Query 001207
Match_columns 1123
No_of_seqs 361 out of 2143
Neff 5.5
Searched_HMMs 46136
Date Thu Mar 28 18:43:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001207hhsearch_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 4E-128 1E-132 1129.9 46.0 589 345-1123 3-593 (593)
2 TIGR00593 pola DNA polymerase 100.0 1E-113 2E-118 1068.2 57.0 581 344-1123 303-887 (887)
3 PRK05755 DNA polymerase I; Pro 100.0 5E-108 1E-112 1028.0 59.6 586 343-1123 294-880 (880)
4 PRK14975 bifunctional 3'-5' ex 100.0 1.2E-96 3E-101 884.0 48.6 539 344-1123 2-553 (553)
5 cd08640 DNA_pol_A_plastid_like 100.0 1.7E-85 3.7E-90 749.4 29.5 371 728-1121 1-371 (371)
6 cd08637 DNA_pol_A_pol_I_C Poly 100.0 2.6E-84 5.7E-89 744.8 36.0 376 620-1120 1-377 (377)
7 PF00476 DNA_pol_A: DNA polyme 100.0 5.7E-84 1.2E-88 744.5 32.6 380 619-1122 1-383 (383)
8 cd08643 DNA_pol_A_pol_I_B Poly 100.0 2E-83 4.2E-88 743.0 34.7 368 619-1123 1-429 (429)
9 cd08638 DNA_pol_A_theta DNA po 100.0 1.4E-79 3E-84 704.8 34.4 303 792-1122 46-373 (373)
10 cd08642 DNA_pol_A_pol_I_A Poly 100.0 9.7E-73 2.1E-77 641.5 29.4 274 792-1119 66-377 (378)
11 cd06444 DNA_pol_A Family A pol 100.0 5.4E-73 1.2E-77 644.5 27.2 303 789-1120 26-347 (347)
12 cd08639 DNA_pol_A_Aquificae_li 100.0 1.5E-71 3.2E-76 626.2 24.9 290 788-1120 28-324 (324)
13 cd08641 DNA_pol_gammaA Pol gam 100.0 7.2E-56 1.6E-60 497.3 19.4 250 819-1112 94-400 (425)
14 smart00482 POLAc DNA polymeras 100.0 9.4E-54 2E-58 455.1 21.4 206 854-1082 1-206 (206)
15 PRK10829 ribonuclease D; Provi 99.8 2.2E-18 4.7E-23 198.5 21.9 172 344-581 2-174 (373)
16 PF01612 DNA_pol_A_exo1: 3'-5' 99.8 4.1E-18 8.8E-23 174.1 17.8 173 345-578 1-176 (176)
17 cd06139 DNA_polA_I_Ecoli_like_ 99.8 5.5E-18 1.2E-22 176.4 18.2 182 368-611 6-193 (193)
18 cd06140 DNA_polA_I_Bacillus_li 99.8 4.6E-18 1E-22 175.8 16.5 175 368-611 4-178 (178)
19 COG0349 Rnd Ribonuclease D [Tr 99.8 8.5E-18 1.8E-22 189.7 18.1 170 348-582 1-171 (361)
20 TIGR01388 rnd ribonuclease D. 99.8 1.9E-17 4.1E-22 191.1 20.4 169 347-580 1-169 (367)
21 cd06129 RNaseD_like DEDDy 3'-5 99.7 9.2E-16 2E-20 157.6 14.5 156 354-574 2-160 (161)
22 cd06141 WRN_exo DEDDy 3'-5' ex 99.6 5.5E-15 1.2E-19 152.2 15.0 165 348-574 1-169 (170)
23 cd06146 mut-7_like_exo DEDDy 3 99.6 6.2E-15 1.3E-19 156.2 15.3 172 345-574 1-192 (193)
24 cd06148 Egl_like_exo DEDDy 3'- 99.6 5.5E-15 1.2E-19 156.9 12.4 171 358-580 4-180 (197)
25 smart00474 35EXOc 3'-5' exonuc 99.5 3.4E-13 7.4E-18 136.7 16.6 170 345-577 1-171 (172)
26 cd06142 RNaseD_exo DEDDy 3'-5' 99.5 1.8E-12 3.9E-17 133.5 17.5 167 355-599 3-170 (178)
27 cd06147 Rrp6p_like_exo DEDDy 3 99.4 1E-11 2.2E-16 131.1 16.8 172 343-580 3-175 (192)
28 cd00007 35EXOc 3'-5' exonuclea 99.3 2.5E-11 5.5E-16 120.7 15.5 153 369-576 2-154 (155)
29 cd09018 DEDDy_polA_RNaseD_like 99.3 2.1E-11 4.5E-16 121.9 13.1 149 369-574 1-149 (150)
30 KOG3657 Mitochondrial DNA poly 99.1 1.7E-10 3.7E-15 138.4 9.3 244 821-1098 686-998 (1075)
31 KOG2206 Exosome 3'-5' exoribon 98.9 2.6E-09 5.6E-14 125.5 7.1 176 337-580 187-363 (687)
32 cd06128 DNA_polA_exo DEDDy 3'- 98.8 5E-08 1.1E-12 98.7 14.2 63 425-490 42-104 (151)
33 COG2176 PolC DNA polymerase II 98.7 1.9E-08 4.1E-13 125.4 8.0 116 367-490 421-557 (1444)
34 PRK07942 DNA polymerase III su 98.6 1.5E-07 3.3E-12 102.9 10.9 115 368-490 7-151 (232)
35 PRK05711 DNA polymerase III su 98.6 5.4E-07 1.2E-11 99.1 13.8 112 368-491 5-146 (240)
36 TIGR01406 dnaQ_proteo DNA poly 98.5 4.9E-07 1.1E-11 98.6 11.8 111 369-491 2-142 (225)
37 PRK09146 DNA polymerase III su 98.5 1.9E-06 4.2E-11 94.8 15.0 122 367-490 47-198 (239)
38 PRK06063 DNA polymerase III su 98.5 2.4E-06 5.1E-11 97.6 15.4 113 367-490 15-150 (313)
39 PRK07740 hypothetical protein; 98.5 3.2E-06 6.8E-11 93.4 15.8 111 368-490 60-197 (244)
40 PRK05601 DNA polymerase III su 98.5 6.7E-07 1.4E-11 102.8 10.6 112 368-491 47-209 (377)
41 PRK06310 DNA polymerase III su 98.4 2.5E-06 5.3E-11 94.5 13.8 118 368-490 8-145 (250)
42 PRK06309 DNA polymerase III su 98.4 3.8E-06 8.3E-11 91.9 13.4 119 368-490 3-137 (232)
43 PRK07246 bifunctional ATP-depe 98.3 2.1E-06 4.6E-11 109.2 12.5 117 368-490 8-141 (820)
44 PRK06807 DNA polymerase III su 98.3 3.3E-06 7.1E-11 96.4 12.4 119 367-490 8-144 (313)
45 TIGR01298 RNaseT ribonuclease 98.3 4.7E-06 1E-10 89.3 12.2 48 437-490 106-161 (200)
46 cd06131 DNA_pol_III_epsilon_Ec 98.3 9.7E-06 2.1E-10 83.5 14.1 110 369-490 1-139 (167)
47 TIGR01405 polC_Gram_pos DNA po 98.3 5.2E-06 1.1E-10 108.5 14.0 118 368-490 191-326 (1213)
48 PRK05168 ribonuclease T; Provi 98.3 8.3E-06 1.8E-10 88.1 12.7 124 354-490 7-170 (211)
49 cd06134 RNaseT DEDDh 3'-5' exo 98.2 9.5E-06 2.1E-10 86.1 12.0 48 437-490 103-158 (189)
50 TIGR01407 dinG_rel DnaQ family 98.2 1.1E-05 2.3E-10 103.6 14.2 117 369-490 2-136 (850)
51 TIGR00573 dnaq exonuclease, DN 98.2 2E-05 4.4E-10 85.4 14.1 113 368-490 8-146 (217)
52 cd06137 DEDDh_RNase DEDDh 3'-5 98.2 4.5E-06 9.9E-11 86.3 7.9 111 370-490 1-134 (161)
53 PRK07883 hypothetical protein; 98.1 1.4E-05 3.1E-10 97.7 12.8 120 368-490 16-153 (557)
54 PRK09145 DNA polymerase III su 98.1 5.1E-05 1.1E-09 81.2 14.6 116 368-490 30-172 (202)
55 cd06136 TREX1_2 DEDDh 3'-5' ex 98.1 4.3E-06 9.3E-11 87.8 6.2 59 424-490 84-151 (177)
56 PRK08517 DNA polymerase III su 98.1 5.6E-05 1.2E-09 84.2 14.8 111 367-490 68-202 (257)
57 smart00479 EXOIII exonuclease 98.0 1.8E-05 3.9E-10 80.7 9.5 109 369-490 2-137 (169)
58 PRK08074 bifunctional ATP-depe 98.0 4.4E-05 9.6E-10 98.8 14.9 118 368-490 4-140 (928)
59 PRK06195 DNA polymerase III su 98.0 4.7E-05 1E-09 86.9 12.7 65 421-490 67-136 (309)
60 PRK07247 DNA polymerase III su 98.0 8E-05 1.7E-09 79.8 13.3 117 368-490 6-141 (195)
61 PRK09182 DNA polymerase III su 98.0 8.7E-05 1.9E-09 84.2 13.8 115 368-490 38-173 (294)
62 PRK07983 exodeoxyribonuclease 97.8 0.00014 3E-09 79.4 12.4 46 437-490 75-120 (219)
63 PRK00448 polC DNA polymerase I 97.8 0.00011 2.3E-09 97.8 12.7 117 368-490 420-555 (1437)
64 cd06144 REX4_like DEDDh 3'-5' 97.8 2.5E-05 5.4E-10 80.0 4.8 64 421-490 64-127 (152)
65 cd06149 ISG20 DEDDh 3'-5' exon 97.7 8.6E-05 1.9E-09 76.7 7.6 113 370-490 1-130 (157)
66 cd06145 REX1_like DEDDh 3'-5' 97.7 7.1E-05 1.5E-09 76.7 6.2 62 421-490 62-123 (150)
67 cd06130 DNA_pol_III_epsilon_li 97.7 0.00032 6.8E-09 71.1 10.8 65 421-490 64-133 (156)
68 PRK07748 sporulation inhibitor 97.6 0.00015 3.2E-09 78.1 7.4 66 421-490 79-150 (207)
69 PRK05359 oligoribonuclease; Pr 97.5 0.00042 9.2E-09 73.4 9.1 103 368-475 4-144 (181)
70 cd06125 DnaQ_like_exo DnaQ-lik 97.5 0.00017 3.7E-09 68.5 5.6 75 370-468 1-83 (96)
71 cd06138 ExoI_N N-terminal DEDD 97.4 0.00084 1.8E-08 70.9 10.4 115 370-490 1-160 (183)
72 cd06127 DEDDh DEDDh 3'-5' exon 97.4 0.00069 1.5E-08 67.4 8.8 107 370-487 1-132 (159)
73 COG0847 DnaQ DNA polymerase II 97.3 0.00051 1.1E-08 75.2 8.2 116 368-490 14-151 (243)
74 cd06135 Orn DEDDh 3'-5' exonuc 97.3 0.00064 1.4E-08 71.3 8.5 103 369-476 1-141 (173)
75 cd05160 DEDDy_DNA_polB_exo DED 97.2 0.0027 5.7E-08 67.5 12.0 65 421-490 63-157 (199)
76 cd06133 ERI-1_3'hExo_like DEDD 97.2 0.0018 3.9E-08 66.8 10.4 67 421-490 75-149 (176)
77 PRK11779 sbcB exonuclease I; P 97.2 0.0027 5.9E-08 76.5 13.0 82 367-453 6-111 (476)
78 PRK06722 exonuclease; Provisio 96.9 0.01 2.3E-07 67.1 13.6 67 421-490 77-151 (281)
79 PF13482 RNase_H_2: RNase_H su 96.4 0.0082 1.8E-07 61.6 7.5 156 370-573 1-163 (164)
80 cd05785 DNA_polB_like2_exo Unc 96.4 0.034 7.3E-07 60.3 12.3 114 368-490 10-164 (207)
81 cd05780 DNA_polB_Kod1_like_exo 96.1 0.036 7.7E-07 59.3 10.5 109 422-573 57-195 (195)
82 PTZ00315 2'-phosphotransferase 96.1 0.024 5.1E-07 69.5 10.1 70 421-490 130-225 (582)
83 PF10108 DNA_pol_B_exo2: Predi 95.6 0.066 1.4E-06 58.2 10.0 111 421-574 37-170 (209)
84 KOG2207 Predicted 3'-5' exonuc 95.6 0.071 1.5E-06 64.8 10.9 177 343-576 390-584 (617)
85 cd05781 DNA_polB_B3_exo DEDDy 95.1 0.23 5E-06 53.1 12.2 108 368-489 4-139 (188)
86 cd05782 DNA_polB_like1_exo Unc 94.7 0.31 6.8E-06 52.9 12.1 66 421-490 78-165 (208)
87 cd05784 DNA_polB_II_exo DEDDy 92.3 1.5 3.2E-05 47.3 12.0 65 422-490 52-148 (193)
88 KOG0950 DNA polymerase theta/e 91.3 0.072 1.6E-06 67.7 0.7 197 822-1083 792-989 (1008)
89 COG3359 Predicted exonuclease 91.0 2.6 5.6E-05 47.0 12.0 164 368-579 99-271 (278)
90 cd05783 DNA_polB_B1_exo DEDDy 90.7 3.8 8.2E-05 44.6 13.1 36 421-457 73-113 (204)
91 cd05779 DNA_polB_epsilon_exo D 90.5 2.6 5.7E-05 45.8 11.7 65 422-490 74-163 (204)
92 cd05777 DNA_polB_delta_exo DED 89.9 4.8 0.0001 44.3 13.2 22 553-574 203-224 (230)
93 KOG3657 Mitochondrial DNA poly 87.7 6.7 0.00014 49.9 13.5 72 553-646 359-436 (1075)
94 PHA02528 43 DNA polymerase; Pr 85.8 8.2 0.00018 50.6 13.7 22 552-573 303-324 (881)
95 KOG2249 3'-5' exonuclease [Rep 84.7 3.6 7.7E-05 46.3 8.3 61 421-490 171-235 (280)
96 PF00940 RNA_pol: DNA-dependen 84.0 14 0.00031 44.3 13.7 134 868-1013 87-252 (405)
97 PF00929 RNase_T: Exonuclease; 83.5 0.43 9.4E-06 47.4 0.7 112 370-490 1-141 (164)
98 cd06143 PAN2_exo DEDDh 3'-5' e 71.7 3.8 8.2E-05 43.7 3.5 59 424-490 91-149 (174)
99 PRK05762 DNA polymerase II; Re 71.2 55 0.0012 42.7 14.5 65 422-490 204-301 (786)
100 cd05776 DNA_polB_alpha_exo ina 70.6 17 0.00036 40.3 8.4 109 422-573 83-226 (234)
101 PTZ00166 DNA polymerase delta 61.7 92 0.002 42.1 14.0 23 552-574 461-483 (1054)
102 PHA00452 T3/T7-like RNA polyme 55.0 89 0.0019 41.0 11.8 209 870-1099 499-764 (807)
103 PF09281 Taq-exonuc: Taq polym 53.9 30 0.00065 35.3 5.8 40 445-490 70-110 (138)
104 KOG4373 Predicted 3'-5' exonuc 49.1 43 0.00094 38.9 6.9 107 424-570 172-281 (319)
105 smart00486 POLBc DNA polymeras 46.1 1.8E+02 0.004 34.5 12.1 22 552-573 199-220 (471)
106 TIGR03491 RecB family nuclease 37.2 2.1E+02 0.0046 34.9 10.8 64 422-490 329-405 (457)
107 KOG1798 DNA polymerase epsilon 30.6 2.6E+02 0.0056 38.9 10.3 24 552-575 429-452 (2173)
108 COG1949 Orn Oligoribonuclease 26.7 1E+02 0.0022 32.9 4.8 21 368-388 7-27 (184)
109 PHA02524 43A DNA polymerase su 23.8 2.5E+02 0.0053 35.0 8.1 29 422-451 181-212 (498)
110 PF04857 CAF1: CAF1 family rib 22.6 1E+02 0.0022 34.7 4.4 51 434-490 147-213 (262)
111 PF13384 HTH_23: Homeodomain-l 21.0 86 0.0019 25.8 2.6 36 948-984 8-43 (50)
112 PF04857 CAF1: CAF1 family rib 20.9 88 0.0019 35.2 3.4 30 351-383 9-38 (262)
113 COG2925 SbcB Exonuclease I [DN 20.6 1.1E+03 0.023 28.8 11.8 104 368-475 10-150 (475)
No 1
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.5e-128 Score=1129.87 Aligned_cols=589 Identities=34% Similarity=0.469 Sum_probs=521.9
Q ss_pred eEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCC-CChhh
Q 001207 345 VMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-GGGRD 423 (1123)
Q Consensus 345 y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~-~~~~e 423 (1123)
|..+.+.+.+..+...+..+ +.+++|+||++++++...++| +++..++ ..+|++..+ ...-.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~---~~~a~~~et~~l~~~~~~lvg------~s~~~~~--------~~~yi~~~~~~~~~~ 65 (593)
T COG0749 3 YGTITDLAVLNAWLTKLNAA---ANIAFDTETDGLDPHGADLVG------LSVASEE--------EAAYIPLLHGPEQLN 65 (593)
T ss_pred chhhhHHHHHHHHHHHHhhc---ccceeeccccccCcccCCeeE------EEeeccc--------cceeEeeccchhhhh
Confidence 45667778888888888776 349999999999998877765 4444322 245665543 11123
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~ 503 (1123)
+...|++||+++...+++||+|+|+++|.++|+. .+..||||||+|+++|+.. .+++++|+.+ +++++
T Consensus 66 ~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~-~~~~~DtmlasYll~~~~~---~~~~~~l~~r-------~l~~~- 133 (593)
T COG0749 66 VLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIE-PGVAFDTMLASYLLNPGAG---AHNLDDLAKR-------YLGLE- 133 (593)
T ss_pred hHHHHHHHhhCcccchhccccchhHHHHHHcCCc-ccchHHHHHHHhccCcCcC---cCCHHHHHHH-------hcCCc-
Confidence 7788999999999999999999999999999976 6789999999999999864 6999999987 55554
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 001207 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (1123)
Q Consensus 504 ~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~ 583 (1123)
.+.+ +.++||+.. +.++ ...+ .+....|++.||+++++|+..|.++|.+.
T Consensus 134 ----~~~~---------~~i~~kg~~--~~~~----~~~~--------~~~~~~y~a~~a~~~~~L~~~l~~~l~~~--- 183 (593)
T COG0749 134 ----TITF---------EDIAGKGKK--QLTF----ADVK--------LEKATEYAAEDADATLRLESILEPELLKT--- 183 (593)
T ss_pred ----cchh---------HHhhccccc--cCcc----ccch--------HHHHHHHHHHHHHHHHHHHHHHHHHhhhh---
Confidence 2233 344454431 1111 1122 36678999999999999999999998874
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHH
Q 001207 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQ 663 (1123)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPLv~VLa~ME~~GI~VD~e~L~~l~~~l~~e~e~le~~i~~~~~~~~~~g~~fNi~S~kQ 663 (1123)
..|..+|++|||||+.||+.||.+||.||.++|.++..++..++..++++++++ +|++||++||||
T Consensus 184 --------~~L~~l~~~iE~Pl~~VLa~ME~~Gi~vD~~~L~~l~~el~~~l~~le~eiy~l------aG~~FNi~SPKQ 249 (593)
T COG0749 184 --------PVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELGCELAELEEEIYEL------AGEEFNINSPKQ 249 (593)
T ss_pred --------hhHHHHHHHHhccHHHHHHHhHhcCceecHHHHHHHHHHHHHHHHHHHHHHHHH------hcCcCCCCCHHH
Confidence 467999999999999999999999999999999999999999999999999766 688999999999
Q ss_pred HHHhhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCCCcHHHHHHHHhc
Q 001207 664 LRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARN 743 (1123)
Q Consensus 664 l~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~~~vLe~La~~ 743 (1123)
|+.+||+ |++||. ..++|+||+|||+++||++|+..
T Consensus 250 L~~ILfe--------Kl~Lp~------------------------------------~~kKtktG~yST~~~vLe~L~~~ 285 (593)
T COG0749 250 LGEILFE--------KLGLPP------------------------------------GLKKTKTGNYSTDAEVLEKLADD 285 (593)
T ss_pred HHHHHHH--------hcCCCc------------------------------------cccccCCCCCccHHHHHHHHhhc
Confidence 9999999 799872 12458899999999999999987
Q ss_pred cCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccCCccCCCCe
Q 001207 744 ISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGR 823 (1123)
Q Consensus 744 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dGR 823 (1123)
||+ ++.||+||+|+||.|||+++|+. ++++.+||
T Consensus 286 h~i---------------------------------------------~~~iL~~Rql~KLksTY~d~L~~-~i~~~t~R 319 (593)
T COG0749 286 HPL---------------------------------------------PKLILEYRQLAKLKSTYTDGLPK-LINPDTGR 319 (593)
T ss_pred Ccc---------------------------------------------HHHHHHHHHHHHHHHHhhhccHH-hhCCCCCc
Confidence 664 56799999999999999999997 66666699
Q ss_pred eeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchh
Q 001207 824 VHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFH 902 (1123)
Q Consensus 824 IH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH 902 (1123)
|||+|+| +|+||||||++|||||||+|++.|+.||++|+|++|+++++|||||||||||||+|+|+.|++||.+|.|||
T Consensus 320 IHTsf~Q~~t~TGRLSSsdPNLQNIPiRse~Gr~IR~aFva~~g~~~i~aDYSQIELRilAHls~D~~Ll~AF~~g~DiH 399 (593)
T COG0749 320 IHTSFNQTGTATGRLSSSDPNLQNIPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRILAHLSQDEGLLRAFTEGEDIH 399 (593)
T ss_pred cCcchHHHHHHhhcccCCCCCcccCCcCCHhHHhhhhceeCCCCCeEEEechHHHHHHHHHHhcCCHHHHHHHhcCccHH
Confidence 9999999 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHH
Q 001207 903 SRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLW 982 (1123)
Q Consensus 903 ~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f 982 (1123)
+.||+.+||++.+ +|++++|+.||++|||++||||++|||+++|||..||+.+|++|
T Consensus 400 ~~TA~~vFgv~~~-----------------------~Vt~e~Rr~AKaINFGiiYG~safgLa~~L~I~~~eA~~~I~~Y 456 (593)
T COG0749 400 TATAAEVFGVPIE-----------------------EVTSEQRRKAKAINFGLIYGMSAFGLAQQLGIPRKEAKEYIDRY 456 (593)
T ss_pred HHHHHHHhCCChh-----------------------hCCHHHhhhhhhhccceeeccchhhHHHHcCCChHHHHHHHHHH
Confidence 9999999997543 57889999999999999999999999999999999999999999
Q ss_pred HHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhcc
Q 001207 983 YNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKE 1062 (1123)
Q Consensus 983 ~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~ 1062 (1123)
|++||+|+.|+++++++|+++|||+|++||||++|+++++|...|+++||.|+|+|||||||||+|.|||.++.++.-.+
T Consensus 457 F~rypgv~~ym~~~~~~ar~~GyV~Tl~gRRry~p~i~s~n~~~R~~aER~AiNaPIQGTAADiiK~AMI~vd~~l~~~~ 536 (593)
T COG0749 457 FERYPGVKEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAERAAINAPIQGTAADIIKLAMIKVDKALKEEK 536 (593)
T ss_pred HHhChHHHHHHHHHHHHHHHcCceeecccccccCcccccCCHHHHHHHHHHHhcCcCcccHHHHHHHHHHhHHHHHhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999665555
Q ss_pred CCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccCChhhcC
Q 001207 1063 LGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNWYSAK 1123 (1123)
Q Consensus 1063 ~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~e~~ 1123 (1123)
...||+|||||||+||||+++++++.++|++.|++++ .|+|||.||+.+|+||.|||
T Consensus 537 ~~~rllLQVHDELvfEv~~~e~e~~~~~v~~~Me~a~----~L~VPL~vdv~~g~nW~ea~ 593 (593)
T COG0749 537 LKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENAV----NLSVPLEVDVGIGKNWDEAH 593 (593)
T ss_pred hhhhhHHhhhhhhhhcCcHhHHHHHHHHHHHHHHHhh----ccCCceEEecCCCcChhhcC
Confidence 6789999999999999999999999999999999997 59999999999999999998
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=9.6e-114 Score=1068.25 Aligned_cols=581 Identities=32% Similarity=0.442 Sum_probs=502.9
Q ss_pred CeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCC---CC
Q 001207 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---GG 420 (1123)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~---~~ 420 (1123)
.|.+|.+.+++..+++. .. .+.+++ ++++++.+.++| ++|+.. .. ...+|++... ..
T Consensus 303 ~~~~~~~~~~~~~~~~~-~~---~~~~~~----~~~~~~~~~~~~----~~~~~~--~~------~~~~~~~~~~~~~~~ 362 (887)
T TIGR00593 303 CAKESEEAAPLANPAEK-AE---VGGFVL----ERLLDQLKKALA----LAFATE--NQ------SYVAYASEADGIPLL 362 (887)
T ss_pred cceEeCCHHHHHHHHHh-Cc---CCeEEE----cCcccccCceeE----EEEEec--CC------CceEEEecccchhhh
Confidence 35678788888887765 22 235777 667776666655 444432 10 1245664321 12
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg 500 (1123)
...+...|+++|+++.+.+|+||+|||+++|.++|+.+.+.+||||||+||++|+.. ++|++|+.+ |++
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~~~----~~l~~la~~-------yl~ 431 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPAQV----STLDTLARR-------YLV 431 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCCCC----CCHHHHHHH-------HcC
Confidence 234567799999999999999999999999999999998889999999999999764 799999987 555
Q ss_pred ccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001207 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1123)
Q Consensus 501 ~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~ 580 (1123)
+. .+.. .+++|++. .+...| .+.+..|||.||.++++||..|.++|++
T Consensus 432 ~~-----~~~~---------~~~~~~~~---------~~~~~~--------~~~~~~ya~~d~~~~~~L~~~l~~~l~~- 479 (887)
T TIGR00593 432 EE-----LILD---------EKIGGKLA---------KFAFPP--------LEEATEYLARRAAATKRLAEELLKELDE- 479 (887)
T ss_pred cc-----cccH---------HHhccCCC---------Cccccc--------HHHHHHHHHHHHHHHHHHHHHHHHHHhh-
Confidence 43 1111 12233221 111123 3557899999999999999999999986
Q ss_pred ccccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCC
Q 001207 581 SWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGS 660 (1123)
Q Consensus 581 ~~~~~~~~~~~~~l~~Ly~~IEmPLv~VLa~ME~~GI~VD~e~L~~l~~~l~~e~e~le~~i~~~~~~~~~~g~~fNi~S 660 (1123)
.++..+|.+|||||++||++||.+||+||.+.|+++..++..+++.+++++++. +|..||++|
T Consensus 480 -----------~~l~~l~~~iE~pl~~vLa~ME~~Gi~vD~~~l~~~~~~~~~~l~~le~~i~~~------~g~~fN~~S 542 (887)
T TIGR00593 480 -----------NKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQELSQEFGEEIADLEEEIYEL------AGEEFNINS 542 (887)
T ss_pred -----------ccHHHHHHHHHHHHHHHHHHHHhCCEEeCHHHHHHHHHHHHHHHHHHHHHHHHH------hCCCCCCCC
Confidence 378999999999999999999999999999999999999999999999999776 467899999
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCCCcHHHHHHH
Q 001207 661 DTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTL 740 (1123)
Q Consensus 661 ~kQl~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~~~vLe~L 740 (1123)
|+||+++||+ ++|||. .++|+|| |||+++||+.|
T Consensus 543 pkQl~~~Lf~--------~lgl~~-------------------------------------~kktktg-~ST~~~vL~~L 576 (887)
T TIGR00593 543 PKQLGEVLFE--------KLGLPV-------------------------------------GKKTKTG-YSTDADVLEKL 576 (887)
T ss_pred HHHHHHHHHH--------hCCCCC-------------------------------------CCCCCCC-CCChHHHHHHh
Confidence 9999999998 678752 2468899 99999999999
Q ss_pred HhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccCCccCC
Q 001207 741 ARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGK 820 (1123)
Q Consensus 741 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~ 820 (1123)
+..||+ +..||+||+++|++|||+++|+. .+.+.
T Consensus 577 ~~~hp~---------------------------------------------~~~ileyR~l~Kl~sty~~~l~~-~i~~~ 610 (887)
T TIGR00593 577 REKHPI---------------------------------------------IALILEYRQLTKLKSTYVDGLPE-LVNPD 610 (887)
T ss_pred hhcCcH---------------------------------------------HHHHHHHHHHHHHHHHHHHHHHH-HhcCC
Confidence 977663 46688999999999999999996 45545
Q ss_pred CCeeeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCC
Q 001207 821 NGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGG 899 (1123)
Q Consensus 821 dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~ 899 (1123)
+||||++||| +|+||||||++|||||||++++.|++||+||+|++|++||++||||||||||||||+|+.|+++|++|.
T Consensus 611 tgRIh~~~~q~~t~TGRlSs~~PNLQNIP~r~~~g~~iR~~Fia~~G~~lv~aDySQIELRilAhls~D~~Li~af~~g~ 690 (887)
T TIGR00593 611 TGRIHTTFNQTGTATGRLSSSNPNLQNIPIRSEEGRKIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGE 690 (887)
T ss_pred CCceeeeeEecccceeeecccCCCccccCCCCcccchhhheEecCCCCeEEEechhHhHHHHHHHHcCCHHHHHHHhcCC
Confidence 5999999998 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHH
Q 001207 900 DFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTV 979 (1123)
Q Consensus 900 DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i 979 (1123)
|||+.||+.+||++.+ +|++++|+.||++|||++||||+++||+++|||.+||++++
T Consensus 691 DiH~~tA~~~fg~~~e-----------------------~vt~~~R~~AK~infGiiYG~g~~~La~~l~is~~eA~~~i 747 (887)
T TIGR00593 691 DIHTETASRLFGVEIE-----------------------DVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFI 747 (887)
T ss_pred ChHHHHHHHHhCCChh-----------------------hCCHHHHhhhhHhhcCcccccchhHHHHHcCCCHHHHHHHH
Confidence 9999999999997653 46789999999999999999999999999999999999999
Q ss_pred HHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHh
Q 001207 980 DLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNAR 1059 (1123)
Q Consensus 980 ~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~ 1059 (1123)
++||++||+|++|++++++.|+++|||+|++||||++|++++.|...|+.++|+|+|+|||||||||+|.||+++++.+.
T Consensus 748 ~~yf~~yp~v~~~~~~~~~~a~~~Gyv~Tl~GRrr~lp~i~s~n~~~r~~aeR~A~N~~iQGsAADi~K~Ami~v~~~l~ 827 (887)
T TIGR00593 748 ERYFARYPGVKDYIENTVEEARKKGYVETLFGRRRYIPDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKRLK 827 (887)
T ss_pred HHHHHHCccHHHHHHHHHHHHHHcCcEEecCCCEeeCCCccccchhhHhHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998544
Q ss_pred hccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccCChhhcC
Q 001207 1060 LKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNWYSAK 1123 (1123)
Q Consensus 1060 l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~e~~ 1123 (1123)
-.+..++|++||||||+||||++++++++++|+++|++++ .|+|||.|++++|+||+|+|
T Consensus 828 ~~~~~~~lvlqVHDElv~Evp~~~~~~v~~~l~~~Me~a~----~l~VPL~v~~~~G~~W~e~~ 887 (887)
T TIGR00593 828 ERKLKARLLLQVHDELIFEAPEEEAEEVAALVKEVMEHAY----PLAVPLEVEVGTGKNWGEAK 887 (887)
T ss_pred hcCCCeEEEeeEceEeeeecCHHHHHHHHHHHHHHHHhhc----CCCCcEEEecCccCCHHhcC
Confidence 3445589999999999999999999999999999999986 68999999999999999998
No 3
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=5.1e-108 Score=1028.00 Aligned_cols=586 Identities=34% Similarity=0.503 Sum_probs=515.8
Q ss_pred CCeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChh
Q 001207 343 SNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGR 422 (1123)
Q Consensus 343 ~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~ 422 (1123)
..|.+|+++++|.++++.+..+ .+++|||||+|++++.+++++ +++++. + ...+|++..+.+ .
T Consensus 294 ~~~~~I~~~~~L~~~l~~l~~~---~~~a~DtEt~~l~~~~~~i~~----i~ls~~--~-------g~~~~ip~~~i~-~ 356 (880)
T PRK05755 294 EDYETILDEEELEAWLAKLKAA---GLFAFDTETTSLDPMQAELVG----LSFAVE--P-------GEAAYIPLDQLD-R 356 (880)
T ss_pred CceEEeCCHHHHHHHHHHhhcc---CeEEEEeccCCCCcccccEEE----EEEEeC--C-------CcEEEEeccccc-H
Confidence 3588999999999999998764 689999999999999887765 444332 2 125677764322 2
Q ss_pred hhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccccc
Q 001207 423 DLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (1123)
Q Consensus 423 evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~ 502 (1123)
.+++.|.++|+++.+.+|+||++||+++|.++|+.+++.+||||+|+||++|+. .++|++|+.+ |++.+
T Consensus 357 ~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~----~~~L~~L~~~-------ylg~~ 425 (880)
T PRK05755 357 EVLAALKPLLEDPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGR----RHGLDSLAER-------YLGHK 425 (880)
T ss_pred HHHHHHHHHHhCCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCC----CCCHHHHHHH-------HhCCC
Confidence 578889999999999999999999999999999988888999999999999975 2899999987 44432
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 001207 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSW 582 (1123)
Q Consensus 503 ~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~ 582 (1123)
.+ ...+++|++. .|...|+ +.+..||+.||.++++||..|.++|.+.
T Consensus 426 -----~~---------~~~~~~gk~~---------~~~~~pl--------e~~~~YAa~Dv~~~~~L~~~L~~~L~~~-- 472 (880)
T PRK05755 426 -----TI---------SFEEVAGKQL---------TFAQVDL--------EEAAEYAAEDADVTLRLHEVLKPKLLEE-- 472 (880)
T ss_pred -----cc---------chHHhcCCCC---------CccccCH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhc--
Confidence 01 1122344321 2333343 4578999999999999999999999863
Q ss_pred ccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHH
Q 001207 583 KLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDT 662 (1123)
Q Consensus 583 ~~~~~~~~~~~l~~Ly~~IEmPLv~VLa~ME~~GI~VD~e~L~~l~~~l~~e~e~le~~i~~~~~~~~~~g~~fNi~S~k 662 (1123)
.+++.+|.++|||++++|+.||.+||+||.++++++..+++.+++.+++++++++ |..||++||+
T Consensus 473 ---------~~l~~l~~eiE~p~~~~l~~me~~Gi~vD~~~~~~~~~~~~~~~~~l~~~~~~~~------g~~fn~~S~~ 537 (880)
T PRK05755 473 ---------PGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELA------GEEFNINSPK 537 (880)
T ss_pred ---------ccHHHHHHHhhchHHHHHHHHHhcCeEeCHHHHHHHHHHHHHHHHHHHHHHHHHh------CCCCCCCCHH
Confidence 3789999999999999999999999999999999999999999999999998774 6789999999
Q ss_pred HHHHhhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCCCcHHHHHHHHh
Q 001207 663 QLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLAR 742 (1123)
Q Consensus 663 Ql~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~~~vLe~La~ 742 (1123)
||+++||+ ++|+|. .++|++| +||++++|+.|+.
T Consensus 538 ql~~~L~~--------~lgl~~-------------------------------------~~kt~~g-~st~~~~L~~l~~ 571 (880)
T PRK05755 538 QLGEILFE--------KLGLPV-------------------------------------GKKTKTG-YSTDAEVLEKLAD 571 (880)
T ss_pred HHHHHHHH--------hcCCCC-------------------------------------CCCCCCC-CCCcHHHHHHHHh
Confidence 99999998 577752 2457788 8999999999987
Q ss_pred ccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccCCccCCCC
Q 001207 743 NISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNG 822 (1123)
Q Consensus 743 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dG 822 (1123)
.||. +..|+|||+++|+++||++++.. .+.+.+|
T Consensus 572 ~~p~---------------------------------------------~~~lle~r~~~kl~sty~~~l~~-~~~~~~~ 605 (880)
T PRK05755 572 DHPI---------------------------------------------PDKILEYRQLSKLKSTYTDALPK-LINPDTG 605 (880)
T ss_pred cChH---------------------------------------------HHHHHHHHHHHHHHHHHHHHHHH-HhccCCC
Confidence 6652 56799999999999999999986 4444446
Q ss_pred eeeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCch
Q 001207 823 RVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDF 901 (1123)
Q Consensus 823 RIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DI 901 (1123)
|||++|+| +|+|||+||++|||||||++++.+..+|+||+|++|++||++||||||+|||||||+|+.|+++|++|.|+
T Consensus 606 rih~~~~~~~t~TGRlss~~PnlQniP~~~~~~~~iR~~f~~~~G~~lv~~DysqiElRilA~ls~D~~l~~~~~~g~Di 685 (880)
T PRK05755 606 RIHTSFNQTVTATGRLSSSDPNLQNIPIRTEEGRRIRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDI 685 (880)
T ss_pred eecceEeecccceeeeeccCCCcccCCCCCccchhhhheEecCCCCEEEEechhhhHHHHHHHHcCCHHHHHHHhcCCCH
Confidence 99999998 99999999999999999999888899999999999999999999999999999999999999999999999
Q ss_pred hHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHH
Q 001207 902 HSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDL 981 (1123)
Q Consensus 902 H~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~ 981 (1123)
|+.+|+.+||++.+ ++++++|+.||++|||++||||+++||+++|+|.+||++++++
T Consensus 686 h~~~A~~~~~~~~~-----------------------~v~~~~R~~aK~~~fg~~YG~g~~~la~~l~is~~eA~~~~~~ 742 (880)
T PRK05755 686 HTATASEVFGVPLE-----------------------EVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDR 742 (880)
T ss_pred HHHHHHHHhCCChh-----------------------hCCHHHHHHHHHHhcchhhCCChHHHHHHcCCCHHHHHHHHHH
Confidence 99999999997543 4577899999999999999999999999999999999999999
Q ss_pred HHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhc
Q 001207 982 WYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLK 1061 (1123)
Q Consensus 982 f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~ 1061 (1123)
||++||+|++|++.+.+.|+++|||+|++||||++|++++.+...|+.++|+|+|++||||||||+|.||+++++.+.-.
T Consensus 743 ~~~~~p~v~~~~~~~~~~a~~~g~v~t~~GR~r~~p~~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~~~~~l~~~ 822 (880)
T PRK05755 743 YFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPDINSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDKALKEE 822 (880)
T ss_pred HHHHCccHHHHHHHHHHHHHHcCCEECCCCCeEeCCcccCCCHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999855444
Q ss_pred cCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccCChhhcC
Q 001207 1062 ELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNWYSAK 1123 (1123)
Q Consensus 1062 ~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~e~~ 1123 (1123)
+++++|++||||||+||||++.+++++++|+++|++++ .|+|||.|++++|+||+|+|
T Consensus 823 ~~~~~l~l~vHDel~~ev~~~~~~~~~~~~~~~me~~~----~l~vpl~v~~~~g~~W~~~~ 880 (880)
T PRK05755 823 GLKSRMLLQVHDELVFEVPEDELEEVKKLVKEVMENAV----ELSVPLVVDVGVGDNWDEAH 880 (880)
T ss_pred CCCceEEEEEcceeEEEeCHHHHHHHHHHHHHHHhCcc----cCCceEEEeCCcCCChHhcC
Confidence 56789999999999999999999999999999999986 68999999999999999998
No 4
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=100.00 E-value=1.2e-96 Score=884.01 Aligned_cols=539 Identities=26% Similarity=0.281 Sum_probs=454.6
Q ss_pred CeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001207 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1123)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~e 423 (1123)
.+.+|++++++..++..+..+ +++++|||+++.++ .++ .+++.. +...+.+|++.
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~---~~~a~DtEf~r~~t---~l~------liQ~~~--------~~~~~liDpl~----- 56 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPA---GVVAGDTETTGDDA---AAA------AAQEGE--------EEPRWVWASTA----- 56 (553)
T ss_pred CceEEeccchhHHHHHHhccC---CceeCCccccCCcc---hhh------eeeecC--------CCceEEECchH-----
Confidence 468999999999999999886 68999999998886 222 223322 23356666531
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~ 503 (1123)
+ +. .+|.++|+.+.+ +||||||+|||++... ..+++|+.++.+ ++++.
T Consensus 57 ~---l~-------------------~~L~~~Gv~~~~-~fDT~LAa~lL~~~~~-~~~~~l~~la~~-------~l~~~- 104 (553)
T PRK14975 57 A---LY-------------------PRLLAAGVRVER-CHDLMLASQLLLGSEG-RAGSSLSAAAAR-------ALGEG- 104 (553)
T ss_pred H---hH-------------------HHHHHCCCccCC-CchHHHHHHHcCCCCC-cCCCCHHHHHHH-------HhCCC-
Confidence 1 11 226677988765 8999999999998651 013899999987 55543
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 001207 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (1123)
Q Consensus 504 ~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~ 583 (1123)
+ .+ .. +. ++|. +|+ ++.+..||+.||.++++||+.|.++|++..-
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 1 01 00 01 2675 554 4678999999999999999999999986300
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHhhhcCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHhhhcCCCC
Q 001207 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVAR----------AEQEAAVNRFRKWASKHCPDA 653 (1123)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPLv~VLa~ME~~GI~VD~e~L~~l~~~l~----------~e~e~le~~i~~~~~~~~~~g 653 (1123)
. ...++..+|.++|||++++|++||.+||+||.+.++++..++. .+++.+++++++.+. .
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 0126889999999999999999999999999999999999888 777888988877752 2
Q ss_pred ccccCCCHHHHHHhhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCCCc
Q 001207 654 KYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVG 733 (1123)
Q Consensus 654 ~~fNi~S~kQl~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~ 733 (1123)
..||++||+||.++| + ++|++. ++|+
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 359999999999999 3 466531 2566
Q ss_pred HHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccc
Q 001207 734 GDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQ 813 (1123)
Q Consensus 734 ~~vLe~La~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~ 813 (1123)
+++| +...|| .+..|++||+++|++|||+++++
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 223333 35789999999999999999988
Q ss_pred cCCccCCCCeeeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHH
Q 001207 814 GSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSML 892 (1123)
Q Consensus 814 ~~~i~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li 892 (1123)
. .++ .|||||++|++ +|+|||+||++|||||||+ .+|+||+|+|||+||++||||||+|||||||+|+.|+
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 89999999998 8999999999999999996 5999999999999999999999999999999999999
Q ss_pred HHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCH
Q 001207 893 DAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSV 972 (1123)
Q Consensus 893 ~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~ 972 (1123)
++|++|.|+|+.||+.+||++.+ + +++|+.||++|||++||||+++|++++| +.
T Consensus 351 ~~~~~g~Dih~~~A~~~~~~~~~-----------------------~--~~~R~~aK~~~~g~~YG~g~~~l~~~~~-~~ 404 (553)
T PRK14975 351 EAFRTGGDLHRLTASVGFGKPEE-----------------------E--KEERALAKAANFGAIYGATSKGLQEYAK-NY 404 (553)
T ss_pred HHHhcCCCHHHHHHHHHhCCCcc-----------------------c--hhHHHHHHHHHHHhhhCCcHHHHHHHcC-CH
Confidence 99999999999999999997542 1 5789999999999999999999999999 99
Q ss_pred HHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHH
Q 001207 973 EEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAML 1052 (1123)
Q Consensus 973 ~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi 1052 (1123)
+||++++++||++||+|++|++.+.+.|+++|||+|++||+|++|++++.+...++.++|+|+|+|||||||||+|.||+
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 HHHHHHhhc-cCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCc-ceeEEEeccccCChhhcC
Q 001207 1053 EISKNARLK-ELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNL-RVDLSVDAKCAQNWYSAK 1123 (1123)
Q Consensus 1053 ~i~~~~~l~-~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L-~VPL~vd~~iG~nW~e~~ 1123 (1123)
++++. +. +.+++|++||||||+||||++.+++++++|+++|+++.. ..+ +|||.|++++|+||+|+|
T Consensus 485 ~~~~~--l~~~~~~~lvl~vHDEl~~e~~~~~~~~~~~~i~~~M~~a~~--~~~~~Vpl~v~~~~g~~w~~~~ 553 (553)
T PRK14975 485 LLRRR--LAEGLDAELVFFVHDEVVVECPEEEAEEVAAAIEEAMEEAGR--LLFGPVPFPVEVAVVESYAEAK 553 (553)
T ss_pred HHHHH--HhhcCCcEEEEEecceeEEEecHHHHHHHHHHHHHHHHHHHh--ccCCCccEEEecCccCCHhhcC
Confidence 99984 43 677899999999999999999999999999999999863 123 599999999999999997
No 5
>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-85 Score=749.41 Aligned_cols=371 Identities=63% Similarity=1.003 Sum_probs=337.9
Q ss_pred CCCCCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhh
Q 001207 728 GWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISN 807 (1123)
Q Consensus 728 G~~St~~~vLe~La~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~st 807 (1123)
|+||++.++|..++..+.. .++.++.|.+... .++....+.++++..||+||+++||+||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~il~~r~~~Kl~st 60 (371)
T cd08640 1 GLPSVDSEALRELAGDPEA--------DILLYEWCYENGV------------SGGEEGKEACEAIEALKEIKSISTLLST 60 (371)
T ss_pred CCCccchHHHHHhcCCccc--------cchhhHHHHHhcc------------CCccccchhhHHHHHHHHHHHHHHHHHH
Confidence 5689999999999976442 1222221111111 1344456788999999999999999999
Q ss_pred hhcccccCCccCCCCeeeecccccCccccccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcC
Q 001207 808 FILPLQGSNVSGKNGRVHCSLNINTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN 887 (1123)
Q Consensus 808 yi~~l~~~~i~~~dGRIH~~~n~~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~ 887 (1123)
|+++|++ .+++.|||||++|++.|+||||||++|||||||++++.++.||+||+|++|++||++||||||||||||||+
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 555789999999997799999999999999999998888899999999999999999999999999999999
Q ss_pred chhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhh
Q 001207 888 CKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARD 967 (1123)
Q Consensus 888 D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~ 967 (1123)
|+.|+++|++|.|||+.||+.+|+.++++|+++++...|.++++++++..+++++++|+.||++|||++||||+++||++
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 99999999999999999999999999999998899999998888888877888999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHH
Q 001207 968 WKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVA 1047 (1123)
Q Consensus 968 lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~ 1047 (1123)
+|||.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|++|++++.+...++.++|+|+|+|||||||||+
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 HHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccCChhh
Q 001207 1048 MCAMLEISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNWYS 1121 (1123)
Q Consensus 1048 K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~e 1121 (1123)
|.||+++++.+...+.+++|++||||||+||||++.+++++++|+++|++++.+ .|+|||.|++++|+||+|
T Consensus 300 K~Ami~i~~~l~~~~~~~~lvlqVHDElv~evp~~~~~~~~~~v~~~Me~~~~~--~l~VPl~v~~~iG~~W~~ 371 (371)
T cd08640 300 MKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGPEEKADEALKIVKDCMENPFFG--PLDVPLEVDGSVGYNWYE 371 (371)
T ss_pred HHHHHHHHHHHhhccCCceEEEEEcceeEEEcCHHHHHHHHHHHHHHHHhcCcc--CCCccEEEeccccCCCCC
Confidence 999999998665667889999999999999999999999999999999998654 689999999999999986
No 6
>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=2.6e-84 Score=744.75 Aligned_cols=376 Identities=37% Similarity=0.556 Sum_probs=346.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHhhcCCCCCCCCCCCCCCcccccccCCCcccccc
Q 001207 620 DREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAE 699 (1123)
Q Consensus 620 D~e~L~~l~~~l~~e~e~le~~i~~~~~~~~~~g~~fNi~S~kQl~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~~ 699 (1123)
|.++|+++..++..+++.++++++.+ +|..||++||+|++++||+ .+|||+
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 78999999999999999999999766 4678999999999999997 577753
Q ss_pred CCCCCcccccchhcccccCCCCccccccCCCCCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccccccccccchhh
Q 001207 700 GKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIF 779 (1123)
Q Consensus 700 ~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~~~vLe~La~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 779 (1123)
..+|++|+ +|+.++|+.|+..||.
T Consensus 52 ----------------------~~~t~~~~-~t~~~~L~~l~~~~p~--------------------------------- 75 (377)
T cd08637 52 ----------------------GKKTKTGY-STDAEVLEKLADEHPI--------------------------------- 75 (377)
T ss_pred ----------------------CCcCCCCC-CchHHHHHhhhhcChH---------------------------------
Confidence 24577885 7888899999876652
Q ss_pred hhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccCCccCCCCeeeecccc-cCccccccccCCCcccCCccccchhhhh
Q 001207 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIR 858 (1123)
Q Consensus 780 ~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR 858 (1123)
+..|++||+++|+++||+++++. .+.+.|||||++|++ +|+||||||++|||||||++++.|..+|
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 56799999999999999999986 344349999999998 9999999999999999999888889999
Q ss_pred ceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCccc
Q 001207 859 QAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLK 938 (1123)
Q Consensus 859 ~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~ 938 (1123)
+||+|++|++||++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||++++
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 999999999999999999999999999999999999999999999999999997553
Q ss_pred ccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCC
Q 001207 939 DAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPA 1018 (1123)
Q Consensus 939 ~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~ 1018 (1123)
+|++++|+.||+++||++||||+.+||+++|+|.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|++|+
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 45778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCC
Q 001207 1019 IKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKP 1098 (1123)
Q Consensus 1019 ~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a 1098 (1123)
+++.+...|+.++|+|+|++||||||||+|.||+++++.+.-.+.+++|+++|||||+||||++.+++++++|+++|+++
T Consensus 280 ~~~~~~~~r~~~~r~a~N~~iQGsaAdi~k~am~~~~~~l~~~~~~~~lvl~vHDEl~~ev~~~~~~~~~~~l~~~M~~~ 359 (377)
T cd08637 280 INSKNRNVRAFAERIAINTPIQGTAADIIKLAMIRVHKALKEEGLKARMLLQVHDELVFEVPEEELEEVAALVKEEMENA 359 (377)
T ss_pred ccCCcHHHhhHHHHhHhcccchhHHHHHHHHHHHHHHHHHHhcCCCeEEEeeEeeeeeEecCHHHHHHHHHHHHHHHhhc
Confidence 99999889999999999999999999999999999998554445578999999999999999999999999999999998
Q ss_pred CCCCCCcceeEEEeccccCChh
Q 001207 1099 FNGKNNLRVDLSVDAKCAQNWY 1120 (1123)
Q Consensus 1099 ~~~~~~L~VPL~vd~~iG~nW~ 1120 (1123)
+ .++|||.|+++||+||+
T Consensus 360 ~----~l~VPl~v~~~ig~~W~ 377 (377)
T cd08637 360 V----ELSVPLKVDVGVGKNWG 377 (377)
T ss_pred c----cCCCcEEEecccCCCCC
Confidence 5 68999999999999996
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=5.7e-84 Score=744.46 Aligned_cols=380 Identities=40% Similarity=0.572 Sum_probs=345.3
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHhhcCCCCCCCCCCCCCCcccccccCCCccccc
Q 001207 619 VDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIA 698 (1123)
Q Consensus 619 VD~e~L~~l~~~l~~e~e~le~~i~~~~~~~~~~g~~fNi~S~kQl~~lLFe~~~~~k~~~l~lp~er~~k~~~~~~~~~ 698 (1123)
||.++|+.+..++..+++.++.++... +|..||++||+|++++||+ ++|+|+
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 799999999999999999998888666 4788999999999999998 677753
Q ss_pred cCCCCCcccccchhcccccCCCCcccccc-CCCCCcHHHHHHHHh-ccCccccccCCCCCCCCCCCcccccccccccccc
Q 001207 699 EGKKTPSKFRNITLRSIGVDLPTEMYTAT-GWPSVGGDALKTLAR-NISAEYDCVDGAHDLDDSGCTEETEYKGAVASNN 776 (1123)
Q Consensus 699 ~~kk~~~~~~~~~l~~~Gi~lp~~~~Tkt-G~~St~~~vLe~La~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 (1123)
..+|++ |.+||++++|+.|+. .|
T Consensus 53 -----------------------~~~t~~~g~~st~~~~L~~l~~~~~-------------------------------- 77 (383)
T PF00476_consen 53 -----------------------TKKTKKKGKPSTDKEVLKKLAEDAH-------------------------------- 77 (383)
T ss_dssp -----------------------SSBETTCSEBHCTHHHHHHHCCCCH--------------------------------
T ss_pred -----------------------CCCCcccchhhhHHHHHHHhhhhhh--------------------------------
Confidence 234555 999999999999986 32
Q ss_pred hhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccCCccCCCCeeeecccc-cCccccccccCCCcccCCccccchh
Q 001207 777 KIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRY 855 (1123)
Q Consensus 777 ~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~ 855 (1123)
+.+..+++||++.|+.+||++++.. .+...|||||++|++ +|+|||+||++|||||||++...|.
T Consensus 78 -------------~~~~~~l~~r~~~kl~~~~~~~~~~-~~~~~dgrih~~~~~~gt~TGRls~~~PNlQniP~~~~~~~ 143 (383)
T PF00476_consen 78 -------------PIAKLLLEYRKLSKLRSTYIDNLLD-KVDPEDGRIHPSFNQTGTATGRLSSSNPNLQNIPKRDPYGK 143 (383)
T ss_dssp -------------THHHHHHHHHHHHHHHHHTTHHHHH-HSBTTTTEE--EEESSSSSSS--EEESSCTSSSSSSSHHHH
T ss_pred -------------hhHHHHHHHHHHHHHHhhhhhHHHH-hccccCCeecceeeecccccCCceeechhhhccccccccCc
Confidence 2467899999999999999999886 455589999999998 9999999999999999999988899
Q ss_pred hhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCC
Q 001207 856 KIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVP 935 (1123)
Q Consensus 856 ~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~ 935 (1123)
++|+||+|++|++||++||||||+|||||||+|+.|+++|.+|.|+|+.+|+.+||.+.+
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 999999999999999999999999999999999999999999999999999999997543
Q ss_pred cccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCccc
Q 001207 936 LLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARR 1015 (1123)
Q Consensus 936 ~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~ 1015 (1123)
++++.+|+.||++|||++||||+.+||+.+|+|.+||++++++||++||+|++|++.+.+.|+++|||+|++||+|+
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 CCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHH
Q 001207 1016 FPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECM 1095 (1123)
Q Consensus 1016 lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~M 1095 (1123)
+|.+++.+...+..++|+|+|++||||||||+|.||+++++.+.-.+.+.+++++|||||+||||++.+++++++|+++|
T Consensus 281 ~p~~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~i~~~l~~~~~~~~l~l~VHDEli~ev~~~~~~~v~~~l~~~M 360 (383)
T PF00476_consen 281 LPNIDSRNKSLRASAERQAVNTPIQGSAADIMKLAMIRIHEALREKGLGARLVLQVHDELIFEVPEDEAEEVAEILKEIM 360 (383)
T ss_dssp CGGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEESSEEEEEEEGGGHHHHHHHHHHHH
T ss_pred CCchhcccchhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCcCceeEEEEcCeeheeecHhHHHHHHHHHHHHH
Confidence 99999998888999999999999999999999999999998655556688999999999999999999999999999999
Q ss_pred cCCCCCCCCcceeEEEeccccCChhhc
Q 001207 1096 SKPFNGKNNLRVDLSVDAKCAQNWYSA 1122 (1123)
Q Consensus 1096 e~a~~~~~~L~VPL~vd~~iG~nW~e~ 1122 (1123)
+++. .++|||.|+++||+||+||
T Consensus 361 ~~~~----~~~vPl~~~~~iG~~W~~~ 383 (383)
T PF00476_consen 361 ENAG----ELRVPLPVEVEIGKNWGEA 383 (383)
T ss_dssp HTSS----HHSSCTCEEEEEESSTTTH
T ss_pred Hhhc----cCCCeEEeecCCCCChhcC
Confidence 9986 4699999999999999997
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=2e-83 Score=743.04 Aligned_cols=368 Identities=23% Similarity=0.238 Sum_probs=325.9
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhh-hcCC--------------------------CCccccCCCHHHHHHhhcCC
Q 001207 619 VDREYLSEIEKVARAEQEAAVNRFRKWAS-KHCP--------------------------DAKYMNVGSDTQLRQLLFGG 671 (1123)
Q Consensus 619 VD~e~L~~l~~~l~~e~e~le~~i~~~~~-~~~~--------------------------~g~~fNi~S~kQl~~lLFe~ 671 (1123)
+|.+....|..++..++..++.++.+.+. ++.+ ...+||++||+||+++||+
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 58889999999999999999999988872 2211 2247999999999999997
Q ss_pred CCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCCCcHHHHHHHHhccCcccccc
Q 001207 672 KPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCV 751 (1123)
Q Consensus 672 ~~~~k~~~l~lp~er~~k~~~~~~~~~~~kk~~~~~~~~~l~~~Gi~lp~~~~TktG~~St~~~vLe~La~~~~~~~~~~ 751 (1123)
++||+ +.++|+||.||||++||+.|. ||+
T Consensus 80 -------~lg~~-------------------------------------~~~~t~~G~~std~~vL~~l~--~p~----- 108 (429)
T cd08643 80 -------KYGWE-------------------------------------PQEFTESGEPKVDEDVLSKLD--YPE----- 108 (429)
T ss_pred -------hcCCC-------------------------------------CCCcCCCCCCCcCHHHHHhcc--chH-----
Confidence 57774 235689999999999999996 553
Q ss_pred CCCCCCCCCCCcccccccccccccchhhhhHHHHHHHhHHHHHHHHHHhHhhhHhhhhcccccC-CccCCCCeeeecccc
Q 001207 752 DGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGS-NVSGKNGRVHCSLNI 830 (1123)
Q Consensus 752 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Lle~r~l~Kl~styi~~l~~~-~i~~~dGRIH~~~n~ 830 (1123)
++.|++||+++|+++||+++...+ ..+++|||||++||+
T Consensus 109 ----------------------------------------~~~ileyr~l~K~~st~~~~~~~~l~~v~~dgRIH~~~nq 148 (429)
T cd08643 109 ----------------------------------------AKLLAEYLLVQKRLGQLADGNNAWLKLVHEDGRIHGAVNT 148 (429)
T ss_pred ----------------------------------------HHHHHHHHHHHHHHHHHHhhHHHHHHHcCCCCceeeeEEe
Confidence 567999999999999999883322 135678999999998
Q ss_pred -cCccccccccCCCcccCCc-cccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCc---hhHHHHHHcCCchhHHH
Q 001207 831 -NTETGRLSARRPNLQNQPA-LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANC---KSMLDAFKAGGDFHSRT 905 (1123)
Q Consensus 831 -~T~TGRlSss~PNLQNIP~-~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D---~~Li~af~~G~DIH~~t 905 (1123)
+|+||||||++|||||||+ ++++|++||+||+|++|++||++||||||||||||||+| +.|++ |..|.|||+.+
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 78888 78899999999
Q ss_pred HhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHH--------
Q 001207 906 AMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKK-------- 977 (1123)
Q Consensus 906 A~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~-------- 977 (1123)
|+. +|+ ++|+.||++|||++||||+++||+.+|++.+||+.
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 985 341 57999999999999999999999999999998887
Q ss_pred ----------------HHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhc
Q 001207 978 ----------------TVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQG 1041 (1123)
Q Consensus 978 ----------------~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQG 1041 (1123)
++++||++||+|++|++.+++.|+++|||+|++||+|++|. +|+|+|++|||
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 99999999999999999999999999999999999999975 48899999999
Q ss_pred hHHHHHHHHHHHHHHHHhhcc----CCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccC
Q 001207 1042 SAADVAMCAMLEISKNARLKE----LGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQ 1117 (1123)
Q Consensus 1042 SAADI~K~AMi~i~~~~~l~~----~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~ 1117 (1123)
|||||||.||+++++.+.-.+ .+++|++||||||+||||++++++++++|+++|+++. ..+.|+|||.|+++||+
T Consensus 345 sAADi~K~Ami~i~~~l~~~g~~~~~~~~lvlqVHDElv~ev~~~~ae~v~~~v~~~Me~a~-~~~~l~VPL~v~~~iG~ 423 (429)
T cd08643 345 AGAILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAG-EHFNFRCPLAGEFDIGR 423 (429)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEccceEEEeCHHHHHHHHHHHHHHHHHhh-hccCCCcceEeecCccC
Confidence 999999999999998554332 3578999999999999999999999999999999985 33468999999999999
Q ss_pred ChhhcC
Q 001207 1118 NWYSAK 1123 (1123)
Q Consensus 1118 nW~e~~ 1123 (1123)
||+|+|
T Consensus 424 nW~e~h 429 (429)
T cd08643 424 NWAETH 429 (429)
T ss_pred CHHHcC
Confidence 999998
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=1.4e-79 Score=704.76 Aligned_cols=303 Identities=34% Similarity=0.478 Sum_probs=284.1
Q ss_pred HHHHHHHHhHhhhHhhhhcccccCCc----cCCCCeeeecccc-cCccccccccCCCcccCCcccc--------------
Q 001207 792 ISALCEVCSIDSLISNFILPLQGSNV----SGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEK-------------- 852 (1123)
Q Consensus 792 i~~Lle~r~l~Kl~styi~~l~~~~i----~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~-------------- 852 (1123)
+..|++||+++|+++||+++++.+ + .+.|||||++|++ +|+||||||++|||||||++..
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 567999999999999999999963 3 2688999999998 8999999999999999999743
Q ss_pred -chhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCC
Q 001207 853 -DRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDK 931 (1123)
Q Consensus 853 -~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~ 931 (1123)
.+..+|+||+|++|++||++||||||||||||||+|+.|+++|++|.|+|+.+|+.+||++.+
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 467899999999999999999999999999999999999999999999999999999997654
Q ss_pred CCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccC
Q 001207 932 PPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLG 1011 (1123)
Q Consensus 932 ~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~G 1011 (1123)
+|++++|+.||++|||++||||+.+||+++|+|.+||++++++||++||+|++|++.+++.|+++|||+|++|
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 4567899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhc-----cCCceEEEEeeceEEEeCCcchHHH
Q 001207 1012 RARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLK-----ELGWKLLLQVHDEVILEGPSESAEV 1086 (1123)
Q Consensus 1012 Rrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~-----~~g~~llLqVHDELv~EVp~~~aee 1086 (1123)
|+|++|++++.++..++.++|+|+|+|||||||||+|.||+++++.+... +.+++|++||||||+||||++.+++
T Consensus 262 Rrr~~p~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~K~ami~i~~~l~~~~~~~~~~~~~lvl~VHDEl~~ev~~~~~~~ 341 (373)
T cd08638 262 RRRYLPEINSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESDVDE 341 (373)
T ss_pred CEEeCCCCCCCCHHHHHHHHHHHhchhhhhHHHHHHHHHHHHHHHHHHhhcccccCCCeEEEEEEccEEEEEeCHHHHHH
Confidence 99999999999999999999999999999999999999999999855432 3678999999999999999999999
Q ss_pred HHHHHHHHHcCCCCCCCCcceeEEEeccccCChhhc
Q 001207 1087 AKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNWYSA 1122 (1123)
Q Consensus 1087 v~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~e~ 1122 (1123)
++++|+++|+++. .+.|||.|++++|+||+|.
T Consensus 342 ~~~~i~~~Me~~~----~l~VPl~v~~~iG~~w~~l 373 (373)
T cd08638 342 VARIIKRSMENAA----KLSVPLPVKVSIGKSWGSL 373 (373)
T ss_pred HHHHHHHHHhCcc----CCCCceEEeecccCCcccC
Confidence 9999999999986 6899999999999999984
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=9.7e-73 Score=641.50 Aligned_cols=274 Identities=26% Similarity=0.353 Sum_probs=247.4
Q ss_pred HHHHHHHHhHhhhHh-hhhcccccCCccCCCCeeeecccc-c-CccccccccCCCcccCCc-------------------
Q 001207 792 ISALCEVCSIDSLIS-NFILPLQGSNVSGKNGRVHCSLNI-N-TETGRLSARRPNLQNQPA------------------- 849 (1123)
Q Consensus 792 i~~Lle~r~l~Kl~s-tyi~~l~~~~i~~~dGRIH~~~n~-~-T~TGRlSss~PNLQNIP~------------------- 849 (1123)
++.||+||++.|+.| ||+++|+. . +.+|||||++|++ + |+||||||++|||||||+
T Consensus 66 ~~~iL~~R~~~k~~s~t~~~~l~~-~-~~~~gRih~~~~~~gat~TGRlss~~pnlQNiP~~~~~~~~~~~~~~~~~d~~ 143 (378)
T cd08642 66 VKRVLELRQELSKTSVKKYEAMER-A-VCSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLKDLDLARELVKSGDFD 143 (378)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHH-H-cCCCCceeeeeeeecchhccccccCCCCcccCCCCcccchHHHHHHhhccchh
Confidence 567999999999998 99999996 3 4578999999998 7 999999999999999999
Q ss_pred ---------cccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccc
Q 001207 850 ---------LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETG 920 (1123)
Q Consensus 850 ---------~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~ 920 (1123)
++..|+.||+||+|+||++||++||||||||||||||+|+.|+++|++|.|||+.||+.+||+|.+++
T Consensus 144 ~~~~~~~~~~~~~~~~iR~aFva~~G~~lvsaDySQIElRVLAhlS~D~~li~af~~g~Dih~~tAs~if~vp~e~~--- 220 (378)
T cd08642 144 ALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKI--- 220 (378)
T ss_pred hhhhhccccccHHHHHhHHheecCCCCEEEEecHHHHHHHHHHHHhCCHHHHHHHhcCCChHHHHHHHHhCCChhhc---
Confidence 55667899999999999999999999999999999999999999999999999999999999876432
Q ss_pred hhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhh----hhhcCCCHHHHHHHHHHHHHhChhHHHHHHHH
Q 001207 921 QVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGL----ARDWKVSVEEAKKTVDLWYNERQEVLTWQEAR 996 (1123)
Q Consensus 921 e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~L----A~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~ 996 (1123)
++++++|+.||++|||++||||+++| ++++|||.+||+.++++||++||+|++||+++
T Consensus 221 ------------------~v~~~~R~~AK~vnfGiiYG~g~~~L~~~aa~~lgis~~EA~~~i~~yf~~yP~v~~~~~~~ 282 (378)
T cd08642 221 ------------------GKNSHLRQKGKVAELALGYGGSVGALKAMGALEMGLTEDELPGIVDAWRNANPNIVKLWWDV 282 (378)
T ss_pred ------------------ccCHHHHHHhhhhhccceeccchHHHHHhhhhhcCCCHHHHHHHHHHHHHHCccHHHHHHHH
Confidence 36789999999999999999999999 88999999999999999999999999999987
Q ss_pred ---HHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeec
Q 001207 997 ---KKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHD 1073 (1123)
Q Consensus 997 ---~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHD 1073 (1123)
...|.++||+.|+ | +| ++|+|||||||||+|.||+++++ .|++|+|||||
T Consensus 283 ~~~~~~a~~~g~v~t~-g-------------------~r-~~~n~IQGtAADi~k~Ami~l~~------~g~~ivLqVHD 335 (378)
T cd08642 283 DKAAKKAVKERKTVKL-G-------------------GK-LVENIVQAIARDCLAEAMLRLEK------AGYDIVMHVHD 335 (378)
T ss_pred HHHHHHHHHcCceEee-h-------------------Hh-hhhcccchhHHHHHHHHHHHHHh------cCCeEEEEECc
Confidence 5667789999997 1 23 45669999999999999999985 36899999999
Q ss_pred eEEEeCCcchHHHHHHHHHHHHcCCCCCCCCcceeEEEeccccCCh
Q 001207 1074 EVILEGPSESAEVAKAIVVECMSKPFNGKNNLRVDLSVDAKCAQNW 1119 (1123)
Q Consensus 1074 ELv~EVp~~~aeev~~~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW 1119 (1123)
|||||||+. ++.++.|+++|++++.| .-.|||.+++.++..|
T Consensus 336 Elv~Evp~~--~~~~~~v~~iM~~~p~w--a~~lPl~a~g~~~~~y 377 (378)
T cd08642 336 EVVIEVPEG--EGSLEEVNEIMAQPPPW--APGLPLNADGFESPYY 377 (378)
T ss_pred eeEEeeccc--hhHHHHHHHHHccCCcc--ccCCcccccccccccc
Confidence 999999983 45778899999999765 3489999999999877
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=5.4e-73 Score=644.52 Aligned_cols=303 Identities=33% Similarity=0.388 Sum_probs=282.6
Q ss_pred hHHHHHHHHHHhHhhhHhhhhcccccCCccCCCCeeeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCCC
Q 001207 789 CDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGN 867 (1123)
Q Consensus 789 ~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G~ 867 (1123)
.|.+..|++||+++|+++||++++++ .++ +|||||++|++ +|+|||+||++|||||||++++.|..+|+||+|++|+
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 56788999999999999999999996 344 69999999998 8999999999999999999988899999999999999
Q ss_pred eEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHh
Q 001207 868 SLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRK 947 (1123)
Q Consensus 868 ~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~ 947 (1123)
+||++||||||||||||||+|+.|+++|.+|.|+|+.+|+.+|+++ +++++|+.
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 46789999
Q ss_pred hHHHhhhhhhC----CChhhhhhhcCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhC---CeEecccCCcccCCCCC
Q 001207 948 AKMLNFSIAYG----KTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRID---NHVHTLLGRARRFPAIK 1020 (1123)
Q Consensus 948 AK~vnfGiiYG----~G~~~LA~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~---GyV~Tl~GRrr~lp~~~ 1020 (1123)
||++|||++|| ||+++|++.+|+|.+||++++++||+.||+|++|++.+++.|++. ||++|++||+|++|+++
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-----------cChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHH
Q 001207 1021 S-----------LTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKA 1089 (1123)
Q Consensus 1021 s-----------~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~ 1089 (1123)
+ .+...+..++|+|+|++||||||||+|.||+++++.+.-.+.+++|+++|||||+||||++.+++++.
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~r~a~N~~IQGsaADi~K~ami~~~~~l~~~~~~~~lvl~VHDElv~evp~~~~~~~~~ 317 (347)
T cd06444 238 WTEVVSDPAAASRARRVRRAAGRFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAA 317 (347)
T ss_pred ccccccccccccccHHHHHHhHHHHhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEccceEEEeCHHHHHHHHH
Confidence 7 45667788899999999999999999999999998554444689999999999999999999999999
Q ss_pred HHHHHHcCCCCCCCCcceeEEEeccccCChh
Q 001207 1090 IVVECMSKPFNGKNNLRVDLSVDAKCAQNWY 1120 (1123)
Q Consensus 1090 ~v~~~Me~a~~~~~~L~VPL~vd~~iG~nW~ 1120 (1123)
+|+++|+++.. ...++|||.|++++|+||+
T Consensus 318 ~l~~~M~~~~~-~~~~~vPl~v~~~ig~~W~ 347 (347)
T cd06444 318 IVREAAEQAVR-LLFGSVPVRFPVKIGVVWR 347 (347)
T ss_pred HHHHHHHHHhh-ccCCCCCEEEEeeecCCCC
Confidence 99999999862 2358999999999999995
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=1.5e-71 Score=626.25 Aligned_cols=290 Identities=34% Similarity=0.513 Sum_probs=265.2
Q ss_pred HhHHHHHHHHHHhHhhhHhhhhcccccCCccCCCCeeeecccc-cCccccccccCCCcccCCccccchhhhhceEEcCCC
Q 001207 788 ACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPG 866 (1123)
Q Consensus 788 ~~~~i~~Lle~r~l~Kl~styi~~l~~~~i~~~dGRIH~~~n~-~T~TGRlSss~PNLQNIP~~~~~g~~iR~~Fia~~G 866 (1123)
.+|.+..|++||+++|+++||+++++. .+++.|||||++|++ +|.|||+||++|||||||+. ..+|++|+|+||
T Consensus 28 ~~p~~~~lle~r~~~kl~~t~~~~l~~-~~~~~~grih~~~~~~gt~TGRlS~~~PnlQniP~~----~~iR~~f~a~~G 102 (324)
T cd08639 28 EHPAVRLLLEYRKLNKLISTFGEKLPK-HIHPVTGRIHPSFNQIGAASGRMSCSNPNLQQIPRE----REFRRCFVAPEG 102 (324)
T ss_pred CChHHHHHHHHHHHhHHHHHHHHHHHH-HccCCCCceeeeEEecccceeehhhccCccccCCCC----cccceeEEcCCC
Confidence 357788999999999999999999986 455678999999997 89999999999999999973 479999999999
Q ss_pred CeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHH
Q 001207 867 NSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERR 946 (1123)
Q Consensus 867 ~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~ 946 (1123)
++||++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||.+++ ++++++|+
T Consensus 103 ~~lv~aDysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~-----------------------~v~~~~R~ 159 (324)
T cd08639 103 NKLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGKPIE-----------------------EITKEERQ 159 (324)
T ss_pred CEEEEechhhhHHHHHHHHhCCHHHHHHHhcCCCHhHHHHHHHhCCChh-----------------------hCCHHHHH
Confidence 9999999999999999999999999999999999999999999997543 45678999
Q ss_pred hhHHHhhhhhhCCChhhhhhhcC------CCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCC
Q 001207 947 KAKMLNFSIAYGKTPVGLARDWK------VSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIK 1020 (1123)
Q Consensus 947 ~AK~vnfGiiYG~G~~~LA~~lg------iS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~ 1020 (1123)
.||++|||++||||+.+|++.++ +|.+||++++++||..||+|+.|++.+. +++.|||+|++||||+++.
T Consensus 160 ~aK~~~fg~~YG~g~~~L~~~l~~~~g~~~s~~eA~~~~~~f~~~~p~v~~~~~~~~--a~~~g~v~Tl~GRrr~~~~-- 235 (324)
T cd08639 160 LAKAVNFGLIYGMSAKGLREYARTNYGVEMSLEEAEKFRESFFFFYKGILRWHHRLK--AKGPIEVRTLLGRRRVFEY-- 235 (324)
T ss_pred HhhhHHHHHHhCCchHHHHHHHhhhcCcCCCHHHHHHHHHHHHHhChhHHHHHHHHH--HhhcCeEECCCCCeecccc--
Confidence 99999999999999999999754 8999999999999999999999999765 6778999999999999842
Q ss_pred ccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCCC
Q 001207 1021 SLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPFN 1100 (1123)
Q Consensus 1021 s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~~ 1100 (1123)
.++|+|+|++||||||||+|.||+++++ .+...+++|+++|||||+||||++.+++++++|+++|+++..
T Consensus 236 --------~~~r~avN~~IQGsaADi~K~ami~i~~--~l~~~~~~lvl~VHDElv~ev~~~~~~~~~~~i~~~Me~a~~ 305 (324)
T cd08639 236 --------FTFTEALNYPIQGTGADILKLALALLVD--RLKDLDAKIVLCVHDEIVLEVPEDEAEEAKKILESSMEEAGK 305 (324)
T ss_pred --------hhhhhHhhhhhhhHHHHHHHHHHHHHHH--HHhcCCCeEEeeeceeeeeecCHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999999999999999998 455578999999999999999999999999999999999862
Q ss_pred CCCCcceeEEEeccccCChh
Q 001207 1101 GKNNLRVDLSVDAKCAQNWY 1120 (1123)
Q Consensus 1101 ~~~~L~VPL~vd~~iG~nW~ 1120 (1123)
...++|||.|+++||+||+
T Consensus 306 -~~~~~VPl~v~~~iG~sW~ 324 (324)
T cd08639 306 -RILKKVPVEVEVSISDSWA 324 (324)
T ss_pred -hcCCCCCeEEecccCCCCC
Confidence 2235899999999999996
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=7.2e-56 Score=497.33 Aligned_cols=250 Identities=21% Similarity=0.218 Sum_probs=227.0
Q ss_pred CCCCeeeecccc-cCcccc------ccccCCCcccCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhH
Q 001207 819 GKNGRVHCSLNI-NTETGR------LSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSM 891 (1123)
Q Consensus 819 ~~dGRIH~~~n~-~T~TGR------lSss~PNLQNIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~L 891 (1123)
..+||||+.+.+ ||+||| +|+++||.+|+|+ +||++|+|+|||+||+|||||||||| ||+|+|+.|
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 899999 8889999999875 89999999999999999999999998 999999999
Q ss_pred H-----HHH---------HcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhh
Q 001207 892 L-----DAF---------KAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAY 957 (1123)
Q Consensus 892 i-----~af---------~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiY 957 (1123)
+ .|| ..|.|||+.||+ +||+ .|+.||++|||++|
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---hhhhhhhcC--CCHHHHHHHHHHHHHhChhHHH-----------------------HHHHHHH-HHHhCCeEec
Q 001207 958 GKT---PVGLARDWK--VSVEEAKKTVDLWYNERQEVLT-----------------------WQEARKK-ESRIDNHVHT 1008 (1123)
Q Consensus 958 G~G---~~~LA~~lg--iS~~EAk~~i~~f~~~yP~Vk~-----------------------~~~~~~~-~A~~~GyV~T 1008 (1123)
|+| +++|+++++ +|.+||++++++||+.||+|+. |++.+.+ .|++.||++|
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 ccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcch-----
Q 001207 1009 LLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSES----- 1083 (1123)
Q Consensus 1009 l~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~~----- 1083 (1123)
++||+ ++|+++++|...+++ +|.|+|+|||||||||+|+|||.++..+...+..++|+|||||||+||||+++
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 999999999887877 99999999999999999999999998555446679999999999999999998
Q ss_pred -HHHHHHHHHHHHcCCCCCCCCc-ceeEEEe
Q 001207 1084 -AEVAKAIVVECMSKPFNGKNNL-RVDLSVD 1112 (1123)
Q Consensus 1084 -aeev~~~v~~~Me~a~~~~~~L-~VPL~vd 1112 (1123)
+.++..++.++|. +. .+.+ +||-.|-
T Consensus 373 lalqi~nlltram~-a~--~lg~~dlPqs~a 400 (425)
T cd08641 373 LALQITNLLTRAMF-AQ--KLGINDLPQSVA 400 (425)
T ss_pred HHHHHHHHHHHHHH-HH--HhccccCCcchh
Confidence 6788888889998 43 2223 5776653
No 14
>smart00482 POLAc DNA polymerase A domain.
Probab=100.00 E-value=9.4e-54 Score=455.11 Aligned_cols=206 Identities=42% Similarity=0.627 Sum_probs=194.6
Q ss_pred hhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCC
Q 001207 854 RYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPP 933 (1123)
Q Consensus 854 g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~ 933 (1123)
|.++|+||+|+||++||++||||||+|||||||+|+.|+++|++|.|+|+.+|+.+||.+++
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 45899999999999999999999999999999999999999999999999999999997654
Q ss_pred CCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHHHHhChhHHHHHHHHHHHHHhCCeEecccCCc
Q 001207 934 VPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYNERQEVLTWQEARKKESRIDNHVHTLLGRA 1013 (1123)
Q Consensus 934 v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRr 1013 (1123)
++++.+|+.||+++||++||||+.+|++++|+|.+||++++++|+++||+|++|++++.+.|+++|||+|++||+
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 456789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeeceEEEeCCcc
Q 001207 1014 RRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHDEVILEGPSE 1082 (1123)
Q Consensus 1014 r~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHDELv~EVp~~ 1082 (1123)
|++|.+++.+...++.++|+|+|++||||||||+|.||+++++.+...+++++|+++|||||+||||++
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 999999988888888899999999999999999999999999865544568899999999999999974
No 15
>PRK10829 ribonuclease D; Provisional
Probab=99.80 E-value=2.2e-18 Score=198.51 Aligned_cols=172 Identities=17% Similarity=0.145 Sum_probs=139.6
Q ss_pred CeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001207 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1123)
Q Consensus 344 ~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~e 423 (1123)
.|.+|+++++|.++++.+..+ +.+|||||+.+.+++.++++. +++. +++..+.||+....
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~---~~lalDtEf~~~~ty~~~l~L------iQl~--------~~~~~~LiD~l~~~--- 61 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAF---PAIALDTEFVRTRTYYPQLGL------IQLY--------DGEQLSLIDPLGIT--- 61 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcC---CeEEEecccccCccCCCceeE------EEEe--------cCCceEEEecCCcc---
Confidence 488999999999999998875 689999999999998877642 3333 23457888987542
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccccc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~ 502 (1123)
.+..|.++|+|+.+.||+|++.+|+.+|. .+|+.+ .++|||++|+++++-.. ++||..|+++ ++|++
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 579866 55899999999998653 3899999987 67654
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 001207 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMS 581 (1123)
Q Consensus 503 ~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~ 581 (1123)
+ .|+. +. .||..+|| ++.|+.||+.||.+++.||+.|.++|.+.+
T Consensus 130 --l-------------------dK~~---~~---sDW~~RPL-------s~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g 174 (373)
T PRK10829 130 --L-------------------DKSE---SR---TDWLARPL-------SERQCEYAAADVFYLLPIAAKLMAETEAAG 174 (373)
T ss_pred --c-------------------Cccc---cc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 1 1211 11 38999998 478999999999999999999999999753
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=99.78 E-value=4.1e-18 Score=174.07 Aligned_cols=173 Identities=30% Similarity=0.443 Sum_probs=130.7
Q ss_pred eEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhh
Q 001207 345 VMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDL 424 (1123)
Q Consensus 345 y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~ev 424 (1123)
|++|+|++++.++++.+... +.+|||+|+++++...... ++.++++..+ ..+++++.........
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 78999999999999999986 5899999999999854332 2356666653 2345555543321125
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccc-cc
Q 001207 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA-YQ 502 (1123)
Q Consensus 425 l~~Lk~~Led~~i~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg-~~ 502 (1123)
...|+++|+++.+.||+||++||+.+|.+ +|+.+.+ ++|||++++++++... +||++|+.+ +++ +.
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 6899999999999864 999999987 454 21
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCcccc-ccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 001207 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKIST-IAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLL 578 (1123)
Q Consensus 503 ~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~-~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~ 578 (1123)
+ .++ ... .+|. .+|+ ++.+..|||.||.++++||+.|.++|+
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 1466 5665 578999999999999999999999874
No 17
>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=5.5e-18 Score=176.37 Aligned_cols=182 Identities=33% Similarity=0.428 Sum_probs=132.7
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCC------CChhhhHhhhhhhhcCCCceEEE
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD------GGGRDLLNEFAPFFEDPSIKKVW 441 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~------~~~~evl~~Lk~~Led~~i~KV~ 441 (1123)
+.++||+|++|++++.+++++ +++..++ ...+|++... .....++..|+++|++..+.+|+
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 589999999999987766654 4444332 1145554321 12345667799999988778999
Q ss_pred eccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchh
Q 001207 442 HNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMK 521 (1123)
Q Consensus 442 HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k 521 (1123)
||++||+++|.++|+.+.+.++||++++|+++|... +++|++++.+ +++.. .+. +.
T Consensus 73 hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~---~~~l~~l~~~-------~l~~~-----~~~---------~~ 128 (193)
T cd06139 73 QNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRR---RHGLDDLAER-------YLGHK-----TIS---------FE 128 (193)
T ss_pred eccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC-----Ccc---------HH
Confidence 999999999999999988889999999999999762 3799999987 44332 011 12
Q ss_pred hhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHH
Q 001207 522 DIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEY 601 (1123)
Q Consensus 522 ~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~~~~~~~~~~~l~~Ly~~I 601 (1123)
.+++++. + . .+|...| ...+..||+.|+.++++|++.|.++|++. .++.++|++|
T Consensus 129 ~~~~k~~--~--~--~~~~~~~--------~~~~~~ya~~d~~~~~~l~~~l~~~l~~~-----------~~~~~l~~~i 183 (193)
T cd06139 129 DLVGKGK--K--Q--ITFDQVP--------LEKAAEYAAEDADITLRLYELLKPKLKEE-----------PGLLELYEEI 183 (193)
T ss_pred HHcCCCc--C--c--CCccccC--------HHHHHHHHHHHHHHHHHHHHHHHHHHhhh-----------hhHHHHHHHH
Confidence 2333321 1 0 1232222 24578899999999999999999999861 3789999999
Q ss_pred hcchHHHHHH
Q 001207 602 WQPFGEILVK 611 (1123)
Q Consensus 602 EmPLv~VLa~ 611 (1123)
||||++||++
T Consensus 184 E~Pl~~vL~~ 193 (193)
T cd06139 184 EMPLIPVLAE 193 (193)
T ss_pred hccHHHHhcC
Confidence 9999999973
No 18
>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=4.6e-18 Score=175.77 Aligned_cols=175 Identities=21% Similarity=0.267 Sum_probs=131.1
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHH
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFD 447 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led~~i~KV~HNaKfD 447 (1123)
..+++|+|+++.+++.++++| +++..+. ..+|++..+. ..+.+.|+++|+++++.|++||+|+|
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 2567764321 02456688999999999999999999
Q ss_pred HHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhccc
Q 001207 448 NHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRR 527 (1123)
Q Consensus 448 l~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~ 527 (1123)
+++|.++|+.+++.+||||||+||++|... +++|++++.+ |++.. ..+ ..++++++
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 55442 001 11223322
Q ss_pred ccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHH
Q 001207 528 KLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGE 607 (1123)
Q Consensus 528 k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~~~~~~~~~~~l~~Ly~~IEmPLv~ 607 (1123)
+ + +...+ .+.+..|+|.|+.++++|++.|.++|++ .+|++||++|||||++
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 3457889999999999999999999987 3799999999999999
Q ss_pred HHHH
Q 001207 608 ILVK 611 (1123)
Q Consensus 608 VLa~ 611 (1123)
||++
T Consensus 175 VL~~ 178 (178)
T cd06140 175 VLAE 178 (178)
T ss_pred HhcC
Confidence 9963
No 19
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=8.5e-18 Score=189.71 Aligned_cols=170 Identities=22% Similarity=0.250 Sum_probs=137.5
Q ss_pred ecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhh
Q 001207 348 VDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNE 427 (1123)
Q Consensus 348 V~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~ 427 (1123)
|++.+.+++++..+..+ ++||+||||.+..++.+++| .++++.++ ....||+... ....+.
T Consensus 1 i~~~~~l~~~~~~~~~~---~~iAiDTEf~r~~t~~p~Lc------LIQi~~~e--------~~~lIdpl~~--~~d~~~ 61 (361)
T COG0349 1 ITTGDLLAAACALLRGS---KAIAIDTEFMRLRTYYPRLC------LIQISDGE--------GASLIDPLAG--ILDLPP 61 (361)
T ss_pred CCchhHHHHHHHHhcCC---CceEEecccccccccCCceE------EEEEecCC--------CceEeccccc--ccccch
Confidence 46778889999998875 68999999999999999885 35555543 3567787642 246788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHc-CCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccccccccc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~r~-GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~ 506 (1123)
|..+|.|+++.||+|++.||+.+|.+. |+ .+.++|||+|||.+++... +|||++|+++ +++++ +
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 5567999999999999764 4999999987 66654 1
Q ss_pred CCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 001207 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSW 582 (1123)
Q Consensus 507 k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~ 582 (1123)
.|+. +. .||..+|| ++.|++||+.||.++++||..|..+|.+.+|
T Consensus 127 ------------------dK~~---q~---SDW~~RPL-------s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r 171 (361)
T COG0349 127 ------------------DKSE---QR---SDWLARPL-------SEAQLEYAAADVEYLLPLYDKLTEELAREGR 171 (361)
T ss_pred ------------------cccc---cc---cccccCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 1211 12 38999998 5789999999999999999999999998654
No 20
>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=99.76 E-value=1.9e-17 Score=191.13 Aligned_cols=169 Identities=18% Similarity=0.105 Sum_probs=135.6
Q ss_pred EecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHh
Q 001207 347 VVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLN 426 (1123)
Q Consensus 347 lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~ 426 (1123)
+|+++++|.++++.+..+ ++||||||+++.+++.+.++. +++ +++...++||+... ..++
T Consensus 1 ~I~t~~~l~~~~~~l~~~---~~ia~DtE~~~~~~y~~~l~L------iQi--------a~~~~~~liD~~~~---~~~~ 60 (367)
T TIGR01388 1 WITTDDELATVCEAVRTF---PFVALDTEFVRERTFWPQLGL------IQV--------ADGEQLALIDPLVI---IDWS 60 (367)
T ss_pred CcCCHHHHHHHHHHHhcC---CEEEEeccccCCCCCCCcceE------EEE--------eeCCeEEEEeCCCc---ccHH
Confidence 488999999999999885 699999999999988776642 333 33345788888643 2477
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhccccccccccccccccc
Q 001207 427 EFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (1123)
Q Consensus 427 ~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~ 506 (1123)
.|+++|+|+.+.||+|++++|+++|.+.|..+++.+|||++|+|++++... +||++|+++ +|++. +
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 899999999999999999999999988766666779999999999998753 799999987 56553 1
Q ss_pred CCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001207 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1123)
Q Consensus 507 k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~ 580 (1123)
.|+. +. .+|..+|+ ++.|..|||.||.+++.||+.|.++|++.
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 27877786 46799999999999999999999999875
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=99.66 E-value=9.2e-16 Score=157.57 Aligned_cols=156 Identities=21% Similarity=0.152 Sum_probs=118.8
Q ss_pred HHHHHHHHH-ccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCC-ceEEEEeCCCCChhhhHhhhhhh
Q 001207 354 AKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNG-KSCIWVDLLDGGGRDLLNEFAPF 431 (1123)
Q Consensus 354 L~~lv~~L~-~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~-~~~~~ID~~~~~~~evl~~Lk~~ 431 (1123)
|.++++.+. .. ++++||||+.+...+..+++ -+++. +. ..++.+|....+ ...+.|+++
T Consensus 2 l~~~~~~l~~~~---~~ig~D~E~~~~~~~~~~~~------liQl~--------~~~~~~~l~d~~~~~--~~~~~L~~l 62 (161)
T cd06129 2 LSSLCEDLSMDG---DVIAFDMEWPPGRRYYGEVA------LIQLC--------VSEEKCYLFDPLSLS--VDWQGLKML 62 (161)
T ss_pred HHHHHHHHhcCC---CEEEEECCccCCCCCCCceE------EEEEE--------ECCCCEEEEecccCc--cCHHHHHHH
Confidence 567888888 53 69999999998876544432 23333 23 447777876432 246778999
Q ss_pred hcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCC
Q 001207 432 FEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNT 510 (1123)
Q Consensus 432 Led~~i~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~ 510 (1123)
|+|+.+.||+|++++|+..|.+ +|+.+.+ +|||++++|++++.. ++||++|+++ +++.. +
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 ccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 511 DEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 511 ~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1123)
.|.. +. .+|..+|| ++.|..|||.||.++++||+.|.
T Consensus 124 --------------~K~~---~~---s~W~~rpL-------t~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 124 --------------DKSI---SC---ADWSYRPL-------TEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred --------------Cccc---ee---ccCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 1111 11 27999998 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=99.62 E-value=5.5e-15 Score=152.25 Aligned_cols=165 Identities=25% Similarity=0.306 Sum_probs=123.0
Q ss_pred ecCHHHHHHHHHHHH-ccccCceEEEeeccccccc--ccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhh
Q 001207 348 VDNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDV--KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDL 424 (1123)
Q Consensus 348 V~t~e~L~~lv~~L~-~a~~~~~VAfDTETtGLd~--~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~ev 424 (1123)
++++.+++++++.+. .. ..++||||+++... ..+.++ .++++ ++..++.+|.... ...
T Consensus 1 ~~~~~~~~~~~~~~~~~~---~~ig~D~E~~~~~~~~~~~~~~------liQl~--------~~~~~~l~~~~~~--~~~ 61 (170)
T cd06141 1 TDSAQDAEEAVKELLGKE---KVVGFDTEWRPSFRKGKRNKVA------LLQLA--------TESRCLLFQLAHM--DKL 61 (170)
T ss_pred CCCHHHHHHHHHHHhcCC---CEEEEeCccCCccCCCCCCCce------EEEEe--------cCCcEEEEEhhhh--hcc
Confidence 357888999999988 53 68999999998765 333321 23333 2344777777542 234
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccc
Q 001207 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1123)
Q Consensus 425 l~~Lk~~Led~~i~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~ 503 (1123)
.+.|+++|+++.+.||+|++++|+..|. .+|+.+.+ +|||++++|++++... ..+|++|+.. +++..
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 5678999999999999999999999997 68998876 4999999999998642 3799999987 55543
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 504 ~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1123)
+. | .|. .+. .+|..+|| ++.|+.|||.||.+++.||+.|.
T Consensus 130 -~~----------k-------~k~---~~~---s~W~~rpL-------t~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 130 -LS----------K-------PKK---VRC---SNWEARPL-------SKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred -cC----------C-------CCC---ccc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 11 0 011 111 28999998 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=99.61 E-value=6.2e-15 Score=156.16 Aligned_cols=172 Identities=19% Similarity=0.207 Sum_probs=123.3
Q ss_pred eEEecCHHHHHHHHHH--HHccccCceEEEeecccccccc--cCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCC
Q 001207 345 VMVVDNVSAAKKVVWM--LTNKYKHLVHACDTEVAKIDVK--QETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG 420 (1123)
Q Consensus 345 y~lV~t~e~L~~lv~~--L~~a~~~~~VAfDTETtGLd~~--~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~ 420 (1123)
+++|++++++.+++.. +... .+|+||+|+++.... ..++ .-+ ||++.+.++.+|....+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~---~vig~D~Ew~~~~~~~~~~~v------~Li--------Qiat~~~~~lid~~~~~ 63 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAG---RVVGIDSEWKPSFLGDSDPRV------AIL--------QLATEDEVFLLDLLALE 63 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccC---CEEEEECccCCCccCCCCCCc------eEE--------EEecCCCEEEEEchhcc
Confidence 5799999999999999 6664 699999999877653 2222 223 33333457778875432
Q ss_pred ---hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCC-----CCccchHHHHHHhcCCCCC-------CCCCCCH
Q 001207 421 ---GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKV-----SGFHADTMHMARLWDSSRR-------TEGGYSL 484 (1123)
Q Consensus 421 ---~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r-~GI~l-----~~~vfDTmIAAyLLdp~~~-------~~gs~sL 484 (1123)
.+...+.|+++|+|+.+.||+|++++|+..|++ +|+.. ...++||+.+++.+..... ....+||
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 HHHhhcccccccccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHH
Q 001207 485 EALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSI 564 (1123)
Q Consensus 485 d~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~ 564 (1123)
.+|+++ +|+.. + .|. .+. .+|..+|| ++.|+.|||.||.
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 999986 55543 1 111 111 28999998 4789999999999
Q ss_pred HHHHHHHHHH
Q 001207 565 NTLKLYKSLK 574 (1123)
Q Consensus 565 ~tlrL~e~L~ 574 (1123)
++++||+.|.
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=99.59 E-value=5.5e-15 Score=156.94 Aligned_cols=171 Identities=23% Similarity=0.285 Sum_probs=119.2
Q ss_pred HHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCC-ceEEEEeCCCCChhhhHhhhhhhhcCCC
Q 001207 358 VWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNG-KSCIWVDLLDGGGRDLLNEFAPFFEDPS 436 (1123)
Q Consensus 358 v~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~-~~~~~ID~~~~~~~evl~~Lk~~Led~~ 436 (1123)
+..|..+ +.+|||||+.++..+ +++ ..+++ ++. ...+.+|+...+.......|+++|+++.
T Consensus 4 ~~~l~~~---~~i~~D~E~~~~~~~-~~~------~LiQi--------a~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 4 IIHLKKQ---KVIGLDCEGVNLGRK-GKL------CLVQI--------ATRTGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhC---CEEEEEcccccCCCC-CCE------EEEEE--------eeCCCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 3445553 689999999877652 232 22333 333 4577788865422235678999999999
Q ss_pred ceEEEeccHHHHHHH-HHcCCCCCCccchHHHHHHhcCCCCC----CCCCCCHHHHhhcccccccccccccccccCCCCc
Q 001207 437 IKKVWHNYSFDNHVL-ENYGLKVSGFHADTMHMARLWDSSRR----TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTD 511 (1123)
Q Consensus 437 i~KV~HNaKfDl~vL-~r~GI~l~~~vfDTmIAAyLLdp~~~----~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~ 511 (1123)
+.||+||+++|+..| +++|+.+.+ +|||++|+|++++... ....+||++++.+ +++.. +
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 5999999999987532 0113699999987 55543 1
Q ss_pred cccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001207 512 EGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1123)
Q Consensus 512 eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~ 580 (1123)
+ +.. .+ .+.+ ..+. .+|..+|+ ++.|+.|||.||.+++.||..|...|.+.
T Consensus 130 ~----k~~--~~-~~~~-~~~~---s~W~~RPL-------t~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 130 S----LKE--DV-KKLM-REDP---KFWALRPL-------TEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred H----HHH--HH-HHHH-hcCc---hhhhcCCC-------CHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 0 100 00 0000 0111 38999998 47899999999999999999999999863
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=99.51 E-value=3.4e-13 Score=136.67 Aligned_cols=170 Identities=25% Similarity=0.233 Sum_probs=119.8
Q ss_pred eEEecCHHHHHHHHHHHH-ccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhh
Q 001207 345 VMVVDNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (1123)
Q Consensus 345 y~lV~t~e~L~~lv~~L~-~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~e 423 (1123)
+.+|++++++..+++.+. .. ..+++|+|+.+..++...++ +++++.+. . .+|+.... ....
T Consensus 1 ~~~i~~~~~~~~~~~~~~~~~---~~l~~~~e~~~~~~~~~~~~------~l~l~~~~-------~-~~~i~~~~-~~~~ 62 (172)
T smart00474 1 VRVVTDSETLEELLEKLRAAG---GEVALDTETTGLNSYSGKLV------LIQISVTG-------E-GAFIIDPL-ALGD 62 (172)
T ss_pred CEEecCHHHHHHHHHHHHhcC---CeEEEeccccCCccCCCCEE------EEEEeEcC-------C-ceEEEEec-cchh
Confidence 468889998888777775 32 47999999887776554443 34443211 1 34443211 1123
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~ 503 (1123)
....|+++|+++.+.+|+||+|+|+++|+++|+.+.+. ||||+|+||++|... .++|+.++.+ +++..
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 35668999999989999999999999998899998875 999999999999753 4799999986 44432
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKL 577 (1123)
Q Consensus 504 ~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL 577 (1123)
.++ .++++ +|..+|+ ...+..||+.||.++++|++.|.++|
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 111 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=99.46 E-value=1.8e-12 Score=133.49 Aligned_cols=167 Identities=23% Similarity=0.259 Sum_probs=117.6
Q ss_pred HHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC
Q 001207 355 KKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED 434 (1123)
Q Consensus 355 ~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led 434 (1123)
.++++.+.. .+.+++|+|+.+.+++.+.++ ++++..+ +..+|++... . .+.+.|+++|++
T Consensus 3 ~~~~~~l~~---~~~l~~~~e~~~~~~~~~~~~------~i~l~~~--------~~~~~i~~~~--~-~~~~~l~~ll~~ 62 (178)
T cd06142 3 EDLCERLAS---AGVIAVDTEFMRLNTYYPRLC------LIQISTG--------GEVYLIDPLA--I-GDLSPLKELLAD 62 (178)
T ss_pred HHHHHHHhc---CCeEEEECCccCCCcCCCceE------EEEEeeC--------CCEEEEeCCC--c-ccHHHHHHHHcC
Confidence 444544433 247999999877765544443 3444322 1256776431 1 245668899999
Q ss_pred CCceEEEeccHHHHHHHHHc-CCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccc
Q 001207 435 PSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEG 513 (1123)
Q Consensus 435 ~~i~KV~HNaKfDl~vL~r~-GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~ee 513 (1123)
+.+.||+||+|+|+++|.++ |+. .+.+|||++|+||++|... ++|++++.+ |++.. + .. ++
T Consensus 63 ~~i~kv~~d~K~~~~~L~~~~gi~-~~~~~D~~laayLl~p~~~----~~l~~l~~~-------~l~~~--~---~~-~~ 124 (178)
T cd06142 63 PNIVKVFHAAREDLELLKRDFGIL-PQNLFDTQIAARLLGLGDS----VGLAALVEE-------LLGVE--L---DK-GE 124 (178)
T ss_pred CCceEEEeccHHHHHHHHHHcCCC-CCCcccHHHHHHHhCCCcc----ccHHHHHHH-------HhCCC--C---Cc-cc
Confidence 99999999999999999887 998 6778999999999999753 699999987 45432 0 00 00
Q ss_pred cccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCch
Q 001207 514 FMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKS 593 (1123)
Q Consensus 514 l~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~~~~~~~~~~~ 593 (1123)
.++ .|..+|++ ..+..|++.||.++++|++.|.++|++. +
T Consensus 125 ---------~~~------------~w~~~~l~-------~~~~~yaa~~a~~l~~L~~~l~~~L~e~------------~ 164 (178)
T cd06142 125 ---------QRS------------DWSKRPLT-------DEQLEYAALDVRYLLPLYEKLKEELEEE------------G 164 (178)
T ss_pred ---------ccc------------cCCCCCCC-------HHHHHHHHHhHHHHHHHHHHHHHHHHHc------------C
Confidence 111 24444442 4578899999999999999999999873 6
Q ss_pred HHHHHH
Q 001207 594 MFDFYQ 599 (1123)
Q Consensus 594 l~~Ly~ 599 (1123)
+.+||.
T Consensus 165 l~~L~~ 170 (178)
T cd06142 165 RLEWAE 170 (178)
T ss_pred cHHHHH
Confidence 777775
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=99.38 E-value=1e-11 Score=131.07 Aligned_cols=172 Identities=27% Similarity=0.263 Sum_probs=123.3
Q ss_pred CCeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChh
Q 001207 343 SNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGR 422 (1123)
Q Consensus 343 ~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~ 422 (1123)
.+|.+|++++++..+++.+... +.+++|+|+....++.+.++ ++++..+. ..+|++... ..
T Consensus 3 ~~~~~i~~~~~l~~~~~~l~~~---~~l~~~~e~~~~~~~~~~~~------~l~l~~~~--------~~~~i~~l~--~~ 63 (192)
T cd06147 3 TPLTFVDTEEKLEELVEKLKNC---KEIAVDLEHHSYRSYLGFTC------LMQISTRE--------EDYIVDTLK--LR 63 (192)
T ss_pred CCcEEECCHHHHHHHHHHHhcC---CeEEEEeEecCCccCCCceE------EEEEecCC--------CcEEEEecc--cc
Confidence 4678997778888877766442 47999998877766555554 45544322 246665321 12
Q ss_pred hhHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccc
Q 001207 423 DLLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAY 501 (1123)
Q Consensus 423 evl~~Lk~~Led~~i~KV~HNaKfDl~vL~-r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~ 501 (1123)
.....|+++|+++.+.||+||+|.|+++|. ++|+.+.+. ||||||+||++|. . ++|+.|+.+ |++.
T Consensus 64 ~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~-fD~~laaYLL~p~-~----~~l~~l~~~-------yl~~ 130 (192)
T cd06147 64 DDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNL-FDTGQAARVLNLP-R----HSLAYLLQK-------YCNV 130 (192)
T ss_pred cchHHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCch-HHHHHHHHHhCCC-c----ccHHHHHHH-------HhCC
Confidence 345568899999999999999999999998 899998887 9999999999997 5 599999987 4543
Q ss_pred cccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001207 502 QKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (1123)
Q Consensus 502 ~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e~ 580 (1123)
. + + | + .+. .+|...|+ ...+..|++.++.++++|++.|.++|+++
T Consensus 131 ~--------~-------~------k-~--~~~---~~~~~~~l-------~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 131 D--------A-------D------K-K--YQL---ADWRIRPL-------PEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred C--------c-------c------h-h--hhc---cccccCCC-------CHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 2 0 0 1 0 011 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=99.33 E-value=2.5e-11 Score=120.70 Aligned_cols=153 Identities=24% Similarity=0.321 Sum_probs=104.6
Q ss_pred eEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHH
Q 001207 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDN 448 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led~~i~KV~HNaKfDl 448 (1123)
.+++|+|+.+.+++..++ .++++..+ ...+|++.... ...+.+.|.++|+++.+.+|+||+++|+
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 588999988777544444 34555432 11455543211 1346667899999998899999999999
Q ss_pred HHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhcccc
Q 001207 449 HVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRK 528 (1123)
Q Consensus 449 ~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k 528 (1123)
++|.++|+...+.++||++|+|+++|... +++|++|+++ |++.. + .. ...+.+++.
T Consensus 67 ~~L~~~~~~~~~~~~D~~~~ayll~~~~~---~~~l~~l~~~-------~l~~~--~---~~---------~~~~~~~~~ 122 (155)
T cd00007 67 VVLARDGIELPGNIFDTMLAAYLLNPGEG---SHSLDDLAKE-------YLGIE--L---DK---------DEQIYGKGA 122 (155)
T ss_pred HHHHHCCCCCCCCcccHHHHHHHhCCCCC---cCCHHHHHHH-------HcCCC--C---cc---------HHHHhcCCC
Confidence 99998888777789999999999999762 3799999987 44332 0 00 011122110
Q ss_pred cccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 529 LKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKK 576 (1123)
Q Consensus 529 ~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~k 576 (1123)
.|..+|+ ...+..|++.|+.++++|++.|.++
T Consensus 123 ---------~~~~~~~-------~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 123 ---------KTFARPL-------SEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred ---------CccccCC-------HHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 0111222 4568899999999999999998765
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=121.90 Aligned_cols=149 Identities=24% Similarity=0.281 Sum_probs=102.5
Q ss_pred eEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHH
Q 001207 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDN 448 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led~~i~KV~HNaKfDl 448 (1123)
++++|+|+.+..++.++++ +++++.++ +..+|++..+. ......|+++|+++.+.||+||+|+|+
T Consensus 1 ~~~~~~e~~~~~~~~~~~~------~l~l~~~~-------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~kv~~d~K~~~ 65 (150)
T cd09018 1 VFAFDTETDSLDNISANLV------LIQLAIEP-------GVAALIPVAHD--YLALELLKPLLEDEKALKVGQNLKYDR 65 (150)
T ss_pred CEEEEeecCCCCCCCceEE------EEEEEcCC-------CcEEEEEcCCc--ccCHHHHHHHhcCCCCceeeecHHHHH
Confidence 3789998877776555543 45554321 12566664321 112456889999999999999999999
Q ss_pred HHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhcccc
Q 001207 449 HVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRK 528 (1123)
Q Consensus 449 ~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k 528 (1123)
+.|.++|+.+.+.+||||+|+||++|... +++|++|+.+ |++.. ++. ..+++++
T Consensus 66 ~~L~~~~~~~~~~~~D~~laayLl~p~~~---~~~l~~l~~~-------~l~~~-----------~~~---~~~~~~~-- 119 (150)
T cd09018 66 GILLNYFIELRGIAFDTMLEAYILNSVAG---RWDMDSLVER-------WLGHK-----------LIK---FESIAGK-- 119 (150)
T ss_pred HHHHHcCCccCCcchhHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC-----------ccc---HHHhcCC--
Confidence 99999999888889999999999999752 2699999987 44432 000 0112222
Q ss_pred cccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 529 LKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 529 ~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~ 574 (1123)
.|..+++ ...+..|++.|+.++++|++.|.
T Consensus 120 ---------~~~~~~~-------~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 120 ---------LWFNQPL-------TEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred ---------CCcccCC-------HHHHHHHHHHHHHHHHHHHHHhc
Confidence 1311222 35688999999999999999874
No 30
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=99.10 E-value=1.7e-10 Score=138.45 Aligned_cols=244 Identities=21% Similarity=0.239 Sum_probs=145.1
Q ss_pred CCeeeecccc-cCccccccccCCCcc--cCCccccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcC---c-----h
Q 001207 821 NGRVHCSLNI-NTETGRLSARRPNLQ--NQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN---C-----K 889 (1123)
Q Consensus 821 dGRIH~~~n~-~T~TGRlSss~PNLQ--NIP~~~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~---D-----~ 889 (1123)
.|-|-+..-. ||.|-|--...=+.- .-| +.-|.+||.+..+|||+.||+||-...|+-|.|.|+. | .
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 3555555554 677766322111111 112 3457899999999999999999999999999988874 1 1
Q ss_pred h-----HHHHHHcCCchhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhh-
Q 001207 890 S-----MLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVG- 963 (1123)
Q Consensus 890 ~-----Li~af~~G~DIH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~- 963 (1123)
+ |...-..|.|+|+.||..+ +..|..||.+|||-|||.|..-
T Consensus 764 a~gwM~Lag~ks~gtdlhs~ta~~l--------------------------------giSr~hakv~Ny~riygag~~fa 811 (1075)
T KOG3657|consen 764 AFGWMTLAGSKSDGTDLHSKTASQL--------------------------------GISRNHAKVFNYARIYGAGQTFA 811 (1075)
T ss_pred hhhhhhhcCccccCchHhHhhhhhc--------------------------------cccHhhhhhccHHHHhcCCcchH
Confidence 1 1111235789999998743 2469999999999999999432
Q ss_pred --hhhhcC--CCHHHHHHHHHHHHHhChhHH-HHHHHHHHHH---------------------------Hh---CCeEec
Q 001207 964 --LARDWK--VSVEEAKKTVDLWYNERQEVL-TWQEARKKES---------------------------RI---DNHVHT 1008 (1123)
Q Consensus 964 --LA~~lg--iS~~EAk~~i~~f~~~yP~Vk-~~~~~~~~~A---------------------------~~---~GyV~T 1008 (1123)
|-.+.+ .+-+||+..-...|..-.|-+ ..+....... ++ .|+-..
T Consensus 812 ~~ll~~fnp~l~~~Ea~~~A~~l~~~tkG~~~~rlk~e~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~gg~es~ 891 (1075)
T KOG3657|consen 812 EKLLMRFNPSLTQSEAKSKASQLFKLTKGDRAKRLKVEVRMVENSLVCKILTIDGIYLIYSIYENEVEPRRLWVGGTESS 891 (1075)
T ss_pred HHhHHhhCCCCchHHHHHHHHHHHHhhcCceeeehHhHHHHhhhhhhchhhhhhhhhhhhhhhhcccchhhhccCchHHH
Confidence 222223 577888766666666555421 1111110000 00 011001
Q ss_pred cc--------CCcccCCCCCccC-hh-----h-hhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhhccCCceEEEEeec
Q 001207 1009 LL--------GRARRFPAIKSLT-RS-----Q-RNHIERAAINTPVQGSAADVAMCAMLEISKNARLKELGWKLLLQVHD 1073 (1123)
Q Consensus 1009 l~--------GRrr~lp~~~s~n-~~-----~-r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l~~~g~~llLqVHD 1073 (1123)
+| +...+.|-+...- .. . -..-.+..+|++||+||-|.+.+-++.+...+.--+..+|+++.|||
T Consensus 892 ~fn~lesia~~~~prtpvlgc~is~sl~~~~~~~~~f~~srinwvvqssavd~lhlllvsm~wl~~~y~i~~rfcisihd 971 (1075)
T KOG3657|consen 892 MFNKLESIATAHDPRTPVLGCQISRSLEKLPEGEPKFLPSRINWVVQSSAVDFLHLLLVSMQWLCDTYKIDARFCISIHD 971 (1075)
T ss_pred HHHHHHHHhhccCCCCCeeccchhhhhcccccCCcccccceeeEEeeccchhHHHHHHHHHHHHHhhcccceEEEEEehH
Confidence 11 1111122211100 00 0 01124568999999999999999998876433333568899999999
Q ss_pred eEEEeCCcchHHHHH--HHHHHHHcCC
Q 001207 1074 EVILEGPSESAEVAK--AIVVECMSKP 1098 (1123)
Q Consensus 1074 ELv~EVp~~~aeev~--~~v~~~Me~a 1098 (1123)
||-+-|.++.+-.++ -.|.++|+.+
T Consensus 972 evrylv~e~d~~raalalqisnl~tr~ 998 (1075)
T KOG3657|consen 972 EVRYLVKEEDAPRAALALQISNLLTRA 998 (1075)
T ss_pred hHHHHhcccccHHHHHHHHHHHHHHHH
Confidence 999999988754332 2234555544
No 31
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=98.87 E-value=2.6e-09 Score=125.47 Aligned_cols=176 Identities=22% Similarity=0.242 Sum_probs=137.8
Q ss_pred hhhccCCCeEEecCHHHHHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeC
Q 001207 337 KLASFYSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDL 416 (1123)
Q Consensus 337 ~l~~~p~~y~lV~t~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~ 416 (1123)
+|.-.| +.+|++..+|.++.+.|... ..+|+|+|+.....|. |. .|+ +||.+.++.+.||.
T Consensus 187 ~le~T~--~~~I~t~~el~~l~~~l~~~---~Efavdlehhsyrsf~----gl---tcl-------mqISTr~ed~iIDt 247 (687)
T KOG2206|consen 187 PLEITP--KVWICTLGELEALPEILDSV---IEFAVDLEHHSYRSFL----GL---TCL-------MQISTRTEDFIIDT 247 (687)
T ss_pred cccccC--ceeeechHHHHHHHHHHhhh---hhhhhhccccchhhhc----Cc---eeE-------EEeeccchhheehh
Confidence 444455 88999999999999988874 4799999999887773 31 122 56666777888887
Q ss_pred CCCChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccc
Q 001207 417 LDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMS 495 (1123)
Q Consensus 417 ~~~~~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~ 495 (1123)
... .+.+..|.+.|.||.+.||+|.+..|+.+|++ +||.+.+ .|||..|+++|+-.+ ++|..|.+.
T Consensus 248 ~~l--~~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvn-Lfdt~~a~r~L~~~r-----~sL~~ll~~----- 314 (687)
T KOG2206|consen 248 FKL--RDHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVN-LFDTIQASRLLGLPR-----PSLAYLLEC----- 314 (687)
T ss_pred HHH--HHHHHHhhhhccCCCeEEEEecCccchhhhhccceEEEEe-chhhHHHHHHhCCCc-----ccHHHHHHH-----
Confidence 642 45667889999999999999999999999987 8998766 799999999999764 799988876
Q ss_pred cccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 496 EDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKK 575 (1123)
Q Consensus 496 ~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~ 575 (1123)
+.++. . .|. + |. .+|.++|| ++.+..||-.|+.+++-+|+.|..
T Consensus 315 --~~~v~------------~---------nk~-y--ql---adwR~rpL-------p~~Mv~yar~dthyllyiyD~lr~ 358 (687)
T KOG2206|consen 315 --VCGVL------------T---------NKK-Y--QL---ADWRIRPL-------PEEMVRYAREDTHYLLYIYDVLRK 358 (687)
T ss_pred --HHhhh------------h---------hhh-h--hh---chhccccC-------cHHHHHHHhhcchhHHHHHHHHHH
Confidence 33332 0 010 1 11 28999998 578999999999999999999998
Q ss_pred HHhhc
Q 001207 576 KLLEM 580 (1123)
Q Consensus 576 kL~e~ 580 (1123)
+|.+.
T Consensus 359 el~~~ 363 (687)
T KOG2206|consen 359 ELKRL 363 (687)
T ss_pred HHHHH
Confidence 88764
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=98.83 E-value=5e-08 Score=98.74 Aligned_cols=63 Identities=32% Similarity=0.492 Sum_probs=56.2
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 425 l~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
...|+++|++..+.|++||+|+++++|.++|+.+.+.+||||||+|||+|... +++|++|+.+
T Consensus 42 ~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~---~~~l~~la~~ 104 (151)
T cd06128 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAG---RHDMDSLAER 104 (151)
T ss_pred HHHHHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCC---CCCHHHHHHH
Confidence 44588899998889999999999999999999999889999999999999753 2599999987
No 33
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=98.72 E-value=1.9e-08 Score=125.40 Aligned_cols=116 Identities=22% Similarity=0.282 Sum_probs=84.9
Q ss_pred CceEEEeecccccccccCccccCcceEEEEee-----------eCCCcccCCCce---EEEEeCC--CCChhhhHhhhhh
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIY-----------SGPEADFGNGKS---CIWVDLL--DGGGRDLLNEFAP 430 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~-----------~~~~I~I~~~~~---~~~ID~~--~~~~~evl~~Lk~ 430 (1123)
+.+|+||.|||||++..+.|+++| +.-+. .+|+-|++...+ .+--+.+ +.+.+++++.|+.
T Consensus 421 atyVVfDiETTGLs~~~d~iIE~a---AvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~ 497 (1444)
T COG2176 421 ATYVVFDIETTGLSPVYDEIIEIA---AVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFRE 497 (1444)
T ss_pred ccEEEEEeecCCcCcccchhhhhe---eeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHHH
Confidence 369999999999999999998733 33333 334444442111 0100111 1235789999999
Q ss_pred hhcCCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 431 FFEDPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 431 ~Led~~i~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
|++|. ..|+||+.||+.+|. ++|+. +.++++||+-+|+-|+|..+ +|+|..||.+
T Consensus 498 ~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~k---sh~Lg~l~kk 557 (1444)
T COG2176 498 FIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFK---SHRLGTLCKK 557 (1444)
T ss_pred HhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhh---hcchHHHHHH
Confidence 99886 589999999999995 35654 56889999999999999876 7999999986
No 34
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.62 E-value=1.5e-07 Score=102.92 Aligned_cols=115 Identities=21% Similarity=0.211 Sum_probs=69.6
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------CC----------ChhhhHh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG----------GGRDLLN 426 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~~----------~~~evl~ 426 (1123)
.+++||+||||+++..++||. +++....+.+..+. ....++++. ++ +..+++.
T Consensus 7 ~~vv~D~ETTGl~p~~d~Iie----ig~v~v~~~g~~~~--~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~ 80 (232)
T PRK07942 7 PLAAFDLETTGVDPETARIVT----AALVVVDADGEVVE--SREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLA 80 (232)
T ss_pred cEEEEEeccCCCCCCCCeeEE----EEEEEEeCCCcccc--ceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHH
Confidence 589999999999998888876 22221111111010 011233221 01 1123444
Q ss_pred hhhhhhcC---CCceEEEeccHHHHHHHH----HcCCCC--CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 427 EFAPFFED---PSIKKVWHNYSFDNHVLE----NYGLKV--SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 427 ~Lk~~Led---~~i~KV~HNaKfDl~vL~----r~GI~l--~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
.+.+++.+ ....+|+||+.||+.+|. ++|+.. ..+++||+.+++.+.+... ++++|++|++.
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 45544421 234679999999999985 456542 3568999999987776432 36899999975
No 35
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.58 E-value=5.4e-07 Score=99.13 Aligned_cols=112 Identities=20% Similarity=0.242 Sum_probs=74.0
Q ss_pred ceEEEeecccccccc-cCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------C---------CChhhhHh
Q 001207 368 LVHACDTEVAKIDVK-QETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------D---------GGGRDLLN 426 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~-~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~---------~~~~evl~ 426 (1123)
.+++|||||||+++. .++||.+| ++.+..+ ...+ ..-..|+.+. + ....+++.
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 589999999999997 68888733 3333211 0000 0112233321 0 11346777
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCC-----CccchHHHHHHhcCCCCCCCCCCCHHHHhhcc
Q 001207 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-----GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (1123)
Q Consensus 427 ~Lk~~Led~~i~KV~HNaKfDl~vL~r----~GI~l~-----~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~ 491 (1123)
.|.+|+++. .+|+||+.||+.+|.+ +|..++ ..++||+.+++.+.|.. .++|++|+.+|
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 554332 34899999999888865 48999999863
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=4.9e-07 Score=98.55 Aligned_cols=111 Identities=26% Similarity=0.274 Sum_probs=72.7
Q ss_pred eEEEeeccccccccc-CccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------C---------CChhhhHhh
Q 001207 369 VHACDTEVAKIDVKQ-ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------D---------GGGRDLLNE 427 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~-d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~---------~~~~evl~~ 427 (1123)
+|+|||||||+++.. ++||++| ++.+..+. ..+ ..-..|+.+. + .+..+++..
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 689999999999975 7887633 23222110 000 0112223221 0 123467788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----HcCC--C-CC--CccchHHHHHHhcCCCCCCCCCCCHHHHhhcc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NYGL--K-VS--GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~----r~GI--~-l~--~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~ 491 (1123)
|.+|+++. ..|+||+.||+.+|. ++|. . +. ..++||+.+++.+.|.. +++|++|+++|
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 88898764 479999999999985 3562 2 22 46899999999888865 48999999863
No 37
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.49 E-value=1.9e-06 Score=94.79 Aligned_cols=122 Identities=17% Similarity=0.140 Sum_probs=72.8
Q ss_pred CceEEEeecccccccccCccccCcceE----------EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhh
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGEVI----------CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPF 431 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~ii----------~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~ 431 (1123)
..+++||+||||+++..++||..|-+. .+....+|+.+|+.....+. | +.. +.+..+++..|.++
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~~~ 126 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHHHH
Confidence 369999999999999989988733100 01111122222221100000 0 000 01245677788888
Q ss_pred hcCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHHhcCCCC--------C--CCCCCCHHHHhhc
Q 001207 432 FEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSR--------R--TEGGYSLEALTGD 490 (1123)
Q Consensus 432 Led~~i~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAyLLdp~~--------~--~~gs~sLd~La~~ 490 (1123)
+.+. ..|+||+.||+.+|.+ .|..+..+++||+..++-+.+.. . ..++++|++++.+
T Consensus 127 ~~~~--~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 198 (239)
T PRK09146 127 LAGK--VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR 198 (239)
T ss_pred hCCC--EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH
Confidence 7653 5799999999999854 35556667899999988665432 0 0135788888875
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.47 E-value=2.4e-06 Score=97.61 Aligned_cols=113 Identities=17% Similarity=0.114 Sum_probs=74.8
Q ss_pred CceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeC---------CCC---------ChhhhHhhh
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDL---------LDG---------GGRDLLNEF 428 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~---------~~~---------~~~evl~~L 428 (1123)
..+++||+||||+++..++||.+| ++.+.. .+..+ .....++.+ .++ ...+++..|
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIg---av~v~~-~g~i~--~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLA---VLGLDA-DGNVE--QSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEE---EEEEEC-Cceee--eEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 369999999999999888888632 222211 11000 000112211 111 135677888
Q ss_pred hhhhcCCCceEEEeccHHHHHHHHH----cCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 429 APFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 429 k~~Led~~i~KV~HNaKfDl~vL~r----~GI~l~-~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+++. ..|+||+.||+.+|.+ +|+.++ +.++||+..++.+.+... +|+|++|++.
T Consensus 89 ~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~---~~kL~~l~~~ 150 (313)
T PRK06063 89 AELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLP---NLRLETLAAH 150 (313)
T ss_pred HHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCC---CCCHHHHHHH
Confidence 8888764 5899999999999853 576544 458999999998776544 6999999975
No 39
>PRK07740 hypothetical protein; Provisional
Probab=98.46 E-value=3.2e-06 Score=93.36 Aligned_cols=111 Identities=18% Similarity=0.192 Sum_probs=73.7
Q ss_pred ceEEEeeccccccccc-CccccCcceEEEEee------------eCCCcccCCCceEEEEeCCC---------CChhhhH
Q 001207 368 LVHACDTEVAKIDVKQ-ETPVDHGEVICFSIY------------SGPEADFGNGKSCIWVDLLD---------GGGRDLL 425 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~-d~Ivg~g~ii~~sl~------------~~~~I~I~~~~~~~~ID~~~---------~~~~evl 425 (1123)
.+|+||+||||+++.. ++|+..| ++.+. .+|..+++... . ...+ .+..+++
T Consensus 60 ~~vv~D~ETTGl~p~~~deIIeIg---aV~~~~~~i~~~~f~~lv~P~~~i~~~~--~--~ltGIt~e~l~~ap~~~evl 132 (244)
T PRK07740 60 PFVVFDLETTGFSPQQGDEILSIG---AVKTKGGEVETDTFYSLVKPKRPIPEHI--L--ELTGITAEDVAFAPPLAEVL 132 (244)
T ss_pred CEEEEEEeCCCCCCCCCCeEEEEE---EEEEECCEEEEEEEEEEeCcCCCCChhh--e--eccCCCHHHHhCCCCHHHHH
Confidence 6899999999999876 6777632 22221 12222221100 0 0011 1245677
Q ss_pred hhhhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 426 NEFAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 426 ~~Lk~~Led~~i~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|.+|+++. ..|+||+.||+.+|.+ .+..+...++||+.+++.+.|... +++|++++..
T Consensus 133 ~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~---~~sL~~l~~~ 197 (244)
T PRK07740 133 HRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD---FPTLDDALAY 197 (244)
T ss_pred HHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC---CCCHHHHHHH
Confidence 7888888664 5899999999999854 344555678999999998877643 6999999974
No 40
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.46 E-value=6.7e-07 Score=102.83 Aligned_cols=112 Identities=11% Similarity=0.081 Sum_probs=76.5
Q ss_pred ceEEEeecccccccccCccccCcceEEEEee------------eCCCcccCCCceEEEEeC-----C--CCChhhhHhhh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIY------------SGPEADFGNGKSCIWVDL-----L--DGGGRDLLNEF 428 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~------------~~~~I~I~~~~~~~~ID~-----~--~~~~~evl~~L 428 (1123)
.+++||+||||+++..++||.+| ++.+. .+|..+++. ..+-- + .....++++.|
T Consensus 47 ~fVvlDiETTGLdp~~drIIeIg---AV~i~~~g~ive~f~tLVnP~~~~~p----~~LHGIT~e~La~AP~f~eVl~el 119 (377)
T PRK05601 47 PFVAVSIQTSGIHPSTSRLITID---AVTLTADGEEVEHFHAVLNPGEDPGP----FHLHGLSAEEFAQGKRFSQILKPL 119 (377)
T ss_pred CEEEEEEECCCCCCCCCeEEEEE---EEEEEcCCEEEEEEEEEECcCCCCCC----ccccCCCHHHHhcCCCHHHHHHHH
Confidence 69999999999999999887622 22222 222211110 00000 0 01256788899
Q ss_pred hhhhcCCCceEEEeccHHHHHHHHH----c----------------------------CCCCCCccchHHHHHHhcCCCC
Q 001207 429 APFFEDPSIKKVWHNYSFDNHVLEN----Y----------------------------GLKVSGFHADTMHMARLWDSSR 476 (1123)
Q Consensus 429 k~~Led~~i~KV~HNaKfDl~vL~r----~----------------------------GI~l~~~vfDTmIAAyLLdp~~ 476 (1123)
.+|+++. .+|+||+.||+.||.+ . ++.+++.++||+-.++.+.|..
T Consensus 120 ~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l 197 (377)
T PRK05601 120 DRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVAL 197 (377)
T ss_pred HHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCC
Confidence 9999764 5899999999999853 1 2344456899999999999876
Q ss_pred CCCCCCCHHHHhhcc
Q 001207 477 RTEGGYSLEALTGDR 491 (1123)
Q Consensus 477 ~~~gs~sLd~La~~~ 491 (1123)
. +|.|..|+.+|
T Consensus 198 ~---~~rL~~La~~l 209 (377)
T PRK05601 198 D---DIRIRGVAHTL 209 (377)
T ss_pred C---CCCHHHHHHHh
Confidence 5 69999999863
No 41
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.42 E-value=2.5e-06 Score=94.53 Aligned_cols=118 Identities=24% Similarity=0.305 Sum_probs=74.0
Q ss_pred ceEEEeecccccccccCccccCcceE--------EEEeeeCCCcccCCCceEEE-E---eCCC-CChhhhHhhhhhhhcC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVI--------CFSIYSGPEADFGNGKSCIW-V---DLLD-GGGRDLLNEFAPFFED 434 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii--------~~sl~~~~~I~I~~~~~~~~-I---D~~~-~~~~evl~~Lk~~Led 434 (1123)
.+|+||+||||+++..++||++|-|. .+....+|+.+|+.....+. | +..+ ....++++.+.+++.+
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 68999999999999888888732100 11112233333331110000 0 0000 1235677788888866
Q ss_pred CCceEEEeccHHHHHHHH----HcCCCCC---CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 435 PSIKKVWHNYSFDNHVLE----NYGLKVS---GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 435 ~~i~KV~HNaKfDl~vL~----r~GI~l~---~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
.. .+|+||+.||+.+|. ++|+... ..++||+-.++.+.+.. +++|+.|+..
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 589999999999985 3566543 45899999999865432 4899999975
No 42
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=98.36 E-value=3.8e-06 Score=91.94 Aligned_cols=119 Identities=20% Similarity=0.207 Sum_probs=74.8
Q ss_pred ceEEEeecccccccccCccccCcce-----EEEEeeeCCCcccCCCceEEE-E--e-CCC-CChhhhHhhhhhhhcCCCc
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEV-----ICFSIYSGPEADFGNGKSCIW-V--D-LLD-GGGRDLLNEFAPFFEDPSI 437 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~i-----i~~sl~~~~~I~I~~~~~~~~-I--D-~~~-~~~~evl~~Lk~~Led~~i 437 (1123)
.+++|||||||+++..++||+.|-+ ..+....+|+.+|+.....+. | + ..+ ....++++.|.+|+.+. .
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 5899999999999988888763210 012222234433332110000 0 0 000 12346677888888653 3
Q ss_pred eEEEec-cHHHHHHHH----HcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 438 KKVWHN-YSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 438 ~KV~HN-aKfDl~vL~----r~GI~l~-~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+|| +.||+.+|. ++|+... ..++||+-.++.+.|... .++|..|+..
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 4676643 468999999887777543 5899999875
No 43
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.35 E-value=2.1e-06 Score=109.17 Aligned_cols=117 Identities=20% Similarity=0.276 Sum_probs=77.8
Q ss_pred ceEEEeecccccccccCccccCc-------ceE-EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHG-------EVI-CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFED 434 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g-------~ii-~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Led 434 (1123)
.+++||+||||+++ .++||.+| +++ .++...+|+.+|+.....+. | +.. ..+..++++.|.+++++
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 68999999999987 47887633 111 12222334333331100000 0 000 01245778888889876
Q ss_pred CCceEEEeccHHHHHHHHH----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 435 PSIKKVWHNYSFDNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 435 ~~i~KV~HNaKfDl~vL~r----~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
. ..|+||+.||+.+|.+ .|..+.++++||+..++.+.|... +|+|++|+..
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 5899999999999964 577777788999999998888654 6999999975
No 44
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.33 E-value=3.3e-06 Score=96.41 Aligned_cols=119 Identities=20% Similarity=0.230 Sum_probs=76.2
Q ss_pred CceEEEeecccccccccCccccCcc-------eE-EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhc
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGE-------VI-CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFE 433 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~-------ii-~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Le 433 (1123)
..+|+||+||||+++..++|+.+|- ++ .+....+|..+++.....+. | +.. ..+..++++.|..|+.
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 3589999999999998888876331 00 11122223333321100000 0 000 0124567888888887
Q ss_pred CCCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 434 DPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 434 d~~i~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+. ..|+||+.||+.+|.+ +|+. +.++++||+..++.+.+... +++|++|++.
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 4699999999999864 5764 44678999998887777654 5899999974
No 45
>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=98.31 E-value=4.7e-06 Score=89.29 Aligned_cols=48 Identities=27% Similarity=0.096 Sum_probs=36.1
Q ss_pred ceEEEeccHHHHHHHHH----cCCCC----CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 437 IKKVWHNYSFDNHVLEN----YGLKV----SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 437 i~KV~HNaKfDl~vL~r----~GI~l----~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
...|+||+.||+.+|.+ +|... ...++||+..++.+.| .++|+.++++
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~------~~~L~~l~~~ 161 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG------QTVLAKACQA 161 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC------cccHHHHHHH
Confidence 35899999999999864 45431 2347899999987664 3689999975
No 46
>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=98.31 E-value=9.7e-06 Score=83.46 Aligned_cols=110 Identities=25% Similarity=0.296 Sum_probs=69.6
Q ss_pred eEEEeeccccccc-ccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 001207 369 VHACDTEVAKIDV-KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (1123)
Q Consensus 369 ~VAfDTETtGLd~-~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~--------------------~~~~evl~~ 427 (1123)
+|+||+||||+++ ..++|+.+| ++.+..+ .+ .. ..-..++.+.. .+..+++..
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig---~v~v~~~-~~-~~-~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~ 74 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIG---CVELINR-RL-TG-NTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADE 74 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEE---EEEEECC-cE-ec-cEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHH
Confidence 4899999999998 667777622 2222211 01 00 01122332210 113456778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~r----~GI~----l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
|.+|+++. ..|+||+.||+.+|.+ +|+. .+..++||+.+++.+.+.. .++|++++++
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 2346899998888777654 4899999986
No 47
>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=98.28 E-value=5.2e-06 Score=108.51 Aligned_cols=118 Identities=24% Similarity=0.329 Sum_probs=78.4
Q ss_pred ceEEEeecccccccccCccccCcc-------eE-EEEeeeCCCcccCCCceE---EEEe-CC-CCChhhhHhhhhhhhcC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGE-------VI-CFSIYSGPEADFGNGKSC---IWVD-LL-DGGGRDLLNEFAPFFED 434 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~-------ii-~~sl~~~~~I~I~~~~~~---~~ID-~~-~~~~~evl~~Lk~~Led 434 (1123)
.+|+||+||||+++..++|+.+|- ++ .|....+|..+|+..... +--+ .. ..+..++++.|.+|+.+
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 699999999999999999887331 00 122222233222210000 0000 00 11346788899999976
Q ss_pred CCceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 435 PSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 435 ~~i~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
. .+|+||+.||+.+|++ +|+. +...++||+..++.+.|... .++|++|+.+
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 5799999999999863 5664 44678999999999888764 6999999975
No 48
>PRK05168 ribonuclease T; Provisional
Probab=98.25 E-value=8.3e-06 Score=88.09 Aligned_cols=124 Identities=17% Similarity=0.087 Sum_probs=71.0
Q ss_pred HHHHHHHHHccccCceEEEeecccccccccCccccCcceEEEEeeeC-CC-cccCCCceEEEEeCC-------------C
Q 001207 354 AKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-ADFGNGKSCIWVDLL-------------D 418 (1123)
Q Consensus 354 L~~lv~~L~~a~~~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~-~~-I~I~~~~~~~~ID~~-------------~ 418 (1123)
+.-+-.++... .+++||+||||+++..++|+.+| ++.+... .+ +.+.. .-..++.+. +
T Consensus 7 ~~~~~~~~~~~---~~vv~D~ETTGl~~~~d~IieIg---aV~v~~d~~g~i~~~~-~f~~lv~P~~~~~i~~~~~~ihG 79 (211)
T PRK05168 7 LNPLKDRFRGF---LPVVIDVETAGFNAKTDALLEIA---AVTLKMDEQGWLYPDE-TLHFHVEPFEGANLEPEALAFNG 79 (211)
T ss_pred cchHHHHhcCC---ceEEEEeeCCCCCCCCCEEEEEe---EEEEEecCCCcEeccc-eEEEEECCCCCCCCCHHHHhhcC
Confidence 34444556554 58999999999999888887633 2322210 01 11100 011122210 0
Q ss_pred ----------CChhhhHhhhhhhhcC-------CCceEEEeccHHHHHHHHH----cCCC---CC-CccchHHHHHHhcC
Q 001207 419 ----------GGGRDLLNEFAPFFED-------PSIKKVWHNYSFDNHVLEN----YGLK---VS-GFHADTMHMARLWD 473 (1123)
Q Consensus 419 ----------~~~~evl~~Lk~~Led-------~~i~KV~HNaKfDl~vL~r----~GI~---l~-~~vfDTmIAAyLLd 473 (1123)
.+..+++..+.+++.+ .....|+||+.||+.+|.+ +|+. +. ..++||+..++.+.
T Consensus 80 It~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~ 159 (211)
T PRK05168 80 IDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL 159 (211)
T ss_pred CCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc
Confidence 0112234444444431 1346899999999999853 5653 11 24799999998765
Q ss_pred CCCCCCCCCCHHHHhhc
Q 001207 474 SSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 474 p~~~~~gs~sLd~La~~ 490 (1123)
+ .++|+.++.+
T Consensus 160 ~------~~~L~~l~~~ 170 (211)
T PRK05168 160 G------QTVLAKACQA 170 (211)
T ss_pred C------CCCHHHHHHH
Confidence 4 2689998875
No 49
>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=9.5e-06 Score=86.13 Aligned_cols=48 Identities=25% Similarity=0.094 Sum_probs=36.9
Q ss_pred ceEEEeccHHHHHHHHH----cCCC---C-CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 437 IKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 437 i~KV~HNaKfDl~vL~r----~GI~---l-~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
...|+||+.||+.+|.+ +|+. . +..++||+.+++.+.+ .++|++++.+
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~------~~~L~~l~~~ 158 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG------QTVLAKACQA 158 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC------CCcHHHHHHH
Confidence 46899999999999853 5662 2 2347999999988765 3689999975
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=98.20 E-value=1.1e-05 Score=103.63 Aligned_cols=117 Identities=20% Similarity=0.246 Sum_probs=76.9
Q ss_pred eEEEeecccccccccCccccCc-------ceE-EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcCC
Q 001207 369 VHACDTEVAKIDVKQETPVDHG-------EVI-CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFEDP 435 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~d~Ivg~g-------~ii-~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Led~ 435 (1123)
+++||+||||+++..++||.+| +++ .++...+|+.+|+.....+. | +.. .....++++.|.+++++.
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 7999999999998888888633 111 12222233333321110000 0 000 012356778888888764
Q ss_pred CceEEEeccHHHHHHHHH----cCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 436 SIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 436 ~i~KV~HNaKfDl~vL~r----~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+||+.||+.+|.+ +|+. ++++++||+-.++.+.|... +++|.+|++.
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 5899999999999853 6776 45678999999998888654 6999999975
No 51
>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=98.19 E-value=2e-05 Score=85.38 Aligned_cols=113 Identities=17% Similarity=0.141 Sum_probs=70.4
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------C---------CChhhhHhh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------D---------GGGRDLLNE 427 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~---------~~~~evl~~ 427 (1123)
.+++||+||||+++..+ ||.+| ++.+..+ ...+ ..-..++.+. + .+..++++.
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-RITG--NKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred CEEEEEecCCCCCCCCC-EEEEE---EEEEECC-CEee--eEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 69999999999999777 77632 2222211 1100 0011222211 0 123567778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC--CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK--VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~r----~GI~--l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
|..|+.+. ..|+||+.||+.+|.+ ++.. ....++||+-.++.+.|... .++++|.+|+..
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 3322 33567899988877665432 125899999975
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=98.16 E-value=4.5e-06 Score=86.27 Aligned_cols=111 Identities=17% Similarity=0.101 Sum_probs=69.5
Q ss_pred EEEeecccccccccCccccCc-------ceEEEEeeeCCCcccCCCceEEEEeCCCCC----------------hhhhHh
Q 001207 370 HACDTEVAKIDVKQETPVDHG-------EVICFSIYSGPEADFGNGKSCIWVDLLDGG----------------GRDLLN 426 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g-------~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~----------------~~evl~ 426 (1123)
|+||+||||+++..++|+..| +++ +....+|..+|+... ....++. .+++++
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-IDSLVRPSVRVTDWR----TRFSGVTPADLEEAAKAGKTIFGWEAARA 75 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEE-EeccccCCCCCCccc----eeccCCCHHHHhhhhhcCCccccHHHHHH
Confidence 589999999999888876522 111 122222322222111 0011111 024567
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 427 EFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 427 ~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
.|.+++++.. .+|+||+.||+.+|... .+.++||+..++.+.+......+++|+.|+.+
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 34588999999988775310026999999976
No 53
>PRK07883 hypothetical protein; Validated
Probab=98.14 E-value=1.4e-05 Score=97.74 Aligned_cols=120 Identities=18% Similarity=0.110 Sum_probs=73.5
Q ss_pred ceEEEeecccccccccCccccCcc-------eE-EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGE-------VI-CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFED 434 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~-------ii-~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Led 434 (1123)
.+|+||+||||+++..++|+.+|- ++ .+....+|+.+|+.....+- | +.. ..+..+++..|..|+++
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 699999999999998888876331 00 11222222222211000000 0 000 01234677788888876
Q ss_pred CCceEEEeccHHHHHHHH----HcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 435 PSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 435 ~~i~KV~HNaKfDl~vL~----r~GI~l~-~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
. ..|+||+.||+.+|. ++|+... ..++||+..++-+.+... ..+++|++|+..
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 468999988876555211 126999999974
No 54
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.10 E-value=5.1e-05 Score=81.25 Aligned_cols=116 Identities=14% Similarity=0.096 Sum_probs=70.3
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------C---------CChhhhHhh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------D---------GGGRDLLNE 427 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~---------~~~~evl~~ 427 (1123)
.+|+||+||||+++..++|+.+| ++.+. +..+.... .-..++.+. + .+..++++.
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 68999999999999888887632 22222 11111100 111223221 0 124567788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccchHHHHHH-hcCCCC-CCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMAR-LWDSSR-RTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~r-----~GI~l~~~vfDTmIAAy-LLdp~~-~~~gs~sLd~La~~ 490 (1123)
|..|+++. .+|+||+.||+.+|.+ +|..++..++|++-..+ ...... ....+++|+++++.
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 5899999999999853 46666667889874432 111111 01125899999975
No 55
>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=98.10 E-value=4.3e-06 Score=87.83 Aligned_cols=59 Identities=29% Similarity=0.288 Sum_probs=41.5
Q ss_pred hHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 424 LLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 424 vl~~Lk~~Led--~~i~KV~HNa-KfDl~vL~----r~GI~l~--~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+.+.|..|+.. .....|+||+ .||+.+|. ++|+.+. ..++||+.+++.+.+ +|++|+.+
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 346899998886553 68888764
No 56
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.07 E-value=5.6e-05 Score=84.20 Aligned_cols=111 Identities=22% Similarity=0.261 Sum_probs=72.1
Q ss_pred CceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-------------------CCChhhhHhh
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------------DGGGRDLLNE 427 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-------------------~~~~~evl~~ 427 (1123)
..+++||+||||+++..++|+.+| ++.+..+. + +. .-..++.+. ..+..+++..
T Consensus 68 ~~~vv~DiETTG~~~~~~~IIEIG---Av~v~~g~-i-~~--~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 68 QVFCFVDIETNGSKPKKHQIIEIG---AVKVKNGE-I-ID--RFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CCEEEEEEeCCCCCCCCCeEEEEE---EEEEECCE-E-EE--EEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 368999999999999888887633 22222110 0 00 001122110 1124578888
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
|..|+++. ..|+||+.||+.+|. ++|.. +.++.+||+-.++.+-+.. +++|++|++.
T Consensus 141 f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~----~~~L~~L~~~ 202 (257)
T PRK08517 141 FRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP----RYGLSFLKEL 202 (257)
T ss_pred HHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCC----CCCHHHHHHH
Confidence 99998764 479999999999985 35654 3466889997776544433 4999999974
No 57
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.04 E-value=1.8e-05 Score=80.70 Aligned_cols=109 Identities=22% Similarity=0.249 Sum_probs=71.1
Q ss_pred eEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC--------------------CCChhhhHhhh
Q 001207 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL--------------------DGGGRDLLNEF 428 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~--------------------~~~~~evl~~L 428 (1123)
+++||+||||+++..++|+..| ++.+..+ .+ . ..-..++.+. +.+..+++..|
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig---~v~~~~~-~~--~-~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIA---AVDVDGG-RI--I-VVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEE---EEEEECC-Ee--E-EEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 7999999999998877777622 2222211 00 0 0001222220 11245677888
Q ss_pred hhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 429 APFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 429 k~~Led~~i~KV~HNa-KfDl~vL~r----~GI~l~--~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+++. ..|+||+ .||+.+|.+ +|+..+ ..++||+..++.+.+.. +++|++|++.
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 4688998 999999964 565433 34799999998877654 4999999975
No 58
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.03 E-value=4.4e-05 Score=98.79 Aligned_cols=118 Identities=21% Similarity=0.235 Sum_probs=76.0
Q ss_pred ceEEEeeccccccccc-CccccCc-------ceE-EEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhc
Q 001207 368 LVHACDTEVAKIDVKQ-ETPVDHG-------EVI-CFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFE 433 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~-d~Ivg~g-------~ii-~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Le 433 (1123)
.+++||+||||+++.. ++||.+| +++ .++...+|+.+|+.....+- | +.. .....+++..|..+++
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 6777633 111 12222233333321100000 0 000 0124567788888987
Q ss_pred CCCceEEEeccHHHHHHHHH----cCCCC-CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 434 DPSIKKVWHNYSFDNHVLEN----YGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 434 d~~i~KV~HNaKfDl~vL~r----~GI~l-~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+. ..|+||+.||+.+|.+ +|+.. .+.++||+-.++.+.|... +|+|++|++.
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 57653 4678999999998888754 6999999975
No 59
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.00 E-value=4.7e-05 Score=86.91 Aligned_cols=65 Identities=22% Similarity=0.229 Sum_probs=50.6
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~----r~GI~l~-~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..++++.|.+|+.+. ..|+||+.||+.+|. ++|+.++ ..++||+..++-+.|... +|+|..|+..
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 456778888888653 589999999999985 3576643 468999998887766654 5999999975
No 60
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=97.98 E-value=8e-05 Score=79.78 Aligned_cols=117 Identities=15% Similarity=0.125 Sum_probs=68.5
Q ss_pred ceEEEeecccccccccCccccCcc-------e-EEEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGE-------V-ICFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFED 434 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~-------i-i~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Led 434 (1123)
.+++||+||||++. .++||.+|- + ..++....|..+++.....+. | +.. ..+..++++.|..|+++
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 466776330 0 012222233333322110000 0 000 01246788889999976
Q ss_pred CCceEEEeccH-HHHHHHHHcCCCCCC-ccchHH---HHHHhc-CCCCCCCCCCCHHHHhhc
Q 001207 435 PSIKKVWHNYS-FDNHVLENYGLKVSG-FHADTM---HMARLW-DSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 435 ~~i~KV~HNaK-fDl~vL~r~GI~l~~-~vfDTm---IAAyLL-dp~~~~~gs~sLd~La~~ 490 (1123)
. .+|+||+. ||+.+|.++|+.+.. ..+||. .+.+.. .+... +|+|.+|+++
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 345654 222222 23333 5999999975
No 61
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=97.96 E-value=8.7e-05 Score=84.23 Aligned_cols=115 Identities=16% Similarity=0.064 Sum_probs=66.6
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeC-CC-c-ccCCCceEEEEeCC-----------CCCh------hhhHhh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-A-DFGNGKSCIWVDLL-----------DGGG------RDLLNE 427 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~-~~-I-~I~~~~~~~~ID~~-----------~~~~------~evl~~ 427 (1123)
.+++|||||||+++..++||.+| ++.+..+ .+ + .+.. ....++++. ++.. ....+.
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 47999999999999999988733 2222110 01 1 1110 111223221 1110 012345
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHcCCCCC-CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~-~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+..++++. ..+|+||+.||+.+|.+.+..+. ..+.|||.......+... +++|++|+..
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 36799999999999987543332 346788765443333332 6999999975
No 62
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.85 E-value=0.00014 Score=79.36 Aligned_cols=46 Identities=37% Similarity=0.284 Sum_probs=37.7
Q ss_pred ceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 437 IKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 437 i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..+|+||+.||+.+|... .+.++||+-+|+.+.|... +++..|+..
T Consensus 75 ~~lVaHNa~FD~~~L~~~----~~~~idTl~lar~l~p~~~----~~l~~L~~~ 120 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEM----PGEWICTMKLARRLWPGIK----YSNMALYKS 120 (219)
T ss_pred CEEEEeCcHhhHHHHhCc----CCCcEeHHHHHHHHccCCC----CCHHHHHHH
Confidence 368999999999999743 3568999999998888753 899999864
No 63
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.80 E-value=0.00011 Score=97.76 Aligned_cols=117 Identities=21% Similarity=0.296 Sum_probs=76.9
Q ss_pred ceEEEeecccccccccCccccCcc-------eE-EEEeeeCCCcccCC------CceEEEEeCCCCChhhhHhhhhhhhc
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGE-------VI-CFSIYSGPEADFGN------GKSCIWVDLLDGGGRDLLNEFAPFFE 433 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~-------ii-~~sl~~~~~I~I~~------~~~~~~ID~~~~~~~evl~~Lk~~Le 433 (1123)
.+|+||+||||+++..++|+..|- ++ .|+...+|+.+++. +.+...+. ...+..++++.|..|+.
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 689999999999998888876331 00 12222233322211 00000000 01134567788888886
Q ss_pred CCCceEEEeccHHHHHHHH----HcCCC-CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 434 DPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 434 d~~i~KV~HNaKfDl~vL~----r~GI~-l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+ ..+|+||+.||+.+|. ++|+. +...++||+-+++.+.|... .++|+.|+.+
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 55678999999998887654 6999999986
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=97.77 E-value=2.5e-05 Score=80.01 Aligned_cols=64 Identities=19% Similarity=0.142 Sum_probs=45.4
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..++++.|..|+++. ..|+||+.||+.+|.. +. +...++||.....+..+.. ..+|+|++|+++
T Consensus 64 ~~~~~~~l~~~l~~~--vlVgHn~~fD~~~L~~-~~-~~~~~~dt~~l~~~~~~~~--~~~~sL~~l~~~ 127 (152)
T cd06144 64 FEEVQKKVAELLKGR--ILVGHALKNDLKVLKL-DH-PKKLIRDTSKYKPLRKTAK--GKSPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHHHhCCC--EEEEcCcHHHHHHhcC-cC-CCccEEEeEEeeccccccC--CCChhHHHHHHH
Confidence 457888899999763 5799999999999963 21 2245789877655554421 126999999975
No 65
>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=97.70 E-value=8.6e-05 Score=76.67 Aligned_cols=113 Identities=19% Similarity=0.173 Sum_probs=64.9
Q ss_pred EEEeecccccccc--cCcccc------CcceEEEEeeeCCCcccCCCceEEE-E---eCC-CCChhhhHhhhhhhhcCCC
Q 001207 370 HACDTEVAKIDVK--QETPVD------HGEVICFSIYSGPEADFGNGKSCIW-V---DLL-DGGGRDLLNEFAPFFEDPS 436 (1123)
Q Consensus 370 VAfDTETtGLd~~--~d~Ivg------~g~ii~~sl~~~~~I~I~~~~~~~~-I---D~~-~~~~~evl~~Lk~~Led~~ 436 (1123)
|+||+||||+++. .+.|+. .|+++ +....+|..+|+...+.+- | +.. ..+.+++++.|..++.+.
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~-~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l~~~- 78 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVL-YDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGK- 78 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEE-EEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHcCCC-
Confidence 5899999999986 233322 11211 2223334333332110000 0 000 123567888899999754
Q ss_pred ceEEEeccHHHHHHHHHcCCCCCCccchHHHH---HH-hcCCCCCCCCCCCHHHHhhc
Q 001207 437 IKKVWHNYSFDNHVLENYGLKVSGFHADTMHM---AR-LWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 437 i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIA---Ay-LLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+||+.||+.+|... .+...+.||... .+ ...|... +|+|+.|+++
T Consensus 79 -vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~---~~~L~~L~~~ 130 (157)
T cd06149 79 -VVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENC---RVSLKVLAKR 130 (157)
T ss_pred -EEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccC---ChhHHHHHHH
Confidence 58999999999999643 123346788643 22 2355433 5999999986
No 66
>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=97.66 E-value=7.1e-05 Score=76.66 Aligned_cols=62 Identities=16% Similarity=0.015 Sum_probs=48.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..++++.|.+|+... ..+|+||+.||+.+|... .+.++||+..++.+.+... +|+|+.|+.+
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 467788899999632 358999999999999753 2457999998887665443 5999999986
No 67
>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=97.65 E-value=0.00032 Score=71.10 Aligned_cols=65 Identities=28% Similarity=0.253 Sum_probs=50.7
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCC-CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~----r~GI~l-~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..+++..|..++++ ...|+||+.||+.+|. ++|+.. +..++||+..+..+.+... +++|+.|++.
T Consensus 64 ~~~v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~---~~~L~~l~~~ 133 (156)
T cd06130 64 FPEVWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP---NHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC---CCCHHHHHHH
Confidence 34677888889876 3689999999999985 357653 4568999988887776543 6999999975
No 68
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=97.57 E-value=0.00015 Score=78.07 Aligned_cols=66 Identities=15% Similarity=0.111 Sum_probs=47.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~----r~GI~l~--~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..++++.|.+|+++.. ..++|++.||+.+|. ++|+..+ ..+.|++...+.+.+... .++|++++++
T Consensus 79 ~~evl~~f~~~~~~~~-~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~---~~~L~~~~~~ 150 (207)
T PRK07748 79 FEELVEKLAEYDKRCK-PTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN---QTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHHHhCcCC-eEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC---CCCHHHHHHH
Confidence 5678888999998733 246677899999995 3576543 457888877765554332 5899999975
No 69
>PRK05359 oligoribonuclease; Provisional
Probab=97.47 E-value=0.00042 Score=73.35 Aligned_cols=103 Identities=13% Similarity=0.130 Sum_probs=63.2
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEe-------------------------CC--CCC
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVD-------------------------LL--DGG 420 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID-------------------------~~--~~~ 420 (1123)
.+|++|+||||+|+..++|++.| ++.+. +..+.+... ...++. .. +.+
T Consensus 4 ~~vvlD~ETTGLdp~~d~IieIg---aV~~~-~~~~~~~~~-~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 4 NLIWIDLEMTGLDPERDRIIEIA---TIVTD-ADLNILAEG-PVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred cEEEEEeecCCCCCCCCeEEEEE---EEEEc-CCceEcccc-eEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 68999999999999999988733 33221 111111100 000110 00 012
Q ss_pred hhhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCccch--HH-HHHHhcCCC
Q 001207 421 GRDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHAD--TM-HMARLWDSS 475 (1123)
Q Consensus 421 ~~evl~~Lk~~Led----~~i~KV~HNaKfDl~vL~r----~GI~l~~~vfD--Tm-IAAyLLdp~ 475 (1123)
..+++..|.+|+.+ .....++||+.||+.+|.+ +|..+.+++.| |+ -+++.+.|.
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 2235699999999999965 36667667777 66 577777764
No 70
>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=97.47 E-value=0.00017 Score=68.54 Aligned_cols=75 Identities=28% Similarity=0.335 Sum_probs=52.1
Q ss_pred EEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCC-ceEEEeccHHHH
Q 001207 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPS-IKKVWHNYSFDN 448 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led~~-i~KV~HNaKfDl 448 (1123)
++||+||+|++++.++|++ +++..+. ....++++ |.+++++.. ..+|+||+.||+
T Consensus 1 ~~~DiEt~~~~~~~~~i~~------i~~~~~~------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~ 56 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIE------IALADVN------PEDTAVID------------LKDILRDKPLAILVGHNGSFDL 56 (96)
T ss_pred CEEEEECCCCCCCCCcEEE------EEEEEcc------CCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhH
Confidence 4799999999999887764 4333221 01234443 667777765 578999999999
Q ss_pred HHHHH----cCCCC---CCccchHHHH
Q 001207 449 HVLEN----YGLKV---SGFHADTMHM 468 (1123)
Q Consensus 449 ~vL~r----~GI~l---~~~vfDTmIA 468 (1123)
.+|.+ +|+.. ...++||+.+
T Consensus 57 ~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 57 PFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 98853 45543 3568999988
No 71
>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=97.40 E-value=0.00084 Score=70.89 Aligned_cols=115 Identities=14% Similarity=0.137 Sum_probs=64.8
Q ss_pred EEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-------------C----------CChhhhHh
Q 001207 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------D----------GGGRDLLN 426 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-------------~----------~~~~evl~ 426 (1123)
+.||+||||+++..++|+..| ++.+.. ....+. ....++.+. + .+..++++
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig---~v~v~~-~~~~~~--~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFA---AIRTDE-NFNEIE--PFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEEEE---EEEECC-CCCCcc--ceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 469999999999888887622 222211 111110 011122110 0 11234667
Q ss_pred hhhhhhcCCCceEEEec-cHHHHHHHHH----cCCCC-------CCccchHHHHHHhcC---CCC-------CCCCCCCH
Q 001207 427 EFAPFFEDPSIKKVWHN-YSFDNHVLEN----YGLKV-------SGFHADTMHMARLWD---SSR-------RTEGGYSL 484 (1123)
Q Consensus 427 ~Lk~~Led~~i~KV~HN-aKfDl~vL~r----~GI~l-------~~~vfDTmIAAyLLd---p~~-------~~~gs~sL 484 (1123)
.|..++.++....|+|| +.||+.+|.+ +|+.. .+..+||+-.++++. |.. ....+|+|
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 7999999853 45431 123468886666532 310 00125899
Q ss_pred HHHhhc
Q 001207 485 EALTGD 490 (1123)
Q Consensus 485 d~La~~ 490 (1123)
++|+++
T Consensus 155 ~~l~~~ 160 (183)
T cd06138 155 EDLAQA 160 (183)
T ss_pred HHHHHH
Confidence 999986
No 72
>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=97.37 E-value=0.00069 Score=67.43 Aligned_cols=107 Identities=25% Similarity=0.209 Sum_probs=66.7
Q ss_pred EEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-----------C---------CChhhhHhhhh
Q 001207 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------D---------GGGRDLLNEFA 429 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-----------~---------~~~~evl~~Lk 429 (1123)
|.+|+||||+++..++|+. ++..........+. ....++.+. + .+..+++..|.
T Consensus 1 v~~D~Ettg~~~~~~~iie----i~~v~~~~~~~~~~--~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIE----IGAVKVDGGIEIVE--RFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred CeEEeeCCCcCCCCCeEEE----EEEEEEECCcChhh--hhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHH
Confidence 5789999999988888876 33222221100000 001122111 0 12346777888
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----cCC-CCCCccchHHHHHHhcCCCCCCCCCCCHHHH
Q 001207 430 PFFEDPSIKKVWHNYSFDNHVLEN----YGL-KVSGFHADTMHMARLWDSSRRTEGGYSLEAL 487 (1123)
Q Consensus 430 ~~Led~~i~KV~HNaKfDl~vL~r----~GI-~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~L 487 (1123)
.++++ ..+|+||+.||..+|.+ +|. .....++||+..++.+.+... .+++..+
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 234568999988887776543 5777776
No 73
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.34 E-value=0.00051 Score=75.18 Aligned_cols=116 Identities=23% Similarity=0.252 Sum_probs=75.4
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeee------------CCCcccCCCceEEE-E--e-CC-CCChhhhHhhhhh
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYS------------GPEADFGNGKSCIW-V--D-LL-DGGGRDLLNEFAP 430 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~------------~~~I~I~~~~~~~~-I--D-~~-~~~~~evl~~Lk~ 430 (1123)
.+++||+||||+++..++||.+| ++.+.. +|..+|+.....+. | . .. .....++.+.+..
T Consensus 14 ~~vv~D~ETtg~~~~~~~iieIg---av~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~ 90 (243)
T COG0847 14 RFVVIDLETTGLNPKKDRIIEIG---AVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLD 90 (243)
T ss_pred cEEEEecccCCCCCCCCceEEEE---eEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHH
Confidence 57999999999999888888633 233322 12222221100000 0 0 00 0012567777888
Q ss_pred hhcCCCceEEEeccHHHHHHHHH----cCCCC-CCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 431 FFEDPSIKKVWHNYSFDNHVLEN----YGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 431 ~Led~~i~KV~HNaKfDl~vL~r----~GI~l-~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
++.+. ...|+||+.||+.+|.. +++.+ ...+.||+-.++-..|+.. .++|+.|+.+
T Consensus 91 ~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~---~~~L~~l~~~ 151 (243)
T COG0847 91 FIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFD---RSSLDALAER 151 (243)
T ss_pred HHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCc---cchHHHHHHH
Confidence 88774 46899999999999953 56654 3457899999999998843 5999999985
No 74
>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=97.34 E-value=0.00064 Score=71.27 Aligned_cols=103 Identities=13% Similarity=0.104 Sum_probs=62.1
Q ss_pred eEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeC------------------CC---------CCh
Q 001207 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDL------------------LD---------GGG 421 (1123)
Q Consensus 369 ~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~------------------~~---------~~~ 421 (1123)
++.||+||||+++..++|+..| ++.+ .+..+.+.. ....++.+ .+ .+.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIg---aV~~-~~~~~~i~~-~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~ 75 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIA---CIIT-DGDLNIIAE-GPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTL 75 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEE---EEEE-eCCCceecC-ceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCH
Confidence 3789999999999888887633 2222 221111110 00111111 01 124
Q ss_pred hhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCccchH---HHHHHhcCCCC
Q 001207 422 RDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHADT---MHMARLWDSSR 476 (1123)
Q Consensus 422 ~evl~~Lk~~Led----~~i~KV~HNaKfDl~vL~r----~GI~l~~~vfDT---mIAAyLLdp~~ 476 (1123)
.+++..|.+|+.+ .....++||+.||+.+|.+ +|..+.++..|| ..+++.+.|..
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 2456789999999999964 465555667787 44666666643
No 75
>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=97.24 E-value=0.0027 Score=67.51 Aligned_cols=65 Identities=23% Similarity=0.344 Sum_probs=47.5
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC----------------------C-ccchHHHHHH
Q 001207 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS----------------------G-FHADTMHMAR 470 (1123)
Q Consensus 421 ~~evl~~Lk~~Led--~~i~KV~HNa-KfDl~vL~----r~GI~l~----------------------~-~vfDTmIAAy 470 (1123)
..+.+..|..++.+ +. .+|+||. .||+.+|. ++|+... + .++|++..++
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 34567777777764 44 4899998 89999984 3576651 2 3689998888
Q ss_pred hcCCCCCCCCCCCHHHHhhc
Q 001207 471 LWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 471 LLdp~~~~~gs~sLd~La~~ 490 (1123)
-..+ .. +|+|+.++..
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 76
>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=97.24 E-value=0.0018 Score=66.82 Aligned_cols=67 Identities=12% Similarity=0.013 Sum_probs=46.4
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r----~GI~----l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..++++.|.+|+.+.....++|+..||..++.+ .+.. ....++|++-.+..+.+... .++|++++..
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 456788888999874113577778999887643 3332 33468899988886666532 5999999975
No 77
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.21 E-value=0.0027 Score=76.51 Aligned_cols=82 Identities=12% Similarity=0.075 Sum_probs=48.6
Q ss_pred CceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCC-------------C----------CChhh
Q 001207 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------D----------GGGRD 423 (1123)
Q Consensus 367 ~~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~-------------~----------~~~~e 423 (1123)
..++++|+||||+++..++|+.+| ++.+..+ .+.+.. ....++.+. + .+..+
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiA---aVrvd~~-~~~i~e-~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e 80 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFA---GIRTDAD-LNIIGE-PLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAE 80 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEE---EEEEeCC-Cceecc-eeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHH
Confidence 368999999999999999988633 2322211 011110 001122110 0 11245
Q ss_pred hHhhhhhhhcCCCceEEEec-cHHHHHHHHH
Q 001207 424 LLNEFAPFFEDPSIKKVWHN-YSFDNHVLEN 453 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HN-aKfDl~vL~r 453 (1123)
++..+..++..+....|+|| +.||..+|++
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~ 111 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRY 111 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHH
Confidence 66677788864445689997 7899999865
No 78
>PRK06722 exonuclease; Provisional
Probab=96.94 E-value=0.01 Score=67.12 Aligned_cols=67 Identities=12% Similarity=0.010 Sum_probs=44.0
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCCC----ccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVSG----FHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r----~GI~l~~----~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..+++..|.+|+++. ..|+||+.||+.+|.+ +|+..+. .++|++-.++-+.+... ...++|+++++.
T Consensus 77 f~eVl~ef~~fig~~--~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~-~~~~sL~~l~~~ 151 (281)
T PRK06722 77 FPQIIEKFIQFIGED--SIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELF-EHTPSLQSAVEQ 151 (281)
T ss_pred HHHHHHHHHHHHCCC--cEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhc-cCCCCHHHHHHH
Confidence 467888999999764 3578889999999864 6765432 24687754443222210 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=96.43 E-value=0.0082 Score=61.60 Aligned_cols=156 Identities=19% Similarity=0.252 Sum_probs=70.5
Q ss_pred EEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCC--ChhhhHhhhhhhhcCCCceEEEec-cHH
Q 001207 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDG--GGRDLLNEFAPFFEDPSIKKVWHN-YSF 446 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~--~~~evl~~Lk~~Led~~i~KV~HN-aKf 446 (1123)
+.||+||+|+++....+.. +|+....+.. ...+...... ..+..+.....++.+.. .+|+|| ..|
T Consensus 1 l~~DIET~Gl~~~~~~i~l----iG~~~~~~~~-------~~~~~~~~~~~~~ee~~~~~~~~~l~~~~-~iv~yng~~F 68 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYL----IGVADFDDDE-------IITFIQWFAEDPDEEEIILEFFELLDEAD-NIVTYNGKNF 68 (164)
T ss_dssp --EEEEESS-GG-G---EE----EEEEE-ETTT-------TE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTT
T ss_pred CcEEecCCCCCCCCCCEEE----EEEEEeCCCc-------eEEeeHhhccCcHHHHHHHHHHHHHhcCC-eEEEEeCccc
Confidence 4699999999986655432 3444333321 1212221111 11122222124555544 468888 589
Q ss_pred HHHHHHH----cCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhh
Q 001207 447 DNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKD 522 (1123)
Q Consensus 447 Dl~vL~r----~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~ 522 (1123)
|+.+|++ +++......+|++...+-... . +++|+.++.. +++.. +.+++-|..+. .
T Consensus 69 D~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~---~~~Lk~ve~~--------lg~~~------~~~~~~G~~~~-~ 128 (164)
T PF13482_consen 69 DIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--E---SYSLKNVEKF--------LGIER------RDDDISGSESV-K 128 (164)
T ss_dssp HHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--C---CTT--SHHH-------------------------HHHHHH-H
T ss_pred CHHHHHHHHHHcCCCcccchhhHHHHHHhccC--C---CCCHHHHhhh--------ccccc------ccCCCCHHHHH-H
Confidence 9999964 454434567899887763222 2 5899999874 44330 11112222111 1
Q ss_pred hhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 523 IFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSL 573 (1123)
Q Consensus 523 lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L 573 (1123)
.|..-. . + .++. ..+....|+..|+..|.+|++.|
T Consensus 129 ~~~~~~--~--~--~~~~----------~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 129 LYKEYL--E--T--GDPE----------ALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHH-----T--T--GGTS------------HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHH--h--c--CCHH----------HHHHHHHHHHHHHHHHHHHHHHh
Confidence 121100 0 0 0111 15678999999999999999976
No 80
>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=96.40 E-value=0.034 Score=60.33 Aligned_cols=114 Identities=21% Similarity=0.250 Sum_probs=64.0
Q ss_pred ceEEEeeccccccccc---CccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC--CCceEEEe
Q 001207 368 LVHACDTEVAKIDVKQ---ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED--PSIKKVWH 442 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~---d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led--~~i~KV~H 442 (1123)
+.++||.|+.+..... +.. ....|+.++.....+ . ...+.....+..+.+..|..++.+ |. .+++|
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~-~~d~Ii~Is~~~~~~------~-~~~~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDR-GDDRIIIVALRDNRG------W-EEVLHAEDAAEKELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCC-CCCeEEEEecccCCC------c-eeeeccCCCCHHHHHHHHHHHHHHhCCC-EEecc
Confidence 5799999997654321 111 112345666543221 0 111111112345677777777764 55 46899
Q ss_pred cc-HHHHHHHH----HcCCCCC------------------------------Cc-cchHHHHHHhcCCCCCCCCCCCHHH
Q 001207 443 NY-SFDNHVLE----NYGLKVS------------------------------GF-HADTMHMARLWDSSRRTEGGYSLEA 486 (1123)
Q Consensus 443 Na-KfDl~vL~----r~GI~l~------------------------------~~-vfDTmIAAyLLdp~~~~~gs~sLd~ 486 (1123)
|. .||+.+|. ++|+.+. +. ++|++.+..-.+....+-.+|+|++
T Consensus 81 N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~ 160 (207)
T cd05785 81 NIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKA 160 (207)
T ss_pred CCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHH
Confidence 97 89999984 3566541 12 3798877664322110112699999
Q ss_pred Hhhc
Q 001207 487 LTGD 490 (1123)
Q Consensus 487 La~~ 490 (1123)
+|..
T Consensus 161 Va~~ 164 (207)
T cd05785 161 VAKH 164 (207)
T ss_pred HHHH
Confidence 9986
No 81
>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=96.10 E-value=0.036 Score=59.31 Aligned_cols=109 Identities=22% Similarity=0.334 Sum_probs=66.7
Q ss_pred hhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC----------------------C-ccchHHHHHHh
Q 001207 422 RDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS----------------------G-FHADTMHMARL 471 (1123)
Q Consensus 422 ~evl~~Lk~~Led--~~i~KV~HNa-KfDl~vL~----r~GI~l~----------------------~-~vfDTmIAAyL 471 (1123)
.+.+..|..++.. +. .+++||. .||+..|. .+|+.++ + ..+|++..++-
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 4566777777765 65 4899995 69999984 2566532 1 26788877764
Q ss_pred cCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhH
Q 001207 472 WDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREE 551 (1123)
Q Consensus 472 Ldp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~ 551 (1123)
.. ... +|+|+.++++ +||.++ .++-++ ....+|.. .+ .
T Consensus 136 ~~-~l~---sy~L~~v~~~-------~Lg~~k--------~d~~~~-~i~~~~~~---------------~~-------~ 173 (195)
T cd05780 136 TL-NLT---RYTLERVYEE-------LFGIEK--------EDVPGE-EIAEAWDS---------------GE-------N 173 (195)
T ss_pred hC-CCC---cCcHHHHHHH-------HhCCCC--------CcCCHH-HHHHHHhC---------------CC-------c
Confidence 22 222 6999999986 555430 111111 01111111 00 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001207 552 RELWISYSAFDSINTLKLYKSL 573 (1123)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1123)
.....+|+..||..+++|...|
T Consensus 174 ~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 174 LERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred hHHHHHHhHHHHHHHHHHHhhC
Confidence 4567899999999999998753
No 82
>PTZ00315 2'-phosphotransferase; Provisional
Probab=96.09 E-value=0.024 Score=69.55 Aligned_cols=70 Identities=14% Similarity=0.010 Sum_probs=43.8
Q ss_pred hhhhHhhhhhhhcCCC--------ceEEEeccHHHHH-HHHH-------cCCCCCC-ccchH-HHHHHhcCCCC------
Q 001207 421 GRDLLNEFAPFFEDPS--------IKKVWHNYSFDNH-VLEN-------YGLKVSG-FHADT-MHMARLWDSSR------ 476 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~--------i~KV~HNaKfDl~-vL~r-------~GI~l~~-~vfDT-mIAAyLLdp~~------ 476 (1123)
..+++..|..||.+.. -..++||+.||+. +|.. .|+.+.. .++|. ...+.++.|..
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 4578888999987653 1368999999995 6632 3665433 34453 25555555421
Q ss_pred --CCCCCCCHHHHhhc
Q 001207 477 --RTEGGYSLEALTGD 490 (1123)
Q Consensus 477 --~~~gs~sLd~La~~ 490 (1123)
....+++|+++++.
T Consensus 210 ~~~~~~~~~L~~al~~ 225 (582)
T PTZ00315 210 ATPPLGPSDMPDMLQM 225 (582)
T ss_pred cccccCCcCHHHHHHH
Confidence 01125899999874
No 83
>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=95.61 E-value=0.066 Score=58.24 Aligned_cols=111 Identities=23% Similarity=0.338 Sum_probs=71.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCCC------------------ccchHHHHHHhcCCCCC
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVSG------------------FHADTMHMARLWDSSRR 477 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNa-KfDl~vL~r----~GI~l~~------------------~vfDTmIAAyLLdp~~~ 477 (1123)
..+.+..|..+++.....+|+||. .||+.+|.. +|+.++. .-+|||-.-...+...
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 456788888888876667899995 699999842 7887643 1268776654444332
Q ss_pred CCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHH
Q 001207 478 TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWIS 557 (1123)
Q Consensus 478 ~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~ 557 (1123)
..+|+.||.- +|+. + -.++.|. ..|.. +++...++...
T Consensus 116 ---~~sLd~la~~--------lgiP-----g--K~~idGs-------------------~V~~~-----y~~g~i~~I~~ 153 (209)
T PF10108_consen 116 ---RTSLDELAAL--------LGIP-----G--KDDIDGS-------------------QVAEL-----YQEGDIDEIRE 153 (209)
T ss_pred ---cCCHHHHHHH--------cCCC-----C--CCCCCHH-------------------HHHHH-----HHcCCHHHHHH
Confidence 4899999974 4442 0 0011111 01111 11122566789
Q ss_pred HHHHHHHHHHHHHHHHH
Q 001207 558 YSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 558 YAA~DA~~tlrL~e~L~ 574 (1123)
||..||..|..||-++.
T Consensus 154 YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 154 YCEKDVLNTYLLYLRFE 170 (209)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999998875
No 84
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.55 E-value=0.071 Score=64.81 Aligned_cols=177 Identities=18% Similarity=0.180 Sum_probs=101.4
Q ss_pred CCeEEecCHHHHHHHH-HHHHccccCceEEEeeccccc-ccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCC
Q 001207 343 SNVMVVDNVSAAKKVV-WMLTNKYKHLVHACDTEVAKI-DVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG 420 (1123)
Q Consensus 343 ~~y~lV~t~e~L~~lv-~~L~~a~~~~~VAfDTETtGL-d~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~ 420 (1123)
..+.+|+++.+++.++ ..+.+. ..+|++|.|-..- .....+++ - +|+..+...++||.....
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--LRYVGIDSEWKPSKKVSDSKLA------I--------LQIFFKDCVYLIDCVKLE 453 (617)
T ss_pred cceeeeCCHHHHHHHHHHHhhhc--CEEEEEccccCcccCCChhHHH------H--------HHHHhcCeEEEeehHHhh
Confidence 4578999999999987 344443 3689999997643 11011110 0 344444556677765421
Q ss_pred --hhhhHh-hhhhhhcCCCceEEEeccHHHHHHHHH------cCCCCC---CccchHHHHHHhcCCCCC----CCCCCCH
Q 001207 421 --GRDLLN-EFAPFFEDPSIKKVWHNYSFDNHVLEN------YGLKVS---GFHADTMHMARLWDSSRR----TEGGYSL 484 (1123)
Q Consensus 421 --~~evl~-~Lk~~Led~~i~KV~HNaKfDl~vL~r------~GI~l~---~~vfDTmIAAyLLdp~~~----~~gs~sL 484 (1123)
..+.+. .+..+|+++.+.|||.+...|++++++ ....+. +.+-++.++-.+.+-... +...-+|
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 345689999999999999999999983 122221 123344444444332110 0001222
Q ss_pred HHHhhcccccccccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHH
Q 001207 485 EALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSI 564 (1123)
Q Consensus 485 d~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~ 564 (1123)
..|.. .++|+.--|. ..-.+|.-+|+. ..|+.|||.|+.
T Consensus 534 ~~Lt~--------------------------------~llg~~lnKt--eqcsnWqcrpLr-------~nQi~yaalDa~ 572 (617)
T KOG2207|consen 534 ADLTD--------------------------------CLLGKKLNKT--EQCSNWQCRPLR-------RNQIYYAALDAV 572 (617)
T ss_pred hhhhH--------------------------------HHhhhhcccc--cccchhhcCCch-------hhHHHHHHhcch
Confidence 22221 1233321110 111279999984 579999999999
Q ss_pred HHHHHHHHHHHH
Q 001207 565 NTLKLYKSLKKK 576 (1123)
Q Consensus 565 ~tlrL~e~L~~k 576 (1123)
.+..++..+.+.
T Consensus 573 ~~~~ifkkv~~v 584 (617)
T KOG2207|consen 573 VLVEIFKKVCSV 584 (617)
T ss_pred hhHHHHHHHHhh
Confidence 999999877643
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=95.14 E-value=0.23 Score=53.10 Aligned_cols=108 Identities=20% Similarity=0.229 Sum_probs=61.5
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC--CCceEEEec-c
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED--PSIKKVWHN-Y 444 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~~~evl~~Lk~~Led--~~i~KV~HN-a 444 (1123)
+.++||.||++..-+... +...|+++++....+ ...++.. ...+..+.+..|..++.. |. .++++| .
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 579999999853322111 113456666654221 1122222 112345677777777764 44 478999 5
Q ss_pred HHHHHHHH----HcCCCCC-----C----------------ccchHHHHHHhcCCCCCCCCCCCHHHHhh
Q 001207 445 SFDNHVLE----NYGLKVS-----G----------------FHADTMHMARLWDSSRRTEGGYSLEALTG 489 (1123)
Q Consensus 445 KfDl~vL~----r~GI~l~-----~----------------~vfDTmIAAyLLdp~~~~~gs~sLd~La~ 489 (1123)
.||+.+|. .+|+.+. + ..+|.+-..+-... .. +++|+.+|.
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 3676542 0 15677665553322 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=94.73 E-value=0.31 Score=52.92 Aligned_cols=66 Identities=26% Similarity=0.340 Sum_probs=45.2
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC-----------------CccchHHHHHHhcCCCCCC
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS-----------------GFHADTMHMARLWDSSRRT 478 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNa-KfDl~vL~r----~GI~l~-----------------~~vfDTmIAAyLLdp~~~~ 478 (1123)
..+.+..|..++++....+|+||. .||+.+|.. +|+.++ +..+|++-+..-.+..
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~--- 154 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGAR--- 154 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCcc---
Confidence 356777888888763346899996 799999853 677533 1267888766543331
Q ss_pred CCCCCHHHHhhc
Q 001207 479 EGGYSLEALTGD 490 (1123)
Q Consensus 479 ~gs~sLd~La~~ 490 (1123)
.+++|+.++..
T Consensus 155 -~~~~L~~va~~ 165 (208)
T cd05782 155 -ARASLDLLAKL 165 (208)
T ss_pred -CCCCHHHHHHH
Confidence 25999999864
No 87
>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=92.34 E-value=1.5 Score=47.28 Aligned_cols=65 Identities=23% Similarity=0.359 Sum_probs=40.5
Q ss_pred hhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC------------------------Cc-cchHHHHH
Q 001207 422 RDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS------------------------GF-HADTMHMA 469 (1123)
Q Consensus 422 ~evl~~Lk~~Led--~~i~KV~HNa-KfDl~vL~----r~GI~l~------------------------~~-vfDTmIAA 469 (1123)
.+.+..|..++.. |. .+++||. .||+..|. .+|+... |. .+|++-..
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 4566666766654 44 4799995 78999884 2455431 21 57876554
Q ss_pred HhcCCCCCCCCCCCHHHHhhc
Q 001207 470 RLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 470 yLLdp~~~~~gs~sLd~La~~ 490 (1123)
+--..... +|+|++++.+
T Consensus 131 k~~~~kl~---sy~L~~Va~~ 148 (193)
T cd05784 131 KTATYHFE---SFSLENVAQE 148 (193)
T ss_pred HHccCCCC---cCCHHHHHHH
Confidence 32111222 6999999986
No 88
>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]
Probab=91.26 E-value=0.072 Score=67.66 Aligned_cols=197 Identities=15% Similarity=0.139 Sum_probs=126.5
Q ss_pred CeeeecccccCccccccccCCCcccCCcc-ccchhhhhceEEcCCCCeEEeecccchhHHHHHHhcCchhHHHHHHcCCc
Q 001207 822 GRVHCSLNINTETGRLSARRPNLQNQPAL-EKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGD 900 (1123)
Q Consensus 822 GRIH~~~n~~T~TGRlSss~PNLQNIP~~-~~~g~~iR~~Fia~~G~~lVsaDySQIELRIlAhlS~D~~Li~af~~G~D 900 (1123)
|++|+-+.-.+. | -+.+|+||+|.+ .-++.-+++-|+...--..|..+|.+.+.||.|+++++..+.....
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 GVIESFIEKCVS-G---QSVRNLQNVQKRKRLYVALALQKLINESPIRTVAEKYKVERGRLQALLSNASSFASLIT---- 863 (1008)
T ss_pred chHHHHHHHhhh-c---cccccccchhHHHHHHHHHHHHHHHhhCcHHHHHHHhCchHHHHHHHHhcchhHHHHHH----
Confidence 677766542111 1 356799999964 1234456777777666678999999999999999999977655443
Q ss_pred hhHHHHhhhccccchhhccchhhhcccCCCCCCCCcccccchHHHHhhHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHH
Q 001207 901 FHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKDAFASERRKAKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVD 980 (1123)
Q Consensus 901 IH~~tA~~if~~~~e~v~~~e~~~~w~~~~~~~v~~~~~vt~~~R~~AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~ 980 (1123)
.|- +. +.|. -++.-+.-.++.+|++|...|..-..++-..++....
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 1231 2566788899999999999999989999999999999
Q ss_pred HHHHhChhHHHHHHHHHHHHHhCCeEecccCCcccCCCCCccChhhhhhhhhhhhhhhhhchHHHHHHHHHHHHHHHHhh
Q 001207 981 LWYNERQEVLTWQEARKKESRIDNHVHTLLGRARRFPAIKSLTRSQRNHIERAAINTPVQGSAADVAMCAMLEISKNARL 1060 (1123)
Q Consensus 981 ~f~~~yP~Vk~~~~~~~~~A~~~GyV~Tl~GRrr~lp~~~s~n~~~r~~aeR~AvN~~IQGSAADI~K~AMi~i~~~~~l 1060 (1123)
-|++.|+.+..+.........+.=+..+.+++..-+-. ..+...--.+||..-.+-+.+.+....
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 99999999999876655444333333333333221110 011111114555555555555444332
Q ss_pred ccCCceEEEEeeceEEEeCCcch
Q 001207 1061 KELGWKLLLQVHDEVILEGPSES 1083 (1123)
Q Consensus 1061 ~~~g~~llLqVHDELv~EVp~~~ 1083 (1123)
+.. |||...++|+-.
T Consensus 975 -----~~~---~w~~~~a~~~i~ 989 (1008)
T KOG0950|consen 975 -----REF---HWEVLVALPEIH 989 (1008)
T ss_pred -----HHh---hhhHhhhcchhh
Confidence 111 999998888754
No 89
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=91.01 E-value=2.6 Score=46.95 Aligned_cols=164 Identities=17% Similarity=0.077 Sum_probs=88.1
Q ss_pred ceEEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCCCC-hhhhHhhhhhhhcCCC-ceEEEec-c
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG-GRDLLNEFAPFFEDPS-IKKVWHN-Y 444 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~~~-~~evl~~Lk~~Led~~-i~KV~HN-a 444 (1123)
.++-||+||||++...+.|. +++.+.. + +..++|-..-.+ .+.-...+..|+.+++ -.+|.+| .
T Consensus 99 ~~~FFDiETTGL~~ag~~I~----~~g~a~~-~--------~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGk 165 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTIT----LVGGARG-V--------DDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGK 165 (278)
T ss_pred ceEEEeeeccccCCCCCeEE----EEEEEEc-c--------CceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCc
Confidence 37789999999998433332 1222221 1 123444332111 1112223455665542 2468888 4
Q ss_pred HHHHHHHHH---cCC--CCCCccchHHHHHHhcCCC-CCCCCCCCHHHHhhcccccccccccccccccCCCCcccccccc
Q 001207 445 SFDNHVLEN---YGL--KVSGFHADTMHMARLWDSS-RRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKI 518 (1123)
Q Consensus 445 KfDl~vL~r---~GI--~l~~~vfDTmIAAyLLdp~-~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~ 518 (1123)
.||..++++ ..+ .+...-||.|-.++-+.-. .. +.+|+.+=+ +||+.. .++.-|..
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 699999983 323 3456679999999866622 12 367766543 455531 11121221
Q ss_pred chhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 001207 519 SMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLE 579 (1123)
Q Consensus 519 s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~e~L~~kL~e 579 (1123)
+. +++.. |..-+ ...+......|.-.|+..+..|+..+.+++.+
T Consensus 228 ~p-~lyr~------------~~~~~----dp~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 228 GP-ELYRL------------YRRYG----DPGLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred hH-HHHHH------------HHHcC----CHHHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 11 11110 11100 00124567889999999999999999887764
No 90
>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=90.75 E-value=3.8 Score=44.56 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=26.9
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHH----HcCCC
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLE----NYGLK 457 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNa-KfDl~vL~----r~GI~ 457 (1123)
..+.+..|..++.+.. .+|++|. .||+..|. ++|+.
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 3567778888887764 6789995 79999984 36776
No 91
>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=90.52 E-value=2.6 Score=45.81 Aligned_cols=65 Identities=26% Similarity=0.323 Sum_probs=39.3
Q ss_pred hhhHhhhhhhhcC--CCceEEEec-cHHHHHHHH----HcCCCCC-------C----------ccchHHHHHHhcCC-CC
Q 001207 422 RDLLNEFAPFFED--PSIKKVWHN-YSFDNHVLE----NYGLKVS-------G----------FHADTMHMARLWDS-SR 476 (1123)
Q Consensus 422 ~evl~~Lk~~Led--~~i~KV~HN-aKfDl~vL~----r~GI~l~-------~----------~vfDTmIAAyLLdp-~~ 476 (1123)
.+.+..|..++.+ |. .++++| ..||+.+|. .+|+.+. + ..+|.+-...--.- ..
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 469999 479999984 2566533 0 14566654432111 11
Q ss_pred CCCCCCCHHHHhhc
Q 001207 477 RTEGGYSLEALTGD 490 (1123)
Q Consensus 477 ~~~gs~sLd~La~~ 490 (1123)
++++|+.+|+.
T Consensus 153 ---~sysLd~Va~~ 163 (204)
T cd05779 153 ---GSQGLKAVTKA 163 (204)
T ss_pred ---CCccHHHHHHH
Confidence 25899999976
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=89.87 E-value=4.8 Score=44.31 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001207 553 ELWISYSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 553 e~~l~YAA~DA~~tlrL~e~L~ 574 (1123)
....+|+..||..+++|...|.
T Consensus 203 ~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 203 RRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred HHHHHhhHHHHHHHHHHHHHHh
Confidence 4678999999999999999875
No 93
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=87.70 E-value=6.7 Score=49.95 Aligned_cols=72 Identities=25% Similarity=0.309 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHHHHHHhhhcC---cccCHH---HHHH
Q 001207 553 ELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEG---MLVDRE---YLSE 626 (1123)
Q Consensus 553 e~~l~YAA~DA~~tlrL~e~L~~kL~e~~~~~~~~~~~~~~l~~Ly~~IEmPLv~VLa~ME~~G---I~VD~e---~L~~ 626 (1123)
.....|||.|+.+|.+++..+-+..-++ | |-.-.|+.|-.-| .+|+.. ++.+
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 4567899999999999999998876543 2 3334677777777 567744 4444
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 001207 627 IEKVARAEQEAAVNRFRKWA 646 (1123)
Q Consensus 627 l~~~l~~e~e~le~~i~~~~ 646 (1123)
.+..++.-...++.+|.+.+
T Consensus 417 ~e~tYeq~~~~~~~kl~~~A 436 (1075)
T KOG3657|consen 417 AEQTYEQLKTEAKRKIIESA 436 (1075)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444444444555555554
No 94
>PHA02528 43 DNA polymerase; Provisional
Probab=85.81 E-value=8.2 Score=50.62 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001207 552 RELWISYSAFDSINTLKLYKSL 573 (1123)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1123)
.....+|+..||..+++|...+
T Consensus 303 ~~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 303 HQKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999974
No 95
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=84.66 E-value=3.6 Score=46.29 Aligned_cols=61 Identities=20% Similarity=0.105 Sum_probs=39.3
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccchHHHHH---HhcCCCCCCCCCCCHHHHhhc
Q 001207 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMA---RLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 421 ~~evl~~Lk~~Led~~i~KV~HNaKfDl~vL~r-~GI~l~~~vfDTmIAA---yLLdp~~~~~gs~sLd~La~~ 490 (1123)
...+-.....+|.+. .+|||.+..|+.+|.- |- ...+.||.--- .++... +..||+.|++.
T Consensus 171 f~~aQ~ev~klL~gR--IlVGHaLhnDl~~L~l~hp---~s~iRDTs~~~pl~k~~~~~----~tpSLK~Lt~~ 235 (280)
T KOG2249|consen 171 FKVAQKEVLKLLKGR--ILVGHALHNDLQALKLEHP---RSMIRDTSKYPPLMKLLSKK----ATPSLKKLTEA 235 (280)
T ss_pred HHHHHHHHHHHHhCC--EEeccccccHHHHHhhhCc---hhhhcccccCchHHHHhhcc----CCccHHHHHHH
Confidence 445666777888764 5799999999999852 31 12355665322 222222 25899999986
No 96
>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=83.97 E-value=14 Score=44.32 Aligned_cols=134 Identities=20% Similarity=0.124 Sum_probs=82.4
Q ss_pred eEEeecccchhHHHHHHhcCchhHHHHHH-----cCCchhHHHHhhhccccchhh---ccchhhhcccCCCCCCCCcccc
Q 001207 868 SLIVADYGQLELRILAHLANCKSMLDAFK-----AGGDFHSRTAMNMYPHIRNAV---ETGQVLLEWHGEDKPPVPLLKD 939 (1123)
Q Consensus 868 ~lVsaDySQIELRIlAhlS~D~~Li~af~-----~G~DIH~~tA~~if~~~~e~v---~~~e~~~~w~~~~~~~v~~~~~ 939 (1123)
+-|..|-|-==+-.+|.|.+|+.+..+.+ .-.|||+.+|..+-....+.. ........|..
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 44677777777889999999999888765 236999999876543322210 11112233321
Q ss_pred cchHHHHhhHHHhhhhhhCCChhhhhhhcC-------C-----------CHHHHHHHHHHHHHhChhHH---HHHHHHHH
Q 001207 940 AFASERRKAKMLNFSIAYGKTPVGLARDWK-------V-----------SVEEAKKTVDLWYNERQEVL---TWQEARKK 998 (1123)
Q Consensus 940 vt~~~R~~AK~vnfGiiYG~G~~~LA~~lg-------i-----------S~~EAk~~i~~f~~~yP~Vk---~~~~~~~~ 998 (1123)
..-.|+..|+..--++||.+..|.+.++. . ..--|+.+.+.+...||+.+ +|++.+..
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 13569999999999999999999987651 1 12236777888888999765 56666655
Q ss_pred HHHhCCe-E--ecccCCc
Q 001207 999 ESRIDNH-V--HTLLGRA 1013 (1123)
Q Consensus 999 ~A~~~Gy-V--~Tl~GRr 1013 (1123)
.+.+.+- | .|+.|-.
T Consensus 235 ~~~~~~~pv~W~tP~Gl~ 252 (405)
T PF00940_consen 235 IIAKLNKPVSWTTPLGLP 252 (405)
T ss_dssp HHHCTCB-EEEEETTSEE
T ss_pred HHHccCCcEEEECCCCCE
Confidence 5544332 2 3555543
No 97
>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=83.47 E-value=0.43 Score=47.37 Aligned_cols=112 Identities=24% Similarity=0.316 Sum_probs=61.7
Q ss_pred EEEeecccccccccCccccCcceEEEEeeeCCCcccCCCceEEEEeCCC---C-------------------ChhhhHhh
Q 001207 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---G-------------------GGRDLLNE 427 (1123)
Q Consensus 370 VAfDTETtGLd~~~d~Ivg~g~ii~~sl~~~~~I~I~~~~~~~~ID~~~---~-------------------~~~evl~~ 427 (1123)
|+||+||||+++..+.|+..| ++.+..+...... .-..++.+.. . ...++...
T Consensus 1 v~~D~Ettg~~~~~~~iieig---~v~~~~~~~~~~~--~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIG---AVKVDDDENEEVE--SFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEE---EEEEETTTTEEEE--EEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEE---EEEeeCCccccce--eeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHh
Confidence 689999999999777787622 3333322100000 0112232211 0 11335666
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----Hc-CCCCC--CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NY-GLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 428 Lk~~Led~~i~KV~HNaKfDl~vL~----r~-GI~l~--~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
|..++... ...|+||+.||..++. ++ +...+ ..++||+...+...+... .++|+.|++.
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 77788632 4689999999886653 22 22222 346677766665544432 3688888875
No 98
>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=71.70 E-value=3.8 Score=43.70 Aligned_cols=59 Identities=19% Similarity=0.079 Sum_probs=38.7
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+...|..++. +...+|||.+..|+.+|+-. .+...++||-+...+ |... ..+|+.|+..
T Consensus 91 v~~~l~~li~-~~tILVGHsL~nDL~aL~l~--hp~~~viDTa~l~~~--~~~r---~~sLk~La~~ 149 (174)
T cd06143 91 AYLKLRLLVD-LGCIFVGHGLAKDFRVINIQ--VPKEQVIDTVELFHL--PGQR---KLSLRFLAWY 149 (174)
T ss_pred HHHHHHHHcC-CCCEEEeccchhHHHHhcCc--CCCcceEEcHHhccC--CCCC---ChhHHHHHHH
Confidence 4445666664 34468999999999998521 122458899754322 3222 5899999987
No 99
>PRK05762 DNA polymerase II; Reviewed
Probab=71.16 E-value=55 Score=42.74 Aligned_cols=65 Identities=26% Similarity=0.462 Sum_probs=41.1
Q ss_pred hhhHhhhhhhhc--CCCceEEEecc-HHHHHHHH----HcCCCCC-------------------------C-ccchHHHH
Q 001207 422 RDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVLE----NYGLKVS-------------------------G-FHADTMHM 468 (1123)
Q Consensus 422 ~evl~~Lk~~Le--d~~i~KV~HNa-KfDl~vL~----r~GI~l~-------------------------~-~vfDTmIA 468 (1123)
.+.+..|..++. ||+ .+++||. .||+..|. .+|+.+. + .++|++..
T Consensus 204 ~~LL~~F~~~i~~~DPD-IIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~ 282 (786)
T PRK05762 204 KALLEKFNAWFAEHDPD-VIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDA 282 (786)
T ss_pred HHHHHHHHHHHHhcCCC-EEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHH
Confidence 456666666665 455 4799995 79999984 2566431 1 15677766
Q ss_pred HHhcCCCCCCCCCCCHHHHhhc
Q 001207 469 ARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 469 AyLLdp~~~~~gs~sLd~La~~ 490 (1123)
.+-..-... +|+|+.++.+
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 100
>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=70.58 E-value=17 Score=40.34 Aligned_cols=109 Identities=24% Similarity=0.290 Sum_probs=64.5
Q ss_pred hhhHhhhhhhhc--CCCceEEEecc-HHHHHHHH----HcCCCC---------------------------CC-ccchHH
Q 001207 422 RDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVLE----NYGLKV---------------------------SG-FHADTM 466 (1123)
Q Consensus 422 ~evl~~Lk~~Le--d~~i~KV~HNa-KfDl~vL~----r~GI~l---------------------------~~-~vfDTm 466 (1123)
.+.+..|..++. ||++ ++|||+ .||+.+|. .+|+.. .| .+.|+.
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 345566666554 6774 799997 89999873 133321 11 156888
Q ss_pred HHHHhcCCCCCCCCCCCHHHHhhcccccccccccccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhH
Q 001207 467 HMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEE 546 (1123)
Q Consensus 467 IAAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~ 546 (1123)
..++=+-. .. +|+|++++.. +|+.+ ..++ ...++.. .|.. +
T Consensus 162 ~~~k~~~~-~~---sY~L~~va~~-------~Lg~~--------k~di----~~~~i~~------------~~~~-~--- 202 (234)
T cd05776 162 LSAKELIR-CK---SYDLTELSQQ-------VLGIE--------RQDI----DPEEILN------------MYND-S--- 202 (234)
T ss_pred HHHHHHhC-CC---CCChHHHHHH-------HhCcC--------cccC----CHHHHHH------------HHhC-H---
Confidence 87774432 22 6999999986 45432 0111 0011110 1111 0
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 547 LQREERELWISYSAFDSINTLKLYKSL 573 (1123)
Q Consensus 547 l~~~~~e~~l~YAA~DA~~tlrL~e~L 573 (1123)
......++|+..||..+++|...|
T Consensus 203 ---~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 203 ---ESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 124567899999999999998876
No 101
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=61.73 E-value=92 Score=42.12 Aligned_cols=23 Identities=30% Similarity=0.332 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 001207 552 RELWISYSAFDSINTLKLYKSLK 574 (1123)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L~ 574 (1123)
......|+..||..+++|...|.
T Consensus 461 ~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 461 RRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999998764
No 102
>PHA00452 T3/T7-like RNA polymerase
Probab=54.98 E-value=89 Score=41.01 Aligned_cols=209 Identities=14% Similarity=0.091 Sum_probs=114.0
Q ss_pred EeecccchhHHHHHHhcCchhHHHHHH-----cCCchhHHHHhhhccccchhhccc-----hhhhcccCCCCCCCCcccc
Q 001207 870 IVADYGQLELRILAHLANCKSMLDAFK-----AGGDFHSRTAMNMYPHIRNAVETG-----QVLLEWHGEDKPPVPLLKD 939 (1123)
Q Consensus 870 VsaDySQIELRIlAhlS~D~~Li~af~-----~G~DIH~~tA~~if~~~~e~v~~~-----e~~~~w~~~~~~~v~~~~~ 939 (1123)
|..|-|.==+-.+|.|.+|....++.+ .-.|||+.+|..+-.........+ .....|..
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 444555555677889999988877664 236999999976533211110000 00001110
Q ss_pred cchHHHHhhHHHhhhhhhCCChhhhhhhc-------CCCH--------H----HHHHHHHHHHHhChh---HHHHHHHHH
Q 001207 940 AFASERRKAKMLNFSIAYGKTPVGLARDW-------KVSV--------E----EAKKTVDLWYNERQE---VLTWQEARK 997 (1123)
Q Consensus 940 vt~~~R~~AK~vnfGiiYG~G~~~LA~~l-------giS~--------~----EAk~~i~~f~~~yP~---Vk~~~~~~~ 997 (1123)
....|+..|+.+-=++||.+..|.++++ ++.. + -|+.+.++..+.||+ +..|+..+.
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 1235999999999999999999987654 2221 1 267778888888986 456888877
Q ss_pred HHHH-hCCe-E--ecccCCcccCCCCCccC-------------------hhhhhhhhhh--hhhhhhhchHHHHHHHHHH
Q 001207 998 KESR-IDNH-V--HTLLGRARRFPAIKSLT-------------------RSQRNHIERA--AINTPVQGSAADVAMCAML 1052 (1123)
Q Consensus 998 ~~A~-~~Gy-V--~Tl~GRrr~lp~~~s~n-------------------~~~r~~aeR~--AvN~~IQGSAADI~K~AMi 1052 (1123)
..+. +.+. | .|+.|-...-|=.+... ......-.++ +.|.+=+==|+=+ .|.
T Consensus 647 ~~i~~~~~~pv~W~TP~GlpV~Q~Y~k~~~~~v~t~~~~~~~i~~~~~~~~~d~~Kq~~a~~PNFIHSLDAsHm---~~t 723 (807)
T PHA00452 647 KLLAAKGAEALHWTTPTGFPVWQEYRKPEEKRVRLRLMGVARVQLYVNTDTIDARKHASGIAPNFVHSLDASHL---RLT 723 (807)
T ss_pred HHHHHhcCCCEEEECCCCCEEEeeecCCCcEEEEEeeccceeEEeccCCCCCCHHHHhcccCCchhhhhhHHHH---HHH
Confidence 7665 3321 1 35555433221100000 0000000111 3455433223322 222
Q ss_pred HHHHHHhhccCCceEEEEeeceEEEeCCcchHHHHHHHHHHHHcCCC
Q 001207 1053 EISKNARLKELGWKLLLQVHDEVILEGPSESAEVAKAIVVECMSKPF 1099 (1123)
Q Consensus 1053 ~i~~~~~l~~~g~~llLqVHDELv~EVp~~~aeev~~~v~~~Me~a~ 1099 (1123)
-+ .+.+.|..-+..|||..... ...++.+..+|++.+-.-+
T Consensus 724 ~~----~~~~~g~~~fa~VHDsfwTh--a~dvd~m~~~lRe~FV~ly 764 (807)
T PHA00452 724 VV----ACAEKGIESFAVIHDSFGTH--AADADNLHRAIRETFVEMY 764 (807)
T ss_pred HH----HHHhcCCCcEEEeccCcccC--hhhHHHHHHHHHHHHHHHh
Confidence 22 12234555578999997654 4456777777877665543
No 103
>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=53.88 E-value=30 Score=35.30 Aligned_cols=40 Identities=25% Similarity=0.189 Sum_probs=22.4
Q ss_pred HHHHHH-HHHcCCCCCCccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 445 SFDNHV-LENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 445 KfDl~v-L~r~GI~l~~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
..|+.+ +.+.|+.+. +--|.|+.+||+||.. .+...++.+
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 467898774 3579999999999963 567777776
No 104
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=49.11 E-value=43 Score=38.92 Aligned_cols=107 Identities=21% Similarity=0.146 Sum_probs=63.9
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHH--cCCCCCCccchHHH-HHHhcCCCCCCCCCCCHHHHhhccccccccccc
Q 001207 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLEN--YGLKVSGFHADTMH-MARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (1123)
Q Consensus 424 vl~~Lk~~Led~~i~KV~HNaKfDl~vL~r--~GI~l~~~vfDTmI-AAyLLdp~~~~~gs~sLd~La~~~~~~~~~~Lg 500 (1123)
+...|+.||+|+....|+-+...|..-|.+ |++.+. ...|... +.-.+++... ..+.+.|+.. .++
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 455677889999999999999999988865 666552 2333221 1112232221 2455666654 222
Q ss_pred ccccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhHHHHHHHHHHHHHHHHHHHH
Q 001207 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLY 570 (1123)
Q Consensus 501 ~~~~l~k~~~~eel~GK~s~k~lfgK~k~kkq~s~~kdw~~~pl~~l~~~~~e~~l~YAA~DA~~tlrL~ 570 (1123)
+. |+. ....+. ... .+|...|+ +.+|+.||+-||.+.+.|+
T Consensus 241 ~~-------------~~~-------v~l~~~-i~m-sdw~~~~L-------s~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 241 YY-------------GKD-------VRLDKE-IRM-SDWSVYPL-------SDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cc-------------ccc-------cccChh-ccc-ccceeeec-------cHHHHHHHHhHHHHHHHHH
Confidence 21 110 000000 111 27999887 4689999999999999999
No 105
>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=46.09 E-value=1.8e+02 Score=34.49 Aligned_cols=22 Identities=36% Similarity=0.622 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 001207 552 RELWISYSAFDSINTLKLYKSL 573 (1123)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L 573 (1123)
......|+..|+..+++|+..+
T Consensus 199 ~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 199 RDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999876
No 106
>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=37.24 E-value=2.1e+02 Score=34.95 Aligned_cols=64 Identities=16% Similarity=0.198 Sum_probs=37.4
Q ss_pred hhhHhhhhhhhcC-CCceEEEeccHHHHHHHHH----cCCCCC------CccchHHHHHH--hcCCCCCCCCCCCHHHHh
Q 001207 422 RDLLNEFAPFFED-PSIKKVWHNYSFDNHVLEN----YGLKVS------GFHADTMHMAR--LWDSSRRTEGGYSLEALT 488 (1123)
Q Consensus 422 ~evl~~Lk~~Led-~~i~KV~HNaKfDl~vL~r----~GI~l~------~~vfDTmIAAy--LLdp~~~~~gs~sLd~La 488 (1123)
..++..|.+|+.. +...++.+| .|....|++ +|.... ..++|.....+ ++.|. ++|||+.++
T Consensus 329 ~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~----~sysLK~v~ 403 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPI----ESYSLKSIA 403 (457)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCC----CCCCHHHHH
Confidence 4466777777764 333445555 787777764 454311 13456553333 44454 369999999
Q ss_pred hc
Q 001207 489 GD 490 (1123)
Q Consensus 489 ~~ 490 (1123)
..
T Consensus 404 ~~ 405 (457)
T TIGR03491 404 RW 405 (457)
T ss_pred HH
Confidence 74
No 107
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=30.62 E-value=2.6e+02 Score=38.91 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 001207 552 RELWISYSAFDSINTLKLYKSLKK 575 (1123)
Q Consensus 552 ~e~~l~YAA~DA~~tlrL~e~L~~ 575 (1123)
...+..|+..||.+|+-||-+...
T Consensus 429 PQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 429 PQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred chhhhhcchHHHHHHHHHHHHHhh
Confidence 355788999999999999876543
No 108
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=26.71 E-value=1e+02 Score=32.94 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=18.9
Q ss_pred ceEEEeecccccccccCcccc
Q 001207 368 LVHACDTEVAKIDVKQETPVD 388 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg 388 (1123)
..|=+|+|.||||+..++|++
T Consensus 7 nLiWIDlEMTGLd~~~drIIE 27 (184)
T COG1949 7 NLIWIDLEMTGLDPERDRIIE 27 (184)
T ss_pred ceEEEeeeeccCCcCcceEEE
Confidence 467799999999999999987
No 109
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=23.79 E-value=2.5e+02 Score=35.05 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=21.0
Q ss_pred hhhHhhhhhhhc--CCCceEEEec-cHHHHHHH
Q 001207 422 RDLLNEFAPFFE--DPSIKKVWHN-YSFDNHVL 451 (1123)
Q Consensus 422 ~evl~~Lk~~Le--d~~i~KV~HN-aKfDl~vL 451 (1123)
.+.+..|..++. ||. .++||| ..||+..|
T Consensus 181 ~eLL~~F~~~i~~~DPD-IItGYNi~nFDlPYL 212 (498)
T PHA02524 181 VDLLLNYIQLWKANTPD-LVFGWNSEGFDIPYI 212 (498)
T ss_pred HHHHHHHHHHHHHhCCC-EEEeCCCcccCHHHH
Confidence 456666777665 466 479999 47999987
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=22.59 E-value=1e+02 Score=34.70 Aligned_cols=51 Identities=24% Similarity=0.147 Sum_probs=36.4
Q ss_pred CCCceEEEeccHHHHHHHHH--cCCCCC--------------CccchHHHHHHhcCCCCCCCCCCCHHHHhhc
Q 001207 434 DPSIKKVWHNYSFDNHVLEN--YGLKVS--------------GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (1123)
Q Consensus 434 d~~i~KV~HNaKfDl~vL~r--~GI~l~--------------~~vfDTmIAAyLLdp~~~~~gs~sLd~La~~ 490 (1123)
+..+.+|+||+-+|+..|.+ .| +++ +.++||..++...... ..+|+.|+..
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 34478999999999998765 34 443 2378999999877632 4799999975
No 111
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.00 E-value=86 Score=25.76 Aligned_cols=36 Identities=14% Similarity=0.164 Sum_probs=21.4
Q ss_pred hHHHhhhhhhCCChhhhhhhcCCCHHHHHHHHHHHHH
Q 001207 948 AKMLNFSIAYGKTPVGLARDWKVSVEEAKKTVDLWYN 984 (1123)
Q Consensus 948 AK~vnfGiiYG~G~~~LA~~lgiS~~EAk~~i~~f~~ 984 (1123)
+..+-+-.. |.+...+|+.+|||.......+++|.+
T Consensus 8 ~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 8 AQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp --HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred HHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 333433334 999999999999999888888888753
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=20.89 E-value=88 Score=35.23 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHccccCceEEEeeccccccccc
Q 001207 351 VSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQ 383 (1123)
Q Consensus 351 ~e~L~~lv~~L~~a~~~~~VAfDTETtGLd~~~ 383 (1123)
.+++..+.+.|..+ .+||||+|++|+....
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 45567777778775 6999999999988754
No 113
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=20.61 E-value=1.1e+03 Score=28.84 Aligned_cols=104 Identities=10% Similarity=0.041 Sum_probs=58.8
Q ss_pred ceEEEeecccccccccCccccCcceEEEEee-------------eCCC-cccCCCceEEEEeCC--------CCChhhhH
Q 001207 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIY-------------SGPE-ADFGNGKSCIWVDLL--------DGGGRDLL 425 (1123)
Q Consensus 368 ~~VAfDTETtGLd~~~d~Ivg~g~ii~~sl~-------------~~~~-I~I~~~~~~~~ID~~--------~~~~~evl 425 (1123)
.++-.|-||.|.+|..+++..++ |+-.. .+|. =-++... +..|-.. +.+..+..
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 58899999999999998875422 22211 1111 0001111 1222110 11223455
Q ss_pred hhhhhhhcCCCceEEEec-cHHHHHHHH----HcCCCC-----CC-----ccchHHHHHHhcCCC
Q 001207 426 NEFAPFFEDPSIKKVWHN-YSFDNHVLE----NYGLKV-----SG-----FHADTMHMARLWDSS 475 (1123)
Q Consensus 426 ~~Lk~~Led~~i~KV~HN-aKfDl~vL~----r~GI~l-----~~-----~vfDTmIAAyLLdp~ 475 (1123)
..+...|..|+...+|+| +.||=.+-+ +.-+++ .+ -+.|.+-++|-|.|.
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 667777888988889998 789877753 322332 11 156777777777774
Done!