~~kKtktG~yST~~~vLe~L~~ 284 (593)
T COG0749 249 QLGEILFE--------KLGLPP------------------------------------GLKKTKTGNYSTDAEVLEKLAD 284 (593)
T ss_pred HHHHHHHH--------hcCCCc------------------------------------cccccCCCCCccHHHHHHHHhh
Confidence 99999999 799972 1246899999999999999998
Q ss_pred ccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccCCccCCCC
Q 001267 743 NISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNG 822 (1112)
Q Consensus 743 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dG 822 (1112)
.||+ ++.||+||+|+||.|||+++|++ ++++.+|
T Consensus 285 ~h~i---------------------------------------------~~~iL~~Rql~KLksTY~d~L~~-~i~~~t~ 318 (593)
T COG0749 285 DHPL---------------------------------------------PKLILEYRQLAKLKSTYTDGLPK-LINPDTG 318 (593)
T ss_pred cCcc---------------------------------------------HHHHHHHHHHHHHHHHhhhccHH-hhCCCCC
Confidence 7775 35699999999999999999997 6777779
Q ss_pred ceeecccc-cCcccccccCCCCcccCCCCccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCc
Q 001267 823 RVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDF 901 (1112)
Q Consensus 823 RIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~Di 901 (1112)
||||+|+| +|+||||||++|||||||+|++.|+.||++|+|++||.++++||||||||||||+|+|+.|++||.+|.||
T Consensus 319 RIHTsf~Q~~t~TGRLSSsdPNLQNIPiRse~Gr~IR~aFva~~g~~~i~aDYSQIELRilAHls~D~~Ll~AF~~g~Di 398 (593)
T COG0749 319 RIHTSFNQTGTATGRLSSSDPNLQNIPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRILAHLSQDEGLLRAFTEGEDI 398 (593)
T ss_pred ccCcchHHHHHHhhcccCCCCCcccCCcCCHhHHhhhhceeCCCCCeEEEechHHHHHHHHHHhcCCHHHHHHHhcCccH
Confidence 99999998 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHH
Q 001267 902 HSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDL 981 (1112)
Q Consensus 902 H~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ 981 (1112)
|+.||+.+||++.+ +|++++|+.||++|||++||||++|||+++|||..||+.+|++
T Consensus 399 H~~TA~~vFgv~~~-----------------------~Vt~e~Rr~AKaINFGiiYG~safgLa~~L~I~~~eA~~~I~~ 455 (593)
T COG0749 399 HTATAAEVFGVPIE-----------------------EVTSEQRRKAKAINFGLIYGMSAFGLAQQLGIPRKEAKEYIDR 455 (593)
T ss_pred HHHHHHHHhCCChh-----------------------hCCHHHhhhhhhhccceeeccchhhHHHHcCCChHHHHHHHHH
Confidence 99999999998543 5688999999999999999999999999999999999999999
Q ss_pred HHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhc
Q 001267 982 WYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLK 1061 (1112)
Q Consensus 982 ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~ 1061 (1112)
||++||+|+.|+++++++|+++|||+|++||||++|+++++|...|+.+||.|+|+|||||||||+|.|||.++..+.-.
T Consensus 456 YF~rypgv~~ym~~~~~~ar~~GyV~Tl~gRRry~p~i~s~n~~~R~~aER~AiNaPIQGTAADiiK~AMI~vd~~l~~~ 535 (593)
T COG0749 456 YFERYPGVKEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAERAAINAPIQGTAADIIKLAMIKVDKALKEE 535 (593)
T ss_pred HHHhChHHHHHHHHHHHHHHHcCceeecccccccCcccccCCHHHHHHHHHHHhcCcCcccHHHHHHHHHHhHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999966555
Q ss_pred CCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCCCCCCcccccccC
Q 001267 1062 ELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHPMFGKSSRLHYDV 1111 (1112)
Q Consensus 1062 ~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a~~~~~~~l~~d~ 1111 (1112)
+...||+|||||||+||||+++ ++++.++|++.||++ ....|||.||+
T Consensus 536 ~~~~rllLQVHDELvfEv~~~e-~e~~~~~v~~~Me~a-~~L~VPL~vdv 583 (593)
T COG0749 536 KLKARLLLQVHDELVFEVPKEE-LEEVKKLLKAIMENA-VNLSVPLEVDV 583 (593)
T ss_pred chhhhhHHhhhhhhhhcCcHhH-HHHHHHHHHHHHHHh-hccCCceEEec
Confidence 5678999999999999999985 999999999999999 88999999996
No 2
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5e-110 Score=1033.23 Aligned_cols=607 Identities=28% Similarity=0.355 Sum_probs=509.9
Q ss_pred chhhhhcccCCcccccccccccccchhhhhhchhhHHHHhhhhccCCCeEEecCHHHHHHHHHHHhccCCCcEEEEEecc
Q 001267 297 LVSFKRSNQKNPKNDAAEGTGQNKKASENENSEKLEILRSKLASFYSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEV 376 (1112)
Q Consensus 297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTET 376 (1112)
...|++++|+++++.+.............+.+ .....|.+|.+.+++..+++. ... +.+++
T Consensus 267 ~~~~~~lef~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~---- 327 (887)
T TIGR00593 267 YALLQELEFKSLLDRLENLESPVIDDHAPVLT-----------EKTSCAKESEEAAPLANPAEK-AEV---GGFVL---- 327 (887)
T ss_pred HHHHHHhCCccHHHHhcccccccccccccccc-----------cccccceEeCCHHHHHHHHHh-CcC---CeEEE----
Confidence 56789999999999883100000000000000 001146678788888888765 222 46777
Q ss_pred CCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC---CChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH
Q 001267 377 AKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---GGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN 453 (1112)
Q Consensus 377 tGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~---~~~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r 453 (1112)
++++++...++| ++|+.. + + ...+|++... .....++..|+++|+++.+.+|+||+|||+++|.+
T Consensus 328 ~~~~~~~~~~~~----~~~~~~--~-----~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~ 395 (887)
T TIGR00593 328 ERLLDQLKKALA----LAFATE--N-----Q-SYVAYASEADGIPLLTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKR 395 (887)
T ss_pred cCcccccCceeE----EEEEec--C-----C-CceEEEecccchhhhhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHh
Confidence 567776666665 444432 1 0 1245665321 11234567799999999999999999999999999
Q ss_pred cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCC
Q 001267 454 YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDG 533 (1112)
Q Consensus 454 ~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~ 533 (1112)
+|+.+.+.+||||||+||++|+.. ++|++|+.+ |+++. .+. +.+++|++.
T Consensus 396 ~gi~~~~~~~Dt~la~yll~~~~~----~~l~~la~~-------yl~~~-----~~~---------~~~~~~~~~----- 445 (887)
T TIGR00593 396 EGIELGGVIFDTMLAAYLLDPAQV----STLDTLARR-------YLVEE-----LIL---------DEKIGGKLA----- 445 (887)
T ss_pred CCCCCCCcchhHHHHHHHcCCCCC----CCHHHHHHH-------HcCcc-----ccc---------HHHhccCCC-----
Confidence 999998889999999999999764 799999987 45442 111 122333321
Q ss_pred CCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHHHHHHhh
Q 001267 534 SAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGEILVKME 613 (1112)
Q Consensus 534 s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME 613 (1112)
.+...| .+.+..|||.|+.+|++||..|.++|.+ .++..+|.+||||++++|+.||
T Consensus 446 ----~~~~~~--------~~~~~~ya~~d~~~~~~L~~~l~~~l~~------------~~l~~l~~~iE~pl~~vLa~ME 501 (887)
T TIGR00593 446 ----KFAFPP--------LEEATEYLARRAAATKRLAEELLKELDE------------NKLLSLYREIELPLSKVLAEME 501 (887)
T ss_pred ----Cccccc--------HHHHHHHHHHHHHHHHHHHHHHHHHHhh------------ccHHHHHHHHHHHHHHHHHHHH
Confidence 111123 3567899999999999999999999986 4789999999999999999999
Q ss_pred hcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCC
Q 001267 614 TEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNT 693 (1112)
Q Consensus 614 ~~GI~VD~e~L~~L~~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~ 693 (1112)
.+||+||.+.|+++..++..+++.++++|++. +|..||++||+||+++||+ ++|||+
T Consensus 502 ~~Gi~vD~~~l~~~~~~~~~~l~~le~~i~~~------~g~~fN~~SpkQl~~~Lf~--------~lgl~~--------- 558 (887)
T TIGR00593 502 KTGIKVDADYLQELSQEFGEEIADLEEEIYEL------AGEEFNINSPKQLGEVLFE--------KLGLPV--------- 558 (887)
T ss_pred hCCEEeCHHHHHHHHHHHHHHHHHHHHHHHHH------hCCCCCCCCHHHHHHHHHH--------hCCCCC---------
Confidence 99999999999999999999999999999776 4678999999999999998 688863
Q ss_pred ccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCccccccccccc
Q 001267 694 EGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVA 773 (1112)
Q Consensus 694 ~~~~~~~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 773 (1112)
.++|+|| |||+++||+.|+..||+
T Consensus 559 ----------------------------~kktktg-~ST~~~vL~~L~~~hp~--------------------------- 582 (887)
T TIGR00593 559 ----------------------------GKKTKTG-YSTDADVLEKLREKHPI--------------------------- 582 (887)
T ss_pred ----------------------------CCCCCCC-CCChHHHHHHhhhcCcH---------------------------
Confidence 1468899 99999999999987774
Q ss_pred ccchhhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCcc
Q 001267 774 SNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEK 852 (1112)
Q Consensus 774 ~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~ 852 (1112)
+..||+||+++|++|||+++|+. .+.+.+||||++||| +|+||||||++|||||||++++
T Consensus 583 ------------------~~~ileyR~l~Kl~sty~~~l~~-~i~~~tgRIh~~~~q~~t~TGRlSs~~PNLQNIP~r~~ 643 (887)
T TIGR00593 583 ------------------IALILEYRQLTKLKSTYVDGLPE-LVNPDTGRIHTTFNQTGTATGRLSSSNPNLQNIPIRSE 643 (887)
T ss_pred ------------------HHHHHHHHHHHHHHHHHHHHHHH-HhcCCCCceeeeeEecccceeeecccCCCccccCCCCc
Confidence 35688999999999999999997 465556999999998 9999999999999999999999
Q ss_pred chhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCC
Q 001267 853 DRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKP 932 (1112)
Q Consensus 853 ~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p 932 (1112)
.|+.||+||+|++|++||++||||||||||||||+|+.|+++|++|.|||+.||+.+||++++
T Consensus 644 ~g~~iR~~Fia~~G~~lv~aDySQIELRilAhls~D~~Li~af~~g~DiH~~tA~~~fg~~~e----------------- 706 (887)
T TIGR00593 644 EGRKIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVEIE----------------- 706 (887)
T ss_pred ccchhhheEecCCCCeEEEechhHhHHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHhCCChh-----------------
Confidence 999999999999999999999999999999999999999999999999999999999998654
Q ss_pred CCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCC
Q 001267 933 PVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGR 1012 (1112)
Q Consensus 933 ~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GR 1012 (1112)
+|++++|+.||++|||++||||+++||+++|||.+||++++++||++||+|++|++++++.|+++|||+|++||
T Consensus 707 ------~vt~~~R~~AK~infGiiYG~g~~~La~~l~is~~eA~~~i~~yf~~yp~v~~~~~~~~~~a~~~Gyv~Tl~GR 780 (887)
T TIGR00593 707 ------DVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFARYPGVKDYIENTVEEARKKGYVETLFGR 780 (887)
T ss_pred ------hCCHHHHhhhhHhhcCcccccchhHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCcEEecCCC
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHH
Q 001267 1013 ARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIV 1092 (1112)
Q Consensus 1013 rr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v 1092 (1112)
||++|+++++|...|+.++|+|+|+|||||||||+|.||+++++.+.-.+..++|+|||||||+||||+++ ++++.++|
T Consensus 781 rr~lp~i~s~n~~~r~~aeR~A~N~~iQGsAADi~K~Ami~v~~~l~~~~~~~~lvlqVHDElv~Evp~~~-~~~v~~~l 859 (887)
T TIGR00593 781 RRYIPDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKRLKERKLKARLLLQVHDELIFEAPEEE-AEEVAALV 859 (887)
T ss_pred EeeCCCccccchhhHhHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCeEEEeeEceEeeeecCHHH-HHHHHHHH
Confidence 99999999999999999999999999999999999999999999554444568999999999999999986 99999999
Q ss_pred HHHhcCCCCCCcccccccC
Q 001267 1093 LANAMHPMFGKSSRLHYDV 1111 (1112)
Q Consensus 1093 ~~~Me~a~~~~~~~l~~d~ 1111 (1112)
+++||++ +...+||.||+
T Consensus 860 ~~~Me~a-~~l~VPL~v~~ 877 (887)
T TIGR00593 860 KEVMEHA-YPLAVPLEVEV 877 (887)
T ss_pred HHHHHhh-cCCCCcEEEec
Confidence 9999999 77899999986
No 3
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=1.2e-104 Score=995.25 Aligned_cols=601 Identities=32% Similarity=0.444 Sum_probs=519.6
Q ss_pred hhhhhcccCCcccccccccccccchhhhhhchhhHHHHhhhhccCCCeEEecCHHHHHHHHHHHhccCCCcEEEEEeccC
Q 001267 298 VSFKRSNQKNPKNDAAEGTGQNKKASENENSEKLEILRSKLASFYSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVA 377 (1112)
Q Consensus 298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETt 377 (1112)
..|.+++|+++++..+ +.. . ++ ..+.+|.+|+++++|.++++.+..+ .+++|||||+
T Consensus 269 ~~~~~~~~~~~~~~~~-~~~------~--~~-----------~~~~~~~~I~~~~~L~~~l~~l~~~---~~~a~DtEt~ 325 (880)
T PRK05755 269 ALFKELEFKSLLRRAA-AAE------A--AP-----------LDEEDYETILDEEELEAWLAKLKAA---GLFAFDTETT 325 (880)
T ss_pred HHHHHhCcHHHHHHhh-ccc------c--cc-----------CCCCceEEeCCHHHHHHHHHHhhcc---CeEEEEeccC
Confidence 3559999999998752 100 0 00 0134688999999999999998765 6899999999
Q ss_pred CCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCC
Q 001267 378 KIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLK 457 (1112)
Q Consensus 378 GLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~ 457 (1112)
|++++.+++++ ++++ ..+ ...+|+|..+.+ ..+++.|.++|+++.+.+|+||++||+++|.++|+.
T Consensus 326 ~l~~~~~~i~~----i~ls--~~~-------g~~~~ip~~~i~-~~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~~gi~ 391 (880)
T PRK05755 326 SLDPMQAELVG----LSFA--VEP-------GEAAYIPLDQLD-REVLAALKPLLEDPAIKKVGQNLKYDLHVLARYGIE 391 (880)
T ss_pred CCCcccccEEE----EEEE--eCC-------CcEEEEeccccc-HHHHHHHHHHHhCCCCcEEEeccHhHHHHHHhCCCC
Confidence 99998877765 3443 322 125677764332 257888999999999999999999999999999998
Q ss_pred CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCc
Q 001267 458 VSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGK 537 (1112)
Q Consensus 458 l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~ 537 (1112)
+++++||||+|+||++|+. .++|++|+.+ |++.+ . ..+++++|++.
T Consensus 392 ~~~~~~DT~iAa~Ll~~~~----~~~L~~L~~~-------ylg~~-----~---------~~~~~~~gk~~--------- 437 (880)
T PRK05755 392 LRGIAFDTMLASYLLDPGR----RHGLDSLAER-------YLGHK-----T---------ISFEEVAGKQL--------- 437 (880)
T ss_pred cCCCcccHHHHHHHcCCCC----CCCHHHHHHH-------HhCCC-----c---------cchHHhcCCCC---------
Confidence 8888999999999999975 2899999997 44432 0 11223444321
Q ss_pred cccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCc
Q 001267 538 ISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGM 617 (1112)
Q Consensus 538 ~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI 617 (1112)
.|+.+|+ +.+..||+.||.++++||..|.++|.+. .+++.+|.++|||++++|+.||.+||
T Consensus 438 ~~~~~pl--------e~~~~YAa~Dv~~~~~L~~~L~~~L~~~-----------~~l~~l~~eiE~p~~~~l~~me~~Gi 498 (880)
T PRK05755 438 TFAQVDL--------EEAAEYAAEDADVTLRLHEVLKPKLLEE-----------PGLLELYEEIELPLVPVLARMERNGI 498 (880)
T ss_pred CccccCH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhc-----------ccHHHHHHHhhchHHHHHHHHHhcCe
Confidence 2333343 4678999999999999999999999863 37899999999999999999999999
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCCcccc
Q 001267 618 LVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVI 697 (1112)
Q Consensus 618 ~VD~e~L~~L~~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~ 697 (1112)
+||.++++++..+++.+++.+++++++++ |..||++||+|++++||+ ++|||.
T Consensus 499 ~vD~~~~~~~~~~~~~~~~~l~~~~~~~~------g~~fn~~S~~ql~~~L~~--------~lgl~~------------- 551 (880)
T PRK05755 499 KVDREYLKELSAELAQRLAELEQEIYELA------GEEFNINSPKQLGEILFE--------KLGLPV------------- 551 (880)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHHHHHHHh------CCCCCCCCHHHHHHHHHH--------hcCCCC-------------
Confidence 99999999999999999999999997764 568999999999999998 678863
Q ss_pred ccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccch
Q 001267 698 AEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNK 777 (1112)
Q Consensus 698 ~~~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 777 (1112)
.++|++| +||++++|+.|+..||.
T Consensus 552 ------------------------~~kt~~g-~st~~~~L~~l~~~~p~------------------------------- 575 (880)
T PRK05755 552 ------------------------GKKTKTG-YSTDAEVLEKLADDHPI------------------------------- 575 (880)
T ss_pred ------------------------CCCCCCC-CCCcHHHHHHHHhcChH-------------------------------
Confidence 2457788 89999999999977663
Q ss_pred hhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchhh
Q 001267 778 IFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYK 856 (1112)
Q Consensus 778 ~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~ 856 (1112)
++.|++||+++|+++||+++|.. .+.+.+||||++|+| +|+|||+||++|||||||++++.+..
T Consensus 576 --------------~~~lle~r~~~kl~sty~~~l~~-~~~~~~~rih~~~~~~~t~TGRlss~~PnlQniP~~~~~~~~ 640 (880)
T PRK05755 576 --------------PDKILEYRQLSKLKSTYTDALPK-LINPDTGRIHTSFNQTVTATGRLSSSDPNLQNIPIRTEEGRR 640 (880)
T ss_pred --------------HHHHHHHHHHHHHHHHHHHHHHH-HhccCCCeecceEeecccceeeeeccCCCcccCCCCCccchh
Confidence 46799999999999999999986 454445699999998 99999999999999999999888899
Q ss_pred hcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCc
Q 001267 857 IRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPL 936 (1112)
Q Consensus 857 iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~ 936 (1112)
+|+||+|++|++||++||||||+|||||+|+|+.|+++|++|.|+|+.||+.+||++++
T Consensus 641 iR~~f~~~~G~~lv~~DysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~~~~~~--------------------- 699 (880)
T PRK05755 641 IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLE--------------------- 699 (880)
T ss_pred hhheEecCCCCEEEEechhhhHHHHHHHHcCCHHHHHHHhcCCCHHHHHHHHHhCCChh---------------------
Confidence 99999999999999999999999999999999999999999999999999999997644
Q ss_pred ccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccC
Q 001267 937 LKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRF 1016 (1112)
Q Consensus 937 ~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~l 1016 (1112)
+|++++|+.||++|||++||||+++||+++|||.+||++++++||++||+|++|++.+.++|+++|||+|++||||++
T Consensus 700 --~v~~~~R~~aK~~~fg~~YG~g~~~la~~l~is~~eA~~~~~~~~~~~p~v~~~~~~~~~~a~~~g~v~t~~GR~r~~ 777 (880)
T PRK05755 700 --EVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYL 777 (880)
T ss_pred --hCCHHHHHHHHHHhcchhhCCChHHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCCEECCCCCeEeC
Confidence 456789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHh
Q 001267 1017 PAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANA 1096 (1112)
Q Consensus 1017 p~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~M 1096 (1112)
|++++.+...|+.++|+|+|++||||||||+|.||+++++.+.-.+++++|++||||||+||||++. ++++.++|+++|
T Consensus 778 p~~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~~~~~l~~~~~~~~l~l~vHDel~~ev~~~~-~~~~~~~~~~~m 856 (880)
T PRK05755 778 PDINSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDKALKEEGLKSRMLLQVHDELVFEVPEDE-LEEVKKLVKEVM 856 (880)
T ss_pred CcccCCCHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEEEEcceeEEEeCHHH-HHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999998654445678999999999999999986 889999999999
Q ss_pred cCCCCCCcccccccC
Q 001267 1097 MHPMFGKSSRLHYDV 1111 (1112)
Q Consensus 1097 e~a~~~~~~~l~~d~ 1111 (1112)
|++ +...+||.||.
T Consensus 857 e~~-~~l~vpl~v~~ 870 (880)
T PRK05755 857 ENA-VELSVPLVVDV 870 (880)
T ss_pred hCc-ccCCceEEEeC
Confidence 999 77899999985
No 4
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=100.00 E-value=2.2e-92 Score=845.62 Aligned_cols=529 Identities=24% Similarity=0.227 Sum_probs=443.3
Q ss_pred CeEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001267 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1112)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~ 423 (1112)
.|.+|+++++|..+|..+..+ +++++|||+++.++ .+ |+ +|+..+...+.||++.
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~---~~~a~DtEf~r~~t---~l-------~l-------iQ~~~~~~~~liDpl~----- 56 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPA---GVVAGDTETTGDDA---AA-------AA-------AQEGEEEPRWVWASTA----- 56 (553)
T ss_pred CceEEeccchhHHHHHHhccC---CceeCCccccCCcc---hh-------he-------eeecCCCceEEECchH-----
Confidence 467999999999999999887 68999999998876 22 21 2333334456667541
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcc
Q 001267 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1112)
Q Consensus 424 vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~ 503 (1112)
++ . .+|.++|+.+.+ +||||||+|||+++.. ..+++|+.++.+ ++++.
T Consensus 57 ~l---~-------------------~~L~~~Gv~~~~-~fDT~LAa~lL~~~~~-~~~~~l~~la~~-------~l~~~- 104 (553)
T PRK14975 57 AL---Y-------------------PRLLAAGVRVER-CHDLMLASQLLLGSEG-RAGSSLSAAAAR-------ALGEG- 104 (553)
T ss_pred Hh---H-------------------HHHHHCCCccCC-CchHHHHHHHcCCCCC-cCCCCHHHHHHH-------HhCCC-
Confidence 11 1 226677988765 8999999999999651 013899999987 55443
Q ss_pred cccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 001267 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (1112)
Q Consensus 504 ~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~ 583 (1112)
+ .| .. +. ++|. +|+ .+.+..||+.||.++++||+.|.++|++..-
T Consensus 105 -l----------~k---------~~---~~---sdw~-rpl-------s~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~- 149 (553)
T PRK14975 105 -L----------DK---------PP---QT---SALS-DPP-------DEEQLLYAAADADVLLELYAVLADQLNRIAA- 149 (553)
T ss_pred -C----------CC---------hh---hh---cccc-ccc-------hHHHHHHHHHHhHHHHHHHHHHHHHHHhhhc-
Confidence 0 01 00 01 2575 554 4778999999999999999999999986300
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHhhhcCCCC
Q 001267 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVAR----------AEQEAAVNRFRKWASKHCPDA 653 (1112)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~e~L~~L~~~l~----------~e~e~leeei~~~~~~~~~~g 653 (1112)
. ...++..+|.++|||++++|++||.+||+||.+.++++..++. .+++.+++++++.++ .
T Consensus 150 ---~--~~~g~l~ll~~~E~~~~~~l~~me~~Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g-----~ 219 (553)
T PRK14975 150 ---A--AHPGRLRLLAAAESAGALAAAEMELAGLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALG-----R 219 (553)
T ss_pred ---c--cchhHHHHHHHHHhhHHHHHHHHHHhCeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhC-----C
Confidence 0 0027889999999999999999999999999999999999888 777889999877652 2
Q ss_pred ccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCc
Q 001267 654 KYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVG 733 (1112)
Q Consensus 654 ~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std 733 (1112)
..||++||+||+++| + ++|+|. ++|+
T Consensus 220 ~~~n~~S~~ql~~~L-~--------~~g~~~---------------------------------------------~~t~ 245 (553)
T PRK14975 220 PRLNPDSPQQVLRAL-R--------RAGIEL---------------------------------------------PSTR 245 (553)
T ss_pred CCCCCCCHHHHHHHH-H--------HCCCCC---------------------------------------------CCCc
Confidence 349999999999999 3 566642 2566
Q ss_pred HHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccc
Q 001267 734 GDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQ 813 (1112)
Q Consensus 734 ~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~ 813 (1112)
+++| +...|| .+..|++||++.|+++||+++++
T Consensus 246 ~~~L--~~~~hp---------------------------------------------~~~~ile~r~~~kl~st~~~~~~ 278 (553)
T PRK14975 246 KWEL--REIDHP---------------------------------------------AVEPLLEYRKLSKLLSANGWAWL 278 (553)
T ss_pred HHHh--ccCCCc---------------------------------------------hHHHHHHHHHHHHHHHHHHHHHH
Confidence 7888 333444 25679999999999999999988
Q ss_pred cCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHH
Q 001267 814 GSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSML 892 (1112)
Q Consensus 814 ~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li 892 (1112)
. .++ .|||||++|++ +|+|||+||++|||||||+ .+|+||+|+|||+||++||||||+|||||||+|+.|+
T Consensus 279 ~-~~~-~~grih~~~~~~gt~TGRlss~~pnlQniP~------~iR~~f~a~~G~~lv~aDysqiElRvlA~ls~D~~l~ 350 (553)
T PRK14975 279 D-YWV-RDGRFHPEYVPGGVVTGRWASRGPNAQQIPR------DIRSAFVADPGWKLVVADASQIELRVLAAYSGDERMI 350 (553)
T ss_pred H-Hhc-cCCcccceeeecceeecccccCCCccccCCH------HHhceEEcCCCCEEEEechhhhHHHHHHHHcCCHHHH
Confidence 6 344 79999999998 8999999999999999997 6999999999999999999999999999999999999
Q ss_pred HHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCH
Q 001267 893 DAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSV 972 (1112)
Q Consensus 893 ~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~ 972 (1112)
++|++|.|+|+.||+.+||+++++ +++|+.||++|||++||||+++|++.+| +.
T Consensus 351 ~~~~~g~Dih~~~A~~~~~~~~~~-------------------------~~~R~~aK~~~~g~~YG~g~~~l~~~~~-~~ 404 (553)
T PRK14975 351 EAFRTGGDLHRLTASVGFGKPEEE-------------------------KEERALAKAANFGAIYGATSKGLQEYAK-NY 404 (553)
T ss_pred HHHhcCCCHHHHHHHHHhCCCccc-------------------------hhHHHHHHHHHHHhhhCCcHHHHHHHcC-CH
Confidence 999999999999999999975431 4789999999999999999999999999 99
Q ss_pred HHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHH
Q 001267 973 EEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAML 1052 (1112)
Q Consensus 973 ~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi 1052 (1112)
+||+.++++||++||+|++|++.+.+.|+++|||+|++||+|++|++++.+...++.++|+|+|+|||||||||+|.||+
T Consensus 405 ~ea~~~~~~~~~~~p~v~~~~~~~~~~a~~~g~v~T~~GR~~~~~~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~k~am~ 484 (553)
T PRK14975 405 GEAARLLERLRRAYPRAVGWVERAAREGERGGVVRTLLGRTSPPPGFAWRARRRARSRGRFTRNFPVQGTAADWAKLALA 484 (553)
T ss_pred HHHHHHHHHHHHHCccHHHHHHHHHHHHHHCCeEECCCCCeecCCCccccChhHHhHhhhhhcCccchhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999988899999999999999999999999999
Q ss_pred HHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCCCCC--CcccccccC
Q 001267 1053 EISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHPMFG--KSSRLHYDV 1111 (1112)
Q Consensus 1053 ~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a~~~--~~~~l~~d~ 1111 (1112)
++++.+.. +.+++|++||||||+||||++. ++++.++|+++|+++.-- +.+||.||+
T Consensus 485 ~~~~~l~~-~~~~~lvl~vHDEl~~e~~~~~-~~~~~~~i~~~M~~a~~~~~~~Vpl~v~~ 543 (553)
T PRK14975 485 LLRRRLAE-GLDAELVFFVHDEVVVECPEEE-AEEVAAAIEEAMEEAGRLLFGPVPFPVEV 543 (553)
T ss_pred HHHHHHhh-cCCcEEEEEecceeEEEecHHH-HHHHHHHHHHHHHHHHhccCCCccEEEec
Confidence 99984322 6678999999999999999986 899999999999987211 368888875
No 5
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=100.00 E-value=8.7e-81 Score=714.31 Aligned_cols=369 Identities=35% Similarity=0.497 Sum_probs=339.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCCcccccc
Q 001267 620 DREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAE 699 (1112)
Q Consensus 620 D~e~L~~L~~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~~~ 699 (1112)
|.++|+++.+++..+++.++++++.+ .|..||++||+|++++||+ .+|||+
T Consensus 1 d~~~l~~~~~~~~~~~~~l~~~~~~l------~g~~fn~~S~~qv~~~L~~--------~lgl~~--------------- 51 (377)
T cd08637 1 DTEYLEELSEELEKELAELEEEIYEL------AGEEFNINSPKQLGEVLFE--------KLGLPV--------------- 51 (377)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH------hCCCCCCCCHHHHHHHHHH--------hCCCCC---------------
Confidence 78999999999999999999999765 4668999999999999997 678763
Q ss_pred CCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhh
Q 001267 700 GKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIF 779 (1112)
Q Consensus 700 ~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 779 (1112)
.++|++|. +|+.++|+.|+..||.
T Consensus 52 ----------------------~~~t~~~~-~t~~~~L~~l~~~~p~--------------------------------- 75 (377)
T cd08637 52 ----------------------GKKTKTGY-STDAEVLEKLADEHPI--------------------------------- 75 (377)
T ss_pred ----------------------CCcCCCCC-CchHHHHHhhhhcChH---------------------------------
Confidence 24577885 7888899999877663
Q ss_pred hhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchhhhc
Q 001267 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIR 858 (1112)
Q Consensus 780 ~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR 858 (1112)
+..|++||+++|+++||++++.+ .+.+.|||||++|++ +|+||||||++|||||||++++.|..+|
T Consensus 76 ------------~~~lle~r~l~k~~~t~~~~l~~-~~~~~dgrih~~~~~~gt~TGRlS~~~PNlQniP~~~~~~~~~R 142 (377)
T cd08637 76 ------------VELILEYRELTKLKSTYVDALPK-LINPKTGRIHTSFNQTVTATGRLSSSDPNLQNIPIRTEEGREIR 142 (377)
T ss_pred ------------HHHHHHHHHHHHHHHHHHHHHHH-HcCCCCCceeeeeeeccccccchhcccCccccCCCCccchHhHH
Confidence 46789999999999999999986 344449999999998 9999999999999999999888889999
Q ss_pred ceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCccc
Q 001267 859 QAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLK 938 (1112)
Q Consensus 859 ~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~ 938 (1112)
+||+|++||+||++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||++++
T Consensus 143 ~~f~~~~G~~lv~aDysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~----------------------- 199 (377)
T cd08637 143 KAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPE----------------------- 199 (377)
T ss_pred HheeCCCCCEEEEechhHhHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCChh-----------------------
Confidence 999999999999999999999999999999999999999999999999999998654
Q ss_pred ccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCC
Q 001267 939 DAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPA 1018 (1112)
Q Consensus 939 ~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~ 1018 (1112)
+|++++|+.||+++||++||||+.+||+++|+|.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|++|+
T Consensus 200 ~v~~~~R~~aK~~~~g~~YG~g~~~la~~lg~s~~eA~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~t~~GRrr~~~~ 279 (377)
T cd08637 200 EVTPEMRRIAKAVNFGIIYGISAFGLSQQLGISRKEAKEYIDRYFARYPGVKEYMEETVEEAREKGYVETLFGRRRYIPE 279 (377)
T ss_pred hCCHHHHhhhhHhhcchhcCcchhHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCcEEccCCCEEeCCc
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcC
Q 001267 1019 IKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMH 1098 (1112)
Q Consensus 1019 ~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~ 1098 (1112)
+.+.+...|+.++|+|+|++||||||||+|.||+++++.+.-.+.+++|+++|||||+||||++. ++++.++|+++|++
T Consensus 280 ~~~~~~~~r~~~~r~a~N~~iQGsaAdi~k~am~~~~~~l~~~~~~~~lvl~vHDEl~~ev~~~~-~~~~~~~l~~~M~~ 358 (377)
T cd08637 280 INSKNRNVRAFAERIAINTPIQGTAADIIKLAMIRVHKALKEEGLKARMLLQVHDELVFEVPEEE-LEEVAALVKEEMEN 358 (377)
T ss_pred ccCCcHHHhhHHHHhHhcccchhHHHHHHHHHHHHHHHHHHhcCCCeEEEeeEeeeeeEecCHHH-HHHHHHHHHHHHhh
Confidence 99999888999999999999999999999999999998654445578999999999999999986 88999999999999
Q ss_pred CCCCCcccccccC
Q 001267 1099 PMFGKSSRLHYDV 1111 (1112)
Q Consensus 1099 a~~~~~~~l~~d~ 1111 (1112)
+ +...+||.||+
T Consensus 359 ~-~~l~VPl~v~~ 370 (377)
T cd08637 359 A-VELSVPLKVDV 370 (377)
T ss_pred c-ccCCCcEEEec
Confidence 9 87899999986
No 6
>cd08640 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including
Probab=100.00 E-value=1.7e-81 Score=715.45 Aligned_cols=361 Identities=59% Similarity=0.892 Sum_probs=327.1
Q ss_pred CCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhhhh
Q 001267 728 GWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISN 807 (1112)
Q Consensus 728 G~~Std~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~st 807 (1112)
|+||++.++|..++..+.. +.++++.|..... .+.....+.++++..||+||+++||+||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~il~~r~~~Kl~st 60 (371)
T cd08640 1 GLPSVDSEALRELAGDPEA--------DILLYEWCYENGV------------SGGEEGKEACEAIEALKEIKSISTLLST 60 (371)
T ss_pred CCCccchHHHHHhcCCccc--------cchhhHHHHHhcc------------CCccccchhhHHHHHHHHHHHHHHHHHH
Confidence 4579999999999976432 2222222222111 1233345678999999999999999999
Q ss_pred hhcccccCCccCCCCceeecccccCcccccccCCCCcccCCCCccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcC
Q 001267 808 FILPLQGSNVSGKNGRVHCSLNINTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN 887 (1112)
Q Consensus 808 yv~~l~~~~v~~~dGRIH~s~n~~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~ 887 (1112)
|+++|++ .+++.|||||++|+|.|+||||||++|||||||++++.+..+|+||+|++|++||++||||||||||||||+
T Consensus 61 y~~~l~~-~~~~~dgRih~~~~~~t~TGRlSs~~PNLQNiP~~~~~~~~iR~~Fva~~G~~lv~aDySQiElRvlA~lS~ 139 (371)
T cd08640 61 FIIPLQE-LLNDSTGRIHCSLNINTETGRLSSRNPNLQNQPALEKDRYKIRKAFIASPGNTLIVADYSQLELRLLAHMTR 139 (371)
T ss_pred HHHHHHH-HccCCCCCeeeeEeeccceeehhcCCCCCCCCCCCCccccchhheEecCCCCEEEEechhhhhHHHHHHHcC
Confidence 9999997 465788999999997799999999999999999998888899999999999999999999999999999999
Q ss_pred chHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccchhh
Q 001267 888 CKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARD 967 (1112)
Q Consensus 888 D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~ 967 (1112)
|+.|+++|++|.|+|+.||+.+||+++++|++++++.+|+++++++++..+++++++|+.||++|||++||||+++||++
T Consensus 140 D~~Li~af~~g~DiH~~tA~~if~~~~e~v~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~AK~infGi~YG~g~~~La~~ 219 (371)
T cd08640 140 CKSMIEAFNAGGDFHSRTASGMYPHVAEAVANGEVLLEWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAYGKTAHGLAKD 219 (371)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHhCCCHHHhccccccccccccccccccccccccHHHHHHHHHHHHHHHhccchhHHHHH
Confidence 99999999999999999999999999999998899999999998888878888999999999999999999999999999
Q ss_pred hCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHH
Q 001267 968 WKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVA 1047 (1112)
Q Consensus 968 lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~ 1047 (1112)
+|||.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|++|++++.+...++.++|+|+|+|||||||||+
T Consensus 220 lgis~~eA~~~i~~f~~~fP~v~~~~~~~~~~a~~~Gyv~T~~GRrr~lp~i~s~~~~~~~~~eR~avN~~IQGsAADI~ 299 (371)
T cd08640 220 WKVKLKEAERTVDAWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGHAERAAINTPIQGSAADIA 299 (371)
T ss_pred cCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCcEEccCCCEEECCCcccccHhhhhhhHHHHHhhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999998888999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCCCC--CCcccccccC
Q 001267 1048 MCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHPMF--GKSSRLHYDV 1111 (1112)
Q Consensus 1048 K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a~~--~~~~~l~~d~ 1111 (1112)
|.||+++++.+...+.+++|++||||||+||||++. ++++.++|+++|+++ + ...+||.||+
T Consensus 300 K~Ami~i~~~l~~~~~~~~lvlqVHDElv~evp~~~-~~~~~~~v~~~Me~~-~~~~l~VPl~v~~ 363 (371)
T cd08640 300 MKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGPEEK-ADEALKIVKDCMENP-FFGPLDVPLEVDG 363 (371)
T ss_pred HHHHHHHHHHHhhccCCceEEEEEcceeEEEcCHHH-HHHHHHHHHHHHHhc-CccCCCccEEEec
Confidence 999999999665667889999999999999999985 899999999999999 5 5689999986
No 7
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=100.00 E-value=7.3e-80 Score=708.90 Aligned_cols=371 Identities=37% Similarity=0.493 Sum_probs=335.5
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCCccccc
Q 001267 619 VDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIA 698 (1112)
Q Consensus 619 VD~e~L~~L~~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~~ 698 (1112)
||.++|+.+..++..+++.+++++... +|..||++||+|++++||+ ++|||+
T Consensus 1 ~d~~~~~~~~~~~~~~~~~~~~~~~~~------~g~~fN~~S~~q~~~~L~~--------~lgl~~-------------- 52 (383)
T PF00476_consen 1 VDREYLEQQSEELDAKLRELEAKAYKL------AGEEFNPNSPKQLAEVLFE--------ELGLPP-------------- 52 (383)
T ss_dssp ETHHHHHHHHHHHHHHHHHHHHHHHHH------HTSCSSTTTHHHHHHHHHT--------TSSSTT--------------
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhHHh------cCCccCCCCHHHHHHHHHH--------cCCCCC--------------
Confidence 799999999999999999999888665 4788999999999999998 688863
Q ss_pred cCCCCCcccccchhcccccCCCCcccccc-CCCcCcHHHHHHHHh-ccCccccccCCCCCCCCCCCcccccccccccccc
Q 001267 699 EGKKTPSKFRNITLRSIGVDLPTEMYTAT-GWPSVGGDALKTLAR-NISAEYDCVDGAHDLDDSGCTEETEYKGAVASNN 776 (1112)
Q Consensus 699 ~~kk~~~~~~~~~l~~~G~~lp~~~~Tkt-G~~Std~~vLe~La~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 776 (1112)
..+|++ |.+||++++|+.|+. .||
T Consensus 53 -----------------------~~~t~~~g~~st~~~~L~~l~~~~~~------------------------------- 78 (383)
T PF00476_consen 53 -----------------------TKKTKKKGKPSTDKEVLKKLAEDAHP------------------------------- 78 (383)
T ss_dssp -----------------------SSBETTCSEBHCTHHHHHHHCCCCHT-------------------------------
T ss_pred -----------------------CCCCcccchhhhHHHHHHHhhhhhhh-------------------------------
Confidence 123444 999999999999986 333
Q ss_pred hhhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchh
Q 001267 777 KIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRY 855 (1112)
Q Consensus 777 ~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~ 855 (1112)
.+..+++||++.|+.+||++++.. .+...|||||++|++ +|+|||+||++|||||||++...|.
T Consensus 79 --------------~~~~~l~~r~~~kl~~~~~~~~~~-~~~~~dgrih~~~~~~gt~TGRls~~~PNlQniP~~~~~~~ 143 (383)
T PF00476_consen 79 --------------IAKLLLEYRKLSKLRSTYIDNLLD-KVDPEDGRIHPSFNQTGTATGRLSSSNPNLQNIPKRDPYGK 143 (383)
T ss_dssp --------------HHHHHHHHHHHHHHHHHTTHHHHH-HSBTTTTEE--EEESSSSSSS--EEESSCTSSSSSSSHHHH
T ss_pred --------------hHHHHHHHHHHHHHHhhhhhHHHH-hccccCCeecceeeecccccCCceeechhhhccccccccCc
Confidence 467799999999999999999886 455589999999997 9999999999999999999988889
Q ss_pred hhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCC
Q 001267 856 KIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVP 935 (1112)
Q Consensus 856 ~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~ 935 (1112)
.+|+||+|++||+||++||||||+|||||||+|+.|+++|.+|.|+|+.+|+.+||++.+
T Consensus 144 ~~R~~f~a~~G~~lv~aD~sqiElRvlA~ls~D~~l~~~~~~g~D~h~~~a~~~~~~~~~-------------------- 203 (383)
T PF00476_consen 144 EIRSAFVAPPGYVLVSADYSQIELRVLAHLSGDENLIEAFRNGEDIHTETASDIFGKPYE-------------------- 203 (383)
T ss_dssp GGGGGEEGSSTEEEEEEEESSHHHHHHHHHHTHHHHHHHHHTTCCHHHHHHHHHTTCHGG--------------------
T ss_pred ccceeEecCccceeeeeehhhhhHHHHHHhcccHHHHHhhcccccHHHHHHHHhcCCCcc--------------------
Confidence 999999999999999999999999999999999999999999999999999999997654
Q ss_pred cccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCccc
Q 001267 936 LLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARR 1015 (1112)
Q Consensus 936 ~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~ 1015 (1112)
++++.+|+.||++|||++||||+.+||+.+|+|.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|+
T Consensus 204 ---~v~~~~R~~aK~~~~g~~YG~g~~~la~~l~~s~~eA~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~t~~gr~r~ 280 (383)
T PF00476_consen 204 ---EVTKEERQKAKTVNFGLIYGMGAKGLAEQLGISEEEAKELIDAFFEAFPGVKKWMERVKKRARENGYVETLFGRRRY 280 (383)
T ss_dssp ---GTTHHHHHHHHHHHHHHHTT-THHHHHHHHTSCHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHSEEECTTSSEEE
T ss_pred ---ccchhhHHHHhHHHHhhhhccCHHHHHHHccCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHhcCCeEEEecccccc
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHH
Q 001267 1016 FPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLAN 1095 (1112)
Q Consensus 1016 lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~ 1095 (1112)
+|.+.+.+...+..++|+|+|++||||||||+|.||++++..+.-.+.+++++++|||||+||||++. ++++.++|+++
T Consensus 281 ~p~~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~i~~~l~~~~~~~~l~l~VHDEli~ev~~~~-~~~v~~~l~~~ 359 (383)
T PF00476_consen 281 LPNIDSRNKSLRASAERQAVNTPIQGSAADIMKLAMIRIHEALREKGLGARLVLQVHDELIFEVPEDE-AEEVAEILKEI 359 (383)
T ss_dssp CGGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEESSEEEEEEEGGG-HHHHHHHHHHH
T ss_pred CCchhcccchhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCcCceeEEEEcCeeheeecHhH-HHHHHHHHHHH
Confidence 99999998889999999999999999999999999999998665556788999999999999999986 99999999999
Q ss_pred hcCCCCCCcccccccC
Q 001267 1096 AMHPMFGKSSRLHYDV 1111 (1112)
Q Consensus 1096 Me~a~~~~~~~l~~d~ 1111 (1112)
|+.+ ....+||.+|+
T Consensus 360 M~~~-~~~~vPl~~~~ 374 (383)
T PF00476_consen 360 MENA-GELRVPLPVEV 374 (383)
T ss_dssp HHTS-SHHSSCTCEEE
T ss_pred HHhh-ccCCCeEEeec
Confidence 9999 55689999885
No 8
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=100.00 E-value=3.1e-78 Score=698.62 Aligned_cols=356 Identities=21% Similarity=0.179 Sum_probs=312.9
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhh-hcC--------------------------CCCccccCCCHHHHHHHhhCC
Q 001267 619 VDREYLSEIEKVARAEQEAAVNRFRKWAS-KHC--------------------------PDAKYMNVGSDTQLRQLLFGG 671 (1112)
Q Consensus 619 VD~e~L~~L~~~l~~e~e~leeei~~~~~-~~~--------------------------~~g~~fNi~S~kQL~~lLFe~ 671 (1112)
+|.+....|..++..++..++.++.+.+. ++. .....||++||+||+++||+
T Consensus 1 ~d~~~a~~l~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fN~~S~~ql~~~L~~- 79 (429)
T cd08643 1 FNQEKAAKLYAQLAGRREDLENELQEVFPPWYVSDGFVPKKRTTNNSVRGYVKGAPYTKIKLVTFNPSSRKHIAKRLKA- 79 (429)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccccccccCccccCCcccceecCCCccccCCccCCCCCHHHHHHHHHH-
Confidence 58889999999999999999999988762 111 12347999999999999997
Q ss_pred CCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCcccccc
Q 001267 672 KPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCV 751 (1112)
Q Consensus 672 ~~~~k~~~l~Lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~~~~~~~~~~ 751 (1112)
++|||+ .++|+||+||||++||+.|. ||+
T Consensus 80 -------~lg~~~-------------------------------------~~~t~~G~~std~~vL~~l~--~p~----- 108 (429)
T cd08643 80 -------KYGWEP-------------------------------------QEFTESGEPKVDEDVLSKLD--YPE----- 108 (429)
T ss_pred -------hcCCCC-------------------------------------CCcCCCCCCCcCHHHHHhcc--chH-----
Confidence 677753 25689999999999999996 663
Q ss_pred CCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhhhhhhcccccC-CccCCCCceeecccc
Q 001267 752 DGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGS-NVSGKNGRVHCSLNI 830 (1112)
Q Consensus 752 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styv~~l~~~-~v~~~dGRIH~s~n~ 830 (1112)
++.|++||+++|+++||+++.+.+ ..+++|||||++|||
T Consensus 109 ----------------------------------------~~~ileyr~l~K~~st~~~~~~~~l~~v~~dgRIH~~~nq 148 (429)
T cd08643 109 ----------------------------------------AKLLAEYLLVQKRLGQLADGNNAWLKLVHEDGRIHGAVNT 148 (429)
T ss_pred ----------------------------------------HHHHHHHHHHHHHHHHHHhhHHHHHHHcCCCCceeeeEEe
Confidence 467999999999999999883322 124578999999998
Q ss_pred -cCcccccccCCCCcccCCC-CccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCc---hHHHHHHHcCCCchhHH
Q 001267 831 -NTETGRLSARRPNLQNQPA-LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANC---KSMLDAFKAGGDFHSRT 905 (1112)
Q Consensus 831 -~T~TGRlSss~PNLQNIP~-~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D---~~Li~af~~G~DiH~~t 905 (1112)
+|+||||||++|||||||+ ++++|+++|+||+|++|++||++||||||||||||||+| +.|++ |..|.|||+.|
T Consensus 149 ~gt~TGRlSss~PNLQnIP~~~~~~G~~iR~~Fva~~G~~lv~aDySQiELRiLAhls~d~~~~~l~~-~~~~~DiH~~t 227 (429)
T cd08643 149 NGAVTGRATHFSPNMAQVPAVGSPYGKECRELFGVPPGWSLVGADASGLELRCLAHYLARYDGGAYTR-KVLGGDIHWAN 227 (429)
T ss_pred CCccccccccCCCcccCCCCCCcccchhhhheEecCCCCEEEEecHHHHHHHHHHHHhcccchHHHHh-hhcccchhHHH
Confidence 8999999999999999994 678899999999999999999999999999999999998 78877 78899999999
Q ss_pred HhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHH--------
Q 001267 906 AMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKK-------- 977 (1112)
Q Consensus 906 A~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~-------- 977 (1112)
|+. +|+ ++|+.||++|||++||||+++||+.+|++.+||+.
T Consensus 228 a~~-~g~------------------------------~~R~~AK~i~fGiiYG~g~~~La~~lg~~~~eA~~~~~~~~~~ 276 (429)
T cd08643 228 AQA-MGL------------------------------LSRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQT 276 (429)
T ss_pred HHH-hCh------------------------------HHHhhhHHHHHHHHHCCChhHHHHHhCCCHHHHHhhhhccccc
Confidence 985 441 58999999999999999999999999999998887
Q ss_pred ----------------HHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhh
Q 001267 978 ----------------TVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQG 1041 (1112)
Q Consensus 978 ----------------~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQG 1041 (1112)
++++||++||+|++|++.+++.|+++|||+|++||+|++|. .|+|+|+||||
T Consensus 277 ~~~~~~~~~~~~~g~~~~~~f~~~~P~v~~~~~~~~~~a~~~Gyv~tl~GRrr~~~~------------~r~A~Nt~iQG 344 (429)
T cd08643 277 KKGTIKKIADKAKGRVVRANFLKGLPALGKLIKKVKEAAKKRGHLVGLDGRRIRVRS------------AHAALNTLLQS 344 (429)
T ss_pred ccchhhhhhhhhhHHHHHHHHHHhCccHHHHHHHHHHHHHhCCceeCCCCCcccCch------------HHHHhChhhhh
Confidence 99999999999999999999999999999999999999974 48899999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcC----CCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCCC--CCCcccccccC
Q 001267 1042 SAADVAMCAMLEISKNARLKE----LGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHPM--FGKSSRLHYDV 1111 (1112)
Q Consensus 1042 SAADI~K~AMi~i~~~~~l~~----~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a~--~~~~~~l~~d~ 1111 (1112)
|||||+|.||+++++.+.-.+ .+++|++||||||+||||++. ++++.++|+++|+++. +...+||.||+
T Consensus 345 sAADi~K~Ami~i~~~l~~~g~~~~~~~~lvlqVHDElv~ev~~~~-ae~v~~~v~~~Me~a~~~~~l~VPL~v~~ 419 (429)
T cd08643 345 AGAILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGI-AEEVGKIAVEAAEKAGEHFNFRCPLAGEF 419 (429)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEccceEEEeCHHH-HHHHHHHHHHHHHHhhhccCCCcceEeec
Confidence 999999999999999654333 357899999999999999985 9999999999999984 35689999885
No 9
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=100.00 E-value=1.3e-75 Score=670.86 Aligned_cols=294 Identities=33% Similarity=0.407 Sum_probs=273.5
Q ss_pred HHHHHHHHhHhhhhhhhhcccccCCc----cCCCCceeecccc-cCcccccccCCCCcccCCCCcc--------------
Q 001267 792 ISALCEVCSIDSLISNFILPLQGSNV----SGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEK-------------- 852 (1112)
Q Consensus 792 i~~Lle~r~l~Kl~styv~~l~~~~v----~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~-------------- 852 (1112)
++.|++||+++|+++||+++++.+ + .+.|||||++|++ +|+||||||++|||||||+++.
T Consensus 46 ~~~ile~r~l~Kl~sty~~~~~~~-~~~~~~~~~grih~~~~~~gt~TGRlSs~~PNlQniP~~~~~~~~~~~~~~~~~~ 124 (373)
T cd08638 46 PKLILEYRKLSKLLTTYVEPLLLL-CKLSSSLQMYRIHPTWNQTGTATGRLSSSEPNLQNVPKDFEIKDAPSPPAGSEGD 124 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-hhcccCCCCCeEeeEEEEccceeeeeeeccCCcCCCCCCCccccccccccccccc
Confidence 467999999999999999999963 3 2678999999998 8999999999999999999753
Q ss_pred -chhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCC
Q 001267 853 -DRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDK 931 (1112)
Q Consensus 853 -~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~ 931 (1112)
.+..+|+||+|++||+||++||||||||||||+|+|+.|+++|++|.|+|+.+|+.+||++++
T Consensus 125 ~~~~~iR~~f~a~~G~~lv~~DysqiElRvlA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~---------------- 188 (373)
T cd08638 125 IPTISLRHAFIPPPGRVLLSADYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVE---------------- 188 (373)
T ss_pred hhhhhhhheeeCCCCCEEEEechhhhHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCChh----------------
Confidence 467899999999999999999999999999999999999999999999999999999998654
Q ss_pred CCCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccC
Q 001267 932 PPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLG 1011 (1112)
Q Consensus 932 p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~G 1011 (1112)
+|++++|+.||++|||++||||+.+||+++|+|.+||++++++||++||+|++|++.+++.|+++|||+|++|
T Consensus 189 -------~v~~~~R~~aK~~~fg~~YG~g~~~La~~l~~s~~eA~~~i~~f~~~~p~v~~~~~~~~~~a~~~g~v~T~~G 261 (373)
T cd08638 189 -------EVTDEERQQAKQLVYGILYGMGAKSLAEQLGVSEEEAKQFIESFKNAYPGVRRFIRETIERARRNGFVETLTG 261 (373)
T ss_pred -------hCCHHHHHHHhHHHHhhHhCCcHHHHHHHhCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCcEEccCC
Confidence 3567899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhc-----CCCceEEeEccceeeeeecchhcHH
Q 001267 1012 RARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLK-----ELGWKLLLQVLFFFSFSFFSIIVIV 1086 (1112)
Q Consensus 1012 Rrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~-----~~~~~llLqVHDElv~Ev~~~~~ae 1086 (1112)
|+|++|++++.++..++.++|+|+|+|||||||||+|.||+++++.+... +.+++|++||||||+||||++. ++
T Consensus 262 Rrr~~p~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~K~ami~i~~~l~~~~~~~~~~~~~lvl~VHDEl~~ev~~~~-~~ 340 (373)
T cd08638 262 RRRYLPEINSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESD-VD 340 (373)
T ss_pred CEEeCCCCCCCCHHHHHHHHHHHhchhhhhHHHHHHHHHHHHHHHHHHhhcccccCCCeEEEEEEccEEEEEeCHHH-HH
Confidence 99999999999999999999999999999999999999999999865432 3578999999999999999985 89
Q ss_pred HHHHHHHHHhcCCCCCCcccccccC
Q 001267 1087 SCQGIVLANAMHPMFGKSSRLHYDV 1111 (1112)
Q Consensus 1087 ~~~~~v~~~Me~a~~~~~~~l~~d~ 1111 (1112)
++.++|+++|+++ ....+||.||+
T Consensus 341 ~~~~~i~~~Me~~-~~l~VPl~v~~ 364 (373)
T cd08638 341 EVARIIKRSMENA-AKLSVPLPVKV 364 (373)
T ss_pred HHHHHHHHHHhCc-cCCCCceEEee
Confidence 9999999999999 56789998875
No 10
>cd08642 DNA_pol_A_pol_I_A Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. P
Probab=100.00 E-value=3.2e-70 Score=620.11 Aligned_cols=325 Identities=22% Similarity=0.236 Sum_probs=275.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhhCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccc
Q 001267 629 KVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFR 708 (1112)
Q Consensus 629 ~~l~~e~e~leeei~~~~~~~~~~g~~fNi~S~kQL~~lLFe~~~~~k~~~l~Lp~er~~k~~~~~~~~~~~kk~~~~~~ 708 (1112)
......++.++++|++.+ |.. |++||+||+++||+ ++++|.+ ..
T Consensus 7 ~~~~~~k~~l~~~i~~~~------g~~-n~~SpkQL~~~Lf~--------~~~l~~~-------------~~-------- 50 (378)
T cd08642 7 ACDDQYKEELLEEAKELT------GLD-NPNSPAQLKDWLNE--------QGGEVDS-------------LL-------- 50 (378)
T ss_pred HHHHHHHHHHHHHHHHHh------CCC-CCCCHHHHHHHHHH--------cCCCCCC-------------Cc--------
Confidence 344556677888886664 555 99999999999998 6777520 01
Q ss_pred cchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHH
Q 001267 709 NITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREA 788 (1112)
Q Consensus 709 ~~~l~~~G~~lp~~~~TktG~~Std~~vLe~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 788 (1112)
++| | ||+.|+..||+
T Consensus 51 --------------k~t------t---vl~~l~~~~~~------------------------------------------ 65 (378)
T cd08642 51 --------------KKD------V---VALLLKTAPGD------------------------------------------ 65 (378)
T ss_pred --------------hhH------H---HHHHhcccCcH------------------------------------------
Confidence 111 2 88888866542
Q ss_pred hHHHHHHHHHHhHhhhhh-hhhcccccCCccCCCCceeecccc-c-CcccccccCCCCcccCCC----------------
Q 001267 789 CDAISALCEVCSIDSLIS-NFILPLQGSNVSGKNGRVHCSLNI-N-TETGRLSARRPNLQNQPA---------------- 849 (1112)
Q Consensus 789 ~~~i~~Lle~r~l~Kl~s-tyv~~l~~~~v~~~dGRIH~s~n~-~-T~TGRlSss~PNLQNIP~---------------- 849 (1112)
++.||+||++.|+.| ||+++|+. . +++|||||++|+| + |+||||||++|||||||+
T Consensus 66 ---~~~iL~~R~~~k~~s~t~~~~l~~-~-~~~~gRih~~~~~~gat~TGRlss~~pnlQNiP~~~~~~~~~~~~~~~~~ 140 (378)
T cd08642 66 ---VKRVLELRQELSKTSVKKYEAMER-A-VCSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLKDLDLARELVKSG 140 (378)
T ss_pred ---HHHHHHHHHHHhhccHHHHHHHHH-H-cCCCCceeeeeeeecchhccccccCCCCcccCCCCcccchHHHHHHhhcc
Confidence 456999999999999 99999997 3 4578999999998 8 999999999999999999
Q ss_pred ------------CccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhcccccccc
Q 001267 850 ------------LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAV 917 (1112)
Q Consensus 850 ------------~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v 917 (1112)
++..|+.||+||+|++|++|+++||||||+|||||||+|+.|+++|++|.|||+.||+.+||+|.+++
T Consensus 141 d~~~~~~~~~~~~~~~~~~iR~aFva~~G~~lvsaDySQIElRVLAhlS~D~~li~af~~g~Dih~~tAs~if~vp~e~~ 220 (378)
T cd08642 141 DFDALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKI 220 (378)
T ss_pred chhhhhhhccccccHHHHHhHHheecCCCCEEEEecHHHHHHHHHHHHhCCHHHHHHHhcCCChHHHHHHHHhCCChhhc
Confidence 56678899999999999999999999999999999999999999999999999999999999876532
Q ss_pred ccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccc----hhhhCCCHHHHHHHHHHHHHhChhHHHHH
Q 001267 918 ETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGL----ARDWKVSVEEAKKTVDLWYNERQEVLTWQ 993 (1112)
Q Consensus 918 ~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~L----a~~lgis~~EAk~~id~ff~~yP~Vk~~~ 993 (1112)
++++++|+.||++|||++||||+++| ++++|||.+||+.++++||++||+|++||
T Consensus 221 ---------------------~v~~~~R~~AK~vnfGiiYG~g~~~L~~~aa~~lgis~~EA~~~i~~yf~~yP~v~~~~ 279 (378)
T cd08642 221 ---------------------GKNSHLRQKGKVAELALGYGGSVGALKAMGALEMGLTEDELPGIVDAWRNANPNIVKLW 279 (378)
T ss_pred ---------------------ccCHHHHHHhhhhhccceeccchHHHHHhhhhhcCCCHHHHHHHHHHHHHHCccHHHHH
Confidence 36789999999999999999999999 88999999999999999999999999999
Q ss_pred HHH---HHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeE
Q 001267 994 EAR---KKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQ 1070 (1112)
Q Consensus 994 ~~~---~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLq 1070 (1112)
+++ ...|.++||+.|+ | +| ++|+|||||||||+|.||+++++ .+++|+||
T Consensus 280 ~~~~~~~~~a~~~g~v~t~-g-------------------~r-~~~n~IQGtAADi~k~Ami~l~~------~g~~ivLq 332 (378)
T cd08642 280 WDVDKAAKKAVKERKTVKL-G-------------------GK-LVENIVQAIARDCLAEAMLRLEK------AGYDIVMH 332 (378)
T ss_pred HHHHHHHHHHHHcCceEee-h-------------------Hh-hhhcccchhHHHHHHHHHHHHHh------cCCeEEEE
Confidence 987 6667789999987 1 23 45669999999999999999986 35899999
Q ss_pred ccceeeeeecchhcHHHHHHHHHHHhcCCC-CCCccccccc
Q 001267 1071 VLFFFSFSFFSIIVIVSCQGIVLANAMHPM-FGKSSRLHYD 1110 (1112)
Q Consensus 1071 VHDElv~Ev~~~~~ae~~~~~v~~~Me~a~-~~~~~~l~~d 1110 (1112)
|||||+||||+. +...+.|+++|+++. |---+||+.+
T Consensus 333 VHDElv~Evp~~---~~~~~~v~~iM~~~p~wa~~lPl~a~ 370 (378)
T cd08642 333 VHDEVVIEVPEG---EGSLEEVNEIMAQPPPWAPGLPLNAD 370 (378)
T ss_pred ECceeEEeeccc---hhHHHHHHHHHccCCccccCCccccc
Confidence 999999999983 235567999999862 2224677654
No 11
>cd06444 DNA_pol_A Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication. DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-
Probab=100.00 E-value=1.3e-69 Score=615.76 Aligned_cols=294 Identities=31% Similarity=0.330 Sum_probs=273.4
Q ss_pred hHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchhhhcceEEcCCCC
Q 001267 789 CDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGN 867 (1112)
Q Consensus 789 ~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~ 867 (1112)
+|.++.|++||+++|+++||+++|++ .++ .|||||++|++ +|+|||+||++|||||||+++..|..+|+||+|++|+
T Consensus 26 hp~~~~ile~r~~~Kl~st~~~~~~~-~~~-~~gRih~~~~~~gT~TGRlSs~~PNlQniP~~~~~g~~iR~~f~a~~G~ 103 (347)
T cd06444 26 HPAVPLLLEYKKLAKLWSANGWPWLD-QWV-RDGRFHPEYVPGGTVTGRWASRGGNAQQIPRRDPLGRDIRQAFVADPGW 103 (347)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHH-Hhc-ccCccccEEEEcccceeeeccCCCccccCCCCCchhhhhhheEecCCCC
Confidence 57788999999999999999999997 344 59999999998 8999999999999999999988899999999999999
Q ss_pred eEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHh
Q 001267 868 SLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRK 947 (1112)
Q Consensus 868 ~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~ 947 (1112)
+||++||||||||||||||+|+.|+++|.+|.|+|+.+|+.+|+++ +++++|+.
T Consensus 104 ~lv~aDysqiElRilA~ls~D~~l~~~f~~g~Dih~~~A~~~~~~~--------------------------v~~~~R~~ 157 (347)
T cd06444 104 TLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATASAMFGVP--------------------------VGGGERQH 157 (347)
T ss_pred EEEEechhHHHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCC--------------------------CCHHHHHH
Confidence 9999999999999999999999999999999999999999999852 45789999
Q ss_pred hHHHhhhhhhC----CCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhC---CeEecccCCcccCCCCC
Q 001267 948 AKMLNFSIAYG----KTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRID---NHVHTLLGRARRFPAIK 1020 (1112)
Q Consensus 948 AK~vnfGiiYG----~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~---GyV~Tl~GRrr~lp~~~ 1020 (1112)
||++|||++|| ||+++|++.+|+|.+||++++++||+.||+|++|++.+++.|++. ||++|++||+|++|++.
T Consensus 158 AK~~~fg~~YG~~~~~g~~~L~~~~~is~~ea~~~~~~f~~~~p~v~~~~~~~~~~a~~~~~~g~v~T~~GR~r~~~~~~ 237 (347)
T cd06444 158 AKIANLGAMYGATSGISARLLAQLRRISTKEAAALIELFFSRFPAFPKAMEYVEDAARRGERGGYVRTLLGRRSPPPDIR 237 (347)
T ss_pred HHHHHHHHHhCCchhhhHHHHHHHhCCCHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhccCCceEEEeCCcEeecCCCc
Confidence 99999999999 999999999999999999999999999999999999999999998 99999999999999988
Q ss_pred c-----------cChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHH
Q 001267 1021 S-----------LTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQ 1089 (1112)
Q Consensus 1021 s-----------~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~ 1089 (1112)
+ .+...+..++|+|+|++||||||||+|.||+++++.+...+.+++|++||||||+||||++. ++++.
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~r~a~N~~IQGsaADi~K~ami~~~~~l~~~~~~~~lvl~VHDElv~evp~~~-~~~~~ 316 (347)
T cd06444 238 WTEVVSDPAAASRARRVRRAAGRFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEE-AEAVA 316 (347)
T ss_pred ccccccccccccccHHHHHHhHHHHhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEccceEEEeCHHH-HHHHH
Confidence 6 45666778899999999999999999999999998654445689999999999999999985 89999
Q ss_pred HHHHHHhcCCC--CCCcccccccC
Q 001267 1090 GIVLANAMHPM--FGKSSRLHYDV 1111 (1112)
Q Consensus 1090 ~~v~~~Me~a~--~~~~~~l~~d~ 1111 (1112)
.+|+++|+++. |...+||.||+
T Consensus 317 ~~l~~~M~~~~~~~~~~vPl~v~~ 340 (347)
T cd06444 317 AIVREAAEQAVRLLFGSVPVRFPV 340 (347)
T ss_pred HHHHHHHHHHhhccCCCCCEEEEe
Confidence 99999999984 35789999885
No 12
>cd08639 DNA_pol_A_Aquificae_like Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nucleas
Probab=100.00 E-value=1.1e-67 Score=593.94 Aligned_cols=280 Identities=31% Similarity=0.422 Sum_probs=254.8
Q ss_pred hHHHHHHHHHHhHhhhhhhhhcccccCCccCCCCceeecccc-cCcccccccCCCCcccCCCCccchhhhcceEEcCCCC
Q 001267 789 CDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGN 867 (1112)
Q Consensus 789 ~~~i~~Lle~r~l~Kl~styv~~l~~~~v~~~dGRIH~s~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~ 867 (1112)
+|+++.|++||+++|+++||++++++ .+.+.|||||++|++ +|+|||+||++|||||||+. ..+|+||+|+||+
T Consensus 29 ~p~~~~lle~r~~~kl~~t~~~~l~~-~~~~~~grih~~~~~~gt~TGRlS~~~PnlQniP~~----~~iR~~f~a~~G~ 103 (324)
T cd08639 29 HPAVRLLLEYRKLNKLISTFGEKLPK-HIHPVTGRIHPSFNQIGAASGRMSCSNPNLQQIPRE----REFRRCFVAPEGN 103 (324)
T ss_pred ChHHHHHHHHHHHhHHHHHHHHHHHH-HccCCCCceeeeEEecccceeehhhccCccccCCCC----cccceeEEcCCCC
Confidence 57788999999999999999999986 455678999999997 99999999999999999973 3799999999999
Q ss_pred eEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHh
Q 001267 868 SLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRK 947 (1112)
Q Consensus 868 ~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~ 947 (1112)
+||++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||++++ ++++++|+.
T Consensus 104 ~lv~aDysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~-----------------------~v~~~~R~~ 160 (324)
T cd08639 104 KLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGKPIE-----------------------EITKEERQL 160 (324)
T ss_pred EEEEechhhhHHHHHHHHhCCHHHHHHHhcCCCHhHHHHHHHhCCChh-----------------------hCCHHHHHH
Confidence 999999999999999999999999999999999999999999997654 356789999
Q ss_pred hHHHhhhhhhCCCcccchhhhC------CCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCc
Q 001267 948 AKMLNFSIAYGKTPVGLARDWK------VSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKS 1021 (1112)
Q Consensus 948 AK~vnfGiiYG~g~~~La~~lg------is~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s 1021 (1112)
||++|||++||||+.+|++.++ +|.+||++++++||..||+++.|++.+. +++.|||+|++||||+++.
T Consensus 161 aK~~~fg~~YG~g~~~L~~~l~~~~g~~~s~~eA~~~~~~f~~~~p~v~~~~~~~~--a~~~g~v~Tl~GRrr~~~~--- 235 (324)
T cd08639 161 AKAVNFGLIYGMSAKGLREYARTNYGVEMSLEEAEKFRESFFFFYKGILRWHHRLK--AKGPIEVRTLLGRRRVFEY--- 235 (324)
T ss_pred hhhHHHHHHhCCchHHHHHHHhhhcCcCCCHHHHHHHHHHHHHhChhHHHHHHHHH--HhhcCeEECCCCCeecccc---
Confidence 9999999999999999999764 8999999999999999999999998765 6788999999999999842
Q ss_pred cChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCCCC
Q 001267 1022 LTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHPMF 1101 (1112)
Q Consensus 1022 ~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a~~ 1101 (1112)
.++|+|+|++||||||||+|.||+++++ .+...+++|++||||||+||||++. ++++.++|+++|+++.-
T Consensus 236 -------~~~r~avN~~IQGsaADi~K~ami~i~~--~l~~~~~~lvl~VHDElv~ev~~~~-~~~~~~~i~~~Me~a~~ 305 (324)
T cd08639 236 -------FTFTEALNYPIQGTGADILKLALALLVD--RLKDLDAKIVLCVHDEIVLEVPEDE-AEEAKKILESSMEEAGK 305 (324)
T ss_pred -------hhhhhHhhhhhhhHHHHHHHHHHHHHHH--HHhcCCCeEEeeeceeeeeecCHHH-HHHHHHHHHHHHHHHHH
Confidence 3579999999999999999999999998 4555789999999999999999986 89999999999998731
Q ss_pred --CCcccccccC
Q 001267 1102 --GKSSRLHYDV 1111 (1112)
Q Consensus 1102 --~~~~~l~~d~ 1111 (1112)
...+||.||+
T Consensus 306 ~~~~~VPl~v~~ 317 (324)
T cd08639 306 RILKKVPVEVEV 317 (324)
T ss_pred hcCCCCCeEEec
Confidence 2479999885
No 13
>cd08641 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-nu
Probab=100.00 E-value=4.1e-55 Score=490.78 Aligned_cols=238 Identities=18% Similarity=0.181 Sum_probs=217.0
Q ss_pred CCCCceeecccc-cCcccc------cccCCCCcccCCCCccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHH
Q 001267 819 GKNGRVHCSLNI-NTETGR------LSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSM 891 (1112)
Q Consensus 819 ~~dGRIH~s~n~-~T~TGR------lSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~L 891 (1112)
..+|||||.+++ ||+||| +|+++||.+|+|+ +||++|+|+|||+||+|||||||||| ||+++|+.|
T Consensus 94 ~~~Gri~p~~~~~GtvTgRa~~~tW~tas~~~~~~iG~------eiR~aF~ap~G~~lVgADySQiELRi-A~lsgD~~l 166 (425)
T cd08641 94 PGYGAILPQVVPMGTITRRAVEPTWLTASNAKKNRVGS------ELKAMVQAPPGYSFVGADVDSQELWI-ASVLGDAHF 166 (425)
T ss_pred CCCCeEeeeeecCcccccccccccccccCCCCcchhhH------HHHhheecCCCCEEEEEchhHHHHHH-HHHcCCHhh
Confidence 468999999998 999999 8889999999876 89999999999999999999999998 999999999
Q ss_pred H-----HHH---------HcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhh
Q 001267 892 L-----DAF---------KAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAY 957 (1112)
Q Consensus 892 i-----~af---------~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiY 957 (1112)
+ .|| .+|.|||+.||+ +||+ .|+.||++|||++|
T Consensus 167 ~~~~~~~AF~~~~l~g~k~~g~DIH~~TA~-i~gi-------------------------------sR~~AK~~NfG~IY 214 (425)
T cd08641 167 GGIHGATAIGWMTLQGKKSEGTDLHSKTAS-ILGI-------------------------------SRDHAKVFNYGRIY 214 (425)
T ss_pred hhccccchhhhhhhcccccCCCCHHHHHHH-HhCC-------------------------------CHHHhHHHHHHHHH
Confidence 9 899 889999999999 7773 29999999999999
Q ss_pred CCC---cccchhhhC--CCHHHHHHHHHHHHHhChhHHH-----------------------HHHHHHH-HHHhCCeEec
Q 001267 958 GKT---PVGLARDWK--VSVEEAKKTVDLWYNERQEVLT-----------------------WQEARKK-ESRIDNHVHT 1008 (1112)
Q Consensus 958 G~g---~~~La~~lg--is~~EAk~~id~ff~~yP~Vk~-----------------------~~~~~~~-~A~~~GyV~T 1008 (1112)
|+| +++|++++| +|.+||++++++||++||+|+. |++.+.+ .|++.||++|
T Consensus 215 G~g~~~a~~L~~~l~~~is~~EA~~~i~~yF~~y~gVr~~~~~~~~~~~~~~~~~w~gg~es~m~n~le~~A~~~g~~tT 294 (425)
T cd08641 215 GAGQPFAERLLMQFNPRLTPAEATEKAKQMYAATKGIRIAIQRSTKGKRLFKRPFWSGGSESIMFNKLEEIAAQSQPRTP 294 (425)
T ss_pred CCCchhhHHHHHHhcCcCCHHHHHHHHHHHHHhCcChhhhhcccccccccccccccccchHHHHHHHHHHHHHhcCCCcC
Confidence 999 899999999 9999999999999999999999 8888888 9999999999
Q ss_pred ccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecchh-----
Q 001267 1009 LLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSII----- 1083 (1112)
Q Consensus 1009 l~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~----- 1083 (1112)
++||+ ++|++.++|...++. +|.|+|+|||||||||+|+|||.++..+...+..++|+|||||||+|||++++
T Consensus 295 llGrr-~~~~l~s~n~~~~~~-~rsaIN~pIQGSAADiiKlaMV~m~~~l~~~~i~aRmlLqVHDEL~feV~eed~yr~a 372 (425)
T cd08641 295 VLGAC-ITSALLEPNLVKNEF-MTSRINWVVQSSAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAA 372 (425)
T ss_pred ccCCE-echhhcccchhHHHH-HHHHhcccchhhHHHHHHHHHHHHHHHHHhcCCCceEEEEECeEeeeeccHHHHHHHH
Confidence 99999 999999999887777 99999999999999999999999998655456779999999999999999874
Q ss_pred cHHHHHHHHHHHhc
Q 001267 1084 VIVSCQGIVLANAM 1097 (1112)
Q Consensus 1084 ~ae~~~~~v~~~Me 1097 (1112)
.+..+..++.++|.
T Consensus 373 lalqi~nlltram~ 386 (425)
T cd08641 373 LALQITNLLTRAMF 386 (425)
T ss_pred HHHHHHHHHHHHHH
Confidence 14455556666665
No 14
>smart00482 POLAc DNA polymerase A domain.
Probab=100.00 E-value=1.3e-53 Score=453.29 Aligned_cols=206 Identities=39% Similarity=0.561 Sum_probs=194.7
Q ss_pred hhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCC
Q 001267 854 RYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPP 933 (1112)
Q Consensus 854 g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~ 933 (1112)
|.++|+||+|+||+++|++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||++++
T Consensus 1 g~~iR~~f~a~~G~~lv~~DysqiElRilA~ls~D~~l~~~~~~g~D~h~~~A~~~~g~~~~------------------ 62 (206)
T smart00482 1 GREIRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEE------------------ 62 (206)
T ss_pred CchhhheeeCCCCCEEEEeeHHHHHHHHHHHHcCCHHHHHHHhcCCCHHHHHHHHHhCCChh------------------
Confidence 35899999999999999999999999999999999999999999999999999999998654
Q ss_pred CCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCc
Q 001267 934 VPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRA 1013 (1112)
Q Consensus 934 v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRr 1013 (1112)
++++++|+.||+++||++||||+.+|++++|+|.+||++++++||++||+|++|++.+.+.|+++|||.|++||+
T Consensus 63 -----~v~~~~R~~aK~~~~g~~YG~g~~~la~~lg~s~~ea~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~t~~Gr~ 137 (206)
T smart00482 63 -----EVTKELRRAAKAINFGIIYGMGAKGLAEQLGISEAEAKELIKAYFARFPGVKRYIKRTLEEARRKGYVTTLFGRR 137 (206)
T ss_pred -----hCCHHHHHHHhHHHHHhhhccchhHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHhCCEEEecCCCe
Confidence 356789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEccceeeeeecch
Q 001267 1014 RRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVLFFFSFSFFSI 1082 (1112)
Q Consensus 1014 r~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVHDElv~Ev~~~ 1082 (1112)
|++|.+.+.+...++.++|+|+|++||||||||+|.||+++++.+...+.+++|+++|||||+||||++
T Consensus 138 r~~~~~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~~~~~~~~~~~~~~~vl~vHDElv~evp~~ 206 (206)
T smart00482 138 RYIPDIDSRNPVLRAAAERAAVNAPIQGSAADILKLAMIKMDEALKEKGLRARLLLQVHDELVFEVPEE 206 (206)
T ss_pred eeCCCCCCCCHHHHhHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEEeeceeEEeecCCC
Confidence 999999988888888899999999999999999999999999965544568899999999999999974
No 15
>PRK10829 ribonuclease D; Provisional
Probab=99.81 E-value=1.1e-18 Score=200.58 Aligned_cols=218 Identities=16% Similarity=0.118 Sum_probs=159.7
Q ss_pred CeEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001267 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1112)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~ 423 (1112)
.|.+|+++++|.++|+.+..+ +.+|||||+.+..++.+.++ + |||+++...+.||+....
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~---~~lalDtEf~~~~ty~~~l~-------L-------iQl~~~~~~~LiD~l~~~--- 61 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAF---PAIALDTEFVRTRTYYPQLG-------L-------IQLYDGEQLSLIDPLGIT--- 61 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcC---CeEEEecccccCccCCCcee-------E-------EEEecCCceEEEecCCcc---
Confidence 488999999999999999886 68999999999998877653 2 445555567889987542
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhc
Q 001267 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (1112)
Q Consensus 424 vL~~Lk~~Led~~v~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~ 502 (1112)
.+..|.++|+|+.+.||+|++.+|+.+|. .+|+.+ .++|||++||++++-+. ++||..|++. ++|++
T Consensus 62 d~~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p-~~~fDTqiaa~~lg~~~----~~gl~~Lv~~-------~lgv~ 129 (373)
T PRK10829 62 DWSPFKALLRDPQVTKFLHAGSEDLEVFLNAFGELP-QPLIDTQILAAFCGRPL----SCGFASMVEE-------YTGVT 129 (373)
T ss_pred chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCCCc-CCeeeHHHHHHHcCCCc----cccHHHHHHH-------HhCCc
Confidence 47889999999999999999999999984 578866 56899999999998654 4899999987 66654
Q ss_pred ccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 001267 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSW 582 (1112)
Q Consensus 503 ~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~ 582 (1112)
+ .|+. +. ++|..+|| ++.|+.||+.||.+++.||+.|.++|.+.++
T Consensus 130 --l-------------------dK~~---~~---sDW~~RPL-------s~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~ 175 (373)
T PRK10829 130 --L-------------------DKSE---SR---TDWLARPL-------SERQCEYAAADVFYLLPIAAKLMAETEAAGW 175 (373)
T ss_pred --c-------------------Cccc---cc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 1 1211 11 38999998 4789999999999999999999999987532
Q ss_pred c---cCCCCCCCchHHHHHHHHhcchHHHHHHhhhcC-cccCHHHHHHHHHHHHHH
Q 001267 583 K---LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEG-MLVDREYLSEIEKVARAE 634 (1112)
Q Consensus 583 ~---~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~G-I~VD~e~L~~L~~~l~~e 634 (1112)
. .++ ...+...-..+..+-.++....| ..++...|..++....-+
T Consensus 176 ~~w~~ee-------~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~lavl~~L~~WR 224 (373)
T PRK10829 176 LPAALDE-------CRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWR 224 (373)
T ss_pred HHHHHHH-------HHHHHhccccCCChHHHHHHhccccCCCHHHHHHHHHHHHHH
Confidence 1 110 11111110112333344555556 556777777776654443
No 16
>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=99.79 E-value=2.1e-18 Score=175.75 Aligned_cols=173 Identities=30% Similarity=0.443 Sum_probs=130.4
Q ss_pred eEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhh
Q 001267 345 VMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDL 424 (1112)
Q Consensus 345 y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~v 424 (1112)
|++|+|++++.++++.+.+. +.+|||+||++++...... ++.++++..+ ...+++++........
T Consensus 1 y~~v~~~~~l~~~~~~l~~~---~~~a~D~E~~~~~~~~~~~----~~~~iq~~~~--------~~~~i~~~~~~~~~~~ 65 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNA---KVLAFDTETTGLDPYSYNP----KIALIQLATG--------EGCYIIDPIDLGDNWI 65 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTT---SEEEEEEEEETSTSTTSSE----EEEEEEEEES--------CEEEEECGTTSTTTTH
T ss_pred CEecCCHHHHHHHHHHHcCC---CeEEEEEEECCCCccccCC----eEEEEEEecC--------CCceeeeeccccccch
Confidence 78999999999999999987 5899999999999854332 2345555543 3345555544321125
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchh-hc
Q 001267 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA-YQ 502 (1112)
Q Consensus 425 L~~Lk~~Led~~v~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg-~~ 502 (1112)
...|+++|+++.+.||+||++||+.+|.+ +|+.+.+ ++|||+|++++++... +||++|+.+ +++ ..
T Consensus 66 ~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~-~~D~~l~~~~l~~~~~----~~L~~L~~~-------~l~~~~ 133 (176)
T PF01612_consen 66 LDALKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKN-VFDTMLAAYLLDPTRS----YSLKDLAEE-------YLGNID 133 (176)
T ss_dssp HHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SS-EEEHHHHHHHTTTSTT----SSHHHHHHH-------HHSEEE
T ss_pred HHHHHHHHhCCCccEEEEEEechHHHHHHHhccccCC-ccchhhhhhccccccc----ccHHHHHHH-------Hhhhcc
Confidence 78899999999999999999999999988 8998865 6899999999999763 999999987 444 21
Q ss_pred ccccCCCCcccccccchhhhhhcccccccCCCCCcccc-ccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 001267 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKIST-IAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLL 578 (1112)
Q Consensus 503 ~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~-~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLe 578 (1112)
+ .+. .+. .+|. .+|+ ++.+..|||.||.++++||+.|.++|+
T Consensus 134 --~-------------------~~~---~~~---~~~~~~~~l-------~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 134 --L-------------------DKK---EQM---SDWRKARPL-------SEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp ----------------------GHC---CTT---SSTTTSSS--------HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred --C-------------------cHH---Hhh---ccCCcCCCC-------hHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 0 000 001 2566 5665 578999999999999999999999874
No 17
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.5e-18 Score=195.51 Aligned_cols=217 Identities=19% Similarity=0.175 Sum_probs=160.6
Q ss_pred ecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhh
Q 001267 348 VDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNE 427 (1112)
Q Consensus 348 V~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~ 427 (1112)
|++.+.++.++..+.++ ++||+||||+++.++.+++|- |||..+.....||+... ...++.
T Consensus 1 i~~~~~l~~~~~~~~~~---~~iAiDTEf~r~~t~~p~LcL--------------IQi~~~e~~~lIdpl~~--~~d~~~ 61 (361)
T COG0349 1 ITTGDLLAAACALLRGS---KAIAIDTEFMRLRTYYPRLCL--------------IQISDGEGASLIDPLAG--ILDLPP 61 (361)
T ss_pred CCchhHHHHHHHHhcCC---CceEEecccccccccCCceEE--------------EEEecCCCceEeccccc--ccccch
Confidence 46778899999998886 689999999999999988742 34444444677888642 245788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHc-CCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhccccc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r~-GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~ 506 (1112)
|..+|.|+.+.||+|++.||+.+|.+. |+ .+.++|||+|||.+++... ++||++|+++ +++++ +
T Consensus 62 l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~-~p~plfdTqiAa~l~g~~~----~~gl~~Lv~~-------ll~v~--l- 126 (361)
T COG0349 62 LVALLADPNVVKIFHAARFDLEVLLNLFGL-LPTPLFDTQIAAKLAGFGT----SHGLADLVEE-------LLGVE--L- 126 (361)
T ss_pred HHHHhcCCceeeeeccccccHHHHHHhcCC-CCCchhHHHHHHHHhCCcc----cccHHHHHHH-------HhCCc--c-
Confidence 999999999999999999999999886 55 4567999999999998764 4999999997 56554 1
Q ss_pred CCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCC
Q 001267 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDG 586 (1112)
Q Consensus 507 ~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~ 586 (1112)
.|+. +. +||..+|| ++.|+.||+.||.++++||..|..+|.+.+|.
T Consensus 127 ------------------dK~~---q~---SDW~~RPL-------s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~--- 172 (361)
T COG0349 127 ------------------DKSE---QR---SDWLARPL-------SEAQLEYAAADVEYLLPLYDKLTEELAREGRL--- 172 (361)
T ss_pred ------------------cccc---cc---cccccCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCch---
Confidence 1211 12 48999998 47899999999999999999999999986542
Q ss_pred CCCCCchHHHHHHHHh----cchHHHHHHhhhc-CcccCHHHHHHHHHHHHHHHHH
Q 001267 587 KPVPGKSMFDFYQEYW----QPFGEILVKMETE-GMLVDREYLSEIEKVARAEQEA 637 (1112)
Q Consensus 587 ~~~~~~~l~~Ly~~IE----mPL~~VLa~ME~~-GI~VD~e~L~~L~~~l~~e~e~ 637 (1112)
....+-|.-++ .+..+-.++-+.. ....+...|..++..+.-+...
T Consensus 173 -----~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a~~~~p~~la~l~~La~wRe~~ 223 (361)
T COG0349 173 -----EWAEDEFRLLPTRRTYKVLPEDAWREIKIAHSLDPRELAVLRELAAWRERE 223 (361)
T ss_pred -----HHHHHHHHHhhhccccccChHhHHHHhhhhhcCChHHHHHHHHHHHHHHHH
Confidence 11122222222 2234455666666 4667788888877655544333
No 18
>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=99.78 E-value=5.3e-18 Score=176.00 Aligned_cols=182 Identities=34% Similarity=0.446 Sum_probs=133.0
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC------CChhhhHhhhhhhhcCCCceEEE
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD------GGGRDLLNEFAPFFEDPSIKKVW 441 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~------~~~~~vL~~Lk~~Led~~v~KV~ 441 (1112)
+.++||+|++|++++.+.+++ +++..++ ...+|++..+ .....++..|+++|++..+.+|+
T Consensus 6 ~~~a~d~e~~~~~~~~~~i~~------l~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~ 72 (193)
T cd06139 6 KVFAFDTETTSLDPMQAELVG------ISFAVEP-------GEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVG 72 (193)
T ss_pred CeEEEEeecCCCCcCCCeEEE------EEEEcCC-------CCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEe
Confidence 689999999999987766654 4444332 1245554322 12345667799999988778999
Q ss_pred eccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhh
Q 001267 442 HNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMK 521 (1112)
Q Consensus 442 HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k 521 (1112)
||++||+++|.++|+.+.+.++||++++|+++|+.. +++|++++.+ +++.. ...+.
T Consensus 73 hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~---~~~l~~l~~~-------~l~~~--------------~~~~~ 128 (193)
T cd06139 73 QNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRR---RHGLDDLAER-------YLGHK--------------TISFE 128 (193)
T ss_pred eccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC--------------CccHH
Confidence 999999999999999988889999999999999763 3799999987 44332 01122
Q ss_pred hhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHH
Q 001267 522 DIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEY 601 (1112)
Q Consensus 522 ~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~~l~~Ly~~I 601 (1112)
.+++++. +. .+|...| ...+..||+.|+.++++|++.|.++|++. .++.++|++|
T Consensus 129 ~~~~k~~--~~----~~~~~~~--------~~~~~~ya~~d~~~~~~l~~~l~~~l~~~-----------~~~~~l~~~i 183 (193)
T cd06139 129 DLVGKGK--KQ----ITFDQVP--------LEKAAEYAAEDADITLRLYELLKPKLKEE-----------PGLLELYEEI 183 (193)
T ss_pred HHcCCCc--Cc----CCccccC--------HHHHHHHHHHHHHHHHHHHHHHHHHHhhh-----------hhHHHHHHHH
Confidence 3344321 11 1232222 24578899999999999999999999851 3789999999
Q ss_pred hcchHHHHHH
Q 001267 602 WQPFGEILVK 611 (1112)
Q Consensus 602 EmPL~~VLa~ 611 (1112)
|||+++||++
T Consensus 184 E~Pl~~vL~~ 193 (193)
T cd06139 184 EMPLIPVLAE 193 (193)
T ss_pred hccHHHHhcC
Confidence 9999999973
No 19
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.78 E-value=7e-18 Score=194.32 Aligned_cols=169 Identities=18% Similarity=0.109 Sum_probs=136.7
Q ss_pred EecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHh
Q 001267 347 VVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLN 426 (1112)
Q Consensus 347 lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~ 426 (1112)
+|+++++|.++++.+.++ ++||||||+++.+++.+.++ + +||+++...++||+... ..+.
T Consensus 1 ~I~t~~~l~~~~~~l~~~---~~ia~DtE~~~~~~y~~~l~-------L-------iQia~~~~~~liD~~~~---~~~~ 60 (367)
T TIGR01388 1 WITTDDELATVCEAVRTF---PFVALDTEFVRERTFWPQLG-------L-------IQVADGEQLALIDPLVI---IDWS 60 (367)
T ss_pred CcCCHHHHHHHHHHHhcC---CEEEEeccccCCCCCCCcce-------E-------EEEeeCCeEEEEeCCCc---ccHH
Confidence 488999999999999886 69999999999998876653 2 45555566788898743 2478
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhccccc
Q 001267 427 EFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (1112)
Q Consensus 427 ~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~ 506 (1112)
.|+++|+|+.+.||+|++++|+++|.+.|..+++.+|||++|+||++++.. +||+.|+++ +|++. +
T Consensus 61 ~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~----~~l~~Lv~~-------~Lg~~--l- 126 (367)
T TIGR01388 61 PLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMS----MGYAKLVQE-------VLGVE--L- 126 (367)
T ss_pred HHHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCC----ccHHHHHHH-------HcCCC--C-
Confidence 899999999999999999999999988766666779999999999999753 799999987 55543 1
Q ss_pred CCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001267 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1112)
Q Consensus 507 ~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~ 580 (1112)
.|+. +. ++|..+|| ++.|..|||.||.+++.||+.|.++|++.
T Consensus 127 ------------------~K~~---~~---sdW~~rPL-------~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~ 169 (367)
T TIGR01388 127 ------------------DKSE---SR---TDWLARPL-------TDAQLEYAAADVTYLLPLYAKLMERLEES 169 (367)
T ss_pred ------------------Cccc---cc---ccCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 1111 11 37877887 46799999999999999999999999874
No 20
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.77 E-value=3.4e-18 Score=176.33 Aligned_cols=174 Identities=21% Similarity=0.266 Sum_probs=130.8
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHH
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFD 447 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led~~v~KV~HNaKfD 447 (1112)
..+++|+|+++.+++.++++| +++..+. ..+|++..+. ..+...|+++|+++.+.|++||+|+|
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~------i~l~~~~--------~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d~K~~ 67 (178)
T cd06140 4 DEVALYVELLGENYHTADIIG------LALANGG--------GAYYIPLELA--LLDLAALKEWLEDEKIPKVGHDAKRA 67 (178)
T ss_pred CceEEEEEEcCCCcceeeEEE------EEEEeCC--------cEEEEeccch--HHHHHHHHHHHhCCCCceeccchhHH
Confidence 468999999999987766654 4444321 2567774321 02456688999999999999999999
Q ss_pred HHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhccc
Q 001267 448 NHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRR 527 (1112)
Q Consensus 448 l~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~ 527 (1112)
+++|.++|+.+++++||||||+||++|+.. +++|++|+.+ |++.. ..+ ..++++++
T Consensus 68 ~~~l~~~gi~~~~~~fDt~laaYLL~p~~~---~~~l~~l~~~-------yl~~~-----~~~---------~~~~~~~~ 123 (178)
T cd06140 68 YVALKRHGIELAGVAFDTMLAAYLLDPTRS---SYDLADLAKR-------YLGRE-----LPS---------DEEVYGKG 123 (178)
T ss_pred HHHHHHCCCcCCCcchhHHHHHHHcCCCCC---CCCHHHHHHH-------HcCCC-----Ccc---------hHHhcCCC
Confidence 999999999998889999999999999864 4899999987 45432 011 11233332
Q ss_pred ccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHH
Q 001267 528 KLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGE 607 (1112)
Q Consensus 528 k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~ 607 (1112)
+ + +...+ .+.+..|+|.|+.++++|++.|.++|++ .++.+||++|||||++
T Consensus 124 ~--~-------~~~~~--------~~~~~~y~~~~a~~l~~l~~~l~~~L~~------------~~l~~L~~~iE~PL~~ 174 (178)
T cd06140 124 A--K-------FAVPD--------EEVLAEHLARKAAAIARLAPKLEEELEE------------NEQLELYYEVELPLAE 174 (178)
T ss_pred C--C-------cccCC--------HHHHHHHHHHHHHHHHHHHHHHHHHHHH------------hHHHHHHHHHHhhHHH
Confidence 1 0 11111 3557889999999999999999999987 4799999999999999
Q ss_pred HHH
Q 001267 608 ILV 610 (1112)
Q Consensus 608 VLa 610 (1112)
||+
T Consensus 175 VL~ 177 (178)
T cd06140 175 VLA 177 (178)
T ss_pred Hhc
Confidence 996
No 21
>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=99.68 E-value=4.3e-16 Score=159.68 Aligned_cols=156 Identities=21% Similarity=0.153 Sum_probs=120.0
Q ss_pred HHHHHHHHh-ccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCC-ceEEEEeCCCCChhhhHhhhhhh
Q 001267 354 AKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNG-KSCIWVDLLDGGGRDLLNEFAPF 431 (1112)
Q Consensus 354 L~~lv~~L~-~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~-~~~~~ID~~~~~~~~vL~~Lk~~ 431 (1112)
|.++++.|. .. +.|+||||+.+...+...+ |+ +||+++ ..++.+|+...+ ...+.|+++
T Consensus 2 l~~~~~~l~~~~---~~ig~D~E~~~~~~~~~~~-------~l-------iQl~~~~~~~~l~d~~~~~--~~~~~L~~l 62 (161)
T cd06129 2 LSSLCEDLSMDG---DVIAFDMEWPPGRRYYGEV-------AL-------IQLCVSEEKCYLFDPLSLS--VDWQGLKML 62 (161)
T ss_pred HHHHHHHHhcCC---CEEEEECCccCCCCCCCce-------EE-------EEEEECCCCEEEEecccCc--cCHHHHHHH
Confidence 677888888 64 6899999999887654332 21 344444 557778876532 246778999
Q ss_pred hcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCC
Q 001267 432 FEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNT 510 (1112)
Q Consensus 432 Led~~v~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~ 510 (1112)
|+++.+.||+|+++.|+..|.+ +|+.+.+ +|||++++|++++.. ++||++|+.+ +++.. +
T Consensus 63 L~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~-~~D~~~aa~ll~~~~----~~~L~~l~~~-------~lg~~--l----- 123 (161)
T cd06129 63 LENPSIVKALHGIEGDLWKLLRDFGEKLQR-LFDTTIAANLKGLPE----RWSLASLVEH-------FLGKT--L----- 123 (161)
T ss_pred hCCCCEEEEEeccHHHHHHHHHHcCCCccc-HhHHHHHHHHhCCCC----CchHHHHHHH-------HhCCC--C-----
Confidence 9999999999999999999976 8998866 599999999999864 3799999987 55543 1
Q ss_pred cccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 511 DEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 511 ~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1112)
.|. .+. ++|..+|| ++.|..|||.||.+++.||++|.
T Consensus 124 --------------~K~---~~~---s~W~~rpL-------t~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 124 --------------DKS---ISC---ADWSYRPL-------TEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred --------------Ccc---cee---ccCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 111 111 38999998 47899999999999999999875
No 22
>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=99.63 E-value=3.4e-15 Score=153.48 Aligned_cols=165 Identities=25% Similarity=0.291 Sum_probs=124.1
Q ss_pred ecCHHHHHHHHHHHh-ccCCCcEEEEEeccCCCCc--ccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhh
Q 001267 348 VDNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDV--KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDL 424 (1112)
Q Consensus 348 V~t~e~L~~lv~~L~-~a~~~~~VAfDTETtGLd~--~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~v 424 (1112)
++++.+++++++.+. .. ..|+||||+++... ..+.+ .. +||+++..++++|+... ...
T Consensus 1 ~~~~~~~~~~~~~~~~~~---~~ig~D~E~~~~~~~~~~~~~------~l--------iQl~~~~~~~l~~~~~~--~~~ 61 (170)
T cd06141 1 TDSAQDAEEAVKELLGKE---KVVGFDTEWRPSFRKGKRNKV------AL--------LQLATESRCLLFQLAHM--DKL 61 (170)
T ss_pred CCCHHHHHHHHHHHhcCC---CEEEEeCccCCccCCCCCCCc------eE--------EEEecCCcEEEEEhhhh--hcc
Confidence 357888999999998 54 68999999998765 22222 11 34444455777887643 234
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcc
Q 001267 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1112)
Q Consensus 425 L~~Lk~~Led~~v~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~ 503 (1112)
...|+++|+++.+.||+|++++|+..|. .+|+.+.+ +|||++++|++++... ..||.+|+.. +++..
T Consensus 62 ~~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~-~~Dl~~aa~ll~~~~~---~~~l~~l~~~-------~l~~~- 129 (170)
T cd06141 62 PPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRG-VVDLSHLAKRVGPRRK---LVSLARLVEE-------VLGLP- 129 (170)
T ss_pred cHHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCC-eeeHHHHHHHhCCCcC---CccHHHHHHH-------HcCcc-
Confidence 5678899999999999999999999997 68998876 4999999999999642 3799999987 45443
Q ss_pred cccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 504 ~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1112)
+ .|.+. .+. ++|..+|| ++.|+.|||.||.+++.||+.|.
T Consensus 130 -~-------------------~k~k~-~~~---s~W~~rpL-------t~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 130 -L-------------------SKPKK-VRC---SNWEARPL-------SKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred -c-------------------CCCCC-ccc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 11000 111 38999998 47899999999999999999875
No 23
>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=99.62 E-value=5.1e-15 Score=156.52 Aligned_cols=172 Identities=19% Similarity=0.207 Sum_probs=124.8
Q ss_pred eEEecCHHHHHHHHHH--HhccCCCcEEEEEeccCCCCcc--cCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCC
Q 001267 345 VMVVDNVSAAKKVVWM--LTNKYKHLVHACDTEVAKIDVK--QETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG 420 (1112)
Q Consensus 345 y~lV~t~e~L~~lv~~--L~~a~~~~~VAfDTETtGLd~~--~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~ 420 (1112)
+++|++++++.+++.. +... +.|+||+|+++.... ...+ |+ +||++++.++.+|+...+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~---~vig~D~Ew~~~~~~~~~~~v-------~L-------iQiat~~~~~lid~~~~~ 63 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAG---RVVGIDSEWKPSFLGDSDPRV-------AI-------LQLATEDEVFLLDLLALE 63 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccC---CEEEEECccCCCccCCCCCCc-------eE-------EEEecCCCEEEEEchhcc
Confidence 4799999999999999 6664 689999999877653 1211 11 455555567888876432
Q ss_pred ---hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCC-----CCccchHHHHHHhcCCCCC-------CCCCCCH
Q 001267 421 ---GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKV-----SGFHADTMHMARLWDSSRR-------TEGGYSL 484 (1112)
Q Consensus 421 ---~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r-~GI~l-----~~~vfDTmIAAyLLdp~~~-------~~~s~sL 484 (1112)
.+...+.|+++|+|+.+.||+|++++|+..|.+ +|+.. ...++||+.+++.+..... ....+||
T Consensus 64 ~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL 143 (193)
T cd06146 64 NLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGL 143 (193)
T ss_pred ccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCH
Confidence 123456689999999999999999999999985 56531 2458999998887653210 0125899
Q ss_pred HHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHH
Q 001267 485 EALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSI 564 (1112)
Q Consensus 485 d~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~ 564 (1112)
.+|+++ +|+.. + .|. .+. ++|..+|| ++.|+.|||.||.
T Consensus 144 ~~l~~~-------~lg~~--l-------------------~K~---~q~---SdW~~rpL-------s~~Qi~YAA~Da~ 182 (193)
T cd06146 144 ADLVQE-------VLGKP--L-------------------DKS---EQC---SNWERRPL-------REEQILYAALDAY 182 (193)
T ss_pred HHHHHH-------HhCCC--c-------------------Ccc---ccc---CCCCCCCC-------CHHHHHHHHHHHH
Confidence 999987 45432 1 111 111 38999998 4789999999999
Q ss_pred HHHHHHHHHH
Q 001267 565 NTLKLYKSLK 574 (1112)
Q Consensus 565 ~tlrL~e~L~ 574 (1112)
++++||++|.
T Consensus 183 ~l~~l~~~L~ 192 (193)
T cd06146 183 CLLEVFDKLL 192 (193)
T ss_pred HHHHHHHHHh
Confidence 9999999885
No 24
>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=99.62 E-value=2.6e-15 Score=159.07 Aligned_cols=170 Identities=23% Similarity=0.310 Sum_probs=120.4
Q ss_pred HHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCC-ceEEEEeCCCCChhhhHhhhhhhhcCCC
Q 001267 358 VWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNG-KSCIWVDLLDGGGRDLLNEFAPFFEDPS 436 (1112)
Q Consensus 358 v~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~-~~~~~ID~~~~~~~~vL~~Lk~~Led~~ 436 (1112)
++.|.++ +.||||||+.++... +.+ |+ +||++. ...+.+|+...+.......|+++|+++.
T Consensus 4 ~~~l~~~---~~i~~D~E~~~~~~~-~~~-------~L-------iQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 4 IIHLKKQ---KVIGLDCEGVNLGRK-GKL-------CL-------VQIATRTGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhC---CEEEEEcccccCCCC-CCE-------EE-------EEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 4455554 689999999877652 222 22 444444 5677889875432235678999999999
Q ss_pred ceEEEeccHHHHHHH-HHcCCCCCCccchHHHHHHhcCCCCC----CCCCCCHHHHHhccccccccchhhcccccCCCCc
Q 001267 437 IKKVWHNYSFDNHVL-ENYGLKVSGFHADTMHMARLWDSSRR----TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTD 511 (1112)
Q Consensus 437 v~KV~HNaKfDl~vL-~r~GI~l~~~vfDTmIAAyLLdp~~~----~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~ 511 (1112)
+.||+||+++|+..| .++|+.+.+ +|||++|+|++++... .....||++++.+ +++.. +
T Consensus 66 i~Kv~h~~k~D~~~L~~~~gi~~~~-~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~-------~l~~~--~------ 129 (197)
T cd06148 66 ILKVIHDCRRDSDALYHQYGIKLNN-VFDTQVADALLQEQETGGFNPDRVISLVQLLDK-------YLYIS--I------ 129 (197)
T ss_pred ccEEEEechhHHHHHHHhcCccccc-eeeHHHHHHHHHHHhcCCccccccccHHHHHHH-------hhCCC--h------
Confidence 999999999999999 568998866 5999999999988532 0113699999987 45432 0
Q ss_pred ccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 001267 512 EGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLE 579 (1112)
Q Consensus 512 eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee 579 (1112)
+ +.. . ..+.+ ..+. .+|..+|| ++.|+.|||.||.+++.||..|.+.|.+
T Consensus 130 ~----k~~--~-~~~~~-~~~~---s~W~~RPL-------t~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 130 S----LKE--D-VKKLM-REDP---KFWALRPL-------TEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred H----HHH--H-HHHHH-hcCc---hhhhcCCC-------CHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 0 100 0 00000 0111 38999998 4789999999999999999999999986
No 25
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.53 E-value=2e-13 Score=137.99 Aligned_cols=170 Identities=25% Similarity=0.228 Sum_probs=119.8
Q ss_pred eEEecCHHHHHHHHHHHh-ccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001267 345 VMVVDNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1112)
Q Consensus 345 y~lV~t~e~L~~lv~~L~-~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~ 423 (1112)
+.+|++++++..+++.+. .. ..+++|+|+.+...+...+++ ++++... . .+|+.... ....
T Consensus 1 ~~~i~~~~~~~~~~~~~~~~~---~~l~~~~e~~~~~~~~~~~~~------l~l~~~~-------~-~~~i~~~~-~~~~ 62 (172)
T smart00474 1 VRVVTDSETLEELLEKLRAAG---GEVALDTETTGLNSYSGKLVL------IQISVTG-------E-GAFIIDPL-ALGD 62 (172)
T ss_pred CEEecCHHHHHHHHHHHHhcC---CeEEEeccccCCccCCCCEEE------EEEeEcC-------C-ceEEEEec-cchh
Confidence 468899999998887775 32 479999998877765555543 4433211 1 23443211 1123
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcc
Q 001267 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1112)
Q Consensus 424 vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~ 503 (1112)
....|+++|+++.+.+|+||+|+|+++|+++|+.+.+. |||++|+||++|... .++|+.++.. +++..
T Consensus 63 ~~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~-~D~~laayll~p~~~---~~~l~~l~~~-------~l~~~- 130 (172)
T smart00474 63 DLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENI-FDTMLAAYLLLGGPS---KHGLATLLKE-------YLGVE- 130 (172)
T ss_pred hHHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccch-hHHHHHHHHHcCCCC---cCCHHHHHHH-------HhCCC-
Confidence 35668899999999999999999999999899998875 999999999999753 4799999987 44332
Q ss_pred cccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKL 577 (1112)
Q Consensus 504 ~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL 577 (1112)
.++ .++++ +|..+|+ ...+..||+.||.++++|++.|.++|
T Consensus 131 -------~~~---------~~~~~----------~~~~~~l-------~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 131 -------LDK---------EEQKS----------DWGARPL-------SEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred -------CCc---------ccCcc----------ccccCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 011 11111 3422332 35688999999999999999998876
No 26
>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=99.49 E-value=6.9e-13 Score=136.30 Aligned_cols=168 Identities=23% Similarity=0.262 Sum_probs=118.0
Q ss_pred HHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhc
Q 001267 354 AKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFE 433 (1112)
Q Consensus 354 L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Le 433 (1112)
|.++++.+... +.+++|+|+.+..++...++ ++++.. +...+|+++... .....|+++|+
T Consensus 2 ~~~~~~~l~~~---~~l~~~~e~~~~~~~~~~~~------~i~l~~--------~~~~~~i~~~~~---~~~~~l~~ll~ 61 (178)
T cd06142 2 LEDLCERLASA---GVIAVDTEFMRLNTYYPRLC------LIQIST--------GGEVYLIDPLAI---GDLSPLKELLA 61 (178)
T ss_pred HHHHHHHHhcC---CeEEEECCccCCCcCCCceE------EEEEee--------CCCEEEEeCCCc---ccHHHHHHHHc
Confidence 34555555332 48999999877665444443 344332 122567764321 24566889999
Q ss_pred CCCceEEEeccHHHHHHHHHc-CCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcc
Q 001267 434 DPSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDE 512 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~r~-GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~e 512 (1112)
++.+.||+||+|+|+++|.++ |+. .+.+|||++|+||++|... ++|++++.+ |++.. + .. +
T Consensus 62 ~~~i~kv~~d~K~~~~~L~~~~gi~-~~~~~D~~laayLl~p~~~----~~l~~l~~~-------~l~~~--~---~~-~ 123 (178)
T cd06142 62 DPNIVKVFHAAREDLELLKRDFGIL-PQNLFDTQIAARLLGLGDS----VGLAALVEE-------LLGVE--L---DK-G 123 (178)
T ss_pred CCCceEEEeccHHHHHHHHHHcCCC-CCCcccHHHHHHHhCCCcc----ccHHHHHHH-------HhCCC--C---Cc-c
Confidence 999999999999999999887 998 6778999999999999753 699999987 44332 0 00 0
Q ss_pred cccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCc
Q 001267 513 GFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGK 592 (1112)
Q Consensus 513 el~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~ 592 (1112)
+ .++ .|..+|++ ..+..|++.|+.++++|++.|.++|++ .
T Consensus 124 ~---------~~~------------~w~~~~l~-------~~~~~yaa~~a~~l~~L~~~l~~~L~e------------~ 163 (178)
T cd06142 124 E---------QRS------------DWSKRPLT-------DEQLEYAALDVRYLLPLYEKLKEELEE------------E 163 (178)
T ss_pred c---------ccc------------cCCCCCCC-------HHHHHHHHHhHHHHHHHHHHHHHHHHH------------c
Confidence 0 111 34444542 457889999999999999999999987 3
Q ss_pred hHHHHHH
Q 001267 593 SMFDFYQ 599 (1112)
Q Consensus 593 ~l~~Ly~ 599 (1112)
++.+||.
T Consensus 164 ~l~~L~~ 170 (178)
T cd06142 164 GRLEWAE 170 (178)
T ss_pred CcHHHHH
Confidence 6788775
No 27
>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=99.41 E-value=4.1e-12 Score=133.75 Aligned_cols=173 Identities=27% Similarity=0.257 Sum_probs=123.9
Q ss_pred CCCeEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCCh
Q 001267 342 YSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGG 421 (1112)
Q Consensus 342 ~~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~ 421 (1112)
.++|.+|++++++..+++.+... +.+++|+|+....++...++ ++++..+. ..+|++....
T Consensus 2 ~~~~~~i~~~~~l~~~~~~l~~~---~~l~~~~e~~~~~~~~~~~~------~l~l~~~~--------~~~~i~~l~~-- 62 (192)
T cd06147 2 ETPLTFVDTEEKLEELVEKLKNC---KEIAVDLEHHSYRSYLGFTC------LMQISTRE--------EDYIVDTLKL-- 62 (192)
T ss_pred CCCcEEECCHHHHHHHHHHHhcC---CeEEEEeEecCCccCCCceE------EEEEecCC--------CcEEEEeccc--
Confidence 35688997778888877776443 47999998877666555554 34444322 2456653211
Q ss_pred hhhHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchh
Q 001267 422 RDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (1112)
Q Consensus 422 ~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg 500 (1112)
......|+++|+++.+.||+||+|.|+++|. ++|+.+.+. ||||||+||++|. . ++|+.|+.+ |++
T Consensus 63 ~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~-fD~~laaYLL~p~-~----~~l~~l~~~-------yl~ 129 (192)
T cd06147 63 RDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNL-FDTGQAARVLNLP-R----HSLAYLLQK-------YCN 129 (192)
T ss_pred ccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCch-HHHHHHHHHhCCC-c----ccHHHHHHH-------HhC
Confidence 2345568899999999999999999999998 889998887 9999999999997 5 599999987 443
Q ss_pred hcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001267 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1112)
Q Consensus 501 ~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee~ 580 (1112)
.. + + | + .+. .+|...|+ ...+..|++.|+.++++|++.|.++|+++
T Consensus 130 ~~------~---------~------k-~--~~~---~~~~~~~l-------~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 130 VD------A---------D------K-K--YQL---ADWRIRPL-------PEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred CC------c---------c------h-h--hhc---cccccCCC-------CHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 31 0 0 1 0 111 12433332 24577899999999999999999999875
No 28
>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=99.35 E-value=2e-11 Score=121.08 Aligned_cols=153 Identities=25% Similarity=0.317 Sum_probs=104.4
Q ss_pred EEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHH
Q 001267 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDN 448 (1112)
Q Consensus 369 ~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led~~v~KV~HNaKfDl 448 (1112)
.+++|+|+.+..++..++ .++++..+ ...+|++.... ...+.+.|.++|+++.+.+|+||+++|+
T Consensus 2 ~l~~d~e~~~~~~~~~~i------~~~~l~~~--------~~~~~i~~~~~-~~~~~~~l~~~l~~~~~~~v~~~~k~d~ 66 (155)
T cd00007 2 EVAFDTETTGLNYHRGKL------VGIQIATA--------GEAAYIPDELE-LEEDLEALKELLEDEDITKVGHDAKFDL 66 (155)
T ss_pred ceEEEEecCCCCcCCCeE------EEEEEEEC--------CcEEEEEcCCC-HHHHHHHHHHHHcCCCCcEEeccHHHHH
Confidence 589999988777544444 34444431 11455543221 1346677899999998899999999999
Q ss_pred HHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccc
Q 001267 449 HVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRK 528 (1112)
Q Consensus 449 ~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k 528 (1112)
++|.++|+.+.+.++||++|+|+++|... +++|++|+++ +++.. ... .....++++
T Consensus 67 ~~L~~~~~~~~~~~~D~~~~ayll~~~~~---~~~l~~l~~~-------~l~~~-----~~~---------~~~~~~~~~ 122 (155)
T cd00007 67 VVLARDGIELPGNIFDTMLAAYLLNPGEG---SHSLDDLAKE-------YLGIE-----LDK---------DEQIYGKGA 122 (155)
T ss_pred HHHHHCCCCCCCCcccHHHHHHHhCCCCC---cCCHHHHHHH-------HcCCC-----Ccc---------HHHHhcCCC
Confidence 99998888777789999999999999763 3799999997 33321 000 011222210
Q ss_pred cccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 529 LKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKK 576 (1112)
Q Consensus 529 ~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~k 576 (1112)
. |..+|+ ...+..|++.|+.++++|++.|.++
T Consensus 123 --------~-~~~~~~-------~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 123 --------K-TFARPL-------SEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred --------C-ccccCC-------HHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 0 111222 4668899999999999999998765
No 29
>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=99.30 E-value=2.1e-11 Score=121.48 Aligned_cols=148 Identities=24% Similarity=0.252 Sum_probs=101.9
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHHH
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNH 449 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led~~v~KV~HNaKfDl~ 449 (1112)
+++|+|+.+..++.++++ +++++.++ ...+|++..+. ......|+++|+++.+.|++||+|+|++
T Consensus 2 ~~~~~e~~~~~~~~~~~~------~l~l~~~~-------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~kv~~d~K~~~~ 66 (150)
T cd09018 2 FAFDTETDSLDNISANLV------LIQLAIEP-------GVAALIPVAHD--YLALELLKPLLEDEKALKVGQNLKYDRG 66 (150)
T ss_pred EEEEeecCCCCCCCceEE------EEEEEcCC-------CcEEEEEcCCc--ccCHHHHHHHhcCCCCceeeecHHHHHH
Confidence 789998877776555544 34444321 12566764321 1124568899999999999999999999
Q ss_pred HHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhccccc
Q 001267 450 VLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKL 529 (1112)
Q Consensus 450 vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~ 529 (1112)
.|.++|+.+.+.+|||++|+||++|... +++|++|+.+ +++.. ..+ .++++++
T Consensus 67 ~L~~~~~~~~~~~~D~~laayLl~p~~~---~~~l~~l~~~-------~l~~~-----~~~---------~~~~~~~--- 119 (150)
T cd09018 67 ILLNYFIELRGIAFDTMLEAYILNSVAG---RWDMDSLVER-------WLGHK-----LIK---------FESIAGK--- 119 (150)
T ss_pred HHHHcCCccCCcchhHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC-----ccc---------HHHhcCC---
Confidence 9999999888889999999999999752 2699999987 44332 000 0112222
Q ss_pred ccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 530 KKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 530 kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1112)
.|..+++ ...+..||+.|+.++.+|++.|.
T Consensus 120 --------~~~~~~~-------~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 120 --------LWFNQPL-------TEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred --------CCcccCC-------HHHHHHHHHHHHHHHHHHHHHhc
Confidence 1311222 35678899999999999999874
No 30
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=99.14 E-value=4.5e-11 Score=143.14 Aligned_cols=246 Identities=18% Similarity=0.198 Sum_probs=147.1
Q ss_pred CCceeecccc-cCcccccccCCCCcc--cCCCCccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcC---c-----h
Q 001267 821 NGRVHCSLNI-NTETGRLSARRPNLQ--NQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN---C-----K 889 (1112)
Q Consensus 821 dGRIH~s~n~-~T~TGRlSss~PNLQ--NIP~~~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~---D-----~ 889 (1112)
.|-|-+.... ||.|-|--..-=+.- .-| +-.|.++|.+..|+||+.||+||-...|+.|.|.|+. | .
T Consensus 686 ~gaI~p~vvp~gtitrrave~tw~tasNs~~--~Rigselkamvqappgy~LVgaDvdsqElwiaa~lgda~~~~~hg~t 763 (1075)
T KOG3657|consen 686 YGAIAPQVVPAGTITRRAVEPTWLTASNARP--DRIGSELKAMVQAPPGYRLVGADVDSQELWIAALLGDASAEGVHGKT 763 (1075)
T ss_pred hhccCccccccchhhhhhhhhhhhhhcccCh--hhhhHHHHHhhcCCCcceEeeccccHHHHHHHHHhhhhhhhcccCcc
Confidence 3556666554 677766221110110 112 2356799999999999999999999999999988873 1 1
Q ss_pred H-----HHHHHHcCCCchhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccc
Q 001267 890 S-----MLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGL 964 (1112)
Q Consensus 890 ~-----Li~af~~G~DiH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~L 964 (1112)
. |...-.+|.|+|+.||..+ +..|..||.+|||.|||.|.. +
T Consensus 764 a~gwM~Lag~ks~gtdlhs~ta~~l--------------------------------giSr~hakv~Ny~riygag~~-f 810 (1075)
T KOG3657|consen 764 AFGWMTLAGSKSDGTDLHSKTASQL--------------------------------GISRNHAKVFNYARIYGAGQT-F 810 (1075)
T ss_pred hhhhhhhcCccccCchHhHhhhhhc--------------------------------cccHhhhhhccHHHHhcCCcc-h
Confidence 1 1112235789999999743 257999999999999999954 3
Q ss_pred hh----hhC--CCHHHHHHHHHHHHHhChhHHH-HHHHHHHHHH------------------------------hCCeEe
Q 001267 965 AR----DWK--VSVEEAKKTVDLWYNERQEVLT-WQEARKKESR------------------------------IDNHVH 1007 (1112)
Q Consensus 965 a~----~lg--is~~EAk~~id~ff~~yP~Vk~-~~~~~~~~A~------------------------------~~GyV~ 1007 (1112)
|. +.+ .+-+||+..-...|..-.|-+. .+........ ..|+-.
T Consensus 811 a~~ll~~fnp~l~~~Ea~~~A~~l~~~tkG~~~~rlk~e~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~gg~es 890 (1075)
T KOG3657|consen 811 AEKLLMRFNPSLTQSEAKSKASQLFKLTKGDRAKRLKVEVRMVENSLVCKILTIDGIYLIYSIYENEVEPRRLWVGGTES 890 (1075)
T ss_pred HHHhHHhhCCCCchHHHHHHHHHHHHhhcCceeeehHhHHHHhhhhhhchhhhhhhhhhhhhhhhcccchhhhccCchHH
Confidence 33 222 6778888777777766665221 1111110000 001100
Q ss_pred cccCC--------cccCCCCCcc-Chhh------hhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHhcCCCceEEeEcc
Q 001267 1008 TLLGR--------ARRFPAIKSL-TRSQ------RNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVL 1072 (1112)
Q Consensus 1008 Tl~GR--------rr~lp~~~s~-n~~~------r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l~~~~~~llLqVH 1072 (1112)
.+|.+ .-+.|-+... .+.+ ...-.+..+|++||+||.|.+.+.++.+...+.--+..+|+++.||
T Consensus 891 ~~fn~lesia~~~~prtpvlgc~is~sl~~~~~~~~~f~~srinwvvqssavd~lhlllvsm~wl~~~y~i~~rfcisih 970 (1075)
T KOG3657|consen 891 SMFNKLESIATAHDPRTPVLGCQISRSLEKLPEGEPKFLPSRINWVVQSSAVDFLHLLLVSMQWLCDTYKIDARFCISIH 970 (1075)
T ss_pred HHHHHHHHHhhccCCCCCeeccchhhhhcccccCCcccccceeeEEeeccchhHHHHHHHHHHHHHhhcccceEEEEEeh
Confidence 11111 1111111100 0000 0012356889999999999999999988754333346789999999
Q ss_pred ceeeeeecchhcHHHHH-HHHHHHhcCCCC
Q 001267 1073 FFFSFSFFSIIVIVSCQ-GIVLANAMHPMF 1101 (1112)
Q Consensus 1073 DElv~Ev~~~~~ae~~~-~~v~~~Me~a~~ 1101 (1112)
|||-+-|.++..-..|- --|.++|.++||
T Consensus 971 devrylv~e~d~~raalalqisnl~tr~~~ 1000 (1075)
T KOG3657|consen 971 DEVRYLVKEEDAPRAALALQISNLLTRAMF 1000 (1075)
T ss_pred HhHHHHhcccccHHHHHHHHHHHHHHHHHH
Confidence 99999988764222221 124466766655
No 31
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=98.85 E-value=3.6e-09 Score=124.22 Aligned_cols=175 Identities=22% Similarity=0.247 Sum_probs=137.6
Q ss_pred hhccCCCeEEecCHHHHHHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC
Q 001267 338 LASFYSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL 417 (1112)
Q Consensus 338 ~~~~~~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~ 417 (1112)
++..| +.+|++..+|.++.+.|... ..+|+|+|+.....+. |. .|+ +||++..+.+.||..
T Consensus 188 le~T~--~~~I~t~~el~~l~~~l~~~---~Efavdlehhsyrsf~----gl---tcl-------mqISTr~ed~iIDt~ 248 (687)
T KOG2206|consen 188 LEITP--KVWICTLGELEALPEILDSV---IEFAVDLEHHSYRSFL----GL---TCL-------MQISTRTEDFIIDTF 248 (687)
T ss_pred ccccC--ceeeechHHHHHHHHHHhhh---hhhhhhccccchhhhc----Cc---eeE-------EEeeccchhheehhH
Confidence 34445 88999999999999998875 4699999998877663 31 233 677788778888876
Q ss_pred CCChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccc
Q 001267 418 DGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSE 496 (1112)
Q Consensus 418 ~~~~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~ 496 (1112)
.. .+.+..|.+.+.+|.+.||+|.+.-|+.+|++ +||.+.+ .|||..|+++|+-.. ++|..|.+.
T Consensus 249 ~l--~~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvn-Lfdt~~a~r~L~~~r-----~sL~~ll~~------ 314 (687)
T KOG2206|consen 249 KL--RDHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVN-LFDTIQASRLLGLPR-----PSLAYLLEC------ 314 (687)
T ss_pred HH--HHHHHHhhhhccCCCeEEEEecCccchhhhhccceEEEEe-chhhHHHHHHhCCCc-----ccHHHHHHH------
Confidence 43 45667899999999999999999999999987 7988755 799999999998764 799988876
Q ss_pred cchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 497 DKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKK 576 (1112)
Q Consensus 497 ~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~k 576 (1112)
+.++. + .| ++ |. .+|.++|| ++.+..||-.|+.+++-+|+.|...
T Consensus 315 -~~~v~--------------~-------nk-~y--ql---adwR~rpL-------p~~Mv~yar~dthyllyiyD~lr~e 359 (687)
T KOG2206|consen 315 -VCGVL--------------T-------NK-KY--QL---ADWRIRPL-------PEEMVRYAREDTHYLLYIYDVLRKE 359 (687)
T ss_pred -HHhhh--------------h-------hh-hh--hh---chhccccC-------cHHHHHHHhhcchhHHHHHHHHHHH
Confidence 33331 0 01 11 11 28999998 4789999999999999999999988
Q ss_pred Hhhc
Q 001267 577 LLEM 580 (1112)
Q Consensus 577 Lee~ 580 (1112)
|...
T Consensus 360 l~~~ 363 (687)
T KOG2206|consen 360 LKRL 363 (687)
T ss_pred HHHH
Confidence 7653
No 32
>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=98.84 E-value=4.1e-08 Score=99.13 Aligned_cols=64 Identities=31% Similarity=0.476 Sum_probs=56.7
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 001267 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (1112)
Q Consensus 425 L~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~ 491 (1112)
...|+++|++..+.|++||+|+++++|.++|+.+.+.+||||||+|||+|... +++|++|+.+|
T Consensus 42 ~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~---~~~l~~la~~y 105 (151)
T cd06128 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAG---RHDMDSLAERW 105 (151)
T ss_pred HHHHHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCC---CCCHHHHHHHH
Confidence 44588899998889999999999999999999998889999999999999753 26999999873
No 33
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=98.78 E-value=1.1e-08 Score=127.47 Aligned_cols=119 Identities=23% Similarity=0.324 Sum_probs=85.2
Q ss_pred CcEEEEEeccCCCCcccCcccccc-------ceE-EEEeeeCCCcccCCCceE---EEEeCCC--CChhhhHhhhhhhhc
Q 001267 367 HLVHACDTEVAKIDVKQETPVDHG-------EVI-CFSIYSGPEADFGNGKSC---IWVDLLD--GGGRDLLNEFAPFFE 433 (1112)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~IVG~g-------~Ii-~fsi~~~~~IqI~~~~~~---~~ID~~~--~~~~~vL~~Lk~~Le 433 (1112)
+.+|+||.|||||++..++|+++| +++ -+..+.+|+-||+...+. +--+.+. .+.++++..|++|++
T Consensus 421 atyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~~~~ 500 (1444)
T COG2176 421 ATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFREFIG 500 (1444)
T ss_pred ccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHHHHhc
Confidence 369999999999999999998743 111 122233444444432110 0001111 125679999999998
Q ss_pred CCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 434 DPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
|. ..|+||+.||+.+|. ++|+. +.++++||+-+||.|+|..+ +|+|..||++
T Consensus 501 d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~k---sh~Lg~l~kk 557 (1444)
T COG2176 501 DS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFK---SHRLGTLCKK 557 (1444)
T ss_pred Cc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhh---hcchHHHHHH
Confidence 86 479999999999985 35654 66889999999999999876 7999999986
No 34
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.64 E-value=3e-07 Score=101.05 Aligned_cols=112 Identities=20% Similarity=0.241 Sum_probs=74.7
Q ss_pred cEEEEEeccCCCCcc-cCccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHh
Q 001267 368 LVHACDTEVAKIDVK-QETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLN 426 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~-~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~ 426 (1112)
.+|+|||||||+++. .++||++| ++.+..+ ...+ .....||.+.. ....+++.
T Consensus 5 r~vvlDtETTGldp~~~drIIEIG---aV~v~~~--~~~~-~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~ 78 (240)
T PRK05711 5 RQIVLDTETTGLNQREGHRIIEIG---AVELINR--RLTG-RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVAD 78 (240)
T ss_pred eEEEEEeeCCCcCCCCCCeEEEEE---EEEEECC--EEec-cEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHH
Confidence 589999999999987 68888743 3332211 1111 11123443311 01345777
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCC-----CccchHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 001267 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-----GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (1112)
Q Consensus 427 ~Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~l~-----~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~ 491 (1112)
.|.+|+++. .+|+||+.||+.+|.+ +|..++ ..++||+.+++.+.|+. .++|++|+.+|
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~----~~~L~aL~~~~ 146 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK----RNSLDALCKRY 146 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC----CCCHHHHHHHC
Confidence 888888764 4799999999999853 553332 34899999999888875 48999999863
No 35
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.59 E-value=2.3e-07 Score=101.31 Aligned_cols=115 Identities=22% Similarity=0.217 Sum_probs=69.7
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC-----------CC----------hhhhHh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------GG----------GRDLLN 426 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~-----------~~----------~~~vL~ 426 (1112)
.+++||+||||+++..++||.+| +.....++..+. ....++++.. +. ..+++.
T Consensus 7 ~~vv~D~ETTGl~p~~d~Iieig----~v~v~~~g~~~~--~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~ 80 (232)
T PRK07942 7 PLAAFDLETTGVDPETARIVTAA----LVVVDADGEVVE--SREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLA 80 (232)
T ss_pred cEEEEEeccCCCCCCCCeeEEEE----EEEEeCCCcccc--ceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHH
Confidence 68999999999999888887632 211111111110 1122343310 11 123444
Q ss_pred hhhhhhcC---CCceEEEeccHHHHHHHH----HcCCC--CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 427 EFAPFFED---PSIKKVWHNYSFDNHVLE----NYGLK--VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 427 ~Lk~~Led---~~v~KV~HNaKfDl~vL~----r~GI~--l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.|.+++.+ ....+|+||+.||+.+|. ++|.. ...+++||+.+++.+.+... ++++|++|+..
T Consensus 81 e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~--~~~~L~~l~~~ 151 (232)
T PRK07942 81 EIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK--GKRTLTALCEH 151 (232)
T ss_pred HHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC--CCCCHHHHHHH
Confidence 44444421 234679999999999985 45654 23568999999987776432 25899999975
No 36
>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=98.54 E-value=9.1e-07 Score=96.32 Aligned_cols=111 Identities=26% Similarity=0.273 Sum_probs=73.3
Q ss_pred EEEEEeccCCCCccc-CccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 001267 369 VHACDTEVAKIDVKQ-ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (1112)
Q Consensus 369 ~VAfDTETtGLd~~~-d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~~ 427 (1112)
+|+|||||||+++.. ++||++| ++.+..+. ..+ .....||.+.. .+..+++..
T Consensus 2 ~vvlD~ETTGl~p~~~d~IIEIg---av~~~~~~--~~~-~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~ 75 (225)
T TIGR01406 2 QIILDTETTGLDPKGGHRIVEIG---AVELVNRM--LTG-DNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADE 75 (225)
T ss_pred EEEEEeeCCCcCCCCCCeEEEEE---EEEEECCc--Eec-ceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHH
Confidence 689999999999875 7888744 22222110 000 01122333210 113467788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----HcCC--C-CC--CccchHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NYGL--K-VS--GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~----r~GI--~-l~--~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~ 491 (1112)
|.+|+.+. ..|+||+.||+.+|. ++|. . +. ..++||+.+++.+.|.. +++|++|+++|
T Consensus 76 f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~----~~~L~~L~~~~ 142 (225)
T TIGR01406 76 FLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ----RNSLDALCKRF 142 (225)
T ss_pred HHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC----CCCHHHHHHhc
Confidence 88888764 479999999999985 3562 2 22 46899999999888875 48999999863
No 37
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.49 E-value=1.9e-06 Score=94.73 Aligned_cols=121 Identities=18% Similarity=0.157 Sum_probs=72.3
Q ss_pred cEEEEEeccCCCCcccCccccccceE----------EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI----------CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFF 432 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii----------~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~L 432 (1112)
.+++||+||||+++..++||.+|-+. .+....+|+.+|+.....+- | +..+ .+..+++..|.+++
T Consensus 48 ~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~~~~ 127 (239)
T PRK09146 48 PFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEAL 127 (239)
T ss_pred CEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 69999999999999889988744111 01111122222211100000 0 0000 12356777888887
Q ss_pred cCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHHhcCCCC--------CC--CCCCCHHHHHhc
Q 001267 433 EDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSR--------RT--EGGYSLEALTGD 490 (1112)
Q Consensus 433 ed~~v~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAyLLdp~~--------~~--~~s~sLd~La~~ 490 (1112)
.+. ..|+||+.||+.+|.+ .|..+..+++||+..++-+.+.. .. ..+++|++++.+
T Consensus 128 ~~~--~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 198 (239)
T PRK09146 128 AGK--VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR 198 (239)
T ss_pred CCC--EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH
Confidence 653 5799999999999854 34556677899999998765432 00 025778888875
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.49 E-value=1.1e-06 Score=100.22 Aligned_cols=112 Identities=17% Similarity=0.109 Sum_probs=74.9
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC---------CC---------ChhhhHhhhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL---------DG---------GGRDLLNEFA 429 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~---------~~---------~~~~vL~~Lk 429 (1112)
.+++||+||||+++..++||.+| ++.+. ..+..+ . ....++.+. ++ ...+++..|.
T Consensus 16 ~fvvlD~ETTGl~p~~d~IIeIg---av~v~-~~g~i~-~-~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~ 89 (313)
T PRK06063 16 GWAVVDVETSGFRPGQARIISLA---VLGLD-ADGNVE-Q-SVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVA 89 (313)
T ss_pred CEEEEEEECCCCCCCCCEEEEEE---EEEEE-CCceee-e-EEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHH
Confidence 69999999999999888888733 22221 111000 0 011122211 11 1346778888
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----cCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 430 PFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 430 ~~Led~~v~KV~HNaKfDl~vL~r----~GI~l~-~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+|+++. ..|+||+.||+.+|.+ +|+.++ +.++||+..++.+.+... +|+|++|+..
T Consensus 90 ~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~---~~kL~~l~~~ 150 (313)
T PRK06063 90 ELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLP---NLRLETLAAH 150 (313)
T ss_pred HHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCC---CCCHHHHHHH
Confidence 888764 5899999999999854 576543 458999999988877654 6999999975
No 39
>PRK07740 hypothetical protein; Provisional
Probab=98.48 E-value=1.2e-06 Score=96.49 Aligned_cols=114 Identities=19% Similarity=0.205 Sum_probs=73.9
Q ss_pred cEEEEEeccCCCCccc-CccccccceE---------EEEeeeCCCcccCCCceEEEEeCCC---------CChhhhHhhh
Q 001267 368 LVHACDTEVAKIDVKQ-ETPVDHGEVI---------CFSIYSGPEADFGNGKSCIWVDLLD---------GGGRDLLNEF 428 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~-d~IVG~g~Ii---------~fsi~~~~~IqI~~~~~~~~ID~~~---------~~~~~vL~~L 428 (1112)
++|+||+||||+++.. ++|+.+|-+. .|.....|..+++... . ...+ .+..+++..|
T Consensus 60 ~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~--~--~ltGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 60 PFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHI--L--ELTGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred CEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhh--e--eccCCCHHHHhCCCCHHHHHHHH
Confidence 6999999999999865 7787643111 0111112222221110 0 0011 1245677788
Q ss_pred hhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 429 APFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 429 k~~Led~~v~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.+|+++. ..|+||+.||+.+|.+ .+..+...++||+.+++.+.|... +++|++++..
T Consensus 136 ~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~---~~sL~~l~~~ 197 (244)
T PRK07740 136 YAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD---FPTLDDALAY 197 (244)
T ss_pred HHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC---CCCHHHHHHH
Confidence 8888764 5899999999999854 344555679999999998887654 6999999974
No 40
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.46 E-value=1.9e-06 Score=95.23 Aligned_cols=118 Identities=24% Similarity=0.306 Sum_probs=73.6
Q ss_pred cEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFED 434 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Led 434 (1112)
.+|+||+||||+++..++||++|-|. .+....+|+.+|+.....+. | +..+ ....+++..|.+++.+
T Consensus 8 ~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~fl~~ 87 (250)
T PRK06310 8 EFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKE 87 (250)
T ss_pred cEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHHhCC
Confidence 68999999999999888888743110 11112223222321110000 0 0000 1134577788888866
Q ss_pred CCceEEEeccHHHHHHHHH----cCCCCC---CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 435 PSIKKVWHNYSFDNHVLEN----YGLKVS---GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 435 ~~v~KV~HNaKfDl~vL~r----~GI~l~---~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.. ..|+||+.||+.+|.+ +|+... ..++||+-.++.+.+.. +++|+.|+..
T Consensus 88 ~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~----~~~L~~l~~~ 145 (250)
T PRK06310 88 GD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSP----NNSLEALAVH 145 (250)
T ss_pred CC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCC----CCCHHHHHHH
Confidence 33 5899999999999853 566542 45899999999864432 5899999975
No 41
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=98.44 E-value=2.4e-06 Score=93.41 Aligned_cols=119 Identities=19% Similarity=0.205 Sum_probs=74.8
Q ss_pred cEEEEEeccCCCCcccCccccccce-----EEEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcCCCc
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEV-----ICFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFEDPSI 437 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~I-----i~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Led~~v 437 (1112)
.+++|||||||+++..++||++|-+ ..+....+|+.+|+.....+- | +..+ ....+++..|.+|+.+. .
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~-~ 81 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD-N 81 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC-C
Confidence 5899999999999988888873311 012222233333322110000 0 0000 11345677788888653 3
Q ss_pred eEEEec-cHHHHHHHH----HcCCCC-CCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 438 KKVWHN-YSFDNHVLE----NYGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 438 ~KV~HN-aKfDl~vL~----r~GI~l-~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..|+|| +.||+.+|. ++|+.. ...++||+-.++.+.|... .++|..|+..
T Consensus 82 ~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~---~~~L~~l~~~ 137 (232)
T PRK06309 82 ILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLP---KHNLQYLRQV 137 (232)
T ss_pred EEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCC---CCCHHHHHHH
Confidence 589999 589999985 467663 3568999999987777654 5899999875
No 42
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.39 E-value=8.5e-07 Score=101.90 Aligned_cols=113 Identities=8% Similarity=-0.004 Sum_probs=76.7
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC---------C---------CChhhhHhhhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL---------D---------GGGRDLLNEFA 429 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~---------~---------~~~~~vL~~Lk 429 (1112)
.+|+||+||||+++..++||.+| ++.+..+ +. +. .....+|.+. + ....+++..|.
T Consensus 47 ~fVvlDiETTGLdp~~drIIeIg---AV~i~~~-g~-iv-e~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 47 PFVAVSIQTSGIHPSTSRLITID---AVTLTAD-GE-EV-EHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CEEEEEEECCCCCCCCCeEEEEE---EEEEEcC-CE-EE-EEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 69999999999999989888633 2222110 00 00 0001122110 1 12467888999
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----c----------------------------CCCCCCccchHHHHHHhcCCCCC
Q 001267 430 PFFEDPSIKKVWHNYSFDNHVLEN----Y----------------------------GLKVSGFHADTMHMARLWDSSRR 477 (1112)
Q Consensus 430 ~~Led~~v~KV~HNaKfDl~vL~r----~----------------------------GI~l~~~vfDTmIAAyLLdp~~~ 477 (1112)
+|+++. .+|+||+.||+.||.+ . ++.+++.++||+-.|+.+.|...
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 999865 4899999999999854 1 23444568999999999998765
Q ss_pred CCCCCCHHHHHhcc
Q 001267 478 TEGGYSLEALTGDR 491 (1112)
Q Consensus 478 ~~~s~sLd~La~~~ 491 (1112)
+|.|..|+.+|
T Consensus 199 ---~~rL~~La~~l 209 (377)
T PRK05601 199 ---DIRIRGVAHTL 209 (377)
T ss_pred ---CCCHHHHHHHh
Confidence 69999999863
No 43
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.39 E-value=1.7e-06 Score=109.94 Aligned_cols=117 Identities=19% Similarity=0.261 Sum_probs=78.1
Q ss_pred cEEEEEeccCCCCcccCccccccc-------eE-EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGE-------VI-CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFED 434 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~-------Ii-~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Led 434 (1112)
.+|+||+||||+++ .++||.+|- |+ .++...+|+.+|+.....+- | +..+ .+..+++..|.+++++
T Consensus 8 ~~vvvD~ETTGl~~-~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~l~~ 86 (820)
T PRK07246 8 KYAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIED 86 (820)
T ss_pred CEEEEEEecCCcCC-CCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHHhCC
Confidence 69999999999987 478887441 11 12222333333322100000 0 0000 1245678888899876
Q ss_pred CCceEEEeccHHHHHHHHH----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 435 PSIKKVWHNYSFDNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 435 ~~v~KV~HNaKfDl~vL~r----~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
. ..|+||+.||+.+|.+ .|..+.++.+||+..++.+.|... +|+|++|+..
T Consensus 87 ~--~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~---~~~L~~L~~~ 141 (820)
T PRK07246 87 C--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE---KYSLSHLSRE 141 (820)
T ss_pred C--EEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 4 4799999999999864 577777788999999998888764 6999999975
No 44
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.36 E-value=2.1e-06 Score=97.81 Aligned_cols=119 Identities=21% Similarity=0.220 Sum_probs=76.6
Q ss_pred CcEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhc
Q 001267 367 HLVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFE 433 (1112)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~~~~~-I---D~~-~~~~~~vL~~Lk~~Le 433 (1112)
..+|+||+||||+++..++|+++|-+. .+....+|+.+++.....+- | +.. ..+..+++..|.+|+.
T Consensus 8 ~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl~ 87 (313)
T PRK06807 8 LDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLH 87 (313)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 368999999999999888888744111 12222223222221100000 0 000 0124567888888887
Q ss_pred CCCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 434 DPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+. ..|+||+.||+.+|.+ +|+. +.++++||+..++.+.+..+ +++|++|+..
T Consensus 88 ~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~---~~kL~~L~~~ 144 (313)
T PRK06807 88 TN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAP---NHKLETLKRM 144 (313)
T ss_pred CC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 65 3699999999999864 5764 45678999998887777654 6899999974
No 45
>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=98.32 E-value=8.6e-06 Score=83.68 Aligned_cols=110 Identities=24% Similarity=0.274 Sum_probs=70.3
Q ss_pred EEEEEeccCCCCc-ccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 001267 369 VHACDTEVAKIDV-KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (1112)
Q Consensus 369 ~VAfDTETtGLd~-~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~~ 427 (1112)
+|+||+||||+++ ..++||.+| ++.+..+. + . ......++.+.. ....+++..
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig---~v~v~~~~-~-~-~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~ 74 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIG---CVELINRR-L-T-GNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADE 74 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEE---EEEEECCc-E-e-ccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHH
Confidence 4899999999998 667787633 12221110 1 0 001122333321 013456778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~----l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
|.+++++. ..|+||+.||+.+|.+ +|+. .+..++||+.+++.+.|.. .++|+++++.
T Consensus 75 l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~----~~~L~~l~~~ 139 (167)
T cd06131 75 FLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK----PNSLDALCKR 139 (167)
T ss_pred HHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC----CCCHHHHHHH
Confidence 88888764 4799999999999853 4442 2346899998888777754 4899999986
No 46
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=98.29 E-value=1e-05 Score=86.65 Aligned_cols=48 Identities=27% Similarity=0.119 Sum_probs=36.1
Q ss_pred ceEEEeccHHHHHHHHH----cCCC---C-CCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 437 IKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 437 v~KV~HNaKfDl~vL~r----~GI~---l-~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
...|+||+.||+.+|.+ +|.. + ...++||+..++.+.|. ++|+.++++
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~------~~L~~l~~~ 161 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ------TVLAKACQA 161 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc------ccHHHHHHH
Confidence 35899999999999864 4542 1 23478999999877653 679999975
No 47
>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=98.29 E-value=4.7e-06 Score=90.10 Aligned_cols=113 Identities=18% Similarity=0.172 Sum_probs=70.8
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~~ 427 (1112)
.+|+||+||||+++..+ ||.+| ++.+..+ +. +. .....++.+.. .+..+++..
T Consensus 8 ~fvv~D~ETTGl~~~~~-IIeIg---av~v~~~-~~-~~-~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 8 TETTGDNETTGLYAGHD-IIEIG---AVEIINR-RI-TG-NKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred CEEEEEecCCCCCCCCC-EEEEE---EEEEECC-CE-ee-eEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 69999999999998777 87633 2222211 11 00 01112222210 113467778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCC--CCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGL--KVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI--~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
|.+|+.+. ..|+||+.||+.+|.+ .+. .....++||+-.++.+.|..+ ..+++|.+|+..
T Consensus 81 ~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~-~~~~~L~~l~~~ 146 (217)
T TIGR00573 81 FADYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFP-GKRNTLDALCKR 146 (217)
T ss_pred HHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCC-CCCCCHHHHHHH
Confidence 88888663 5799999999999964 232 233568899988877766432 125789999975
No 48
>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=98.23 E-value=3.3e-06 Score=110.15 Aligned_cols=118 Identities=23% Similarity=0.291 Sum_probs=78.8
Q ss_pred cEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCceE---EEE-eCC-CCChhhhHhhhhhhhcC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSC---IWV-DLL-DGGGRDLLNEFAPFFED 434 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~~~---~~I-D~~-~~~~~~vL~~Lk~~Led 434 (1112)
.+|+||+||||+++..++|+++|.+. .|....+|+.+|+..... +.- +.. ..+..++++.|.+|+.+
T Consensus 191 ~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl~~ 270 (1213)
T TIGR01405 191 TYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEFFKD 270 (1213)
T ss_pred cEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhCC
Confidence 69999999999999989998744111 122222232222211000 000 000 01245788899999976
Q ss_pred CCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 435 PSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 435 ~~v~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
. ..|+||+.||+.+|.+ +|+. +..+++||+..++.+.|... .++|++|+.+
T Consensus 271 ~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k---~~kL~~Lak~ 326 (1213)
T TIGR01405 271 S--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYK---SHRLGNICKK 326 (1213)
T ss_pred C--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCC---CCCHHHHHHH
Confidence 4 5799999999999864 5764 44678999999999888765 6999999985
No 49
>PRK05168 ribonuclease T; Provisional
Probab=98.22 E-value=1.1e-05 Score=87.07 Aligned_cols=123 Identities=17% Similarity=0.093 Sum_probs=70.7
Q ss_pred HHHHHHHhccCCCcEEEEEeccCCCCcccCccccccceEEEEeeeC-CC-cccCCCceEEEEeCC-C------------C
Q 001267 355 KKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-ADFGNGKSCIWVDLL-D------------G 419 (1112)
Q Consensus 355 ~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~-~~-IqI~~~~~~~~ID~~-~------------~ 419 (1112)
.-+-.++... .+++||+||||+++..++||++| ++.+... .+ +.+.. ....++.+. + +
T Consensus 8 ~~~~~~~~~~---~~vv~D~ETTGl~~~~d~IieIg---aV~v~~d~~g~i~~~~-~f~~lv~P~~~~~i~~~~~~ihGI 80 (211)
T PRK05168 8 NPLKDRFRGF---LPVVIDVETAGFNAKTDALLEIA---AVTLKMDEQGWLYPDE-TLHFHVEPFEGANLEPEALAFNGI 80 (211)
T ss_pred chHHHHhcCC---ceEEEEeeCCCCCCCCCEEEEEe---EEEEEecCCCcEeccc-eEEEEECCCCCCCCCHHHHhhcCC
Confidence 3344556554 58999999999999888888743 2222211 01 11111 111233220 0 0
Q ss_pred ----------ChhhhHhhhhhhhcC-------CCceEEEeccHHHHHHHHH----cCCC---C-CCccchHHHHHHhcCC
Q 001267 420 ----------GGRDLLNEFAPFFED-------PSIKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDS 474 (1112)
Q Consensus 420 ----------~~~~vL~~Lk~~Led-------~~v~KV~HNaKfDl~vL~r----~GI~---l-~~~vfDTmIAAyLLdp 474 (1112)
+..+++..+.+++.+ .....|+||+.||+.+|.+ +|+. + +..++||+..++.+.+
T Consensus 81 t~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~ 160 (211)
T PRK05168 81 DPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG 160 (211)
T ss_pred CchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC
Confidence 112233344444431 1346899999999999854 5642 1 1247999999987755
Q ss_pred CCCCCCCCCHHHHHhc
Q 001267 475 SRRTEGGYSLEALTGD 490 (1112)
Q Consensus 475 ~~~~~~s~sLd~La~~ 490 (1112)
. ++|+.++.+
T Consensus 161 ~------~~L~~l~~~ 170 (211)
T PRK05168 161 Q------TVLAKACQA 170 (211)
T ss_pred C------CCHHHHHHH
Confidence 3 679998875
No 50
>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=98.22 E-value=1.2e-05 Score=102.93 Aligned_cols=117 Identities=20% Similarity=0.233 Sum_probs=77.0
Q ss_pred EEEEEeccCCCCcccCccccccce-------E-EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcCC
Q 001267 369 VHACDTEVAKIDVKQETPVDHGEV-------I-CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFEDP 435 (1112)
Q Consensus 369 ~VAfDTETtGLd~~~d~IVG~g~I-------i-~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Led~ 435 (1112)
+|+||+||||+++..++||.+|-+ + .++...+|+.+++.....+- | +..+ ....+++..|.+++++.
T Consensus 2 ~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l~~~ 81 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHhCCC
Confidence 799999999999888888874311 1 12222233322221110000 0 0000 11356778888888764
Q ss_pred CceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 436 SIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 436 ~v~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..|+||+.||+.+|.+ +|+. ++++++||+-.++.+.|... +++|.+|+..
T Consensus 82 --~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~---~~~L~~l~~~ 136 (850)
T TIGR01407 82 --IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEE---SYQLSELSEA 136 (850)
T ss_pred --EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCC---CCCHHHHHHH
Confidence 4899999999999854 6776 46778999999998888655 6999999975
No 51
>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=98.22 E-value=1.2e-05 Score=85.17 Aligned_cols=48 Identities=25% Similarity=0.102 Sum_probs=36.8
Q ss_pred ceEEEeccHHHHHHHHH----cCCC---C-CCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 437 IKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 437 v~KV~HNaKfDl~vL~r----~GI~---l-~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
...|+||+.||+.+|.+ +|+. . +..++||+.+++.+.+. ++|++++.+
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~------~~L~~l~~~ 158 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ------TVLAKACQA 158 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC------CcHHHHHHH
Confidence 46899999999999854 5662 1 23479999999887653 679999875
No 52
>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=98.21 E-value=2.4e-06 Score=88.16 Aligned_cols=111 Identities=17% Similarity=0.106 Sum_probs=69.9
Q ss_pred EEEEeccCCCCcccCcccccc-------ceEEEEeeeCCCcccCCCceEEEEeCCCCC----------------hhhhHh
Q 001267 370 HACDTEVAKIDVKQETPVDHG-------EVICFSIYSGPEADFGNGKSCIWVDLLDGG----------------GRDLLN 426 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g-------~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~----------------~~~vL~ 426 (1112)
|+||+||||+++..++|+.+| +++ +....+|..+++.... ...++. .+++++
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~-~~~~v~P~~~i~~~~~----~i~GIt~~~l~~a~~~~~~~~~~~~~~~ 75 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL-IDSLVRPSVRVTDWRT----RFSGVTPADLEEAAKAGKTIFGWEAARA 75 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEE-EeccccCCCCCCccce----eccCCCHHHHhhhhhcCCccccHHHHHH
Confidence 589999999999888887633 111 2222223222221110 001111 014567
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 427 EFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 427 ~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.|.+++++.. ..|+||+.||+.+|... .+.++||+..++.+.|......+++|+.|+.+
T Consensus 76 ~~~~~i~~~~-vlVgHn~~fD~~fL~~~----~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~ 134 (161)
T cd06137 76 ALWKFIDPDT-ILVGHSLQNDLDALRMI----HTRVVDTAILTREAVKGPLAKRQWSLRTLCRD 134 (161)
T ss_pred HHHHhcCCCc-EEEeccHHHHHHHHhCc----CCCeeEehhhhhhccCCCcCCCCccHHHHHHH
Confidence 7888887633 58999999999999753 34588999999988775410016999999986
No 53
>PRK07883 hypothetical protein; Validated
Probab=98.15 E-value=8.7e-06 Score=99.47 Aligned_cols=120 Identities=18% Similarity=0.098 Sum_probs=73.8
Q ss_pred cEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFED 434 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Led 434 (1112)
.+|+||+||||+++..+.|+.+|-|. .|....+|+.+++.....+- | +..+ .+..+++..|.+|+++
T Consensus 16 ~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~fl~~ 95 (557)
T PRK07883 16 TFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARG 95 (557)
T ss_pred CEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHhcC
Confidence 69999999999999888888744111 12222222222211000000 0 0000 1134677788888876
Q ss_pred CCceEEEeccHHHHHHHH----HcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 435 PSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 435 ~~v~KV~HNaKfDl~vL~----r~GI~l~-~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
. ..|+||+.||+.+|. ++|+... ..++||+..++-+.+... ..+++|++|+..
T Consensus 96 ~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~-~~~~~L~~L~~~ 153 (557)
T PRK07883 96 A--VLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDE-APNVRLSTLARL 153 (557)
T ss_pred C--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCC-CCCCCHHHHHHH
Confidence 3 579999999999985 4677654 568999998876555211 126999999974
No 54
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.15 E-value=1.1e-05 Score=89.68 Aligned_cols=110 Identities=22% Similarity=0.261 Sum_probs=72.2
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC----------C---------CChhhhHhhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL----------D---------GGGRDLLNEF 428 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~----------~---------~~~~~vL~~L 428 (1112)
.+++||+||||+++..++|+++| ++.+..+. + +. ....++.+. + .+..+++..|
T Consensus 69 ~~vv~DiETTG~~~~~~~IIEIG---Av~v~~g~-i-~~--~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 69 VFCFVDIETNGSKPKKHQIIEIG---AVKVKNGE-I-ID--RFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CEEEEEEeCCCCCCCCCeEEEEE---EEEEECCE-E-EE--EEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 69999999999999888888744 22222111 0 00 001122211 0 1245688889
Q ss_pred hhhhcCCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 429 APFFEDPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 429 k~~Led~~v~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.+|+++. ..|+||+.||+.+|. ++|.. +.++.+||+-.++.+-+.. +++|++|++.
T Consensus 142 ~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~----~~~L~~L~~~ 202 (257)
T PRK08517 142 RLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP----RYGLSFLKEL 202 (257)
T ss_pred HHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCC----CCCHHHHHHH
Confidence 9998764 479999999999985 45654 4466889997776554443 4899999974
No 55
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=98.14 E-value=1.6e-05 Score=89.94 Aligned_cols=115 Identities=16% Similarity=0.062 Sum_probs=67.4
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeC-CC-c-ccCCCceEEEEeCCC-----------CCh------hhhHhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-A-DFGNGKSCIWVDLLD-----------GGG------RDLLNE 427 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~-~~-I-qI~~~~~~~~ID~~~-----------~~~------~~vL~~ 427 (1112)
.+|+|||||||+++..++||++| ++.+... .+ + ++.. ....++++.. +.. ....+.
T Consensus 38 ~~vvlD~ETTGLd~~~d~IIEIg---~V~v~~~~~g~i~~v~~-~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~~ 113 (294)
T PRK09182 38 LGVILDTETTGLDPRKDEIIEIG---MVAFEYDDDGRIGDVLD-TFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA 113 (294)
T ss_pred eEEEEEeeCCCCCCCCCeEEEEE---EEEEEecCCCceeeeee-EEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHHH
Confidence 57999999999999989998743 2222110 01 1 1111 1122333211 100 112345
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~-~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+..+++.. ...|+||+.||+.+|.+.+..+. ..+.||+.......+... +++|++|+..
T Consensus 114 l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~---~~kL~~La~~ 173 (294)
T PRK09182 114 VDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFE---GTKLGYLAGQ 173 (294)
T ss_pred HHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCC---CCCHHHHHHH
Confidence 67777664 35799999999999987654332 346788765443333333 6999999975
No 56
>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=98.13 E-value=3.7e-06 Score=88.15 Aligned_cols=59 Identities=29% Similarity=0.288 Sum_probs=41.4
Q ss_pred hHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 424 LLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 424 vL~~Lk~~Led--~~v~KV~HNa-KfDl~vL~----r~GI~l~--~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+.+.|.+|+.. .....|+||+ .||+.+|. ++|+.+. ..++||+.+++.+.+ +|++|+.+
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~--------~L~~l~~~ 151 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ--------SLGSLYKR 151 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh--------hHHHHHHH
Confidence 44556666653 2346899998 89999985 4676543 346899999886643 68888764
No 57
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.12 E-value=4.4e-05 Score=81.57 Aligned_cols=116 Identities=14% Similarity=0.097 Sum_probs=70.4
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~~ 427 (1112)
.+|+||+||||+++..++|+.+| ++.+. +..+.... ....+|.+.. .+..+++..
T Consensus 30 ~~vviD~ETTGl~~~~d~IieIg---aV~~~-~~~~~~~~-~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 30 EWVALDCETTGLDPRRAEIVSIA---AVKIR-GNRILTSE-RLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CEEEEEeECCCCCCCCCceEEEE---EEEEE-CCEEeecC-ceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 68999999999999888888733 22222 11111111 1122333210 113567788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHH-hcCCCCC-CCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMAR-LWDSSRR-TEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAy-LLdp~~~-~~~s~sLd~La~~ 490 (1112)
|.+++++. ..|+||+.||+.+|.+ .|..++..++||+-..+ ....... ...+++|++++..
T Consensus 105 ~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~ 172 (202)
T PRK09145 105 LLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKH 172 (202)
T ss_pred HHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHH
Confidence 88888764 4799999999999853 36666667889864432 1111111 0125899999975
No 58
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.09 E-value=3.3e-05 Score=99.71 Aligned_cols=118 Identities=20% Similarity=0.242 Sum_probs=76.3
Q ss_pred cEEEEEeccCCCCccc-Cccccccc-------eE-EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhc
Q 001267 368 LVHACDTEVAKIDVKQ-ETPVDHGE-------VI-CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFE 433 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~-d~IVG~g~-------Ii-~fsi~~~~~IqI~~~~~~~~-I---D~~~-~~~~~vL~~Lk~~Le 433 (1112)
.+|+||+||||+++.. ++||.+|- |+ .+....+|+.+|+.....+- | +..+ ....+++..|..+++
T Consensus 4 ~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l~ 83 (928)
T PRK08074 4 RFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83 (928)
T ss_pred CEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHhC
Confidence 5899999999998764 67876431 11 12222233322221100000 0 0000 124567788888987
Q ss_pred CCCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 434 DPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+. ..|+||+.||+.+|.+ .|+. +.++++||+-.++.+.|... +|+|++|++.
T Consensus 84 ~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~---~~~L~~l~~~ 140 (928)
T PRK08074 84 GA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAE---SYKLRDLSEE 140 (928)
T ss_pred CC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCC---CCCHHHHHHh
Confidence 64 5799999999999864 5765 34678999999999888765 6999999975
No 59
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=98.06 E-value=5.1e-05 Score=81.17 Aligned_cols=117 Identities=15% Similarity=0.145 Sum_probs=69.3
Q ss_pred cEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFED 434 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~~~~~-I---D~~-~~~~~~vL~~Lk~~Led 434 (1112)
.+|+||+||||++. .++||.+|-+. .+.....|..+++.....+- | +.. +.+..+++..|..|+++
T Consensus 6 ~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f~~~ 84 (195)
T PRK07247 6 TYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVGE 84 (195)
T ss_pred eEEEEEeeCCCCCC-CCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHHHCC
Confidence 58999999999985 56777644111 12222233323322110000 0 000 01245788899999976
Q ss_pred CCceEEEeccH-HHHHHHHHcCCCCCC-ccchHH---HHHHhc-CCCCCCCCCCCHHHHHhc
Q 001267 435 PSIKKVWHNYS-FDNHVLENYGLKVSG-FHADTM---HMARLW-DSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 435 ~~v~KV~HNaK-fDl~vL~r~GI~l~~-~vfDTm---IAAyLL-dp~~~~~~s~sLd~La~~ 490 (1112)
. .+|+||+. ||+.+|.++|+.+.+ ..+||+ .+.+.. .|+.. +|+|.+|+++
T Consensus 85 ~--~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~---~~~L~~La~~ 141 (195)
T PRK07247 85 L--PLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIA---NLKLQTVADF 141 (195)
T ss_pred C--eEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCC---CCCHHHHHHh
Confidence 5 47999995 899999998887654 345664 222322 23333 6999999975
No 60
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.05 E-value=4.1e-05 Score=87.24 Aligned_cols=65 Identities=22% Similarity=0.229 Sum_probs=50.8
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~----r~GI~l~-~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..++++.|.+|+.+. ..|+||+.||+.+|. ++|+..+ ..++||+..++-+.|..+ +++|+.|+..
T Consensus 67 f~ev~~~~~~fl~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~---~~~L~~L~~~ 136 (309)
T PRK06195 67 FDKIWEKIKHYFNNN--LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNID---NARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCC---cCCHHHHHHH
Confidence 356778888888653 589999999999985 3576643 568999998887777654 6999999975
No 61
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.03 E-value=3.8e-05 Score=78.18 Aligned_cols=109 Identities=22% Similarity=0.250 Sum_probs=71.2
Q ss_pred EEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC--------------------CCChhhhHhhh
Q 001267 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL--------------------DGGGRDLLNEF 428 (1112)
Q Consensus 369 ~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~--------------------~~~~~~vL~~L 428 (1112)
+|+||+||||+++..++|+.+| ++.+..+. +. .....+|.+. +.+..+++..|
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig---~v~~~~~~---~~-~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIA---AVDVDGGR---II-VVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEE---EEEEECCE---eE-EEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 7999999999998777787633 22222110 00 0011233221 01235677888
Q ss_pred hhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 429 APFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 429 k~~Led~~v~KV~HNa-KfDl~vL~r----~GI~l~--~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..++++. ..|+||+ .||+.+|.+ +|+..+ ..++||+-.++.+.+.. +++|++|++.
T Consensus 75 ~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~----~~~L~~l~~~ 137 (169)
T smart00479 75 LEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR----KYSLKKLAER 137 (169)
T ss_pred HHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC----CCCHHHHHHH
Confidence 8999764 3688888 999999865 565433 34799999998877654 4899999975
No 62
>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=98.03 E-value=1.7e-05 Score=81.70 Aligned_cols=63 Identities=17% Similarity=0.071 Sum_probs=45.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHH---HH-hcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHM---AR-LWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIA---Ay-LLdp~~~~~~s~sLd~La~~ 490 (1112)
..+++..|.+++.+. ..|+||+.||+.+|... .+...+.||... .+ ...|... +|+|+.|+++
T Consensus 64 ~~~v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~---~~~L~~L~~~ 130 (157)
T cd06149 64 FAVAQKEILKILKGK--VVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENC---RVSLKVLAKR 130 (157)
T ss_pred HHHHHHHHHHHcCCC--EEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccC---ChhHHHHHHH
Confidence 467888899999764 58999999999999643 123456788642 22 2355443 6999999986
No 63
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.97 E-value=5.9e-05 Score=82.07 Aligned_cols=46 Identities=37% Similarity=0.257 Sum_probs=37.8
Q ss_pred ceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 437 IKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 437 v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
...|+||+.||+.+|... .+.++||+-+|+.+.|+. .+++..|+..
T Consensus 75 ~~lVaHNa~FD~~~L~~~----~~~~idTl~lar~l~p~~----~~~l~~L~~~ 120 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEM----PGEWICTMKLARRLWPGI----KYSNMALYKS 120 (219)
T ss_pred CEEEEeCcHhhHHHHhCc----CCCcEeHHHHHHHHccCC----CCCHHHHHHH
Confidence 368999999999999643 356899999999888875 3899999874
No 64
>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=97.79 E-value=2e-05 Score=80.59 Aligned_cols=63 Identities=19% Similarity=0.149 Sum_probs=45.4
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCC-CCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSS-RRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~-~~~~~s~sLd~La~~ 490 (1112)
..+++..|.+++++. ..|+||+.||+.+|.. +. +...++||.....+..+. .. +++|++|++.
T Consensus 64 ~~~~~~~l~~~l~~~--vlVgHn~~fD~~~L~~-~~-~~~~~~dt~~l~~~~~~~~~~---~~sL~~l~~~ 127 (152)
T cd06144 64 FEEVQKKVAELLKGR--ILVGHALKNDLKVLKL-DH-PKKLIRDTSKYKPLRKTAKGK---SPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHHHhCCC--EEEEcCcHHHHHHhcC-cC-CCccEEEeEEeeccccccCCC---ChhHHHHHHH
Confidence 456888899999763 4799999999999963 21 224578987765555442 22 6999999975
No 65
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.77 E-value=0.00014 Score=96.62 Aligned_cols=117 Identities=21% Similarity=0.253 Sum_probs=76.7
Q ss_pred cEEEEEeccCCCCcccCccccccceE--------EEEeeeCCCcccCCCc------eEEEEeCCCCChhhhHhhhhhhhc
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGK------SCIWVDLLDGGGRDLLNEFAPFFE 433 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii--------~fsi~~~~~IqI~~~~------~~~~ID~~~~~~~~vL~~Lk~~Le 433 (1112)
.+|+||+||||+++..++|+.+|.+. .|....+|+.+++... +...+. ...+..+++..|..|+.
T Consensus 420 ~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~-~aps~~EaL~~f~~fig 498 (1437)
T PRK00448 420 TYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVK-DAPSIEEVLPKFKEFCG 498 (1437)
T ss_pred cEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHc-CCCCHHHHHHHHHHHhC
Confidence 69999999999999888888743111 1222222222221100 000000 01124567778888876
Q ss_pred CCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 434 DPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+ ...|+||+.||+.+|. ++|+. +...++||+-+++.+.|... .++|+.|+.+
T Consensus 499 g--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k---~~kL~~LAk~ 555 (1437)
T PRK00448 499 D--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELK---SHRLNTLAKK 555 (1437)
T ss_pred C--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccc---cccHHHHHHH
Confidence 5 4689999999999874 46774 55678999999998888654 6999999985
No 66
>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=97.74 E-value=0.0002 Score=72.39 Aligned_cols=64 Identities=28% Similarity=0.295 Sum_probs=50.6
Q ss_pred hhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 422 RDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 422 ~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.+++..|..++++. ..|+||+.||+.+|.+ +|+. ++..++||+..++.+.+... +++|+.|++.
T Consensus 65 ~~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~---~~~L~~l~~~ 133 (156)
T cd06130 65 PEVWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP---NHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC---CCCHHHHHHH
Confidence 46778888898773 5899999999999853 5765 34568999998887777654 6999999975
No 67
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=97.59 E-value=0.00019 Score=77.07 Aligned_cols=66 Identities=15% Similarity=0.101 Sum_probs=47.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~----r~GI~l~--~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..+++..|.+|+++... .++|++.||+.+|. ++|+..+ +.++|++...+.+.+... .++|++++++
T Consensus 79 ~~evl~~f~~~~~~~~~-~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~---~~~L~~~~~~ 150 (207)
T PRK07748 79 FEELVEKLAEYDKRCKP-TIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN---QTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHHHhCcCCe-EEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC---CCCHHHHHHH
Confidence 46788889999987332 46677899999985 3576533 457888877765555433 5899999975
No 68
>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=97.58 E-value=8.5e-05 Score=75.99 Aligned_cols=62 Identities=16% Similarity=0.015 Sum_probs=48.1
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..+++..|.+|+.+. ..+|+||+.||+.+|... .+.++||+..++.+.+... +|+|+.|+.+
T Consensus 62 ~~~v~~~~~~fl~~~-~vlVgHn~~fD~~fL~~~----~~~~iDT~~l~r~~~~~~~---~~~L~~L~~~ 123 (150)
T cd06145 62 LEDVQKKLLSLISPD-TILVGHSLENDLKALKLI----HPRVIDTAILFPHPRGPPY---KPSLKNLAKK 123 (150)
T ss_pred HHHHHHHHHHHhCCC-CEEEEcChHHHHHHhhcc----CCCEEEcHHhccccCCCCC---ChhHHHHHHH
Confidence 456788899999632 358999999999999753 2458999998887665443 5999999986
No 69
>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=97.51 E-value=0.00014 Score=68.97 Aligned_cols=75 Identities=29% Similarity=0.356 Sum_probs=51.8
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCC-ceEEEeccHHHH
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPS-IKKVWHNYSFDN 448 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led~~-v~KV~HNaKfDl 448 (1112)
++||+||+|++++.++|++ +++. ... ....++++ |.+++++.. ..+|+||+.||+
T Consensus 1 ~~~DiEt~~~~~~~~~i~~----i~~~--~~~------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~ 56 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIE----IALA--DVN------PEDTAVID------------LKDILRDKPLAILVGHNGSFDL 56 (96)
T ss_pred CEEEEECCCCCCCCCcEEE----EEEE--Ecc------CCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhH
Confidence 4799999999998887765 3332 221 11234443 667777765 578999999999
Q ss_pred HHHHH----cCCCC---CCccchHHHH
Q 001267 449 HVLEN----YGLKV---SGFHADTMHM 468 (1112)
Q Consensus 449 ~vL~r----~GI~l---~~~vfDTmIA 468 (1112)
.+|.+ +|+.. ..+++||+.+
T Consensus 57 ~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 57 PFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 98854 45542 3568999987
No 70
>PRK05359 oligoribonuclease; Provisional
Probab=97.49 E-value=0.00037 Score=73.71 Aligned_cols=103 Identities=13% Similarity=0.133 Sum_probs=63.1
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeC--------------C----C---------CC
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDL--------------L----D---------GG 420 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~--------------~----~---------~~ 420 (1112)
.+|++|+|||||++..++|+++| ++.+ .+..+.+..+ ...++.+ . + .+
T Consensus 4 ~~vvlD~ETTGLdp~~d~IieIg---aV~~-~~~~~~~~~~-~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 4 NLIWIDLEMTGLDPERDRIIEIA---TIVT-DADLNILAEG-PVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred cEEEEEeecCCCCCCCCeEEEEE---EEEE-cCCceEcccc-eEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 68999999999999999998744 2222 1111111110 0011100 0 1 12
Q ss_pred hhhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCccch--HH-HHHHhcCCC
Q 001267 421 GRDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHAD--TM-HMARLWDSS 475 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led----~~v~KV~HNaKfDl~vL~r----~GI~l~~~vfD--Tm-IAAyLLdp~ 475 (1112)
..+++..|.+|+++ .....++||+.||+.+|.+ .|..+.++++| |+ -+++.+.|.
T Consensus 79 ~~e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~ 144 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPE 144 (181)
T ss_pred HHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChh
Confidence 45677788888853 2234699999999999965 36667677777 66 477777774
No 71
>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=97.45 E-value=0.00056 Score=67.91 Aligned_cols=107 Identities=25% Similarity=0.239 Sum_probs=67.1
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhhhh
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNEFA 429 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~--------------------~~~~~vL~~Lk 429 (1112)
|.+|+||||+++..++|+.+| ....... ..+.. ....++.+.. .+..+++..|.
T Consensus 1 v~~D~Ettg~~~~~~~iiei~----~v~~~~~-~~~~~-~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIG----AVKVDGG-IEIVE-RFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEE----EEEEECC-cChhh-hhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHH
Confidence 578999999998888887632 2222211 00000 0012222210 11345777888
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----cCC-CCCCccchHHHHHHhcCCCCCCCCCCCHHHH
Q 001267 430 PFFEDPSIKKVWHNYSFDNHVLEN----YGL-KVSGFHADTMHMARLWDSSRRTEGGYSLEAL 487 (1112)
Q Consensus 430 ~~Led~~v~KV~HNaKfDl~vL~r----~GI-~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~L 487 (1112)
.++++ ..+|+||+.||..+|.+ +|. .....++||+..++.+.+... .+++..+
T Consensus 75 ~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~---~~~l~~~ 132 (159)
T cd06127 75 EFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLR---SHRLGLL 132 (159)
T ss_pred HHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCC---cCchHHH
Confidence 88877 46899999999999865 332 234568999988887776544 5778777
No 72
>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=97.43 E-value=0.00078 Score=71.05 Aligned_cols=115 Identities=14% Similarity=0.142 Sum_probs=65.0
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC-------------C----------CChhhhHh
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------D----------GGGRDLLN 426 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~-------------~----------~~~~~vL~ 426 (1112)
+.||+||||+++..++||.+| ++.+.. .+..+ . ....++.+. + ....+++.
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig---~v~v~~-~~~~~-~-~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFA---AIRTDE-NFNEI-E-PFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEEEE---EEEECC-CCCCc-c-ceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 469999999999888888733 222211 11111 0 111222110 0 01234667
Q ss_pred hhhhhhcCCCceEEEec-cHHHHHHHHH----cCCCC-------CCccchHHHHHHhcC---CCC------C-CCCCCCH
Q 001267 427 EFAPFFEDPSIKKVWHN-YSFDNHVLEN----YGLKV-------SGFHADTMHMARLWD---SSR------R-TEGGYSL 484 (1112)
Q Consensus 427 ~Lk~~Led~~v~KV~HN-aKfDl~vL~r----~GI~l-------~~~vfDTmIAAyLLd---p~~------~-~~~s~sL 484 (1112)
.|.+++..+....|+|| +.||+.+|.+ +|... .+..+||+-.++++. |.. . ...+|+|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 77788865444578997 7999999854 45431 123468886666532 310 0 0125889
Q ss_pred HHHHhc
Q 001267 485 EALTGD 490 (1112)
Q Consensus 485 d~La~~ 490 (1112)
++|+.+
T Consensus 155 ~~l~~~ 160 (183)
T cd06138 155 EDLAQA 160 (183)
T ss_pred HHHHHH
Confidence 999986
No 73
>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=97.40 E-value=0.00049 Score=71.99 Aligned_cols=103 Identities=14% Similarity=0.128 Sum_probs=62.4
Q ss_pred EEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC------------------C---------CCh
Q 001267 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL------------------D---------GGG 421 (1112)
Q Consensus 369 ~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~------------------~---------~~~ 421 (1112)
++.||+||||+++..++|+++| ++.+ .+..+++... ...++.+. + .+.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIg---aV~~-~~~~~~i~~~-f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~ 75 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIA---CIIT-DGDLNIIAEG-PELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTL 75 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEE---EEEE-eCCCceecCc-eeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCH
Confidence 3789999999999888888743 2222 2211122110 01112110 1 123
Q ss_pred hhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCccchH---HHHHHhcCCCC
Q 001267 422 RDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHADT---MHMARLWDSSR 476 (1112)
Q Consensus 422 ~~vL~~Lk~~Led----~~v~KV~HNaKfDl~vL~r----~GI~l~~~vfDT---mIAAyLLdp~~ 476 (1112)
.+++..|.+|+.+ .....++||+.||+.+|.+ .|..+.++..|| ..+++.+.|+.
T Consensus 76 ~~vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~ 141 (173)
T cd06135 76 AQAEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEI 141 (173)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHh
Confidence 5677788888864 2456789999999999864 465555667887 44666666653
No 74
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.36 E-value=0.0011 Score=72.48 Aligned_cols=113 Identities=22% Similarity=0.205 Sum_probs=75.6
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC-----------C---------ChhhhHhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLNE 427 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~-----------~---------~~~~vL~~ 427 (1112)
.+++||+||||+++..++||.+| ++.+..+. + .......|+.+.. + ...++++.
T Consensus 14 ~~vv~D~ETtg~~~~~~~iieIg---av~~~~~~-i--~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~ 87 (243)
T COG0847 14 RFVVIDLETTGLNPKKDRIIEIG---AVTLEDGR-I--VERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPE 87 (243)
T ss_pred cEEEEecccCCCCCCCCceEEEE---eEEEECCe-e--ecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHH
Confidence 57999999999999888888743 23222221 0 0000012222210 0 12467777
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCCC-CCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~l-~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+.+++.+. ...|+||+.||+.+|.. +++.+ ...+.||+-.++-..|+.. .++|+.|+.+
T Consensus 88 ~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~---~~~L~~l~~~ 151 (243)
T COG0847 88 FLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFD---RSSLDALAER 151 (243)
T ss_pred HHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCc---cchHHHHHHH
Confidence 88888774 46899999999999853 45553 3557899999999999843 5999999985
No 75
>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=97.33 E-value=0.0013 Score=67.82 Aligned_cols=67 Identities=12% Similarity=0.013 Sum_probs=46.6
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~----l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..++++.|.+|+.+.....+.|+..||..++.+ .+.. ....++|++-.+..+.+..+ .++|++++..
T Consensus 75 ~~~vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~---~~~L~~l~~~ 149 (176)
T cd06133 75 FPEVLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK---RTGLSKALEY 149 (176)
T ss_pred HHHHHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 356788888999874113567778999887643 3331 33568899988887666543 5999999975
No 76
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.32 E-value=0.0019 Score=77.65 Aligned_cols=81 Identities=12% Similarity=0.080 Sum_probs=48.2
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCC-------------CC----------Chhhh
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------DG----------GGRDL 424 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~-------------~~----------~~~~v 424 (1112)
.++++|+||||+++..++|+.+| ++.+..+ .+.++. ....++.+. ++ +..++
T Consensus 7 ~fvv~D~ETTGLdP~~DrIIeiA---aVrvd~~-~~~i~e-~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 7 TFLWHDYETFGANPALDRPAQFA---GIRTDAD-LNIIGE-PLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred cEEEEEEECCCCCCCCCeeEEEE---EEEEeCC-Cceecc-eeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 69999999999999999998743 2222111 011111 011222111 01 12345
Q ss_pred HhhhhhhhcCCCceEEEec-cHHHHHHHHH
Q 001267 425 LNEFAPFFEDPSIKKVWHN-YSFDNHVLEN 453 (1112)
Q Consensus 425 L~~Lk~~Led~~v~KV~HN-aKfDl~vL~r 453 (1112)
+..+.+++..+....|+|| +.||..++++
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~ 111 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRY 111 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHH
Confidence 6677778864445689997 7899999865
No 77
>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=97.31 E-value=0.0022 Score=68.00 Aligned_cols=65 Identities=23% Similarity=0.350 Sum_probs=47.5
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHHH----cCCCCC----------------------C-ccchHHHHHH
Q 001267 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLEN----YGLKVS----------------------G-FHADTMHMAR 470 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led--~~v~KV~HNa-KfDl~vL~r----~GI~l~----------------------~-~vfDTmIAAy 470 (1112)
..+.+..|..++.+ ++ ..++||. .||+.+|.. +|+... + .++|++..++
T Consensus 63 E~~lL~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r 141 (199)
T cd05160 63 EKELLKRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYK 141 (199)
T ss_pred HHHHHHHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHH
Confidence 34577777777765 44 4899998 899999842 566551 1 3689998888
Q ss_pred hcCCCCCCCCCCCHHHHHhc
Q 001267 471 LWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 471 LLdp~~~~~~s~sLd~La~~ 490 (1112)
-..+ .. +|+|++++..
T Consensus 142 ~~~~-l~---sy~L~~v~~~ 157 (199)
T cd05160 142 RDFK-LK---SYTLDAVAEE 157 (199)
T ss_pred HhcC-cc---cCCHHHHHHH
Confidence 6655 33 6999999986
No 78
>PRK06722 exonuclease; Provisional
Probab=97.27 E-value=0.0024 Score=72.05 Aligned_cols=67 Identities=13% Similarity=0.020 Sum_probs=44.0
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCCC----ccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVSG----FHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r----~GI~l~~----~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..+++..|.+|+++.. .|+||+.||+.+|.+ +|+..+. .++|++-.++-+.+... ...++|+++++.
T Consensus 77 f~eVl~ef~~fig~~~--lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~-~~~~sL~~l~~~ 151 (281)
T PRK06722 77 FPQIIEKFIQFIGEDS--IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELF-EHTPSLQSAVEQ 151 (281)
T ss_pred HHHHHHHHHHHHCCCc--EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhc-cCCCCHHHHHHH
Confidence 4678889999997643 578889999999864 5765432 24687755443333211 013789999975
No 79
>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=96.73 E-value=0.0044 Score=63.45 Aligned_cols=156 Identities=19% Similarity=0.237 Sum_probs=69.7
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCC--hhhhHhhhhhhhcCCCceEEEec-cHH
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG--GRDLLNEFAPFFEDPSIKKVWHN-YSF 446 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~--~~~vL~~Lk~~Led~~v~KV~HN-aKf 446 (1112)
+.||+||+|+++....+.. +|+....+. ....+....... .+..+.....++.+.. ..|+|| ..|
T Consensus 1 l~~DIET~Gl~~~~~~i~l----iG~~~~~~~-------~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~-~iv~yng~~F 68 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYL----IGVADFDDD-------EIITFIQWFAEDPDEEEIILEFFELLDEAD-NIVTYNGKNF 68 (164)
T ss_dssp --EEEEESS-GG-G---EE----EEEEE-ETT-------TTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTT
T ss_pred CcEEecCCCCCCCCCCEEE----EEEEEeCCC-------ceEEeeHhhccCcHHHHHHHHHHHHHhcCC-eEEEEeCccc
Confidence 4699999999986554432 333332222 111122211111 1122222114555544 468888 579
Q ss_pred HHHHHHH----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhh
Q 001267 447 DNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKD 522 (1112)
Q Consensus 447 Dl~vL~r----~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~ 522 (1112)
|+.+|.+ +++......+|++..++-... . +++|+.++.. +|+.. +.+++-|... -.
T Consensus 69 D~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~---~~~Lk~ve~~--------lg~~~------~~~~~~G~~~-~~ 128 (164)
T PF13482_consen 69 DIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--E---SYSLKNVEKF--------LGIER------RDDDISGSES-VK 128 (164)
T ss_dssp HHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--C---CTT--SHHH-------------------------HHHHH-HH
T ss_pred CHHHHHHHHHHcCCCcccchhhHHHHHHhccC--C---CCCHHHHhhh--------ccccc------ccCCCCHHHH-HH
Confidence 9999964 454434568899887763222 2 5899999874 44331 1011112111 11
Q ss_pred hhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 523 IFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSL 573 (1112)
Q Consensus 523 lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L 573 (1112)
.+..- ... .++. ..+....|+..|+..|.+|+++|
T Consensus 129 ~~~~~--~~~----~~~~----------~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 129 LYKEY--LET----GDPE----------ALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHH-----TT----GGTS------------HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHH--Hhc----CCHH----------HHHHHHHHHHHHHHHHHHHHHHh
Confidence 12110 000 0111 14678999999999999999986
No 80
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.60 E-value=0.015 Score=70.32 Aligned_cols=178 Identities=18% Similarity=0.193 Sum_probs=105.8
Q ss_pred CCeEEecCHHHHHHHH-HHHhccCCCcEEEEEeccCCC-CcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCC
Q 001267 343 SNVMVVDNVSAAKKVV-WMLTNKYKHLVHACDTEVAKI-DVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG 420 (1112)
Q Consensus 343 ~~y~lV~t~e~L~~lv-~~L~~a~~~~~VAfDTETtGL-d~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~ 420 (1112)
..+.+|+++.++..++ +.+.+. ..+|++|.|-..- .....++ + + +|+..+...++||.....
T Consensus 390 ~~i~~V~~e~El~~l~l~~l~~e--~~yVGiDsEwkps~~v~dsk~-------~--I-----lQif~~~~v~Lidc~~l~ 453 (617)
T KOG2207|consen 390 ESIGMVGNEKELRDLLLESLSEE--LRYVGIDSEWKPSKKVSDSKL-------A--I-----LQIFFKDCVYLIDCVKLE 453 (617)
T ss_pred cceeeeCCHHHHHHHHHHHhhhc--CEEEEEccccCcccCCChhHH-------H--H-----HHHHhcCeEEEeehHHhh
Confidence 3578999999999987 344443 2699999997643 1111111 0 0 466666667778875421
Q ss_pred --hhhhHh-hhhhhhcCCCceEEEeccHHHHHHHHH------cCCCCC---CccchHHHHHHhcCCCCC----CCCCCCH
Q 001267 421 --GRDLLN-EFAPFFEDPSIKKVWHNYSFDNHVLEN------YGLKVS---GFHADTMHMARLWDSSRR----TEGGYSL 484 (1112)
Q Consensus 421 --~~~vL~-~Lk~~Led~~v~KV~HNaKfDl~vL~r------~GI~l~---~~vfDTmIAAyLLdp~~~----~~~s~sL 484 (1112)
..+++. .+..+|+++.+.|||.+...|++++++ .-+.+. +.+-++.++-.+.+-... .....+|
T Consensus 454 ~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L 533 (617)
T KOG2207|consen 454 NLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGL 533 (617)
T ss_pred hchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhh
Confidence 223333 355689999999999999999999983 222222 223344455444432110 0001233
Q ss_pred HHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHH
Q 001267 485 EALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSI 564 (1112)
Q Consensus 485 d~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~ 564 (1112)
..|... ++|+.--|. ..-.+|.-+|+. ..|+.|||-|+.
T Consensus 534 ~~Lt~~--------------------------------llg~~lnKt--eqcsnWqcrpLr-------~nQi~yaalDa~ 572 (617)
T KOG2207|consen 534 ADLTDC--------------------------------LLGKKLNKT--EQCSNWQCRPLR-------RNQIYYAALDAV 572 (617)
T ss_pred hhhhHH--------------------------------Hhhhhcccc--cccchhhcCCch-------hhHHHHHHhcch
Confidence 333321 223221110 112379999984 578999999999
Q ss_pred HHHHHHHHHHHHH
Q 001267 565 NTLKLYKSLKKKL 577 (1112)
Q Consensus 565 ~tlrL~e~L~~kL 577 (1112)
.+..++.++.+..
T Consensus 573 ~~~~ifkkv~~vv 585 (617)
T KOG2207|consen 573 VLVEIFKKVCSVV 585 (617)
T ss_pred hhHHHHHHHHhhc
Confidence 9999999876543
No 81
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=96.42 E-value=0.016 Score=62.91 Aligned_cols=111 Identities=23% Similarity=0.349 Sum_probs=70.9
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCCC------------------ccchHHHHHHhcCCCCC
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVSG------------------FHADTMHMARLWDSSRR 477 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNa-KfDl~vL~r----~GI~l~~------------------~vfDTmIAAyLLdp~~~ 477 (1112)
..+.+..|..+++.....+|+||. .||+.+|.. +|+.++. ..+|||-+-...+...
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~- 115 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKA- 115 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccc-
Confidence 456888888888876677899996 599999853 7887642 2368776644444332
Q ss_pred CCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHH
Q 001267 478 TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWIS 557 (1112)
Q Consensus 478 ~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~ 557 (1112)
..+|+.||.- +|+. + -.++-|. ...+++ ++...+....
T Consensus 116 ---~~sLd~la~~--------lgiP-----g--K~~idGs-~V~~~y-----------------------~~g~i~~I~~ 153 (209)
T PF10108_consen 116 ---RTSLDELAAL--------LGIP-----G--KDDIDGS-QVAELY-----------------------QEGDIDEIRE 153 (209)
T ss_pred ---cCCHHHHHHH--------cCCC-----C--CCCCCHH-HHHHHH-----------------------HcCCHHHHHH
Confidence 4899999974 4432 0 0011110 001111 1222466789
Q ss_pred HHHHHHHHHHHHHHHHH
Q 001267 558 YSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 558 YAA~DA~~tlrL~e~L~ 574 (1112)
||..||..|..||-++.
T Consensus 154 YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 154 YCEKDVLNTYLLYLRFE 170 (209)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999998774
No 82
>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=96.34 E-value=0.043 Score=59.39 Aligned_cols=112 Identities=20% Similarity=0.256 Sum_probs=63.5
Q ss_pred cEEEEEeccCCCCccc---CccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC--CCceEEEe
Q 001267 368 LVHACDTEVAKIDVKQ---ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED--PSIKKVWH 442 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~---d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led--~~v~KV~H 442 (1112)
..++||+|+.+..... +.. ....|++++.....+ ...+ +.....+..+.+..|..++.. |+ .+++|
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~-~~d~Ii~Is~~~~~~------~~~~-~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDR-GDDRIIIVALRDNRG------WEEV-LHAEDAAEKELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCC-CCCeEEEEecccCCC------ceee-eccCCCCHHHHHHHHHHHHHHhCCC-EEecc
Confidence 5799999997654321 011 112345555543221 1111 111112345677777777764 55 46799
Q ss_pred cc-HHHHHHHH----HcCCCCC------------------------------Cc-cchHHHHHHhcCC---CCCCCCCCC
Q 001267 443 NY-SFDNHVLE----NYGLKVS------------------------------GF-HADTMHMARLWDS---SRRTEGGYS 483 (1112)
Q Consensus 443 Na-KfDl~vL~----r~GI~l~------------------------------~~-vfDTmIAAyLLdp---~~~~~~s~s 483 (1112)
|. .||+.+|. ++|+.+. +. ++|++.+..-.+. ... +++
T Consensus 81 N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~---sys 157 (207)
T cd05785 81 NIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLP---SYG 157 (207)
T ss_pred CCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCC---CCC
Confidence 97 89999984 3566541 12 3798877664322 223 699
Q ss_pred HHHHHhcc
Q 001267 484 LEALTGDR 491 (1112)
Q Consensus 484 Ld~La~~~ 491 (1112)
|+++|..+
T Consensus 158 L~~Va~~~ 165 (207)
T cd05785 158 LKAVAKHF 165 (207)
T ss_pred HHHHHHHh
Confidence 99999863
No 83
>PTZ00315 2'-phosphotransferase; Provisional
Probab=96.25 E-value=0.015 Score=71.08 Aligned_cols=70 Identities=14% Similarity=0.012 Sum_probs=43.7
Q ss_pred hhhhHhhhhhhhcCCC--------ceEEEeccHHHHH-HHHH-------cCCCCCCc-cchH-HHHHHhcCCCC------
Q 001267 421 GRDLLNEFAPFFEDPS--------IKKVWHNYSFDNH-VLEN-------YGLKVSGF-HADT-MHMARLWDSSR------ 476 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~--------v~KV~HNaKfDl~-vL~r-------~GI~l~~~-vfDT-mIAAyLLdp~~------ 476 (1112)
..+++..|..||.+.. -..++||+.||+. +|.+ .|+.+... ++|. ...+.++.|+.
T Consensus 130 F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~ 209 (582)
T PTZ00315 130 FPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGG 209 (582)
T ss_pred HHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccc
Confidence 4578889999987653 1368999999995 6632 36654333 4453 25565655521
Q ss_pred --CCCCCCCHHHHHhc
Q 001267 477 --RTEGGYSLEALTGD 490 (1112)
Q Consensus 477 --~~~~s~sLd~La~~ 490 (1112)
.....++|+++++.
T Consensus 210 ~~~~~~~~~L~~al~~ 225 (582)
T PTZ00315 210 ATPPLGPSDMPDMLQM 225 (582)
T ss_pred cccccCCcCHHHHHHH
Confidence 00125889998874
No 84
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.15 E-value=0.034 Score=59.31 Aligned_cols=109 Identities=22% Similarity=0.330 Sum_probs=66.6
Q ss_pred hhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC----------------------C-ccchHHHHHHh
Q 001267 422 RDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS----------------------G-FHADTMHMARL 471 (1112)
Q Consensus 422 ~~vL~~Lk~~Led--~~v~KV~HNa-KfDl~vL~----r~GI~l~----------------------~-~vfDTmIAAyL 471 (1112)
.+.+..|..++.. ++ ..++||. .||+..|. ++|+.++ + ..+|++..++-
T Consensus 57 ~~lL~~F~~~i~~~dpd-iivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~ 135 (195)
T cd05780 57 KEMIKRFIEIVKEKDPD-VIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR 135 (195)
T ss_pred HHHHHHHHHHHHHcCCC-EEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh
Confidence 4567777777765 65 4899996 69999984 2566532 1 26788877764
Q ss_pred cCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhH
Q 001267 472 WDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREE 551 (1112)
Q Consensus 472 Ldp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~ 551 (1112)
.. ... +++|+++++. +||.++ .++-++ .+..++..+ + .
T Consensus 136 ~~-~l~---sy~L~~v~~~-------~Lg~~k--------~d~~~~-~i~~~~~~~---------------~-------~ 173 (195)
T cd05780 136 TL-NLT---RYTLERVYEE-------LFGIEK--------EDVPGE-EIAEAWDSG---------------E-------N 173 (195)
T ss_pred hC-CCC---cCcHHHHHHH-------HhCCCC--------CcCCHH-HHHHHHhCC---------------C-------c
Confidence 22 223 6999999986 455430 111110 011111110 0 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001267 552 RELWISYSAFDSINTLKLYKSL 573 (1112)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1112)
.....+|+..||..|++|...|
T Consensus 174 ~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 174 LERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred hHHHHHHhHHHHHHHHHHHhhC
Confidence 3567899999999999998753
No 85
>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=95.45 E-value=0.29 Score=52.27 Aligned_cols=108 Identities=20% Similarity=0.228 Sum_probs=61.3
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC--CCceEEEecc-
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED--PSIKKVWHNY- 444 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~~~~vL~~Lk~~Led--~~v~KV~HNa- 444 (1112)
..++||+||++..-+... +...|+++++....+ ...++.. ...+..+.+..|..++.. |. .++++|.
T Consensus 4 ~~l~fDIEt~~~~gfp~~--~~d~Ii~Is~~~~~g------~~~~~~~-~~~~E~~lL~~F~~~i~~~dPd-~i~gyN~~ 73 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNP--RRDPIIVISLATSNG------DVEFILA-EGLDDRKIIREFVKYVKEYDPD-IIVGYNSN 73 (188)
T ss_pred eEEEEEEEecCCCCCCCC--CCCCEEEEEEEeCCC------CEEEEEe-cCCCHHHHHHHHHHHHHHcCCC-EEEecCCC
Confidence 579999999854322111 123456666654221 1122221 112234677777777764 44 3789994
Q ss_pred HHHHHHHH----HcCCCCC-----C----------------ccchHHHHHHhcCCCCCCCCCCCHHHHHh
Q 001267 445 SFDNHVLE----NYGLKVS-----G----------------FHADTMHMARLWDSSRRTEGGYSLEALTG 489 (1112)
Q Consensus 445 KfDl~vL~----r~GI~l~-----~----------------~vfDTmIAAyLLdp~~~~~~s~sLd~La~ 489 (1112)
.||+.+|. ++|+.+. + ..+|.+-..+-... .+ +++|+++|.
T Consensus 74 ~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~-l~---~y~L~~Va~ 139 (188)
T cd05781 74 AFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE-VK---VKTLENVAE 139 (188)
T ss_pred cCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC-CC---CCCHHHHHH
Confidence 79999984 3565442 0 15677766553322 22 699999986
No 86
>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=94.80 E-value=0.17 Score=54.79 Aligned_cols=66 Identities=27% Similarity=0.359 Sum_probs=45.3
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC-----------------CccchHHHHHHhcCCCCCC
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS-----------------GFHADTMHMARLWDSSRRT 478 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNa-KfDl~vL~r----~GI~l~-----------------~~vfDTmIAAyLLdp~~~~ 478 (1112)
..+.+..|..++++....+|+||. .||+.+|.. +|+.++ +..+|++-+..-.+. ..
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~-~~- 155 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGA-RA- 155 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCc-cC-
Confidence 346778888888764446899996 799999853 677433 126788877654333 12
Q ss_pred CCCCCHHHHHhc
Q 001267 479 EGGYSLEALTGD 490 (1112)
Q Consensus 479 ~~s~sLd~La~~ 490 (1112)
+++|+.+|..
T Consensus 156 --~~~L~~va~~ 165 (208)
T cd05782 156 --RASLDLLAKL 165 (208)
T ss_pred --CCCHHHHHHH
Confidence 5899999874
No 87
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=92.85 E-value=1.3 Score=49.10 Aligned_cols=164 Identities=19% Similarity=0.146 Sum_probs=87.4
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCCCC-hhhhHhhhhhhhcCCCc-eEEEecc-
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG-GRDLLNEFAPFFEDPSI-KKVWHNY- 444 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~~~-~~~vL~~Lk~~Led~~v-~KV~HNa- 444 (1112)
.++-||+|||||+...+.| ..+....+. ...++|-..-.+ ...-...+..|+.+++. .+|.+|.
T Consensus 99 ~~~FFDiETTGL~~ag~~I------~~~g~a~~~-------~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGk 165 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTI------TLVGGARGV-------DDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGK 165 (278)
T ss_pred ceEEEeeeccccCCCCCeE------EEEEEEEcc-------CceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCc
Confidence 4778999999999843332 222222211 112334221111 11122334555655422 4688885
Q ss_pred HHHHHHHHH---cCC--CCCCccchHHHHHHhcCCC-CCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccc
Q 001267 445 SFDNHVLEN---YGL--KVSGFHADTMHMARLWDSS-RRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKI 518 (1112)
Q Consensus 445 KfDl~vL~r---~GI--~l~~~vfDTmIAAyLLdp~-~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~ 518 (1112)
.||+.+++| .-+ .+...-||.|..++-+.-. .. +.+|+.+=+ +||+.. .++.-|..
T Consensus 166 aFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~---~c~Lk~VEr--------~LGi~R-------~edtdG~~ 227 (278)
T COG3359 166 AFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLP---RCGLKTVER--------ILGIRR-------EEDTDGYD 227 (278)
T ss_pred ccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCC---CCChhhHHH--------HhCccc-------cccCCCcc
Confidence 599999984 323 3556689999999866522 22 366776543 455431 01111111
Q ss_pred hhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 001267 519 SMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLE 579 (1112)
Q Consensus 519 s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~e~L~~kLee 579 (1112)
+. +++.. +.+.+ .| .+......|.-.|+..+..|++.+.+++.+
T Consensus 228 ~p-~lyr~--~~~~~--------dp------~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 228 GP-ELYRL--YRRYG--------DP------GLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred hH-HHHHH--HHHcC--------CH------HHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 11 11110 11110 01 124566789999999999999999887754
No 88
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=92.24 E-value=1.7 Score=46.78 Aligned_cols=65 Identities=23% Similarity=0.362 Sum_probs=40.5
Q ss_pred hhhHhhhhhhhcC--CCceEEEecc-HHHHHHHHH----cCCCCC------------------------Cc-cchHHHHH
Q 001267 422 RDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLEN----YGLKVS------------------------GF-HADTMHMA 469 (1112)
Q Consensus 422 ~~vL~~Lk~~Led--~~v~KV~HNa-KfDl~vL~r----~GI~l~------------------------~~-vfDTmIAA 469 (1112)
.+.+..|..++.. |+ ..++||. .||+..|.+ +|+.+. +. .+|++-..
T Consensus 52 ~~lL~~f~~~i~~~dPD-vi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~ 130 (193)
T cd05784 52 KSLLLALIAWFAQYDPD-IIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDAL 130 (193)
T ss_pred HHHHHHHHHHHHhhCCC-EEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHH
Confidence 4566676666654 44 4799995 799999842 455431 11 57876554
Q ss_pred HhcCCCCCCCCCCCHHHHHhc
Q 001267 470 RLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 470 yLLdp~~~~~~s~sLd~La~~ 490 (1112)
+--..... +|+|+++|..
T Consensus 131 k~~~~kl~---sy~L~~Va~~ 148 (193)
T cd05784 131 KTATYHFE---SFSLENVAQE 148 (193)
T ss_pred HHccCCCC---cCCHHHHHHH
Confidence 42111233 6999999986
No 89
>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=90.65 E-value=2.3 Score=46.19 Aligned_cols=65 Identities=26% Similarity=0.317 Sum_probs=39.1
Q ss_pred hhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC-------C----------ccchHHHHHHhcCC-CC
Q 001267 422 RDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS-------G----------FHADTMHMARLWDS-SR 476 (1112)
Q Consensus 422 ~~vL~~Lk~~Led--~~v~KV~HNa-KfDl~vL~----r~GI~l~-------~----------~vfDTmIAAyLLdp-~~ 476 (1112)
.+.+..|..++.+ |. .++++|. .||+..|. ++|+.+. + ..+|.+-...--.- ..
T Consensus 74 ~~lL~~f~~~i~~~~Pd-~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~ 152 (204)
T cd05779 74 KALLQRFFEHIREVKPH-IIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQ 152 (204)
T ss_pred HHHHHHHHHHHHHhCCC-EEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCC
Confidence 4566677777654 44 3699995 79999984 2566532 0 14566654432111 11
Q ss_pred CCCCCCCHHHHHhc
Q 001267 477 RTEGGYSLEALTGD 490 (1112)
Q Consensus 477 ~~~~s~sLd~La~~ 490 (1112)
++++|+.+|+.
T Consensus 153 ---~sysLd~Va~~ 163 (204)
T cd05779 153 ---GSQGLKAVTKA 163 (204)
T ss_pred ---CCccHHHHHHH
Confidence 15899999986
No 90
>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]
Probab=90.31 E-value=0.1 Score=66.32 Aligned_cols=208 Identities=13% Similarity=0.097 Sum_probs=132.8
Q ss_pred CceeecccccCcccccccCCCCcccCCCC-ccchhhhcceEEcCCCCeEEEecccchhHHHHHHhcCchHHHHHHHcCCC
Q 001267 822 GRVHCSLNINTETGRLSARRPNLQNQPAL-EKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGD 900 (1112)
Q Consensus 822 GRIH~s~n~~T~TGRlSss~PNLQNIP~~-~~~g~~iR~~Fia~~G~~lvsaDySQIELRIlAhlS~D~~Li~af~~G~D 900 (1112)
|++|+-+.--+.| -+.+|+||.|.+ .-++.-++.-|+...--..|..+|.+.+.||.||++++..+.....
T Consensus 792 G~~e~fi~~~~~g----qs~~~~~~~~~~~r~y~~l~L~~li~espi~~V~~kYk~~rg~lqall~~a~~~a~~It---- 863 (1008)
T KOG0950|consen 792 GVIESFIEKCVSG----QSVRNLQNVQKRKRLYVALALQKLINESPIRTVAEKYKVERGRLQALLSNASSFASLIT---- 863 (1008)
T ss_pred chHHHHHHHhhhc----cccccccchhHHHHHHHHHHHHHHHhhCcHHHHHHHhCchHHHHHHHHhcchhHHHHHH----
Confidence 6677655431111 456799999974 2234466777777766778999999999999999999977665544
Q ss_pred chhHHHhhhccccccccccchhhhcccCCCCCCCCcccccChHHHHhhHHHhhhhhhCCCcccchhhhCCCHHHHHHHHH
Q 001267 901 FHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVD 980 (1112)
Q Consensus 901 iH~~tA~~ifg~~~e~v~~~~~~~~w~~~~~p~v~~~~~vt~~~R~~AK~vnfGiiYG~g~~~La~~lgis~~EAk~~id 980 (1112)
.|- +. +.|. -++.-+.-.++.+|++|.+.|..-..+|-..+++...
T Consensus 864 --------~Fc---e~-------l~w~----------------~~~~l~~~~~~rl~~g~~~eL~~Lmrv~~~~~~RAr~ 909 (1008)
T KOG0950|consen 864 --------FFC---ES-------IQWF----------------PLRALLSEFYGRLSFGGHAELIPLMRVPDVKAERARQ 909 (1008)
T ss_pred --------HHH---HH-------hhhc----------------chHHHHHHHHHHHhccchhhhhhhhcCchhHHHHHHH
Confidence 111 00 1232 3566778899999999999999999999999999999
Q ss_pred HHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhHhhhhhhHHHHHHHHHHHHHHHHHHh
Q 001267 981 LWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARL 1060 (1112)
Q Consensus 981 ~ff~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~~eR~avN~~IQGSAADI~K~AMi~i~~~~~l 1060 (1112)
-|++.|+.+..+.........+.=+..+.+++...+-. ..+...-..+||..-.+-+.+++....
T Consensus 910 lf~Agf~tv~~iA~a~p~klvkel~~si~~~~a~~i~~-----------s~~~~l~~t~~~~~~e~~~~~iv~~es---- 974 (1008)
T KOG0950|consen 910 LFKAGFTSVGSIANATPEKLVKELPISISMKQATQIVA-----------SAKDELRKTGKGLMEEIEATKIVDIES---- 974 (1008)
T ss_pred HHHhhccchHHHhcCChHHHHHHhhccccHHHhhhHHh-----------hhhHHHHHhhcccceecchHHHHHHHH----
Confidence 99999999999876655444443333333333222110 001111114555555555555544332
Q ss_pred cCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcCC
Q 001267 1061 KELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMHP 1099 (1112)
Q Consensus 1061 ~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~a 1099 (1112)
+.. ||+...++++-. . + -+.+.|++-
T Consensus 975 -----~~~---~w~~~~a~~~i~-~--~--~~~~~ls~~ 1000 (1008)
T KOG0950|consen 975 -----REF---HWEVLVALPEIH-V--L--KLQESLSHL 1000 (1008)
T ss_pred -----HHh---hhhHhhhcchhh-H--H--hHHHHhhcc
Confidence 111 999999988843 1 1 245666654
No 91
>PF00940 RNA_pol: DNA-dependent RNA polymerase; InterPro: IPR002092 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 phage-type enzymes are family of single chain polymerases found in bacteriophages and mitochondria [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=90.22 E-value=3.7 Score=49.13 Aligned_cols=133 Identities=20% Similarity=0.123 Sum_probs=81.9
Q ss_pred eEEEecccchhHHHHHHhcCchHHHHHHH-----cCCCchhHHHhhhccccccc---cccchhhhcccCCCCCCCCcccc
Q 001267 868 SLIVADYGQLELRILAHLANCKSMLDAFK-----AGGDFHSRTAMNMYPHIRNA---VETGQVLLEWHGEDKPPVPLLKD 939 (1112)
Q Consensus 868 ~lvsaDySQIELRIlAhlS~D~~Li~af~-----~G~DiH~~tA~~ifg~~~e~---v~~~~~~~~w~~~~~p~v~~~~~ 939 (1112)
+-|..|-|.==+-.+|.|.+|+.+.++.+ .-.|||+.+|..+-...... ......+.+|..
T Consensus 87 lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip~~~p~DiY~~V~~~v~~~l~~~~~~~~~~~~~~~~l~----------- 155 (405)
T PF00940_consen 87 LPVHQDGSCSGLQHYSALLRDEVGAKAVNLIPSDKPQDIYSEVAEEVKKRLEEDADDAEEDNSLAKWLK----------- 155 (405)
T ss_dssp SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSSSSS---HHHHHHHHHHHHHHHHHHEHHCCHHHHHHCC-----------
T ss_pred ceeeecCcccHHHHHHHHccCHhhChhcCCCCCCCCCchHHHHHHHHHHHHHHhhcccccchHHHHHhc-----------
Confidence 34667877777889999999999888875 24699999987654322221 011122233431
Q ss_pred cChHHHHhhHHHhhhhhhCCCcccchhhhC-------CC-----------HHHHHHHHHHHHHhChhHHH---HHHHHHH
Q 001267 940 AFASERRKAKMLNFSIAYGKTPVGLARDWK-------VS-----------VEEAKKTVDLWYNERQEVLT---WQEARKK 998 (1112)
Q Consensus 940 vt~~~R~~AK~vnfGiiYG~g~~~La~~lg-------is-----------~~EAk~~id~ff~~yP~Vk~---~~~~~~~ 998 (1112)
....|+..|...--++||.+..|.++++. .. .--|+.+.+.+.+.||+.+. |++.+..
T Consensus 156 -~~i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~~~~~la~~i~~~i~~~~~~a~~~m~wL~~~a~ 234 (405)
T PF00940_consen 156 -GGITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYKAAMYLAKIIFEAIKEVFPGARNIMDWLQEIAK 234 (405)
T ss_dssp -CT--HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHH
T ss_pred -CCCChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 13579999999999999999999987651 11 22367778888888997765 5555555
Q ss_pred HHHhCCe-E--ecccCC
Q 001267 999 ESRIDNH-V--HTLLGR 1012 (1112)
Q Consensus 999 ~A~~~Gy-V--~Tl~GR 1012 (1112)
.+.+.+- | .|+.|-
T Consensus 235 ~~~~~~~pv~W~tP~Gl 251 (405)
T PF00940_consen 235 IIAKLNKPVSWTTPLGL 251 (405)
T ss_dssp HHHCTCB-EEEEETTSE
T ss_pred HHHccCCcEEEECCCCC
Confidence 4444331 2 355554
No 92
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=90.08 E-value=5.4 Score=43.85 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001267 553 ELWISYSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 553 e~~l~YAA~DA~~tlrL~e~L~ 574 (1112)
....+|+..||..+++|+.+|.
T Consensus 203 ~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 203 RRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred HHHHHhhHHHHHHHHHHHHHHh
Confidence 4678999999999999999874
No 93
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=89.93 E-value=5.4 Score=43.32 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=26.9
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHH----HcCCC
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLE----NYGLK 457 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNa-KfDl~vL~----r~GI~ 457 (1112)
..+.+..|.+++.+.. ..|++|. .||+..|. ++|+.
T Consensus 73 E~~lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~ 113 (204)
T cd05783 73 EKELIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIP 113 (204)
T ss_pred HHHHHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCC
Confidence 3567788888887764 6789995 69999984 36766
No 94
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=87.17 E-value=1.8 Score=48.52 Aligned_cols=61 Identities=20% Similarity=0.092 Sum_probs=39.6
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHH---HHhcCCCCCCCCCCCHHHHHhc
Q 001267 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHM---ARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 421 ~~~vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIA---AyLLdp~~~~~~s~sLd~La~~ 490 (1112)
...+-..+.++|.+. .+|||.+..|+.+|.- | +...+.||.-- -.++.... ..||+.|++.
T Consensus 171 f~~aQ~ev~klL~gR--IlVGHaLhnDl~~L~l~h---p~s~iRDTs~~~pl~k~~~~~~----tpSLK~Lt~~ 235 (280)
T KOG2249|consen 171 FKVAQKEVLKLLKGR--ILVGHALHNDLQALKLEH---PRSMIRDTSKYPPLMKLLSKKA----TPSLKKLTEA 235 (280)
T ss_pred HHHHHHHHHHHHhCC--EEeccccccHHHHHhhhC---chhhhcccccCchHHHHhhccC----CccHHHHHHH
Confidence 445666777888774 4799999999999852 2 12335576432 22222222 5899999987
No 95
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=86.85 E-value=6 Score=50.29 Aligned_cols=72 Identities=25% Similarity=0.309 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcC---cccCHH---HHHH
Q 001267 553 ELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEG---MLVDRE---YLSE 626 (1112)
Q Consensus 553 e~~l~YAA~DA~~tlrL~e~L~~kLee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~G---I~VD~e---~L~~ 626 (1112)
.....|||.|+.+|.+++..+-+..-+. | |-...|+.|-.-| .+||.. |+.+
T Consensus 359 q~L~~YCA~Dv~aThqVf~~lfP~Fler------c----------------PHPaTlagMLsmGsvyLPvN~nW~rYin~ 416 (1075)
T KOG3657|consen 359 QPLMNYCARDVIATHQVFFRLFPLFLER------C----------------PHPATLAGMLSMGSVYLPVNSNWERYINE 416 (1075)
T ss_pred HHHHHHHhhhhHHHHHHHHHHhHHHHHh------C----------------CChHhHHHHHhcCcEEeeccccHHHHHHH
Confidence 4567899999999999999988875542 1 4444566666667 567744 4444
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 001267 627 IEKVARAEQEAAVNRFRKWA 646 (1112)
Q Consensus 627 L~~~l~~e~e~leeei~~~~ 646 (1112)
.+...+.-+..++.+|.+.+
T Consensus 417 ~e~tYeq~~~~~~~kl~~~A 436 (1075)
T KOG3657|consen 417 AEQTYEQLKTEAKRKIIESA 436 (1075)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444444444555555544
No 96
>PHA02528 43 DNA polymerase; Provisional
Probab=84.56 E-value=12 Score=49.04 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001267 552 RELWISYSAFDSINTLKLYKSL 573 (1112)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1112)
.....+|+..||..+++|..++
T Consensus 303 ~~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 303 HQKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999984
No 97
>PRK05762 DNA polymerase II; Reviewed
Probab=71.44 E-value=50 Score=43.02 Aligned_cols=65 Identities=26% Similarity=0.490 Sum_probs=40.8
Q ss_pred hhhHhhhhhhhc--CCCceEEEecc-HHHHHHHHH----cCCCCC-------------------------C-ccchHHHH
Q 001267 422 RDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVLEN----YGLKVS-------------------------G-FHADTMHM 468 (1112)
Q Consensus 422 ~~vL~~Lk~~Le--d~~v~KV~HNa-KfDl~vL~r----~GI~l~-------------------------~-~vfDTmIA 468 (1112)
.+.+..|..++. ||++ .++||. .||+..|.+ +|+.+. + .++|++..
T Consensus 204 ~~LL~~F~~~i~~~DPDI-IvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~ 282 (786)
T PRK05762 204 KALLEKFNAWFAEHDPDV-IIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDA 282 (786)
T ss_pred HHHHHHHHHHHHhcCCCE-EEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHH
Confidence 456666666665 4553 799995 699999842 565431 1 15677766
Q ss_pred HHhcCCCCCCCCCCCHHHHHhc
Q 001267 469 ARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 469 AyLLdp~~~~~~s~sLd~La~~ 490 (1112)
.+-..-... +++|+.++..
T Consensus 283 ~k~~~~~l~---sysL~~Va~~ 301 (786)
T PRK05762 283 LKSATWVFD---SFSLEYVSQR 301 (786)
T ss_pred HHHhhccCC---CCCHHHHHHH
Confidence 553321222 6999999986
No 98
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=71.43 E-value=15 Score=40.52 Aligned_cols=109 Identities=24% Similarity=0.272 Sum_probs=64.0
Q ss_pred hhhHhhhhhhhc--CCCceEEEecc-HHHHHHHHH----cCCCC---------------------------CCc-cchHH
Q 001267 422 RDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVLEN----YGLKV---------------------------SGF-HADTM 466 (1112)
Q Consensus 422 ~~vL~~Lk~~Le--d~~v~KV~HNa-KfDl~vL~r----~GI~l---------------------------~~~-vfDTm 466 (1112)
.+.+..|..++. ||++ .+|||. .||+.+|.+ +|+.. .|. +.|+.
T Consensus 83 ~~LL~~f~~~i~~~DPDi-ivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~ 161 (234)
T cd05776 83 RALLNFFLAKLQKIDPDV-LVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTY 161 (234)
T ss_pred HHHHHHHHHHHhhcCCCE-EEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccH
Confidence 345555555553 6774 799997 899998732 23321 111 56888
Q ss_pred HHHHhcCCCCCCCCCCCHHHHHhccccccccchhhcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhH
Q 001267 467 HMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEE 546 (1112)
Q Consensus 467 IAAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~ 546 (1112)
..++=+-. .. +|+|++++.. +|+.+ . .++ ..+++.. .|.. +
T Consensus 162 ~~~k~~~~-~~---sY~L~~va~~-------~Lg~~-----k---~di----~~~~i~~------------~~~~-~--- 202 (234)
T cd05776 162 LSAKELIR-CK---SYDLTELSQQ-------VLGIE-----R---QDI----DPEEILN------------MYND-S--- 202 (234)
T ss_pred HHHHHHhC-CC---CCChHHHHHH-------HhCcC-----c---ccC----CHHHHHH------------HHhC-H---
Confidence 87764433 33 6999999986 44432 0 111 0111110 1111 0
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 547 LQREERELWISYSAFDSINTLKLYKSL 573 (1112)
Q Consensus 547 ~~~~~~e~~l~YAA~DA~~tlrL~e~L 573 (1112)
......++|+..||..+++|..+|
T Consensus 203 ---~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 203 ---ESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 114567899999999999999876
No 99
>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=68.85 E-value=4 Score=43.46 Aligned_cols=59 Identities=17% Similarity=0.034 Sum_probs=38.7
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 424 vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+...|..++. +...+|||.+..|+.+|.-. .+...++||-+.-. .|... ..+|..|+..
T Consensus 91 v~~~l~~li~-~~tILVGHsL~nDL~aL~l~--hp~~~viDTa~l~~--~~~~r---~~sLk~La~~ 149 (174)
T cd06143 91 AYLKLRLLVD-LGCIFVGHGLAKDFRVINIQ--VPKEQVIDTVELFH--LPGQR---KLSLRFLAWY 149 (174)
T ss_pred HHHHHHHHcC-CCCEEEeccchhHHHHhcCc--CCCcceEEcHHhcc--CCCCC---ChhHHHHHHH
Confidence 4445666664 34468999999999998521 12345889975432 23222 5899999987
No 100
>PHA00452 T3/T7-like RNA polymerase
Probab=61.45 E-value=39 Score=44.11 Aligned_cols=207 Identities=13% Similarity=0.035 Sum_probs=114.2
Q ss_pred EEecccchhHHHHHHhcCchHHHHHHH-----cCCCchhHHHhhhccccccccccc-----hhhhcccCCCCCCCCcccc
Q 001267 870 IVADYGQLELRILAHLANCKSMLDAFK-----AGGDFHSRTAMNMYPHIRNAVETG-----QVLLEWHGEDKPPVPLLKD 939 (1112)
Q Consensus 870 vsaDySQIELRIlAhlS~D~~Li~af~-----~G~DiH~~tA~~ifg~~~e~v~~~-----~~~~~w~~~~~p~v~~~~~ 939 (1112)
|..|-|.==+-.+|.|.+|....++.+ .-.|||+.+|..+-.....+...+ .....|..
T Consensus 499 I~qDgSCnGlQHyAAL~rD~~ga~~VNL~p~d~p~DvY~~Va~~v~~~i~~d~~~~~~~~~~~~~~~l~----------- 567 (807)
T PHA00452 499 VAMDGTCSGLQHFSAMLRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDAINGTDNTRALARLWLA----------- 567 (807)
T ss_pred cccCCcccHHHHHHHHhCCHHhHHHhCCCCCCCCccHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHh-----------
Confidence 444666555678888999998877764 246999999976532211111000 00111211
Q ss_pred cChHHHHhhHHHhhhhhhCCCcccchhhh-------CCCH--------H----HHHHHHHHHHHhChhHH---HHHHHHH
Q 001267 940 AFASERRKAKMLNFSIAYGKTPVGLARDW-------KVSV--------E----EAKKTVDLWYNERQEVL---TWQEARK 997 (1112)
Q Consensus 940 vt~~~R~~AK~vnfGiiYG~g~~~La~~l-------gis~--------~----EAk~~id~ff~~yP~Vk---~~~~~~~ 997 (1112)
....|+..|...--.+||.+..|.++++ |+.. + -|+.+.+...+.||+.+ .|+..+.
T Consensus 568 -~~i~RkvvKqtVMT~vYGvT~~g~~~qI~~~l~~~~~~~~~~~~~~~~~~~yla~~i~~ai~~~f~~a~~im~wL~~~a 646 (807)
T PHA00452 568 -YGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQPGIDEGDGAMFTNQAASYMAKLIWDAISETVPAAVEAMNWLQQAA 646 (807)
T ss_pred -CCCChhhcccccccceeCCchhhhHHHHHHHHHhcCCCcccchhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 1246999999999999999999987654 3221 1 26777888888888555 5877777
Q ss_pred HHHH-hCC-eE--ecccCCcccCCCCCccC-------------------hhhhhhhhhh--hHhhhhhhHHHHHHHHHHH
Q 001267 998 KESR-IDN-HV--HTLLGRARRFPAIKSLT-------------------RSQRNHIERA--AINTPVQGSAADVAMCAML 1052 (1112)
Q Consensus 998 ~~A~-~~G-yV--~Tl~GRrr~lp~~~s~n-------------------~~~r~~~eR~--avN~~IQGSAADI~K~AMi 1052 (1112)
..+. +.+ .| .|+.|-...=|-..... ........++ +.|++=+==|+ -|.+..+
T Consensus 647 ~~i~~~~~~pv~W~TP~GlpV~Q~Y~k~~~~~v~t~~~~~~~i~~~~~~~~~d~~Kq~~a~~PNFIHSLDAs-Hm~~t~~ 725 (807)
T PHA00452 647 KLLAAKGAEALHWTTPTGFPVWQEYRKPEEKRVRLRLMGVARVQLYVNTDTIDARKHASGIAPNFVHSLDAS-HLRLTVV 725 (807)
T ss_pred HHHHHhcCCCEEEECCCCCEEEeeecCCCcEEEEEeeccceeEEeccCCCCCCHHHHhcccCCchhhhhhHH-HHHHHHH
Confidence 6665 332 11 35555432211100000 0000001111 34653332222 2222222
Q ss_pred HHHHHHHhcCCCceEEeEccceeeeeecchhcHHHHHHHHHHHhcC
Q 001267 1053 EISKNARLKELGWKLLLQVLFFFSFSFFSIIVIVSCQGIVLANAMH 1098 (1112)
Q Consensus 1053 ~i~~~~~l~~~~~~llLqVHDElv~Ev~~~~~ae~~~~~v~~~Me~ 1098 (1112)
.+. +.|..-+..|||........ ++.+..+|++.+-.
T Consensus 726 ~~~------~~g~~~fa~VHDsfwTha~d---vd~m~~~lRe~FV~ 762 (807)
T PHA00452 726 ACA------EKGIESFAVIHDSFGTHAAD---ADNLHRAIRETFVE 762 (807)
T ss_pred HHH------hcCCCcEEEeccCcccChhh---HHHHHHHHHHHHHH
Confidence 222 23555578999998876444 67777788876643
No 101
>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=59.59 E-value=22 Score=36.25 Aligned_cols=40 Identities=25% Similarity=0.189 Sum_probs=22.5
Q ss_pred HHHHHH-HHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 445 SFDNHV-LENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 445 KfDl~v-L~r~GI~l~~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
..|+.+ +.+.|+.+. +--|-|+.|||+||.. .....++.+
T Consensus 70 AK~LAv~a~~~G~~v~-PGDDPlLlAYLlDPsN-----t~p~~varR 110 (138)
T PF09281_consen 70 AKDLAVHALREGVVVE-PGDDPLLLAYLLDPSN-----TNPEGVARR 110 (138)
T ss_dssp HHHHHHHHHHTT-----B---HHHHHHHH-TT-------SHHHHHHH
T ss_pred HHHHHHHHHhcCcccC-CCCCcchhhhhcCccC-----CChHHHHHH
Confidence 345555 467898764 4679999999999974 567777876
No 102
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=58.96 E-value=1.3e+02 Score=40.84 Aligned_cols=22 Identities=27% Similarity=0.276 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001267 553 ELWISYSAFDSINTLKLYKSLK 574 (1112)
Q Consensus 553 e~~l~YAA~DA~~tlrL~e~L~ 574 (1112)
.....|+..||..+++|..+|.
T Consensus 462 ~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 462 RRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999998764
No 103
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=57.02 E-value=1.2e+02 Score=33.66 Aligned_cols=54 Identities=17% Similarity=0.153 Sum_probs=32.8
Q ss_pred cCCCceEEEeccHHHHHHHHH--cCCCCCC--------------ccchHHHHHHhcCCCCCCCCCCCHHHHHh
Q 001267 433 EDPSIKKVWHNYSFDNHVLEN--YGLKVSG--------------FHADTMHMARLWDSSRRTEGGYSLEALTG 489 (1112)
Q Consensus 433 ed~~v~KV~HNaKfDl~vL~r--~GI~l~~--------------~vfDTmIAAyLLdp~~~~~~s~sLd~La~ 489 (1112)
-++.+.+|..+..||...|-+ -+..++. .++|+.+++.....-.. ..||..||.
T Consensus 139 ~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l---~~GL~~lA~ 208 (239)
T KOG0304|consen 139 LDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSL---KGGLQRLAD 208 (239)
T ss_pred ccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhh---hcCHHHHHH
Confidence 357889999999999988754 1333332 24566666665543111 356666665
No 104
>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=57.01 E-value=7.4 Score=38.44 Aligned_cols=112 Identities=24% Similarity=0.316 Sum_probs=62.2
Q ss_pred EEEEeccCCCCcccCccccccceEEEEeeeCCCcccCCCceEEEEeCCC---C-------------------ChhhhHhh
Q 001267 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---G-------------------GGRDLLNE 427 (1112)
Q Consensus 370 VAfDTETtGLd~~~d~IVG~g~Ii~fsi~~~~~IqI~~~~~~~~ID~~~---~-------------------~~~~vL~~ 427 (1112)
|+|||||||+++..+.|+++| .+.+..+..... .....++.+.. . ...+++..
T Consensus 1 v~~D~Ettg~~~~~~~iieig---~v~~~~~~~~~~--~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIG---AVKVDDDENEEV--ESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEE---EEEEETTTTEEE--EEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEE---EEEeeCCccccc--eeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHh
Confidence 689999999999777887633 222222110000 00112332211 0 01235666
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----c-CCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----Y-GLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~r----~-GI~l~--~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
|..++... ...|+||+.||+.++.+ + +...+ ..++||+...+...+... .++|+.|++.
T Consensus 76 ~~~~~~~~-~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~l~~~ 141 (164)
T PF00929_consen 76 FEEFLKKN-DILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRK---KYSLDDLAEY 141 (164)
T ss_dssp HHHHHHHH-TEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHH---HHSHHHHHHH
T ss_pred hhhhhhcc-cccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccc---cCCHHHHHHH
Confidence 77888632 46899999998866532 3 22222 346777766665555432 3678888874
No 105
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=46.18 E-value=50 Score=38.39 Aligned_cols=107 Identities=21% Similarity=0.139 Sum_probs=63.7
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHH--cCCCCCCccchHHH-HHHhcCCCCCCCCCCCHHHHHhccccccccchh
Q 001267 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLEN--YGLKVSGFHADTMH-MARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (1112)
Q Consensus 424 vL~~Lk~~Led~~v~KV~HNaKfDl~vL~r--~GI~l~~~vfDTmI-AAyLLdp~~~~~~s~sLd~La~~~~~~~~~~Lg 500 (1112)
+...|+.||+|+....|+-+.+.|..-|.+ |++.+. ...|.-. +.-.++++.. ..+.+.|+.. .++
T Consensus 172 IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~-~~~dlr~~~~d~~g~~~~---~~s~e~i~~~-------~~~ 240 (319)
T KOG4373|consen 172 IPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIG-ELEDLRLLVNDSLGGSMP---NDSFEEIVSE-------TLG 240 (319)
T ss_pred chHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHH-hhhhHHhhcchhhccCcc---CccHHHHHHH-------Hhh
Confidence 445666789999999999999999988865 665542 1233221 1112333222 2556666654 222
Q ss_pred hcccccCCCCcccccccchhhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHH
Q 001267 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLY 570 (1112)
Q Consensus 501 ~~~~l~~~~~~eel~GK~s~k~lfgK~k~kkq~s~~~~w~~~pL~~~~~~~~e~~l~YAA~DA~~tlrL~ 570 (1112)
+. |+. ....+. .. ..+|...||+ ..|+.||+-||.+.+.|+
T Consensus 241 ~~-------------~~~-------v~l~~~-i~-msdw~~~~Ls-------~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 241 YY-------------GKD-------VRLDKE-IR-MSDWSVYPLS-------DDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cc-------------ccc-------cccChh-cc-cccceeeecc-------HHHHHHHHhHHHHHHHHH
Confidence 21 110 000000 11 1389998884 789999999999999999
No 106
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=42.65 E-value=3.7e+02 Score=31.89 Aligned_cols=22 Identities=36% Similarity=0.622 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001267 552 RELWISYSAFDSINTLKLYKSL 573 (1112)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1112)
......|+..|+..+++|+..+
T Consensus 199 ~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 199 RDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4668999999999999999886
No 107
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=42.14 E-value=1.8e+02 Score=40.20 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 001267 552 RELWISYSAFDSINTLKLYKSLKK 575 (1112)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L~~ 575 (1112)
...+..|...||.+|.-||-+...
T Consensus 429 PQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 429 PQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred chhhhhcchHHHHHHHHHHHHHhh
Confidence 356788999999999999976543
No 108
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=39.29 E-value=2.2e+02 Score=34.78 Aligned_cols=64 Identities=16% Similarity=0.204 Sum_probs=37.4
Q ss_pred hhhHhhhhhhhcC-CCceEEEeccHHHHHHHHH----cCCCCC------CccchHHHHHH--hcCCCCCCCCCCCHHHHH
Q 001267 422 RDLLNEFAPFFED-PSIKKVWHNYSFDNHVLEN----YGLKVS------GFHADTMHMAR--LWDSSRRTEGGYSLEALT 488 (1112)
Q Consensus 422 ~~vL~~Lk~~Led-~~v~KV~HNaKfDl~vL~r----~GI~l~------~~vfDTmIAAy--LLdp~~~~~~s~sLd~La 488 (1112)
..++..|.+|+.. +...++.+| .|....|++ +|.... ..++|.....+ ++.|.. ++||+.++
T Consensus 329 ~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~----sysLK~v~ 403 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIE----SYSLKSIA 403 (457)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCC----CCCHHHHH
Confidence 3466777777765 333344445 787877765 454310 13466654332 445543 69999999
Q ss_pred hc
Q 001267 489 GD 490 (1112)
Q Consensus 489 ~~ 490 (1112)
.-
T Consensus 404 ~~ 405 (457)
T TIGR03491 404 RW 405 (457)
T ss_pred HH
Confidence 73
No 109
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=29.33 E-value=5.7e+02 Score=30.98 Aligned_cols=104 Identities=11% Similarity=0.075 Sum_probs=58.5
Q ss_pred cEEEEEeccCCCCcccCccccccceEEEEe-------------eeCCC-cccCCCceEEEEeCC--------CCChhhhH
Q 001267 368 LVHACDTEVAKIDVKQETPVDHGEVICFSI-------------YSGPE-ADFGNGKSCIWVDLL--------DGGGRDLL 425 (1112)
Q Consensus 368 ~~VAfDTETtGLd~~~d~IVG~g~Ii~fsi-------------~~~~~-IqI~~~~~~~~ID~~--------~~~~~~vL 425 (1112)
.++-.|-||.|.++..+++..++ |+.. +.+|. =-++.+. +.+|-.. +.+..+..
T Consensus 10 tF~~yDYETfG~~Pa~DRPaQFA---giRTD~~~NiIgeP~~fyCkpsdDyLP~P~-a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 10 TFLFYDYETFGVHPALDRPAQFA---GIRTDIEFNIIGEPIVFYCKPADDYLPQPG-AVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred cEEEEehhhcCCCcccccchhhh---eeeccccccccCCCeEEEecCccccCCCCC-ceeeecCCHHHHHhcCCChHHHH
Confidence 58899999999999988775421 2211 11111 0011111 1122110 01123455
Q ss_pred hhhhhhhcCCCceEEEec-cHHHHHHHH----HcCCCC-----C--C---ccchHHHHHHhcCCC
Q 001267 426 NEFAPFFEDPSIKKVWHN-YSFDNHVLE----NYGLKV-----S--G---FHADTMHMARLWDSS 475 (1112)
Q Consensus 426 ~~Lk~~Led~~v~KV~HN-aKfDl~vL~----r~GI~l-----~--~---~vfDTmIAAyLLdp~ 475 (1112)
..+...|..|....+|+| +.||=.+-+ +.-+++ + + -+.|.+-|+|-|.|+
T Consensus 86 ~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPe 150 (475)
T COG2925 86 ARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPE 150 (475)
T ss_pred HHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcc
Confidence 666677888888889998 789887743 322332 1 1 146777788877774
No 110
>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=28.77 E-value=55 Score=36.80 Aligned_cols=51 Identities=24% Similarity=0.147 Sum_probs=36.1
Q ss_pred CCCceEEEeccHHHHHHHHH--cCCCCC--------------CccchHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 001267 434 DPSIKKVWHNYSFDNHVLEN--YGLKVS--------------GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1112)
Q Consensus 434 d~~v~KV~HNaKfDl~vL~r--~GI~l~--------------~~vfDTmIAAyLLdp~~~~~~s~sLd~La~~ 490 (1112)
+..+.+|+||+-+|+..|.+ .| +++ ..++||..++...... ..+|+.|+..
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~-----~~~L~~l~~~ 213 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIG-PLPETLEEFKELLRELFPRIYDTKYLAEECPGK-----STSLQELAEE 213 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS------SSHHHHHHH
T ss_pred ccCCcEEEeChHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcccccHHHHHHhcccc-----ccCHHHHHHH
Confidence 34478999999999998865 24 333 2378999999877632 4799999975
No 111
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=26.98 E-value=29 Score=41.05 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=33.0
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCC
Q 001267 428 FAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSR 476 (1112)
Q Consensus 428 Lk~~Led~~v~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~ 476 (1112)
+++.|+...+ +. +++-+...+. .+++.+.+ ++||++|..|+.+..
T Consensus 241 yK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~n-VkDtQia~sLve~~e 286 (458)
T KOG2405|consen 241 YKRELESLEK--VI-DRIRLIEQLDTTYHSALKN-VKDTQIASSLVEPSE 286 (458)
T ss_pred chhhhhhcce--eh-hhhhhhHHHHhHHHHHHHh-hHHHHHHHHHhhhHH
Confidence 5566665432 44 8888888775 46777766 799999999999854
No 112
>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=24.87 E-value=77 Score=35.66 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhccCCCcEEEEEeccCCCCccc
Q 001267 351 VSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQ 383 (1112)
Q Consensus 351 ~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~ 383 (1112)
.+++..+.+.|..+ .+||+|+|++|+....
T Consensus 9 ~~~l~~i~~~i~~~---~fvaiD~EftGl~~~~ 38 (262)
T PF04857_consen 9 EEELPEILQAISKA---DFVAIDTEFTGLVSKP 38 (262)
T ss_dssp HHHHHHHHHHHHHS---SEEEEEEEES-S-SSS
T ss_pred HHHHHHHHHHHhhC---CEEEEEeeccccccCC
Confidence 45677777888886 6999999999988754
No 113
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=20.68 E-value=2.6e+02 Score=34.77 Aligned_cols=29 Identities=24% Similarity=0.413 Sum_probs=20.9
Q ss_pred hhhHhhhhhhhc--CCCceEEEecc-HHHHHHH
Q 001267 422 RDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVL 451 (1112)
Q Consensus 422 ~~vL~~Lk~~Le--d~~v~KV~HNa-KfDl~vL 451 (1112)
.+.+..|..++. ||++ ++|||. .||+..|
T Consensus 181 ~eLL~~F~~~i~~~DPDI-ItGYNi~nFDlPYL 212 (498)
T PHA02524 181 VDLLLNYIQLWKANTPDL-VFGWNSEGFDIPYI 212 (498)
T ss_pred HHHHHHHHHHHHHhCCCE-EEeCCCcccCHHHH
Confidence 356666666665 4664 799995 7999987
Done!