Query 001780
Match_columns 1014
No_of_seqs 472 out of 1908
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 09:09:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001780.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001780hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0969 DNA polymerase delta, 100.0 3E-254 6E-259 2130.7 64.3 927 71-1013 56-1062(1066)
2 PTZ00166 DNA polymerase delta 100.0 6E-212 1E-216 1970.9 89.7 934 73-1014 26-1054(1054)
3 KOG0968 DNA polymerase zeta, c 100.0 4E-141 9E-146 1238.6 50.5 704 301-1014 657-1488(1488)
4 KOG0970 DNA polymerase alpha, 100.0 9E-128 2E-132 1127.9 50.4 831 86-977 328-1333(1429)
5 PRK05761 DNA polymerase I; Rev 100.0 5E-121 1E-125 1121.8 63.1 672 94-898 20-776 (787)
6 PRK05762 DNA polymerase II; Re 100.0 4E-120 8E-125 1122.3 68.4 681 89-898 2-779 (786)
7 COG0417 PolB DNA polymerase el 100.0 5E-118 1E-122 1101.4 64.3 708 117-899 8-781 (792)
8 PHA03036 DNA polymerase; Provi 100.0 3E-119 6E-124 1093.2 50.2 621 247-887 113-986 (1004)
9 TIGR00592 pol2 DNA polymerase 100.0 5E-117 1E-121 1128.2 65.2 722 117-887 322-1172(1172)
10 PHA02528 43 DNA polymerase; Pr 100.0 1E-106 3E-111 994.9 56.1 659 118-892 13-868 (881)
11 cd05533 POLBc_delta DNA polyme 100.0 1.7E-99 4E-104 869.9 36.7 392 497-890 2-393 (393)
12 cd05534 POLBc_zeta DNA polymer 100.0 2.6E-98 6E-103 871.3 36.5 421 465-892 1-448 (451)
13 cd05532 POLBc_alpha DNA polyme 100.0 8.7E-88 1.9E-92 775.4 32.2 377 496-894 6-390 (400)
14 PF00136 DNA_pol_B: DNA polyme 100.0 2.4E-86 5.2E-91 782.8 28.3 421 465-892 1-450 (466)
15 cd05536 POLBc_B3 DNA polymeras 100.0 3.5E-85 7.5E-90 747.0 35.5 367 497-897 3-370 (371)
16 cd05537 POLBc_Pol_II DNA polym 100.0 1.8E-81 3.8E-86 713.8 34.4 348 497-889 2-370 (371)
17 cd05530 POLBc_B1 DNA polymeras 100.0 1.2E-78 2.6E-83 688.5 35.8 349 497-887 12-371 (372)
18 cd00145 POLBc DNA polymerase t 100.0 3.3E-78 7E-83 679.2 30.9 320 497-887 2-323 (323)
19 cd05538 POLBc_Pol_II_B DNA pol 100.0 5.2E-76 1.1E-80 663.5 31.3 329 497-876 2-336 (347)
20 cd05531 POLBc_B2 DNA polymeras 100.0 1E-73 2.2E-78 646.7 33.9 336 496-889 3-352 (352)
21 PHA03334 putative DNA polymera 100.0 2.4E-68 5.2E-73 643.8 32.3 356 402-773 516-998 (1545)
22 KOG1798 DNA polymerase epsilon 100.0 1.3E-65 2.8E-70 611.3 46.4 714 117-886 69-1119(2173)
23 smart00486 POLBc DNA polymeras 100.0 1.2E-65 2.7E-70 605.6 35.4 377 300-681 1-470 (471)
24 cd05535 POLBc_epsilon DNA poly 100.0 5.7E-54 1.2E-58 495.9 26.8 304 567-886 218-613 (621)
25 PHA02524 43A DNA polymerase su 100.0 1.3E-51 2.7E-56 475.9 26.3 279 300-595 104-479 (498)
26 PF03104 DNA_pol_B_exo1: DNA p 100.0 4.2E-41 9.1E-46 379.2 14.6 256 125-402 1-258 (325)
27 TIGR00592 pol2 DNA polymerase 100.0 1.6E-40 3.6E-45 425.4 -1.9 376 199-615 128-618 (1172)
28 PHA02523 43B DNA polymerase su 100.0 5.5E-37 1.2E-41 333.7 16.9 286 601-892 37-377 (391)
29 cd05777 DNA_polB_delta_exo DED 100.0 1.1E-29 2.4E-34 273.4 15.2 151 297-447 2-229 (230)
30 cd05778 DNA_polB_zeta_exo inac 99.9 5.3E-25 1.1E-29 237.0 13.5 139 301-439 3-231 (231)
31 cd05779 DNA_polB_epsilon_exo D 99.9 3.2E-23 6.8E-28 218.4 11.9 135 301-438 1-203 (204)
32 cd05780 DNA_polB_Kod1_like_exo 99.9 2.8E-22 6.1E-27 210.7 13.1 130 300-441 1-195 (195)
33 PHA02563 DNA polymerase; Provi 99.9 4.5E-21 9.8E-26 228.5 18.3 272 420-746 170-543 (630)
34 cd05781 DNA_polB_B3_exo DEDDy 99.8 4.7E-21 1E-25 200.1 12.0 122 300-441 1-188 (188)
35 cd05783 DNA_polB_B1_exo DEDDy 99.8 1.8E-19 3.8E-24 190.4 12.2 95 298-400 1-105 (204)
36 cd05160 DEDDy_DNA_polB_exo DED 99.8 1.8E-19 3.9E-24 189.8 11.7 96 304-400 1-97 (199)
37 cd05785 DNA_polB_like2_exo Unc 99.8 1.5E-19 3.3E-24 191.4 10.9 85 298-400 5-92 (207)
38 cd05784 DNA_polB_II_exo DEDDy 99.8 8.1E-19 1.7E-23 183.8 11.1 85 300-400 1-85 (193)
39 cd05776 DNA_polB_alpha_exo ina 99.7 2.8E-18 6.1E-23 185.4 8.5 142 300-446 1-231 (234)
40 PF14260 zf-C4pol: C4-type zin 99.6 4.1E-15 8.9E-20 131.6 6.9 71 926-996 1-73 (73)
41 cd05782 DNA_polB_like1_exo Unc 99.3 3.9E-12 8.4E-17 135.2 9.8 104 318-439 45-207 (208)
42 PF10108 DNA_pol_B_exo2: Predi 98.6 1.8E-07 4E-12 98.5 9.8 110 318-444 3-172 (209)
43 PF13482 RNase_H_2: RNase_H su 98.0 4.7E-06 1E-10 85.1 5.3 116 305-441 1-163 (164)
44 PHA02735 putative DNA polymera 97.9 0.00011 2.3E-09 82.6 12.4 106 420-540 203-312 (716)
45 PF08490 DUF1744: Domain of un 97.9 0.00023 4.9E-09 82.8 15.2 256 439-729 117-396 (396)
46 COG3359 Predicted exonuclease 97.4 0.00048 1E-08 73.2 8.5 75 303-399 99-173 (278)
47 PRK06309 DNA polymerase III su 96.6 0.0034 7.4E-08 68.2 6.5 86 303-400 3-98 (232)
48 cd06125 DnaQ_like_exo DnaQ-lik 96.3 0.0072 1.6E-07 56.5 5.7 61 305-400 1-61 (96)
49 TIGR00573 dnaq exonuclease, DN 96.0 0.01 2.2E-07 63.9 6.0 86 302-400 7-104 (217)
50 PRK06310 DNA polymerase III su 96.0 0.013 2.8E-07 64.4 6.8 90 301-400 6-105 (250)
51 smart00479 EXOIII exonuclease 95.9 0.027 5.9E-07 57.2 8.3 86 304-400 2-98 (169)
52 cd06136 TREX1_2 DEDDh 3'-5' ex 95.9 0.021 4.6E-07 59.4 7.5 92 305-400 2-116 (177)
53 cd06138 ExoI_N N-terminal DEDD 95.8 0.014 3.1E-07 60.9 6.0 89 305-400 1-102 (183)
54 PRK09145 DNA polymerase III su 95.8 0.019 4.1E-07 61.0 6.7 91 301-400 28-128 (202)
55 PRK08517 DNA polymerase III su 95.8 0.018 3.9E-07 63.6 6.6 91 301-400 67-164 (257)
56 PRK05711 DNA polymerase III su 95.7 0.022 4.7E-07 62.3 6.9 89 300-400 2-103 (240)
57 cd06130 DNA_pol_III_epsilon_li 95.6 0.021 4.7E-07 57.4 5.9 83 305-400 2-94 (156)
58 PF08996 zf-DNA_Pol: DNA Polym 95.5 0.0079 1.7E-07 63.3 2.7 60 921-980 16-93 (188)
59 cd06135 Orn DEDDh 3'-5' exonuc 95.5 0.027 5.8E-07 58.4 6.3 89 305-400 2-111 (173)
60 cd06127 DEDDh DEDDh 3'-5' exon 95.4 0.019 4E-07 57.1 4.8 84 305-400 1-96 (159)
61 PRK07740 hypothetical protein; 95.4 0.034 7.3E-07 61.0 7.0 91 300-400 57-158 (244)
62 PRK09146 DNA polymerase III su 95.4 0.031 6.7E-07 61.1 6.6 91 301-400 46-146 (239)
63 PRK07942 DNA polymerase III su 95.3 0.046 1E-06 59.5 7.9 92 301-400 5-110 (232)
64 PRK05359 oligoribonuclease; Pr 95.3 0.041 8.9E-07 57.6 7.2 91 303-400 4-115 (181)
65 PRK06807 DNA polymerase III su 95.3 0.033 7.1E-07 63.3 6.6 89 301-400 7-105 (313)
66 PRK06063 DNA polymerase III su 95.2 0.047 1E-06 62.1 7.6 89 301-400 14-111 (313)
67 cd06131 DNA_pol_III_epsilon_Ec 95.1 0.054 1.2E-06 55.4 7.0 86 305-400 2-98 (167)
68 PRK05168 ribonuclease T; Provi 94.9 0.086 1.9E-06 56.5 8.4 92 300-400 15-131 (211)
69 PRK07247 DNA polymerase III su 94.8 0.079 1.7E-06 56.1 7.5 89 303-400 6-102 (195)
70 PF03175 DNA_pol_B_2: DNA poly 94.7 0.0054 1.2E-07 73.3 -1.9 45 568-624 329-373 (459)
71 TIGR01406 dnaQ_proteo DNA poly 94.6 0.077 1.7E-06 57.5 7.1 86 303-400 1-99 (225)
72 PRK07883 hypothetical protein; 94.6 0.062 1.3E-06 65.8 7.0 89 301-400 14-112 (557)
73 PRK11779 sbcB exonuclease I; P 94.2 0.14 2.9E-06 61.4 8.4 93 300-400 4-111 (476)
74 TIGR01405 polC_Gram_pos DNA po 94.2 0.12 2.6E-06 68.2 8.6 88 302-400 190-287 (1213)
75 KOG1798 DNA polymerase epsilon 94.2 0.33 7.2E-06 62.8 11.8 249 438-728 1586-1867(2173)
76 cd06134 RNaseT DEDDh 3'-5' exo 93.9 0.13 2.8E-06 54.1 6.8 91 304-400 7-119 (189)
77 PRK06195 DNA polymerase III su 93.9 0.1 2.2E-06 59.3 6.3 85 303-400 2-97 (309)
78 PRK05601 DNA polymerase III su 93.9 0.18 4E-06 57.9 8.3 91 299-400 43-142 (377)
79 PRK09182 DNA polymerase III su 93.6 0.19 4.1E-06 56.7 7.7 31 300-335 35-65 (294)
80 TIGR01298 RNaseT ribonuclease 93.5 0.25 5.3E-06 52.6 8.2 92 303-400 9-122 (200)
81 PF00929 RNase_T: Exonuclease; 93.2 0.21 4.6E-06 49.5 6.7 88 305-400 1-100 (164)
82 TIGR01407 dinG_rel DnaQ family 92.9 0.17 3.7E-06 65.3 6.8 87 303-400 1-97 (850)
83 PRK07748 sporulation inhibitor 92.5 0.3 6.4E-06 52.2 7.0 97 301-400 3-110 (207)
84 cd06144 REX4_like DEDDh 3'-5' 92.1 0.28 6.2E-06 49.6 5.9 38 358-399 56-93 (152)
85 PRK08074 bifunctional ATP-depe 91.8 0.32 6.9E-06 63.3 7.4 88 303-400 4-101 (928)
86 cd06137 DEDDh_RNase DEDDh 3'-5 91.1 0.33 7.1E-06 49.7 5.2 83 305-400 1-101 (161)
87 TIGR03491 RecB family nuclease 90.9 0.79 1.7E-05 55.0 9.0 75 303-400 285-360 (457)
88 PRK07246 bifunctional ATP-depe 90.7 0.38 8.2E-06 61.7 6.4 87 302-400 7-103 (820)
89 PHA03181 helicase-primase prim 89.2 19 0.0004 45.0 18.4 162 609-789 459-643 (764)
90 cd06149 ISG20 DEDDh 3'-5' exon 89.0 0.68 1.5E-05 47.2 5.5 84 305-400 1-94 (157)
91 cd06133 ERI-1_3'hExo_like DEDD 88.9 1.2 2.5E-05 45.7 7.3 94 305-400 2-107 (176)
92 cd06145 REX1_like DEDDh 3'-5' 88.0 0.97 2.1E-05 45.7 5.8 84 305-400 1-93 (150)
93 PHA03144 helicase-primase prim 87.0 28 0.0006 43.6 18.1 162 609-789 450-629 (746)
94 PRK06722 exonuclease; Provisio 86.6 1.6 3.4E-05 49.0 6.9 92 303-400 6-107 (281)
95 COG2176 PolC DNA polymerase II 86.0 1 2.3E-05 57.8 5.6 91 299-400 418-518 (1444)
96 COG0847 DnaQ DNA polymerase II 83.8 2.3 5E-05 46.2 6.6 90 302-400 13-112 (243)
97 PF01612 DNA_pol_A_exo1: 3'-5' 82.7 4.5 9.9E-05 41.0 7.9 29 369-400 65-94 (176)
98 PRK14714 DNA polymerase II lar 77.3 1.5 3.2E-05 57.1 2.5 106 877-1010 623-741 (1337)
99 PRK07983 exodeoxyribonuclease 76.6 6.2 0.00014 42.6 6.8 80 304-400 2-91 (219)
100 PRK00448 polC DNA polymerase I 74.6 3.8 8.2E-05 55.4 5.4 88 302-400 419-516 (1437)
101 PHA03140 helicase-primase prim 71.9 1.6E+02 0.0035 37.2 17.5 137 609-764 457-613 (772)
102 cd06139 DNA_polA_I_Ecoli_like_ 60.0 62 0.0013 33.3 10.0 78 303-400 6-84 (193)
103 PTZ00315 2'-phosphotransferase 53.4 49 0.0011 40.8 8.8 94 302-398 56-169 (582)
104 PHA02952 EEV maturation protei 53.2 32 0.0007 42.5 7.2 39 361-400 249-291 (648)
105 PF03337 Pox_F12L: Poxvirus F1 47.8 49 0.0011 41.1 7.5 95 299-400 189-293 (651)
106 PF13240 zinc_ribbon_2: zinc-r 46.0 10 0.00022 26.1 0.9 21 925-945 1-22 (23)
107 PRK05755 DNA polymerase I; Pro 45.3 55 0.0012 42.8 8.1 73 301-400 314-387 (880)
108 KOG3657 Mitochondrial DNA poly 44.9 19 0.00041 45.2 3.5 23 420-442 358-380 (1075)
109 PRK04023 DNA polymerase II lar 42.6 18 0.00039 46.5 2.9 105 877-1010 589-695 (1121)
110 PF03833 PolC_DP2: DNA polymer 40.1 9.4 0.0002 48.1 0.0 62 877-947 617-678 (900)
111 PF13248 zf-ribbon_3: zinc-rib 38.9 16 0.00035 25.7 1.0 22 924-945 3-25 (26)
112 PF03175 DNA_pol_B_2: DNA poly 36.9 16 0.00034 43.9 1.2 32 497-529 205-236 (459)
113 cd06141 WRN_exo DEDDy 3'-5' ex 33.2 71 0.0015 32.5 5.2 21 422-442 149-169 (170)
114 PF10571 UPF0547: Uncharacteri 31.7 28 0.0006 24.8 1.2 22 925-946 2-24 (26)
115 cd06129 RNaseD_like DEDDy 3'-5 29.4 1.1E+02 0.0024 31.0 5.8 21 422-442 140-160 (161)
116 TIGR03826 YvyF flagellar opero 28.0 20 0.00044 35.9 0.1 29 924-952 4-34 (137)
117 PRK00420 hypothetical protein; 27.1 31 0.00067 33.4 1.2 24 922-945 22-49 (112)
118 PF08408 DNA_pol_B_3: DNA poly 26.4 26 0.00056 35.2 0.5 43 401-445 88-130 (149)
119 TIGR03826 YvyF flagellar opero 26.2 24 0.00053 35.3 0.3 26 922-947 80-105 (137)
120 PF08988 DUF1895: Protein of u 25.1 1.4E+02 0.003 26.4 4.7 39 575-613 18-60 (68)
121 PF09889 DUF2116: Uncharacteri 24.9 80 0.0017 27.1 3.1 22 924-945 4-27 (59)
122 TIGR02501 type_III_yscE type I 23.5 1.5E+02 0.0034 26.0 4.7 46 573-619 15-64 (67)
123 PRK06266 transcription initiat 21.6 1E+02 0.0022 32.4 3.8 41 924-964 118-169 (178)
124 COG1645 Uncharacterized Zn-fin 20.1 46 0.00099 33.1 0.8 23 922-944 27-52 (131)
No 1
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=2.6e-254 Score=2130.69 Aligned_cols=927 Identities=67% Similarity=1.124 Sum_probs=895.8
Q ss_pred ccCccCCCCCCCCCCCCCCeeEEEEEeEEeeecCCccccCccccCCceEEEEEEEecCCcEEEEEEeCcceEEEEecCCC
Q 001780 71 RLAKWARPPLSSGYVSQCQSIMFQQLDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQG 150 (1014)
Q Consensus 71 ~~~~~~r~~~~~~~~~~~~~l~Fq~lD~d~~~~~~~~~~~~~~~~~~pvIrLFGvT~~G~SV~v~V~gF~PYFYV~~p~~ 150 (1014)
..++|.||++| .++|...+|.|||+|+|.+++.+ +...+.+|+||+||+|.+|+|||||||||.|||||++|.+
T Consensus 56 ~~~~w~Rp~~p-~~~p~~~~i~fqq~~~e~y~~~~-----~~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g 129 (1066)
T KOG0969|consen 56 EHSRWARPALP-ALDPIKNDIEFQQIDIEFYVENG-----SGTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNG 129 (1066)
T ss_pred ccccccCCCCC-ccCcccccceEEEeehhhhccCC-----CcccCCCceEEEeeeccCCCeEEEEEecccceEEecCCCC
Confidence 34789999996 67999999999999999986532 2445678999999999999999999999999999999999
Q ss_pred CCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccCCCcccEEEEEEcChhhHHHHHHHHhcCccccCCC
Q 001780 151 MGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVASCRGILDRGIQLDGLG 230 (1014)
Q Consensus 151 ~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~~~~~~flKI~~~~P~~v~klR~~le~g~~~~~l~ 230 (1014)
+.++++..+.+.|+..+.. ..+..+++|+|+++|||+++++.+|+||++++|.++.++|..|++|....+.+
T Consensus 130 ~~~e~i~~~~~~l~~~~~~--------~av~~ve~~~k~~l~~~~g~~k~~f~kit~~lP~~~~~~r~~lergv~~~~~~ 201 (1066)
T KOG0969|consen 130 FGPEHIGKFQQALDVKVTA--------HAVDHVEVVSKESLYGYQGDTKQPFLKITVTLPRMVAAARRLLERGVFISGKG 201 (1066)
T ss_pred CCHHHHHHHHHHHHHHHHH--------hHHHHHHHHhhhhhheecCCCCceeEEEecccHHHHHHhHHHHHhcccccccC
Confidence 9999999999999988764 25888999999999999999999999999999999999999999994444332
Q ss_pred C-ccceeeecccccceeeeeecCCcceeEEEEeccceeccccccccceeeeeeeccccccCCCCCCcCCCCCcEEEEEEE
Q 001780 231 M-KSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDI 309 (1014)
Q Consensus 231 ~-~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~~~pplrilSfDI 309 (1014)
. ..+++||+||+|.+|||+|++|.||+|+++|+++|..+..+.|.||+|+++.|+++++|+++|+|.++||+|+|||||
T Consensus 202 ~~~~~~~yEsNi~f~lrfmvd~~iVG~~wi~lp~gk~~~~~~~~s~cqlEv~v~y~~lishp~eG~w~~~APlrvlSfDI 281 (1066)
T KOG0969|consen 202 EKVGFTTYESNIDFVLRFMVDCDIVGMNWIELPAGKYRIRDNRVSRCQLEVSVNYKDLISHPAEGEWSKIAPLRVLSFDI 281 (1066)
T ss_pred cceeeeEecCCccEEEEEEecCccccceeEEeccchheeccchhcccceEEEEeecccccccccCcccccccccccceeE
Confidence 2 257899999999999999999999999999999998887799999999999999999999999999999999999999
Q ss_pred EEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEec
Q 001780 310 ECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYN 389 (1014)
Q Consensus 310 E~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyN 389 (1014)
||.+++|.||+|+.||||||++++...|+..||++++|+|++|++|.|++|.++.+|++||.+|.+||++.|||||+|||
T Consensus 282 ECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~V~~~~~e~elL~~W~~firevDPDvI~GYN 361 (1066)
T KOG0969|consen 282 ECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSNVHSYETEKELLESWRKFIREVDPDVIIGYN 361 (1066)
T ss_pred EeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCceeEEeccHHHHHHHHHHHHHhcCCCeEeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcccccc---------------------------------------------------------------------
Q 001780 390 ICKFDLPYLIE--------------------------------------------------------------------- 400 (1014)
Q Consensus 390 i~~FDlpyL~~--------------------------------------------------------------------- 400 (1014)
+.+||+|||++
T Consensus 362 i~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfDllqvi~Rd~KLrSytLNaV 441 (1066)
T KOG0969|consen 362 ICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFDLLQVILRDYKLRSYTLNAV 441 (1066)
T ss_pred ccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeeehHHHHHHHhhhhhhcchhhh
Confidence 99999999999
Q ss_pred --------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHH
Q 001780 401 --------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLS 472 (1014)
Q Consensus 401 --------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s 472 (1014)
||||||+.|+++|+|+.++|+|||.||||||+||+||+++||.+.||+|||||||+|++++++|||||||.|
T Consensus 442 s~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDAYLPlRLlekLM~ivNy~EMARVTGVP~syLltRGqqIKVlS 521 (1066)
T KOG0969|consen 442 SAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEKLMVIVNYTEMARVTGVPISYLLTRGQQIKVLS 521 (1066)
T ss_pred HHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhhcchHHHHHHHHHHHhHHhhhhhhCCcHHHHHhCCcchHHHH
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCccccCCCcCCCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCC
Q 001780 473 QLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPE 552 (1014)
Q Consensus 473 ~L~r~a~~~~~viP~~~~~~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~ 552 (1014)
||+|+|+++++++|+.+.++++...||||+|+||.+|||+.||++|||+||||||||||||||||++.+++.++++ ++
T Consensus 522 qLlRkakq~~~~~P~i~~~~s~~e~yEGatVIEp~kGfY~~PIATLDFaSLYPSIMmahNLCYtTLl~~~t~~~l~--~~ 599 (1066)
T KOG0969|consen 522 QLLRKAKQKDFVIPNIKSQGSDDEQYEGATVIEPRKGFYDKPIATLDFASLYPSIMMAHNLCYTTLLTKETVEKLG--DE 599 (1066)
T ss_pred HHHHHHhhcCeeeeeecccCCccccccccEEeecccccCCCCceeeehhhhhhHHHHHhhhhheeccccchhhhcC--cc
Confidence 9999999999999999877665459999999999999999999999999999999999999999999999888876 78
Q ss_pred ceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChH
Q 001780 553 CVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIE 632 (1014)
Q Consensus 553 ~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~ 632 (1014)
+|+.||+|++||+.++|+|+||+||++||.+||++|++||+++||+++++||+||+||||+|||+||||||+.|++||.+
T Consensus 600 ~~~~TP~g~yFv~~~~rkGlLP~ILe~ll~aRKraK~dlk~ekDp~kr~vldGRQLAlKisANSvYGFTGAtvGkLPCle 679 (1066)
T KOG0969|consen 600 DYTRTPTGDYFVKTEVRKGLLPEILEDLLTARKRAKADLKKEKDPFKRAVLDGRQLALKISANSVYGFTGATVGKLPCLE 679 (1066)
T ss_pred ceeECCCCCeeeehhhhccccHHHHHHHHHHHHHHHHHHHhccCHHHHhhhcchhhheeecccccccccccccCccceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEe
Q 001780 633 ISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFE 712 (1014)
Q Consensus 633 iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~E 712 (1014)
|+.|||++||+||++|+.+||++|+++|||++++.|||||||||||+|+..++++||++|+|+|++|+..|++||+||||
T Consensus 680 IS~SVT~yGR~MI~~TK~~Ve~~y~~~ngy~~da~ViYGDTDSVMv~Fgv~~v~~am~lg~eaa~~vs~~F~~PIkLEFE 759 (1066)
T KOG0969|consen 680 ISQSVTAYGRQMIEKTKKLVEEKYTIKNGYSHDAVVIYGDTDSVMVKFGVSDVEEAMKLGREAAEYVSSKFVKPIKLEFE 759 (1066)
T ss_pred echhhHHHHHHHHHHHHHHHHHHhhhccCCccccEEEecCCceEEEecCchhHHHHHHHhHHHHHHHHhcCCCCceeEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccceecccceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCC
Q 001780 713 KVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRM 792 (1014)
Q Consensus 713 kvy~~~ll~~KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v 792 (1014)
|||+|+||++||||||++|++|+.++++|.||+|+||||+|+||++++..+|+.||.++|+++|.++++++|++|+.|++
T Consensus 760 KvY~PYLLInKKRYAGL~~t~pd~~DkmD~kGietVRRDnc~LV~~v~~~~L~kiLi~rdv~gA~~fvk~~IsDlL~nri 839 (1066)
T KOG0969|consen 760 KVYFPYLLINKKRYAGLLWTNPDVFDKMDCKGIETVRRDNCPLVANVVNTVLRKILIERDVEGALAFVKDTISDLLCNRI 839 (1066)
T ss_pred eeecceEEeccceeeeeEeccCCcCccccccccchhccCCchHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccceeEeecccCCcccccCcchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhH
Q 001780 793 DLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHY 872 (1014)
Q Consensus 793 ~~~~lvi~k~l~k~~~~Y~~~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~y 872 (1014)
|++.|||+|+|+|..++|.+++|||++|+||++||+|++|..||||||||+.+++|+++|+|+|||.||++||+|||+.|
T Consensus 840 DiS~LVItK~Ltkagd~Y~~kqaHveLAermrkRD~gtaP~lGDRVpYVIi~~akg~~ay~rsEDP~fVLenNipiD~~y 919 (1066)
T KOG0969|consen 840 DISLLVITKELTKAGDDYAAKQAHVELAERMRKRDAGTAPNLGDRVPYVIIAAAKGAPAYERSEDPLYVLENNIPIDTRY 919 (1066)
T ss_pred ceeeeeeeehhcccccchhhhhhhHHHHHHhhhcCCCCCCccCCcCcEEEEecccCCchhcCCCCCeEEecCCCCcchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcchhhHHHhhccccccchhhhhcCCccceeeecCCCCcccccccccccccccccccccC--cccCCcCCCChHHHH
Q 001780 873 YLENQISKPLLRIFEPILKNASKELLSGDHTRSISISTPSNSGIMKFAKRQLSCIGCKALISN--GTLCSHCKGREAELY 950 (1014)
Q Consensus 873 Yi~~qi~~pl~ri~~~i~g~~~~~l~~g~~~r~~~~~~~~~~~~~~f~~~~~~C~~C~~~~~~--~~~C~~C~~~~~~~~ 950 (1014)
||++||.+||.|||+||+|+.+++++.|+|||.+.+.+++.||+|+|++++.+|++|+.++.. +++|.+|..+.+++|
T Consensus 920 YL~nQlsKPllrIfePILg~~~~~l~~g~htR~~~v~~~~~gGl~~F~kk~~tC~gCk~~~~~~~~~~C~~C~~r~~~ly 999 (1066)
T KOG0969|consen 920 YLENQLSKPLLRIFEPILGDAEKELLRGDHTRTITVTTSKVGGLMAFAKKVETCLGCKAPLRKGEQALCENCLPRSSELY 999 (1066)
T ss_pred HHhhhhhhhHHHHhhhhhCchhhccccccceeEEEeecccccchhhhhhhcccccccccccccccchhhhhhcccHHHHH
Confidence 999999999999999999998788999999999999999999999999999999999999876 579999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHcccccCCCCCcccccCCCCCcceeecchhhhHHHHHHhhccCC
Q 001780 951 CKTVSQVQELEVLFGRLWTQCQECQGSLHQDVLCTSRDCPIFYRRKKAQKDMAEAKLQLDRWN 1013 (1014)
Q Consensus 951 ~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~c~~~~cp~~y~r~~~~~~~~~~~~~~~~~~ 1013 (1014)
++.+..++++|.+|+++|++||+||||+|++|+|+|+||||||||.|++++|+++.+.|+||+
T Consensus 1000 qk~v~~~~~lee~fsrlWt~Cqrcqgs~h~~vic~~rdCpifymr~kv~keL~~~~~~l~rf~ 1062 (1066)
T KOG0969|consen 1000 QKQVSHVNDLEEKFSRLWTECQRCQGSLHEEVICSNRDCPIFYMRQKVRKELQEQVDRLRRFG 1062 (1066)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhheeccCCCCchhhHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999999999999999999999999996
No 2
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=5.8e-212 Score=1970.87 Aligned_cols=934 Identities=58% Similarity=1.009 Sum_probs=877.0
Q ss_pred CccCCCCCCCCCCCCCCeeEEEEEeEEee------ecCCccccCccccCCceEEEEEEEecCCcEEEEEEeCcceEEEEe
Q 001780 73 AKWARPPLSSGYVSQCQSIMFQQLDIDYV------IGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYIS 146 (1014)
Q Consensus 73 ~~~~r~~~~~~~~~~~~~l~Fq~lD~d~~------~~~~~~~~~~~~~~~~pvIrLFGvT~~G~SV~v~V~gF~PYFYV~ 146 (1014)
..|.|+++|+ +...++|.|||+|+||+ ++.|+.++++...+++|+|||||+|++|+|||||||||+|||||+
T Consensus 26 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pvIRlFGvTe~G~SV~v~V~gF~PYFYV~ 103 (1054)
T PTZ00166 26 FSKLRRPLPP--ISLQKDLVFFQLDADYTEKDDKSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIE 103 (1054)
T ss_pred HHhccCCCCc--ccccCCceEEEEeeeccccccccccCccccCCCccCCCceEEEEEEecCCCCEEEEEEeCCceEEEEe
Confidence 4588999977 44788899999999997 677778888887788999999999999999999999999999999
Q ss_pred cCCCCCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccCCCcccEEEEEEcChhhHHHHHHHHhcCccc
Q 001780 147 CPQGMGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVASCRGILDRGIQL 226 (1014)
Q Consensus 147 ~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~~~~~~flKI~~~~P~~v~klR~~le~g~~~ 226 (1014)
+|++++++++..+++.|+..+...+..+.....|.+|++|+|++||||+++++.+|+||++.+|++++++|+.|++|..+
T Consensus 104 ~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~VeiV~k~sl~gY~~~~~~~flKIt~~~P~~v~klR~~Le~g~~~ 183 (1054)
T PTZ00166 104 APPNFLPEDSQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVV 183 (1054)
T ss_pred cCCCCCHHHHHHHHHHHHHHHhhcccccccCCceEEEEEEEeeeeceeCCCCceeEEEEEEcCHHHHHHHHHHHHcCCcc
Confidence 99999988999999999987764221222345799999999999999998778999999999999999999999998654
Q ss_pred cCCC---CccceeeecccccceeeeeecCCcceeEEEEeccceecccc--ccccceeeeeeeccccccCCCCCCcCCCCC
Q 001780 227 DGLG---MKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAK--TLSYCQLEFDCLYSDIISRHPEGEFSKMAP 301 (1014)
Q Consensus 227 ~~l~---~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~--k~S~C~~E~~v~~~~~~~~~~~~~~~~~pp 301 (1014)
++.- +..+++||+||+|++|||||++|.||+|+++++++|.+++. +.|||++|++|+++++++++++++|.++||
T Consensus 184 ~~~~~~~~~~~~vyEsnI~f~lRFmID~~I~g~~Wi~i~~~~~~~~~~~~~~s~c~~E~~~~~~~l~~~~~~~~~~~~pp 263 (1054)
T PTZ00166 184 CGGGWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAP 263 (1054)
T ss_pred cccccccccccceeecCCCHHHHHHhccCCCceeEEEecCcceeecccccCCCcceEEEEEehhheeecccccccCCCCC
Confidence 3321 12368999999999999999999999999999998877654 799999999999999999998889999999
Q ss_pred cEEEEEEEEEccCCCC-CCCCCCCceeEEEEEeeccCccc-cceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHH
Q 001780 302 FRILSFDIECAGRKGH-FPEPTHDPVIQVANLVTLQGEKQ-PFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIRE 379 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~-fP~~~~D~Ii~Is~~v~~~g~~~-~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~ 379 (1014)
||||||||||.++.|. ||+|+.|||||||++++..|... ++.+.+|++++|+++.|++|..|++|++||.+|+++|++
T Consensus 264 lrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i~g~~V~~f~sE~eLL~~f~~~I~~ 343 (1054)
T PTZ00166 264 LRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIA 343 (1054)
T ss_pred cEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccCCCceEEEeCCHHHHHHHHHHHHHh
Confidence 9999999999998884 99999999999999888888765 788999999999999999999999999999999999999
Q ss_pred hCCCEEEEecccCCCcccccc-----------------------------------------------------------
Q 001780 380 VDPDVMIGYNICKFDLPYLIE----------------------------------------------------------- 400 (1014)
Q Consensus 380 ~DPDIIiGyNi~~FDlpyL~~----------------------------------------------------------- 400 (1014)
+|||||+|||+++||||||++
T Consensus 344 ~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~~ 423 (1054)
T PTZ00166 344 VDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDY 423 (1054)
T ss_pred cCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEEEEHHHHHHHhc
Confidence 999999999999999999988
Q ss_pred ------------------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhc
Q 001780 401 ------------------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462 (1014)
Q Consensus 401 ------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl 462 (1014)
|+|++++.|.++|++++++|++++.||++||.|+++|+++|+++.+++||||++|+|+++++
T Consensus 424 kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~~~~~~~e~arv~gip~~~v~ 503 (1054)
T PTZ00166 424 KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLL 503 (1054)
T ss_pred CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccCCChHHhh
Confidence 56788889999999999999999999999999999999999999999999999999999999
Q ss_pred ccccHHHHHHHHHHHHhhcCccccCCCcC-CCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccCh
Q 001780 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQA-GSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTP 541 (1014)
Q Consensus 463 ~rG~~~~v~s~L~r~a~~~~~viP~~~~~-~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~ 541 (1014)
+||||++++|+|+|+|+++|+++|+.... .....+|+||+|+||++|||++||++|||+||||||||||||||||++++
T Consensus 504 ~rG~q~kv~s~Llr~~~~~~~viP~~~~~~~~~~~~yeGg~VleP~~G~y~~pV~vLDF~SLYPSIiia~NlcysTl~~~ 583 (1054)
T PTZ00166 504 TRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPP 583 (1054)
T ss_pred cCCcchhHHHHHHHHHHhcCeeccCchhccccccCCCCCceeecCCCCCeeCceEEeecCCcccHHHHhcCCCcceeecc
Confidence 99999999999999999999999987653 22234899999999999999999999999999999999999999999988
Q ss_pred hhhhccCCCCCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceeccccc
Q 001780 542 EDARKLNLPPECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFT 621 (1014)
Q Consensus 542 ~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~ 621 (1014)
.+... ++++++..+|+|.+|+++++++||||++|++|+++|+++|+.||+++||.++++||+||+|||++|||+||||
T Consensus 584 ~~~~~--~~~~~~~~~p~g~~Fv~~~~r~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~ 661 (1054)
T PTZ00166 584 NDANN--YPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVLNGRQLALKISANSVYGYT 661 (1054)
T ss_pred hhhcc--CCCcceeecCCCceeeecCCCCcccHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhhhhhcccccccc
Confidence 75443 2467889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccc-CCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHH
Q 001780 622 GATV-GQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYIS 700 (1014)
Q Consensus 622 G~~~-~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs 700 (1014)
|+++ |||||.++|++||++||++|++|+++||+.+++.|||.||++|||||||||||++++.+.+|++++|++++++||
T Consensus 662 G~~~~gr~~c~~iA~sIT~~GR~~i~~t~~~ie~~~~~~~g~~~g~~VIYGDTDSvfV~~~~~~~~ea~~~g~e~a~~Is 741 (1054)
T PTZ00166 662 GAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERIS 741 (1054)
T ss_pred ccccCCccccHHHHHHHHHHHHHHHHHHHHHHHHhccccccCcCCeEEEecCCCceEEEeCCccHHHHHHHHHHHHHHHH
Confidence 9999 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCceeEEEeeeeccceecccceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHH
Q 001780 701 GTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYV 780 (1014)
Q Consensus 701 ~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v 780 (1014)
+.|++||+|||||||.|++|++||||||+.|+++++.+++++||+|+||||||+++|++++++|+.||.++|+++|++|+
T Consensus 742 ~~~~~pi~LefEkvy~~~ll~~KKrYag~~~~~~~~~~k~d~KGie~vRRD~c~~~k~~~~~vl~~il~~~d~~~a~~~~ 821 (1054)
T PTZ00166 742 KKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFT 821 (1054)
T ss_pred HhcCCCcEEEEeeeeeeeeecccceEEEEEEecCCCCceeeeeeeEEEeccchHHHHHHHHHHHHHHHccCCHHHHHHHH
Confidence 99999999999999999999999999999999888778999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCCccceeEeecccCCcccccCcchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhh
Q 001780 781 KSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIY 860 (1014)
Q Consensus 781 ~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~ 860 (1014)
++.+.+|++|++|+++|+|+|+|+|. +|++++|||++|+||++||+|.+|+.||||+|||+++.+|.++++||++|.|
T Consensus 822 ~~~~~~l~~~~v~i~~lvi~k~l~k~--~Y~~~~phv~~A~rl~~rd~~~~p~~GdrI~YViv~~~~~~~~~~ra~~p~~ 899 (1054)
T PTZ00166 822 KGKISDLLQNRIDISLLVITKSLGKD--DYEGRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLY 899 (1054)
T ss_pred HHHHHHHHcCCCCHHHEEEEEEechh--hCCCCCcHHHHHHHHHHhCcCcCCCCCCEEEEEEEECCCCcchhhhccCHHH
Confidence 99999999999999999999999994 9999999999999999999999999999999999999888899999999999
Q ss_pred hhccCCCcChhHHHhhcchhhHHHhhccccccchhhhhcCCccceeeecCCCCcccccccccccccccccccccCcccCC
Q 001780 861 VLENNIPIDTHYYLENQISKPLLRIFEPILKNASKELLSGDHTRSISISTPSNSGIMKFAKRQLSCIGCKALISNGTLCS 940 (1014)
Q Consensus 861 ~~~~~~~iD~~yYi~~qi~~pl~ri~~~i~g~~~~~l~~g~~~r~~~~~~~~~~~~~~f~~~~~~C~~C~~~~~~~~~C~ 940 (1014)
+++++++||++|||+ ||+|||.|||+||+++ +.+|+.|+|+|.+.+++++.|++++|++++.+|++|+.++..+++|.
T Consensus 900 ~~~~~~~iD~~YYi~-ql~~pl~Ri~~~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~c~ 977 (1054)
T PTZ00166 900 VLENNIPIDTQYYLD-QIKNPLLRIFEGVMDN-PDSLFSGEHTRHITISSSSKGGLSKFVKKQLQCLGCKSVIKEGALCD 977 (1054)
T ss_pred HHhcCCCCCHHHHHH-HHHHHHHHHHHHhhcC-HHHHhccCccceeeecCCCcccHHHHHhcCcccCCCCCCCCCCCcCc
Confidence 999999999999999 9999999999999776 89999999999999999999999999999999999999998889999
Q ss_pred cC-CCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCCcccccCCCCCcceeecchhhhHHHHHHhhccCC--C
Q 001780 941 HC-KGREAELYCKTVSQVQELEVLFGRLWTQCQECQGSLHQDVLCTSRDCPIFYRRKKAQKDMAEAKLQLDRWN--F 1014 (1014)
Q Consensus 941 ~C-~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~c~~~~cp~~y~r~~~~~~~~~~~~~~~~~~--~ 1014 (1014)
+| ..+.+++|..++.+++.+|.+|.++|++||+|+|++|++|+|+|+||||||+|+|+++||++++++|+||+ |
T Consensus 978 ~c~~~~~~~~~~~~~~~~~~~e~~~~~~~~~c~~c~g~~~~~~~c~~~dc~i~y~r~k~~~~~~~~~~~~~~~~~~~ 1054 (1054)
T PTZ00166 978 NCNQNKEPSIYGKKLAKRRHKEAEYSQLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFGLDW 1054 (1054)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCcccCCCCchhheehhHHHHHHHHHHHHHhhccCC
Confidence 99 67788999999999999999999999999999999999999999999999999999999999999999998 7
No 3
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=4.1e-141 Score=1238.61 Aligned_cols=704 Identities=33% Similarity=0.564 Sum_probs=617.0
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCc----cccceeEEEeccc-c----------CCcCcceEeecCC
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGE----KQPFIRNVMTLKS-C----------APIVGVDVMSFET 365 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~----~~~~~~~vf~l~~-~----------~~~~~~~V~~~~~ 365 (1014)
-|+++|+.+++.+++++-|||..|+|-+|.+++..+.. ..-+...++.++. | ..+.|..|..+.+
T Consensus 657 ~Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~gv~Vv~~~~~ds~~~t~~~~~~~~~~V~~~~s 736 (1488)
T KOG0968|consen 657 LLTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVGVIVVDKVCPDSHVQTTTLGGIYGCRVVVMES 736 (1488)
T ss_pred eeeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcccceeeeeEEEEeccCccccccccccCCcCCceEEEehh
Confidence 46999999999999999999999999999988765511 1112234555442 1 3456889999999
Q ss_pred HHHHHHHHHHHHHHhCCCEEEEecccCCCcccccc---------------------------------------------
Q 001780 366 ERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE--------------------------------------------- 400 (1014)
Q Consensus 366 E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~--------------------------------------------- 400 (1014)
|.||++++.+++.++||||++||++++++|+||++
T Consensus 737 E~elf~ev~~~i~q~DPDIl~GyEi~~~SWGyl~eR~~~l~~di~~~lsRv~~~~~~n~~d~~~ewg~tt~S~i~i~GR~ 816 (1488)
T KOG0968|consen 737 ELELFEEVAKLIVQYDPDILLGYEIHNLSWGYLIERAKLLGIDISRDLSRVKCYEKTNESDDEREWGYTTISGINIVGRH 816 (1488)
T ss_pred HHHHHHHHHHHHHhcCcceeeeeeecccchHHHHHHHHHhcchHHHHHhcCCChhhhhhhhhhhhccceeeccccccchh
Confidence 99999999999999999999999999999999998
Q ss_pred --------cccc----------------------cchhHHHhhcCC-hhhhhHHhhhhhccccchHHHHhhhhhhHhHHH
Q 001780 401 --------KEDV----------------------HHSIISDLQNGN-AETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVE 449 (1014)
Q Consensus 401 --------kedv----------------------~~~~i~~l~~~~-~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e 449 (1014)
+.+| .+..+++||++. ...|.+++.|.++.+.+.+.|+.++..+....|
T Consensus 817 ~lNiWRilR~eV~L~nYtlEsv~~nVL~kk~P~~~~~~Lt~~~~s~~~~~r~~~l~y~l~Ra~~NlelLsq~d~i~k~~E 896 (1488)
T KOG0968|consen 817 VLNIWRILRSEVALTNYTLESVVFNVLRKKIPMFDFAVLTRWWKSKRSAERNDVLNYLLSRARLNLELLSQLDWILKNSE 896 (1488)
T ss_pred hhhHHHHHhhhhhhhhccHHHHHHHHHHhhcCCCcHHHHHHHHhcccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhHH
Confidence 0011 123466777654 345789999999999999999999999999999
Q ss_pred HHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcC-CCCCCcCCc-ceeeeccCceEEeeeEeeeccccchHH
Q 001780 450 MARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQA-GSEQGTYEG-ATVLEARAGFYEKPIATLDFASLYPSI 527 (1014)
Q Consensus 450 ~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~-~~~~~~yeG-g~VleP~~G~y~~pV~~LDF~SLYPSI 527 (1014)
|||+.||+|..|++||+|+||||||+|.|+.+||+.|++..+ ...+.+.|. ++||||++.||++||+||||+||||||
T Consensus 897 ~ARv~GIdF~sV~tRGSQ~rVESmllRiAk~~Nyi~~SPs~kQv~~q~A~EcvPLVMEPeS~fY~~PViVLDFQSLYPSi 976 (1488)
T KOG0968|consen 897 MARVIGIDFHSVLTRGSQFRVESMLLRIAKPMNYIAPSPSHKQVAMQGAPECVPLVMEPESAFYFDPVIVLDFQSLYPSI 976 (1488)
T ss_pred HHHhhcceeeEEeeccchhhHHHHHHHHhcccccccCCccHHHHhhcCCccccceeecchhhhccCceEEEEchhhcchH
Confidence 999999999999999999999999999999999999987542 233445664 999999999999999999999999999
Q ss_pred HHHhCCCcccccChhhh-h-----ccC-----CC-------CCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHH
Q 001780 528 MMAYNLCYSTLVTPEDA-R-----KLN-----LP-------PECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKA 589 (1014)
Q Consensus 528 iia~Nlc~sT~~~~~~~-~-----~~~-----~~-------~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~ 589 (1014)
|||||+||||++++-.. . .|| ++ .+++.++|||.+|||+++|+|+||++|+++|++|.++|+
T Consensus 977 vIAYNyCySTcLG~v~~l~~~~e~~LG~s~~s~~~dil~~~~ndV~isPNgv~yVK~sVRkgvLpkmLeEIL~tRiMVKk 1056 (1488)
T KOG0968|consen 977 VIAYNYCYSTCLGKVGNLNQMNEIKLGVSKYSLPPDILVLAKNDVTISPNGVMYVKPSVRKGVLPKMLEEILATRIMVKK 1056 (1488)
T ss_pred HHhHHHHHHHhhhHHHhhccccceeeeeeeccCCHHHHHHHhcceeeCCCceEEechhhhhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999997421 1 122 22 247889999999999999999999999999999999999
Q ss_pred HhhhcC-ChHHHHHhHHHhhhccccceeccccccccc-CCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccce
Q 001780 590 DLKEAK-DPLEKAVLDGRQLALKISANSVYGFTGATV-GQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAE 667 (1014)
Q Consensus 590 ~mk~~~-d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~-~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~ 667 (1014)
.||..+ +..++++||+||+|||++||.+||||.|++ |||||.++|++|..+||++|++++++|+.. -.|||+
T Consensus 1057 aMK~~~~~~~L~RiLnaRQLALKLiANVTYGYTsA~FSGRMPCaElADsIV~~GRETLEraIe~Vn~~------d~w~Ak 1130 (1488)
T KOG0968|consen 1057 AMKRTKDNKKLKRILNARQLALKLIANVTYGYTSANFSGRMPCAELADSIVQKGRETLERAIEMVNRG------DYWGAK 1130 (1488)
T ss_pred HHHHhcchHHHHHHhhhHHHHHHHHhhccccccccccCCCCchHHHHHHHHHhhHHHHHHHHHHHhcC------CcCCeE
Confidence 999998 778999999999999999999999999999 999999999999999999999999999973 248999
Q ss_pred EEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCC-CccceeEeeee
Q 001780 668 VIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPE-KFDKMDTKGIE 746 (1014)
Q Consensus 668 VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~-~~~k~~~KGie 746 (1014)
||||||||+||.+++.+.+|||++|++||+.||+.+|+|+.|+|||||+|++|++||||+|+.|+.++ +.+.+|+||||
T Consensus 1131 VVYGDTDSmFVlL~GaT~eeAF~IGq~iAe~VT~~NP~PV~LKfEKVY~PCvL~tKKRYVG~~YEs~~Qk~PiFDAKGIE 1210 (1488)
T KOG0968|consen 1131 VVYGDTDSMFVLLPGATVEEAFEIGQEIAEAVTNSNPKPVVLKFEKVYHPCVLLTKKRYVGFMYESPNQKEPIFDAKGIE 1210 (1488)
T ss_pred EEEcCCCceEEEecCccHHHHHHHHHHHHHHHHhcCCCCeEEEeeeecccceeeeccceeeeeeccCcccCCccccccce
Confidence 99999999999999999999999999999999999999999999999999999999999999999887 56789999999
Q ss_pred eccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccccC---cchHHHHHHHH
Q 001780 747 TVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEV---KAAHVELAERM 823 (1014)
Q Consensus 747 ~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~---~~~hv~~A~r~ 823 (1014)
|||||+||++.++++++|++||..+|++.++.|+.+++.+++.|+++++||++.|+++.. .|.. .+|.+.+|+|+
T Consensus 1211 TVRRDtcPavakilEksL~LlFetkdlS~IK~y~q~~~~ki~~Gkvs~qDF~FaKEvRl~--~~~~~~~~pP~avva~r~ 1288 (1488)
T KOG0968|consen 1211 TVRRDTCPAVAKILEKSLRLLFETKDLSKIKKYLQNVCNKIQEGKVSFQDFCFAKEVRLE--KYYSASAAPPGAVVARRR 1288 (1488)
T ss_pred eeeccCcHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCcchhhheeeeeecce--eccccccCCchHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999983 4443 36789999999
Q ss_pred HHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhcc-CCCcChhHHHhhcchhhHHHhhccccccchhhhhcC--
Q 001780 824 RKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLEN-NIPIDTHYYLENQISKPLLRIFEPILKNASKELLSG-- 900 (1014)
Q Consensus 824 ~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~-~~~iD~~yYi~~qi~~pl~ri~~~i~g~~~~~l~~g-- 900 (1014)
+..||..+|++|+||||||++|.+|+.+++|+.+|++++++ .+++|..|||.+||+|||.|+|+.| |.+..+|+..
T Consensus 1289 i~~DpR~EPqygERVPYvII~G~pG~~L~~~vvsP~efL~~~~~rLn~~YYINk~iiPpL~Rvf~Li-G~~v~~W~~Emp 1367 (1488)
T KOG0968|consen 1289 ITKDPRHEPQYGERVPYVIIDGVPGSTLYSRVVSPEEFLRNPTYRLNTFYYINKQIIPPLDRVFNLI-GADVDSWYHEMP 1367 (1488)
T ss_pred hccCCccCccccccCCeEEEeCCCCCcHHHHhcCHHHHhcCCceeccceeeehhhccchHHHHhhhc-ccchhhHHHhcc
Confidence 99999999999999999999999999999999999999976 6999999999999999999999977 7789999872
Q ss_pred CccceeeecCCC-Ccc--cccccccccccccccccccCcccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCC
Q 001780 901 DHTRSISISTPS-NSG--IMKFAKRQLSCIGCKALISNGTLCSHCKGREAELYCKTVSQVQELEVLFGRLWTQCQECQGS 977 (1014)
Q Consensus 901 ~~~r~~~~~~~~-~~~--~~~f~~~~~~C~~C~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 977 (1014)
.|+|+-...++. .+| +..|+ .+.+|..|-.++....+|..|.+++.++...++.+.+++|+++.+|.++|..|+|+
T Consensus 1368 k~krtS~~~te~e~~~~tid~f~-ts~hC~~c~~~~~~~~lC~~Clqnp~~~a~~~v~~~~~l~re~~~L~~iCr~Cs~~ 1446 (1488)
T KOG0968|consen 1368 KSKRTSLKLTETEKGGITIDTFV-TSKHCSSCCSRIGSTQLCSDCLQNPSATALALVQKGRELERERSQLITICRSCSGS 1446 (1488)
T ss_pred ccccccccccccccCCceeeEEE-eeccccchhcccccchhHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 233332222222 222 44553 57889998677777899999999999999999999999999999999999999986
Q ss_pred C---CCcccccCCCCCcceeecchhhhHHHHHH-hhccCC-C
Q 001780 978 L---HQDVLCTSRDCPIFYRRKKAQKDMAEAKL-QLDRWN-F 1014 (1014)
Q Consensus 978 ~---~~~~~c~~~~cp~~y~r~~~~~~~~~~~~-~~~~~~-~ 1014 (1014)
. .+.|.|.|.+||+||.|.|+++.+....+ ..+-|+ |
T Consensus 1447 ~~~~~~~v~C~S~~C~V~y~r~k~er~l~~qae~~~k~l~~w 1488 (1488)
T KOG0968|consen 1447 SQRDGQVVKCNSLTCPVFYTRSKVERYLRAQAETAHKMLGSW 1488 (1488)
T ss_pred ccccccccccccccCchhhhHHHHHHHHHhhHHHHHHHhccC
Confidence 4 35899999999999999999999995433 344444 6
No 4
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=9e-128 Score=1127.88 Aligned_cols=831 Identities=27% Similarity=0.422 Sum_probs=658.2
Q ss_pred CCCCeeEEEEEeEEeeecCCccccCccccCCceEEEEEEE---e-cCCcEEEEEEeCcceEEEEecCC-C-CC-------
Q 001780 86 SQCQSIMFQQLDIDYVIGDSNRELLPLSSGSAAIIRIFGV---T-REGHSVCCKVHGFEPYFYISCPQ-G-MG------- 152 (1014)
Q Consensus 86 ~~~~~l~Fq~lD~d~~~~~~~~~~~~~~~~~~pvIrLFGv---T-~~G~SV~v~V~gF~PYFYV~~p~-~-~~------- 152 (1014)
...+.|.|+|+|+.+.+. +...+|.|||+ + +.+.|||+.|.|...-+|+ .|. . ..
T Consensus 328 ~e~~~l~f~wlDaYee~~-----------~~~g~l~LFGKVk~~~~t~~Sccv~V~ni~R~lyf-lPR~~~l~~~~~e~~ 395 (1429)
T KOG0970|consen 328 VEDGSLRFFWLDAYEEVY-----------KAPGTLYLFGKVKLSGDTYVSCCVVVKNICRVLYF-LPRPIKLSAAVGEDS 395 (1429)
T ss_pred cccceEEEEEehhhHHHh-----------CCCceEEEEeeeeccCCCceEEEEEEcCeeeEEEe-cccccccccccCCcc
Confidence 357789999999887732 22378999998 3 3578999999999999998 342 1 11
Q ss_pred -CCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccC---CCcccEEEEEEcChhhHHHHHHHHhcCccccC
Q 001780 153 -PDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQ---QKSQPFLKIVVALPTMVASCRGILDRGIQLDG 228 (1014)
Q Consensus 153 -~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~---~~~~~flKI~~~~P~~v~klR~~le~g~~~~~ 228 (1014)
++...++..++...+...- ...-.+..+|++. |.|+. ....+||||.+. ...++|...| +|.+|++
T Consensus 396 ~~~s~~dv~~E~~~~l~~k~-----~~~~fk~k~v~~~--yafe~~dvp~~~dyLeV~y~--~~~p~LP~Dl-kgdsfsh 465 (1429)
T KOG0970|consen 396 IPESKRDVYKEVGSLLSNKL-----GLTEFKSKPVKKN--YAFELPDVPMKSDYLEVLYS--YETPKLPSDL-KGDSFSH 465 (1429)
T ss_pred chhhHHHHHHHHHHHHHhhh-----hhhHhhhhhhhhh--hccccCCCCCCCcceEEecc--ccCCCCcccc-ccchHHH
Confidence 2244666666666554310 0111223334443 33332 346889999986 4445565555 5778888
Q ss_pred CCCccceeeecccccceeeeeecCCcceeEEEEeccceeccccccccceeeeeeeccccccCCCCCCcCCCCCcEEEEEE
Q 001780 229 LGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFD 308 (1014)
Q Consensus 229 l~~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~~~pplrilSfD 308 (1014)
+|+ +|...+.||+++++|+|+||++|.. |...+.+.|||++|+.|..++.+....+.. .++|||++||+.
T Consensus 466 vfg-------t~tn~lE~fll~rKimGPCWlkv~~--~s~~~~~~SwCk~Ev~v~sP~nI~~~~~~~-a~~Ppl~llsL~ 535 (1429)
T KOG0970|consen 466 VFG-------TNTNPLERFLLSRKIMGPCWLKVKG--YSDPPRNASWCKVEVTVKSPQNITVVCSKK-APPPPLTLLSLN 535 (1429)
T ss_pred Hhc-------cCccHHHHHHHhccccCceEEEeec--CCCCCCCccceeeEEEecCCcceEEeecCC-CCCCCeeEEEee
Confidence 887 4677777999999999999999984 543334899999999997665555443322 668999999999
Q ss_pred EEEccCCCCCCCCCCCceeEEEEEeecc-----Cccccce-eEEEeccc---cC---------CcCcceEeecCCHHHHH
Q 001780 309 IECAGRKGHFPEPTHDPVIQVANLVTLQ-----GEKQPFI-RNVMTLKS---CA---------PIVGVDVMSFETERDVL 370 (1014)
Q Consensus 309 IE~~~~~g~fP~~~~D~Ii~Is~~v~~~-----g~~~~~~-~~vf~l~~---~~---------~~~~~~V~~~~~E~eLL 370 (1014)
|+|.. .|.-+..+|+|||..+... +.+.|.. ++.++|.. ++ ......|..+.+|+.||
T Consensus 536 i~T~~----N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v~~~~sErALL 611 (1429)
T KOG0970|consen 536 IRTSM----NPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKVVLHNSERALL 611 (1429)
T ss_pred eeehh----ccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCceEEecCHHHHH
Confidence 99987 4556678999999665432 2222222 22122210 10 00123488999999999
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccccc----------------------------------------c-------
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIEKE----------------------------------------D------- 403 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ke----------------------------------------d------- 403 (1014)
..|+..++..|||+|+|||+.+|++..|+++- |
T Consensus 612 s~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD~~~~a~~ 691 (1429)
T KOG0970|consen 612 SHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCDLNLAARE 691 (1429)
T ss_pred HHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEeehHHHHHh
Confidence 99999999999999999999999999997600 0
Q ss_pred -----------------------ccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcch
Q 001780 404 -----------------------VHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460 (1014)
Q Consensus 404 -----------------------v~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~ 460 (1014)
+....|...|. +.++.-.++..++.|+.+.++|+.+|+.++.+.+|+.++|.-+.+
T Consensus 692 lik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~-~s~~L~~ll~~~~~d~~~~l~i~~~l~~LpLs~qlTnIaGni~~R 770 (1429)
T KOG0970|consen 692 LIKAQSYSLSELSQQILKEERKEINANEIPKMYE-DSKSLTYLLEHTITDAELILQIMFRLNALPLSKQLTNIAGNIWAR 770 (1429)
T ss_pred hhccccccHHHHHHHHHhhhcccCCHhHhhhhcc-ChHHHHHHHHHHhHHHHHHHHHHHHhccchHHHHHHHHHhHHHHH
Confidence 00111222222 123355678889999999999999999999999999999999999
Q ss_pred hcccccHHHHHHHHHHHHhhcCccccCCCcC------------C-------CCCCcCCcceeeeccCceEEeeeEeeecc
Q 001780 461 LLSRGQSIKVLSQLLRKAKQKNLVIPNVKQA------------G-------SEQGTYEGATVLEARAGFYEKPIATLDFA 521 (1014)
Q Consensus 461 vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~------------~-------~~~~~yeGg~VleP~~G~y~~pV~~LDF~ 521 (1014)
.+..|...|.|.+|||+++++||++|++... + ..+++|.||+|+||++|||++.|++||||
T Consensus 771 TL~G~RAeRnEylLLH~F~~~~fIvPDK~~ssk~~~d~d~~~eg~d~~~~~KKk~kYaGGLVlePkkGlYe~~VLllDFN 850 (1429)
T KOG0970|consen 771 TLQGGRAERNEYLLLHEFYKNGFIVPDKQNSSKAQKDADETEEGADEPSKGKKKAKYAGGLVLEPKKGLYEKYVLLLDFN 850 (1429)
T ss_pred HhhccchhhhhHHHHHHHHHCCccCCCccchhhhhhhhhhhhccccccccccccccccCceeeccccchhhheeEEEEcc
Confidence 9999999999999999999999999987520 1 12368999999999999999999999999
Q ss_pred ccchHHHHHhCCCcccccCh-hhhhccCCCCCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHH
Q 001780 522 SLYPSIMMAYNLCYSTLVTP-EDARKLNLPPECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEK 600 (1014)
Q Consensus 522 SLYPSIiia~Nlc~sT~~~~-~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~ 600 (1014)
|||||||++|||||||+-.- .+ .++....|. ++..+||||++|+.|++.|+++|++||...+|.++
T Consensus 851 SLYPSIIQEyNICFTTv~~~~~d-------~Dqlp~lP~------s~~~~GiLPr~l~~LVerRk~VK~lMK~~~tp~~~ 917 (1429)
T KOG0970|consen 851 SLYPSIIQEYNICFTTVDRFSVD-------SDQLPRLPS------SSSEQGILPRLLENLVERRKEVKKLMKQELTPEKR 917 (1429)
T ss_pred ccchHHHHHhhheeeeccccccC-------cccCCCCCC------ccccCCccHHHHHHHHHHHHHHHHHHhcCCCHHHH
Confidence 99999999999999999652 11 223444553 34689999999999999999999999999999999
Q ss_pred HHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEc
Q 001780 601 AVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQF 680 (1014)
Q Consensus 601 ~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~ 680 (1014)
.+||+||+|||++|||||||+|++++|||..++|+.||..||++|++|+++|+.. |++|||||||||||+.
T Consensus 918 ~q~DIRQqALKLTANSMYGCLGf~~SRFyAkpLAaLVT~KGReiLm~Tk~Lve~m---------nl~VIYGDTDSvMInT 988 (1429)
T KOG0970|consen 918 KQLDIRQQALKLTANSMYGCLGFVNSRFYAKPLAALVTYKGREILMNTKDLVEKM---------NLEVIYGDTDSVMINT 988 (1429)
T ss_pred HhhhHHHHHHhhhhccchhhcccccchhhhhhHHHHHhhhhHHHHHHHHHHHHhc---------CeEEEEcCCceEEeeC
Confidence 9999999999999999999999999999999999999999999999999999984 8899999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCCC-ccceeEeeeeeccCchHHHHHHH
Q 001780 681 GVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEK-FDKMDTKGIETVRRDNCLLVKNL 759 (1014)
Q Consensus 681 ~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~-~~k~~~KGie~vRRD~~~l~k~~ 759 (1014)
+..|.++|+++|.++.+.||+.+ +-++|++++||.++||++||+|||+..++.++ ...++.||+++||||||+++|++
T Consensus 989 n~td~~~a~kig~~~k~~VNkrY-k~LEIDiDgVfkrlLLlkKKKYAAL~l~~dgkg~~~~E~KGLDmvRRDwc~Lake~ 1067 (1429)
T KOG0970|consen 989 NSTDYEEALKIGNEFKQAVNKRY-KLLEIDIDGVFKRLLLLKKKKYAALTLNKDGKGVERIEVKGLDMVRRDWCQLAKEI 1067 (1429)
T ss_pred CCccHHHHHHHHHHHHHHHHHHh-hhheeehhHHHHHHHHHhhhhheeEEecCCCCCceeeeecccchhHHHHHHHHHHH
Confidence 99999999999999999999998 57999999999999999999999999875544 24899999999999999999999
Q ss_pred HHHHHHHHhcCCChhhHH----HHHHHHHHHHHcCCCCccceeEeecccCCcccccC--cchHHHHHHHHHHhcCCCCCC
Q 001780 760 VTECLHKILVDRDIPGAV----QYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEV--KAAHVELAERMRKRDAATAPN 833 (1014)
Q Consensus 760 ~~~vl~~il~~~d~~~a~----~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~--~~~hv~~A~r~~~rd~g~~p~ 833 (1014)
..-||+.||.+++.++++ +++.++-.+|.+|.||+++|+|+|+|+|+|++|.+ .+|||+||.||++|+ +..++
T Consensus 1068 g~~vLd~ILs~~~~ee~veaI~d~L~kI~~k~~~G~vpl~~fvI~k~LtK~Pe~Yp~~kslPhVqVALrm~~~G-~~~~k 1146 (1429)
T KOG0970|consen 1068 GKAVLDKILSDKSREEIVEAIHDELRKISEKLENGNVPLEKFVITKTLTKNPEAYPDGKSLPHVQVALRMNKRG-KRKVK 1146 (1429)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCccchhheeeehhccCChhhCCCcccCcHHHHHHHHHHhc-Ccccc
Confidence 999999999999877665 45666667788999999999999999999999986 489999999999985 58999
Q ss_pred CCCeeEEEEEecCC-CCccccccCChhhhhc--cCCCcChhHHHhhcchhhHHHhhccccccchhhhhc--CCccceeee
Q 001780 834 VGDRVPYVIIKAAK-GAKAYERSEDPIYVLE--NNIPIDTHYYLENQISKPLLRIFEPILKNASKELLS--GDHTRSISI 908 (1014)
Q Consensus 834 ~GdrV~YVi~~~~~-~~~~~~ra~~p~~~~~--~~~~iD~~yYi~~qi~~pl~ri~~~i~g~~~~~l~~--g~~~r~~~~ 908 (1014)
.||.|+|||+++.+ +.++.+||.+|.++.. +++.||+.|||.+||+||+.|+++||.|.++..+.. |.+++.+..
T Consensus 1147 ~gDvV~yVI~~~D~~~~~As~RAyh~~e~~~~~~~l~iD~~YYLa~QIhPvV~Rlve~Iegt~a~riae~LGlDstkyr~ 1226 (1429)
T KOG0970|consen 1147 AGDVVPYVICKEDGIDNPASERAYHPDEVMPDEDNLAIDYNYYLAQQIHPVVERLVEPIEGTDAVRIAECLGLDSTKYRR 1226 (1429)
T ss_pred cCCeEEEEEecCCCCCCchhhcccChHhhCccCcceeechhhHhhhhcchhHHHHhhhhcccCHHHHHHHhCCCchhhhh
Confidence 99999999996544 4456799999998874 359999999999999999999999999997766543 655544432
Q ss_pred cCCC-------Cc------ccccc---cccccccccccccccC----------------cccCCcCCCCh---H-HHHHH
Q 001780 909 STPS-------NS------GIMKF---AKRQLSCIGCKALISN----------------GTLCSHCKGRE---A-ELYCK 952 (1014)
Q Consensus 909 ~~~~-------~~------~~~~f---~~~~~~C~~C~~~~~~----------------~~~C~~C~~~~---~-~~~~~ 952 (1014)
.... .+ ...+| ......|+.|+++... +.-|.+|.... + .+..+
T Consensus 1227 ~~~~q~~~~a~s~~~s~~td~~~~~~ce~~~l~CptC~~~~~~~~~~~~~s~~~~~~~l~~~Ca~Cq~~~~~~~~~i~nq 1306 (1429)
T KOG0970|consen 1227 HEGNQKENSALSPDESTLTDVERFKDCEPLTLRCPTCSTENSRAFAVDKVSEMSRKEVLSLYCARCQQEPIESPASITNQ 1306 (1429)
T ss_pred hhcchhhhhhhCCCcchhcchhhhccccceEEECCCCCCcccccccccCcccchhhhHhhhcChhhhcCCccchHHHHHH
Confidence 2100 11 12233 2456899999886432 23499998866 3 45555
Q ss_pred HHHHHHHHHHHHHHHHHHcc--cccCC
Q 001780 953 TVSQVQELEVLFGRLWTQCQ--ECQGS 977 (1014)
Q Consensus 953 ~~~~~~~~~~~~~~~~~~C~--~C~~~ 977 (1014)
+..+++....+|+..|++|. .|...
T Consensus 1307 ~~~qir~fV~~yy~g~lvCdd~tC~~~ 1333 (1429)
T KOG0970|consen 1307 VERQIRCFVSLYYLGWLVCDDPTCGFR 1333 (1429)
T ss_pred HHHHHHHHHHHHhhhheeecCcccccc
Confidence 66789999999999999996 48743
No 5
>PRK05761 DNA polymerase I; Reviewed
Probab=100.00 E-value=4.9e-121 Score=1121.79 Aligned_cols=672 Identities=25% Similarity=0.328 Sum_probs=554.2
Q ss_pred EEEeEEeeecCCccccCccccCCceEEEEEEEecCCcEEEEEEe-CcceEEEEecCCCCCCCcHHHHHHHHHHHHhhhcc
Q 001780 94 QQLDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVH-GFEPYFYISCPQGMGPDDISHFHQILEGRMREANR 172 (1014)
Q Consensus 94 q~lD~d~~~~~~~~~~~~~~~~~~pvIrLFGvT~~G~SV~v~V~-gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~ 172 (1014)
+.||++|. .. ++.|+|++||++ +|..+.+... ||+||||+..|++. +.+... .. .
T Consensus 20 ~lld~~Y~----------~~-~~~~vi~l~~~~-~~~~~~~~d~~gfkPYfy~~~~~~~-------~~~~~~-~~-~--- 75 (787)
T PRK05761 20 YLLSVDYD----------GK-LGKAVVKLYDPE-TGKIYKWYDRTGHKPYFLTDLDPDE-------IDKIPK-IL-R--- 75 (787)
T ss_pred eEEEEEEe----------cc-CCeeEEEEEecC-CCeEEEEEcCCCCCCeEEecCChHH-------HHhhhh-hh-c---
Confidence 79999998 43 456999999996 6655555544 59999999766531 111111 11 1
Q ss_pred CCCCCcceEEEEEEeecccccccCCCcccEEEEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeeeeecC
Q 001780 173 NSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCN 252 (1014)
Q Consensus 173 ~~~~~~~V~~Ie~V~K~sl~gy~~~~~~~flKI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFmID~~ 252 (1014)
...+..++++.+.++|+|+ ..+++||++.+|.+++++|+.++++ +.+||+||+|++|||+|++
T Consensus 76 ----~~~~~~~e~~~~~~~~~~~---~~~~~kI~~~~p~~v~~~r~~~~~~----------~~~~EaDI~f~~RyliD~~ 138 (787)
T PRK05761 76 ----HPSFDHLEIVEKYDGLRDK---KVKVTKIVVKDPLAVRRLRLSVRDI----------PRAWEADIKYEFRYIYDNG 138 (787)
T ss_pred ----CCCeeeEEEEEEEeccCCC---cceEEEEEECCHHHHHHHHHHHHhh----------hhheeCCCChHHheEEeCC
Confidence 2458889999999998877 4799999999999999999998863 4789999999999999999
Q ss_pred CcceeEEEEeccceeccccccccceeeeeeeccccccCCCCCCcC-----CCCCcEEEEEEEEEccCC-CCCCCCCCCce
Q 001780 253 IVGGNWIEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFS-----KMAPFRILSFDIECAGRK-GHFPEPTHDPV 326 (1014)
Q Consensus 253 I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~-----~~pplrilSfDIE~~~~~-g~fP~~~~D~I 326 (1014)
|.||+|++++.+.+.... ..|+.|+...+... +....+|. ..|||++|||||||.+.. |.||+
T Consensus 139 i~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~P~lk~lsfDIE~~~~~~g~~P~------ 207 (787)
T PRK05761 139 LIPGMPYDVKNGLESVEP---EILVEEIKKAFKDE--RKLAEDWLPIFEAPIPKIKRIAIDIEVYTPAKGRIPD------ 207 (787)
T ss_pred CCCCceEEeccccccccc---ccccccccccchhh--hhhhhhhhhhccCCCCCcceEEEEEEeccCcCCCCCC------
Confidence 999999999876543332 22666665544322 11222332 469999999999999864 56664
Q ss_pred eEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccccccccc---
Q 001780 327 IQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKED--- 403 (1014)
Q Consensus 327 i~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ked--- 403 (1014)
++|++||.+|+++|+++||||+ ||+++||||||.++-.
T Consensus 208 -------------------------------------~~E~eLL~~f~~~i~~~dPdi~--yN~~~FDlPYL~~Ra~~lg 248 (787)
T PRK05761 208 -------------------------------------DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLG 248 (787)
T ss_pred -------------------------------------CCHHHHHHHHHHHHHhcCCEEE--EcCCcchHHHHHHHHHHhC
Confidence 4999999999999999999976 9999999999998110
Q ss_pred ------------------------------------cc---c--hhHHHhhcC----------ChhhhhHHhhhhhcccc
Q 001780 404 ------------------------------------VH---H--SIISDLQNG----------NAETRRRLAVYCLKDAY 432 (1014)
Q Consensus 404 ------------------------------------v~---~--~~i~~l~~~----------~~~~r~~l~~Y~lkDa~ 432 (1014)
++ + ..+.+...| +..++++|+.||++||.
T Consensus 249 i~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~ 328 (787)
T PRK05761 249 IPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAE 328 (787)
T ss_pred CCchhcccccCCCceEEechhheeecceeeeeccceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHH
Confidence 00 0 011121111 12357899999999999
Q ss_pred chHHHH--hhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCc----CC-------CCCCcCC
Q 001780 433 LPQRLL--DKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQ----AG-------SEQGTYE 499 (1014)
Q Consensus 433 l~~~L~--~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~----~~-------~~~~~ye 499 (1014)
|+++|+ .+...+.++++|||++|+|++++...|++.+++++|+++|+++|+++|++.. .. ....+|+
T Consensus 329 l~~~L~~f~~~~~l~~~~elarit~lpl~~v~r~~~g~~i~~~l~~~a~~~~~liP~~~~~~~~~~~~~~~~~~~~~~y~ 408 (787)
T PRK05761 329 ITLKLTFFNNELVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDILRLDHEVYKKAIIKGKKYR 408 (787)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHCcCHHHHhccCHHHHHHHHHHHHHHhCCEeCCCCccccccccccccccccccCCcC
Confidence 999985 5778899999999999999999954455788999999999999999998754 21 0124899
Q ss_pred cceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHHHHH
Q 001780 500 GATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEILEE 579 (1014)
Q Consensus 500 Gg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~ 579 (1014)
||+|++|++|+|++ |++|||+|||||||++|||||+|++.+...... +....+.|..|++ .+.|++|.+|+.
T Consensus 409 Gg~V~~P~~G~y~~-V~vlDF~SLYPSIi~~~Ni~p~T~~~~~~~~~~-----~~~~~~~~~~~~~--~~~gl~~~il~~ 480 (787)
T PRK05761 409 GGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKCHY-----DDEVPELGHSVCD--DRPGLTSVLVGL 480 (787)
T ss_pred CcEEeccCCCceee-EEEeeecccchHHHHHhCCChhhccCccccccc-----cCCCCCCCceeec--CCCCchHHHHHH
Confidence 99999999999998 999999999999999999999999876421110 1111245666664 689999999999
Q ss_pred HHHHHHHHHHHhhhcC--ChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhcc
Q 001780 580 LLAARKRAKADLKEAK--DPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFT 657 (1014)
Q Consensus 580 Ll~~R~~~K~~mk~~~--d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~ 657 (1014)
|++.|+++|+.|++.+ |+.++++||++|+|+|++|||+|||+|++++||||.++|++||++||++|+.|++++++.
T Consensus 481 l~~~R~~~k~~~~~~~~~~~~~~~~ld~~Q~AlKi~~NS~YGy~G~~~~r~~~~~~A~~IT~~GR~~l~~t~~~ie~~-- 558 (787)
T PRK05761 481 LRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEEL-- 558 (787)
T ss_pred HHHHHHHHHHHhhccCCCCHHHHHHHHHHHHhheeeeecccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHc--
Confidence 9999999999998764 789999999999999999999999999999999999999999999999999999999984
Q ss_pred ccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceec-ccceeEEEeccCCCC
Q 001780 658 TVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLI-SKKRYAGLYWTNPEK 736 (1014)
Q Consensus 658 ~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~-~KKRYagl~~~~~~~ 736 (1014)
|++|||||||||||+++. .++ .++++++|++.+ +|+|||||+|.+++|. +||||||+. .
T Consensus 559 -------g~~VIYGDTDSvfv~~~~--~~~----~~~l~~~i~~~~--~i~LE~Ek~y~~~l~~~~KKrYag~~-----~ 618 (787)
T PRK05761 559 -------GLKVLYGDTDSLFVWGPT--KES----LEELIKEIEERT--GIDLEVDKTYDWVAFSGLKKNYFGVL-----K 618 (787)
T ss_pred -------CCEEEEEeCceEEEECCC--HHH----HHHHHHHHHHhC--CCceEEEEEEEEEEEecccceEEEEe-----c
Confidence 889999999999999765 222 257888899988 4999999999999875 999999998 3
Q ss_pred ccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChh-------hHHHHHHHHHHHHHcCCCCccceeEeecccCCccc
Q 001780 737 FDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIP-------GAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDD 809 (1014)
Q Consensus 737 ~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~-------~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~ 809 (1014)
.+++++||+|+||||||+|+|++++++|+.||.++|++ ++.+++++.+.+|++|++|+++|+|+|+|+|.+++
T Consensus 619 dgki~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~~~~~~~~~~~~~~~~v~~~~~~l~~g~~~~~~lvi~k~l~k~~~~ 698 (787)
T PRK05761 619 DGKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEIEDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDE 698 (787)
T ss_pred CCeEEEEEEEEEeCCchHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHHHHHcCCCCHHHEEEEeeecCCHHH
Confidence 47899999999999999999999999999999999999 89999999999999999999999999999999999
Q ss_pred ccC-cchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHhhcc
Q 001780 810 YEV-KAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFEP 888 (1014)
Q Consensus 810 Y~~-~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~ 888 (1014)
|++ .+|||.+|+++++ .|..+++||||+|||+++.+++ .|.++ +++.+||++||++ ||.|++.||+++
T Consensus 699 Y~~~~~~hv~aa~~~~~--~g~~~~~Gd~I~YVi~~~~~~~-------~p~~~-~~~~~iD~~yYi~-~l~~~~~~il~~ 767 (787)
T PRK05761 699 YTKNTPQHVKAALQLRD--YGVEVSPGDIISYVKVDDKRGV-------KPVQL-AKLSEIDVEKYIE-LLRSALEQILSA 767 (787)
T ss_pred hcCCCchHHHHHHHHHh--CCCCCCCCCEEEEEEEcCCCCC-------Chhhh-cccCCcCHHHHHH-HHHHHHHHHHHH
Confidence 987 5799999999875 4899999999999999875532 24433 4678999999998 999999999998
Q ss_pred ccccchhhhh
Q 001780 889 ILKNASKELL 898 (1014)
Q Consensus 889 i~g~~~~~l~ 898 (1014)
+ |.+..+|.
T Consensus 768 ~-g~~~~~l~ 776 (787)
T PRK05761 768 L-GVSWDDIR 776 (787)
T ss_pred h-CCCHHHHc
Confidence 7 77777775
No 6
>PRK05762 DNA polymerase II; Reviewed
Probab=100.00 E-value=3.8e-120 Score=1122.34 Aligned_cols=681 Identities=27% Similarity=0.397 Sum_probs=562.6
Q ss_pred CeeEEEEEeEEeeecCCccccCccccCCceEEEEEEEecCCcEEEEEEeCcceEEEEecCCCCCCCcHHHHHHHHHHHHh
Q 001780 89 QSIMFQQLDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMR 168 (1014)
Q Consensus 89 ~~l~Fq~lD~d~~~~~~~~~~~~~~~~~~pvIrLFGvT~~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~ 168 (1014)
+.+.|++||++|.+ . +++|+||+||+|++|.++|+++.||+||||+..+.. .....+....
T Consensus 2 ~~~~~~lL~~~~~~----------~-~~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~-------~~~~~~~~~~- 62 (786)
T PRK05762 2 MLQQGFILTRHYRD----------T-PGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDE-------RAESLLAGEI- 62 (786)
T ss_pred CceEEEEEeeEEEE----------E-CCeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchh-------hhHHHHhhcc-
Confidence 34789999999983 2 346999999999999999999999999999975332 1111222110
Q ss_pred hhccCCCCCcceEEEEEEeecccccccCCCcccEEEEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeee
Q 001780 169 EANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFM 248 (1014)
Q Consensus 169 ~~~~~~~~~~~V~~Ie~V~K~sl~gy~~~~~~~flKI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFm 248 (1014)
...++. ..+..|.+ .++..+++.+++.+.++++.+.++ ++.+||+||+|..|||
T Consensus 63 -----------~~~~~~---~~l~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~---------~~~i~EaDI~~~~R~l 116 (786)
T PRK05762 63 -----------GVRLSP---LALKDFHR---RPVLGLYCRQHRQLTRLPKRLREG---------GVDVYEADIRFPERYL 116 (786)
T ss_pred -----------cceeec---cceecccC---CeeeEEEeccHHHHHHHHHHHHHc---------CCeEEECCCChhHhhe
Confidence 112222 24555553 468899999999999999988762 5889999999999999
Q ss_pred eecCCcceeEEEEeccceeccccccccceeeeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCceeE
Q 001780 249 IDCNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQ 328 (1014)
Q Consensus 249 ID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~ 328 (1014)
||++|.|++|+++.... +++..++ ...++.+.+ .| .|+|++|||||||++. ++|++
T Consensus 117 id~~i~~~~w~~~~~~~--------~~~~~~~--~~~~i~~~~---~~--~p~lrvlsfDIE~~~~---------~~i~s 172 (786)
T PRK05762 117 MERFITPCVWFSGEVEQ--------YTTDGVL--RNARLKPAP---DY--RPPLKVVSLDIETSNK---------GELYS 172 (786)
T ss_pred eeCCCCCcEEEEEEeec--------cccceeE--EecceeeCC---CC--CCCCeEEEEEEEEcCC---------CceEE
Confidence 99999999999886311 1233433 334444321 24 3999999999999863 26888
Q ss_pred EEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccccccc-------
Q 001780 329 VANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK------- 401 (1014)
Q Consensus 329 Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~k------- 401 (1014)
|++. |...+ .+++++.+.+..+..|..|+||++||.+|+++|+++|||||+|||+++||||||.++
T Consensus 173 I~~~----~~~~~---~vi~ig~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~ 245 (786)
T PRK05762 173 IGLE----GCGQR---PVIMLGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP 245 (786)
T ss_pred eeec----CCCCC---eEEEEECCCCCCcceEEEcCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCC
Confidence 8853 22222 577777665433334888999999999999999999999999999999999999981
Q ss_pred --------c------c---------c---------------------------------------c----chhHHHhhcC
Q 001780 402 --------E------D---------V---------------------------------------H----HSIISDLQNG 415 (1014)
Q Consensus 402 --------e------d---------v---------------------------------------~----~~~i~~l~~~ 415 (1014)
. . + + .++|.++|.
T Consensus 246 ~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~- 324 (786)
T PRK05762 246 LRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFA- 324 (786)
T ss_pred cccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHh-
Confidence 0 0 0 0 012233332
Q ss_pred ChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCCCCC
Q 001780 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQ 495 (1014)
Q Consensus 416 ~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~~~~ 495 (1014)
+++.+++.||++||.++++|++++++++.+.|||+++|+|++++. |++..++++|+++|+++|+++|++.... ..
T Consensus 325 --~~~~~l~~Y~l~Da~lt~~L~~kl~ll~~~~ela~l~g~~~~~v~--~~~~~~e~lll~~~~~~g~v~P~~~~~~-~~ 399 (786)
T PRK05762 325 --EDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVG--GSVAAFEHLYLPRAHRAGYVAPNLGERP-GE 399 (786)
T ss_pred --hhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCHHHhC--ccHHhHHHHHHHHHHHCCEeCCCccccc-cc
Confidence 457889999999999999999999999999999999999999985 7788889999999999999999875422 24
Q ss_pred CcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHH
Q 001780 496 GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPE 575 (1014)
Q Consensus 496 ~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~ 575 (1014)
.|+||+|++|++|+|++ |++|||+|||||||++|||||+|++..... ++.+...+|+|.+|++ ++|++|+
T Consensus 400 -~y~Gg~V~~p~~G~y~~-V~~lDF~SLYPSIi~~~Ni~p~T~~~~~~~-----~~~~~~~~~~~~~f~k---~~gilp~ 469 (786)
T PRK05762 400 -ASPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQ-----PPEESVAGFLGARFSR---EKHFLPE 469 (786)
T ss_pred -ccCccEEecCCCCCcCc-eEEEEchhhhHHHHHHhCcCccceecCCCC-----CCcccccCCCCccccc---cCcchHH
Confidence 89999999999999997 999999999999999999999999854321 1234466889999965 8999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhh
Q 001780 576 ILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDK 655 (1014)
Q Consensus 576 iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~ 655 (1014)
+|++|+++|+++|+.|++ .+|+|+|++|||+|||+|++++||||.++|++||++||++|+.|++++++.
T Consensus 470 ~l~~l~~~R~~~K~~~~~-----------~~q~a~Ki~~Ns~YG~~g~~~~r~~~~~~A~~it~~Gr~~l~~~~~~~~~~ 538 (786)
T PRK05762 470 IVERLWEGRDEAKREMNK-----------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQ 538 (786)
T ss_pred HHHHHHHHHHHHHHHHHH-----------HHHHHHHhhhhhcccccccccccccChHHHHHHHHhHHHHHHHHHHHHHHC
Confidence 999999999999999985 689999999999999999999999999999999999999999999999984
Q ss_pred ccccCCccccceEEEecCccceEEcC-CCCHHHHHHHHHHHHHHHHhc----------CCCceeEEEeeeeccceec---
Q 001780 656 FTTVGGYEHNAEVIYGDTDSVMVQFG-VPTVEAAMKLGREAADYISGT----------FIKPIKLEFEKVYYPYLLI--- 721 (1014)
Q Consensus 656 ~~~~~gy~~~~~VIYGDTDSv~V~~~-~~~~~ea~~lg~eia~~vs~~----------~~~pi~Le~Ekvy~~~ll~--- 721 (1014)
|++||||||||+||+++ ..+.+++.++|+++++.||+. ++.|++||||++|.+++|.
T Consensus 539 ---------g~~viYgDTDSifv~~~~~~~~~~~~~~~~~l~~~in~~~~~~l~~~~~~~~~l~le~E~vy~~~~l~~~r 609 (786)
T PRK05762 539 ---------GYQVIYGDTDSTFVWLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALELEFEKHYRRFFMPTIR 609 (786)
T ss_pred ---------CCEEEeecCCceEEEcCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCceEEEEeeeeehhcccccc
Confidence 88999999999999998 578999999999999999984 3678999999999999994
Q ss_pred -----ccceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccc
Q 001780 722 -----SKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSL 796 (1014)
Q Consensus 722 -----~KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~ 796 (1014)
+||||||+.|++ +..+++++||+|+||||||+++|++++++++.||.++++ .+|+++.+++|++|++| ++
T Consensus 610 g~~~~~KKrYag~~~~~-~~~~~~~~KGle~vRrD~~~~~k~~~~~vl~~il~~~~~---~~~~~~~~~~l~~~~~~-~~ 684 (786)
T PRK05762 610 GAEEGSKKRYAGLIQEG-DGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEPY---VDYVREVIDKLRAGELD-EK 684 (786)
T ss_pred ccchhhhheEEEEEEcc-CCCceEEEEeeEEECCChHHHHHHHHHHHHHHHhcCCCH---HHHHHHHHHHHHcCCCc-hh
Confidence 999999999843 346899999999999999999999999999999999887 78999999999999999 99
Q ss_pred eeEeecccCCccccc-CcchHHHHHHHHHHhcCCC----CCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChh
Q 001780 797 LVITKGLTKTGDDYE-VKAAHVELAERMRKRDAAT----APNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTH 871 (1014)
Q Consensus 797 lvi~k~l~k~~~~Y~-~~~~hv~~A~r~~~rd~g~----~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~ 871 (1014)
|+|+|+|+|.+++|+ +.+|||.+|+++++++... .++.||+|+|||+..+++ ++. ..+.+||++
T Consensus 685 lv~~k~l~k~~~~Y~~~~~phv~aa~~~~~~~~~~~~~~~~~~g~~I~Yvi~~~g~~-~~~----------~~~~~iD~~ 753 (786)
T PRK05762 685 LVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYKVGRPLQYQNGGKIGYVITVNGPE-PLE----------YRKSPIDYD 753 (786)
T ss_pred EEEEehcCCCHHHcCCCCCHHHHHHHHHHhcCcccCCcccCCCCCEEEEEEEeCCCC-cHH----------hcCCCCCHH
Confidence 999999999999999 6689999999998875332 135799999999643222 221 237899999
Q ss_pred HHHhhcchhhHHHhhccccccchhhhh
Q 001780 872 YYLENQISKPLLRIFEPILKNASKELL 898 (1014)
Q Consensus 872 yYi~~qi~~pl~ri~~~i~g~~~~~l~ 898 (1014)
|||++||.|++.||+.++ |.+..++.
T Consensus 754 yYi~kql~p~~~ril~~~-~~~~~~~~ 779 (786)
T PRK05762 754 YYIEKQLQPVADRILPFF-GDDFATLK 779 (786)
T ss_pred HHHHHhhHHHHHHHHhhh-CCCHHHHh
Confidence 999999999999999987 77677766
No 7
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.3e-118 Score=1101.38 Aligned_cols=708 Identities=38% Similarity=0.602 Sum_probs=607.5
Q ss_pred ceEEEEEEEecCCcEEEEEEeCcceEEEEecCCCCCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccC
Q 001780 117 AAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQ 196 (1014)
Q Consensus 117 ~pvIrLFGvT~~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~ 196 (1014)
.|.+++||.+++|++|++.+.+|.||||+..+.. .+.+. +....+... .......+...+... |.
T Consensus 8 ~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~---------~~~~~~~~~~~~~~~--~~- 72 (792)
T COG0417 8 FPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNS-RPEDY--VLKILNRRL---------DDVLELEEVENVPDP--YL- 72 (792)
T ss_pred ceEEEEeeecCCCCEEEEEecCCCCcEEEecCCC-cccch--hhhhccccc---------cccceeeeeeeeecc--cc-
Confidence 5999999999999999999999999999988765 11111 111111000 011122222233333 33
Q ss_pred CCcccEEEEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeeeeecCCcceeEEEEeccceeccccccccc
Q 001780 197 QKSQPFLKIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYC 276 (1014)
Q Consensus 197 ~~~~~flKI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C 276 (1014)
..+.+.+||+...|..++++|+.+.+. ..+ ...+||+||+|..|||+|++|.+|.|+.++........ ...
T Consensus 73 ~~~~~~~~i~~~~p~~v~~~r~~~~~~--~~~----~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~~~~~~~~~-~~~-- 143 (792)
T COG0417 73 GREVEVLKIYARDPQAVRKLREKVKRE--LEG----VVDIFEADIPFAMRYLIDKGIRPMVWVSVDVEDIGSIH-SLF-- 143 (792)
T ss_pred CCcccceeeEecCHHHHHHHHHHHhhh--hhc----cceEeecCCCcchheeeecCCCCceEEEeeeccccchh-hcc--
Confidence 446789999999999999999988752 111 36899999999999999999999999999853322110 000
Q ss_pred eeeeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcC
Q 001780 277 QLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIV 356 (1014)
Q Consensus 277 ~~E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~ 356 (1014)
....+..+|+|++|||||||.++.+.+|++..|++++|+......+... ....++...
T Consensus 144 ---------------~~~~~~~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~-------~~~~~~~~~ 201 (792)
T COG0417 144 ---------------LEHREDVRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI-------EVFIYTSGE 201 (792)
T ss_pred ---------------cccccCcCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc-------ccccccCCC
Confidence 1123466899999999999999999999999999999998776544321 122244556
Q ss_pred cceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccccccc-----------------------------------
Q 001780 357 GVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK----------------------------------- 401 (1014)
Q Consensus 357 ~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~k----------------------------------- 401 (1014)
+..|..+.+|.+||.+|.+++..+|||||+|||+++||||||.++
T Consensus 202 ~~~v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl 281 (792)
T COG0417 202 GFSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDL 281 (792)
T ss_pred CceeEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEec
Confidence 677999999999999999999999999999999999999999881
Q ss_pred -----------------------------ccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHH
Q 001780 402 -----------------------------EDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMAR 452 (1014)
Q Consensus 402 -----------------------------edv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~ar 452 (1014)
+++++..+.++|+..+.+..+++.||+.|+.|+.+++.+.+.+..++|+|+
T Consensus 282 ~~~~~~~~~~~~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~l~~~~e~s~ 361 (792)
T COG0417 282 YPALRRRPLNLKSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLKNELLPLLIELSR 361 (792)
T ss_pred HHHHhhhhcccccccHHHHHHHhcccccccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 222233444455555556789999999999999999999999999999999
Q ss_pred HhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCCCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhC
Q 001780 453 VTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYN 532 (1014)
Q Consensus 453 v~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~N 532 (1014)
++|+|++++..+|++.+++++|+++|++.|+++|++...... ..|+||+|++|.+|+|++ |++|||+|||||||++||
T Consensus 362 vsg~~~~~~~~~~~~~~~~~~l~~~a~~~~~~iP~~~~~~~~-~~~~Gg~V~~P~~Gly~~-V~vLDF~SLYPSII~~~N 439 (792)
T COG0417 362 VSGLPLDDVTRAGSGARVEGLLLREAKRRGELIPNKEERPER-KKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYN 439 (792)
T ss_pred HhCCCHHHHcccchhHHHHHHHHHHHhhcCEeccCccccchh-hhcCCCEEccCCccccCc-EEEEEccccChHHHHHhC
Confidence 999999999999999999999999999999999998653332 379999999999999999 999999999999999999
Q ss_pred CCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccc
Q 001780 533 LCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKI 612 (1014)
Q Consensus 533 lc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi 612 (1014)
|||+|+..+... ...+|+|..+..++.++|++|++|++|++.|.++|+.||+.+++.++.+||+||+||||
T Consensus 440 i~p~T~~~~~~~---------~~~~~~~~~~~~~~~~~G~lp~il~~L~~~R~~~K~~~k~~~~~~e~~~~d~rQ~AlKv 510 (792)
T COG0417 440 ISPDTLVEEDCS---------DDYSPPGVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEKDPSERKLLDGRQLALKV 510 (792)
T ss_pred CCcceecCCCcc---------ccccCCCCcccccccCCCchHHHHHHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHH
Confidence 999999876532 23456676677777899999999999999999999999999999999999999999999
Q ss_pred cceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHH
Q 001780 613 SANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLG 692 (1014)
Q Consensus 613 ~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg 692 (1014)
+|||+|||+|++++||||.++|++||++||++|..|++++|+. |++|||||||||||+.+....+||++.+
T Consensus 511 l~NS~YGy~G~~~~rf~~~e~a~~VT~~gR~ii~~t~~~ae~~---------G~~ViyGDTDSlfv~~~~~~~~ea~~~~ 581 (792)
T COG0417 511 LANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEM---------GLRVIYGDTDSLFVTLPGATYEEAIKIG 581 (792)
T ss_pred HHhhccccccccCCccCCHHHHHHHHHHHHHHHHHHHHHHHHc---------CCEEEEECCceeEEEcCCCchHHHHHHH
Confidence 9999999999999999999999999999999999999999995 7799999999999999988899999999
Q ss_pred HHHHHHHHhcCCCceeEEEeeeeccceecc-cceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCC
Q 001780 693 REAADYISGTFIKPIKLEFEKVYYPYLLIS-KKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDR 771 (1014)
Q Consensus 693 ~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~-KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~ 771 (1014)
++++++||..++.+|+||||++|++++|.. ||||||+.++++ ++++||+|+||||||+++|++|++||+.||.++
T Consensus 582 ~~l~~~vn~~~~~~i~lE~e~~y~~~ll~~~KKRYag~~~~g~----~~~vKG~e~~RrD~~~l~k~~q~~vl~~il~~~ 657 (792)
T COG0417 582 EELVEEVNERLPSGIELEVEKVYKRFLLPTAKKRYAGLLEDGD----KIEVKGLETVRRDWPELVKEFQREVLEVLLSGR 657 (792)
T ss_pred HHHHHHHhhcCCCCeEEEeeehhhhhhccccccceEEEeccCC----EEEEeeeEEEecCccHHHHHHHHHHHHHHHcCC
Confidence 999999999999999999999999999998 999999996532 899999999999999999999999999999999
Q ss_pred ChhhH-HHHHHHHHHHHHcCCCCccceeEeecccCCcccccCcchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCc
Q 001780 772 DIPGA-VQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAK 850 (1014)
Q Consensus 772 d~~~a-~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~ 850 (1014)
|+++| ..+++..+.++++|++++++|+|+|+|++.+++|.+.+||+.+|+|++++ |..+.+|++|+|||+++. .+
T Consensus 658 ~~e~~~~~~~~~v~~~l~~~~~~~~~lvi~k~l~k~~~ey~~~~p~~~~a~~~~~~--g~~~~~g~~i~Yvi~~~~--~~ 733 (792)
T COG0417 658 DVEEALAKYVRDVIEKLRNGEVPIEKLVISKRLTRPLSEYKANKPHVVVAARLRKR--GINVKPGDRIPYVIVKGK--GK 733 (792)
T ss_pred CHHHHHHHHHHHHHHHHHcCCcCHHHheeeeeeccChhhhcCCCcHHHHHHHHHhC--CCCCCCCCEeEEEEecCC--Cc
Confidence 99999 99999999999999999999999999999999999999999999999877 899999999999999986 47
Q ss_pred cccccCChhhhhccCCCcChhHHHhhcchhhHHHhhccccccchhhhhc
Q 001780 851 AYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFEPILKNASKELLS 899 (1014)
Q Consensus 851 ~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~i~g~~~~~l~~ 899 (1014)
..+||++|.++.+++.+||++||+++||+||+.||+++|.+. ..++..
T Consensus 734 ~~~ra~~~~~~~~~~~~iD~~YY~~~Ql~~~~~ril~~i~~~-~~~~~~ 781 (792)
T COG0417 734 LVERAEPPELVDEENSPIDYEYYITKQLLPALERILEPIGGN-FAELKG 781 (792)
T ss_pred ccccccCceecccccccCCHHHHHhccchHHHHHHHHHhccc-Hhhhcc
Confidence 889999999998888999999999999999999999999554 666654
No 8
>PHA03036 DNA polymerase; Provisional
Probab=100.00 E-value=2.9e-119 Score=1093.18 Aligned_cols=621 Identities=24% Similarity=0.354 Sum_probs=529.2
Q ss_pred eeeecCCcceeEEEEeccceeccccccccceeeeeee-ccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCc
Q 001780 247 FMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCL-YSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDP 325 (1014)
Q Consensus 247 FmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~-~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~ 325 (1014)
|.+-++|.+-|=+.+....-+..+ ..| ..|+ ++.+-.-+.. ...-|++.|||||||.. .|.||.|..||
T Consensus 113 f~~~n~i~p~gcy~i~~~~~~~~~---~~~---y~c~~p~~~f~~~i~---~~~~~~~~lsfDIEC~~-~g~FPs~~~~p 182 (1004)
T PHA03036 113 FYVLNNISPDGCYRIDIDKLEKIN---NKC---YHCDDPKKCFANKIP---RFDIPRSYLFLDIECHF-DKKFPSVFINP 182 (1004)
T ss_pred EEEecCcCCccceecCHHHhcccc---CCc---eeeCCHHHHhcCcCC---CccCcceeEEEEEEecc-CCCCCCcccCc
Confidence 788899988777777644332222 123 2232 2222111110 11247899999999995 88899999999
Q ss_pred eeEEEE-EeeccC--------------ccccceeEEEeccccCCc---CcceEeecCCHHHHHHHHHHHHHHhCCCEEEE
Q 001780 326 VIQVAN-LVTLQG--------------EKQPFIRNVMTLKSCAPI---VGVDVMSFETERDVLLAWRDFIREVDPDVMIG 387 (1014)
Q Consensus 326 Ii~Is~-~v~~~g--------------~~~~~~~~vf~l~~~~~~---~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiG 387 (1014)
|++||+ .+...| +.++..+.++++..|+++ .+..+..|.+|++|| +|++++.+.|||+|+|
T Consensus 183 vshIs~~~~~~~~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~ 261 (1004)
T PHA03036 183 VSHISCCYIDLSGKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKELILCSEIVLL-RIAKKLLELEFDYVVT 261 (1004)
T ss_pred ceEEEEEEEecCCCeeEEEEeccccccccccccceeeeeeccccccccCCceeeecCCHHHHH-HHHHHHHhcCCCEEEe
Confidence 999995 566666 344455677888888877 688999999999988 7799999999999999
Q ss_pred ecccCCCcccccc-------------------------------------------------------------------
Q 001780 388 YNICKFDLPYLIE------------------------------------------------------------------- 400 (1014)
Q Consensus 388 yNi~~FDlpyL~~------------------------------------------------------------------- 400 (1014)
||+++||||||.+
T Consensus 262 yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L 341 (1004)
T PHA03036 262 FNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEKL 341 (1004)
T ss_pred ccCCCcchHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCccccceEEecccCCeEEEEhHHHHhhhcCc
Confidence 9999999999988
Q ss_pred --------------------------------------------------------------------------------
Q 001780 401 -------------------------------------------------------------------------------- 400 (1014)
Q Consensus 401 -------------------------------------------------------------------------------- 400 (1014)
T Consensus 342 ~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~t~ny~~i~~~~~~k~~~k~~~~~~~~~~~~~ 421 (1004)
T PHA03036 342 DSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLSTGNYVTINDDDICKILDKDIIENSFTVKVIC 421 (1004)
T ss_pred ccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhcccceeeecccchhhhcccccccccceeeeec
Confidence
Q ss_pred ---------------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccc
Q 001780 401 ---------------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRG 465 (1014)
Q Consensus 401 ---------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG 465 (1014)
|+||++++|.+.|+ .++|++++.||++||.||++|+++++++..+.++|+.+.+|..+++..|
T Consensus 422 ~~~~~~~~~~~~~~~KdDV~~~~i~~~~~--~~~r~rla~YClkDa~L~l~L~~~l~~~~~v~~~a~~~~lp~~~~i~~~ 499 (1004)
T PHA03036 422 KNNYIPGDTYTLSFGKDDVDLSDMYKNYN--LEIALEMARYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYR 499 (1004)
T ss_pred ccccccccceeecccccCCCHHHHHHHhC--hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhheEeee
Confidence 45666777888886 4789999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHhhcCccccCCCcCCCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhh-
Q 001780 466 QSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDA- 544 (1014)
Q Consensus 466 ~~~~v~s~L~r~a~~~~~viP~~~~~~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~- 544 (1014)
||+++.+||+|.|.++|+++|.... ..+.+|+||+|+||++|+|++||++|||+||||||||+|||||||+++....
T Consensus 500 ~s~~i~~qllr~~~~~~~i~p~~~~--~~~~~YeGa~VlEP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~ 577 (1004)
T PHA03036 500 ASTLIKGPLLKLLLEEKTILVRSET--KNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVND 577 (1004)
T ss_pred eccccccHHHHHHHHCCcccccCCC--CccCCcCceEEecCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccc
Confidence 9999999999999999999994322 2233799999999999999989999999999999999999999999864210
Q ss_pred hc---------c--CCCCCcee---eCCCC-----ceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHH
Q 001780 545 RK---------L--NLPPECVN---KTPSG-----ETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDG 605 (1014)
Q Consensus 545 ~~---------~--~~~~~~~~---~~p~g-----~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~ 605 (1014)
++ + ..++.++. ..|++ ..|+.+++++||||++|++|+++|+++|++||+++|+.++++||+
T Consensus 578 ~~~~~~i~~~~i~~~~p~~dy~~v~~~~~~~~~v~~~~vf~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~~~d~~e~~~lD~ 657 (1004)
T PHA03036 578 NRLEAEINKQELRRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIYDS 657 (1004)
T ss_pred cccccccccccccccCCCccceeeeccCCcccccccceeecCCCCcChHHHHHHHHHHHHHHHHHHhhCCChHHHHHHHH
Confidence 00 0 11222322 23432 346677789999999999999999999999999999999999999
Q ss_pred HhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhc-----------------------------
Q 001780 606 RQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKF----------------------------- 656 (1014)
Q Consensus 606 rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~----------------------------- 656 (1014)
+|+|+|++|||+|||+|+++|||||.++|++||++||+||+.|+++|++.+
T Consensus 658 rQlAlKI~aNS~YG~~G~~~~rly~~~iA~sVTa~GR~mI~~tk~~Ve~~~~~~~~~~l~~~p~~~f~~~~r~~~~~~~~ 737 (1004)
T PHA03036 658 MQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSVLNGSKLINGKLILANCPINPFFKDDRSIDTNYDT 737 (1004)
T ss_pred HHHHHHHHHhcccccccccCccccCHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhccccccccccccccccccc
Confidence 999999999999999999999999999999999999999999999987633
Q ss_pred cccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhc-CCCceeEEEeeeeccceecccceeEEEeccCC-
Q 001780 657 TTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGT-FIKPIKLEFEKVYYPYLLISKKRYAGLYWTNP- 734 (1014)
Q Consensus 657 ~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~-~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~- 734 (1014)
..+++|.+|++|||||||||||+++..+.++++++|+++++.||+. |++|++|||||||.++||++||||||+.|+++
T Consensus 738 ~l~~~~~~g~kVIYGDTDSVFV~~~~~d~eea~~ig~ela~~In~~lf~~pikLEfEKVY~~lLLl~KKRYAGl~~~~~~ 817 (1004)
T PHA03036 738 NLPVEYNFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASS 817 (1004)
T ss_pred cccccccCCcEEEEEecCeeEEEcCCCCHHHHHHHHHHHHHHHHHHhcCCCeEEEehhhHHHHHhhhhhheeeEeecccc
Confidence 1345677899999999999999999999999999999999999985 89999999999999999999999999998765
Q ss_pred --CCccceeEeeeeeccCchHHHHHHHHHHHHHHH---hcCCC---hhhHHHHHHHHHHHHHc----CCCCccceeEeec
Q 001780 735 --EKFDKMDTKGIETVRRDNCLLVKNLVTECLHKI---LVDRD---IPGAVQYVKSTISDLLM----NRMDLSLLVITKG 802 (1014)
Q Consensus 735 --~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~i---l~~~d---~~~a~~~v~~~i~~l~~----~~v~~~~lvi~k~ 802 (1014)
+..+++++||+|+||||||+|+|++++++++.| |.+++ .+.|++++++.+.+|.. |++|+++|+|||+
T Consensus 818 ~~~~~~kid~KGie~VRRD~c~fvK~v~~~vi~~L~~iL~~~d~~~~~~~i~~Lk~~i~dL~~n~~~~~vple~LviSk~ 897 (1004)
T PHA03036 818 TDGSVPERVNKGTSETRRDVSKFHKYMIKIYKTRLLDMLSEGNMNSNQVCIDILRSLEKDLIIEFDSRSAPLEMFLLSRT 897 (1004)
T ss_pred CCCCceEEEEECceeEeCchHHHHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhhhc
Confidence 345689999999999999999999999976654 87776 56889999998888765 4999999999999
Q ss_pred ccCCcccccCc-chHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCC--------CCccccccCChhhhhccCCCcChhHH
Q 001780 803 LTKTGDDYEVK-AAHVELAERMRKRDAATAPNVGDRVPYVIIKAAK--------GAKAYERSEDPIYVLENNIPIDTHYY 873 (1014)
Q Consensus 803 l~k~~~~Y~~~-~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~--------~~~~~~ra~~p~~~~~~~~~iD~~yY 873 (1014)
+++ .|+++ +||+++|+||++|+++ .|+.||||+||++.+.. +.+.|+|||||.|+++|+++||++||
T Consensus 898 l~~---~Yk~~~~ph~~la~r~~~r~~~-~p~iGDRv~YV~i~~~~~~w~~~~~~~~~ye~aeDp~yvl~~~~~I~~e~Y 973 (1004)
T PHA03036 898 HHC---NYKSPDNPNMYLVNEYNKNNPE-KIEIGERYYFAYICPINLPWQKKLVNIKTYERIIDRSFKLKSNERIFYEVY 973 (1004)
T ss_pred ccc---cCCCCCCCHHHHHHHHHhhCCC-CCCCCCEEEEEEEECCCccccccccCcccceeecCccccccCCCceeHHHH
Confidence 998 49986 9999999999999988 99999999999998755 67899999999999999999999999
Q ss_pred HhhcchhhHHHhhc
Q 001780 874 LENQISKPLLRIFE 887 (1014)
Q Consensus 874 i~~qi~~pl~ri~~ 887 (1014)
++ ||+.++.+++.
T Consensus 974 ~~-~l~~~v~n~l~ 986 (1004)
T PHA03036 974 FK-RLATEVVNLLD 986 (1004)
T ss_pred HH-HHHHHHHHHhc
Confidence 99 79999998875
No 9
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=4.6e-117 Score=1128.17 Aligned_cols=722 Identities=26% Similarity=0.407 Sum_probs=592.8
Q ss_pred ceEEEEEEEecCCcEEEEEEeCcc-eEEEEecCCCCCCC---------cHHHHHHHHHH-HHhhhccCCCCCcceEEEEE
Q 001780 117 AAIIRIFGVTREGHSVCCKVHGFE-PYFYISCPQGMGPD---------DISHFHQILEG-RMREANRNSKVPQFVRHIEM 185 (1014)
Q Consensus 117 ~pvIrLFGvT~~G~SV~v~V~gF~-PYFYV~~p~~~~~~---------~~~~~~~~L~~-~l~~~~~~~~~~~~V~~Ie~ 185 (1014)
.+++.+||+..+|.|+|+.|.||. ..++++.+.....+ .+.++...... .+.+. ...-.+...
T Consensus 322 ~G~~~lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~------~k~dv~~k~ 395 (1172)
T TIGR00592 322 LGVVLLFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGY------KKEKFRAKP 395 (1172)
T ss_pred CCeEEEecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhc------CcCceeeEE
Confidence 377999998777899999999987 56667765432211 22333322222 11110 111122233
Q ss_pred EeecccccccCC-----CcccEEEEEEcChhhHHHHHHHHhc--CccccCCCCccceeeecccccceeeeeecCCcceeE
Q 001780 186 VQKRSIMYYQQQ-----KSQPFLKIVVALPTMVASCRGILDR--GIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNW 258 (1014)
Q Consensus 186 V~K~sl~gy~~~-----~~~~flKI~~~~P~~v~klR~~le~--g~~~~~l~~~~~~~yEanI~~~lRFmID~~I~G~~W 258 (1014)
+.+. |.+... ....+++|.+..+..+..+....+. |.++. .+|++|.....||+++++++|+||
T Consensus 396 I~~~--~~~~~~~~~v~y~~~~lkv~y~l~~~~~~l~~l~~~~~g~~~~-------~vf~~n~g~~erfll~rki~gp~W 466 (1172)
T TIGR00592 396 IAKK--YEFEAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFW-------HVFGSNTGNLERFLLLRKIKGPCW 466 (1172)
T ss_pred ehhh--ccCCCCccCCcCCcceEEEEEccCccchhhhhhhhhccCCcch-------heeccCHHHHHHHHhcCCCCCCce
Confidence 3332 333321 2357999999877666666554442 33333 467899999999999999999999
Q ss_pred EEEeccceeccccccccceeeeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCc
Q 001780 259 IEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGE 338 (1014)
Q Consensus 259 i~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~ 338 (1014)
+.+........ .+.|||++|+.+..+.++.. +.+..+||+++|+|+||+ +||....++|+|||+++...+.
T Consensus 467 L~i~~p~~~~~-~~~S~c~yEga~v~~p~v~~---g~~~~~pPl~vLdFsi~S-----lyPsi~~~~nl~iS~~v~~~~~ 537 (1172)
T TIGR00592 467 LAVKGPDELEY-PRRSWCKYEGGYVKPPNVEK---GLDKTPPPLVVLDFSMKS-----LNPSIIRNEIVSIPDTLHREFA 537 (1172)
T ss_pred EEeCCCcccCc-CCccccceEEEEecCccccc---cccCCCCCeEEEEeeeEE-----ecCccccCceEEEEEEEeeccc
Confidence 99976544321 14789999999986654332 344557999999999993 4899999999999988765421
Q ss_pred -----cccceeEEEec----cccC----------CcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccccc
Q 001780 339 -----KQPFIRNVMTL----KSCA----------PIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLI 399 (1014)
Q Consensus 339 -----~~~~~~~vf~l----~~~~----------~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~ 399 (1014)
..+.....|+. ..|. .+.+..|..+.+|++||.+|++.++++|||+++|||+.+|||+||.
T Consensus 538 ~d~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~ 617 (1172)
T TIGR00592 538 LDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLA 617 (1172)
T ss_pred ccCCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHH
Confidence 11112222322 1122 2345678999999999999999999999999999999999999988
Q ss_pred c----------------------------------------------------------------cccccchhHHHhhcC
Q 001780 400 E----------------------------------------------------------------KEDVHHSIISDLQNG 415 (1014)
Q Consensus 400 ~----------------------------------------------------------------kedv~~~~i~~l~~~ 415 (1014)
+ |.++++..|.++|.
T Consensus 618 nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~- 696 (1172)
T TIGR00592 618 NRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYS- 696 (1172)
T ss_pred HHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHh-
Confidence 7 23455677888887
Q ss_pred ChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCC---
Q 001780 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAG--- 492 (1014)
Q Consensus 416 ~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~--- 492 (1014)
+++.+.+++.||++||.|+++|+.+|++++.+.++|+++|.+++.++.+|+|.+++++|+|+++++||++|++....
T Consensus 697 ~~~~~~~~~~y~~~Da~l~~~L~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~~~~~~~i~P~~~~~~~~~ 776 (1172)
T TIGR00592 697 ESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQ 776 (1172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHHHHhCCEEccCcccccccc
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999864210
Q ss_pred --------------CCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCC
Q 001780 493 --------------SEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTP 558 (1014)
Q Consensus 493 --------------~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p 558 (1014)
....+|+||+|++|++|||++||++|||+|||||||++|||||||++.+.+. +++...|
T Consensus 777 ~~~~~~~~~~~~~~~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~t~~~~~~~-------~~~~~~~ 849 (1172)
T TIGR00592 777 KLGDEDEEIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDE-------DELPELP 849 (1172)
T ss_pred ccccccccccccccccccCcCCCeEecCCCCcccCCEEEEEcCCccHHHHHHhCcCccccCCCCcc-------hhcccCC
Confidence 1124899999999999999999999999999999999999999999875421 1222222
Q ss_pred CCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHH
Q 001780 559 SGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVT 638 (1014)
Q Consensus 559 ~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT 638 (1014)
.++.++||||++|++|+++|+++|+.||+..||.++++||.||+|||++|||+|||+|+++|||||.++|++||
T Consensus 850 ------~~~~~~Gilp~il~~L~~~R~~~K~~mk~~~~~~~~~~~d~~Q~AlKi~aNS~YG~lG~~~~r~~~~~~A~~iT 923 (1172)
T TIGR00592 850 ------DSELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVT 923 (1172)
T ss_pred ------cccccCcchHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHhhhccccccccccccccChHHHHHHH
Confidence 24568999999999999999999999999889999999999999999999999999999999999999999999
Q ss_pred HhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccc
Q 001780 639 SYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPY 718 (1014)
Q Consensus 639 ~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ 718 (1014)
++||++|+.|++++++. |++|||||||||||+++..+.++++++|+++++.||+.|+ |++||||++|.++
T Consensus 924 ~~GR~~l~~~~~~~e~~---------g~~VIYGDTDSv~v~~~~~~~~e~~~~~~~~~~~in~~~~-~l~le~e~vy~~~ 993 (1172)
T TIGR00592 924 AKGREILEHTRQLVEEM---------NLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRL 993 (1172)
T ss_pred HHHHHHHHHHHHHHHHc---------CCEEEEecCCeEEEEcCCCCHHHHHHHHHHHHHHHhhcCC-ceEEeehhhhHhh
Confidence 99999999999999984 7899999999999999999999999999999999999997 8999999999999
Q ss_pred eecccceeEEEeccCCCCc---cceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHH----HcCC
Q 001780 719 LLISKKRYAGLYWTNPEKF---DKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDL----LMNR 791 (1014)
Q Consensus 719 ll~~KKRYagl~~~~~~~~---~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l----~~~~ 791 (1014)
||++||||||+.++++... .++++||+|+||||||+|+|++++++|+.||.++++++|++++++.+.++ .+|+
T Consensus 994 ll~~KKrYa~l~~~~~~~g~~~~k~~~KGle~vRrD~~~l~k~~~~~vl~~il~~~~~~~~~~~i~~~l~~~~~~l~~g~ 1073 (1172)
T TIGR00592 994 LLLKKKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKNVLNGE 1073 (1172)
T ss_pred HhhhccceEEEeeccCcCCCcceeEEeecceEEECCcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999998754332 38999999999999999999999999999999999999887777666555 4599
Q ss_pred CCccceeEeecccCCccccc--CcchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhh--ccCCC
Q 001780 792 MDLSLLVITKGLTKTGDDYE--VKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVL--ENNIP 867 (1014)
Q Consensus 792 v~~~~lvi~k~l~k~~~~Y~--~~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~--~~~~~ 867 (1014)
+|+++|+|+|+|+|.+++|. +.+|||++|+||++++ |..++.||||+|||++++++...++||++|.++. +++++
T Consensus 1074 ~~~~~lvi~k~l~k~~~~Y~~~~~~phv~~A~~~~~~~-g~~~~~G~~I~Yvi~~~~~~~~~~~ra~~~~~~~~~~~~l~ 1152 (1172)
T TIGR00592 1074 VPLEKFVINKQLTRDPKDYPDGASLPHVHVALRINARG-GRKVKAGDVVSYVICKDGGNLSARQRAYALEELQRKHNNLI 1152 (1172)
T ss_pred CCHHHeeehhhccCCHHHcCCCCCChHHHHHHHHHHhc-CCCCCCCCEEEEEEEeCCCCcchhhhccChHHhhccCCCCC
Confidence 99999999999999999999 5689999999999874 7889999999999999877766778999998875 45799
Q ss_pred cChhHHHhhcchhhHHHhhc
Q 001780 868 IDTHYYLENQISKPLLRIFE 887 (1014)
Q Consensus 868 iD~~yYi~~qi~~pl~ri~~ 887 (1014)
||++|||++||+||+.|||+
T Consensus 1153 iD~~yYi~~qi~p~~~Ri~e 1172 (1172)
T TIGR00592 1153 YDTQYYLEHQIHPVVLRILE 1172 (1172)
T ss_pred cCHHHHHHhhcHHHHHHhhC
Confidence 99999999999999999986
No 10
>PHA02528 43 DNA polymerase; Provisional
Probab=100.00 E-value=1.2e-106 Score=994.93 Aligned_cols=659 Identities=23% Similarity=0.297 Sum_probs=524.8
Q ss_pred eEEEEEEEecCCcEEEEEEeCcceEEEEecCCCCCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccCC
Q 001780 118 AIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQQ 197 (1014)
Q Consensus 118 pvIrLFGvT~~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~~ 197 (1014)
..|..=|+.++|+.....|+ |.|.+|+.+.++. .+..|.
T Consensus 13 ~~~~~r~~~~~g~~~~~~~~-~~ptl~~~~~~~~--------------------------------------~~~~~~-- 51 (881)
T PHA02528 13 DNILERYIDDNGKERSRKVK-YEPTLFVHANEES--------------------------------------KYKDIY-- 51 (881)
T ss_pred CEEEEEEEcCCCcEEEEeec-cCcceEEecCCCc--------------------------------------cccccC--
Confidence 34555556678999999986 9999999775420 111222
Q ss_pred CcccEEEEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeeeeecCCcceeEEEEeccceeccccccccce
Q 001780 198 KSQPFLKIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQ 277 (1014)
Q Consensus 198 ~~~~flKI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~ 277 (1014)
..+...+++.+.+...++.+.++.. ++.+| ++|+.|.+.-| +.|. .
T Consensus 52 -~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~----------~merfi~~~~~-----~~~~-~-------- 97 (881)
T PHA02528 52 -GKNCRPKKFDSMRDARKWMKRMKDV---------GFEAL----------GMDDFKLQYIS-----DTYP-G-------- 97 (881)
T ss_pred -CCEEeEEECCCHHHHHHHHHHHHhc---------CCcee----------ehhHHhhhhhh-----hhcC-C--------
Confidence 1578889999998888887776541 23333 78888888766 2221 0
Q ss_pred eeeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCC--CCceeEEEEEeeccCccccceeEEEecc-----
Q 001780 278 LEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPT--HDPVIQVANLVTLQGEKQPFIRNVMTLK----- 350 (1014)
Q Consensus 278 ~E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~--~D~Ii~Is~~v~~~g~~~~~~~~vf~l~----- 350 (1014)
+.++ ..|+||++||||||+++.| ||+|+ .|||++||.. +..+. + -.+|.++
T Consensus 98 ---------------~~~~-~~p~lrv~s~DIE~~~~~g-fP~p~~~~d~IisIsl~-~~~~~-~---~~v~~~~~~~~~ 155 (881)
T PHA02528 98 ---------------EIKY-DRSKIRIANLDIEVTAEDG-FPDPEEAKYEIDAITHY-DSIDD-R---FYVFDLGSVEEW 155 (881)
T ss_pred ---------------CCCC-CCCCccEEEEEEEECCCCC-CCCcccCCCcEEEEEEe-cCCCC-E---EEEEEecCcccc
Confidence 0122 2489999999999998776 99999 7899999952 11111 1 1245442
Q ss_pred ----ccC---CcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccc-----------------------
Q 001780 351 ----SCA---PIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE----------------------- 400 (1014)
Q Consensus 351 ----~~~---~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~----------------------- 400 (1014)
++. ...+.++..|++|++||.+|+++|++.|||||+|||+++||||||++
T Consensus 156 ~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~ 235 (881)
T PHA02528 156 DAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKER 235 (881)
T ss_pred cccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccc
Confidence 111 12346677899999999999999999999999999999999999988
Q ss_pred ---------------------------------------------------cccccchhHHHhhcCChhhhhHHhhhhhc
Q 001780 401 ---------------------------------------------------KEDVHHSIISDLQNGNAETRRRLAVYCLK 429 (1014)
Q Consensus 401 ---------------------------------------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lk 429 (1014)
|.++++++|.++|.+ +..+++.||++
T Consensus 236 ~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~---d~~~l~~Ynl~ 312 (881)
T PHA02528 236 TIENMYGREEIAYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRET---DHQKYIEYNII 312 (881)
T ss_pred cccccccccceeEEEcceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhc---CHHHHHHHHHH
Confidence 222233456666653 34789999999
Q ss_pred cccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHH-HHHHHHHhhcCccccCCCcCCCCCCcCCcceeeeccC
Q 001780 430 DAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVL-SQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARA 508 (1014)
Q Consensus 430 Da~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~-s~L~r~a~~~~~viP~~~~~~~~~~~yeGg~VleP~~ 508 (1014)
||.|+++|+.+++++.+++|||+++|+|+++++ +|++++ ++|+++++++|+++|+.... ..+ +|+||+|+||+|
T Consensus 313 Da~Lv~~L~~kl~ll~~~~e~ArltGi~l~~v~---sq~~~~~~lll~~~~r~g~viP~~~~~-~~~-~y~Gg~V~eP~p 387 (881)
T PHA02528 313 DVELVDRLDDKRKLIELVLSMAYYAKINFEDVF---SPIKTWDAIIFNSLKEEKIVIPENKSH-KKQ-KYAGAFVKEPVP 387 (881)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHhc---chHhHHHHHHHHHHHHcCcccCCcccc-CCC-CCCCcEEecCCC
Confidence 999999999999999999999999999999985 356655 67899999999999987542 224 899999999999
Q ss_pred ceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhc--------cCCCCCceeeCCCCceeeecCCcCCCcHHHHHHH
Q 001780 509 GFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARK--------LNLPPECVNKTPSGETFVKSNLQKGILPEILEEL 580 (1014)
Q Consensus 509 G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~--------~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~L 580 (1014)
|+|++ |++|||+|||||||++|||||+|++++..... ...+.+++..+|+|.+|++ .++||||++|++|
T Consensus 388 GlY~~-VvVLDF~SLYPSIIiayNIcp~Tlv~~~~~~~~~~~~~~~~~~~~~~~~~~p~G~~F~k--~~~GiLP~iL~~L 464 (881)
T PHA02528 388 GAYRW-VVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYINKTAPRPSDEYSCSPNGWMYRK--DIRGVIPTEIKKV 464 (881)
T ss_pred Ccccc-eEEEeccccChHHHHHhCCChhhccccccccccccccccccCCCCCceeEcCCCCeEeC--CCCeehHHHHHHH
Confidence 99985 99999999999999999999999997642111 1122456778999999986 3899999999999
Q ss_pred HHHHHHHHHHhhhcC-C--------------------------------------------------hHHHHHhHHHhhh
Q 001780 581 LAARKRAKADLKEAK-D--------------------------------------------------PLEKAVLDGRQLA 609 (1014)
Q Consensus 581 l~~R~~~K~~mk~~~-d--------------------------------------------------~~~~~~ld~rQ~A 609 (1014)
+++|+++|+.||+++ | +.++++||.+|+|
T Consensus 465 l~~R~~~Kk~Mk~~~~~~~~~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~d~~Q~A 544 (881)
T PHA02528 465 FDQRKIYKKKMLAAERNAELIKTILEDLNDSVDTPIDVDYYFDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMA 544 (881)
T ss_pred HHHHHHHHHHHHhccccccccccccccccccccccccccccccchhhhhhhhcccchhhhhhhhhhhHHHHHHHHHHHHH
Confidence 999999999998654 1 1457899999999
Q ss_pred ccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCC-HH--
Q 001780 610 LKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPT-VE-- 686 (1014)
Q Consensus 610 lKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~-~~-- 686 (1014)
+||+|||+|||+|+.++||||.++|+|||++||.+|+.+++.+++.++..+|..++++|||||||||||+++..- ..
T Consensus 545 ~KI~~NS~YG~lG~~~~r~y~~~~A~aiT~~Gr~~I~~i~~~~~e~l~~~~~~~g~~~VIYGDTDSvfV~~~~~~~~~~~ 624 (881)
T PHA02528 545 RKILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDYVIYGDTDSIYVNLDPLVEKVGE 624 (881)
T ss_pred HHHHHHhhhhhccCcCccCCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhcccCCcEEEEEcCCeeEEEeCCcchhhhh
Confidence 999999999999999999999999999999999999988888877555445555457999999999999996431 00
Q ss_pred ----HHHHH-------H------------HHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCCC---ccce
Q 001780 687 ----AAMKL-------G------------REAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEK---FDKM 740 (1014)
Q Consensus 687 ----ea~~l-------g------------~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~---~~k~ 740 (1014)
+...+ + .|++++++... +++.|+||++|.+++|.+||||||+.|+++++ .+++
T Consensus 625 ~~~~~~~~lv~~~~~~~~~~l~~~~~~~~~el~e~~~~~~-~~~~m~~ek~~~~~~~~sKKRYAgl~~~~~g~~~~~~kl 703 (881)
T PHA02528 625 DKFKDTNHWVDFLDKFCKERMEPYIDSSYRELCEYMNNYE-HLMFMDREAIAGPGFWTAKKRYALNVWDSEGTRYAEPKL 703 (881)
T ss_pred ccchhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhc-cccchhHHHHhhHhhhhccccEEEEeccCCCcccCCCeE
Confidence 11111 1 26777787755 46999999999999999999999999987653 3799
Q ss_pred eEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccc--------cC
Q 001780 741 DTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDY--------EV 812 (1014)
Q Consensus 741 ~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y--------~~ 812 (1014)
++||+|+||||||+++|++|+++++.||.+++ +++++|+++++.++++ +|++++.+. ++++++++| ++
T Consensus 704 ~~kGlEtvRsD~~~lak~~q~~vi~~Il~~~~-e~~~~yvk~~i~~~~~--~d~~~i~~~-~~~~~l~~Y~~~~~~y~k~ 779 (881)
T PHA02528 704 KIMGIETQRSSTPKAVQKALKEAIRRILQEGE-ESLQEYIKEFEKEFRK--LDYEEIAFV-SSANNIAKYSDDKGIPGKG 779 (881)
T ss_pred EEecceeeecchHHHHHHHHHHHHHHHHhCCc-HhHHHHHHHHHHHHHc--CCHHHEEee-eccCCHHHhcccccccccC
Confidence 99999999999999999999999999998865 9999999999999997 999999988 899999998 45
Q ss_pred cchHHHHHH---HHHHhcCCC-CCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCc--ChhHHHhhc------chh
Q 001780 813 KAAHVELAE---RMRKRDAAT-APNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPI--DTHYYLENQ------ISK 880 (1014)
Q Consensus 813 ~~~hv~~A~---r~~~rd~g~-~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~i--D~~yYi~~q------i~~ 880 (1014)
.+|||.+|+ ++.+++.|. .++.|++|.||++++++ +.++||....++-+-...+ |.+||+++| ++|
T Consensus 780 ~pphV~aA~~~~~~~~~~~g~~~~~~G~kI~~v~lk~~~--~~~~~~~~~~~~~~~p~~~~~d~~~~iD~~~~~~k~~~~ 857 (881)
T PHA02528 780 CPIHIRGALLYNRAVKGTLGYPPIQEGEKVMVLPLKEPN--PIGENCIAWPSGTELPKEIRSDLLKWVDYNLLFEKSFIK 857 (881)
T ss_pred CCHHHHHHHHHHHHHhhhcCCcccCCCCEEEEEEEeCCC--CCCCceEeccccccCHHHHhhchhheechhhhhhhhhhh
Confidence 589999998 776642366 78999999999999744 6778887666543323456 999999999 999
Q ss_pred hHHHhhcccccc
Q 001780 881 PLLRIFEPILKN 892 (1014)
Q Consensus 881 pl~ri~~~i~g~ 892 (1014)
|+.||++++ |.
T Consensus 858 p~~~il~~~-g~ 868 (881)
T PHA02528 858 PLKNITEAI-GW 868 (881)
T ss_pred HHHHHHHHh-CC
Confidence 999999998 55
No 11
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=100.00 E-value=1.7e-99 Score=869.90 Aligned_cols=392 Identities=78% Similarity=1.213 Sum_probs=376.9
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
+|+||+|++|++|||++||++|||+|||||||++|||||||++++.+... ++++++..+|+|.+|+++++++||||++
T Consensus 2 ~Y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~~--~~~~~~~~~p~~~~f~~~~~~~Gilp~i 79 (393)
T cd05533 2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKK--LPPEDYIKTPNGDYFVKSSVRKGLLPEI 79 (393)
T ss_pred CCCCeEeccCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCccccc--CCCcceEECCCCceeecCCCCCCchHHH
Confidence 79999999999999999999999999999999999999999998764332 2356788999999999988899999999
Q ss_pred HHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhc
Q 001780 577 LEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKF 656 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~ 656 (1014)
|++|++.|+++|+.||+++||.++++||.+|+|+|++|||+|||+|+++|||||.++|++||++||++|+.|++++++.+
T Consensus 80 L~~Ll~~R~~~K~~mk~~~d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~~r~~~~~~A~~iT~~GR~~l~~~~~~ie~~~ 159 (393)
T cd05533 80 LEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKY 159 (393)
T ss_pred HHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhhheeeeecccccccccCCccchHHHHHHHHhHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCCC
Q 001780 657 TTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEK 736 (1014)
Q Consensus 657 ~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~ 736 (1014)
.+.+||.+|++|||||||||||+++..+.++++++|+++++.||+.|+.|++||||++|.++|+++||||||+.|++++.
T Consensus 160 ~~~~g~~~~~~VIYGDTDSvfv~~~~~~~~~~~~~~~ei~~~i~~~~~~~i~Le~E~vy~~~ll~~KKrYag~~~~~~~~ 239 (393)
T cd05533 160 TKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPDK 239 (393)
T ss_pred cccccCCCceEEEecCCCceEEEcCCCCHHHHHHHHHHHHHHHHhcCCCCeEEeeHHHHHHHHHHHHhhheEEEeecCCC
Confidence 88899999999999999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred ccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccccCcchH
Q 001780 737 FDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816 (1014)
Q Consensus 737 ~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~~h 816 (1014)
.+++++||+|++|||||+|+|++++++|+.||.++|++++++++++.+++|++|++|+++|+|+|+|+|.+++|+..+||
T Consensus 240 ~~ki~~KGle~vRRD~~~~~k~~~~~vl~~il~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~i~k~l~k~~~~Y~~~~ph 319 (393)
T cd05533 240 HDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNKIDISLLVITKALTKTADDYAGKQAH 319 (393)
T ss_pred CceeEEeceEEEcccchHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHcCCCCHHHEEEEeeecCChhhcCCCCch
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHhhcccc
Q 001780 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFEPIL 890 (1014)
Q Consensus 817 v~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~i~ 890 (1014)
|++|+||+++++|..|++||||+|||+++.++.++++||++|.++++++++||++|||++||+|||.|||+||+
T Consensus 320 v~~A~rl~~~~~g~~~~~G~rI~Yvi~~~~~~~~~~~~a~~~~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~~~ 393 (393)
T cd05533 320 VELAERMRKRDPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPIL 393 (393)
T ss_pred HHHHHHHHhcCCCCCCCCCCEEEEEEEECCCCCcHHhhccCHHHHHhcCCCCChHHHHHhcchHHHHHHHhhhC
Confidence 99999999998899999999999999998778889999999999999999999999999999999999999984
No 12
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=100.00 E-value=2.6e-98 Score=871.28 Aligned_cols=421 Identities=37% Similarity=0.628 Sum_probs=380.7
Q ss_pred ccHHHHHHHHHHHHhhcCccccCCCcCC-C-CCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChh
Q 001780 465 GQSIKVLSQLLRKAKQKNLVIPNVKQAG-S-EQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPE 542 (1014)
Q Consensus 465 G~~~~v~s~L~r~a~~~~~viP~~~~~~-~-~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~ 542 (1014)
|||++||++|+|+|+++|+++|+..... . ..+.++||+|+||++|+|++||++|||+||||||||+|||||||+++..
T Consensus 1 g~q~rve~~llr~~~~~g~~~p~~~~~~~~~~~~~~~g~~V~eP~~G~y~~~V~vLDF~SLYPSIi~~~Nic~sT~~~~~ 80 (451)
T cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80 (451)
T ss_pred CCeEEeHHHHHHHHHHcCEEeecCchhccccccccccCcEeecCCcCcccCceEEEecccccHHHHHHhCcCcccccccc
Confidence 8999999999999999999999874321 1 1336789999999999999999999999999999999999999998742
Q ss_pred hh-----hc---------------cCCCCCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCC-hHHHH
Q 001780 543 DA-----RK---------------LNLPPECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKD-PLEKA 601 (1014)
Q Consensus 543 ~~-----~~---------------~~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d-~~~~~ 601 (1014)
+. .. ....++++..+|+|..|+++++++||||++|++|++.|+++|+.||++++ +.+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~~~~~~~ 160 (451)
T cd05534 81 EELNGGGKFGFLGVKLYLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQR 160 (451)
T ss_pred cccccccccccccccccccccccccccCCCcEEECCCcceeecCCCCCCchHHHHHHHHHHHHHHHHHHhhCCCCHHHHH
Confidence 10 00 00113457789999999998889999999999999999999999999886 89999
Q ss_pred HhHHHhhhccccceeccccccccc-CCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEc
Q 001780 602 VLDGRQLALKISANSVYGFTGATV-GQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQF 680 (1014)
Q Consensus 602 ~ld~rQ~AlKi~aNS~YG~~G~~~-~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~ 680 (1014)
+||.+|+|+|++|||+|||+|+++ |||||.++|++||++||++|++|++++++. ..+|++|||||||||||++
T Consensus 161 ~ld~~Q~AlKi~~NS~YGy~G~~~~gr~~~~~iA~~IT~~GR~~l~~~~~~ie~~------~~~g~~VIYGDTDSvfv~~ 234 (451)
T cd05534 161 ILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIEST------PKWGAKVVYGDTDSLFVLL 234 (451)
T ss_pred HHHHHHHHHHHHhhccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHhhc------cccCceEEeecccceeEec
Confidence 999999999999999999999997 799999999999999999999999999982 1248999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCC-CCccceeEeeeeeccCchHHHHHHH
Q 001780 681 GVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNP-EKFDKMDTKGIETVRRDNCLLVKNL 759 (1014)
Q Consensus 681 ~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~-~~~~k~~~KGie~vRRD~~~l~k~~ 759 (1014)
++.+.++++++|++++++||+.|+.|++||||++|.++++++||||||+.|+++ +..+++++||+|+||||||+|+|++
T Consensus 235 ~~~~~~~~~~~~~~i~~~in~~~~~~i~le~E~vy~~~ll~~KKrYag~~~~~~~~~~~ki~~KGle~vRrD~~~~~k~~ 314 (451)
T cd05534 235 PGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAVQKI 314 (451)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCCCceeeHHHHHHHHHHHhhhhEEEEEEecCCCCCceEEeecceEEecccHHHHHHH
Confidence 988999999999999999999999999999999999999999999999998764 3457999999999999999999999
Q ss_pred HHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCc-ccccCcchHHHHHHHHHHhcCCCCCCCCCee
Q 001780 760 VTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTG-DDYEVKAAHVELAERMRKRDAATAPNVGDRV 838 (1014)
Q Consensus 760 ~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~-~~Y~~~~~hv~~A~r~~~rd~g~~p~~GdrV 838 (1014)
++++|+.||.++|++++.+++++.+.+|++|++|+++|+|+|+|+++. +.|+..+|||.+|+|+++++++..|+.||||
T Consensus 315 ~~~vl~~il~~~d~~~~~~~l~~~~~~l~~g~~~~~dlii~k~l~~~~y~~~~~~p~hv~~A~k~~~~~~~~~~~~G~rI 394 (451)
T cd05534 315 LEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATLPAGAIVALRRMEKDPRAEPQYGERV 394 (451)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHHHHHcCCCCHHHeEEEEEeeccccCccCCCChHHHHHHHHHHhCCCCCCCCCCEE
Confidence 999999999999999999999999999999999999999999999874 3344567999999999999889999999999
Q ss_pred EEEEEecCCCCccccccCChhhh-hccCCCcChhHHHhhcchhhHHHhhcccccc
Q 001780 839 PYVIIKAAKGAKAYERSEDPIYV-LENNIPIDTHYYLENQISKPLLRIFEPILKN 892 (1014)
Q Consensus 839 ~YVi~~~~~~~~~~~ra~~p~~~-~~~~~~iD~~yYi~~qi~~pl~ri~~~i~g~ 892 (1014)
+|||++|.++.++++||++|.++ .+++++||++|||++||+||+.|||++| |.
T Consensus 395 ~YViv~~~~~~~~~~ra~~~~~~~~~~~~~iD~~yYi~~Qi~~~~~ril~~~-g~ 448 (451)
T cd05534 395 PYVVVRGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIPALDRLFNLV-GV 448 (451)
T ss_pred EEEEEeCCCCCcHHHhccCHHHHhhcCCCCCChHHHHHhcCHHHHHHHHHHc-CC
Confidence 99999998788899999999854 5678999999999999999999999997 54
No 13
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=100.00 E-value=8.7e-88 Score=775.39 Aligned_cols=377 Identities=37% Similarity=0.603 Sum_probs=345.7
Q ss_pred CcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHH
Q 001780 496 GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPE 575 (1014)
Q Consensus 496 ~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~ 575 (1014)
.+|+||+|+||++|+|++||++|||+|||||||++|||||||+++..+... . ... ..|+.++.++||||+
T Consensus 6 ~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~------~--~~~--~~~~~~~~~~Gilp~ 75 (400)
T cd05532 6 AKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDE------D--DEE--PPLPPSDQEKGILPR 75 (400)
T ss_pred CCcCCceeecCCCCcccCceEEEeccccchHHHHHhcCChhhccccccccc------C--Ccc--ccccccccCCCchHH
Confidence 389999999999999999999999999999999999999999987542111 0 011 234455689999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhh
Q 001780 576 ILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDK 655 (1014)
Q Consensus 576 iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~ 655 (1014)
+|++|+++|+++|+.||+.+|+.++++||.+|+|+|++|||+|||+|+++|||||.++|++||++||++|+.|++++++.
T Consensus 76 ~l~~l~~~R~~~K~~~k~~~d~~~~~~~d~~Q~alKi~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~ 155 (400)
T cd05532 76 IIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKM 155 (400)
T ss_pred HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhhcccccccccccccChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999985
Q ss_pred ccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCC
Q 001780 656 FTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPE 735 (1014)
Q Consensus 656 ~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~ 735 (1014)
|++|||||||||||+++..+.++++++|+++++.||+.|+ +++||||++|.+++|++||||||+.|++++
T Consensus 156 ---------g~~ViYgDTDSifv~~~~~~~~~~~~~~~~i~~~in~~~~-~i~le~e~iy~~~ll~~KKrYag~~~~~~~ 225 (400)
T cd05532 156 ---------NLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYK-KLEIDIDGVFKRLLLLKKKKYAALKVVDDD 225 (400)
T ss_pred ---------CCEEEEeCCCeEEEecCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhHHHHhhhhhcceEEEeecCC
Confidence 8899999999999999988999999999999999999996 899999999999999999999999988654
Q ss_pred -CccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChh----hHHHHHHHHHHHHHcCCCCccceeEeecccCCcccc
Q 001780 736 -KFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIP----GAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDY 810 (1014)
Q Consensus 736 -~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~----~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y 810 (1014)
..+++++||+|++|||||+|+|++++++++.||.+++.+ .+.+++++.+.+|.+|++|+++|+|+|+|+|++++|
T Consensus 226 ~~~~k~~~KGie~~RrD~~~~~k~~~~~vl~~ll~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~lii~k~l~k~~~~Y 305 (400)
T cd05532 226 KGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEY 305 (400)
T ss_pred ccceeeEEeceeEEecccHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHcCCCCHHHEEEeecccCChHHc
Confidence 347899999999999999999999999999999998854 455888899999999999999999999999999999
Q ss_pred cC--cchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhh-ccCCCcChhHHHhhcchhhHHHhhc
Q 001780 811 EV--KAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVL-ENNIPIDTHYYLENQISKPLLRIFE 887 (1014)
Q Consensus 811 ~~--~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~-~~~~~iD~~yYi~~qi~~pl~ri~~ 887 (1014)
+. .+||+++|+||+++ |..+.+||||+|||++++++.++++||++|.++. +++.+||++|||++||+|||.|||+
T Consensus 306 ~~~~~~~hv~~A~rl~~~--g~~~~~G~rI~Yvi~~~~~~~~~~~ra~~~~~~~~~~~~~iD~~yYi~~qi~~pl~ri~~ 383 (400)
T cd05532 306 PDKKSLPHVQVALRMNKR--GRKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISRLCE 383 (400)
T ss_pred CCCCCCcHHHHHHHHHHc--CCCCCCCCEEEEEEEeCCCCCchhhhccCHHHHhhccCCCCChHHHHHHhhHHHHHHHHH
Confidence 98 58999999999987 5889999999999999877777899999999988 5789999999999999999999999
Q ss_pred cccccch
Q 001780 888 PILKNAS 894 (1014)
Q Consensus 888 ~i~g~~~ 894 (1014)
||.+...
T Consensus 384 ~~~~~~~ 390 (400)
T cd05532 384 PIEGTDA 390 (400)
T ss_pred hccCCCH
Confidence 9977643
No 14
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=100.00 E-value=2.4e-86 Score=782.82 Aligned_cols=421 Identities=48% Similarity=0.750 Sum_probs=369.8
Q ss_pred ccHHHHHHHHHHHHhhcCccccCCCcC-------CCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCccc
Q 001780 465 GQSIKVLSQLLRKAKQKNLVIPNVKQA-------GSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYST 537 (1014)
Q Consensus 465 G~~~~v~s~L~r~a~~~~~viP~~~~~-------~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT 537 (1014)
|||++++|+|+++|+++|+++|+.... .....+|+||+|++|++|+|++++.+|||+|||||||++|||||||
T Consensus 1 gq~~~v~~~ll~~~~~~~~~~p~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G~~~~v~~~lDF~SLYPsii~~~Ni~~~T 80 (466)
T PF00136_consen 1 GQQIRVESLLLREAHRRNYIIPSKKERPEGFTSKSEQKEKYEGGYVLEPKPGLYENVVSVLDFASLYPSIIIAYNICPET 80 (466)
T ss_dssp -CHHHHHHHHHHHHHHTTBE-B-HHHHHHTHHHHHHHCTCEEEC-BE--HSSEEEEEEEEEEETTHHHHHHHHTTHSTTT
T ss_pred CchhhHHHHHHHHHHHCCEEeeCCcccccccccccccccccccceeeccccccccCceeeeecccccHHHHHhccCCcce
Confidence 899999999999999999999986543 1123489999999999999999666899999999999999999999
Q ss_pred ccChhh--hhccCC--CCC---ceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHH-HHHhHHHhhh
Q 001780 538 LVTPED--ARKLNL--PPE---CVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLE-KAVLDGRQLA 609 (1014)
Q Consensus 538 ~~~~~~--~~~~~~--~~~---~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~-~~~ld~rQ~A 609 (1014)
+++..+ ..++.- ..+ .....+.+..|++...++|+||.+|+.|++.|+++|+.|++.+|+.+ ++.||++|+|
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gilp~~l~~~l~~R~~~K~~~~~~~~~~~~~~~~d~~Q~a 160 (466)
T PF00136_consen 81 IVDDDECKDNEVSPDIKYDYGPFIVGSPVGVRFVKKGVRPGILPEILEELLEKRKEIKKLMKKAKDPDEEYAILDARQLA 160 (466)
T ss_dssp BTCTTHCSSEEEHTTCCCCTCEEEECSCCSEEEESSTCSHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_pred EecchhhhcccccccccccccceeecCCceeeecccCcccccChHHHHHHHHHHHHHhhhhhhhccchhhHHHHHHHHHh
Confidence 998751 111100 001 12245667789999999999999999999999999999999988876 9999999999
Q ss_pred ccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHH
Q 001780 610 LKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAM 689 (1014)
Q Consensus 610 lKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~ 689 (1014)
+||+|||+|||+|++++||||.++|++||++||++|+.|++++++.. +|++|||||||||||+++..+.++++
T Consensus 161 ~Ki~~NS~YG~~g~~~~r~~~~~~a~~iT~~GR~~i~~~~~~~~~~~-------~g~~viYgDTDSv~v~~~~~~~~~~~ 233 (466)
T PF00136_consen 161 LKIIANSFYGYLGAKNSRFYCKEIAEAITATGREIIKKAIEIIEEME-------FGFEVIYGDTDSVFVQFPDSDKEDAK 233 (466)
T ss_dssp HHHHHTTHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHHS-------CTEEEEEEETTEEEEECTTCHHHHHH
T ss_pred hcccceeeEeecCccccchhhhhhhheehhhhHhhHHHHHHHHHhhc-------ccceEEEEcccceEEecCCCcHHHHH
Confidence 99999999999999999999999999999999999999999999951 38899999999999999998889999
Q ss_pred HHHHHHHHHHHhc-CCCceeEEEeeeeccceecccceeEEEeccCCCCc-cceeEeeeeeccCchHHHHHHHHHHHHHHH
Q 001780 690 KLGREAADYISGT-FIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKF-DKMDTKGIETVRRDNCLLVKNLVTECLHKI 767 (1014)
Q Consensus 690 ~lg~eia~~vs~~-~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~~-~k~~~KGie~vRRD~~~l~k~~~~~vl~~i 767 (1014)
+.+++++++|++. ++.||+||||++|.+++|++||||||+.|++.++. +++++||+|++|||+|+|+|++++++|+.|
T Consensus 234 ~~~~~l~~~i~~~~~~~~i~le~E~~y~~~~l~~KKrY~~~~~~~~~~~~~~~~~kG~e~~RrD~~~~~k~~~~~~l~~i 313 (466)
T PF00136_consen 234 KKGEELAKEINSELFPSPIKLEFEKVYRWFILLAKKRYAGLKYDNEGKKKGKIKIKGLELVRRDWCPFVKDIQREVLEII 313 (466)
T ss_dssp HHHHHHHHHHHHHSCSTTHEEEEEEEEEEEEEEETTEEEEEETCCCEEETSEEEEESSSGGSSSSTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhhcCCCceeeecccEEEEEEEccCCccceeeeecccccceeEEeccccccCchhHHHHHHHHHHHHHH
Confidence 9999999999987 58999999999999999999999999999876553 899999999999999999999999999999
Q ss_pred hcCCChhhHH--------HHHHHHHHHHHcCCCCccceeEeecccCCcccccCcch-HHHHHHHHHHhcCCCCCCCCCee
Q 001780 768 LVDRDIPGAV--------QYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAA-HVELAERMRKRDAATAPNVGDRV 838 (1014)
Q Consensus 768 l~~~d~~~a~--------~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~~-hv~~A~r~~~rd~g~~p~~GdrV 838 (1014)
|.+.+.+.+. +++++...++.++++++++|++++++++++++|+...+ |+.+|+||++++++..|+.||||
T Consensus 314 l~~~~~~~~~~~i~~~~~e~l~~~~~~l~~~~~~~~~li~~k~l~k~~~~Y~~~~~~hv~~a~rl~~~~~~~~p~~GdrI 393 (466)
T PF00136_consen 314 LKGKDPEEAVEKIKEVIIEYLKKYIEKLRNGEVPIEDLIISKRLSKDLEEYKKKTPPHVRAAKRLKKRGPGYKPQKGDRI 393 (466)
T ss_dssp HTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCSHGGGGHEEEECCSCGGGCSSSHHHHHHHHHHHHCTTHCTCTGTTSEE
T ss_pred hCCCCHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHhhhccCCcccccccCCcHHHHHHHHHhhhcccCCcCCCEe
Confidence 9999988763 56777777899999999999999999999999998765 99999999998778999999999
Q ss_pred EEEEEec---CCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHhhcccccc
Q 001780 839 PYVIIKA---AKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFEPILKN 892 (1014)
Q Consensus 839 ~YVi~~~---~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~i~g~ 892 (1014)
+|||+++ ..+..+++++++|.++.+++.+||++||+++||+||+.|+|+++.+.
T Consensus 394 ~Yvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~iD~~yYi~~ql~~pl~ril~~~~~~ 450 (466)
T PF00136_consen 394 PYVIVKGPSKKKGPKPSERAEDPEYVKENNLPIDYEYYIEKQLLPPLERILEPLGWN 450 (466)
T ss_dssp EEEEBSSSSTTHCEEESCSEETTTHHHHTTS-BSHHHHHHTTHHHHHHHHHHTCTTT
T ss_pred EEEEEcCccccccccchhhccChhhhhccCCCcchHHHHhhccHHHHHHHHHHhcCC
Confidence 9999998 34567889999999999999999999999999999999999999765
No 15
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=100.00 E-value=3.5e-85 Score=746.95 Aligned_cols=367 Identities=37% Similarity=0.570 Sum_probs=335.0
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
+|+||+|++|++|+|++ |++|||+|||||||++|||||||++.+... +.....++|..|++ .++||+|++
T Consensus 3 ~y~Gg~V~~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~-------~~~~~~~~~~~f~~--~~~Gilp~i 72 (371)
T cd05536 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCE-------DCDVEPQVGHKFRK--DPPGFIPSV 72 (371)
T ss_pred CCCceEEeCCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCcc-------ccccCCCCCcEEec--CCCCchHHH
Confidence 79999999999999998 999999999999999999999999876421 11223457888876 489999999
Q ss_pred HHHHHHHHHHHHHHhhhcCCh-HHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhh
Q 001780 577 LEELLAARKRAKADLKEAKDP-LEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDK 655 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~mk~~~d~-~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~ 655 (1014)
|++|+++|+++|+.||+.+++ .++++||++|+|+||+|||+|||+|+++|||||.++|++||+.||++|+.|++++++.
T Consensus 73 l~~ll~~R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~i~~~ 152 (371)
T cd05536 73 LEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEK 152 (371)
T ss_pred HHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHhccccccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 999999999999999988754 8899999999999999999999999999999999999999999999999999999984
Q ss_pred ccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCCC
Q 001780 656 FTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPE 735 (1014)
Q Consensus 656 ~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~ 735 (1014)
|++|||||||||||+++..+. +++.+++++++|++.++ ++||||++|.++++++||||||+.
T Consensus 153 ---------g~~VIYgDTDSvfv~~~~~~~--~~~~~~~l~~~i~~~~~--i~le~E~vy~~~l~~~KKrY~g~~----- 214 (371)
T cd05536 153 ---------GFKVIYGDTDSLFVKIDGADA--VKKKVKKLLKYINEELP--LELEIEKFYKRGFFVTKKRYAGLT----- 214 (371)
T ss_pred ---------CCEEEEEcCcccEEeecCchH--HHHHHHHHHHHHHhcCC--eeEEEeeeeHHHHHhhhceeEEEc-----
Confidence 889999999999999987653 56677899999999985 999999999999999999999985
Q ss_pred CccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccccCcch
Q 001780 736 KFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAA 815 (1014)
Q Consensus 736 ~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~~ 815 (1014)
..+++++||+|++|||||+|+|++++++|+.||.++|+++|++++++.+++|++|++|+++|+|+|+|+|.+++|++++|
T Consensus 215 ~~g~i~~KG~e~~RrD~~~~~k~~~~~~l~~ll~~~~~~~~~~~~~~~~~~l~~g~~~~~dlii~k~l~k~~~~Y~~~~~ 294 (371)
T cd05536 215 EDGKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATGP 294 (371)
T ss_pred cCCeEEEEeeeeEeCccHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCCCHHHeEEeHHhcCCHHHhCCCCc
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHhhccccccchh
Q 001780 816 HVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFEPILKNASK 895 (1014)
Q Consensus 816 hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~~i~g~~~~ 895 (1014)
|+.+|+||+++ |..+++||||+|||+++++ +.++|++++.++ ++++++|++||+++||+|||.|||+++ |.+.+
T Consensus 295 hv~~a~~l~~~--g~~~~~G~rI~Yvi~~~~~--~~~dr~~p~~~~-~~~~~iD~~yYi~~qi~~pl~ril~~~-g~~~~ 368 (371)
T cd05536 295 HVAAAKKLAKR--GYKVRPGTKIGYVIVKGSG--KISDRAYPYDMV-DEKHKYDAEYYIDNQVLPAVLRILEAF-GYKEE 368 (371)
T ss_pred HHHHHHHHHhc--CCCCCCCCEEEEEEEECCC--cccccccCHHHh-ccCCCCCHHHHHHHhcHHHHHHHHHHh-CCCHH
Confidence 99999999987 6789999999999998743 578999987665 478999999999999999999999987 66565
Q ss_pred hh
Q 001780 896 EL 897 (1014)
Q Consensus 896 ~l 897 (1014)
+|
T Consensus 369 ~l 370 (371)
T cd05536 369 DL 370 (371)
T ss_pred Hc
Confidence 54
No 16
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=100.00 E-value=1.8e-81 Score=713.82 Aligned_cols=348 Identities=31% Similarity=0.463 Sum_probs=308.9
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
.++||+|++|++|+|++ |++|||+|||||||++|||||+|++...... ..++....|+|.+|++ ++||||++
T Consensus 2 ~~~Gg~V~eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~~~~----~~~~~~~~~~~~~f~~---~~Gilp~~ 73 (371)
T cd05537 2 SSPGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAP----DPEDLIPGFLGARFSR---EKHILPDL 73 (371)
T ss_pred CCCCcEEeCCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCCCCC----CccccccCCCCCeEec---CCCchHHH
Confidence 46899999999999997 9999999999999999999999997643211 1234567889999986 35999999
Q ss_pred HHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhc
Q 001780 577 LEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKF 656 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~ 656 (1014)
|++|+++|+++|+.|+. .+|+|+|++|||+|||+|++++||||.++|++||++||++|+.|++++++.
T Consensus 74 l~~l~~~R~~~K~~~~~-----------~~q~AlKi~~Ns~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~- 141 (371)
T cd05537 74 IARLWAARDEAKREKNA-----------PLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQ- 141 (371)
T ss_pred HHHHHHHHHHHHHhccH-----------HHHHhHhhheecceeecccccccccChHHHHHHHHHHHHHHHHHHHHHHHc-
Confidence 99999999999998752 479999999999999999999999999999999999999999999999984
Q ss_pred cccCCccccceEEEecCccceEEcCC-CCHHHHHHHHHHHHHHHHhcC----------CCceeEEEeeeeccceec----
Q 001780 657 TTVGGYEHNAEVIYGDTDSVMVQFGV-PTVEAAMKLGREAADYISGTF----------IKPIKLEFEKVYYPYLLI---- 721 (1014)
Q Consensus 657 ~~~~gy~~~~~VIYGDTDSv~V~~~~-~~~~ea~~lg~eia~~vs~~~----------~~pi~Le~Ekvy~~~ll~---- 721 (1014)
|++|||||||||||+++. .+.+++.++|+++++.||+.| +.|++|||||+|.+++|+
T Consensus 142 --------g~~ViYgDTDSvfV~~~~~~~~~~~~~~~~~l~~~In~~~~~~~~~~~~~~~~l~Le~Ekvy~~~ll~~~~~ 213 (371)
T cd05537 142 --------GYQVIYGDTDSTFVWLGEELDAAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRG 213 (371)
T ss_pred --------CCEEEEecCCceEEecCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCceEEEeeeeeeeeeecccc
Confidence 889999999999999986 689999999999999999865 457999999999999986
Q ss_pred ----ccceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccce
Q 001780 722 ----SKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLL 797 (1014)
Q Consensus 722 ----~KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~l 797 (1014)
+||||||+.|+. ..+++++||+|+||||||+|+|++++++|+.||.+++++ +|+++.+.+|++|++| ++|
T Consensus 214 ~~~~~KKrYag~~~~~--~~~~i~~KGle~vRrD~~~l~k~~~~~vl~~il~~~~~~---~~~~~~~~~l~~g~~~-~~l 287 (371)
T cd05537 214 SDEGSKKRYAGLKSTD--GGDELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYE---GFIKETVEELLAGELD-ELL 287 (371)
T ss_pred ccccccceEEEEEEEC--CCcEEEeecceeEecchHHHHHHHHHHHHHHHhcCCCHH---HHHHHHHHHHHcCCCc-hHh
Confidence 799999999862 357999999999999999999999999999999998764 8899999999999999 999
Q ss_pred eEeecccCCcccccC-cchHHHHHHHHHHhcCC-CCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHh
Q 001780 798 VITKGLTKTGDDYEV-KAAHVELAERMRKRDAA-TAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLE 875 (1014)
Q Consensus 798 vi~k~l~k~~~~Y~~-~~~hv~~A~r~~~rd~g-~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~ 875 (1014)
+|+|+|+|.+++|++ .+|||.+|++|++++.. ..|..||||+|||++++.+ | +.+++++||++|||+
T Consensus 288 vi~k~L~k~~~~Y~~~~~phv~aa~~~~~~~~~~~~~~~gd~I~YVi~~~g~~---------~--~~~~~~~iD~~yYi~ 356 (371)
T cd05537 288 VYRKRLRRPLSEYTKNVPPHVQAARLADQINRELGRPRQYQWIEYVITVNGPE---------P--LEYRTSPLDYQHYID 356 (371)
T ss_pred EEehhcCCCHHHcCCCCCcHHHHHHHHHhcCCccCCCCCCCEEEEEEecCCcc---------h--HhhcCCCCCHHHHHH
Confidence 999999999999984 58999999999988532 2467899999999984221 1 223569999999999
Q ss_pred hcchhhHHHhhccc
Q 001780 876 NQISKPLLRIFEPI 889 (1014)
Q Consensus 876 ~qi~~pl~ri~~~i 889 (1014)
+||+|++.|||+++
T Consensus 357 ~qi~p~~~ril~~~ 370 (371)
T cd05537 357 KQLKPIADSILPFL 370 (371)
T ss_pred hccHHHHHHHHHhc
Confidence 99999999999976
No 17
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=100.00 E-value=1.2e-78 Score=688.47 Aligned_cols=349 Identities=28% Similarity=0.397 Sum_probs=301.4
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
+|+||+|++|++|+|++ |++|||+|||||||++|||||||++.+... +....+|++.++++ ..++||+|++
T Consensus 12 ~y~Gg~V~~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~~~~-------~~~~~~p~~~~~~~-~~~~Gilp~i 82 (372)
T cd05530 12 KYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCE-------CKTNEVPEVGHWVC-KKRPGITSQI 82 (372)
T ss_pred CCCCCEeecCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccCccc-------ccceecCCCCceEE-ecCCCccHHH
Confidence 89999999999999999 999999999999999999999999976321 11233454444432 3689999999
Q ss_pred HHHHHHHHHHHHHHh-hhcC-ChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHh
Q 001780 577 LEELLAARKRAKADL-KEAK-DPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVED 654 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~m-k~~~-d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~ 654 (1014)
|+.|++.|+++|+.| +..+ ||.++.+||++|+|+||+|||+|||+|+.++||||.++|++||++||++|+.|++++++
T Consensus 83 l~~L~~~R~~~~k~~~k~~~~d~~~~~~ld~~Q~alKi~~NS~YG~~g~~~~~~~~~~~A~~it~~GR~~l~~~~~~~~~ 162 (372)
T cd05530 83 IGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARE 162 (372)
T ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHhccccccccccCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999976555 4455 89999999999999999999999999999999999999999999999999999999987
Q ss_pred hccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceec-ccceeEEEeccC
Q 001780 655 KFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLI-SKKRYAGLYWTN 733 (1014)
Q Consensus 655 ~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~-~KKRYagl~~~~ 733 (1014)
. |++|||||||||||+++.. +. .++++++|++.+ +++||||++|.+++|. +||||||+.
T Consensus 163 ~---------g~~VIYGDTDSvfv~~~~~--~~----~~~i~~~i~~~~--~i~le~E~~y~~~ll~~~KKrY~g~~--- 222 (372)
T cd05530 163 L---------GLKVLYGDTDSLFLWNPPQ--EQ----LEDLVEWVEKEL--GLDLELDKEYRYVVFSGLKKNYLGVT--- 222 (372)
T ss_pred C---------CcEEEEEeccceEEecCCh--hH----HHHHHHHHhhcc--CceEEEEEEEeeeeeccccccEEEEe---
Confidence 3 8899999999999997642 22 357788888877 5999999999987765 799999986
Q ss_pred CCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChh-------hHHHHHHHHHHHHHcCCCCccceeEeecccCC
Q 001780 734 PEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIP-------GAVQYVKSTISDLLMNRMDLSLLVITKGLTKT 806 (1014)
Q Consensus 734 ~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~-------~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~ 806 (1014)
..+++++||+|++|||||+|+|++++++|+.||..++++ .+.+++++.+.+|.+|++|+++|+|+|+|+|.
T Consensus 223 --~~gki~~KGie~~RrD~~~~~k~~~~~vl~~ll~~~~~~~~~~~~~~i~~~~~~~~~~l~~g~~~~~~lvi~k~L~K~ 300 (372)
T cd05530 223 --KDGSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEDFEKAREKIRDIVKGVYKRLKKKEYTLDQLAFKVMLSKP 300 (372)
T ss_pred --cCCcEEEEeEEEEeCCchHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHheeehhccCC
Confidence 247899999999999999999999999999999987654 36678889999999999999999999999999
Q ss_pred cccccC-cchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHh
Q 001780 807 GDDYEV-KAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRI 885 (1014)
Q Consensus 807 ~~~Y~~-~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri 885 (1014)
+++|++ .+|||.+|++|.++ |..+++||||+|||++|.++...++.+ +..+||++||++ +|.+|+.+|
T Consensus 301 ~~~Y~~~~~phv~aa~~~~~~--g~~~~~G~~I~YVi~~~~~~~~p~~~~--------~~~~iD~~yYi~-~l~~a~~~i 369 (372)
T cd05530 301 PEEYTKNTPQHVKAARQLEKY--GRNVEAGDIISYVKVKGKEGVKPVQLA--------RLDEVDVEKYVE-IMRSTLEQI 369 (372)
T ss_pred HHHhcCCCCHHHHHHHHHHhc--CCCCCCCCEEEEEEEeCCCCCchhhhc--------cCCCCCHHHHHH-HHHHHHHHH
Confidence 999985 57999999998765 789999999999999987665433322 345899999999 699999998
Q ss_pred hc
Q 001780 886 FE 887 (1014)
Q Consensus 886 ~~ 887 (1014)
++
T Consensus 370 ~~ 371 (372)
T cd05530 370 LG 371 (372)
T ss_pred hc
Confidence 76
No 18
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), 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 B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=100.00 E-value=3.3e-78 Score=679.19 Aligned_cols=320 Identities=45% Similarity=0.677 Sum_probs=294.2
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
+|+||+|++|++|+|++ |++|||+|||||||++|||||||++...+... .+ .+.|..|+.+++++|++|.+
T Consensus 2 ~y~Gg~V~~P~~G~~~~-V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~~----~~----~~~~~~~~~~~~~~Gilp~i 72 (323)
T cd00145 2 PYEGGYVFDPIPGLYEN-VIVLDFKSLYPSIIITYNLSPTTLVGNGEIAA----PE----DYIGVGFRSPKDRKGLLPRI 72 (323)
T ss_pred CCCCcEEecCcccccCc-eEEeecCCccHHHHHHhCCCcccccccccccC----cc----cccCccccccCCCCCCCHHH
Confidence 79999999999999985 99999999999999999999999997653321 11 12255677777899999999
Q ss_pred HHHHHHHHHHHHHHhhhcCC-hHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhh
Q 001780 577 LEELLAARKRAKADLKEAKD-PLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDK 655 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~mk~~~d-~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~ 655 (1014)
|++|++.|+++|+.||+.++ +.++.+||.+|+|+|++|||+|||+|+++|||||.++|++||++||++|+.|++++++.
T Consensus 73 L~~Ll~~R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~G~~~~r~~~~~~A~~IT~~GR~~l~~~~~~ie~~ 152 (323)
T cd00145 73 LEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEH 152 (323)
T ss_pred HHHHHHHHHHHHHHHhhCcCCHHHHHHHHHHhhhhheeeecceeecccccccCCChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999998874 99999999999999999999999999999999999999999999999999999999984
Q ss_pred ccccCCccccceEEEecCccceEEcCC-CCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCC
Q 001780 656 FTTVGGYEHNAEVIYGDTDSVMVQFGV-PTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNP 734 (1014)
Q Consensus 656 ~~~~~gy~~~~~VIYGDTDSv~V~~~~-~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~ 734 (1014)
|++|||||||||||+++. .+.++++++|+++++.| .++.||+||||++|.++++++||||||+.|+++
T Consensus 153 ---------g~~VIYGDTDSifv~~~~~~~~~~~~~~~~~~~~~i--~~~~~i~le~E~vy~~~ll~~KKrYag~~~~~~ 221 (323)
T cd00145 153 ---------GARVIYGDTDSIFVSLPKMGTKEDAIKEGREILQEL--ADEHLLELEFEKVYLPFFLGKKKRYAGLDIWKG 221 (323)
T ss_pred ---------CCEEEEECCCceEEEeCCCCCHHHHHHHHHHHHHHh--CCCCCeEEEEchhhHHHHHhhhhhEEEEEEEcC
Confidence 889999999999999998 78999999999999999 567899999999999999999999999998876
Q ss_pred CCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccccCcc
Q 001780 735 EKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKA 814 (1014)
Q Consensus 735 ~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~~ 814 (1014)
+..+++++||+|+||||||+++|++++++|+.||.+ +.+.+++++.+.+|
T Consensus 222 ~~~~~~~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~---~~~~~~v~~~~~~l--------------------------- 271 (323)
T cd00145 222 QDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEE---ERKVEAVKEYIDEL--------------------------- 271 (323)
T ss_pred CCCceEEEEcceEEecCcHHHHHHHHHHHHHHHHcC---CchHHHHHHHHHHh---------------------------
Confidence 557899999999999999999999999999999986 55778888888777
Q ss_pred hHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhhHHHhhc
Q 001780 815 AHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIFE 887 (1014)
Q Consensus 815 ~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~pl~ri~~ 887 (1014)
|||+|||++++++..+++||++|+++++++++||++||+++|++||+.|||+
T Consensus 272 ---------------------~~i~yvi~~~~~~~~~~~ra~~~~~~~~~~~~iD~~yY~~~~~~~~~~ri~~ 323 (323)
T cd00145 272 ---------------------DKVKYVVTRGGKGVPDYERADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323 (323)
T ss_pred ---------------------ccccEEEEcCCCCCCcccccCChhhhcccCCCCChHHHHHhccHhHHHHhcC
Confidence 8999999999888888999999999999999999999999999999999985
No 19
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=100.00 E-value=5.2e-76 Score=663.52 Aligned_cols=329 Identities=25% Similarity=0.330 Sum_probs=296.9
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPEI 576 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~i 576 (1014)
+|+||+|++|.+|+|++ |++|||+|||||||++|||||+. .+.||+|.+
T Consensus 2 ~~~GG~v~~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~~------------------------------~~~Gilp~i 50 (347)
T cd05538 2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRICPAR------------------------------DSLGIFLAL 50 (347)
T ss_pred CcCCceEcccCCcCcCc-eEEEEcccchHHHHHHhCCCCCC------------------------------CCCcccHHH
Confidence 69999999999999997 99999999999999999999841 267999999
Q ss_pred HHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhc
Q 001780 577 LEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKF 656 (1014)
Q Consensus 577 L~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~ 656 (1014)
|++|+++|.++|+.||+++||.++.+||.+|+|+|+++||+|||+|++++||||.++|++||++||++|+.|++++++.
T Consensus 51 l~~Ll~~R~~~K~~~k~~~~~~~~~~~d~~Q~AlKi~~NS~YG~lG~~~~r~~~~~~A~~iT~~GR~~L~~~~~~~e~~- 129 (347)
T cd05538 51 LKYLVELRLAAKESARAAARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRR- 129 (347)
T ss_pred HHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhhhhchhhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999973
Q ss_pred cccCCccccceEEEecCccceEEcCCC-C-HHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceecccceeEEEeccCC
Q 001780 657 TTVGGYEHNAEVIYGDTDSVMVQFGVP-T-VEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNP 734 (1014)
Q Consensus 657 ~~~~gy~~~~~VIYGDTDSv~V~~~~~-~-~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~ 734 (1014)
|++|||||||||||+++.. + .++ +++++++|++.++.+++||||++|.++++.+||||||+.
T Consensus 130 --------g~~VIygDTDSi~v~~~~~~~~~~~----~~~~~~~i~~~~~~~i~le~e~~y~~~l~~~KKrYa~~~---- 193 (347)
T cd05538 130 --------GATPVEVDTDGIYFIPPNGVDTEDE----EEELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLD---- 193 (347)
T ss_pred --------CCEEEEEcCCeeEEEeCCCCChHHH----HHHHHHHHHHhCCCCeEEEEhHHHHHHHhhcCceEEEEe----
Confidence 8899999999999998643 2 222 367889999999999999999999999999999999975
Q ss_pred CCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeEeecccCCcccccCc-
Q 001780 735 EKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVK- 813 (1014)
Q Consensus 735 ~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi~k~l~k~~~~Y~~~- 813 (1014)
..+++++||+|+||||||+|+|++++++|+.||. .+.+++.+++++.+.+|.+|++|+++|+|+|+|+|.+++|.++
T Consensus 194 -~~gki~~KG~e~vRrD~~~~~k~~~~~vl~~ll~-~~~~~~~~~~~~~~~~l~~~~~~~~~l~i~k~l~k~~~~Y~~~~ 271 (347)
T cd05538 194 -YDGKLIVKGSAFRSRGIEPFLREFLREAVRLLLQ-GDGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEEYLQKV 271 (347)
T ss_pred -cCCcEEEECCCcccCCchHHHHHHHHHHHHHHHc-CChHHHHHHHHHHHHHHHcCCCCHHHEEEEeecCCCHHHHhhhh
Confidence 3478999999999999999999999999999995 5778899999999999999999999999999999999999653
Q ss_pred ---chHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhh
Q 001780 814 ---AAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLEN 876 (1014)
Q Consensus 814 ---~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~ 876 (1014)
.+|..+|.+++.+ .|..+++||+|+|||+++++|.++++||+.++.+-.+..++|++||+++
T Consensus 272 ~~~~~~~~~a~~~a~~-~g~~~~~G~~I~Yvi~~~~~g~~~~~ra~~~~~~~~~~~~~d~~yY~~~ 336 (347)
T cd05538 272 RAGKRNPAAAYEIALA-RPREWRAGDRVTYYVSGTGKGVSVYENCRLVADYDPAHPDENTGFYAER 336 (347)
T ss_pred hcccCChhHHHHHHHh-cCCCCCCCCEEEEEEEeCCCCCCHHHhhccHHHhCCCccccCHHHHHHH
Confidence 2454434444332 4889999999999999998889999999988777666788999999995
No 20
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=100.00 E-value=1e-73 Score=646.71 Aligned_cols=336 Identities=28% Similarity=0.413 Sum_probs=293.0
Q ss_pred CcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhccCCCCCceeeCCCCceeeecCCcCCCcHH
Q 001780 496 GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGILPE 575 (1014)
Q Consensus 496 ~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~~~~~~~~~~~~p~g~~fvk~~~~~Gilp~ 575 (1014)
.+|+||+|++|++|+|++ |++|||+|||||||++|||||+|++..... +....+.+..|++ +++||+|+
T Consensus 3 ~~~~Gg~V~~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~~~~--------~~~~~~~~~~~~~--~~~gilp~ 71 (352)
T cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCE--------CRDHVYLGHRICL--KRRGFLPE 71 (352)
T ss_pred cCCCCcEEecCCCCccCc-eEEEEccccchHHHHHhCCChhhccccCcc--------cccCCCCCceEec--CCCCchHH
Confidence 379999999999999998 999999999999999999999999865321 1112355666654 68999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhh
Q 001780 576 ILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDK 655 (1014)
Q Consensus 576 iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~ 655 (1014)
+|++|+++|.++|+.||+.+++ |.+|+|+|++|||+|||+|+++++|+|.++|++||+.||++|+.|++++|+.
T Consensus 72 ~l~~l~~~R~~~K~~~k~~~~~------d~~q~AlKi~~NS~YGylG~~~~~f~~~~~A~~vT~~GR~~L~~~~~~~e~~ 145 (352)
T cd05531 72 VLEPLLERRLEYKRLKKEEDPY------AGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEM 145 (352)
T ss_pred HHHHHHHHHHHHHHHhhcCCCc------hHHHhhheeeeecccccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999987653 9999999999999999999999999999999999999999999999999984
Q ss_pred ccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCceeEEEeeeeccceec-------ccceeEE
Q 001780 656 FTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLI-------SKKRYAG 728 (1014)
Q Consensus 656 ~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi~Le~Ekvy~~~ll~-------~KKRYag 728 (1014)
|++||||||||+||+++.. ..+++++|++.++ ++||+|++|.+++|+ +||||+|
T Consensus 146 ---------g~~VIygDTDSvfv~~~~~--------~~~~~~~i~~~~~--i~l~le~~y~~~~~~~~~~~~~~kKrY~g 206 (352)
T cd05531 146 ---------GFRVLHGIVDSLWIQGRGD--------IEELAREIEERTG--IPLKLEGHYDWIVFLPERDGLGAPNRYFG 206 (352)
T ss_pred ---------CCEEEEEccccceeecCch--------HHHHHHHHHHhcC--CceEEEEEEEEEEeeccccccCcceeEEE
Confidence 8899999999999997321 2467778888774 788999999987654 6899999
Q ss_pred EeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChh-------hHHHHHHHHHHHHHcCCCCccceeEee
Q 001780 729 LYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIP-------GAVQYVKSTISDLLMNRMDLSLLVITK 801 (1014)
Q Consensus 729 l~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~-------~a~~~v~~~i~~l~~~~v~~~~lvi~k 801 (1014)
+.. .+++++||+|+||||||+|+|++++++|+.||.++|++ ++.+++++...+|.+|+ +++|+|+|
T Consensus 207 ~~~-----~g~i~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~lvi~k 279 (352)
T cd05531 207 RLS-----DGEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLKLREEALDLFRRYLQRLREGD--LEDLIIEK 279 (352)
T ss_pred ecC-----CCcEEEEeeEEEeCCchHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhcCC--hHHEEEEE
Confidence 974 47899999999999999999999999999999999986 45567888888899887 99999999
Q ss_pred cccCCcccccCcchHHHHHHHHHHhcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhhccCCCcChhHHHhhcchhh
Q 001780 802 GLTKTGDDYEVKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKP 881 (1014)
Q Consensus 802 ~l~k~~~~Y~~~~~hv~~A~r~~~rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~~~~~~iD~~yYi~~qi~~p 881 (1014)
+|+|.+++|+..+|| +|++|+++ |..+++||+|+|||+++.++.+. .+++.++|++||++ ||.|+
T Consensus 280 ~l~k~~~~Y~~~~~~--~a~~l~~~--g~~~~~G~~I~Yvi~~~~~~~~~----------~~~~~~~D~~yYi~-~l~~~ 344 (352)
T cd05531 280 KISKRSSEYKVLAST--ALKALRAK--GVSVVPGMKIEYIVRDGKRPVPD----------LGNDEGYDTKYYRE-LLERA 344 (352)
T ss_pred EecCCHHHcCCchHH--HHHHHHhC--CCCCCCCCEEEEEEEECCCCCcc----------ccccCCCCHHHHHH-HHHHH
Confidence 999999999998888 78988876 78899999999999988655322 35778999999997 89999
Q ss_pred HHHhhccc
Q 001780 882 LLRIFEPI 889 (1014)
Q Consensus 882 l~ri~~~i 889 (1014)
..+|+.++
T Consensus 345 ~~~il~~~ 352 (352)
T cd05531 345 AEELLFPL 352 (352)
T ss_pred HHHhccCC
Confidence 99998763
No 21
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=100.00 E-value=2.4e-68 Score=643.76 Aligned_cols=356 Identities=23% Similarity=0.264 Sum_probs=287.5
Q ss_pred ccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccc--------cHHHHHHH
Q 001780 402 EDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRG--------QSIKVLSQ 473 (1014)
Q Consensus 402 edv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG--------~~~~v~s~ 473 (1014)
+||||++|.++|++++++|+|++.||++||+|+++|+++|+++.+++||+|+|+.+....++|| ||+|++|+
T Consensus 516 eDV~YkeI~~lf~~g~e~RaRla~YCLkDA~LvlrLlkkl~~h~e~~eraRvT~~id~~~l~RG~v~fdG~vQQIKV~s~ 595 (1545)
T PHA03334 516 DDVKYTEMDGMFTAGGAALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRATYNIDYVAHGRGVMNFCGFVQSTKSVEV 595 (1545)
T ss_pred cCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCceeecccceecccCccchhhHHHH
Confidence 8999999999999999999999999999999999999999999999999999998876666666 99999999
Q ss_pred HHHHHh-hcCcccc-----------CCCcC-CCCCCcCCcceeeeccCce-----EEeeeEeeeccccchHHHHHhCCCc
Q 001780 474 LLRKAK-QKNLVIP-----------NVKQA-GSEQGTYEGATVLEARAGF-----YEKPIATLDFASLYPSIMMAYNLCY 535 (1014)
Q Consensus 474 L~r~a~-~~~~viP-----------~~~~~-~~~~~~yeGg~VleP~~G~-----y~~pV~~LDF~SLYPSIiia~Nlc~ 535 (1014)
++++|+ +.|+++| ..... .....+|+||+|++|++|+ |++||++|||+||||||||+|||||
T Consensus 596 lL~kA~~~~~~~ia~~~i~~s~ilP~~~~~~~~~~~~YeGAtVLEP~~Gf~~~~~Y~~PVaVLDFASLYPSIIiahNLCY 675 (1545)
T PHA03334 596 PLLKARLRIGIFVATGRIAESLCMPEKYARDCRQKIKLKGGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISP 675 (1545)
T ss_pred HHHHHHHhcCcccccccccccccCCcccccccccccccCCeEeecCCCCccccccCCCcEEEEEccccchHHHHHhCCCc
Confidence 998887 7777764 22111 1223479999999999999 6789999999999999999999999
Q ss_pred ccccChhhhhcc-CCCCCceeeCCCC--------------ceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHH
Q 001780 536 STLVTPEDARKL-NLPPECVNKTPSG--------------ETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPLEK 600 (1014)
Q Consensus 536 sT~~~~~~~~~~-~~~~~~~~~~p~g--------------~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~ 600 (1014)
||++.+...+++ ++..-++...|.| ..+++.....+++|.+|++||++|+++|++||+++||.++
T Consensus 676 eTLV~~~c~~~~~~~~~~d~~k~p~gy~~~~~vy~V~~~~~~~P~~~rf~SiLp~LL~eLL~~RK~~Kk~MKk~kDp~er 755 (1545)
T PHA03334 676 EAIVDPDCTARVRGWVVFDWKKIDRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLK 755 (1545)
T ss_pred ccccCccchhhhccccccccccCCcccCccccceeeccccCcCCCcceecchHHHHHHHHHHHHHHHHHHHhhCCCHHHH
Confidence 999977543321 1111111111111 1122223446899999999999999999999999999999
Q ss_pred HHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEc
Q 001780 601 AVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQF 680 (1014)
Q Consensus 601 ~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~ 680 (1014)
.+||+||+|+|++|||+|||+|+ ++|++||++||+||+.+++++++. .|++|||||||||||++
T Consensus 756 ~iLD~rQlALKVtANSvYGytG~--------~cA~lVTa~GRemI~~t~~~IE~e--------~G~~VIYGDTDSVfV~~ 819 (1545)
T PHA03334 756 SYHNQLQNEMKICANSHYGVAPH--------ACQHLITTLGRHKIKLVEEFIKKE--------PGMTVNYGDTDSVMFQL 819 (1545)
T ss_pred HHHHHHHHHHHHHHHhhcCcchh--------HHHHHHHHHHHHHHHHHHHHHHHh--------CCCEEEEEeCCceEEEe
Confidence 99999999999999999999975 468899999999999999999943 48999999999999999
Q ss_pred CCCC-----------HHHHHHHHHHHHHHHHhcC--------------------------------------C-----Cc
Q 001780 681 GVPT-----------VEAAMKLGREAADYISGTF--------------------------------------I-----KP 706 (1014)
Q Consensus 681 ~~~~-----------~~ea~~lg~eia~~vs~~~--------------------------------------~-----~p 706 (1014)
+..+ .++.++++++.+++++... + .|
T Consensus 820 p~~d~~~~~~d~v~~~~~~~~~~~~~~~~~s~~~~~~~~~~k~~~~~~~v~~~L~~l~~~l~d~m~~~l~~~~~~~~~~p 899 (1545)
T PHA03334 820 PPDDAETYLEDTVTLEDEERAPLEYTLEEWSAEAVNHVTKAKTKREGETVQSILSDLNTVLYDDMIERLRYVDEGGSVEP 899 (1545)
T ss_pred CccccccccccccchhhhhhhhhhhhHHHHHHHHHHHHHhhhhhcccchHHHHHHHHHHHHHHHHHHhheEeCCCCcEee
Confidence 7432 2344445544444433210 0 01
Q ss_pred -----------------------------eeEEEeeeeccceecccceeEEEeccCCCC---ccceeEeeeeeccCchHH
Q 001780 707 -----------------------------IKLEFEKVYYPYLLISKKRYAGLYWTNPEK---FDKMDTKGIETVRRDNCL 754 (1014)
Q Consensus 707 -----------------------------i~Le~Ekvy~~~ll~~KKRYagl~~~~~~~---~~k~~~KGie~vRRD~~~ 754 (1014)
-+|+||..-.-.++++||||+...|+.++. ..|++++|+|++|+..+.
T Consensus 900 ~~~~~~~~~~d~~~g~~~~~~~~f~~~~ItkL~yEn~stv~~~~aKK~Yi~~vhd~e~~~~~~pKlK~~G~ea~KSStpg 979 (1545)
T PHA03334 900 FKDGEDWWVVDPLDGIWTYVRDPFSSELITKLCYENTSTVTCRLAKKMYIYTNHELNNGPLGNTKIKMRGMQANKSSAAG 979 (1545)
T ss_pred ccCCCceeeecCCCceEEEeccchhHhHHHHHhhhcchhhhhhhhhhhhheeeeecCCcccccceeeeccccccccCCcH
Confidence 158888877777889999999999996643 468999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCh
Q 001780 755 LVKNLVTECLHKILVDRDI 773 (1014)
Q Consensus 755 l~k~~~~~vl~~il~~~d~ 773 (1014)
+++.+.+++++.||.+.-+
T Consensus 980 a~r~~~~d~i~lI~~ggal 998 (1545)
T PHA03334 980 ATRRITNDFVNLIFKGGAL 998 (1545)
T ss_pred HHHHHHHHHHHHHhcCCeE
Confidence 9999999999999987643
No 22
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-65 Score=611.26 Aligned_cols=714 Identities=22% Similarity=0.309 Sum_probs=534.3
Q ss_pred ceEEEEEEEecCCcEEEEEEeCcceEEEEecCCCCCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEeecccccccC
Q 001780 117 AAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQ 196 (1014)
Q Consensus 117 ~pvIrLFGvT~~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K~sl~gy~~ 196 (1014)
...+.+|.++++|.++.+.+. |+||||+.+.++. -.++.++|...+.+ .|.+|++|.|++|.-++.
T Consensus 69 ~S~VD~yFi~~dG~~Fk~~~p-y~PYFyiAt~d~~----e~~Ve~yL~Kky~g---------~i~~ie~v~kEDL~lkNH 134 (2173)
T KOG1798|consen 69 ISAVDLYFIDDDGSSFKVKYP-YRPYFYIATRDGM----ELEVEEYLRKKYEG---------QIADIEIVHKEDLDLKNH 134 (2173)
T ss_pred eeEEEEEEEccCCCeEEEeec-ccceEEEeecccc----HHHHHHHHHHHHhh---------hhhheeEecHhhcCchhh
Confidence 478999999999999999997 9999999887653 34577788887755 588999999999875552
Q ss_pred --CCcccEEEEEEcChhhHHHHHHHHh----cC-cccc------CC-------------CCccceeeecccccceeeeee
Q 001780 197 --QKSQPFLKIVVALPTMVASCRGILD----RG-IQLD------GL-------------GMKSFMTYESNVLFALRFMID 250 (1014)
Q Consensus 197 --~~~~~flKI~~~~P~~v~klR~~le----~g-~~~~------~l-------------~~~~~~~yEanI~~~lRFmID 250 (1014)
+-+..|+|++|.+-..+-++|+.|. ++ ..+. .+ .......-|.||||+.|+.||
T Consensus 135 LsGlqk~yiKlsF~t~~~L~~vrK~l~~iV~~N~~q~~a~daY~~~ls~~~~~~~q~D~ld~IvDiREYDVPyHvR~sID 214 (2173)
T KOG1798|consen 135 LSGLQKTYIKLSFDTVNQLVEVRKDLRPIVKRNKAQFDALDAYTNILSGNLNGRDQGDALDSIVDIREYDVPYHVRVSID 214 (2173)
T ss_pred hhcccccEEEEEEecHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhccCCcccchHhhhhhHhhcCCceEEEEeec
Confidence 3457899999999888877766654 22 1111 00 011245778899999999999
Q ss_pred cCCcceeEEEEeccceeccccccccceeeeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCceeEEE
Q 001780 251 CNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVA 330 (1014)
Q Consensus 251 ~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is 330 (1014)
.+|+.+-|+.+.... .++.+.-++ +-...|.++||+|||||+..+-+|||++.|+|+|||
T Consensus 215 ~~IrvG~WY~V~~~~------------~~v~i~~r~--------~~i~radp~VlAFDIETtKlPLKFPDae~DqIMMIS 274 (2173)
T KOG1798|consen 215 LDIRVGQWYNVSYNS------------GPVEIERRT--------DLIERADPRVLAFDIETTKLPLKFPDAESDQIMMIS 274 (2173)
T ss_pred CCeeeeeeeeeeeec------------cceEEEecc--------cccccCCceEEEEeeecccCCCCCCCcccceEEEEE
Confidence 999999999987311 112221111 112347889999999999999999999999999999
Q ss_pred EEeeccCccccceeEE-------EeccccCCcC-cceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccccc
Q 001780 331 NLVTLQGEKQPFIRNV-------MTLKSCAPIV-GVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402 (1014)
Q Consensus 331 ~~v~~~g~~~~~~~~v-------f~l~~~~~~~-~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ke 402 (1014)
+++..+|.... .|.+ |...+...-. -..|...++|.+||.+|++.|++..|.||++||++.|||||+..+.
T Consensus 275 YMiDGqGfLIt-NREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra 353 (2173)
T KOG1798|consen 275 YMIDGQGFLIT-NREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARA 353 (2173)
T ss_pred EEecCceEEEe-chhhhccchhhcccCCccccccceEEecCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHH
Confidence 99987775210 1111 2222222222 2567888999999999999999999999999999999999998811
Q ss_pred c-------------------------------------------------------------ccchhHHHhhcCChhhhh
Q 001780 403 D-------------------------------------------------------------VHHSIISDLQNGNAETRR 421 (1014)
Q Consensus 403 d-------------------------------------------------------------v~~~~i~~l~~~~~~~r~ 421 (1014)
. |.++.|..+.. |..+
T Consensus 354 ~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~---EkPQ 430 (2173)
T KOG1798|consen 354 KIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAM---EKPQ 430 (2173)
T ss_pred HhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhh---hCch
Confidence 1 11122332222 3456
Q ss_pred HHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCC---------
Q 001780 422 RLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAG--------- 492 (1014)
Q Consensus 422 ~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~--------- 492 (1014)
+++.|+..||..++-|..|. +++..+.|+.+..++.+.+|..|++..+|.+|+-+|...|.++||+..+.
T Consensus 431 ~lasYSVSDAVATYyLYMkY-VhPFIFsLctIIPl~PDevLRKGSGTLCE~LLmVeA~~~NIv~PNK~~e~~~~f~dGhl 509 (2173)
T KOG1798|consen 431 TLASYSVSDAVATYYLYMKY-VHPFIFSLCTIIPLNPDEVLRKGSGTLCEALLMVEAYHANIVFPNKHTEDPEKFYDGHL 509 (2173)
T ss_pred hhhhcchHHHHHHHHHHHHH-hhhHHhhhhhccccChHHHHhcCcchHHHHHHHHHHHhcCeecCCcCccchhhhccCee
Confidence 89999999999999998886 67888999999999999999999999999999999999999999986532
Q ss_pred -CCCCcCCcceeeeccCceEEe----------------------------------------------------------
Q 001780 493 -SEQGTYEGATVLEARAGFYEK---------------------------------------------------------- 513 (1014)
Q Consensus 493 -~~~~~yeGg~VleP~~G~y~~---------------------------------------------------------- 513 (1014)
..+ .|-||+|-.-++|+++.
T Consensus 510 leSE-TYVGGHVE~LesGVFRSDip~~F~~dp~a~~eLi~~l~~~L~~~l~vE~k~~vd~v~nfeEv~~~I~~kL~~lrd 588 (2173)
T KOG1798|consen 510 LESE-TYVGGHVECLESGVFRSDIPTEFRMDPSAYEELIDELGETLDFALTVENKVRVDEVTNFEEVKDEILEKLEELRD 588 (2173)
T ss_pred eeee-eeechhhhhHhcccccccCcccccCCHHHHHHHHHHHHHHHHHHHhhhcccchhhhcCHHHHHHHHHHHHHHhcC
Confidence 124 89999999999998764
Q ss_pred --------eeEeeeccccchHHHHHhCCCcccccChhhhhc-------------cCCC---------CCcee--------
Q 001780 514 --------PIATLDFASLYPSIMMAYNLCYSTLVTPEDARK-------------LNLP---------PECVN-------- 555 (1014)
Q Consensus 514 --------pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~-------------~~~~---------~~~~~-------- 555 (1014)
-|++||.+||||+||++..|.|..+++.+.|.. +.|. .++|.
T Consensus 589 ~p~R~E~PlIYHLDVaaMYPNIilTNRLQP~siv~E~~C~~CDfN~P~ktC~Rkm~W~WRGe~~pa~r~EY~~I~~qles 668 (2173)
T KOG1798|consen 589 VPIREEGPLIYHLDVAAMYPNIILTNRLQPDSIVDEEICAACDFNKPGKTCKRKMEWAWRGEYFPAKRSEYHRIKKQLES 668 (2173)
T ss_pred CCccccCCeEEEEehhhccCceeeecCCCCcccccHhhhccCCCCCCCcchhhhheeeeeeeEecCcchHHHHHHHHHHh
Confidence 389999999999999999999999998764422 1110 01111
Q ss_pred -eCCCCceee-------------------------------------------ecCCcCCCcHHHHHHHHHHHHHHHHHh
Q 001780 556 -KTPSGETFV-------------------------------------------KSNLQKGILPEILEELLAARKRAKADL 591 (1014)
Q Consensus 556 -~~p~g~~fv-------------------------------------------k~~~~~Gilp~iL~~Ll~~R~~~K~~m 591 (1014)
.-|+|.-|- -+.++..++-..++.+.++|.++|.+.
T Consensus 669 E~f~~~~~~~~~k~F~~L~~~eq~~~~kkRl~~Ysrk~Y~rv~~~~i~eRet~ICqRENpFYVdTVrsFRDRRYeyK~L~ 748 (2173)
T KOG1798|consen 669 ESFPAGAPFSPSKSFHELSREEQAAKLKKRLKDYSRKVYHRVKDTEIEERETTICQRENPFYVDTVRSFRDRRYEYKGLH 748 (2173)
T ss_pred ccCCCCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHhHhcccchhhhhcchhhccCchhhhhHHHhhhhhhHHHHHH
Confidence 112221110 023456788889999999999999887
Q ss_pred hhcC----------ChHH-------HHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHh
Q 001780 592 KEAK----------DPLE-------KAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVED 654 (1014)
Q Consensus 592 k~~~----------d~~~-------~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~ 654 (1014)
|..+ |... --+||+.|+|.|+++||+|||....++|||++|+|.-||.+|..+|+.|+++||.
T Consensus 749 K~wkg~ls~a~~sg~~a~i~eak~mvVlYdSLQLAHKcILNSFYGYVMRKGsRWYSMEMAGIvc~TGAnIIq~AR~lVEr 828 (2173)
T KOG1798|consen 749 KVWKGKLSAAKASGDLARIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCLTGANIIQMARELVER 828 (2173)
T ss_pred HHHHHHHhhhhccCchhhHHhhhheEEehHhHHHHHHHHHhhhhhhhhccccchheeehhheeeccchHHHHHHHHHHHH
Confidence 6421 2221 1369999999999999999999999999999999999999999999999999998
Q ss_pred hccccCCccccceEEEecCccceEEcCCCCHHHH----------------HHHHHHHHHHHHhc----C-----------
Q 001780 655 KFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAA----------------MKLGREAADYISGT----F----------- 703 (1014)
Q Consensus 655 ~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea----------------~~lg~eia~~vs~~----~----------- 703 (1014)
. .+.+--|||+||+-+|++-++-. ..+-..+++..|+. +
T Consensus 829 i----------GrPLELDTDGIWCilP~SFPEnf~Fk~~n~kkvtiSYPc~mLN~~V~e~fTN~QYq~L~dp~~~~Y~t~ 898 (2173)
T KOG1798|consen 829 I----------GRPLELDTDGIWCILPGSFPENFTFKLKNGKKVTISYPCVMLNHLVHEGFTNHQYQELVDPVRLTYVTR 898 (2173)
T ss_pred h----------CCCeeccCCceEEeccCCCccceEEEecCCcEEEEechHHHHHHHHHhccchhhHHHhcCcccceeeec
Confidence 5 26788999999998876543310 01112222222221 1
Q ss_pred -CCceeEEEeeeeccceecc--------cceeEEEeccCCCCccceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChh
Q 001780 704 -IKPIKLEFEKVYYPYLLIS--------KKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIP 774 (1014)
Q Consensus 704 -~~pi~Le~Ekvy~~~ll~~--------KKRYagl~~~~~~~~~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~ 774 (1014)
.+.|.+|.++.|..++|.+ |||||-...+ ..--+.||+|+.||.--.++|.+|.++++.+|.+.+++
T Consensus 899 SEnSIfFEVDGPYkAMILPaSkEEGk~lKKRYAVFN~D----GsLAELKGFEiKRRGEL~lIK~FQs~lF~~FL~GstLE 974 (2173)
T KOG1798|consen 899 SENSIFFEVDGPYKAMILPASKEEGKLLKKRYAVFNED----GSLAELKGFEIKRRGELKLIKVFQSELFKVFLKGSTLE 974 (2173)
T ss_pred ccceEEEEecCceeEEeeccchhhhhhhhheeEEecCC----CchhhhcCceeeecchhhHHHHHHHHHHHHHhCCCcHH
Confidence 1347889999999999974 8999976532 12467899999999999999999999999999999999
Q ss_pred hH---HHHHHHHHHHHHcCC---CC----ccceeEeecccCCcccccC-cchHHHHHHHHHHhcCC--CCCCCCCeeEEE
Q 001780 775 GA---VQYVKSTISDLLMNR---MD----LSLLVITKGLTKTGDDYEV-KAAHVELAERMRKRDAA--TAPNVGDRVPYV 841 (1014)
Q Consensus 775 ~a---~~~v~~~i~~l~~~~---v~----~~~lvi~k~l~k~~~~Y~~-~~~hv~~A~r~~~rd~g--~~p~~GdrV~YV 841 (1014)
++ +..+.+.|-+|+.++ ++ ++.+.-+++.+|.+++|.. +.-.+.-|+||.+- -| ..--.|-+..|+
T Consensus 975 EcY~aVA~Vad~WLDiL~s~G~~l~D~eL~elISEnrSMSk~L~dYg~QKStsitTAkRLaeF-LGd~MvKDkGL~C~yI 1053 (2173)
T KOG1798|consen 975 ECYSAVAAVADRWLDILDSHGADLTDSELLELISENRSMSKKLEDYGGQKSTSITTAKRLAEF-LGDDMVKDKGLACRYI 1053 (2173)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHhhchhhhhhHHHhccccchHHHHHHHHHHH-hchhhhhccCceeEEE
Confidence 75 567788898988653 22 3446678889999999985 55567779998764 23 233578899999
Q ss_pred EEecCCCCccccccCChhh----------hh-----ccC-------CCcChhHHHhhcchhhHHHhh
Q 001780 842 IIKAAKGAKAYERSEDPIY----------VL-----ENN-------IPIDTHYYLENQISKPLLRIF 886 (1014)
Q Consensus 842 i~~~~~~~~~~~ra~~p~~----------~~-----~~~-------~~iD~~yYi~~qi~~pl~ri~ 886 (1014)
|...+.|+++.|||.+..- ++ .+. .-||++||+++ |-.++++|.
T Consensus 1054 Is~~P~g~PVtERAIPVAIF~ae~~vk~~fLRkW~k~~sl~d~dIR~IiDWdYY~eR-LgSaIQKiI 1119 (2173)
T KOG1798|consen 1054 ISRKPEGAPVTERAIPVAIFQAEPPVKKHFLRKWTKDSSLEDTDIRAIIDWDYYRER-LGSAIQKII 1119 (2173)
T ss_pred EEecCCCCCcccccceeEEEecCcHHHHHHHHHHhccCccccCChheeeehHHHHHH-HHHHHHHHh
Confidence 9999999999999964221 11 112 24899999995 555544443
No 23
>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=100.00 E-value=1.2e-65 Score=605.59 Aligned_cols=377 Identities=44% Similarity=0.726 Sum_probs=329.2
Q ss_pred CCcEEEEEEEEEccCCCCCCCCC--CCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHH
Q 001780 300 APFRILSFDIECAGRKGHFPEPT--HDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFI 377 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~--~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i 377 (1014)
|+++++||||||.+..+.||++. .|+|++|+......+...+..+.+|++..+....+..+..|++|++||.+|++++
T Consensus 1 ~~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~lL~~f~~~i 80 (471)
T smart00486 1 PPLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEIDGVEVYEFNNEKELLKAFLEFI 80 (471)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCCCCeEEecCCHHHHHHHHHHHH
Confidence 57899999999999888899998 7999999988776655555667899999998888889999999999999999999
Q ss_pred HHhCCCEEEEecccCCCcccccc---------------------------------------------------------
Q 001780 378 REVDPDVMIGYNICKFDLPYLIE--------------------------------------------------------- 400 (1014)
Q Consensus 378 ~~~DPDIIiGyNi~~FDlpyL~~--------------------------------------------------------- 400 (1014)
++.|||||+|||+.+||||||++
T Consensus 81 ~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~Dl~~~~~~~ 160 (471)
T smart00486 81 KKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVIDLYNLYKNK 160 (471)
T ss_pred HHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEEEEhHHHHHHH
Confidence 99999999999999999999987
Q ss_pred -------------------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchh
Q 001780 401 -------------------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFL 461 (1014)
Q Consensus 401 -------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~v 461 (1014)
|.+++++.|.++|+.+.+.+.+++.||++|+.++++|+.+++.+....+||+++|+++..+
T Consensus 161 ~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l~~~~~~~~~s~~~~~~~~~~ 240 (471)
T smart00486 161 LKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPQRRT 240 (471)
T ss_pred hCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHH
Confidence 2233344566666655567889999999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHHHHHHhhcCccccCCCcCCC--------CCCcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCC
Q 001780 462 LSRGQSIKVLSQLLRKAKQKNLVIPNVKQAGS--------EQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNL 533 (1014)
Q Consensus 462 l~rG~~~~v~s~L~r~a~~~~~viP~~~~~~~--------~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nl 533 (1014)
+.+|++.++++++++++++.|+++|+...... ...+|+||+|++|.+|+|++||+++||+|||||||++|||
T Consensus 241 ~~~g~~~~v~~~l~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~y~gg~v~~p~~g~~~~~v~~lDf~SlYPsii~~~nl 320 (471)
T smart00486 241 LYYGSQIRVESLLLREAKKNNYILPSKSLIDFKGSEPELKKKAKYPGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNL 320 (471)
T ss_pred HhcCcHHHHHHHHHHHHhhCCEEeccchhcccccccccccccccccccEEecCCCCcccCceEEeehhhccHHHHHHhCC
Confidence 99999999999999999999999998654321 1248999999999999999999999999999999999999
Q ss_pred CcccccChhhhh-ccCCC----CCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcCChH--HHHHhHHH
Q 001780 534 CYSTLVTPEDAR-KLNLP----PECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAKDPL--EKAVLDGR 606 (1014)
Q Consensus 534 c~sT~~~~~~~~-~~~~~----~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~--~~~~ld~r 606 (1014)
||+|++...... .+... .......+++..|++.+.++|++|++|++|++.|.++|+.|++.+++. ++..||.+
T Consensus 321 ~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~~~~~~~~~~~d~~ 400 (471)
T smart00486 321 CYSTLVGRGENSGELFLDVEDLLTIKYEKPEGYHFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSR 400 (471)
T ss_pred CCcccccccccccccCCChhhcceeeecCCCcceeecCCCCCeehHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHH
Confidence 999999764311 00000 012345678888998888899999999999999999999999887654 89999999
Q ss_pred hhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcC
Q 001780 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFG 681 (1014)
Q Consensus 607 Q~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~ 681 (1014)
|+|+|+++||+||++|+..+||+|.++|++||+.||++|+.|++++++. |+.++++|||||||||||+++
T Consensus 401 q~a~K~~~Ns~yG~~g~~~~~~~~~~~a~~iT~~gr~~l~~~~~~i~~~-----~~~~~~~viYgDTDSi~v~~~ 470 (471)
T smart00486 401 QLALKLTANSVYGYLGFTNSRLYCKPLAASVTALGREILEKTKELIEKN-----GYPPGFKVIYGDTDSIFVTKP 470 (471)
T ss_pred HHHHHhhhcccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHh-----CCCCCeEEEEecCceEEEecC
Confidence 9999999999999999999999999999999999999999999999986 222358999999999999875
No 24
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=100.00 E-value=5.7e-54 Score=495.92 Aligned_cols=304 Identities=22% Similarity=0.286 Sum_probs=246.7
Q ss_pred CCcCCCcHHHHHHHHHHHHHHHHHhhhcC----------Ch-------HHHHHhHHHhhhccccceecccccccccCCCC
Q 001780 567 NLQKGILPEILEELLAARKRAKADLKEAK----------DP-------LEKAVLDGRQLALKISANSVYGFTGATVGQLP 629 (1014)
Q Consensus 567 ~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~----------d~-------~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~ 629 (1014)
..+.+++...++.+.++|..+|.+.|..+ |+ .+-.+||++|+|+|+++||+|||+|++++|||
T Consensus 218 qrEn~Fyvdtvr~FrdrRy~yK~~~k~~k~~~~~~~~~~~~~~~~~a~~~~~lyDs~Q~A~KiIlNSfYGYlG~~gsRwY 297 (621)
T cd05535 218 QRENPFYVDTVRAFRDRRYEYKGLHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWY 297 (621)
T ss_pred eccCCcHHhhHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccCcCCcccC
Confidence 35679999999999999999998877532 22 12368999999999999999999999999999
Q ss_pred ChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHH---HHHHHHH---------HHH
Q 001780 630 CIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEA---AMKLGRE---------AAD 697 (1014)
Q Consensus 630 ~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~e---a~~lg~e---------ia~ 697 (1014)
+.++|++||++||++|+.|++++|+. |..| |||||||||.+|....++ +++.|++ ++.
T Consensus 298 s~emA~~VT~~GreIIk~tr~lvE~~---------G~~V-egDTDsI~~~lp~~~~e~~~~~~k~g~~~~~~~~~~~LN~ 367 (621)
T cd05535 298 SMEMAGIVCYTGANIIQMARELVEQI---------GRPL-ELDTDGIWCILPKSFPENFTFKTKNGKKVTISYPCVMLNH 367 (621)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhc---------CCEE-EEecCeeEEEcCCCChHHHHHHhhccchhhhhhhHHHHHH
Confidence 99999999999999999999999974 6666 899999999987665443 2222332 233
Q ss_pred HHHhc--------CCC------------ceeEEEeeeeccceec--------ccceeEEEeccCCCCccce-eEeeeeec
Q 001780 698 YISGT--------FIK------------PIKLEFEKVYYPYLLI--------SKKRYAGLYWTNPEKFDKM-DTKGIETV 748 (1014)
Q Consensus 698 ~vs~~--------~~~------------pi~Le~Ekvy~~~ll~--------~KKRYagl~~~~~~~~~k~-~~KGie~v 748 (1014)
.|++. +.. +|++|+|++|.++||. .|||||++.+ ++++ ++||+|+|
T Consensus 368 ~V~~~~tn~qy~~l~~p~~~~y~i~se~~IefEvDG~Yk~mllpask~~~~~~KKRYAv~~~-----dG~i~elKGfEik 442 (621)
T cd05535 368 LVHKKFTNDQYQELVDPSTGTYETRSENSIFFEVDGPYKAMILPASKEEGKLLKKRYAVFNE-----DGSLAELKGFEVK 442 (621)
T ss_pred HHHHHHHHHHhhhccCcccccccccccceeEEEeccceeeeEcccccccccccccceEEEcC-----CCCEEEEeCceee
Confidence 33222 112 4899999999999995 6999998753 3455 89999999
Q ss_pred cCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHH----HHc--CCCC----ccceeEeecccCCcccccC-cchHH
Q 001780 749 RRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISD----LLM--NRMD----LSLLVITKGLTKTGDDYEV-KAAHV 817 (1014)
Q Consensus 749 RRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~----l~~--~~v~----~~~lvi~k~l~k~~~~Y~~-~~~hv 817 (1014)
|||||+|+|++|+++++.||.++++++|+++|++++.+ |.+ +.++ ++.++++++|+|.+++|.+ +++||
T Consensus 443 RRd~~~LaK~fQ~eV~e~iL~g~~~Eea~~~V~~v~~~~ld~L~~~~~~~~d~eLi~li~~~k~LsK~l~eY~~~ks~~V 522 (621)
T cd05535 443 RRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVANYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSI 522 (621)
T ss_pred eCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHhhcccCCCHHHcCCCCCcHH
Confidence 99999999999999999999999999999999988887 555 4565 4557779999999999998 78899
Q ss_pred HHHHHHHH-hcCCCCCCCCCeeEEEEEecCCCCccccccCChhhhh---------------cc---C----CCcChhHHH
Q 001780 818 ELAERMRK-RDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVL---------------EN---N----IPIDTHYYL 874 (1014)
Q Consensus 818 ~~A~r~~~-rd~g~~p~~GdrV~YVi~~~~~~~~~~~ra~~p~~~~---------------~~---~----~~iD~~yYi 874 (1014)
.+|+||++ .+.+.....|+.++|||++++.+.+..+||.++.-+. ++ + --||++||+
T Consensus 523 ~~AkRl~e~lg~~~~~~~G~~i~YII~~~p~~~~vseRAiPv~if~~~~~~~~~~lrkW~~~~~~~~~d~r~iiDW~YY~ 602 (621)
T cd05535 523 TTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVTERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYI 602 (621)
T ss_pred HHHHHHHHhhcCCcccCCCCeEEEEEEeCCCCCCccccccChhhhcCCHHHHHHHHHHHhCCCCcCCCChhhhhchHHHH
Confidence 99999987 3446788899999999999988889999998765331 11 1 238999999
Q ss_pred hhcchhhHHHhh
Q 001780 875 ENQISKPLLRIF 886 (1014)
Q Consensus 875 ~~qi~~pl~ri~ 886 (1014)
++ |...++.|.
T Consensus 603 ~r-l~~~iqKii 613 (621)
T cd05535 603 ER-LGSTIQKII 613 (621)
T ss_pred HH-HHHHHHhee
Confidence 95 666666654
No 25
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=100.00 E-value=1.3e-51 Score=475.93 Aligned_cols=279 Identities=26% Similarity=0.405 Sum_probs=222.8
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCC--CceeEEEEEeeccCccccceeEEEec-------cc------cCCcCcceEeecC
Q 001780 300 APFRILSFDIECAGRKGHFPEPTH--DPVIQVANLVTLQGEKQPFIRNVMTL-------KS------CAPIVGVDVMSFE 364 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~--D~Ii~Is~~v~~~g~~~~~~~~vf~l-------~~------~~~~~~~~V~~~~ 364 (1014)
-.+||..+|||+++. .||+|.. -||.+|+.--+..+..+ + .+|.| +. +....|+.|+.|+
T Consensus 104 ~~i~~~~~DIEv~~~--~fp~~~~a~~~i~~i~~~d~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~ 178 (498)
T PHA02524 104 DDVVIDVVDIEVTAP--EFPEPKYAKYEIDMISHVRLHNGKKT-Y--YIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFE 178 (498)
T ss_pred hhceEEEEEEEecCC--CCCChhhcCCceEEEEeeecccCCcc-E--EEEeccccccCCCcccccccccccCCeEEEEeC
Confidence 357999999999874 4999985 58999985322212211 2 23432 11 1114578999999
Q ss_pred CHHHHHHHHHHHHHHhCCCEEEEecccCCCccccccc-------------------------------------------
Q 001780 365 TERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK------------------------------------------- 401 (1014)
Q Consensus 365 ~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~k------------------------------------------- 401 (1014)
+|++||.+|+++|++.|||||+|||+++||||||+++
T Consensus 179 sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iD 258 (498)
T PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMD 258 (498)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeE
Confidence 9999999999999999999999999999999999881
Q ss_pred ------------------------------ccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhHHHHH
Q 001780 402 ------------------------------EDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMA 451 (1014)
Q Consensus 402 ------------------------------edv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~a 451 (1014)
.+++ ..|.++|. +++++++.||++||.|+++|..++.++..++++|
T Consensus 259 l~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~-~~I~~l~~---~d~~rla~YclkDa~L~~~L~~~~~ll~~~~~la 334 (498)
T PHA02524 259 YMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYE-GPINKFRK---ADHQRYVDYCVRDTDIILLIDGRRCFIDLILSLS 334 (498)
T ss_pred HHHHHHHhhhccCCCCCHHHHHHHhcCCccccch-hhHHHHhc---CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1111 12444543 3568999999999999998887787888888999
Q ss_pred HHhCcCcchhcccccHHHHH-HHHHHHHhhcCccccCCCcCCCCCCcCCcceeeeccCceEEeeeEeeeccccchHHHHH
Q 001780 452 RVTGVPISFLLSRGQSIKVL-SQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMA 530 (1014)
Q Consensus 452 rv~g~p~~~vl~rG~~~~v~-s~L~r~a~~~~~viP~~~~~~~~~~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia 530 (1014)
+++|+|+++++ +|++++ ++|+++|+++|+++|+.+... .+ +|+||+|++|++|+|++ |++|||+|||||||++
T Consensus 335 rvtglpl~~v~---~qikv~~~lllr~~~~~g~viP~~~~~~-~~-~Y~GA~V~eP~~GlY~~-VivLDFaSLYPSII~a 408 (498)
T PHA02524 335 YYAKIRFDDVL---GTIKVWDSIIFNSLVESNVVIPAMKASP-KQ-SFPGAYVKEPVPGGYRY-GLSFDLTSLYPSILRL 408 (498)
T ss_pred HHHCCCHHHhc---cHHHHHHHHHHHHHHHCCEecCCCCCCC-CC-ccCCeEEecCCCccccC-eEEEEccccCHHHHHH
Confidence 99999999985 467766 688999999999999876533 34 89999999999999999 5689999999999999
Q ss_pred hCCCcccccChh---hhhcc-----CCCCCceeeCCCCceeeecCCcCCCcHHHHHHHHHHHHHHHHHhhhcC
Q 001780 531 YNLCYSTLVTPE---DARKL-----NLPPECVNKTPSGETFVKSNLQKGILPEILEELLAARKRAKADLKEAK 595 (1014)
Q Consensus 531 ~Nlc~sT~~~~~---~~~~~-----~~~~~~~~~~p~g~~fvk~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~ 595 (1014)
|||||+|+++.. .++++ ..++++++.+|+|.+|++ .++||||++|++|+++|+++|++|+++.
T Consensus 409 ~NIsPeTl~~~~~~~~~~~~~~~~~~~~~~~~~~~P~G~~F~K--~~~GilP~iLe~Ll~~RK~~Kk~M~~a~ 479 (498)
T PHA02524 409 LNISPEMIAGMFSPARLEDYINKVAPKPSDQFSCAPNGMMYKK--GVVGVLPNETEKVFLQRKSEKKMMLAAI 479 (498)
T ss_pred hCCCHHHhhccccccchhhhccccCCCCCcceEECCCCCEEec--CCCcccHHHHHHHHHHHHHHHHHHHHhH
Confidence 999999997642 23222 113579999999999987 5799999999999999999999999753
No 26
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=100.00 E-value=4.2e-41 Score=379.19 Aligned_cols=256 Identities=39% Similarity=0.728 Sum_probs=209.3
Q ss_pred EecCCcEEEEEEeCcceEEEEecCCCCCCCcHHHHHHHHHHHHhhhccCCCCCcceEEEEEEee-cccccccCCCcccEE
Q 001780 125 VTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMREANRNSKVPQFVRHIEMVQK-RSIMYYQQQKSQPFL 203 (1014)
Q Consensus 125 vT~~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~Ie~V~K-~sl~gy~~~~~~~fl 203 (1014)
.|++|+||||+|+||+||||+..++.... .++.+.++..+.. .....+.+++.|+| ++||||+.+. .+|+
T Consensus 1 ~t~~g~svcv~v~~f~pyfYv~~~~~~~~---~~~~~~~~~~~~~-----~~~~~~~~~~~V~r~~~~~~y~~~~-~~~l 71 (325)
T PF03104_consen 1 MTEDGKSVCVRVHGFRPYFYVLPPESDSP---KDLEQFIEQLLRK-----KFKIDVFKIEKVKRKKSFYGYDGKE-EPFL 71 (325)
T ss_dssp -ECTSEEEEEEEST--EEEEEEESSGGGH---HHHTTHEEHHEET-----TEEEEEEEEEEEEEEEESSEETTEE-EEEE
T ss_pred CCCCCCEEEEEEcCCCEEEEEECCCCccH---HHHHHHHHHHhhh-----ccCCceEEEEEEEeeeeeccCCCCC-ceEE
Confidence 48999999999999999999988765322 2222222111111 12356789999999 9999999654 4599
Q ss_pred EEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeeeeecCCcceeEEEEeccceeccccccccceeeeeee
Q 001780 204 KIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQLEFDCL 283 (1014)
Q Consensus 204 KI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~E~~v~ 283 (1014)
||++.+|..++++++.+++ ...++||+||++++|||+|++|.|++|++++... .....+.|+|+.|+.+.
T Consensus 72 kV~~~~~~~~~~~~~~l~~---------~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~-~~~~~~~s~~~~e~~~~ 141 (325)
T PF03104_consen 72 KVYFSSPRDVRKLRDNLKK---------TFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPS-KPVKDRVSWCDIEFSVD 141 (325)
T ss_dssp EEEESSTTHHHHHHHHHHH---------TEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTE-CHHHHHTCTCSCECECC
T ss_pred EEEECcHHHHHHHHHHHHh---------ccchhhccCCCHHHheeeecCcccceeeeccccc-ccccccccccccccccc
Confidence 9999999999999999875 2478999999999999999999999999999751 11223789999999999
Q ss_pred ccccccCCCCCCcCCCCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcC-cceEee
Q 001780 284 YSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIV-GVDVMS 362 (1014)
Q Consensus 284 ~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~-~~~V~~ 362 (1014)
+.++.+++....+ |||++|||||||.+..+.||++..|+|+|||+++...|...+..+.+|+++.|.... +..|..
T Consensus 142 ~~~~~~~~~~~~~---p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 218 (325)
T PF03104_consen 142 YSNLKPLPDESIP---PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSIEDNVEVIY 218 (325)
T ss_dssp HHHHECHTSSSSG---GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCTTCTTEEEE
T ss_pred ccccccccccccc---cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCCCCCcEEEE
Confidence 9998887754332 999999999999999888999999999999998887766666778899999998877 999999
Q ss_pred cCCHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccccc
Q 001780 363 FETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402 (1014)
Q Consensus 363 ~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ke 402 (1014)
|++|++||.+|+++|+++|||||+|||+++||||||+++-
T Consensus 219 ~~~E~~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~ 258 (325)
T PF03104_consen 219 FDSEKELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERA 258 (325)
T ss_dssp ESSHHHHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHH
T ss_pred ECCHHHHHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHH
Confidence 9999999999999999999999999999999999999943
No 27
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.6e-40 Score=425.38 Aligned_cols=376 Identities=24% Similarity=0.245 Sum_probs=291.1
Q ss_pred cccEEEEEEcChhhHHHHHHHHhcCccccCCCCccceeeecccccceeeeeecCCcceeEEEEeccceecccccccccee
Q 001780 199 SQPFLKIVVALPTMVASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLSYCQL 278 (1014)
Q Consensus 199 ~~~flKI~~~~P~~v~klR~~le~g~~~~~l~~~~~~~yEanI~~~lRFmID~~I~G~~Wi~i~~~~~~~~~~k~S~C~~ 278 (1014)
+..++|+++.+|..++++|..+.. ++. ..+.+|++|++..|+|+|+.+.++.| + .+.... .
T Consensus 128 ~~~~~k~~~~~~~~v~~~~~~~~~---~~~----~~~~~e~di~~~~r~~~d~~~~p~~~---~--~~~~~~--~----- 188 (1172)
T TIGR00592 128 LVSVPKLKFSSPADVPAINDFSNH---HPA----VVDIVKKAIPVSTRYLLEKILIPVPL---K--RAEFAG--G----- 188 (1172)
T ss_pred cccccccccccccchhhccccccc---ccc----ccccccCCCCccccccccccccCCCC---C--cccccc--c-----
Confidence 457899999999999998876543 222 35789999999999999999999865 1 111100 0
Q ss_pred eeeeeccccccCCCCCCcCCCCCcEEEEEEEEEccCCC--CC--CCCCCCceeEEEEE----eeccCccccceeEEEecc
Q 001780 279 EFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKG--HF--PEPTHDPVIQVANL----VTLQGEKQPFIRNVMTLK 350 (1014)
Q Consensus 279 E~~v~~~~~~~~~~~~~~~~~pplrilSfDIE~~~~~g--~f--P~~~~D~Ii~Is~~----v~~~g~~~~~~~~vf~l~ 350 (1014)
......+||++++||||||.+..| .| |++..|+|||||++ +...|+..+..+.+|+++
T Consensus 189 --------------~~~~~~~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~~~~~~~~~~~ 254 (1172)
T TIGR00592 189 --------------DVQMEGDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESEPEARVVTWKK 254 (1172)
T ss_pred --------------cccccCCCcccccccccccccccccccCcccccccccccccccccccccccccCCCccchhhhccC
Confidence 001234699999999999998755 44 55667999999975 455677778888999999
Q ss_pred ccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccc------------------------------
Q 001780 351 SCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE------------------------------ 400 (1014)
Q Consensus 351 ~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~------------------------------ 400 (1014)
+|+++.|+.|..|++|.+||.+|.++|++.|||||+|||+++||||||.+
T Consensus 255 ~~~~~~~~~v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~~~~~~~~~da~~dr~~~~G~~~lfGr~~~~ 334 (1172)
T TIGR00592 255 PDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKLGVVLLFGRDVDH 334 (1172)
T ss_pred ccccCCCccceeccchHHHHhhHHHHHhhcCcchhcccccccCccceecCCceEEeeHHhhhHHhhCCCeEEEecccCCc
Confidence 99999999999999999999999999999999999999999999999987
Q ss_pred -----------------------------------------------------cccccchhHHHhhcCChhhhhHHhhhh
Q 001780 401 -----------------------------------------------------KEDVHHSIISDLQNGNAETRRRLAVYC 427 (1014)
Q Consensus 401 -----------------------------------------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~ 427 (1014)
|++++++.|.+.|.++.+ .+++.||
T Consensus 335 ~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~k~dv~~k~I~~~~~~~~~--~~~v~y~ 412 (1172)
T TIGR00592 335 VSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAP--DIDAPYS 412 (1172)
T ss_pred eeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcCcCceeeEEehhhccCCCC--ccCCcCC
Confidence 234445556666655433 2688999
Q ss_pred hccccchHHHHhhhhhhHhHHHHHHHhCcCcchh--cccccHHHHHHHHHHHHhhcCccccCCCcC---C-CCCCcCCcc
Q 001780 428 LKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFL--LSRGQSIKVLSQLLRKAKQKNLVIPNVKQA---G-SEQGTYEGA 501 (1014)
Q Consensus 428 lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~v--l~rG~~~~v~s~L~r~a~~~~~viP~~~~~---~-~~~~~yeGg 501 (1014)
++|+.+++.|+.++..+.++.+ ++.|.++..+ +++|++++++ +.|++...+++.|..... . ....+|||+
T Consensus 413 ~~~lkv~y~l~~~~~~l~~l~~--~~~g~~~~~vf~~n~g~~erfl--l~rki~gp~WL~i~~p~~~~~~~~S~c~yEga 488 (1172)
T TIGR00592 413 SEYLEVTYELGKEFAPMEALPS--DLKGQTFWHVFGSNTGNLERFL--LLRKIKGPCWLAVKGPDELEYPRRSWCKYEGG 488 (1172)
T ss_pred cceEEEEEccCccchhhhhhhh--hccCCcchheeccCHHHHHHHH--hcCCCCCCceEEeCCCcccCcCCccccceEEE
Confidence 9999999999998888887655 4556666655 6788888874 558899898887753321 1 113389999
Q ss_pred eeeec--cCceEEe--eeEeeecc--ccchHHHHHhCCCcccccChh-hhhccCCCCCc-eeeCC-CCceeee-------
Q 001780 502 TVLEA--RAGFYEK--PIATLDFA--SLYPSIMMAYNLCYSTLVTPE-DARKLNLPPEC-VNKTP-SGETFVK------- 565 (1014)
Q Consensus 502 ~VleP--~~G~y~~--pV~~LDF~--SLYPSIiia~Nlc~sT~~~~~-~~~~~~~~~~~-~~~~p-~g~~fvk------- 565 (1014)
+|++| .+|+|.+ ||++|||+ |||||||++||||++|++... .+++ ..+++ +...+ .+..|..
T Consensus 489 ~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~--~~~~~~~~~~~~~~~~~~~~~~p~~~ 566 (1172)
T TIGR00592 489 YVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDK--PPPEPPYDVHPCVGTRPKDCSFPLDL 566 (1172)
T ss_pred EecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeecccccC--CCCCCccceEEEEEEccCCCCCCchh
Confidence 99999 9999998 89999999 999999999999998887543 1211 11222 21112 1222211
Q ss_pred cCCcCCCcHHHHHHHHHHHHHHHHHhhhcC--ChHHHHHhHHHhhhccccce
Q 001780 566 SNLQKGILPEILEELLAARKRAKADLKEAK--DPLEKAVLDGRQLALKISAN 615 (1014)
Q Consensus 566 ~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~--d~~~~~~ld~rQ~AlKi~aN 615 (1014)
...++|++|..|+.++++|+.+++.|+... ||.....||.+|.|||+++|
T Consensus 567 ~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~n 618 (1172)
T TIGR00592 567 KGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLAN 618 (1172)
T ss_pred hhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHH
Confidence 125789999999999999999999999876 99999999999999999999
No 28
>PHA02523 43B DNA polymerase subunit B; Provisional
Probab=100.00 E-value=5.5e-37 Score=333.69 Aligned_cols=286 Identities=20% Similarity=0.262 Sum_probs=213.3
Q ss_pred HHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccce-EEEecCccceEE
Q 001780 601 AVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAE-VIYGDTDSVMVQ 679 (1014)
Q Consensus 601 ~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~-VIYGDTDSv~V~ 679 (1014)
+.++.+|.|+|+++||+|||+|+.++||||.++|++||++||++|+++.+.+++......+- .|++ |||||||||||+
T Consensus 37 a~~~~~q~AiKIlmNSfYGylG~~~~R~yd~e~A~aVT~~Gre~Ik~i~~~~ney~~~l~~t-~G~~~VIYgDTDSifv~ 115 (391)
T PHA02523 37 QKRNTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERKLNEYINELVKT-TGVDYVCYIDTDSVYLN 115 (391)
T ss_pred HHHhcchHHHHHHHHhhhhhhcCCCceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-cCcceEEEecCCeeEEE
Confidence 45788999999999999999999999999999999999999999997777444322111111 2565 999999999999
Q ss_pred cCCCCHHHH-------------------HH-------HHHHHHHHHHhcCCCceeEEEeeeeccc--------eecccce
Q 001780 680 FGVPTVEAA-------------------MK-------LGREAADYISGTFIKPIKLEFEKVYYPY--------LLISKKR 725 (1014)
Q Consensus 680 ~~~~~~~ea-------------------~~-------lg~eia~~vs~~~~~pi~Le~Ekvy~~~--------ll~~KKR 725 (1014)
++.-..+.. ++ -.+++|++++.. .+.+.+|||++|.++ ++.+|||
T Consensus 116 ~~~~v~~~~~~~~~d~~~~vd~ldk~~~~~iE~~In~sY~el~eymna~-~h~~~m~rE~ia~~f~~s~g~~gfw~~KKR 194 (391)
T PHA02523 116 MEAVVNRVGIDKFRDTNHLIDFLDNLGSKKLEPFIDDSYKELEEYMNHD-HHLLLMDREAIFGAPLGSDGIGGFWTGKKR 194 (391)
T ss_pred ecchHHHHhhhhhccchhhhHHHHHHHHHHhHHHHHHHHHHHHHHhcch-hhhhhhhHHHhccccccccccchhhhhhhh
Confidence 964111000 00 113455555543 356899999999997 8889999
Q ss_pred eEEEeccCCCC-c--cceeEeeeeeccCchHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHcCCCCccceeE---
Q 001780 726 YAGLYWTNPEK-F--DKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVI--- 799 (1014)
Q Consensus 726 Yagl~~~~~~~-~--~k~~~KGie~vRRD~~~l~k~~~~~vl~~il~~~d~~~a~~~v~~~i~~l~~~~v~~~~lvi--- 799 (1014)
|||.+|.+.++ + +++++.|+|++|+|.++++|+++++|+++||.+. -+.+++|+++.+.+.. ++|+++..+
T Consensus 195 YA~~v~d~EG~r~~epklkI~G~E~qrSstp~~~~~~~ke~i~~Il~~~-ee~iqeyi~~~~~ey~--~~~~~~Ia~~s~ 271 (391)
T PHA02523 195 YALNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEG-ESSLQDYFKEFKDEFK--NIPYQDVAAVSS 271 (391)
T ss_pred hhheeeeccCccccCCccceeeeeecccCchHHHHHHHHHHHHHHHhCC-hHHHHHHHHHHHHHHh--cCCHHHhcccCC
Confidence 99998876654 2 6999999999999999999999999999999854 5559999999999885 799999998
Q ss_pred eecccCCcccccC----cchHHHHHHHHHHh---cCC-CCCCCCCeeEEEEEecCCC--Ccccccc---CChhhh-hccC
Q 001780 800 TKGLTKTGDDYEV----KAAHVELAERMRKR---DAA-TAPNVGDRVPYVIIKAAKG--AKAYERS---EDPIYV-LENN 865 (1014)
Q Consensus 800 ~k~l~k~~~~Y~~----~~~hv~~A~r~~~r---d~g-~~p~~GdrV~YVi~~~~~~--~~~~~ra---~~p~~~-~~~~ 865 (1014)
...+.|..+.|.. .+.||..|.-.++. +.+ ..++.|+.|..|..+.+.. +.-.+-. .=|.++ ++=-
T Consensus 272 ~~~I~K~~d~~~~~~kg~p~hvrGal~~N~~~~~~~~~~~i~~GeKvk~l~Lk~~np~~~~c~~~~sgd~iP~ef~~D~~ 351 (391)
T PHA02523 272 ANNIGKNGDALGFPIKGTPYHVKGVLAYNRIAKTDTAIPMISEGEKVMVLPLRDRNPFNEACFAWPSGTPIPPAVEADVL 351 (391)
T ss_pred CCchhhcccccCCCCCCCchhhHHHHHHHHHhcccCCCccccCCCceEEEeccCCCCCCcceEeccCCCCCCHHhhccHH
Confidence 5778888778765 45698776544332 211 1268899999998875332 1222222 123222 2212
Q ss_pred CCcChhHHHhhcchhhHHHhhcccccc
Q 001780 866 IPIDTHYYLENQISKPLLRIFEPILKN 892 (1014)
Q Consensus 866 ~~iD~~yYi~~qi~~pl~ri~~~i~g~ 892 (1014)
--||++--++|.++.||.||++++ |.
T Consensus 352 k~iDy~~mfeKtf~~Pl~~I~ea~-g~ 377 (391)
T PHA02523 352 KYLDINKLFDKTFVKPLSSICEAT-KT 377 (391)
T ss_pred hhccHHHHHHHHHHhHHHHHHHHh-CC
Confidence 347889999999999999999998 54
No 29
>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=99.96 E-value=1.1e-29 Score=273.43 Aligned_cols=151 Identities=78% Similarity=1.330 Sum_probs=138.2
Q ss_pred CCCCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHH
Q 001780 297 SKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDF 376 (1014)
Q Consensus 297 ~~~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~ 376 (1014)
.++||+++|||||||.++.|.||+|+.|||+|||+++...|...+..+.+|++++|.++.++.|..|++|++||.+|+++
T Consensus 2 ~~~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~E~eLL~~f~~~ 81 (230)
T cd05777 2 SKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDF 81 (230)
T ss_pred CCCCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCCCCEEEEECCHHHHHHHHHHH
Confidence 35799999999999999999999999999999999888777766677899999999999999999999999999999999
Q ss_pred HHHhCCCEEEEecccCCCcccccc--------------------------------------------------------
Q 001780 377 IREVDPDVMIGYNICKFDLPYLIE-------------------------------------------------------- 400 (1014)
Q Consensus 377 i~~~DPDIIiGyNi~~FDlpyL~~-------------------------------------------------------- 400 (1014)
|+++|||||+|||+++||||||.+
T Consensus 82 i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iD~~~~~~ 161 (230)
T cd05777 82 VQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQ 161 (230)
T ss_pred HHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEeeeHHHHHH
Confidence 999999999999999999999988
Q ss_pred ---------------------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHhH
Q 001780 401 ---------------------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNY 447 (1014)
Q Consensus 401 ---------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~~ 447 (1014)
|.+++++.|.++|+++++.+.+++.||++||.|+++|+++|+++.++
T Consensus 162 ~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~~~~~ 229 (230)
T cd05777 162 RDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLVNY 229 (230)
T ss_pred HhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHhhHccc
Confidence 34455677888998888899999999999999999999999988764
No 30
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=99.92 E-value=5.3e-25 Score=236.98 Aligned_cols=139 Identities=24% Similarity=0.398 Sum_probs=118.9
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccc---e-eEEEeccccC---------CcCcceEeecCCHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPF---I-RNVMTLKSCA---------PIVGVDVMSFETER 367 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~---~-~~vf~l~~~~---------~~~~~~V~~~~~E~ 367 (1014)
.|++|||||||.++++.||+|+.|||+||++++..++..... . ..+++.++|. .+.+..|..|++|+
T Consensus 3 ~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 82 (231)
T cd05778 3 HLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVESEL 82 (231)
T ss_pred ceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCCHH
Confidence 589999999999999999999999999999887654432211 1 1467777773 56789999999999
Q ss_pred HHHHHHHHHHHHhCCCEEEEecccCCCcccccc-----------------------------------------------
Q 001780 368 DVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE----------------------------------------------- 400 (1014)
Q Consensus 368 eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~----------------------------------------------- 400 (1014)
+||.+|+++|+.+|||||+|||+++||||||++
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~ 162 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHI 162 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEE
Confidence 999999999999999999999999999999988
Q ss_pred -----------------------------cccccchhHHHhh-cCChhhhhHHhhhhhccccchHHHHh
Q 001780 401 -----------------------------KEDVHHSIISDLQ-NGNAETRRRLAVYCLKDAYLPQRLLD 439 (1014)
Q Consensus 401 -----------------------------kedv~~~~i~~l~-~~~~~~r~~l~~Y~lkDa~l~~~L~~ 439 (1014)
|++++++.|++|| +++++.|.+++.||++||.++++|++
T Consensus 163 lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll~ 231 (231)
T cd05778 163 LNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEILD 231 (231)
T ss_pred eEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhhC
Confidence 4566778899997 46678999999999999999999974
No 31
>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=99.89 E-value=3.2e-23 Score=218.44 Aligned_cols=135 Identities=24% Similarity=0.367 Sum_probs=106.8
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCcccc---c-eeE--EEeccccCCcCc-ceEeecCCHHHHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQP---F-IRN--VMTLKSCAPIVG-VDVMSFETERDVLLAW 373 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~---~-~~~--vf~l~~~~~~~~-~~V~~~~~E~eLL~~f 373 (1014)
|+++|||||||.+..|.||+|+.|||||||+++...|.... . ... .|...+|.+..+ ..|..|++|++||.+|
T Consensus 1 ~lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f 80 (204)
T cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80 (204)
T ss_pred CceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCceEEecCCCHHHHHHHH
Confidence 68999999999988888999999999999988765553210 0 011 133334444443 5678899999999999
Q ss_pred HHHHHHhCCCEEEEecccCCCcccccc-----------------------------------------------------
Q 001780 374 RDFIREVDPDVMIGYNICKFDLPYLIE----------------------------------------------------- 400 (1014)
Q Consensus 374 ~~~i~~~DPDIIiGyNi~~FDlpyL~~----------------------------------------------------- 400 (1014)
+++++++|||+|+|||+.+||||||.+
T Consensus 81 ~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~V 160 (204)
T cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAV 160 (204)
T ss_pred HHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHHHH
Confidence 999999999999999999999999988
Q ss_pred --------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHH
Q 001780 401 --------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLL 438 (1014)
Q Consensus 401 --------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~ 438 (1014)
|.++++++|.++|+++ ..+++.||++||.+++.|.
T Consensus 161 a~~~Lg~~K~~~~~~~I~~~~~~~---~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 161 TKAKLGYDPVELDPEDMVPLARED---PQTLASYSVSDAVATYYLY 203 (204)
T ss_pred HHHHhCCCcCcCCHHHHHHHHhCC---cHHHHhccHHHHHHHHHHh
Confidence 3445556677777754 4689999999999999875
No 32
>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=99.87 E-value=2.8e-22 Score=210.73 Aligned_cols=130 Identities=32% Similarity=0.519 Sum_probs=107.2
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHH
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIRE 379 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~ 379 (1014)
|++++++|||||++..| ||+|..|+|+|||+.. .+. ..++++..+.. ..|..|++|++||.+|+++|++
T Consensus 1 p~l~i~~fDIEt~~~~g-~p~~~~d~Ii~Is~~~--~~~-----~~~~~~~~~~~---~~v~~~~~E~~lL~~F~~~i~~ 69 (195)
T cd05780 1 EDLKILSFDIEVLNHEG-EPNPEKDPIIMISFAD--EGG-----NKVITWKKFDL---PFVEVVKTEKEMIKRFIEIVKE 69 (195)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCcEEEEEEec--CCC-----ceEEEecCCCC---CeEEEeCCHHHHHHHHHHHHHH
Confidence 78999999999998777 8999999999999643 221 23555554432 2577899999999999999999
Q ss_pred hCCCEEEEecccCCCcccccc-----------------------------------------------------------
Q 001780 380 VDPDVMIGYNICKFDLPYLIE----------------------------------------------------------- 400 (1014)
Q Consensus 380 ~DPDIIiGyNi~~FDlpyL~~----------------------------------------------------------- 400 (1014)
.|||+|+|||+.+||||||.+
T Consensus 70 ~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~v~~ 149 (195)
T cd05780 70 KDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYE 149 (195)
T ss_pred cCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCcCcHHHHHH
Confidence 999999999999999999988
Q ss_pred ------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhh
Q 001780 401 ------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKL 441 (1014)
Q Consensus 401 ------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl 441 (1014)
|.++++++|.++|..+. .+.+++.||++||.++++|++++
T Consensus 150 ~~Lg~~k~d~~~~~i~~~~~~~~-~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 150 ELFGIEKEDVPGEEIAEAWDSGE-NLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred HHhCCCCCcCCHHHHHHHHhCCC-chHHHHHHhHHHHHHHHHHHhhC
Confidence 34455567777776443 68999999999999999998764
No 33
>PHA02563 DNA polymerase; Provisional
Probab=99.86 E-value=4.5e-21 Score=228.51 Aligned_cols=272 Identities=19% Similarity=0.272 Sum_probs=170.9
Q ss_pred hhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCCCC--CCc
Q 001780 420 RRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSE--QGT 497 (1014)
Q Consensus 420 r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~~~--~~~ 497 (1014)
+.....|+.+|+.+...+++.. .+.+ +......+.+..++-+++.+-.....-+|.......+ ..+
T Consensus 170 ~~e~~~Yl~~D~~il~~~~~i~--------~~~~----f~~~TisS~a~~ifk~~~~~~~~~~~~~p~l~~~~~~fIr~s 237 (630)
T PHA02563 170 DPEELEYIHNDCVIIAGMLDIH--------FSEG----FTRFTTGSDAMTVYKELYQKIKIKYTHFPILDLGFDDFIRKF 237 (630)
T ss_pred cHHHHHHHHHHHHHHHHHHHHH--------HHhc----cccCCcchHHHHHHHHHHhhcccccccCCCCCchHHHHHHHh
Confidence 4577899999986655544321 1222 1222222334455555554211111223543221110 238
Q ss_pred CCcceee---eccCceEEeeeEeeeccccchHHHHHhCCCccccc-Chhhh---hc--c--------------CCCCCc-
Q 001780 498 YEGATVL---EARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLV-TPEDA---RK--L--------------NLPPEC- 553 (1014)
Q Consensus 498 yeGg~Vl---eP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~-~~~~~---~~--~--------------~~~~~~- 553 (1014)
|.||.|. ++.+|++++ +.++|++|||||+|..+++++.+-. ..... .. + ..+.+-
T Consensus 238 Y~GGr~~~~~~~~~~~~~~-~~~yDvnSlYPsaM~~~~~P~g~p~~~~~k~~~~~~~~~~i~~~~~~f~~~ev~~p~~~~ 316 (630)
T PHA02563 238 YRGGRTWYNPKYIGKLIEE-GYVYDVNSLYPYVMYNAKLPYGEPFYEKGKPAELKPDPLYIYNYGALFKLKKGYVPDDML 316 (630)
T ss_pred eeCceeecccccccccccc-ccccccccccHHHHhhccCCCCCceeeccCcccccccccccccceEEEEEEEccCCCccc
Confidence 9999998 899999987 7799999999999999999987622 11100 00 0 000000
Q ss_pred -----------eeeCCCC--------------------------------------ceeeecCCcCCCcHHHHHHHHHHH
Q 001780 554 -----------VNKTPSG--------------------------------------ETFVKSNLQKGILPEILEELLAAR 584 (1014)
Q Consensus 554 -----------~~~~p~g--------------------------------------~~fvk~~~~~Gilp~iL~~Ll~~R 584 (1014)
-.+.|.| ..|- ...+++.+.+..+.+.|
T Consensus 317 i~Ik~~~~~~~~~i~p~g~~~g~~~~~E~~~~~~~~i~le~~ik~y~~~~i~v~~Gy~fe---~~~~~FkeyI~~lY~iK 393 (630)
T PHA02563 317 IQIKSNLDFNGRLVLKVGIVKYVNSGNEYVDLNLNNLDLELEITHYDAFNEEVESGVVFE---CETGLFRDFIDHFYEIK 393 (630)
T ss_pred cceeccccCCCceeeecccEeeEecCceEEEEEeceEEHHHhhhccceeEEEEEEEEEEc---ccCchHHHHHHHHHHHH
Confidence 0011111 1121 23688888999999988
Q ss_pred HHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccC---CCCC---------------------hHHHhhHHHh
Q 001780 585 KRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVG---QLPC---------------------IEISSSVTSY 640 (1014)
Q Consensus 585 ~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~---r~~~---------------------~~iA~sIT~~ 640 (1014)
.+.|+.-+ .++..|+++||.||-+|-.-. ++++ .++|++|||+
T Consensus 394 ~~~K~~~~-------------~~~i~KLlLNSLYGKfg~~p~~~~~~~~l~~~~~l~~~~~~~~~~~~~yv~iAa~ITa~ 460 (630)
T PHA02563 394 TNSKGAKK-------------QNMLAKLMLNSLYGKFALNPDNTGKVPYLDDNGRLDLISNGEENKEPNYIPIAAFITAR 460 (630)
T ss_pred hccccCcc-------------HHHHHHHHHhcccchhhcCccccCceeeecccceeeeecCCccccccccchHHHHHHHH
Confidence 88655321 136899999999999997653 3322 4599999999
Q ss_pred hHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhcCCCce---eEEEeeeecc
Q 001780 641 GRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPI---KLEFEKVYYP 717 (1014)
Q Consensus 641 GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~~~~pi---~Le~Ekvy~~ 717 (1014)
||.+|..+++.+++ .|+|||||||||+...... +.+.+..+. ++++|.++.+
T Consensus 461 aR~~m~~~~~~~~~------------~v~Y~DTDSi~v~~~~~~~-------------L~~~~i~~~eLGk~k~E~~~~~ 515 (630)
T PHA02563 461 ARSNLLSALQYLYE------------KFIYCDTDSIHLEGAETPK-------------LPKDMIDPKELGKWDHEGEFIK 515 (630)
T ss_pred HHHHHHHHHHHhhc------------cEEEECCceEEEecCcccc-------------CchhhCChhHhcceeccceeeE
Confidence 99999999998876 2999999999999765321 111111223 3489999999
Q ss_pred ceecccceeEEEeccCCCCccceeEeeee
Q 001780 718 YLLISKKRYAGLYWTNPEKFDKMDTKGIE 746 (1014)
Q Consensus 718 ~ll~~KKRYagl~~~~~~~~~k~~~KGie 746 (1014)
.+++++|+|+.+..+.. ....+++||++
T Consensus 516 ~~fl~~K~Y~l~~~d~~-~~i~ik~KGi~ 543 (630)
T PHA02563 516 AKYLRPKKYALYAEEVN-GKLKIKCAGMP 543 (630)
T ss_pred EEEEeccEEEEEecCCC-ceEEEEeCCCC
Confidence 99999999966554432 23358889994
No 34
>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=99.84 E-value=4.7e-21 Score=200.14 Aligned_cols=122 Identities=29% Similarity=0.539 Sum_probs=97.4
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHH
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIRE 379 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~ 379 (1014)
|+||+|+|||||++..| ||+|+.|+|+|||++.. .|.. .++. ..+.+|++||.+|+++|++
T Consensus 1 p~l~~l~fDIEt~~~~g-fp~~~~d~Ii~Is~~~~-~g~~-----~~~~------------~~~~~E~~lL~~F~~~i~~ 61 (188)
T cd05781 1 PDLKTLAFDIEVYSKYG-TPNPRRDPIIVISLATS-NGDV-----EFIL------------AEGLDDRKIIREFVKYVKE 61 (188)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCCEEEEEEEeC-CCCE-----EEEE------------ecCCCHHHHHHHHHHHHHH
Confidence 78999999999998776 99999999999997542 3321 1221 1357999999999999999
Q ss_pred hCCCEEEEecccCCCcccccc-----------------------------------------------------------
Q 001780 380 VDPDVMIGYNICKFDLPYLIE----------------------------------------------------------- 400 (1014)
Q Consensus 380 ~DPDIIiGyNi~~FDlpyL~~----------------------------------------------------------- 400 (1014)
+|||+|+|||+++||||||.+
T Consensus 62 ~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~~L 141 (188)
T cd05781 62 YDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAEYL 141 (188)
T ss_pred cCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHHHH
Confidence 999999999999999999988
Q ss_pred -------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhh
Q 001780 401 -------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKL 441 (1014)
Q Consensus 401 -------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl 441 (1014)
|.++.+.+|.++|. +++.+.+++.||++|+.++++|++++
T Consensus 142 g~~k~~~k~~~~~~~i~~~~~-~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 142 GVMKKSERVLIEWYRIYEYWD-DEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCCccccccCCCHHHHHHHHc-CcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 01233345555664 34478899999999999999998763
No 35
>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=99.80 E-value=1.8e-19 Score=190.42 Aligned_cols=95 Identities=29% Similarity=0.478 Sum_probs=75.7
Q ss_pred CCCCcEEEEEEEEEccCC-CCCCCCCC--CceeEEEEEeeccCccccceeEEEecccc-------CCcCcceEeecCCHH
Q 001780 298 KMAPFRILSFDIECAGRK-GHFPEPTH--DPVIQVANLVTLQGEKQPFIRNVMTLKSC-------APIVGVDVMSFETER 367 (1014)
Q Consensus 298 ~~pplrilSfDIE~~~~~-g~fP~~~~--D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~-------~~~~~~~V~~~~~E~ 367 (1014)
++|+||+|||||||.+.. |.||+|+. |+||+||+. ..+|. +.++.++.. ....+..|..|.+|+
T Consensus 1 ~~P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~-~~~~~-----~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 74 (204)
T cd05783 1 PIPKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA-GSDGL-----KRVLVLKREGVEGLEGLLPEGAEVEFFDSEK 74 (204)
T ss_pred CCCCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc-CCCCC-----cEEEEEecCCcccccccCCCCCeEEecCCHH
Confidence 369999999999999865 77999987 899999953 21221 234444321 123567899999999
Q ss_pred HHHHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 368 DVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 368 eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+||.+|+++++++ |+|+|||+.+||||||.+
T Consensus 75 ~lL~~F~~~i~~~--~~iig~N~~~FDlpyl~~ 105 (204)
T cd05783 75 ELIREAFKIISEY--PIVLTFNGDNFDLPYLYN 105 (204)
T ss_pred HHHHHHHHHHhcC--CEEEEeCCCCcCHHHHHH
Confidence 9999999999977 589999999999999998
No 36
>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=99.80 E-value=1.8e-19 Score=189.83 Aligned_cols=96 Identities=42% Similarity=0.707 Sum_probs=76.7
Q ss_pred EEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEecccc-CCcCcceEeecCCHHHHHHHHHHHHHHhCC
Q 001780 304 ILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSC-APIVGVDVMSFETERDVLLAWRDFIREVDP 382 (1014)
Q Consensus 304 ilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~-~~~~~~~V~~~~~E~eLL~~f~~~i~~~DP 382 (1014)
++||||||++..| ||+|..|+|++||++....|....+.........+ ..+.+..|..+++|++||.+|+++++++||
T Consensus 1 v~~~DIEt~~~~~-~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~~i~~~~v~~~~~E~~lL~~f~~~i~~~dp 79 (199)
T cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREYDP 79 (199)
T ss_pred CccEEEeecCCCC-CcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCCCCCCceEEEeCCHHHHHHHHHHHHHhcCC
Confidence 5899999999766 89999999999998776566543222111111111 135678899999999999999999999999
Q ss_pred CEEEEecccCCCcccccc
Q 001780 383 DVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 383 DIIiGyNi~~FDlpyL~~ 400 (1014)
|||+|||+.+||||||.+
T Consensus 80 diivg~N~~~FD~~~L~~ 97 (199)
T cd05160 80 DILTGYNIDDFDLPYLLK 97 (199)
T ss_pred CEEEEeccCCCcHHHHHH
Confidence 999999999999999988
No 37
>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=99.80 E-value=1.5e-19 Score=191.45 Aligned_cols=85 Identities=36% Similarity=0.528 Sum_probs=68.8
Q ss_pred CCCCcEEEEEEEEEccCCCCC-C--CCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHH
Q 001780 298 KMAPFRILSFDIECAGRKGHF-P--EPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWR 374 (1014)
Q Consensus 298 ~~pplrilSfDIE~~~~~g~f-P--~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~ 374 (1014)
..|+|++|||||||.+..|.| | ++..|+|+|||+... .|. ..++.. .+.+|++||.+|+
T Consensus 5 ~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~-~~~-----~~~~~~------------~~~~E~~lL~~f~ 66 (207)
T cd05785 5 TFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN-RGW-----EEVLHA------------EDAAEKELLEELV 66 (207)
T ss_pred CCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC-CCc-----eeeecc------------CCCCHHHHHHHHH
Confidence 468999999999999988764 4 556799999996432 221 112211 2689999999999
Q ss_pred HHHHHhCCCEEEEecccCCCcccccc
Q 001780 375 DFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 375 ~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
++++++|||||+|||+.+||||||.+
T Consensus 67 ~~i~~~dPdii~g~N~~~FD~pyl~~ 92 (207)
T cd05785 67 AIIRERDPDVIEGHNIFRFDLPYLRR 92 (207)
T ss_pred HHHHHhCCCEEeccCCcccCHHHHHH
Confidence 99999999999999999999999988
No 38
>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=99.77 E-value=8.1e-19 Score=183.76 Aligned_cols=85 Identities=25% Similarity=0.432 Sum_probs=73.4
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHH
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIRE 379 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~ 379 (1014)
|||++|||||||++.. +|++|+... .+ .+.+++++.+++..+..|..|++|++||.+|++++++
T Consensus 1 p~l~~~~fDIE~~~~~---------~i~~i~~~~--~~-----~~~i~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~ 64 (193)
T cd05784 1 PKLKVVSLDIETSMDG---------ELYSIGLYG--EG-----QERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQ 64 (193)
T ss_pred CCccEEEEEeecCCCC---------CEEEEEeec--CC-----CCEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHh
Confidence 7999999999998632 899988422 11 2357888888777788999999999999999999999
Q ss_pred hCCCEEEEecccCCCcccccc
Q 001780 380 VDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 380 ~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|||||+|||+++||||||.+
T Consensus 65 ~dPDvi~g~N~~~FD~~yl~~ 85 (193)
T cd05784 65 YDPDIIIGWNVINFDLRLLQR 85 (193)
T ss_pred hCCCEEEECCCcCcCHHHHHH
Confidence 999999999999999999988
No 39
>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=99.74 E-value=2.8e-18 Score=185.37 Aligned_cols=142 Identities=27% Similarity=0.397 Sum_probs=110.5
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeecc----Ccc--ccceeEEEec----ccc---------CCcCcceE
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQ----GEK--QPFIRNVMTL----KSC---------APIVGVDV 360 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~----g~~--~~~~~~vf~l----~~~---------~~~~~~~V 360 (1014)
|||+++|+.|.|.. .+..++.+|+|||++++.. +.. .++....+++ +.. ....+..|
T Consensus 1 Ppl~v~sls~~T~~----n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v 76 (234)
T cd05776 1 PPLTVMSLSIKTVL----NSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKV 76 (234)
T ss_pred CCeEEEEEEeEEEe----cCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcE
Confidence 89999999999986 2444579999999876542 211 1122222332 211 11245679
Q ss_pred eecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccc----------------------------------------
Q 001780 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE---------------------------------------- 400 (1014)
Q Consensus 361 ~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~---------------------------------------- 400 (1014)
..|++|++||.+|+++|+++|||||+|||+.+||||||++
T Consensus 77 ~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl 156 (234)
T cd05776 77 RIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRL 156 (234)
T ss_pred EEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCch
Confidence 9999999999999999999999999999999999999998
Q ss_pred ------------------------------cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhHh
Q 001780 401 ------------------------------KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFN 446 (1014)
Q Consensus 401 ------------------------------kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~~ 446 (1014)
|.++++.+|.++|.+ ++.+.+++.||++||.++++|+.+|++++.
T Consensus 157 ~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~-~~~l~~l~~y~~~Da~l~~~L~~kl~il~L 231 (234)
T cd05776 157 LCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-SESLLKLLEHTEKDAYLILQLMFKLNILPL 231 (234)
T ss_pred hhccHHHHHHHhCCCCCChHHHHHHHhCcCcccCCHHHHHHHHhC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCcC
Confidence 344555677778875 778999999999999999999999998764
No 40
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=99.56 E-value=4.1e-15 Score=131.59 Aligned_cols=71 Identities=44% Similarity=0.979 Sum_probs=66.5
Q ss_pred cccccccccCc--ccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHcccccCCCCCcccccCCCCCcceeec
Q 001780 926 CIGCKALISNG--TLCSHCKGREAELYCKTVSQVQELEVLFGRLWTQCQECQGSLHQDVLCTSRDCPIFYRRK 996 (1014)
Q Consensus 926 C~~C~~~~~~~--~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~c~~~~cp~~y~r~ 996 (1014)
|+.|+..++.+ ++|++|..++......++.+++..|++|.++|++|++|+|+.+.++.|.|+||||||+|+
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~~~~~~~l~~~~~~~E~~~~~l~~iC~~C~~~~~~~~~C~s~DCpV~Y~R~ 73 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDPQQTIYNLLSRLRELERRFNELWTICQSCSGSLHEEIECDSLDCPVFYERV 73 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCcccCCCCCcceeeC
Confidence 89999998863 999999998887777999999999999999999999999999999999999999999996
No 41
>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=99.32 E-value=3.9e-12 Score=135.24 Aligned_cols=104 Identities=23% Similarity=0.343 Sum_probs=75.7
Q ss_pred CCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccc
Q 001780 318 FPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPY 397 (1014)
Q Consensus 318 fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpy 397 (1014)
|+.+..++|++||++....+. . .. .+. -..+.+|++||.+|+++|++++| +|+|||+.+|||||
T Consensus 45 ~l~~~~~~Iv~Is~~~~~~~~-~-~~----~~~---------~~~~~~E~elL~~F~~~i~~~~p-~lv~yNg~~FDlP~ 108 (208)
T cd05782 45 FLPLPFHKVVSISALYRDDDG-G-FL----KVR---------TLDGADEKELLEDFFQLIEKKNP-RLVSFNGRGFDLPV 108 (208)
T ss_pred CCccccCceEEEEEEEEecCC-C-eE----EEe---------ecCCCCHHHHHHHHHHHHHHhCC-EEEecCCCcCCHHH
Confidence 666778999999976532111 1 11 110 12357999999999999999998 89999999999999
Q ss_pred ccc-----------------------------------------------------------cccccchhHHHhhcCChh
Q 001780 398 LIE-----------------------------------------------------------KEDVHHSIISDLQNGNAE 418 (1014)
Q Consensus 398 L~~-----------------------------------------------------------kedv~~~~i~~l~~~~~~ 418 (1014)
|.. |.+++.++|.++|..+
T Consensus 109 L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG~~~K~d~~G~~v~~~y~~g-- 186 (208)
T cd05782 109 LHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEG-- 186 (208)
T ss_pred HHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCCCCCcCCCHHHHHHHHHcC--
Confidence 987 2233344555555432
Q ss_pred hhhHHhhhhhccccchHHHHh
Q 001780 419 TRRRLAVYCLKDAYLPQRLLD 439 (1014)
Q Consensus 419 ~r~~l~~Y~lkDa~l~~~L~~ 439 (1014)
.+.+++.||.+|+..++.|+.
T Consensus 187 ~~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 187 KLDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred ChHHHHHHHHHHHHHHHHHHh
Confidence 378999999999999998864
No 42
>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=98.59 E-value=1.8e-07 Score=98.52 Aligned_cols=110 Identities=21% Similarity=0.389 Sum_probs=77.0
Q ss_pred CCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccc
Q 001780 318 FPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPY 397 (1014)
Q Consensus 318 fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpy 397 (1014)
|+...--.|++||++....+. .+ .+.+++. ...+|++||..|.+++.+..| .++|||+-+||+||
T Consensus 3 Fl~~~f~kIV~Is~~~~~~~~--~~--~v~s~~~----------~~~~E~~lL~~F~~~~~~~~p-~LVs~NG~~FDlP~ 67 (209)
T PF10108_consen 3 FLPLPFHKIVCISVVYADDDG--QF--KVKSLGG----------PDDDEKELLQDFFDLVEKYNP-QLVSFNGRGFDLPV 67 (209)
T ss_pred CCcccCCCeEEEEEEEEecCC--cE--EEEeccC----------CCCCHHHHHHHHHHHHHhCCC-eEEecCCccCCHHH
Confidence 555556789999977443221 12 2333322 224799999999999999998 67999999999999
Q ss_pred ccc------------------------------------------------------------cccccchhHHHhhcCCh
Q 001780 398 LIE------------------------------------------------------------KEDVHHSIISDLQNGNA 417 (1014)
Q Consensus 398 L~~------------------------------------------------------------kedv~~~~i~~l~~~~~ 417 (1014)
|.. |.+++.+++.+++. .
T Consensus 68 L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPgK~~idGs~V~~~y~--~ 145 (209)
T PF10108_consen 68 LCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPGKDDIDGSQVAELYQ--E 145 (209)
T ss_pred HHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCCCCCCCHHHHHHHHH--c
Confidence 987 22333334444442 1
Q ss_pred hhhhHHhhhhhccccchHHHHhhhhhh
Q 001780 418 ETRRRLAVYCLKDAYLPQRLLDKLMFI 444 (1014)
Q Consensus 418 ~~r~~l~~Y~lkDa~l~~~L~~kl~~~ 444 (1014)
.+..+++.||.+|+.-+..|+-++..+
T Consensus 146 g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 146 GDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 246789999999999999887776543
No 43
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.05 E-value=4.7e-06 Score=85.06 Aligned_cols=116 Identities=27% Similarity=0.412 Sum_probs=64.0
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCE
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDV 384 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDI 384 (1014)
+-|||||++ +.| ..+.|++|+......+....+. . +.. .-++|.+.+.++++.+.+ .|.
T Consensus 1 l~~DIET~G---l~~--~~~~i~liG~~~~~~~~~~~~~-~-~~~------------~~~~ee~~~~~~~~~l~~--~~~ 59 (164)
T PF13482_consen 1 LFFDIETTG---LSP--DNDTIYLIGVADFDDDEIITFI-Q-WFA------------EDPDEEEIILEFFELLDE--ADN 59 (164)
T ss_dssp --EEEEESS----GG---G---EEEEEEE-ETTTTE-EE-E-E-G------------GGHHHHHHHHH--HHHHT--T--
T ss_pred CcEEecCCC---CCC--CCCCEEEEEEEEeCCCceEEee-H-hhc------------cCcHHHHHHHHHHHHHhc--CCe
Confidence 469999994 444 3466899986543332221111 1 111 123566666665577774 588
Q ss_pred EEEecccCCCccccccc------------------------------------------ccccchhHHHhh-----cCCh
Q 001780 385 MIGYNICKFDLPYLIEK------------------------------------------EDVHHSIISDLQ-----NGNA 417 (1014)
Q Consensus 385 IiGyNi~~FDlpyL~~k------------------------------------------edv~~~~i~~l~-----~~~~ 417 (1014)
++|||+.+||+|+|..+ +++..+....+| .|++
T Consensus 60 iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~~~~~Lk~ve~~lg~~~~~~~~~G~~~~~~~~~~~~~~~~ 139 (164)
T PF13482_consen 60 IVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFLESYSLKNVEKFLGIERRDDDISGSESVKLYKEYLETGDP 139 (164)
T ss_dssp EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTSCCTT--SHHH-----------HHHHHHHHHH---TTGGT
T ss_pred EEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccCCCCCHHHHhhhcccccccCCCCHHHHHHHHHHHHhcCCH
Confidence 99999999999999881 111222222232 2345
Q ss_pred hhhhHHhhhhhccccchHHHHhhh
Q 001780 418 ETRRRLAVYCLKDAYLPQRLLDKL 441 (1014)
Q Consensus 418 ~~r~~l~~Y~lkDa~l~~~L~~kl 441 (1014)
+.+.+++.||.+|+..+.+|.+.|
T Consensus 140 ~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 140 EALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 667899999999999999998876
No 44
>PHA02735 putative DNA polymerase type B; Provisional
Probab=97.88 E-value=0.00011 Score=82.57 Aligned_cols=106 Identities=22% Similarity=0.216 Sum_probs=66.7
Q ss_pred hhHHhhhhhccccchHHHHhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccccCCCcCC----CCC
Q 001780 420 RRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAG----SEQ 495 (1014)
Q Consensus 420 r~~l~~Y~lkDa~l~~~L~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~viP~~~~~~----~~~ 495 (1014)
...++.|.-.||.|+..|...+ +..|.-..+|+.+-++.|- ...+.|-....+ -|...... -.+
T Consensus 203 ~~dilkyak~da~l~~dl~~e~------~n~~e~ldipmgrp~stgy--la~~yl~~~~~e----kp~lg~~~ma~~~wE 270 (716)
T PHA02735 203 FDDILKYAKIDAELTQDLAIEA------TNEAEELDIPMGRPFSTGY--LAAEYLDANLEE----KPGLGNEAMAKLAWE 270 (716)
T ss_pred HHHHHHHHhhhHHHHHHHHHHH------hhhHhhcCCccCCCcccch--hhHHHHhccccc----CCCCChHHHHHHHHH
Confidence 4568899999999999886543 2345555666666555552 112222111111 12211110 124
Q ss_pred CcCCcceeeeccCceEEeeeEeeeccccchHHHHHhCCCcccccC
Q 001780 496 GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVT 540 (1014)
Q Consensus 496 ~~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~ 540 (1014)
.|-||.+---++|=+-. |+.-|.+|+||+||... =.|.|+..
T Consensus 271 -sYyGGrfeV~KrgnvGE-v~~pDINSaYPaim~dl-PDpKTl~W 312 (716)
T PHA02735 271 -SYAGGRFEVFKRGNVGE-VAAPDINSAYPAILADL-PDPKTLNW 312 (716)
T ss_pred -hhcCCceEEeccCccce-eeeccccccchHHHHhC-CCCcccch
Confidence 79999987778888876 99999999999999982 24677644
No 45
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=97.86 E-value=0.00023 Score=82.85 Aligned_cols=256 Identities=15% Similarity=0.233 Sum_probs=158.8
Q ss_pred hhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHH-HHHhhcCccc---cCCCcC-C-CCCC------cC-Ccceeee
Q 001780 439 DKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLL-RKAKQKNLVI---PNVKQA-G-SEQG------TY-EGATVLE 505 (1014)
Q Consensus 439 ~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~-r~a~~~~~vi---P~~~~~-~-~~~~------~y-eGg~Vle 505 (1014)
.--..+...+++||..+||+..+-. -...-+..+++ |..++.|.|+ |+.... + .+.. .. +-..+.-
T Consensus 117 ~~~~wl~~~i~laRY~~IPlgNl~~-D~~~f~~Di~yAR~L~~~~~VLW~S~~~~PDlGG~e~Dd~~~~~~~~~~~~~~i 195 (396)
T PF08490_consen 117 NLGSWLSERIELARYAHIPLGNLPS-DNPLFLIDIFYARRLRKNNHVLWWSPSPRPDLGGKEEDDNRLLWDMDELESPEI 195 (396)
T ss_pred HHHHHHHHHHHHHHHcCCCcccCCc-chHHHHHHHHHHHHHHHCCeEEeCCCCCCCCCCcchhhhhcccccccccCceEE
Confidence 3334566778999999999987622 12222445555 7888899987 332111 1 1110 01 1122233
Q ss_pred ccCceEEeeeEeeecccc-chHHHHHhCCCcccccChhhh-hccCCCCCceee-----CCCCceeeecCCcCCCcHHHHH
Q 001780 506 ARAGFYEKPIATLDFASL-YPSIMMAYNLCYSTLVTPEDA-RKLNLPPECVNK-----TPSGETFVKSNLQKGILPEILE 578 (1014)
Q Consensus 506 P~~G~y~~pV~~LDF~SL-YPSIiia~Nlc~sT~~~~~~~-~~~~~~~~~~~~-----~p~g~~fvk~~~~~Gilp~iL~ 578 (1014)
-.||+|++-.+.||+..| .-+|..+.-|- .-+- +-.+...+.... ...+..|. ...+-+..+
T Consensus 196 n~pG~Y~~vcvEl~i~~LavnaiL~S~~i~------e~EG~~~~~~~~~~~~~~~~~~~~~~~~~~----e~~~~~~~f- 264 (396)
T PF08490_consen 196 NNPGAYRSVCVELDISNLAVNAILQSSLIN------ELEGSDSAGFNFDTASDASNGSANSSSSYD----ESAFCSAAF- 264 (396)
T ss_pred ECCCccceEEEEEEecceeHHHHHHHhHHh------hhcCCccccccccccccccccccccccccc----cccccHHHH-
Confidence 468999997788999887 44444433221 1000 000000000000 00011111 112222222
Q ss_pred HHHHHHHHHHHHhhhcC--ChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhc
Q 001780 579 ELLAARKRAKADLKEAK--DPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKF 656 (1014)
Q Consensus 579 ~Ll~~R~~~K~~mk~~~--d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~ 656 (1014)
--.|.++|.-++... ++.- -.+.+.+|-.+-...+.||++.+...|-..=+..+.+....+..
T Consensus 265 --~iLr~mv~~w~~d~~~~n~~A-----------D~ll~~f~rWl~sp~S~LyDPaL~~~v~~LmkK~flqLl~Ef~r-- 329 (396)
T PF08490_consen 265 --RILRSMVKSWLRDALKGNSFA-----------DSLLQHFYRWLSSPSSLLYDPALHRMVHNLMKKVFLQLLAEFRR-- 329 (396)
T ss_pred --HHHHHHHHHHHHHHhcCCccH-----------HHHHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHHHHHHH--
Confidence 223444444444311 1111 11257799999999999999999999999888888777777765
Q ss_pred cccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhc--CCCceeEEEeeeeccceecccceeEEE
Q 001780 657 TTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGT--FIKPIKLEFEKVYYPYLLISKKRYAGL 729 (1014)
Q Consensus 657 ~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~--~~~pi~Le~Ekvy~~~ll~~KKRYagl 729 (1014)
.|++|||+|-..|.|.++..++++|...++-+.+.|+++ | +-+.|+..+.|..++++-+.+|+|+
T Consensus 330 -------lG~~VVyA~~~riil~T~K~~~~~A~ay~~yi~~~i~~~~lF-~~l~l~~~~~w~~LlwmD~~NygGi 396 (396)
T PF08490_consen 330 -------LGSKVVYADFNRIILCTGKTSLENAYAYVQYILKSIRSRELF-SWLDLKPVRYWDSLLWMDPYNYGGI 396 (396)
T ss_pred -------cCCEEEEEcCCEEEEECCCCCHHHHHHHHHHHHHHHhccccc-ccEEeEHHHHhhhheEecccccCCC
Confidence 499999999999999999999999999999888888874 4 5689999999999999999999884
No 46
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.41 E-value=0.00048 Score=73.17 Aligned_cols=75 Identities=21% Similarity=0.303 Sum_probs=53.1
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCC
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDP 382 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DP 382 (1014)
.++-|||||++-+ +..++|++.+. ...++....+++.|--+ -+.|..+|..|...+ |-
T Consensus 99 ~~~FFDiETTGL~-----~ag~~I~~~g~--a~~~~~~~~Vrq~~lp~------------p~~E~avle~fl~~~---~~ 156 (278)
T COG3359 99 DVAFFDIETTGLD-----RAGNTITLVGG--ARGVDDTMHVRQHFLPA------------PEEEVAVLENFLHDP---DF 156 (278)
T ss_pred ceEEEeeeccccC-----CCCCeEEEEEE--EEccCceEEEEeecCCC------------cchhhHHHHHHhcCC---Cc
Confidence 6889999999743 24577777763 22333333445444322 147999999887765 66
Q ss_pred CEEEEecccCCCccccc
Q 001780 383 DVMIGYNICKFDLPYLI 399 (1014)
Q Consensus 383 DIIiGyNi~~FDlpyL~ 399 (1014)
.+++.||+..||||||.
T Consensus 157 ~~lvsfNGkaFD~Pfik 173 (278)
T COG3359 157 NMLVSFNGKAFDIPFIK 173 (278)
T ss_pred ceEEEecCcccCcHHHH
Confidence 78999999999999998
No 47
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.62 E-value=0.0034 Score=68.21 Aligned_cols=86 Identities=17% Similarity=0.298 Sum_probs=59.0
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccC----------CcCcceEeecCCHHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCA----------PIVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~----------~~~~~~V~~~~~E~eLL~~ 372 (1014)
+++.||+||++. ++..|.||+||++ .. +....+.. . +++.. .|....|...++..+.+.+
T Consensus 3 ~~vv~D~ETTGl-----~~~~d~IIeig~v-~~-~~~~~f~~-l--v~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 3 ALIFYDTETTGT-----QIDKDRIIEIAAY-NG-VTSESFQT-L--VNPEIPIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred cEEEEEeeCCCC-----CCCCCEEEEEEEE-cC-ccccEEEE-E--eCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 588999999973 3567999999974 21 11121221 1 12211 1233456666788999999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++. +.++++|||+..||+++|.+
T Consensus 73 ~~~fi~--~~~~lVaHN~~~FD~~~L~~ 98 (232)
T PRK06309 73 FIEFCG--TDNILVAHNNDAFDFPLLRK 98 (232)
T ss_pred HHHHHc--CCCEEEEeCCHHHHHHHHHH
Confidence 999985 45799999998999999976
No 48
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=96.29 E-value=0.0072 Score=56.46 Aligned_cols=61 Identities=23% Similarity=0.425 Sum_probs=43.9
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCCCE
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDV 384 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DPDI 384 (1014)
++||||+++.. +..++|++|+......+ . .+ +. + |..++++..|.+
T Consensus 1 ~~~DiEt~~~~-----~~~~~i~~i~~~~~~~~--~-----~~-------------~~-~--------f~~~l~~~~~~v 46 (96)
T cd06125 1 IAIDTEATGLD-----GAVHEIIEIALADVNPE--D-----TA-------------VI-D--------LKDILRDKPLAI 46 (96)
T ss_pred CEEEEECCCCC-----CCCCcEEEEEEEEccCC--C-----EE-------------Ee-h--------HHHHHhhCCCCE
Confidence 47999999743 45689999985442111 1 01 01 1 888888888899
Q ss_pred EEEecccCCCcccccc
Q 001780 385 MIGYNICKFDLPYLIE 400 (1014)
Q Consensus 385 IiGyNi~~FDlpyL~~ 400 (1014)
++|||. +||++||.+
T Consensus 47 ~V~hn~-~fD~~fL~~ 61 (96)
T cd06125 47 LVGHNG-SFDLPFLNN 61 (96)
T ss_pred EEEeCc-HHhHHHHHH
Confidence 999999 899999877
No 49
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.04 E-value=0.01 Score=63.92 Aligned_cols=86 Identities=20% Similarity=0.238 Sum_probs=56.1
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCcc--ccceeEEEeccccCC----------cCcceEeecCCHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEK--QPFIRNVMTLKSCAP----------IVGVDVMSFETERDV 369 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~--~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eL 369 (1014)
.+.++||+||++. +|..| ||+|+.+.-..+.. ..|.. .+++..+ |....+...+...+.
T Consensus 7 ~~fvv~D~ETTGl-----~~~~~-IIeIgav~v~~~~~~~~~f~~---li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev 77 (217)
T TIGR00573 7 DTETTGDNETTGL-----YAGHD-IIEIGAVEIINRRITGNKFHT---YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEI 77 (217)
T ss_pred cCEEEEEecCCCC-----CCCCC-EEEEEEEEEECCCEeeeEEEE---EECcCCCCCHHHHhhcCCCHHHHcCCCCHHHH
Confidence 4678999999972 35667 99999775233321 11111 1122111 222334455678899
Q ss_pred HHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 370 LLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 370 L~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+..|.+++. .++++|||. .||+++|..
T Consensus 78 ~~~~~~~~~---~~~lVaHNa-~FD~~fL~~ 104 (217)
T TIGR00573 78 AEDFADYIR---GAELVIHNA-SFDVGFLNY 104 (217)
T ss_pred HHHHHHHhC---CCEEEEecc-HHHHHHHHH
Confidence 999999985 479999997 799999866
No 50
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.00 E-value=0.013 Score=64.42 Aligned_cols=90 Identities=18% Similarity=0.235 Sum_probs=59.2
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVL 370 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL 370 (1014)
+.+.+.||+||++- +|..|.||+||++....+... .....-+++..+ |....|...++..+++
T Consensus 6 ~~~~v~~D~ETTGl-----~~~~d~IIEIa~v~v~~~~~~--~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~ 78 (250)
T PRK06310 6 DTEFVCLDCETTGL-----DVKKDRIIEFAAIRFTFDEVI--DSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVF 78 (250)
T ss_pred CCcEEEEEEeCCCC-----CCCCCeEEEEEEEEEECCeEE--EEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHH
Confidence 35789999999973 456799999997644322111 111111222211 2223455556788999
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+|.+++. +.++++|||+ .||+++|..
T Consensus 79 ~~~~~fl~--~~~~lvghn~-~FD~~~L~~ 105 (250)
T PRK06310 79 PQIKGFFK--EGDYIVGHSV-GFDLQVLSQ 105 (250)
T ss_pred HHHHHHhC--CCCEEEEECH-HHHHHHHHH
Confidence 99999985 3589999996 599999976
No 51
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=95.91 E-value=0.027 Score=57.16 Aligned_cols=86 Identities=24% Similarity=0.354 Sum_probs=56.4
Q ss_pred EEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCc-cccceeEEEeccccCC----------cCcceEeecCCHHHHHHH
Q 001780 304 ILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGE-KQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 304 ilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~-~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~~ 372 (1014)
++.||+||++. ++..++|++||.+....+. ...|.. + +++..+ +....+..-..+.+.+..
T Consensus 2 ~v~~D~Ettg~-----~~~~~~Iieig~v~~~~~~~~~~f~~--~-v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~ 73 (169)
T smart00479 2 LVVIDCETTGL-----DPGKDEIIEIAAVDVDGGRIIVVFDT--Y-VKPDRPITDYATEIHGITPEMLDDAPTFEEVLEE 73 (169)
T ss_pred EEEEEeeCCCC-----CCCCCeEEEEEEEEEECCEeEEEEEE--E-ECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 67999999973 3457899999977644432 111111 1 121111 112233445678899999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++.. .+++|||...||+.+|..
T Consensus 74 ~~~~l~~---~~~v~~n~~~fD~~~L~~ 98 (169)
T smart00479 74 LLEFLKG---KILVAGNALNFDLRFLKL 98 (169)
T ss_pred HHHHhcC---CEEEEeCCHHHhHHHHHH
Confidence 9998864 578899998999999877
No 52
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=95.90 E-value=0.021 Score=59.42 Aligned_cols=92 Identities=15% Similarity=0.216 Sum_probs=50.4
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccc-----------cceeEEEeccccCCc----------CcceEeec
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQ-----------PFIRNVMTLKSCAPI----------VGVDVMSF 363 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~-----------~~~~~vf~l~~~~~~----------~~~~V~~~ 363 (1014)
..||+||++. +.+.+|+||.||.+.-..|... ...+.-+-+++..++ .+..+..-
T Consensus 2 vv~D~ETTGl----~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~ 77 (177)
T cd06136 2 VFLDLETTGL----PKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHK 77 (177)
T ss_pred eEEeeecCCC----CCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcC
Confidence 5799999973 2256899999997643222100 000001112222111 11122221
Q ss_pred CC-HHHHHHHHHHHHHHhC-CCEEEEecccCCCcccccc
Q 001780 364 ET-ERDVLLAWRDFIREVD-PDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 364 ~~-E~eLL~~f~~~i~~~D-PDIIiGyNi~~FDlpyL~~ 400 (1014)
.. +.++...+.+|+...+ +.+++|||...||+++|..
T Consensus 78 ~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~ 116 (177)
T cd06136 78 APFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRS 116 (177)
T ss_pred CCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHH
Confidence 21 2245555666666554 5699999998999999865
No 53
>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=95.84 E-value=0.014 Score=60.94 Aligned_cols=89 Identities=22% Similarity=0.331 Sum_probs=55.6
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccc--cceeEEEeccc-cC---------CcCcceEee-cCCHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQ--PFIRNVMTLKS-CA---------PIVGVDVMS-FETERDVLL 371 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~--~~~~~vf~l~~-~~---------~~~~~~V~~-~~~E~eLL~ 371 (1014)
+-||+||++. +|..|+||+||.+....+... .+.. ...... .. .|....+.. -.++.++|.
T Consensus 1 ~~~D~ETTGl-----~~~~d~Iieig~v~v~~~~~~~~~~~~-~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGL-----NPSFDQILQFAAIRTDENFNEIEPFNI-FCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCC-----CCCCCceEEEEEEEECCCCCCccceeE-EEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 3589999973 346799999998644322111 1111 111111 00 112223444 467889999
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|..++.+ ..++++|||...||+.+|..
T Consensus 75 ~~~~~~~~-~~~~lVahn~~~FD~~fL~~ 102 (183)
T cd06138 75 KIHRLFNT-PGTCIVGYNNIRFDDEFLRF 102 (183)
T ss_pred HHHHHHcc-CCCcEEeeCchhhHHHHHHH
Confidence 99999874 34689999988899999865
No 54
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.77 E-value=0.019 Score=60.97 Aligned_cols=91 Identities=20% Similarity=0.291 Sum_probs=57.9
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC-------c---CcceEeecCCHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP-------I---VGVDVMSFETERDVL 370 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~-------~---~~~~V~~~~~E~eLL 370 (1014)
+-+.+++|+||++. +|..|+||+|+++....+........-+.+++..+ + ....+..-.++.+.+
T Consensus 28 ~~~~vviD~ETTGl-----~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl 102 (202)
T PRK09145 28 PDEWVALDCETTGL-----DPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEAL 102 (202)
T ss_pred CCCEEEEEeECCCC-----CCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHH
Confidence 34789999999963 45679999999865443321100000011222111 1 122344556889999
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+|.+++. ..+++|||. .||+.+|..
T Consensus 103 ~~~~~~i~---~~~lv~hn~-~fD~~fL~~ 128 (202)
T PRK09145 103 RQLLAFIG---NRPLVGYYL-EFDVAMLNR 128 (202)
T ss_pred HHHHHHHc---CCeEEEeCH-HHHHHHHHH
Confidence 99999986 468999996 699999865
No 55
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.76 E-value=0.018 Score=63.58 Aligned_cols=91 Identities=22% Similarity=0.318 Sum_probs=58.7
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccc-cceeEEEec--c-ccC---CcCcceEeecCCHHHHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQ-PFIRNVMTL--K-SCA---PIVGVDVMSFETERDVLLAW 373 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~-~~~~~vf~l--~-~~~---~~~~~~V~~~~~E~eLL~~f 373 (1014)
..+.+.||+||++ ++|..|+||.||++.-..|... .|...+.+- . .+. .+....+...++..+.+.+|
T Consensus 67 ~~~~vv~DiETTG-----~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 67 DQVFCFVDIETNG-----SKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CCCEEEEEEeCCC-----CCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 4478899999997 2456789999997754444211 111111110 0 000 11223345567889999999
Q ss_pred HHHHHHhCCCEEEEecccCCCcccccc
Q 001780 374 RDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 374 ~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+++. -++++|||. +||+.+|-.
T Consensus 142 ~~fl~---~~v~VaHNa-~FD~~fL~~ 164 (257)
T PRK08517 142 RLFLG---DSVFVAHNV-NFDYNFISR 164 (257)
T ss_pred HHHHC---CCeEEEECH-HHHHHHHHH
Confidence 99986 478999998 799999865
No 56
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=95.69 E-value=0.022 Score=62.27 Aligned_cols=89 Identities=21% Similarity=0.248 Sum_probs=57.4
Q ss_pred CCcEEEEEEEEEccCCCCCCCCC-CCceeEEEEEeeccCcc--ccceeEEEeccccCC----------cCcceEeecCCH
Q 001780 300 APFRILSFDIECAGRKGHFPEPT-HDPVIQVANLVTLQGEK--QPFIRNVMTLKSCAP----------IVGVDVMSFETE 366 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~-~D~Ii~Is~~v~~~g~~--~~~~~~vf~l~~~~~----------~~~~~V~~~~~E 366 (1014)
++++.+.||+||++- +|. .|.||.|+++.-..+.. ..|. ..+++..+ |....+..-+..
T Consensus 2 ~~~r~vvlDtETTGl-----dp~~~drIIEIGaV~v~~~~~~~~~f~---~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f 73 (240)
T PRK05711 2 AIMRQIVLDTETTGL-----NQREGHRIIEIGAVELINRRLTGRNFH---VYIKPDRLVDPEALAVHGITDEFLADKPTF 73 (240)
T ss_pred CCCeEEEEEeeCCCc-----CCCCCCeEEEEEEEEEECCEEeccEEE---EEECcCCcCCHHHhhhcCCCHHHHcCCCCH
Confidence 467999999999973 344 79999999864332211 1111 11222211 122234445677
Q ss_pred HHHHHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 367 RDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 367 ~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+++..|.+|+.. ..++|||. .||+++|..
T Consensus 74 ~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~ 103 (240)
T PRK05711 74 AEVADEFLDFIRG---AELIIHNA-PFDIGFMDY 103 (240)
T ss_pred HHHHHHHHHHhCC---CEEEEEcc-HHhHHHHHH
Confidence 8999999999863 46899998 699999854
No 57
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=95.57 E-value=0.021 Score=57.40 Aligned_cols=83 Identities=17% Similarity=0.177 Sum_probs=51.1
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC-------cC---cceEeecCCHHHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP-------IV---GVDVMSFETERDVLLAWR 374 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~-------~~---~~~V~~~~~E~eLL~~f~ 374 (1014)
.++|+||++ | ..|+|++|+.+.-..|... .+.-+-+++..+ +. ...+..-....+.+.+|.
T Consensus 2 v~~D~Ettg-----~--~~~~ii~ig~v~~~~~~~~--~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~ 72 (156)
T cd06130 2 VAIDFETAN-----A--DRASACSIGLVKVRDGQIV--DTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIK 72 (156)
T ss_pred EEEEEeCCC-----C--CCCceEEEEEEEEECCEEE--EEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHH
Confidence 579999995 2 2578999997654444221 111011111111 11 122333445678899999
Q ss_pred HHHHHhCCCEEEEecccCCCcccccc
Q 001780 375 DFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 375 ~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+++.. ++++|||. .||+.+|..
T Consensus 73 ~~l~~---~~lv~hn~-~fD~~~l~~ 94 (156)
T cd06130 73 PFLGG---SLVVAHNA-SFDRSVLRA 94 (156)
T ss_pred HHhCC---CEEEEeCh-HHhHHHHHH
Confidence 99874 79999997 799999865
No 58
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=95.55 E-value=0.0079 Score=63.28 Aligned_cols=60 Identities=22% Similarity=0.473 Sum_probs=39.3
Q ss_pred cccccccccccccc--C------------cccCCcCCCChH--HHHHHHHHHHHHHHHHHHHHHHHccc--ccCCCCC
Q 001780 921 KRQLSCIGCKALIS--N------------GTLCSHCKGREA--ELYCKTVSQVQELEVLFGRLWTQCQE--CQGSLHQ 980 (1014)
Q Consensus 921 ~~~~~C~~C~~~~~--~------------~~~C~~C~~~~~--~~~~~~~~~~~~~~~~~~~~~~~C~~--C~~~~~~ 980 (1014)
+...+|+.|++... + +..|++|....+ .+..++...+|.+.++|+..|.+|.. |....++
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR~~i~~YY~gwl~Cdd~~C~~~TR~ 93 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIREHISRYYEGWLVCDDPTCGNRTRQ 93 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--HHHHHHHHHHHHHHHHHHHHH--CCCCTCCCHHCCCS
T ss_pred ceEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCceeCcccccCcccc
Confidence 56789999998641 1 578999998766 45566677899999999999999987 9866554
No 59
>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=95.46 E-value=0.027 Score=58.40 Aligned_cols=89 Identities=17% Similarity=0.237 Sum_probs=55.4
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccce-eEEEeccccC-----------------CcCcceEeecCCH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFI-RNVMTLKSCA-----------------PIVGVDVMSFETE 366 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~-~~vf~l~~~~-----------------~~~~~~V~~~~~E 366 (1014)
+.||+||++. +|..|+||+|+.+... +...... ..-..++... .+.+..+..-.++
T Consensus 2 v~iD~ETTGl-----~p~~d~IieIgaV~~~-~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~ 75 (173)
T cd06135 2 VWIDLEMTGL-----DPEKDRILEIACIITD-GDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTL 75 (173)
T ss_pred EEEEEecCCC-----CCCCCeeEEEEEEEEe-CCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCH
Confidence 5799999973 3567999999987543 3211110 0001111110 1111234455678
Q ss_pred HHHHHHHHHHHHHh---CCCEEEEecccCCCcccccc
Q 001780 367 RDVLLAWRDFIREV---DPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 367 ~eLL~~f~~~i~~~---DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+.+..|.+|+... +-.+++|+| ..||+.+|..
T Consensus 76 ~~vl~~~~~f~~~~~~~~~~~lvgh~-~~FD~~fL~~ 111 (173)
T cd06135 76 AQAEAELLEFIKKYVPKGKSPLAGNS-VHQDRRFLDK 111 (173)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecc-hhhCHHHHHH
Confidence 99999999999863 445788877 4799999865
No 60
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=95.42 E-value=0.019 Score=57.11 Aligned_cols=84 Identities=25% Similarity=0.448 Sum_probs=52.4
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccC-c-cccceeEEEeccccCC-------c---CcceEeecCCHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQG-E-KQPFIRNVMTLKSCAP-------I---VGVDVMSFETERDVLLA 372 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g-~-~~~~~~~vf~l~~~~~-------~---~~~~V~~~~~E~eLL~~ 372 (1014)
+.+|+||++. +|..++|++||.+....+ . ...+.. + +.+... + ....+..-....+.+.+
T Consensus 1 v~~D~Ettg~-----~~~~~~iiei~~v~~~~~~~~~~~~~~--~-i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~ 72 (159)
T cd06127 1 VVFDTETTGL-----DPKKDRIIEIGAVKVDGGIEIVERFET--L-VNPGRPIPPEATAIHGITDEMLADAPPFEEVLPE 72 (159)
T ss_pred CeEEeeCCCc-----CCCCCeEEEEEEEEEECCcChhhhhhe--e-eCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHH
Confidence 3689999873 346789999997765433 1 111111 1 111111 1 11122333466788888
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++.. ++++|||+ .||+++|..
T Consensus 73 ~~~~l~~---~~~v~~n~-~fD~~~l~~ 96 (159)
T cd06127 73 FLEFLGG---RVLVAHNA-SFDLRFLNR 96 (159)
T ss_pred HHHHHCC---CEEEEeCc-HhhHHHHHH
Confidence 8888875 89999998 899998876
No 61
>PRK07740 hypothetical protein; Provisional
Probab=95.39 E-value=0.034 Score=61.00 Aligned_cols=91 Identities=23% Similarity=0.347 Sum_probs=58.9
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEE-EeccccCC----------cCcceEeecCCHHH
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNV-MTLKSCAP----------IVGVDVMSFETERD 368 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~v-f~l~~~~~----------~~~~~V~~~~~E~e 368 (1014)
...+++.||+||++ ..|+ ..|+||+|+++....+.. ..... ..+.+..+ |....+.......+
T Consensus 57 ~~~~~vv~D~ETTG---l~p~-~~deIIeIgaV~~~~~~i--~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~e 130 (244)
T PRK07740 57 TDLPFVVFDLETTG---FSPQ-QGDEILSIGAVKTKGGEV--ETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAE 130 (244)
T ss_pred cCCCEEEEEEeCCC---CCCC-CCCeEEEEEEEEEECCEE--EEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHH
Confidence 46679999999986 2332 238999999876544321 01111 11222111 12234555678899
Q ss_pred HHHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 369 VLLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 369 LL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+.+|.+++. -++++|||+ .||+.+|..
T Consensus 131 vl~~f~~fi~---~~~lVahna-~fD~~fL~~ 158 (244)
T PRK07740 131 VLHRFYAFIG---AGVLVAHHA-GHDKAFLRH 158 (244)
T ss_pred HHHHHHHHhC---CCEEEEeCH-HHHHHHHHH
Confidence 9999999875 479999996 799998865
No 62
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.36 E-value=0.031 Score=61.10 Aligned_cols=91 Identities=11% Similarity=0.141 Sum_probs=57.8
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVL 370 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL 370 (1014)
....+.||+||++- +|..|+||+|+.+.-..|.-.........+++..+ |....+..-++..+.+
T Consensus 46 ~~~~vviD~ETTGl-----~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl 120 (239)
T PRK09146 46 EVPFVALDFETTGL-----DAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERIL 120 (239)
T ss_pred cCCEEEEEeECCCC-----CCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHH
Confidence 56899999999973 34689999999765433321000000111222111 2223344455778899
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+|.+++. .++++|||. .||+.+|..
T Consensus 121 ~~l~~~~~---~~~lVaHna-~FD~~fL~~ 146 (239)
T PRK09146 121 DELLEALA---GKVVVVHYR-RIERDFLDQ 146 (239)
T ss_pred HHHHHHhC---CCEEEEECH-HHHHHHHHH
Confidence 99988874 589999996 599999866
No 63
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=95.35 E-value=0.046 Score=59.45 Aligned_cols=92 Identities=23% Similarity=0.273 Sum_probs=57.4
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec-cCccccceeEEEeccccCCc-------Cc---ceEee-cCCHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL-QGEKQPFIRNVMTLKSCAPI-------VG---VDVMS-FETERD 368 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~-~g~~~~~~~~vf~l~~~~~~-------~~---~~V~~-~~~E~e 368 (1014)
..++++||+||++- +|..|+||+|+.+.-. +|... ...-.-+++..++ .| ..+.. -..+.+
T Consensus 5 ~~~~vv~D~ETTGl-----~p~~d~Iieig~v~v~~~g~~~--~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~ 77 (232)
T PRK07942 5 PGPLAAFDLETTGV-----DPETARIVTAALVVVDADGEVV--ESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAE 77 (232)
T ss_pred cCcEEEEEeccCCC-----CCCCCeeEEEEEEEEeCCCccc--cceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHH
Confidence 45789999999973 4677999999976433 24321 1111122222222 11 11211 123467
Q ss_pred HHHHHHHHHHHh--CCCEEEEecccCCCcccccc
Q 001780 369 VLLAWRDFIREV--DPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 369 LL~~f~~~i~~~--DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|..|..++... +-.+++|||. .||+.+|..
T Consensus 78 vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~ 110 (232)
T PRK07942 78 VLAEIADALREAWARGVPVVVFNA-PYDLTVLDR 110 (232)
T ss_pred HHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHH
Confidence 899999988753 4679999998 699999866
No 64
>PRK05359 oligoribonuclease; Provisional
Probab=95.34 E-value=0.041 Score=57.57 Aligned_cols=91 Identities=19% Similarity=0.284 Sum_probs=56.6
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccce-eEEEeccc-----------c------CCcCcceEeecC
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFI-RNVMTLKS-----------C------APIVGVDVMSFE 364 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~-~~vf~l~~-----------~------~~~~~~~V~~~~ 364 (1014)
+.+.+|+||++- +|..|.|+.||++....+- .... ...+.+.. + ..+....+..-.
T Consensus 4 ~~vvlD~ETTGL-----dp~~d~IieIgaV~~~~~~-~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~ 77 (181)
T PRK05359 4 NLIWIDLEMTGL-----DPERDRIIEIATIVTDADL-NILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTV 77 (181)
T ss_pred cEEEEEeecCCC-----CCCCCeEEEEEEEEEcCCc-eEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCC
Confidence 578999999973 4578999999988653321 1110 00111110 0 012222333445
Q ss_pred CHHHHHHHHHHHHHHhC---CCEEEEecccCCCcccccc
Q 001780 365 TERDVLLAWRDFIREVD---PDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 365 ~E~eLL~~f~~~i~~~D---PDIIiGyNi~~FDlpyL~~ 400 (1014)
++.+.+..|++|+...- -.+++|+|+ .||+.||..
T Consensus 78 ~~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~ 115 (181)
T PRK05359 78 SEAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLAR 115 (181)
T ss_pred CHHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHH
Confidence 78999999999997642 245788775 699999866
No 65
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=95.26 E-value=0.033 Score=63.28 Aligned_cols=89 Identities=27% Similarity=0.383 Sum_probs=57.8
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVL 370 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL 370 (1014)
|...+.||+||++- +|..|+||+||++.-..|... .+...-+++..+ +....+...+...+.+
T Consensus 7 ~~~~Vv~DlETTGl-----~p~~~eIIEIgaV~v~~g~i~--~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl 79 (313)
T PRK06807 7 PLDYVVIDFETTGF-----NPYNDKIIQVAAVKYRNHELV--DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVL 79 (313)
T ss_pred CCCEEEEEEECCCC-----CCCCCeEEEEEEEEEECCEEE--EEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHH
Confidence 34789999999752 346789999997654333211 110111222111 1222344556889999
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
..|.+++. -++++|||+ .||+++|..
T Consensus 80 ~~f~~fl~---~~~lVaHNa-~FD~~fL~~ 105 (313)
T PRK06807 80 PLFLAFLH---TNVIVAHNA-SFDMRFLKS 105 (313)
T ss_pred HHHHHHHc---CCeEEEEcH-HHHHHHHHH
Confidence 99999985 567999998 899999876
No 66
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.18 E-value=0.047 Score=62.06 Aligned_cols=89 Identities=19% Similarity=0.246 Sum_probs=57.1
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec-cCccccceeEEEeccccC--------CcCcceEeecCCHHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL-QGEKQPFIRNVMTLKSCA--------PIVGVDVMSFETERDVLL 371 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~-~g~~~~~~~~vf~l~~~~--------~~~~~~V~~~~~E~eLL~ 371 (1014)
|...++||+||++. +|..|.||+|+.+... .|... .....-+++.. .|....|...+.-.+.+.
T Consensus 14 ~~~fvvlD~ETTGl-----~p~~d~IIeIgav~v~~~g~i~--~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~ 86 (313)
T PRK06063 14 PRGWAVVDVETSGF-----RPGQARIISLAVLGLDADGNVE--QSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAG 86 (313)
T ss_pred CCCEEEEEEECCCC-----CCCCCEEEEEEEEEEECCceee--eEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHH
Confidence 46789999999973 4567999999976542 34211 11011112111 112223444456688889
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|.+++. -++++|||. .||+.+|..
T Consensus 87 ~l~~~l~---~~~lVaHNa-~FD~~fL~~ 111 (313)
T PRK06063 87 EVAELLR---GRTLVAHNV-AFDYSFLAA 111 (313)
T ss_pred HHHHHcC---CCEEEEeCH-HHHHHHHHH
Confidence 8888875 579999997 799999865
No 67
>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=95.06 E-value=0.054 Score=55.37 Aligned_cols=86 Identities=16% Similarity=0.215 Sum_probs=53.0
Q ss_pred EEEEEEEccCCCCCCCC-CCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEP-THDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLLAW 373 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~-~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~~f 373 (1014)
+.||+||++. +| ..|.||+|+.+.-..+.... ....+.+++..+ |....+.......+.+..|
T Consensus 2 v~~D~ETTGl-----~~~~~~~iieig~v~v~~~~~~~-~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l 75 (167)
T cd06131 2 IVLDTETTGL-----DPREGHRIIEIGCVELINRRLTG-NTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEF 75 (167)
T ss_pred EEEEeeCCCC-----CCCCCCeEEEEEEEEEECCcEec-cEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHH
Confidence 5799999973 34 56899999976433332110 011111222211 1222344456778999999
Q ss_pred HHHHHHhCCCEEEEecccCCCcccccc
Q 001780 374 RDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 374 ~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+++.. .+++|||+ .||+.+|..
T Consensus 76 ~~~l~~---~~lv~hn~-~fD~~~l~~ 98 (167)
T cd06131 76 LDFIRG---AELVIHNA-SFDVGFLNA 98 (167)
T ss_pred HHHHCC---CeEEEeCh-HHhHHHHHH
Confidence 998764 56899998 699998754
No 68
>PRK05168 ribonuclease T; Provisional
Probab=94.94 E-value=0.086 Score=56.52 Aligned_cols=92 Identities=22% Similarity=0.374 Sum_probs=54.3
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec---cCcc---ccceeEEEeccc--cCC-------cCcce----E
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL---QGEK---QPFIRNVMTLKS--CAP-------IVGVD----V 360 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~---~g~~---~~~~~~vf~l~~--~~~-------~~~~~----V 360 (1014)
-.+..++||+||++. +|..|.||+||.+.-. +|.- ..|.. -+++ ..+ +.|.. +
T Consensus 15 ~~~~~vv~D~ETTGl-----~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~---lv~P~~~~~i~~~~~~ihGIt~e~~~ 86 (211)
T PRK05168 15 RGFLPVVIDVETAGF-----NAKTDALLEIAAVTLKMDEQGWLYPDETLHF---HVEPFEGANLEPEALAFNGIDPDNPL 86 (211)
T ss_pred cCCceEEEEeeCCCC-----CCCCCEEEEEeEEEEEecCCCcEeccceEEE---EECCCCCCCCCHHHHhhcCCCchhhh
Confidence 356789999999973 4567999999976432 2211 11111 1221 111 11211 1
Q ss_pred eecCCHHHHHHHHHHHHHHh------CCCEEEEecccCCCcccccc
Q 001780 361 MSFETERDVLLAWRDFIREV------DPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 361 ~~~~~E~eLL~~f~~~i~~~------DPDIIiGyNi~~FDlpyL~~ 400 (1014)
..-..+.+.+.+|++++.+. +=.+++|||. .||+.+|..
T Consensus 87 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~ 131 (211)
T PRK05168 87 RGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMA 131 (211)
T ss_pred hcCCChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHH
Confidence 11235666777777777642 1258999998 699999865
No 69
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=94.80 E-value=0.079 Score=56.13 Aligned_cols=89 Identities=27% Similarity=0.340 Sum_probs=56.2
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccc-cceeEEEeccc----cC---CcCcceEeecCCHHHHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQ-PFIRNVMTLKS----CA---PIVGVDVMSFETERDVLLAWR 374 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~-~~~~~vf~l~~----~~---~~~~~~V~~~~~E~eLL~~f~ 374 (1014)
+.++||+||++.+ ..|+||+||.+.-..|... .|...+-+-.+ +. .|....|..-++-.+.|.+|.
T Consensus 6 ~~vvlD~EtTGl~------~~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~ 79 (195)
T PRK07247 6 TYIAFDLEFNTVN------GVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79 (195)
T ss_pred eEEEEEeeCCCCC------CCCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHH
Confidence 6789999998632 2578999997654444211 11111100000 11 122334555567889999999
Q ss_pred HHHHHhCCCEEEEecccCCCcccccc
Q 001780 375 DFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 375 ~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+|+. ..+++|||...||+.+|..
T Consensus 80 ~f~~---~~~lVaHNa~~fD~~fL~~ 102 (195)
T PRK07247 80 EFVG---ELPLIGYNAQKSDLPILAE 102 (195)
T ss_pred HHHC---CCeEEEEeCcHhHHHHHHH
Confidence 9986 4579999999999999854
No 70
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=94.66 E-value=0.0054 Score=73.33 Aligned_cols=45 Identities=27% Similarity=0.423 Sum_probs=30.8
Q ss_pred CcCCCcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccc
Q 001780 568 LQKGILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGAT 624 (1014)
Q Consensus 568 ~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~ 624 (1014)
.+.|++++-++.+.+.|...|+..... +.-.|+++||.||=+|-.
T Consensus 329 ~~~~~F~~~i~~~~~~k~~~k~~~~~~------------~~i~KL~lNSlyGkf~~~ 373 (459)
T PF03175_consen 329 EKGGLFKEYIDKLYELKKNAKKKADKE------------KSIAKLLLNSLYGKFGQN 373 (459)
T ss_dssp EES-TTHHHHHHHHHHHHH--HHHHH---------------HHHHHHHHHHHHHS--
T ss_pred cccCchHHHHHHHHHhhhhhccCCchh------------HHHHHHHHhhhhhhhccC
Confidence 357899999999999998887654321 146799999999998854
No 71
>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=94.62 E-value=0.077 Score=57.49 Aligned_cols=86 Identities=15% Similarity=0.227 Sum_probs=54.0
Q ss_pred EEEEEEEEEccCCCCCCCCC-CCceeEEEEEeeccCcc--ccceeEEEeccccCCc----------CcceEeecCCHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPT-HDPVIQVANLVTLQGEK--QPFIRNVMTLKSCAPI----------VGVDVMSFETERDV 369 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~-~D~Ii~Is~~v~~~g~~--~~~~~~vf~l~~~~~~----------~~~~V~~~~~E~eL 369 (1014)
|.+.||+||++. +|. .|.||.|+++.-..+.. ..|.. -+++..++ ....+..-+...+.
T Consensus 1 r~vvlD~ETTGl-----~p~~~d~IIEIgav~~~~~~~~~~~f~~---~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev 72 (225)
T TIGR01406 1 RQIILDTETTGL-----DPKGGHRIVEIGAVELVNRMLTGDNFHV---YVNPERDMPAEAAKVHGITDEFLADKPKFKEI 72 (225)
T ss_pred CEEEEEeeCCCc-----CCCCCCeEEEEEEEEEECCcEecceEEE---EECcCCCCCHHHHhccCCCHHHHhCCCCHHHH
Confidence 568999999972 344 48999999863222211 11111 12222111 12233344677899
Q ss_pred HHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 370 LLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 370 L~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+.+|.+|+.. ..++|||. .||+.+|..
T Consensus 73 ~~~f~~fi~~---~~lVaHNa-~FD~~fL~~ 99 (225)
T TIGR01406 73 ADEFLDFIGG---SELVIHNA-AFDVGFLNY 99 (225)
T ss_pred HHHHHHHhCC---CEEEEEec-HHHHHHHHH
Confidence 9999999863 57899998 699999865
No 72
>PRK07883 hypothetical protein; Validated
Probab=94.60 E-value=0.062 Score=65.77 Aligned_cols=89 Identities=22% Similarity=0.343 Sum_probs=59.6
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHH
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVL 370 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL 370 (1014)
..+.+.||+||++. +|..|+|++|+.+....|... .+...-+++..+ |....+.....+.+.+
T Consensus 14 ~~~~Vv~D~ETTGl-----~p~~~~IIEIgaV~v~~g~iv--~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl 86 (557)
T PRK07883 14 DVTFVVVDLETTGG-----SPAGDAITEIGAVKVRGGEVL--GEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVL 86 (557)
T ss_pred CCCEEEEEEecCCC-----CCCCCeEEEEEEEEEECCEEE--EEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHH
Confidence 45789999999973 456799999997654433211 111111122111 2223445557889999
Q ss_pred HHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 371 LAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 371 ~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
..|.+|+. .++++|||. .||+++|..
T Consensus 87 ~~f~~fl~---~~~lVaHNa-~FD~~fL~~ 112 (557)
T PRK07883 87 PAFLEFAR---GAVLVAHNA-PFDIGFLRA 112 (557)
T ss_pred HHHHHHhc---CCEEEEeCc-HHHHHHHHH
Confidence 99999986 589999998 699999876
No 73
>PRK11779 sbcB exonuclease I; Provisional
Probab=94.19 E-value=0.14 Score=61.40 Aligned_cols=93 Identities=18% Similarity=0.157 Sum_probs=58.0
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCcc---ccceeEEEecccc--C---------CcCcceEee-cC
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEK---QPFIRNVMTLKSC--A---------PIVGVDVMS-FE 364 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~---~~~~~~vf~l~~~--~---------~~~~~~V~~-~~ 364 (1014)
...+.+.||+||++. +|..|.||+||.+....+.. .++. .++-... . .|....+.. -.
T Consensus 4 ~~~~fvv~D~ETTGL-----dP~~DrIIeiAaVrvd~~~~~i~e~~~--~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~ 76 (476)
T PRK11779 4 MQPTFLWHDYETFGA-----NPALDRPAQFAGIRTDADLNIIGEPLV--FYCKPADDYLPSPEAVLITGITPQEALEKGL 76 (476)
T ss_pred CCCcEEEEEEECCCC-----CCCCCeeEEEEEEEEeCCCceecceeE--EEEcCCcCcCCCHHHHHHhCCCHHHHHhcCC
Confidence 356799999999973 46789999999875433211 1111 1111110 0 011112211 23
Q ss_pred CHHHHHHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 365 TERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 365 ~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+|.+++..+.+++.. ...+++|||...||+.+|..
T Consensus 77 ~e~e~~~~i~~~l~~-~~~~lVGhNni~FD~eflr~ 111 (476)
T PRK11779 77 PEAEFAARIHAEFSQ-PGTCILGYNNIRFDDEVTRY 111 (476)
T ss_pred CHHHHHHHHHHHHhc-CCCEEEEeCchhhcHHHHHH
Confidence 688999999999863 23689999999999987755
No 74
>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=94.19 E-value=0.12 Score=68.23 Aligned_cols=88 Identities=22% Similarity=0.384 Sum_probs=60.4
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLL 371 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~ 371 (1014)
-+.++||+||++. +|..|.||+|+++.-..|.. ..+.-+-+++..+ |....+....++.+.|.
T Consensus 190 ~~~VVfDiETTGL-----~~~~d~IIEIGAVkv~~g~i--id~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~ 262 (1213)
T TIGR01405 190 ATYVVFDIETTGL-----SPQYDEIIEFGAVKVKNGRI--IDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLE 262 (1213)
T ss_pred CcEEEEEeEecCC-----CCCCCeEEEEEEEEEECCeE--EEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHH
Confidence 3789999999962 35689999999876544421 1111111222211 22233455678999999
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+|.+|+. ..+++||| ..||+++|..
T Consensus 263 ~f~~fl~---~~iLVaHN-a~FD~~fL~~ 287 (1213)
T TIGR01405 263 KFKEFFK---DSILVAHN-ASFDIGFLNT 287 (1213)
T ss_pred HHHHHhC---CCeEEEEC-hHHHHHHHHH
Confidence 9999986 47999999 7899999987
No 75
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=94.15 E-value=0.33 Score=62.77 Aligned_cols=249 Identities=17% Similarity=0.245 Sum_probs=146.1
Q ss_pred HhhhhhhHhHHHHHHHhCcCcchhcccccHHHHHHHHHHHHhhcCccc-------cCCCcCCCC------CCcCCcceee
Q 001780 438 LDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQLLRKAKQKNLVI-------PNVKQAGSE------QGTYEGATVL 504 (1014)
Q Consensus 438 ~~kl~~~~~~~e~arv~g~p~~~vl~rG~~~~v~s~L~r~a~~~~~vi-------P~~~~~~~~------~~~yeGg~Vl 504 (1014)
+.....+...+++||.+++|+..+=..-.++-+--++.|+.++.|.++ |+......+ +-.-.-.+|.
T Consensus 1586 ~a~~~wl~~~i~~SRY~~VPigNl~~D~~~f~iD~~faR~Lrk~~~vLW~s~~~~PDlGGie~d~~~~s~~~~~~s~~~~ 1665 (2173)
T KOG1798|consen 1586 LASGSWLSHRIKLSRYSHVPIGNLPEDWLTFIIDLFFARKLRKHNHVLWWSKNGVPDLGGIENDEMLLSSELQTTSDTVE 1665 (2173)
T ss_pred HhHHHHHHHHHHHHHhcCCcccCCchHHHHHHHHHHHHHHHHhcCeeEEecCCCCCCCCcccchhhhhhHHhcccccchh
Confidence 333345667789999999999865332223333334558888888876 221110000 0011236666
Q ss_pred eccCceEEeeeEeeeccccchHHHHHhCCCcccccChhhhhc------cCC----CCC-ceeeCCCCceeeecCCcCC--
Q 001780 505 EARAGFYEKPIATLDFASLYPSIMMAYNLCYSTLVTPEDARK------LNL----PPE-CVNKTPSGETFVKSNLQKG-- 571 (1014)
Q Consensus 505 eP~~G~y~~pV~~LDF~SLYPSIiia~Nlc~sT~~~~~~~~~------~~~----~~~-~~~~~p~g~~fvk~~~~~G-- 571 (1014)
--.+|+|++..+.|+.+-|-= .|++....+.. +|. .+. -..-++.|..| +.-+
T Consensus 1666 ln~~G~Y~~v~vel~l~nlav----------ntll~S~lvne~EG~d~~g~~~dv~~~~~~~d~~~~~~~----De~a~~ 1731 (2173)
T KOG1798|consen 1666 LNRPGAYSTVCVELKLSNLAV----------NTLLQSALVNEMEGADFLGVTFDVNDRTAAEDDLTGACY----DETALC 1731 (2173)
T ss_pred hccccccceeEEEEEehHHHH----------HHHHHHhhhhhhhccccccccccccccchhhcccccccc----ccccch
Confidence 678999999667777654433 33333221111 110 000 00112223111 1111
Q ss_pred -----CcHHHHHHHHHHHHHHHHHhhhcCChHHHHHhHHHhhhccccceecccccccccCCCCChHHHhhHHHhhHHHHH
Q 001780 572 -----ILPEILEELLAARKRAKADLKEAKDPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIE 646 (1014)
Q Consensus 572 -----ilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~ 646 (1014)
+|..+|++++..=. + ..+.. | -.+.+..+-.+-...+.++|+++...+--.=+....
T Consensus 1732 ~~~f~VLk~llk~~~~d~~------~-~gN~~----------A-D~iv~~l~~Wl~spss~L~dpaL~~~vh~lmkK~fl 1793 (2173)
T KOG1798|consen 1732 AQAFRVLKQLLKRWVLDAA------K-SGNIY----------A-DLIVQHLSRWLRSPSSKLHDPALHRHVHVLMKKLFL 1793 (2173)
T ss_pred HHHHHHHHHHHHHHHHHHH------h-hcchh----------H-HHHHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHH
Confidence 22223333222111 1 01111 0 123355566666677899999999988887777776
Q ss_pred HHHHHHHhhccccCCccccceEEEecCccceEEcCCCCHHHHHHHHHHHHHHHHhc--CCCceeEEEeeeeccceecccc
Q 001780 647 HTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGT--FIKPIKLEFEKVYYPYLLISKK 724 (1014)
Q Consensus 647 ~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~~~~ea~~lg~eia~~vs~~--~~~pi~Le~Ekvy~~~ll~~KK 724 (1014)
.....++.. |+.|||.|-+=|-++.+..+.+.|....+-+.+.++.. | +-+.|.+-.-|..++++.+-
T Consensus 1794 ~L~~e~~rl---------Ga~iIyA~~nkili~T~K~~~e~A~~y~e~l~ksi~t~~~f-~~l~i~~~r~wd~llwmD~~ 1863 (2173)
T KOG1798|consen 1794 QLLAELRRL---------GAIIIYADFNKILINTGKFSVEAAKAYSEYLLKSISTLPVF-HLLDINPVRYWDSLLWMDAH 1863 (2173)
T ss_pred HHHHHHHhc---------CCeEEEecCCEEEEecCCCCHHHHHHHHHHHHHhhhcccch-hheeccHHHHHHHHhhhccc
Confidence 666666663 89999999999999999999999999888888888774 3 45778877778888888887
Q ss_pred eeEE
Q 001780 725 RYAG 728 (1014)
Q Consensus 725 RYag 728 (1014)
+|-|
T Consensus 1864 n~~g 1867 (2173)
T KOG1798|consen 1864 NYGG 1867 (2173)
T ss_pred cccc
Confidence 7554
No 76
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=93.91 E-value=0.13 Score=54.12 Aligned_cols=91 Identities=22% Similarity=0.291 Sum_probs=50.4
Q ss_pred EEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCc-cc-cce-eEEEeccc--cCCc-------Ccce----EeecCCHH
Q 001780 304 ILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGE-KQ-PFI-RNVMTLKS--CAPI-------VGVD----VMSFETER 367 (1014)
Q Consensus 304 ilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~-~~-~~~-~~vf~l~~--~~~~-------~~~~----V~~~~~E~ 367 (1014)
-++||+||++. +|++|.||+||.+.-..+. .. ... ..-+.+++ ..++ .|.. +..-..+.
T Consensus 7 ~vv~D~ETTGl-----~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~ 81 (189)
T cd06134 7 PVVVDVETGGF-----NPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEK 81 (189)
T ss_pred eEEEEecCCCC-----CCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchH
Confidence 35899999973 4567999999977432221 11 000 11111222 1111 1111 11113445
Q ss_pred HHHHHHHHHHHHh------CCCEEEEecccCCCcccccc
Q 001780 368 DVLLAWRDFIREV------DPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 368 eLL~~f~~~i~~~------DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+-+..|.+++.+. +=.+++|||. .||+.+|..
T Consensus 82 ~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~ 119 (189)
T cd06134 82 EALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNA 119 (189)
T ss_pred HHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHH
Confidence 6677777777643 1258999998 699999865
No 77
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.88 E-value=0.1 Score=59.33 Aligned_cols=85 Identities=16% Similarity=0.175 Sum_probs=54.6
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEecccc--------CC---cCcceEeecCCHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSC--------AP---IVGVDVMSFETERDVLL 371 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~--------~~---~~~~~V~~~~~E~eLL~ 371 (1014)
+.+.||+||++ ++.|.||+|+.+.-..|... ...-.-+++. .. |....|..-+...+.+.
T Consensus 2 ~~vviD~ETTg-------~~~d~IieIgav~v~~g~i~--~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~ 72 (309)
T PRK06195 2 NFVAIDFETAN-------EKRNSPCSIGIVVVKDGEIV--EKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWE 72 (309)
T ss_pred cEEEEEEeCCC-------CCCCceEEEEEEEEECCEEE--EEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHH
Confidence 56899999983 35699999997654444311 1100111111 11 12233444567788999
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|.+++. -++++|||. .||+.+|..
T Consensus 73 ~~~~fl~---~~~lVaHNa-~FD~~fL~~ 97 (309)
T PRK06195 73 KIKHYFN---NNLVIAHNA-SFDISVLRK 97 (309)
T ss_pred HHHHHhC---CCEEEEECc-HHHHHHHHH
Confidence 9998885 489999998 699999865
No 78
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=93.86 E-value=0.18 Score=57.90 Aligned_cols=91 Identities=12% Similarity=0.170 Sum_probs=58.5
Q ss_pred CCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec-cCccccceeEEEeccccCC--------cCcceEeecCCHHHH
Q 001780 299 MAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL-QGEKQPFIRNVMTLKSCAP--------IVGVDVMSFETERDV 369 (1014)
Q Consensus 299 ~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~-~g~~~~~~~~vf~l~~~~~--------~~~~~V~~~~~E~eL 369 (1014)
+.....++|||||++. +|..|.||.|+++.-. .|... ......+++..+ |....+..-++-.++
T Consensus 43 ~~~~~fVvlDiETTGL-----dp~~drIIeIgAV~i~~~g~iv--e~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eV 115 (377)
T PRK05601 43 IEAAPFVAVSIQTSGI-----HPSTSRLITIDAVTLTADGEEV--EHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQI 115 (377)
T ss_pred CCCCCEEEEEEECCCC-----CCCCCeEEEEEEEEEEcCCEEE--EEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHH
Confidence 3456799999999973 5678999999876433 44211 111112222111 112233344566889
Q ss_pred HHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 370 LLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 370 L~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|..|.+|+.. .++++||.. |||.||..
T Consensus 116 l~el~~fL~g---~vLVaHNA~-FD~~FL~~ 142 (377)
T PRK05601 116 LKPLDRLIDG---RTLILHNAP-RTWGFIVS 142 (377)
T ss_pred HHHHHHHhCC---CEEEEECcH-HHHHHHHH
Confidence 9999999873 389999965 99999876
No 79
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=93.55 E-value=0.19 Score=56.70 Aligned_cols=31 Identities=19% Similarity=0.240 Sum_probs=24.4
Q ss_pred CCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec
Q 001780 300 APFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL 335 (1014)
Q Consensus 300 pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~ 335 (1014)
++-+++.+|+||++. +|..|.||+|+.+...
T Consensus 35 ~~~~~vvlD~ETTGL-----d~~~d~IIEIg~V~v~ 65 (294)
T PRK09182 35 FVRLGVILDTETTGL-----DPRKDEIIEIGMVAFE 65 (294)
T ss_pred CCCeEEEEEeeCCCC-----CCCCCeEEEEEEEEEE
Confidence 556899999999973 4577999999977443
No 80
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=93.54 E-value=0.25 Score=52.57 Aligned_cols=92 Identities=20% Similarity=0.324 Sum_probs=49.6
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccC-ccccceeEEE--ecccc--CCcC-------cc----eEeecCCH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQG-EKQPFIRNVM--TLKSC--APIV-------GV----DVMSFETE 366 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g-~~~~~~~~vf--~l~~~--~~~~-------~~----~V~~~~~E 366 (1014)
.-++||+||++. +|.+|.||.||.+.-..+ .........| -+++. .+++ |. .+..-..+
T Consensus 9 ~~vv~D~ETTGl-----~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 9 LPVVVDVETGGF-----NAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred eeEEEEeeCCCC-----CCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 346899999962 456799999997643211 1110000011 11211 1111 11 11122345
Q ss_pred HHHHHHHHHHHHHh------CCCEEEEecccCCCcccccc
Q 001780 367 RDVLLAWRDFIREV------DPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 367 ~eLL~~f~~~i~~~------DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.+.+.+++.++.+. +-.+++|||.. ||+.+|-.
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~-FD~~fL~~ 122 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNAN-FDLGFLNA 122 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECch-hhHHHHHH
Confidence 56666666666422 34589999975 99999865
No 81
>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=93.15 E-value=0.21 Score=49.54 Aligned_cols=88 Identities=22% Similarity=0.436 Sum_probs=54.2
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC------------cCcceEeecCCHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP------------IVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~------------~~~~~V~~~~~E~eLL~~ 372 (1014)
+.||+||++. ++..+.|++||.+.-..+........-..+.+..+ +....+..-....+.+..
T Consensus 1 v~~D~Ettg~-----~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGL-----DPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSS-----TTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCC-----CCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHh
Confidence 4799999984 34678999999875544432011100011111111 111233444566778888
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++... .+++||| ..||.+.+..
T Consensus 76 ~~~~~~~~--~~~v~~n-~~fd~~~l~~ 100 (164)
T PF00929_consen 76 FEEFLKKN--DILVGHN-ASFDIGFLRR 100 (164)
T ss_dssp HHHHHHHH--TEEEETT-CCHEEESSHH
T ss_pred hhhhhhcc--ccccccc-ccchhhHHHH
Confidence 99998843 8999999 8899998865
No 82
>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=92.89 E-value=0.17 Score=65.33 Aligned_cols=87 Identities=22% Similarity=0.311 Sum_probs=57.2
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~~ 372 (1014)
+.+++|+||++. +|..|+||+||++.-..|.. ......-+++..+ |....+..-+...+.+..
T Consensus 1 ~~vvvD~ETTG~-----~~~~~~IIeig~v~v~~~~i--~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~ 73 (850)
T TIGR01407 1 RYAVVDLETTGT-----QLSFDKIIQIGIVVVEDGEI--VDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQE 73 (850)
T ss_pred CEEEEEEECCCC-----CCCCCeEEEEEEEEEECCEE--EEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHH
Confidence 357899999973 45679999999875544421 1111111222111 122334455678899999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++. ..+++|||+ .||+++|..
T Consensus 74 l~~~l~---~~~~VahN~-~fD~~fL~~ 97 (850)
T TIGR01407 74 IYDLLE---DGIFVAHNV-HFDLNFLAK 97 (850)
T ss_pred HHHHhC---CCEEEEeCc-HHHHHHHHH
Confidence 999875 578999997 699999976
No 83
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=92.52 E-value=0.3 Score=52.17 Aligned_cols=97 Identities=16% Similarity=0.202 Sum_probs=58.7
Q ss_pred CcEEEEEEEEEccCCC-CCCCCCCCceeEEEEEeeccCcc-ccceeEEEe-----cc-ccC---CcCcceEeecCCHHHH
Q 001780 301 PFRILSFDIECAGRKG-HFPEPTHDPVIQVANLVTLQGEK-QPFIRNVMT-----LK-SCA---PIVGVDVMSFETERDV 369 (1014)
Q Consensus 301 plrilSfDIE~~~~~g-~fP~~~~D~Ii~Is~~v~~~g~~-~~~~~~vf~-----l~-~~~---~~~~~~V~~~~~E~eL 369 (1014)
+.+.+.||+||++..+ .-|....|+||+|+.+.-..|.. ..|...|-+ +. .+. .|....|..-++..+.
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ev 82 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEEL 82 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHH
Confidence 5688999999997543 23443358999999765433321 112111111 11 011 1223445556788999
Q ss_pred HHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 370 LLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 370 L~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+.+|.+++... +.++++| . +||+.+|..
T Consensus 83 l~~f~~~~~~~-~~~iv~~-~-~fD~~fL~~ 110 (207)
T PRK07748 83 VEKLAEYDKRC-KPTIVTW-G-NMDMKVLKH 110 (207)
T ss_pred HHHHHHHhCcC-CeEEEEE-C-HHHHHHHHH
Confidence 99999998732 3466665 3 699999865
No 84
>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=92.06 E-value=0.28 Score=49.62 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=31.4
Q ss_pred ceEeecCCHHHHHHHHHHHHHHhCCCEEEEecccCCCccccc
Q 001780 358 VDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLI 399 (1014)
Q Consensus 358 ~~V~~~~~E~eLL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~ 399 (1014)
..|..-++..+.+.+|.+++. ..+++|||+ .||+.+|-
T Consensus 56 ~~v~~a~~~~~~~~~l~~~l~---~~vlVgHn~-~fD~~~L~ 93 (152)
T cd06144 56 EHLKDAPDFEEVQKKVAELLK---GRILVGHAL-KNDLKVLK 93 (152)
T ss_pred HHHcCCCCHHHHHHHHHHHhC---CCEEEEcCc-HHHHHHhc
Confidence 345666788999999999986 489999998 59999985
No 85
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=91.79 E-value=0.32 Score=63.34 Aligned_cols=88 Identities=27% Similarity=0.351 Sum_probs=56.8
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~~ 372 (1014)
+++.||+||++. .|. ..|.||+||++.-..|... .+...-+++..+ |....|...+...+.+..
T Consensus 4 ~~vvvD~ETTG~---~p~-~~d~IIeigav~v~~~~i~--~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~ 77 (928)
T PRK08074 4 RFVVVDLETTGN---SPK-KGDKIIQIAAVVVEDGEIL--ERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPE 77 (928)
T ss_pred CEEEEEEeCCCC---CCC-CCCcEEEEEEEEEECCEEE--EEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHH
Confidence 478999999962 222 2489999998765444211 111111222211 222344455678899999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++. ..+++|||+ .||+++|..
T Consensus 78 l~~~l~---~~~~VaHN~-~FD~~fL~~ 101 (928)
T PRK08074 78 IVELLE---GAYFVAHNV-HFDLNFLNE 101 (928)
T ss_pred HHHHhC---CCeEEEECh-HHHHHHHHH
Confidence 999985 578999997 599999976
No 86
>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=91.07 E-value=0.33 Score=49.70 Aligned_cols=83 Identities=20% Similarity=0.326 Sum_probs=47.0
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcC-------c---ceEeecCC-------HH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIV-------G---VDVMSFET-------ER 367 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~-------~---~~V~~~~~-------E~ 367 (1014)
++||+||++- +|..|.|++||++--..|... +.. + +++..++. | ..+..-++ -.
T Consensus 1 v~lD~EttGl-----~~~~d~ii~Ig~V~v~~g~i~-~~~--~-v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~ 71 (161)
T cd06137 1 VALDCEMVGL-----ADGDSEVVRISAVDVLTGEVL-IDS--L-VRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWE 71 (161)
T ss_pred CEEEeeeeeE-----cCCCCEEEEEEEEEcCCCeEE-Eec--c-ccCCCCCCccceeccCCCHHHHhhhhhcCCccccHH
Confidence 3799999863 245799999997654344311 111 0 11111111 1 11111011 13
Q ss_pred HHHHHHHHHHHHhCC-CEEEEecccCCCcccccc
Q 001780 368 DVLLAWRDFIREVDP-DVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 368 eLL~~f~~~i~~~DP-DIIiGyNi~~FDlpyL~~ 400 (1014)
+.+..|.+++. . .+++|||.. ||+.+|-.
T Consensus 72 ~~~~~~~~~i~---~~~vlVgHn~~-fD~~fL~~ 101 (161)
T cd06137 72 AARAALWKFID---PDTILVGHSLQ-NDLDALRM 101 (161)
T ss_pred HHHHHHHHhcC---CCcEEEeccHH-HHHHHHhC
Confidence 66677777775 4 699999985 89999854
No 87
>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=90.90 E-value=0.79 Score=54.98 Aligned_cols=75 Identities=21% Similarity=0.243 Sum_probs=48.3
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCC
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDP 382 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DP 382 (1014)
-.+-||||+. | ...-.+++|+++...|....-....+..+ -.+|++.+.+|++++..+ |
T Consensus 285 ~~~ffDiEt~------P--~~~~~yL~G~~~~~~~~~~~~~~~fla~~------------~~~E~~~~~~f~~~l~~~-~ 343 (457)
T TIGR03491 285 GELIFDIESD------P--DENLDYLHGFLVVDKGQENEKYRPFLAED------------PNTEELAWQQFLQLLQSY-P 343 (457)
T ss_pred ccEEEEecCC------C--CCCCceEEEEEEecCCCCCcceeeeecCC------------chHHHHHHHHHHHHHHHC-C
Confidence 3678999997 3 34556888875543332211011122211 258999999999999886 8
Q ss_pred C-EEEEecccCCCcccccc
Q 001780 383 D-VMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 383 D-IIiGyNi~~FDlpyL~~ 400 (1014)
| -|.-|| +|..++|.+
T Consensus 344 ~~~i~hY~--~~e~~~l~r 360 (457)
T TIGR03491 344 DAPIYHYG--ETEKDSLRR 360 (457)
T ss_pred CCeEEeeC--HHHHHHHHH
Confidence 7 588999 466777666
No 88
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=90.67 E-value=0.38 Score=61.71 Aligned_cols=87 Identities=23% Similarity=0.284 Sum_probs=57.3
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCC----------cCcceEeecCCHHHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAP----------IVGVDVMSFETERDVLL 371 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~----------~~~~~V~~~~~E~eLL~ 371 (1014)
-+.+.||+||++. . + .|+||+||++.-..|... .....-+++..+ |....|..-+...+.+.
T Consensus 7 ~~~vvvD~ETTGl---~--~-~d~IIeIgaV~v~~g~i~--~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~ 78 (820)
T PRK07246 7 RKYAVVDLEATGA---G--P-NASIIQVGIVIIEGGEII--DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVAR 78 (820)
T ss_pred CCEEEEEEecCCc---C--C-CCeEEEEEEEEEECCEEE--EEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHH
Confidence 3688999999973 2 3 489999998754443211 111111222222 22234555677889999
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|.+++. -.+++|||. .||+++|..
T Consensus 79 ~~~~~l~---~~~lVaHN~-~FD~~fL~~ 103 (820)
T PRK07246 79 HIYDLIE---DCIFVAHNV-KFDANLLAE 103 (820)
T ss_pred HHHHHhC---CCEEEEECc-HHHHHHHHH
Confidence 9999876 478999998 599999965
No 89
>PHA03181 helicase-primase primase subunit; Provisional
Probab=89.20 E-value=19 Score=44.99 Aligned_cols=162 Identities=15% Similarity=0.134 Sum_probs=102.9
Q ss_pred hccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCC-----
Q 001780 609 ALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVP----- 683 (1014)
Q Consensus 609 AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~----- 683 (1014)
-||-.+-+++|-+-. -|.++..+|-+.+-.+=....+.+.+. ++-|==..-|+.|=-|+..
T Consensus 459 wLK~aLv~f~G~Lkh-----~~p~~y~aii~i~N~Is~~vE~~A~~~---------~FAiCtYvkDGfWG~F~~~~~~~~ 524 (764)
T PHA03181 459 WLKRPIVEFGGLLKH-----FREDVYKAIIGIGNHISLEVEATASTL---------MFAPCTYVKDGMWGTFIDKANNVI 524 (764)
T ss_pred hHHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhc---------CeeEEeecCCceEEeccccccccc
Confidence 466667777776643 477888888888877766666666553 4444444556665444322
Q ss_pred --C--HHHHH----HHHHHHHHH-HHh---cCC--CceeEEEeeeeccceecccceeEEEeccCCCCccceeEeeeeecc
Q 001780 684 --T--VEAAM----KLGREAADY-ISG---TFI--KPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVR 749 (1014)
Q Consensus 684 --~--~~ea~----~lg~eia~~-vs~---~~~--~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~~~k~~~KGie~vR 749 (1014)
+ ...+. .-.++.+.. +.+ .+| -++.|.+|+||--.++.+-..| .+|+..... -++-|+ .-|
T Consensus 525 ~~~~~~~~a~~~lR~ac~~aA~~~l~~~GL~~p~~~~l~LRlEGvYThAvsW~~n~y--WLwN~~~~~--~~~vGF-P~r 599 (764)
T PHA03181 525 VSPEGNENIFETLRVACNESANRLATSIGLRFPDGINLQMRLEGVYTHAMSWNANCY--WLWNRNTRE--SDFVGF-PKQ 599 (764)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCceEEEeEEeeeeeeecCcce--eeccCCCCC--cceeec-CCC
Confidence 1 12222 112233332 332 233 3578899999999999998888 778754323 334899 457
Q ss_pred CchHHHHHHHHHHHHHHHhcCCC----hhhHHHHHHHHHHHHHc
Q 001780 750 RDNCLLVKNLVTECLHKILVDRD----IPGAVQYVKSTISDLLM 789 (1014)
Q Consensus 750 RD~~~l~k~~~~~vl~~il~~~d----~~~a~~~v~~~i~~l~~ 789 (1014)
.-....+|+.+..+|+.+....+ ++.+.+-.++..++|..
T Consensus 600 ~~~~~~ak~~Ls~lL~~i~~~~~~~~~l~~~~~~a~~~cd~Lv~ 643 (764)
T PHA03181 600 PEFATHAKEALSTLLEEICLCNDTDESLLTIQEKVQKVFEELLY 643 (764)
T ss_pred cHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHHHH
Confidence 77888999999999988776443 55566667777776653
No 90
>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=89.03 E-value=0.68 Score=47.23 Aligned_cols=84 Identities=13% Similarity=0.160 Sum_probs=52.9
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccC----------CcCcceEeecCCHHHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCA----------PIVGVDVMSFETERDVLLAWR 374 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~----------~~~~~~V~~~~~E~eLL~~f~ 374 (1014)
++||+||++. .|..+.++|+.|+.+. ..|... +.. + +++.. .|....+..-++-.+.+.+|.
T Consensus 1 v~~D~EttGl---~~~~~~~~i~~i~~v~-~~g~~~-~~~--l-v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~ 72 (157)
T cd06149 1 VAIDCEMVGT---GPGGRESELARCSIVN-YHGDVL-YDK--Y-IRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEIL 72 (157)
T ss_pred CEEEeEeccc---cCCCCeEEEEEEEEEe-CCCCEE-EEE--e-ECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHH
Confidence 4799999974 3443468888888543 344321 111 1 11111 122234445567789999999
Q ss_pred HHHHHhCCCEEEEecccCCCcccccc
Q 001780 375 DFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 375 ~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+++. -.|++|||. .||+.+|-.
T Consensus 73 ~~l~---~~vlV~Hn~-~~D~~~l~~ 94 (157)
T cd06149 73 KILK---GKVVVGHAI-HNDFKALKY 94 (157)
T ss_pred HHcC---CCEEEEeCc-HHHHHHhcc
Confidence 9985 469999996 689988864
No 91
>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=88.91 E-value=1.2 Score=45.66 Aligned_cols=94 Identities=18% Similarity=0.297 Sum_probs=53.8
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCcc---ccceeEEEecc--c----c---CCcCcceEeecCCHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEK---QPFIRNVMTLK--S----C---APIVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~---~~~~~~vf~l~--~----~---~~~~~~~V~~~~~E~eLL~~ 372 (1014)
+.||+||++..+.---...++|++||++.-..+.. ..|...+-.-. . + ..+....+.......+.+.+
T Consensus 2 vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~~ 81 (176)
T cd06133 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKE 81 (176)
T ss_pred EEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHHH
Confidence 68999999743210002348999999764332221 11111111111 0 0 11222334556788999999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+++....+.++++|+ .||+..|..
T Consensus 82 ~~~~l~~~~~~~~v~~~--~~d~~~l~~ 107 (176)
T cd06133 82 FLEWLGKNGKYAFVTWG--DWDLKDLLQ 107 (176)
T ss_pred HHHHHHhCCCeEEEeec--HhhHHHHHH
Confidence 99999865446777775 688887665
No 92
>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=87.97 E-value=0.97 Score=45.72 Aligned_cols=84 Identities=15% Similarity=0.121 Sum_probs=52.7
Q ss_pred EEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccc-----c---CCcCcceEeec-CCHHHHHHHHHH
Q 001780 305 LSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKS-----C---APIVGVDVMSF-ETERDVLLAWRD 375 (1014)
Q Consensus 305 lSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~-----~---~~~~~~~V~~~-~~E~eLL~~f~~ 375 (1014)
+++|+|+.+-.+ .|+|+.|+.+ ...|.. .|.. .+.... . ..|....+..- +++.+.+.+|.+
T Consensus 1 ~~iD~E~~g~~~------g~ei~~i~~v-~~~~~~-~f~~-lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~ 71 (150)
T cd06145 1 FALDCEMCYTTD------GLELTRVTVV-DENGKV-VLDE-LVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLS 71 (150)
T ss_pred CEEeeeeeeecC------CCEEEEEEEE-eCCCCE-EEEE-eECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHH
Confidence 479999998532 2899999965 334431 1221 111000 1 11222345444 389999999999
Q ss_pred HHHHhCCCEEEEecccCCCcccccc
Q 001780 376 FIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 376 ~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|+. +=.+|+|||.. ||+.+|-.
T Consensus 72 fl~--~~~vlVgHn~~-fD~~fL~~ 93 (150)
T cd06145 72 LIS--PDTILVGHSLE-NDLKALKL 93 (150)
T ss_pred HhC--CCCEEEEcChH-HHHHHhhc
Confidence 995 12599999985 99999854
No 93
>PHA03144 helicase-primase primase subunit; Provisional
Probab=86.98 E-value=28 Score=43.59 Aligned_cols=162 Identities=18% Similarity=0.201 Sum_probs=101.9
Q ss_pred hccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCC-----
Q 001780 609 ALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVP----- 683 (1014)
Q Consensus 609 AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~----- 683 (1014)
.||-.+-+++|-+-. -|.++..+|-+.+-.+=....+.+.+. ++-|==..-|+.|=-|+..
T Consensus 450 wlK~aLv~f~GgL~h-----~~p~~yr~ii~i~N~Is~~vE~~A~~~---------~FAiCtYvkDGfWG~f~~~~~~~~ 515 (746)
T PHA03144 450 WLKAALVSFFGGLQH-----ICPAAYRALIALANAVSRALERAANAV---------GFAVCTYVKDGFWGVLGVDPQDAV 515 (746)
T ss_pred hHHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhc---------CeeEEeecCCceEEeccCCccccc
Confidence 466667777776653 477888888888877666655555553 4444444556665545432
Q ss_pred ------CHHHHHHHHHHHHHHHHhc----CC--CceeEEEeeeeccceecccceeEEEeccCCCCccceeEeeeeeccCc
Q 001780 684 ------TVEAAMKLGREAADYISGT----FI--KPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRD 751 (1014)
Q Consensus 684 ------~~~ea~~lg~eia~~vs~~----~~--~pi~Le~Ekvy~~~ll~~KKRYagl~~~~~~~~~k~~~KGie~vRRD 751 (1014)
..+++-...++.+..+-.. ++ -++.|.+|+||--.++.+-..| .+|+... +.-++-|+-. |.-
T Consensus 516 ~~~a~~~ae~lR~ace~aA~~~L~~~GL~~~~~~~l~LRlEGvyThAvsW~~~~y--WLwN~~~--~~~~~vGFP~-Rs~ 590 (746)
T PHA03144 516 SADALAAAERARAACQAAAEAVLADMGLLLPEGAPLHLRLEGLYTHAVSWSQHGY--WLWNRRT--DTEDFVGFPL-RSA 590 (746)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCceEEEeEEeeeeeeecCcce--eeccCCC--CccceeeccC-chH
Confidence 1112222223333333222 22 3578999999999999998888 7787533 3345589965 777
Q ss_pred hHHHHHHHHHHHHH-HHhcCCChhhHHHHHHHHHHHHHc
Q 001780 752 NCLLVKNLVTECLH-KILVDRDIPGAVQYVKSTISDLLM 789 (1014)
Q Consensus 752 ~~~l~k~~~~~vl~-~il~~~d~~~a~~~v~~~i~~l~~ 789 (1014)
-+..+|+.+..+|+ ..-...+++.+.+-.++..++|..
T Consensus 591 ~a~~ak~aL~~lL~~~~~~~~~~~~~~~~a~~~cd~lv~ 629 (746)
T PHA03144 591 AARAAKAALRALLRAAVADSADAETLRQAAREACDRLVL 629 (746)
T ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHH
Confidence 77778888888885 334455677777777777777653
No 94
>PRK06722 exonuclease; Provisional
Probab=86.63 E-value=1.6 Score=48.97 Aligned_cols=92 Identities=20% Similarity=0.226 Sum_probs=54.4
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccc---cceeEEEe---cc-ccC---CcCcceEeecCCHHHHHHH
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQ---PFIRNVMT---LK-SCA---PIVGVDVMSFETERDVLLA 372 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~---~~~~~vf~---l~-~~~---~~~~~~V~~~~~E~eLL~~ 372 (1014)
+.+.||+||+..++. ....|+||+|+++.-..|..+ .|...+-+ +. .|. .|.+..|..-+.-.+.+..
T Consensus 6 ~~vViD~ETT~~p~~--~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~e 83 (281)
T PRK06722 6 HFIVFDIERNFRPYK--SEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEK 83 (281)
T ss_pred EEEEEEeeCCCCCCC--CCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 678999999742211 234589999997654344211 11111111 10 111 2333455566778899999
Q ss_pred HHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 373 WRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 373 f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
|.+|+.. +.++++|. .||+.+|..
T Consensus 84 f~~fig~---~~lvahna-~FD~~FL~~ 107 (281)
T PRK06722 84 FIQFIGE---DSIFVTWG-KEDYRFLSH 107 (281)
T ss_pred HHHHHCC---CcEEEEEe-HHHHHHHHH
Confidence 9999962 34555564 799999877
No 95
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=86.01 E-value=1 Score=57.77 Aligned_cols=91 Identities=23% Similarity=0.357 Sum_probs=60.9
Q ss_pred CCCcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccC----------CcCcceEeecCCHHH
Q 001780 299 MAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCA----------PIVGVDVMSFETERD 368 (1014)
Q Consensus 299 ~pplrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~----------~~~~~~V~~~~~E~e 368 (1014)
+-.-+-+.|||||++- .|..|.||+||.+.-..|... .+.-|-+++.. .|.+..+..-....+
T Consensus 418 l~datyVVfDiETTGL-----s~~~d~iIE~aAvKikng~iI--d~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~ 490 (1444)
T COG2176 418 LDDATYVVFDIETTGL-----SPVYDEIIEIAAVKIKNGRII--DKFQFFIKPGRPLSATITELTGITDEMLENAPEIEE 490 (1444)
T ss_pred cccccEEEEEeecCCc-----CcccchhhhheeeeeeCCcch--HHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHH
Confidence 3445678899999973 346799999997755555421 11111122211 223334555567788
Q ss_pred HHHHHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 369 VLLAWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 369 LL~~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|..|.+|+. -+|++.|| .+||++||-.
T Consensus 491 vL~kf~~~~~---d~IlVAHN-asFD~gFl~~ 518 (1444)
T COG2176 491 VLEKFREFIG---DSILVAHN-ASFDMGFLNT 518 (1444)
T ss_pred HHHHHHHHhc---CcEEEecc-CccchhHHHH
Confidence 9999999886 57999999 8899999977
No 96
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=83.82 E-value=2.3 Score=46.23 Aligned_cols=90 Identities=22% Similarity=0.382 Sum_probs=55.9
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCc-------CcceEeecCCH---HHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPI-------VGVDVMSFETE---RDVLL 371 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~-------~~~~V~~~~~E---~eLL~ 371 (1014)
.+...||+||++. ++..|.||.|+.+.-..+.... ......+++..++ .|..-....+. .+.+.
T Consensus 13 ~~~vv~D~ETtg~-----~~~~~~iieIgav~~~~~~i~~-~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~ 86 (243)
T COG0847 13 TRFVVIDLETTGL-----NPKKDRIIEIGAVTLEDGRIVE-RSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLP 86 (243)
T ss_pred CcEEEEecccCCC-----CCCCCceEEEEeEEEECCeeec-ceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHH
Confidence 6889999999974 3478999999987554442110 1011112221111 12111122233 78888
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|.+++... .++++|| ..||+++|..
T Consensus 87 ~~~~~i~~~--~~~Vahn-a~fD~~fl~~ 112 (243)
T COG0847 87 EFLDFIGGL--RLLVAHN-AAFDVGFLRV 112 (243)
T ss_pred HHHHHHCCC--CeEEEEc-hhhcHHHHHH
Confidence 888888733 9999999 7899999876
No 97
>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=82.66 E-value=4.5 Score=40.97 Aligned_cols=29 Identities=34% Similarity=0.715 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhCCCE-EEEecccCCCcccccc
Q 001780 369 VLLAWRDFIREVDPDV-MIGYNICKFDLPYLIE 400 (1014)
Q Consensus 369 LL~~f~~~i~~~DPDI-IiGyNi~~FDlpyL~~ 400 (1014)
++..+..++. ||+| .+|||+. ||+..|..
T Consensus 65 ~~~~l~~ll~--~~~i~kv~~n~~-~D~~~L~~ 94 (176)
T PF01612_consen 65 ILDALKELLE--DPNIIKVGHNAK-FDLKWLYR 94 (176)
T ss_dssp HHHHHHHHHT--TTTSEEEESSHH-HHHHHHHH
T ss_pred hHHHHHHHHh--CCCccEEEEEEe-chHHHHHH
Confidence 5666666666 7775 8999984 89999887
No 98
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=77.33 E-value=1.5 Score=57.10 Aligned_cols=106 Identities=17% Similarity=0.421 Sum_probs=65.6
Q ss_pred cchhhHHHhhccccccchhhhhcCCccceeeecC------CCCcccccccccccccccccccccCcccCCcCCCChHHHH
Q 001780 877 QISKPLLRIFEPILKNASKELLSGDHTRSISIST------PSNSGIMKFAKRQLSCIGCKALISNGTLCSHCKGREAELY 950 (1014)
Q Consensus 877 qi~~pl~ri~~~i~g~~~~~l~~g~~~r~~~~~~------~~~~~~~~f~~~~~~C~~C~~~~~~~~~C~~C~~~~~~~~ 950 (1014)
++.||+.-+| || |+ .|-.+|.+..++ ...+|....-.....|+.|++.... ..|++|......
T Consensus 623 ~mkP~~h~LF-Pi-g~------aGG~qR~I~kAa~~a~~~~d~~G~ieVEV~~rkCPkCG~~t~~-~fCP~CGs~te~-- 691 (1337)
T PRK14714 623 KMKPPVHTLF-PI-GE------AGGAQRDVAKAAKHAPDMSDEGGVIEVEVGRRRCPSCGTETYE-NRCPDCGTHTEP-- 691 (1337)
T ss_pred ccCCCCcccc-cc-cc------cCcccccHHHHHHhhhhccccCCeEEEEEEEEECCCCCCcccc-ccCcccCCcCCC--
Confidence 4666666665 55 33 133344443322 1134443433446799999997654 699999987421
Q ss_pred HHHHHHHHHHHHHHHHHHHHcccccCCCCCc-------ccccCCCCCcceeecchhhhHHHHHHhhc
Q 001780 951 CKTVSQVQELEVLFGRLWTQCQECQGSLHQD-------VLCTSRDCPIFYRRKKAQKDMAEAKLQLD 1010 (1014)
Q Consensus 951 ~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~-------~~c~~~~cp~~y~r~~~~~~~~~~~~~~~ 1010 (1014)
-..|++|...+..+ ..|.+.-.+.-++++..+..+..+.+-|.
T Consensus 692 -----------------vy~CPsCGaev~~des~a~~CP~CGtplv~~~~~~i~~~~~~~~A~~~~g 741 (1337)
T PRK14714 692 -----------------VYVCPDCGAEVPPDESGRVECPRCDVELTPYQRRTINVKEEYRSALENVG 741 (1337)
T ss_pred -----------------ceeCccCCCccCCCccccccCCCCCCcccccceEEecHHHHHHHHHHHhC
Confidence 12699998754322 35777777777888888888888766553
No 99
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=76.60 E-value=6.2 Score=42.65 Aligned_cols=80 Identities=19% Similarity=0.224 Sum_probs=41.6
Q ss_pred EEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCc----------CcceEeecCCHHHHHHHH
Q 001780 304 ILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPI----------VGVDVMSFETERDVLLAW 373 (1014)
Q Consensus 304 ilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~----------~~~~V~~~~~E~eLL~~f 373 (1014)
...||+||++.. + .||.|+.+.-.+|... .....-+++..++ ....|.--+.-.+.+..|
T Consensus 2 ~~vlD~ETTGl~-----~---~IieIg~v~v~~~~i~--~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~ 71 (219)
T PRK07983 2 LRVIDTETCGLQ-----G---GIVEIASVDVIDGKIV--NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHY 71 (219)
T ss_pred eEEEEEECCCCC-----C---CCEEEEEEEEECCEEE--EEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHHH
Confidence 457899999742 1 3999987633333211 0000111221121 111222223334444443
Q ss_pred HHHHHHhCCCEEEEecccCCCcccccc
Q 001780 374 RDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 374 ~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
..-++++|||. .||+.+|..
T Consensus 72 ------~~~~~lVaHNa-~FD~~~L~~ 91 (219)
T PRK07983 72 ------YGSEWYVAHNA-SFDRRVLPE 91 (219)
T ss_pred ------cCCCEEEEeCc-HhhHHHHhC
Confidence 25679999997 499998854
No 100
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=74.62 E-value=3.8 Score=55.43 Aligned_cols=88 Identities=19% Similarity=0.349 Sum_probs=57.5
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCc----------CcceEeecCCHHHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPI----------VGVDVMSFETERDVLL 371 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~----------~~~~V~~~~~E~eLL~ 371 (1014)
-+.+.||+||++- ++..|.|++|+.+.-..|....-.. .-+++..++ ....+..-.+..+.|.
T Consensus 419 ~~~VVfDLETTGL-----~~~~deIIEIgAV~V~~G~iie~F~--~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~ 491 (1437)
T PRK00448 419 ATYVVFDVETTGL-----SAVYDEIIEIGAVKIKNGEIIDKFE--FFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLP 491 (1437)
T ss_pred CcEEEEEhhhcCC-----CCchhhhheeeeEEEeCCeEeeeEE--EEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHH
Confidence 4689999999962 3567999999876544443211011 112221111 1223444567889999
Q ss_pred HHHHHHHHhCCCEEEEecccCCCcccccc
Q 001780 372 AWRDFIREVDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 372 ~f~~~i~~~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
.|.+|+. -.++++||. .||+++|..
T Consensus 492 ~f~~fig---g~vLVAHNa-~FD~~fL~~ 516 (1437)
T PRK00448 492 KFKEFCG---DSILVAHNA-SFDVGFINT 516 (1437)
T ss_pred HHHHHhC---CCEEEEeCc-cccHHHHHH
Confidence 9999875 479999999 799999855
No 101
>PHA03140 helicase-primase primase subunit; Provisional
Probab=71.89 E-value=1.6e+02 Score=37.20 Aligned_cols=137 Identities=15% Similarity=0.176 Sum_probs=84.3
Q ss_pred hccccceecccccccccCCCCChHHHhhHHHhhHHHHHHHHHHHHhhccccCCccccceEEEecCccceEEcCCC-----
Q 001780 609 ALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVP----- 683 (1014)
Q Consensus 609 AlKi~aNS~YG~~G~~~~r~~~~~iA~sIT~~GR~~i~~t~~~ve~~~~~~~gy~~~~~VIYGDTDSv~V~~~~~----- 683 (1014)
-||-.+-+++|-+-. -|.++..+|-+.+-.+=....+.+.+. ++-|==..-|+.|=-|+..
T Consensus 457 ~LK~aLv~f~GgLrh-----~~p~~y~aii~i~N~Is~~vE~~A~~~---------~FAiCtYvKDGFWG~F~~~~~~~~ 522 (772)
T PHA03140 457 CLKPALVTFFGGLRH-----IHPPAYKAIIALANAISACVERAANER---------NFAICTYVKDGFWGAFGDLVPGAV 522 (772)
T ss_pred hHHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhc---------CeeEEeeccCceeEeccccccccc
Confidence 356666777776643 477788888888877666665655553 3344444455555444322
Q ss_pred ----CHHHHHHH---HHHHHHHHHh-c----CC--CceeEEEeeeeccceecccceeEEEecc-CCCCccceeEeeeeec
Q 001780 684 ----TVEAAMKL---GREAADYISG-T----FI--KPIKLEFEKVYYPYLLISKKRYAGLYWT-NPEKFDKMDTKGIETV 748 (1014)
Q Consensus 684 ----~~~ea~~l---g~eia~~vs~-~----~~--~pi~Le~Ekvy~~~ll~~KKRYagl~~~-~~~~~~k~~~KGie~v 748 (1014)
....+..+ .++.+..+-. . ++ -++.|.+|+||--.++.+-..| .+|+ ...+.+ +.-|+ .-
T Consensus 523 ~~~~~~~~a~~lR~ace~aA~~~L~~~~GL~~~~~~~l~LRlEGvyThAvsW~~~~y--WLwN~~~~~~~--~~vGF-P~ 597 (772)
T PHA03140 523 SRDAARAAALALRDDCERAVEAVLRDDLGLRPAEGAEPHLRFEGVFTHAVSWCTTGY--WLWNATTGESE--HLVGV-PC 597 (772)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHhcCcCCCCCCCceEEEeEEeeeeeeecCcce--eecccCCCCcc--ceeec-cC
Confidence 11222222 2333333322 2 22 3578899999999999998888 7777 332222 34799 45
Q ss_pred cCchHHHHHHHHHHHH
Q 001780 749 RRDNCLLVKNLVTECL 764 (1014)
Q Consensus 749 RRD~~~l~k~~~~~vl 764 (1014)
|.-....+|+.+..+|
T Consensus 598 rs~a~~~ak~~l~~lL 613 (772)
T PHA03140 598 RSEAARDAKESLAGLL 613 (772)
T ss_pred ccHHHHHHHHHHHHHH
Confidence 7778888888888888
No 102
>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=59.97 E-value=62 Score=33.29 Aligned_cols=78 Identities=24% Similarity=0.439 Sum_probs=44.8
Q ss_pred EEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHhCC
Q 001780 303 RILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDP 382 (1014)
Q Consensus 303 rilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~DP 382 (1014)
..++||+|+.+- ++..+.|+.++.... .+. .+ .+.+... ....-.+..+.+..|.+++.. .
T Consensus 6 ~~~a~d~e~~~~-----~~~~~~i~~l~~~~~-~~~--~~---~~~~~~~------~~~~~~~~~~~~~~l~~~l~~--~ 66 (193)
T cd06139 6 KVFAFDTETTSL-----DPMQAELVGISFAVE-PGE--AY---YIPLGHD------YGGEQLPREEVLAALKPLLED--P 66 (193)
T ss_pred CeEEEEeecCCC-----CcCCCeEEEEEEEcC-CCC--EE---EEecCCC------ccccCCCHHHHHHHHHHHHhC--C
Confidence 468999988642 234567877773221 111 11 1111110 000112567788888888873 4
Q ss_pred C-EEEEecccCCCcccccc
Q 001780 383 D-VMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 383 D-IIiGyNi~~FDlpyL~~ 400 (1014)
+ .++|||. .||+.+|..
T Consensus 67 ~~~~v~hn~-k~d~~~l~~ 84 (193)
T cd06139 67 SIKKVGQNL-KFDLHVLAN 84 (193)
T ss_pred CCcEEeecc-HHHHHHHHH
Confidence 4 6899998 699998864
No 103
>PTZ00315 2'-phosphotransferase; Provisional
Probab=53.38 E-value=49 Score=40.77 Aligned_cols=94 Identities=18% Similarity=0.137 Sum_probs=56.3
Q ss_pred cEEEEEEEEEccCCCCCCCCCCCceeEEEEEeec--cCccc-cceeEEEecc------ccCC---cCcceEeecCCHHHH
Q 001780 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTL--QGEKQ-PFIRNVMTLK------SCAP---IVGVDVMSFETERDV 369 (1014)
Q Consensus 302 lrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~--~g~~~-~~~~~vf~l~------~~~~---~~~~~V~~~~~E~eL 369 (1014)
-..+.||+||++..+ +....|+||.|+++.-. .|.-. .|...|-.-. .|.. |....|..-.+-.+.
T Consensus 56 d~~IV~DlETTgl~~--~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eV 133 (582)
T PTZ00315 56 DAYVVLDFEATCEAD--RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVV 133 (582)
T ss_pred CeEEEEEEecCCCCC--CCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHH
Confidence 578899999987421 11246899999987532 23211 1111111100 1222 223445556677899
Q ss_pred HHHHHHHHHHhCC-------CEEEEecccCCCcc-cc
Q 001780 370 LLAWRDFIREVDP-------DVMIGYNICKFDLP-YL 398 (1014)
Q Consensus 370 L~~f~~~i~~~DP-------DIIiGyNi~~FDlp-yL 398 (1014)
+..|.+|+..... .+++++|+ .||+. +|
T Consensus 134 l~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL 169 (582)
T PTZ00315 134 YCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTML 169 (582)
T ss_pred HHHHHHHHhccccccccccCceEEEecc-HHHHHHHH
Confidence 9999999987641 47888997 58885 44
No 104
>PHA02952 EEV maturation protein; Provisional
Probab=53.18 E-value=32 Score=42.48 Aligned_cols=39 Identities=23% Similarity=0.651 Sum_probs=33.9
Q ss_pred eecCCHHHHHHHHHHHHHH----hCCCEEEEecccCCCcccccc
Q 001780 361 MSFETERDVLLAWRDFIRE----VDPDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 361 ~~~~~E~eLL~~f~~~i~~----~DPDIIiGyNi~~FDlpyL~~ 400 (1014)
+.|++ ++|+..|++++.+ .+-=+++||=..-||+|.|..
T Consensus 249 ~~~~s-k~li~~FL~Wl~e~~~n~~ti~LvGy~Ss~FD~pLL~~ 291 (648)
T PHA02952 249 INFDS-KKLILDFLKWLKEVMTNTSTIILVGYLSSFFDFPLLKA 291 (648)
T ss_pred ecCCH-HHHHHHHHHHHHHHhcCCceEEEEEhhhhhcchHHHHh
Confidence 35566 9999999999998 667789999999999998877
No 105
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=47.79 E-value=49 Score=41.06 Aligned_cols=95 Identities=22% Similarity=0.411 Sum_probs=61.1
Q ss_pred CCCcEEEEEEEEEccCCC----CCC-CCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHH
Q 001780 299 MAPFRILSFDIECAGRKG----HFP-EPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAW 373 (1014)
Q Consensus 299 ~pplrilSfDIE~~~~~g----~fP-~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f 373 (1014)
-|.+-|+.+||+..+... .+| +|....|++|+......+ ..|-.--+.+. +|--.+.|++=+.|+..|
T Consensus 189 RPE~DIl~~di~~ia~~~~W~~~~~~~~~~~~v~ai~v~a~it~-~gp~iymIsty------PG~~F~nf~s~~~li~~F 261 (651)
T PF03337_consen 189 RPEIDILPYDIKAIAQKSNWSKLRPYNPRALKVFAISVNAIITP-NGPSIYMISTY------PGKCFINFDSNKALISDF 261 (651)
T ss_pred CccceeecccHHhhhchhcccccccCCcccceEEEEEEEEEecC-CCceeEEEEec------CCceEEeCCCchHHHHHH
Confidence 478888889988877432 234 444567777653211111 11111112222 233345788888899999
Q ss_pred HHHHHH-hC----CCEEEEecccCCCcccccc
Q 001780 374 RDFIRE-VD----PDVMIGYNICKFDLPYLIE 400 (1014)
Q Consensus 374 ~~~i~~-~D----PDIIiGyNi~~FDlpyL~~ 400 (1014)
+++|.+ .. -=+++||=..-||+|.|..
T Consensus 262 L~Wl~e~~~~n~~ti~LvGy~ss~FD~pLLra 293 (651)
T PF03337_consen 262 LKWLRECIMKNIRTIILVGYFSSFFDFPLLRA 293 (651)
T ss_pred HHHHHHHHhccCceEEEeehhhhhhccHHHHh
Confidence 999998 44 3479999999999999988
No 106
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.03 E-value=10 Score=26.08 Aligned_cols=21 Identities=29% Similarity=0.760 Sum_probs=16.9
Q ss_pred ccccccccccC-cccCCcCCCC
Q 001780 925 SCIGCKALISN-GTLCSHCKGR 945 (1014)
Q Consensus 925 ~C~~C~~~~~~-~~~C~~C~~~ 945 (1014)
.|+.|++++.. ..+|++|..+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 38899999876 5789999754
No 107
>PRK05755 DNA polymerase I; Provisional
Probab=45.30 E-value=55 Score=42.79 Aligned_cols=73 Identities=27% Similarity=0.542 Sum_probs=45.4
Q ss_pred CcEEEEEEEEEccCCCCCCCCCCCceeEEEEEeeccCccccceeEEEeccccCCcCcceEeecCCHHHHHHHHHHHHHHh
Q 001780 301 PFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREV 380 (1014)
Q Consensus 301 plrilSfDIE~~~~~g~fP~~~~D~Ii~Is~~v~~~g~~~~~~~~vf~l~~~~~~~~~~V~~~~~E~eLL~~f~~~i~~~ 380 (1014)
.-.+++||+|+.+. +|..+.|+.|+..+. .|. . ..+.+.. + . .+.+..|.+++.
T Consensus 314 ~~~~~a~DtEt~~l-----~~~~~~i~~i~ls~~-~g~-~----~~ip~~~--------i----~-~~~l~~l~~~L~-- 367 (880)
T PRK05755 314 AAGLFAFDTETTSL-----DPMQAELVGLSFAVE-PGE-A----AYIPLDQ--------L----D-REVLAALKPLLE-- 367 (880)
T ss_pred ccCeEEEEeccCCC-----CcccccEEEEEEEeC-CCc-E----EEEeccc--------c----c-HHHHHHHHHHHh--
Confidence 34689999999863 245677888874321 121 0 1111110 0 1 167788888888
Q ss_pred CCCE-EEEecccCCCcccccc
Q 001780 381 DPDV-MIGYNICKFDLPYLIE 400 (1014)
Q Consensus 381 DPDI-IiGyNi~~FDlpyL~~ 400 (1014)
|+++ ++|||. .||+.+|..
T Consensus 368 d~~v~kV~HNa-kfDl~~L~~ 387 (880)
T PRK05755 368 DPAIKKVGQNL-KYDLHVLAR 387 (880)
T ss_pred CCCCcEEEecc-HhHHHHHHh
Confidence 6775 799998 689998765
No 108
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=44.90 E-value=19 Score=45.19 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=19.8
Q ss_pred hhHHhhhhhccccchHHHHhhhh
Q 001780 420 RRRLAVYCLKDAYLPQRLLDKLM 442 (1014)
Q Consensus 420 r~~l~~Y~lkDa~l~~~L~~kl~ 442 (1014)
...|..||-.|++.+.+++.++-
T Consensus 358 fq~L~~YCA~Dv~aThqVf~~lf 380 (1075)
T KOG3657|consen 358 FQPLMNYCARDVIATHQVFFRLF 380 (1075)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHh
Confidence 34688999999999999999864
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.62 E-value=18 Score=46.51 Aligned_cols=105 Identities=20% Similarity=0.374 Sum_probs=58.1
Q ss_pred cchhhHHHhhccccccchhhhhcCCccceeeecCCCCcccccccccccccccccccccCcccCCcCCCChHHHHHHHHHH
Q 001780 877 QISKPLLRIFEPILKNASKELLSGDHTRSISISTPSNSGIMKFAKRQLSCIGCKALISNGTLCSHCKGREAELYCKTVSQ 956 (1014)
Q Consensus 877 qi~~pl~ri~~~i~g~~~~~l~~g~~~r~~~~~~~~~~~~~~f~~~~~~C~~C~~~~~~~~~C~~C~~~~~~~~~~~~~~ 956 (1014)
++.||..-+| || |+ .|-.+|.+..+... +|...--.....|..|+.... ...|++|......+
T Consensus 589 kMkP~~h~LF-Pi-G~------~GG~~R~i~~A~~~-~g~~eVEVg~RfCpsCG~~t~-~frCP~CG~~Te~i------- 651 (1121)
T PRK04023 589 KMKPPVHVLF-PI-GN------AGGSTRDINKAAKY-KGTIEVEIGRRKCPSCGKETF-YRRCPFCGTHTEPV------- 651 (1121)
T ss_pred cCCCCCcccc-cc-cc------cCcccccHHHHHhc-CCceeecccCccCCCCCCcCC-cccCCCCCCCCCcc-------
Confidence 4566666555 55 33 13344544433321 232222234568999998753 57999998773222
Q ss_pred HHHHHHHHHHHHHHcccccCCCCC--cccccCCCCCcceeecchhhhHHHHHHhhc
Q 001780 957 VQELEVLFGRLWTQCQECQGSLHQ--DVLCTSRDCPIFYRRKKAQKDMAEAKLQLD 1010 (1014)
Q Consensus 957 ~~~~~~~~~~~~~~C~~C~~~~~~--~~~c~~~~cp~~y~r~~~~~~~~~~~~~~~ 1010 (1014)
..|.+|...... ...|...-=|.-..++..+..+..+.+-|.
T Consensus 652 ------------~fCP~CG~~~~~y~CPKCG~El~~~s~~~i~l~~~~~~A~~~lg 695 (1121)
T PRK04023 652 ------------YRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKELYDRALENLG 695 (1121)
T ss_pred ------------eeCccccCcCCCCcCCCCCCCCCccceEEecHHHHHHHHHHHhC
Confidence 238888644332 123444444556677777777777766553
No 110
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=40.14 E-value=9.4 Score=48.13 Aligned_cols=62 Identities=19% Similarity=0.419 Sum_probs=0.0
Q ss_pred cchhhHHHhhccccccchhhhhcCCccceeeecCCCCcccccccccccccccccccccCcccCCcCCCChH
Q 001780 877 QISKPLLRIFEPILKNASKELLSGDHTRSISISTPSNSGIMKFAKRQLSCIGCKALISNGTLCSHCKGREA 947 (1014)
Q Consensus 877 qi~~pl~ri~~~i~g~~~~~l~~g~~~r~~~~~~~~~~~~~~f~~~~~~C~~C~~~~~~~~~C~~C~~~~~ 947 (1014)
++.||..-+| || |+ .|-.+|.+..+.....|...-......|+.|+.... ...|+.|.....
T Consensus 617 kM~P~~h~LF-PI-G~------~GG~~R~i~~A~~~~~g~i~vei~~r~Cp~Cg~~t~-~~~Cp~CG~~T~ 678 (900)
T PF03833_consen 617 KMKPPPHVLF-PI-GE------AGGSRRDIQKAAKKGKGTIEVEIGRRRCPKCGKETF-YNRCPECGSHTE 678 (900)
T ss_dssp -----------------------------------------------------------------------
T ss_pred cCCCCCceec-cc-cc------cCcccccHHHHHhcCCCeeEEeeecccCcccCCcch-hhcCcccCCccc
Confidence 4666666555 55 33 144456665444332222222223468999987533 578888886643
No 111
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=38.89 E-value=16 Score=25.73 Aligned_cols=22 Identities=27% Similarity=0.791 Sum_probs=17.7
Q ss_pred cccccccccccC-cccCCcCCCC
Q 001780 924 LSCIGCKALISN-GTLCSHCKGR 945 (1014)
Q Consensus 924 ~~C~~C~~~~~~-~~~C~~C~~~ 945 (1014)
..|+.|++.+.. ...|++|..+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 579999998765 4799999764
No 112
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=36.92 E-value=16 Score=43.91 Aligned_cols=32 Identities=34% Similarity=0.476 Sum_probs=24.3
Q ss_pred cCCcceeeeccCceEEeeeEeeeccccchHHHH
Q 001780 497 TYEGATVLEARAGFYEKPIATLDFASLYPSIMM 529 (1014)
Q Consensus 497 ~yeGg~VleP~~G~y~~pV~~LDF~SLYPSIii 529 (1014)
+|.||.+.--.+|... +|..+|++|||||+|.
T Consensus 205 s~~GGr~~~~~~~~~~-~i~~yDvnSLYP~~m~ 236 (459)
T PF03175_consen 205 SYYGGRCEVFKPGIKN-KIYYYDVNSLYPSAMK 236 (459)
T ss_dssp EE-GGGB-TEEEESE----EEEEETTHHHHHHH
T ss_pred hcCCceeeeeeccccc-ceeeeeccCCcHHHHh
Confidence 8999999666777776 6999999999999988
No 113
>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=33.22 E-value=71 Score=32.46 Aligned_cols=21 Identities=33% Similarity=0.534 Sum_probs=17.2
Q ss_pred HHhhhhhccccchHHHHhhhh
Q 001780 422 RLAVYCLKDAYLPQRLLDKLM 442 (1014)
Q Consensus 422 ~l~~Y~lkDa~l~~~L~~kl~ 442 (1014)
.-+.|+..||++.+.|.++|.
T Consensus 149 ~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 149 EQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 446899999999999888763
No 114
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=31.73 E-value=28 Score=24.80 Aligned_cols=22 Identities=27% Similarity=0.708 Sum_probs=17.5
Q ss_pred ccccccccccC-cccCCcCCCCh
Q 001780 925 SCIGCKALISN-GTLCSHCKGRE 946 (1014)
Q Consensus 925 ~C~~C~~~~~~-~~~C~~C~~~~ 946 (1014)
+|+.|++.+.. ...|++|....
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 69999998765 47899998654
No 115
>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=29.38 E-value=1.1e+02 Score=31.02 Aligned_cols=21 Identities=24% Similarity=0.313 Sum_probs=15.7
Q ss_pred HHhhhhhccccchHHHHhhhh
Q 001780 422 RLAVYCLKDAYLPQRLLDKLM 442 (1014)
Q Consensus 422 ~l~~Y~lkDa~l~~~L~~kl~ 442 (1014)
.-+.|+..||+....|.++|.
T Consensus 140 ~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 140 DQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 356788888888888877763
No 116
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=27.97 E-value=20 Score=35.91 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=21.5
Q ss_pred cccccccccccC--cccCCcCCCChHHHHHH
Q 001780 924 LSCIGCKALISN--GTLCSHCKGREAELYCK 952 (1014)
Q Consensus 924 ~~C~~C~~~~~~--~~~C~~C~~~~~~~~~~ 952 (1014)
..|..|++.+.. ..+|++|.....+.|.+
T Consensus 4 ~nC~~CgklF~~~~~~iCp~C~~~~e~~f~k 34 (137)
T TIGR03826 4 ANCPKCGRLFVKTGRDVCPSCYEEEEREFEK 34 (137)
T ss_pred ccccccchhhhhcCCccCHHHhHHHHHHHHH
Confidence 489999997654 57999999866555443
No 117
>PRK00420 hypothetical protein; Validated
Probab=27.10 E-value=31 Score=33.40 Aligned_cols=24 Identities=13% Similarity=0.203 Sum_probs=19.0
Q ss_pred cccccccccccccC----cccCCcCCCC
Q 001780 922 RQLSCIGCKALISN----GTLCSHCKGR 945 (1014)
Q Consensus 922 ~~~~C~~C~~~~~~----~~~C~~C~~~ 945 (1014)
...+|+.|+.|+.. ..+|++|...
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCCe
Confidence 35799999998763 3799999873
No 118
>PF08408 DNA_pol_B_3: DNA polymerase family B viral insert; InterPro: IPR013617 This viral domain is found between the exonuclease domain of the DNA polymerase family B (IPR006133 from INTERPRO) and the IPR006134 from INTERPRO domain, connecting the two. ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=26.35 E-value=26 Score=35.16 Aligned_cols=43 Identities=30% Similarity=0.321 Sum_probs=32.0
Q ss_pred cccccchhHHHhhcCChhhhhHHhhhhhccccchHHHHhhhhhhH
Q 001780 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIF 445 (1014)
Q Consensus 401 kedv~~~~i~~l~~~~~~~r~~l~~Y~lkDa~l~~~L~~kl~~~~ 445 (1014)
|+||..+++-.-++ -+.-..++.||+.||.|+.-|.+..++..
T Consensus 88 KDDVdL~dmY~nYn--l~~a~em~~YCiHDacLCkyLw~Yy~i~~ 130 (149)
T PF08408_consen 88 KDDVDLSDMYKNYN--LDIALEMARYCIHDACLCKYLWDYYGIET 130 (149)
T ss_pred CCCCCHHHHHHhcc--HHHHHHHHHHHHhHHHHHHHHHHHcCcce
Confidence 88987776544332 34556899999999999999988766543
No 119
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.16 E-value=24 Score=35.34 Aligned_cols=26 Identities=31% Similarity=0.714 Sum_probs=22.6
Q ss_pred cccccccccccccCcccCCcCCCChH
Q 001780 922 RQLSCIGCKALISNGTLCSHCKGREA 947 (1014)
Q Consensus 922 ~~~~C~~C~~~~~~~~~C~~C~~~~~ 947 (1014)
....|-.|++++..|-+|.+|.....
T Consensus 80 l~~~CE~CG~~I~~Gr~C~~C~~~l~ 105 (137)
T TIGR03826 80 LGYPCERCGTSIREGRLCDSCAGELK 105 (137)
T ss_pred CcCcccccCCcCCCCCccHHHHHHHH
Confidence 45799999999999999999997654
No 120
>PF08988 DUF1895: Protein of unknown function (DUF1895); InterPro: IPR015081 The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown. ; PDB: 1ZW0_B 2P58_A 2UWJ_E 2Q1K_D 3PH0_B.
Probab=25.05 E-value=1.4e+02 Score=26.39 Aligned_cols=39 Identities=23% Similarity=0.296 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHhhhcCChHHHHH----hHHHhhhcccc
Q 001780 575 EILEELLAARKRAKADLKEAKDPLEKAV----LDGRQLALKIS 613 (1014)
Q Consensus 575 ~iL~~Ll~~R~~~K~~mk~~~d~~~~~~----ld~rQ~AlKi~ 613 (1014)
.+...|..++..+|+.|....+|.++.+ +++-|-|++|+
T Consensus 18 ~i~~~L~~a~~~vkr~L~~G~~P~eyQq~q~~~~AieAA~~Vi 60 (68)
T PF08988_consen 18 AIEQQLRQAQSQVKRKLDRGGTPQEYQQLQQQYDAIEAAIAVI 60 (68)
T ss_dssp HHHHHHHHHHHHHHHHHTCTSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999999889987754 45666666665
No 121
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=24.91 E-value=80 Score=27.11 Aligned_cols=22 Identities=27% Similarity=0.687 Sum_probs=17.4
Q ss_pred cccccccccccC-cccCC-cCCCC
Q 001780 924 LSCIGCKALISN-GTLCS-HCKGR 945 (1014)
Q Consensus 924 ~~C~~C~~~~~~-~~~C~-~C~~~ 945 (1014)
.+|+.|++++.. ...|+ .|+..
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~ 27 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREE 27 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHH
Confidence 589999999976 58895 68753
No 122
>TIGR02501 type_III_yscE type III secretion system protein, YseE family. Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized.
Probab=23.52 E-value=1.5e+02 Score=26.02 Aligned_cols=46 Identities=30% Similarity=0.343 Sum_probs=35.1
Q ss_pred cHHHHHHHHHHHHHHHHHhhhcCChHHHHH----hHHHhhhccccceeccc
Q 001780 573 LPEILEELLAARKRAKADLKEAKDPLEKAV----LDGRQLALKISANSVYG 619 (1014)
Q Consensus 573 lp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~----ld~rQ~AlKi~aNS~YG 619 (1014)
.-.++..|.+++..+|+.|+...+|..+.. +++-+.|.+|+ |.+|+
T Consensus 15 ~~~~~~~L~~a~~~lk~qL~~~~tp~qYq~l~~~~~A~~aA~~II-~~l~~ 64 (67)
T TIGR02501 15 ARAIIEQLEAALAELKEQLSRGGDPQQYQEWQLLADAIEAAIKII-EILTG 64 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence 456788999999999999999889987755 45666677776 44443
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.63 E-value=1e+02 Score=32.37 Aligned_cols=41 Identities=27% Similarity=0.454 Sum_probs=26.0
Q ss_pred cccccccccccC------cccCCcCCCChH-----HHHHHHHHHHHHHHHHH
Q 001780 924 LSCIGCKALISN------GTLCSHCKGREA-----ELYCKTVSQVQELEVLF 964 (1014)
Q Consensus 924 ~~C~~C~~~~~~------~~~C~~C~~~~~-----~~~~~~~~~~~~~~~~~ 964 (1014)
-.|+.|+...+. +..|+.|..... .....+..++..++..+
T Consensus 118 Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~~l~~~~ 169 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNSELIKELKEQIKELEEEL 169 (178)
T ss_pred EECCCCCcEEeHHHHhhcCCcCCCCCCCCeecccHHHHHHHHHHHHHHHHHh
Confidence 379999877643 689999987433 34444444565565544
No 124
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.07 E-value=46 Score=33.08 Aligned_cols=23 Identities=17% Similarity=0.430 Sum_probs=18.5
Q ss_pred cccccccccccccC---cccCCcCCC
Q 001780 922 RQLSCIGCKALISN---GTLCSHCKG 944 (1014)
Q Consensus 922 ~~~~C~~C~~~~~~---~~~C~~C~~ 944 (1014)
...+|+.|+.|+-. ..+|+.|..
T Consensus 27 L~~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred HHhhCcccCCcceeeCCeEECCCCCc
Confidence 45799999999833 489999984
Done!