Query 000502
Match_columns 1459
No_of_seqs 445 out of 1985
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:54:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000502.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000502hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0968 DNA polymerase zeta, c 100.0 3E-138 6E-143 1252.6 34.6 938 459-1459 52-1143(1488)
2 PTZ00166 DNA polymerase delta 100.0 4.1E-99 9E-104 971.4 48.5 548 819-1459 145-721 (1054)
3 KOG0969 DNA polymerase delta, 100.0 8.3E-97 2E-101 870.4 28.0 536 829-1459 171-727 (1066)
4 PHA02528 43 DNA polymerase; Pr 100.0 8.2E-78 1.8E-82 758.9 45.3 446 955-1459 104-615 (881)
5 PHA03036 DNA polymerase; Provi 100.0 8.6E-76 1.9E-80 734.1 46.0 460 956-1459 159-761 (1004)
6 PRK05762 DNA polymerase II; Re 100.0 3.9E-74 8.4E-79 727.5 45.8 462 838-1459 85-554 (786)
7 TIGR00592 pol2 DNA polymerase 100.0 1.2E-71 2.6E-76 726.3 45.1 483 856-1459 446-956 (1172)
8 smart00486 POLBc DNA polymeras 100.0 3.5E-70 7.5E-75 649.3 47.9 458 956-1459 2-469 (471)
9 PRK05761 DNA polymerase I; Rev 100.0 2.8E-69 6E-74 680.0 39.0 460 824-1459 91-574 (787)
10 COG0417 PolB DNA polymerase el 100.0 2.6E-68 5.6E-73 674.0 44.8 490 825-1459 72-569 (792)
11 PHA03334 putative DNA polymera 100.0 3.2E-60 6.9E-65 590.7 39.3 453 979-1459 274-819 (1545)
12 KOG0970 DNA polymerase alpha, 100.0 5.5E-61 1.2E-65 583.1 30.9 489 857-1458 469-987 (1429)
13 PHA02524 43A DNA polymerase su 100.0 3.2E-58 7E-63 547.8 35.8 400 933-1390 84-492 (498)
14 cd05534 POLBc_zeta DNA polymer 100.0 2E-54 4.3E-59 517.5 20.9 229 1230-1459 1-234 (451)
15 cd05533 POLBc_delta DNA polyme 100.0 7.4E-45 1.6E-49 429.3 17.7 173 1267-1459 5-183 (393)
16 PF00136 DNA_pol_B: DNA polyme 100.0 2.7E-45 5.8E-50 442.1 11.0 218 1230-1459 1-224 (466)
17 cd00145 POLBc DNA polymerase t 100.0 6E-42 1.3E-46 395.7 17.6 165 1266-1459 4-168 (323)
18 cd05778 DNA_polB_zeta_exo inac 100.0 1.1E-40 2.3E-45 369.0 25.7 222 955-1204 2-231 (231)
19 cd05532 POLBc_alpha DNA polyme 100.0 1.1E-41 2.3E-46 403.5 17.0 163 1266-1459 9-171 (400)
20 cd05536 POLBc_B3 DNA polymeras 100.0 1.7E-41 3.8E-46 398.2 17.0 163 1267-1459 6-168 (371)
21 cd05530 POLBc_B1 DNA polymeras 100.0 2.7E-40 5.9E-45 387.0 17.1 165 1266-1458 14-178 (372)
22 cd05537 POLBc_Pol_II DNA polym 100.0 1.1E-38 2.3E-43 374.1 15.9 153 1267-1459 5-157 (371)
23 cd05777 DNA_polB_delta_exo DED 100.0 4.5E-37 9.8E-42 339.7 25.0 224 954-1211 4-228 (230)
24 cd05531 POLBc_B2 DNA polymeras 100.0 3.7E-38 8E-43 367.5 16.1 155 1266-1458 6-160 (352)
25 cd05538 POLBc_Pol_II_B DNA pol 100.0 9.7E-38 2.1E-42 363.3 15.2 141 1267-1459 5-145 (347)
26 KOG1798 DNA polymerase epsilon 100.0 1.2E-36 2.6E-41 375.8 24.3 447 955-1459 244-844 (2173)
27 TIGR00592 pol2 DNA polymerase 100.0 2.3E-34 5.1E-39 377.1 -7.4 385 954-1399 195-618 (1172)
28 cd05780 DNA_polB_Kod1_like_exo 100.0 3.5E-30 7.5E-35 278.3 24.3 195 955-1206 1-195 (195)
29 cd05779 DNA_polB_epsilon_exo D 100.0 1.1E-28 2.4E-33 268.7 21.4 200 956-1203 1-203 (204)
30 cd05781 DNA_polB_B3_exo DEDDy 100.0 3.3E-28 7.2E-33 262.0 23.1 184 955-1206 1-188 (188)
31 PF03104 DNA_pol_B_exo1: DNA p 100.0 8.9E-29 1.9E-33 283.0 15.3 258 824-1156 63-325 (325)
32 cd05785 DNA_polB_like2_exo Unc 99.9 5E-27 1.1E-31 256.5 21.3 192 954-1203 6-206 (207)
33 cd05784 DNA_polB_II_exo DEDDy 99.9 1E-26 2.2E-31 251.5 23.1 188 955-1204 1-193 (193)
34 cd05776 DNA_polB_alpha_exo ina 99.9 2.3E-27 5E-32 263.4 17.9 220 955-1213 1-233 (234)
35 cd05160 DEDDy_DNA_polB_exo DED 99.9 1.2E-26 2.7E-31 249.9 22.9 198 959-1203 1-198 (199)
36 cd05783 DNA_polB_B1_exo DEDDy 99.9 3.4E-24 7.4E-29 233.8 21.8 190 954-1204 2-202 (204)
37 KOG0969 DNA polymerase delta, 99.9 4.8E-26 1E-30 272.0 4.9 144 19-168 58-242 (1066)
38 PTZ00166 DNA polymerase delta 99.9 3.7E-23 8.1E-28 268.9 15.6 146 9-167 40-229 (1054)
39 cd05535 POLBc_epsilon DNA poly 99.8 9.7E-21 2.1E-25 228.6 13.8 105 1350-1459 219-338 (621)
40 cd05782 DNA_polB_like1_exo Unc 99.8 4.8E-18 1.1E-22 186.2 18.7 166 970-1204 42-207 (208)
41 PHA02563 DNA polymerase; Provi 99.6 4.2E-15 9E-20 183.8 17.5 347 1031-1458 50-487 (630)
42 PHA02523 43B DNA polymerase su 99.6 1.8E-15 3.8E-20 173.5 7.5 75 1384-1459 36-116 (391)
43 KOG0968 DNA polymerase zeta, c 99.3 2.5E-12 5.4E-17 160.4 6.5 169 1-169 1-209 (1488)
44 PF10108 DNA_pol_B_exo2: Predi 99.3 1.9E-10 4.1E-15 126.2 18.5 170 973-1210 3-173 (209)
45 PF03104 DNA_pol_B_exo1: DNA p 99.0 1.7E-10 3.8E-15 132.7 1.9 96 53-162 2-123 (325)
46 PF13482 RNase_H_2: RNase_H su 98.9 6.1E-09 1.3E-13 109.2 11.3 158 960-1206 1-163 (164)
47 PRK05762 DNA polymerase II; Re 98.8 2.1E-09 4.6E-14 138.7 5.5 117 33-160 6-130 (786)
48 PRK05761 DNA polymerase I; Rev 98.3 4.3E-07 9.4E-12 117.3 5.3 109 35-166 21-154 (787)
49 COG3359 Predicted exonuclease 98.2 2.8E-05 6.1E-10 86.6 14.5 160 958-1206 99-265 (278)
50 COG0417 PolB DNA polymerase el 97.7 5.6E-05 1.2E-09 98.5 7.7 115 42-162 6-134 (792)
51 PHA02735 putative DNA polymera 97.6 0.00048 1E-08 81.1 12.6 135 1152-1304 170-309 (716)
52 PRK06310 DNA polymerase III su 97.5 0.0038 8.1E-08 71.3 17.2 105 957-1070 7-114 (250)
53 PRK08517 DNA polymerase III su 97.4 0.0033 7.1E-08 72.2 15.3 103 957-1069 68-172 (257)
54 PRK06309 DNA polymerase III su 97.4 0.0025 5.3E-08 71.9 14.0 102 958-1070 3-107 (232)
55 TIGR03491 RecB family nuclease 97.3 0.0058 1.3E-07 75.5 17.4 122 1025-1205 326-456 (457)
56 PRK06063 DNA polymerase III su 97.3 0.0073 1.6E-07 71.2 17.0 104 957-1069 15-119 (313)
57 PRK07883 hypothetical protein; 97.2 0.0057 1.2E-07 77.3 15.6 104 957-1070 15-121 (557)
58 smart00479 EXOIII exonuclease 97.0 0.017 3.6E-07 60.5 15.2 102 959-1069 2-106 (169)
59 cd06136 TREX1_2 DEDDh 3'-5' ex 97.0 0.011 2.4E-07 63.9 14.3 107 960-1070 2-125 (177)
60 PRK07942 DNA polymerase III su 96.9 0.016 3.4E-07 65.6 15.1 106 957-1069 6-118 (232)
61 PRK06195 DNA polymerase III su 96.8 0.029 6.2E-07 66.1 16.6 100 958-1069 2-105 (309)
62 cd06130 DNA_pol_III_epsilon_li 96.8 0.014 3E-07 60.7 12.4 98 960-1069 2-102 (156)
63 TIGR01405 polC_Gram_pos DNA po 96.7 0.016 3.4E-07 78.8 15.2 102 958-1069 191-295 (1213)
64 TIGR01406 dnaQ_proteo DNA poly 96.7 0.015 3.3E-07 65.5 12.5 100 959-1067 2-105 (225)
65 PRK07740 hypothetical protein; 96.7 0.047 1E-06 62.3 16.4 101 956-1065 58-162 (244)
66 PRK05601 DNA polymerase III su 96.7 0.02 4.3E-07 68.6 13.8 195 956-1206 45-245 (377)
67 PRK06807 DNA polymerase III su 96.7 0.016 3.5E-07 68.4 13.0 103 957-1069 8-113 (313)
68 PRK05711 DNA polymerase III su 96.7 0.02 4.4E-07 65.2 13.2 167 955-1206 2-172 (240)
69 cd06131 DNA_pol_III_epsilon_Ec 96.6 0.014 3.1E-07 61.7 11.1 100 960-1068 2-105 (167)
70 cd06138 ExoI_N N-terminal DEDD 96.6 0.0091 2E-07 64.9 9.3 103 961-1069 2-110 (183)
71 TIGR00573 dnaq exonuclease, DN 96.4 0.019 4.2E-07 64.1 10.8 101 957-1067 7-110 (217)
72 PRK08074 bifunctional ATP-depe 96.3 0.061 1.3E-06 72.1 16.3 102 958-1069 4-109 (928)
73 PRK09146 DNA polymerase III su 96.3 0.091 2E-06 59.9 15.4 102 956-1066 46-151 (239)
74 TIGR01407 dinG_rel DnaQ family 96.2 0.068 1.5E-06 71.0 16.2 101 959-1069 2-105 (850)
75 cd06125 DnaQ_like_exo DnaQ-lik 96.0 0.03 6.4E-07 55.0 8.3 69 961-1070 2-70 (96)
76 PRK07246 bifunctional ATP-depe 95.6 0.19 4E-06 66.7 16.0 100 958-1068 8-110 (820)
77 cd06127 DEDDh DEDDh 3'-5' exon 95.5 0.03 6.6E-07 57.1 6.8 98 961-1067 2-102 (159)
78 PRK11779 sbcB exonuclease I; P 95.5 0.12 2.6E-06 64.4 13.0 104 956-1065 5-115 (476)
79 cd06134 RNaseT DEDDh 3'-5' exo 95.3 0.45 9.7E-06 52.3 15.5 104 960-1069 8-127 (189)
80 PRK07247 DNA polymerase III su 95.3 0.2 4.3E-06 55.6 12.5 93 958-1060 6-101 (195)
81 cd06133 ERI-1_3'hExo_like DEDD 95.1 0.53 1.2E-05 49.9 14.7 104 960-1068 2-114 (176)
82 cd06137 DEDDh_RNase DEDDh 3'-5 94.6 0.11 2.3E-06 55.5 7.9 90 961-1060 2-100 (161)
83 TIGR01298 RNaseT ribonuclease 94.2 1.6 3.5E-05 48.5 16.3 105 958-1068 9-129 (200)
84 PRK09145 DNA polymerase III su 94.0 0.19 4E-06 55.6 8.4 104 957-1069 29-137 (202)
85 PRK07748 sporulation inhibitor 93.8 0.52 1.1E-05 52.4 11.6 110 957-1070 4-119 (207)
86 PRK06722 exonuclease; Provisio 93.8 1.5 3.3E-05 51.4 15.7 106 958-1069 6-115 (281)
87 COG0847 DnaQ DNA polymerase II 93.2 0.55 1.2E-05 52.9 10.6 106 957-1070 13-121 (243)
88 PF01612 DNA_pol_A_exo1: 3'-5' 93.0 1.1 2.4E-05 47.0 12.0 52 1151-1206 119-171 (176)
89 PF03175 DNA_pol_B_2: DNA poly 92.9 0.016 3.5E-07 71.4 -2.2 44 1350-1407 329-372 (459)
90 PRK05168 ribonuclease T; Provi 92.3 0.72 1.6E-05 51.6 10.0 107 957-1069 17-139 (211)
91 PF08490 DUF1744: Domain of un 92.0 8.3 0.00018 47.5 19.1 214 1208-1458 121-345 (396)
92 PRK05359 oligoribonuclease; Pr 91.8 0.82 1.8E-05 50.1 9.4 107 958-1070 4-124 (181)
93 PRK00448 polC DNA polymerase I 91.5 1.9 4.2E-05 60.2 14.4 102 958-1069 420-524 (1437)
94 cd06145 REX1_like DEDDh 3'-5' 91.2 1.1 2.4E-05 47.4 9.3 87 961-1059 2-91 (150)
95 cd06135 Orn DEDDh 3'-5' exonuc 89.8 1.1 2.3E-05 48.6 8.0 102 960-1067 2-117 (173)
96 COG2176 PolC DNA polymerase II 89.7 0.51 1.1E-05 63.0 6.3 103 958-1070 422-527 (1444)
97 KOG1798 DNA polymerase epsilon 85.6 1.1 2.4E-05 60.8 5.6 51 1200-1250 1583-1633(2173)
98 cd06141 WRN_exo DEDDy 3'-5' ex 82.4 19 0.00041 38.3 12.6 54 1150-1206 115-168 (170)
99 cd06144 REX4_like DEDDh 3'-5' 82.4 4.7 0.0001 42.7 7.9 44 1013-1060 50-93 (152)
100 PRK09182 DNA polymerase III su 82.3 3.3 7.1E-05 49.0 7.3 97 956-1063 36-140 (294)
101 PTZ00315 2'-phosphotransferase 81.4 72 0.0016 41.4 18.9 105 957-1065 56-175 (582)
102 cd06139 DNA_polA_I_Ecoli_like_ 81.1 77 0.0017 34.0 16.8 52 1150-1206 109-166 (193)
103 PRK05755 DNA polymerase I; Pro 74.3 37 0.00081 46.0 14.4 70 958-1060 316-386 (880)
104 PF08408 DNA_pol_B_3: DNA poly 73.8 3.2 6.9E-05 44.1 3.4 62 1162-1226 85-146 (149)
105 cd06149 ISG20 DEDDh 3'-5' exon 72.1 8.1 0.00018 41.3 6.2 90 961-1060 2-93 (157)
106 PF00929 RNase_T: Exonuclease; 72.0 2.5 5.4E-05 43.1 2.2 99 960-1066 1-105 (164)
107 PRK07983 exodeoxyribonuclease 47.7 62 0.0013 36.9 7.9 84 960-1059 3-89 (219)
108 cd05767 IgC_MHC_II_alpha Class 38.1 29 0.00063 34.3 3.1 24 45-68 2-29 (94)
109 cd06146 mut-7_like_exo DEDDy 3 33.0 75 0.0016 35.2 5.6 53 1149-1206 139-191 (193)
110 cd05770 IgC_beta2m Class I maj 24.8 70 0.0015 31.7 3.2 25 45-69 2-30 (93)
111 KOG0970 DNA polymerase alpha, 24.5 2E+02 0.0043 39.9 7.8 32 132-163 464-495 (1429)
112 cd06129 RNaseD_like DEDDy 3'-5 23.7 1.2E+02 0.0025 32.5 4.8 66 1136-1206 94-159 (161)
No 1
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=2.8e-138 Score=1252.57 Aligned_cols=938 Identities=35% Similarity=0.475 Sum_probs=723.3
Q ss_pred CccccHhHHhhHHHHhhhhhhccCC-CchhhhhhccccCCCCchhHHHHHHhhhchh---HHhhHHHHHHHHhhcccccc
Q 000502 459 PQATDTEALGLLKWLATSQAAEDLN-SDDELLHETILSPLLPETTIDKVLEKANTDY---ERESQKECQDILDSIEDEVN 534 (1459)
Q Consensus 459 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~ 534 (1459)
+...|+++.|..+|+++++++++++ .+|+.+.+|+|.|..+.+.|.+.||.|..++ ..|||++|+++|+|++-+..
T Consensus 52 ~~v~~a~~~g~~~~~~s~g~l~~i~~k~d~~~t~t~l~~~d~~aqi~k~le~a~~~~~~a~~esq~~~~~~v~sv~~vk~ 131 (1488)
T KOG0968|consen 52 IRVFGANEEGETVCCFSHGVLPYIYVKYDSFATTTDLEVPDFLAQIQKSLEYALALAARANPESQKPNLNAVQSVQLVKG 131 (1488)
T ss_pred ceecccccccceeeeeecccchhhhhhhhhhccccccccccHHHHHHHHHHHHHHHHhhcChhhhcchHHHHHHHHhcCC
Confidence 3568999999999999999999999 9999999999999999999999999999999 99999999999999776544
Q ss_pred cccccccCCCCCCCCCCCCCCCCC----------CccccCCCCCCcccCCCCCCCCCCchhhhhhhhhcccccccccCcc
Q 000502 535 VDGLEERNSSTVDPSNHPETSSHK----------KIPQIDGSSDDLYLLPCSGSSGNSSKKEIKSESIRSFQHQVPQDTW 604 (1459)
Q Consensus 535 ~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 604 (1459)
+.-.-...+-+...++..-++|.+ +||.-..|. +.|.++...+.+.+.+ .-...+.+.
T Consensus 132 ~p~~~~~~~~s~~~k~~l~~~sck~rl~el~rdg~ipnk~is~---------~esh~~y~~~r~~d~n--~~~~~~ikv- 199 (1488)
T KOG0968|consen 132 IPFYGYSFCFSKFLKICLFSPSCKDRLVELFRDGAIPNKVISV---------YESHLPYLLQRMVDHN--LYGCAPIKV- 199 (1488)
T ss_pred CCccccccchhhHHHHHhcCchhHHHHHHHHhcccCCCccccc---------chhccchhhhhhhhcc--cccceeeec-
Confidence 332222223333344444445443 466555555 4444554444444433 112233333
Q ss_pred ccccccccc-cccccccccceecccccCCcccccccccccceeeccccCccCcccccccCCccccccccccc--cc--cc
Q 000502 605 TNAASKCNV-KKKLWGSLPFSVSEQFNKDIETVSCNISSLCVTEVKDHGATGSLVGNELGKSFDALEREDAD--AH--DI 679 (1459)
Q Consensus 605 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~~ 679 (1459)
.+...+|. .|.+||.+||++++. ..+.+. ++.+. ......+++++........++.+.+...+ .+ ++
T Consensus 200 -ds~~~~n~~dnsv~d~~p~t~sdn-~~l~ds--~~~s~----kl~~t~lsd~~~~~~~~~~I~~l~e~~kd~~kcrn~t 271 (1488)
T KOG0968|consen 200 -DSSIIKNDVDNSVFDNVPVTVSDN-LALLDS--CWLSE----KLIHTDLSDTPASSPNSLLITSLAEIWKDEAKCRNLT 271 (1488)
T ss_pred -chhhhcCCcccccccCcceeeCcc-HHHHhh--cCchh----ccCcchhhhccccCCCcceeeehHHhhhhHHHhhccc
Confidence 33455555 999999999999987 233333 33333 45556677777777777778887777665 22 11
Q ss_pred hhcccccCccHHHHHHhhh--ccccCCCCCCccccccc--ccccchhhhhhhhhhhcccccccccccccCCCCCCCc---
Q 000502 680 KEATAVTGGSVRDLMRRKR--SYRESSECEPPRVKRVN--VTGEQKNALSMCEKQLEFDTLQNDECEKCPLKGGTGI--- 752 (1459)
Q Consensus 680 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 752 (1459)
--.....+|+++|+|++++ +.|++...+++..+++. ++++.++ ..+|+...++ +...-|++.+-+|.++
T Consensus 272 ~s~e~~~~s~l~d~~~k~~~~~~~esi~sq~~kse~~~~~~~~~~~E-t~~~~s~~q~---~~~~~E~~~f~~~~~~~~s 347 (1488)
T KOG0968|consen 272 SSDETNSFSKLHDSQFKLKEESSHESISSQHMKSEKLLLNEIKEKHE-TNRRVSRFQG---VLPSNEFCLFYSGARTNES 347 (1488)
T ss_pred cchhhhccCchhhhcccchhhcccCCchHHHHHHHHHHHhhhccCCC-cccccccccc---cccchHHHHHHhcCCCCcc
Confidence 1112567899999999988 44488889999988876 7777765 6666666666 3344455555555444
Q ss_pred ---ccccccccCCC------------------------------CCCCCCCCc-------------------ceee----
Q 000502 753 ---STVCKENMESP------------------------------SPFDTKKED-------------------ASVS---- 776 (1459)
Q Consensus 753 ---~~~~~~~~~~~------------------------------~~~~~~~~~-------------------~~~~---- 776 (1459)
|..|++.|+.. +++.+..+. +.+.
T Consensus 348 ~~~s~~~e~~Vs~~S~~~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~ 427 (1488)
T KOG0968|consen 348 DIDSQNREEHVSQISMSQKGNWSNPPLTAIQMKKETLPNIESILVSSATQLESSNSGTLFLSREEVEICDDLGIVLKSVF 427 (1488)
T ss_pred cccCcchhhccccccccccccccCCCccccchhhhhhhhhhhccccccccccccCCCccccccccccccchhcccccccc
Confidence 44455555511 122211110 0000
Q ss_pred ------------------cC--CCccccccccccc--ccCC--CcccccCCCCC-----------------CCCCCCcCC
Q 000502 777 ------------------VG--DWKADNCKESKFD--ATSV--EPRELQSDHPN-----------------NNDSNLNQG 815 (1459)
Q Consensus 777 ------------------~~--~~~~~~~~~~~~~--~~~~--~~~~~~~~~~~-----------------~~~~~~~~~ 815 (1459)
.. .|+..++...+++ .+.+ |+..-|+.+-- +....+.++
T Consensus 428 nS~a~~~~~~s~~~~l~s~~k~~~~~~~~~s~~~~l~~~~~~~~a~~~~~~~~v~a~~ts~~~~~~~~~~~e~~k~~~q~ 507 (1488)
T KOG0968|consen 428 NSYAERTSTISPLSPLRSAKKMAPKFRQERSPSLQLDDGMVTRIAESQQTRSSVGASKTSIIEQPGEDPMEEDLKYREQA 507 (1488)
T ss_pred cccccccccccccccccchhhhcchhhcCCCCCccccCCcceehhhhhcCccccCCCCCccCCCCCcchhHHHhHHhhcC
Confidence 00 2445555555554 2222 55555555411 111134445
Q ss_pred ccccCCceeccCCceEEeecCCCCCChhHHHHHhhhcCCCcc-----ccccccceeecC-----------CCcccc-cee
Q 000502 816 SLTGVPTLYLNDGSCLYMLRPPFSPPSVDSVHKWLLHDDKGA-----SGDMDKASVEHS-----------SLKGSD-IRP 878 (1459)
Q Consensus 816 ~~~~~p~~y~~d~s~~~~lt~~~sp~s~~~v~~wL~~~~~~~-----~~~~~~r~~~d~-----------~~s~~~-~~~ 878 (1459)
.-.|.|.+--.|+++.++.+ +.|+.+.. -+|-.+++... +..+..+-..|- +..+.| ...
T Consensus 508 ~~~~~~~~~~~d~s~~~~~~--~~p~~d~k-lQ~psD~~~~~~~~~~s~~P~~~~~~~~~~S~~e~~s~~nv~~tgE~l~ 584 (1488)
T KOG0968|consen 508 PEEGIPERQLEDDSNEALSD--GHPKNDYK-LQPPSDDEDSNTMSLKSQKPVERAEADDVDSEVEDDSELNVKGTGEVLE 584 (1488)
T ss_pred cccccccccccccchhhHhh--cCCccccc-cCCCCCccccchhhhhccCchhhhhhccCCccccchhhcCccccceeeE
Confidence 57889999889999888877 33444333 56666554432 011111111111 001111 000
Q ss_pred cchh-hhhcccccCCCCCCCCCCcccccccccccccCCCcccccccccccccCCCCCC-CCCCCccCCcCCCCCCCCCCC
Q 000502 879 VLEE-MHQEADEMISTEPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRS-KPTPLSQIGFQDPASAGAGEQ 956 (1459)
Q Consensus 879 ~~~~-~~~~~~~~s~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~-~~~p~~~~~~~~~~~~~~~~~ 956 (1459)
+... --+...+.+.++.++|.+-. +.+..++..+....++|||+||+..+ ..++.+..|+++++..+.++.
T Consensus 585 ~~s~pd~~~s~k~~~t~s~~d~~~~-------~~~~~~~~~~~~~~e~s~i~~p~~~s~~~~~~~v~~~q~~~~~~~~~~ 657 (1488)
T KOG0968|consen 585 IHSDPDDQSSEKWALTPSAYDQNFK-------SMNEQLFDAAKIENELSQIRGPTAKSVYTFETSVAGAQKSKPVEQTQL 657 (1488)
T ss_pred eecCcccchhhhhccChHHHHhhHH-------HHhhhhhcccchhhhhhhccCCccccccccchhhhcccccccccccce
Confidence 0000 11123344555544444333 34444444456788999999999884 467888889999888899999
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCC-----CceEEEEEEEecCCCcc---c-cccCCCCCcEEEEeCCH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDS-----DHAVEIYVLLYCKSESH---Q-RSLVGIPDCKVFVCSKE 1027 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~-----d~~~ei~vLv~~~~~~~---~-~~~~~i~g~~V~~f~SE 1027 (1459)
|+++++|+|+.+||++.|||.+|+|.+|+||++.+. +.+..++++++....++ . ..+.++.|++|.++.+|
T Consensus 658 Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~gv~Vv~~~~~ds~~~t~~~~~~~~~~V~~~~sE 737 (1488)
T KOG0968|consen 658 LTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVGVIVVDKVCPDSHVQTTTLGGIYGCRVVVMESE 737 (1488)
T ss_pred eeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcccceeeeeEEEEeccCccccccccccCCcCCceEEEehhH
Confidence 999999999999999999999999999999999883 33444555555433121 2 23478889999999999
Q ss_pred HHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHH
Q 000502 1028 IHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAE 1107 (1459)
Q Consensus 1028 kELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g 1107 (1459)
++|+++++++|..+||||++||++++++||||++|++.||+++...++|++.....+.
T Consensus 738 ~elf~ev~~~i~q~DPDIl~GyEi~~~SWGyl~eR~~~l~~di~~~lsRv~~~~~~n~---------------------- 795 (1488)
T KOG0968|consen 738 LELFEEVAKLIVQYDPDILLGYEIHNLSWGYLIERAKLLGIDISRDLSRVKCYEKTNE---------------------- 795 (1488)
T ss_pred HHHHHHHHHHHHhcCcceeeeeeecccchHHHHHHHHHhcchHHHHHhcCCChhhhhh----------------------
Confidence 9999999999999999999999999999999999999999999999999986543210
Q ss_pred hhhhhhhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHH
Q 000502 1108 SLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYR 1187 (1459)
Q Consensus 1108 ~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~r 1187 (1459)
+.....||++|.+++.|.|||+|++||++|.+++|.+|+||+|++++|+++.|.++++.|++||.++....|++
T Consensus 796 ------~d~~~ewg~tt~S~i~i~GR~~lNiWRilR~eV~L~nYtlEsv~~nVL~kk~P~~~~~~Lt~~~~s~~~~~r~~ 869 (1488)
T KOG0968|consen 796 ------SDDEREWGYTTISGINIVGRHVLNIWRILRSEVALTNYTLESVVFNVLRKKIPMFDFAVLTRWWKSKRSAERND 869 (1488)
T ss_pred ------hhhhhhccceeeccccccchhhhhHHHHHhhhhhhhhccHHHHHHHHHHhhcCCCcHHHHHHHHhcccHHHHHH
Confidence 11234799999999999999999999999999999999999999999999999999999999999999889999
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccC
Q 000502 1188 CVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECL 1267 (1459)
Q Consensus 1188 vl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~G 1267 (1459)
++.|+++++.++++|+.++++|.++.||||++||+|.+|++||||+||||||+|.||++|||+|+|+.+||..|+|+||.
T Consensus 870 ~l~y~l~Ra~~NlelLsq~d~i~k~~E~ARv~GIdF~sV~tRGSQ~rVESmllRiAk~~Nyi~~SPs~kQv~~q~A~Ecv 949 (1488)
T KOG0968|consen 870 VLNYLLSRARLNLELLSQLDWILKNSEMARVIGIDFHSVLTRGSQFRVESMLLRIAKPMNYIAPSPSHKQVAMQGAPECV 949 (1488)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHhhHHHHHhhcceeeEEeeccchhhHHHHHHHHhcccccccCCccHHHHhhcCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccc---cCCCcccCCCchhhcccCcccccCCCCce
Q 000502 1268 PLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKEN---TLGVSSFRPDLHVLRDLKDELLIPPNGVM 1344 (1459)
Q Consensus 1268 glVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n---~~Gv~~~~~d~~~l~~Lkd~i~isPngv~ 1344 (1459)
|+||||++.||.|||+||||||||||||||||||||||+|++...+.+ ++|++.|+.+++.+.++++++.++|||++
T Consensus 950 PLVMEPeS~fY~~PViVLDFQSLYPSivIAYNyCySTcLG~v~~l~~~~e~~LG~s~~s~~~dil~~~~ndV~isPNgv~ 1029 (1488)
T KOG0968|consen 950 PLVMEPESAFYFDPVIVLDFQSLYPSIVIAYNYCYSTCLGKVGNLNQMNEIKLGVSKYSLPPDILVLAKNDVTISPNGVM 1029 (1488)
T ss_pred ceeecchhhhccCceEEEEchhhcchHHHhHHHHHHHhhhHHHhhccccceeeeeeeccCCHHHHHHHhcceeeCCCceE
Confidence 999999999999999999999999999999999999999999876544 79999999999999988999999999999
Q ss_pred ecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHH
Q 000502 1345 YVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQ 1424 (1459)
Q Consensus 1345 FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~ 1424 (1459)
|||+++|+|+||+||++||++|.|||++||+++ ++..++++||+||||||++||++||||+|+|||||||.|+||+|++
T Consensus 1030 yVK~sVRkgvLpkmLeEIL~tRiMVKkaMK~~~-~~~~L~RiLnaRQLALKLiANVTYGYTsA~FSGRMPCaElADsIV~ 1108 (1488)
T KOG0968|consen 1030 YVKPSVRKGVLPKMLEEILATRIMVKKAMKRTK-DNKKLKRILNARQLALKLIANVTYGYTSANFSGRMPCAELADSIVQ 1108 (1488)
T ss_pred EechhhhhhhHHHHHHHHHHHHHHHHHHHHHhc-chHHHHHHhhhHHHHHHHHhhccccccccccCCCCchHHHHHHHHH
Confidence 999999999999999999999999999999998 5678999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1425 CGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1425 ~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
+|||+|++||++|+....|||+||||||||+||+|
T Consensus 1109 ~GRETLEraIe~Vn~~d~w~AkVVYGDTDSmFVlL 1143 (1488)
T KOG0968|consen 1109 KGRETLERAIEMVNRGDYWGAKVVYGDTDSMFVLL 1143 (1488)
T ss_pred hhHHHHHHHHHHHhcCCcCCeEEEEcCCCceEEEe
Confidence 99999999999999999999999999999999986
No 2
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=4.1e-99 Score=971.36 Aligned_cols=548 Identities=26% Similarity=0.414 Sum_probs=464.5
Q ss_pred cCCce-eccCC-ceEEeecCCCCCChhHHHHHhhhcCC---------------CccccccccceeecCCCccccceecch
Q 000502 819 GVPTL-YLNDG-SCLYMLRPPFSPPSVDSVHKWLLHDD---------------KGASGDMDKASVEHSSLKGSDIRPVLE 881 (1459)
Q Consensus 819 ~~p~~-y~~d~-s~~~~lt~~~sp~s~~~v~~wL~~~~---------------~~~~~~~~~r~~~d~~~s~~~~~~~~~ 881 (1459)
+-+++ |+.++ ..+++|+. .+|-.+..+.+.|.... ++.|++...|||+|+++.+++|+.+..
T Consensus 145 k~sl~gY~~~~~~~flKIt~-~~P~~v~klR~~Le~g~~~~~~~~~~~~~~~vyEsnI~f~lRFmID~~I~g~~Wi~i~~ 223 (1054)
T PTZ00166 145 KESLMYYKGNGEKDFLKITV-QLPKMVPRLRSLIESGVVVCGGGWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPK 223 (1054)
T ss_pred eeeeceeCCCCceeEEEEEE-cCHHHHHHHHHHHHcCCcccccccccccccceeecCCCHHHHHHhccCCCceeEEEecC
Confidence 34554 76544 68999998 99999999999886541 245999999999999999999999986
Q ss_pred hh--hhc-ccccCCCCCCCCCCcccccccccccccCCCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCce
Q 000502 882 EM--HQE-ADEMISTEPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLT 958 (1459)
Q Consensus 882 ~~--~~~-~~~~s~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~Lt 958 (1459)
+- .+. ..+.|+|++|++|+..++..|.. ++. | ...|+|+
T Consensus 224 ~~~~~~~~~~~~s~c~~E~~~~~~~l~~~~~-------------------~~~------~-------------~~~pplr 265 (1054)
T PTZ00166 224 GKYKIRPPKKKTSTCQIEVDCSYEDLIPLPP-------------------EGE------Y-------------LTIAPLR 265 (1054)
T ss_pred cceeecccccCCCcceEEEEEehhheeeccc-------------------ccc------c-------------CCCCCcE
Confidence 53 233 35789999999999887666650 000 1 1236799
Q ss_pred EEEEEEEeCcCCC-CCCCCCCCcEEEEEEEeecCCCce--EEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHH
Q 000502 959 LLSIEVQAESRGD-LRPDPRYDSINVVALAFENDSDHA--VEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFI 1035 (1459)
Q Consensus 959 iLSIEIet~srg~-lfPDPe~DpI~~Is~~v~~d~d~~--~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFi 1035 (1459)
+|+|||||.++.+ .||+|+.|+|++|++.+...+... ....++.. ..+..+.|..|..|++|++||.+|+
T Consensus 266 ilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl-------~~c~~i~g~~V~~f~sE~eLL~~f~ 338 (1054)
T PTZ00166 266 ILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTL-------KECASIAGANVLSFETEKELLLAWA 338 (1054)
T ss_pred EEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEec-------CccccCCCceEEEeCCHHHHHHHHH
Confidence 9999999987755 499999999999999877654322 12222222 2345667889999999999999999
Q ss_pred HHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhh
Q 000502 1036 KILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAI 1115 (1459)
Q Consensus 1036 dlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~ 1115 (1459)
++|+.+|||||+|||+++||||||++||+.+|+..+..|||.+...... ... ..
T Consensus 339 ~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~-~~~-------------------------~~ 392 (1054)
T PTZ00166 339 EFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVI-KDS-------------------------KF 392 (1054)
T ss_pred HHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccc-ccc-------------------------cc
Confidence 9999999999999999999999999999999998777899976432110 000 01
Q ss_pred hccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHH
Q 000502 1116 IEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGR 1195 (1459)
Q Consensus 1116 ~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkD 1195 (1459)
....||.++.+.+.|.||++||+|++++++++|.+|+|++||+++||++|++++++.|++||..+ ...|+++++||++|
T Consensus 393 ~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~-~~~~~~l~~Y~l~D 471 (1054)
T PTZ00166 393 SSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGS-PETRRRIAVYCLKD 471 (1054)
T ss_pred ccccccccccceeEeeeEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcC-hhhHHHHHHHHHHH
Confidence 12457777777899999999999999999999999999999999999999999999999999754 35689999999999
Q ss_pred HHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccCCeeeeccC
Q 000502 1196 AKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPES 1275 (1459)
Q Consensus 1196 a~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~GglVmEP~s 1275 (1459)
+.|+++|+++++++.++.||||++|+|+.++++||+|+|||++|+|+|+++||++|++...++..+.+++ ||+||||++
T Consensus 472 a~L~~~L~~kl~~~~~~~e~arv~gip~~~v~~rG~q~kv~s~Llr~~~~~~~viP~~~~~~~~~~~~ye-Gg~VleP~~ 550 (1054)
T PTZ00166 472 AILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYE-GATVLEPKK 550 (1054)
T ss_pred HHHHHHHHHHHhHHHHHHHHhhccCCChHHhhcCCcchhHHHHHHHHHHhcCeeccCchhccccccCCCC-CceeecCCC
Confidence 9999999999999999999999999999999999999999999999999999999987654455556677 599999999
Q ss_pred CcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCCh
Q 000502 1276 GFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVL 1355 (1459)
Q Consensus 1276 GfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGIL 1355 (1459)
|||++||+||||+||||||||||||||||+++..... . + ..+.+..+|||.+|+++++|+|||
T Consensus 551 G~y~~pV~vLDF~SLYPSIiia~NlcysTl~~~~~~~--------~-------~--~~~~~~~~p~g~~Fv~~~~r~Gil 613 (1054)
T PTZ00166 551 GFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDAN--------N-------Y--PEDTYVTTPTGDKFVKKEVRKGIL 613 (1054)
T ss_pred CCeeCceEEeecCCcccHHHHhcCCCcceeecchhhc--------c-------C--CCcceeecCCCceeeecCCCCccc
Confidence 9999999999999999999999999999999753110 0 0 124567899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHH
Q 000502 1356 PRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAIS 1435 (1459)
Q Consensus 1356 P~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~ 1435 (1459)
|+||++||++|+++|+.||+.+ |+.++++||+||+|||++|||+||||||.+||||||.++|++||++||++|++|++
T Consensus 614 p~iL~~Ll~~R~~~K~~mk~~~--d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~gr~~c~~iA~sIT~~GR~~i~~t~~ 691 (1054)
T PTZ00166 614 PLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKE 691 (1054)
T ss_pred HHHHHHHHHHHHHHHHHHhhCC--CHHHHHHHHHHHHhhhhhccccccccccccCCccccHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999876 67899999999999999999999999999889999999999999999999999999
Q ss_pred HHhhcC------CCCcEEEEeccceeEEEC
Q 000502 1436 FVNENE------KWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1436 ~Ie~~~------~~GakVIYGDTDSlFV~l 1459 (1459)
+|++.. .||++||||||||+||.+
T Consensus 692 ~ie~~~~~~~g~~~g~~VIYGDTDSvfV~~ 721 (1054)
T PTZ00166 692 LVEKHYTKANGYKHDATVIYGDTDSVMVKF 721 (1054)
T ss_pred HHHHhccccccCcCCeEEEecCCCceEEEe
Confidence 999852 479999999999999974
No 3
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=8.3e-97 Score=870.41 Aligned_cols=536 Identities=27% Similarity=0.426 Sum_probs=458.4
Q ss_pred ceEEeecCCCCCChhHHHHHhhhcCCC--------------ccccccccceeecCCCccccceecchhhhhc-ccccCCC
Q 000502 829 SCLYMLRPPFSPPSVDSVHKWLLHDDK--------------GASGDMDKASVEHSSLKGSDIRPVLEEMHQE-ADEMIST 893 (1459)
Q Consensus 829 s~~~~lt~~~sp~s~~~v~~wL~~~~~--------------~~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~-~~~~s~~ 893 (1459)
+.+++||. ..|.. .+.++.|...|. +.|++-..|||+|.+..+++|..+..+.-+. ..+-|+|
T Consensus 171 ~~f~kit~-~lP~~-~~~~r~~lergv~~~~~~~~~~~~~yEsNi~f~lrfmvd~~iVG~~wi~lp~gk~~~~~~~~s~c 248 (1066)
T KOG0969|consen 171 QPFLKITV-TLPRM-VAAARRLLERGVFISGKGEKVGFTTYESNIDFVLRFMVDCDIVGMNWIELPAGKYRIRDNRVSRC 248 (1066)
T ss_pred ceeEEEec-ccHHH-HHHhHHHHHhcccccccCcceeeeEecCCccEEEEEEecCccccceeEEeccchheeccchhccc
Confidence 46778887 45544 444444444441 2377788899999999999999999987775 3599999
Q ss_pred CCCCCCCcccccccccccccCCCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCC
Q 000502 894 EPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLR 973 (1459)
Q Consensus 894 e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lf 973 (1459)
++|..+++++++-|. .+|+ | ...+++++|||||||-+|++.|
T Consensus 249 qlEv~v~y~~lishp-------------------~eG~------w-------------~~~APlrvlSfDIECagrkg~F 290 (1066)
T KOG0969|consen 249 QLEVSVNYKDLISHP-------------------AEGE------W-------------SKIAPLRVLSFDIECAGRKGVF 290 (1066)
T ss_pred ceEEEEeeccccccc-------------------ccCc------c-------------cccccccccceeEEeccCCCCC
Confidence 999999999999998 1332 1 1236789999999999999999
Q ss_pred CCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCC
Q 000502 974 PDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQG 1053 (1459)
Q Consensus 974 PDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~ 1053 (1459)
|.|+.|||++|+-.+...++...-+. +....+.+.+|.|+.|..+.+|++||..|-++|++.|||||+|||+.+
T Consensus 291 Pe~~~DPvIQIan~v~~~Ge~~pf~r------nvf~l~~capI~G~~V~~~~~e~elL~~W~~firevDPDvI~GYNi~n 364 (1066)
T KOG0969|consen 291 PEAKIDPVIQIANLVTLQGENEPFVR------NVFTLKTCAPIVGSNVHSYETEKELLESWRKFIREVDPDVIIGYNICN 364 (1066)
T ss_pred CccccChHHHHHHHHHHhcCCchHHH------hhhcccCcCCCCCceeEEeccHHHHHHHHHHHHHhcCCCeEecccccc
Confidence 99999999999866554444321110 011235678999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCe
Q 000502 1054 GSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGR 1133 (1459)
Q Consensus 1054 FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GR 1133 (1459)
||+|||++||+.||+..+.-|||.+.... ..+++.|+ +..+|.+..+.+.|.||
T Consensus 365 FDiPYll~RA~~L~Ie~Fp~LGRikn~~s-~irDttfS-------------------------Skq~GtRetK~v~I~GR 418 (1066)
T KOG0969|consen 365 FDIPYLLNRAKTLGIENFPYLGRIKNSRS-VIRDSTFS-------------------------SKQYGTRETKEVNIDGR 418 (1066)
T ss_pred cccceecChHhhcCcccccccceecccce-eeeccccc-------------------------hhhcCcccceEEeecce
Confidence 99999999999999998888999875321 12233333 34577777888999999
Q ss_pred EEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHH
Q 000502 1134 IVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTS 1213 (1459)
Q Consensus 1134 ivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ 1213 (1459)
+.+||+.++++++||.+|||+.|+.|||++.|+|+++..|+++- +|+...|++++.||++|+.|.++|+++|+.|..+.
T Consensus 419 lqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQ-ng~~~TRRRlA~YCLkDAYLPlRLlekLM~ivNy~ 497 (1066)
T KOG0969|consen 419 LQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQ-NGNEQTRRRLAVYCLKDAYLPLRLLEKLMVIVNYT 497 (1066)
T ss_pred eeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhh-cCcHHHHHHHHHHHhhhhcchHHHHHHHHHHHhHH
Confidence 99999999999999999999999999999999999999999985 56667899999999999999999999999999999
Q ss_pred HHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccCCeeeeccCCcccCCeEEeeccccchh
Q 000502 1214 ELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPS 1293 (1459)
Q Consensus 1214 ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPS 1293 (1459)
||||++|+|+..+++||+|+||-|+|+|.|+.++|++|+-.. +-+.+..|| |++|+||..|||+.||++|||+|||||
T Consensus 498 EMARVTGVP~syLltRGqqIKVlSqLlRkakq~~~~~P~i~~-~~s~~e~yE-GatVIEp~kGfY~~PIATLDFaSLYPS 575 (1066)
T KOG0969|consen 498 EMARVTGVPISYLLTRGQQIKVLSQLLRKAKQKDFVIPNIKS-QGSDDEQYE-GATVIEPRKGFYDKPIATLDFASLYPS 575 (1066)
T ss_pred hhhhhhCCcHHHHHhCCcchHHHHHHHHHHhhcCeeeeeecc-cCCcccccc-ccEEeecccccCCCCceeeehhhhhhH
Confidence 999999999999999999999999999999999999987532 223335566 799999999999999999999999999
Q ss_pred HHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHH
Q 000502 1294 MMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAI 1373 (1459)
Q Consensus 1294 IMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~M 1373 (1459)
||||||+||+|++.+.... .|. .++++.+|+|..||+.++|+|+||++|++||..|+.+|+.|
T Consensus 576 IMmahNLCYtTLl~~~t~~---------------~l~--~~~~~~TP~g~yFv~~~~rkGlLP~ILe~ll~aRKraK~dl 638 (1066)
T KOG0969|consen 576 IMMAHNLCYTTLLTKETVE---------------KLG--DEDYTRTPTGDYFVKTEVRKGLLPEILEDLLTARKRAKADL 638 (1066)
T ss_pred HHHHhhhhheeccccchhh---------------hcC--ccceeECCCCCeeeehhhhccccHHHHHHHHHHHHHHHHHH
Confidence 9999999999998532211 111 36788999999999999999999999999999999999999
Q ss_pred HhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcC------CCCcEE
Q 000502 1374 KKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE------KWKAKV 1447 (1459)
Q Consensus 1374 Kk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~------~~GakV 1447 (1459)
|+.+ |++++++||.||+||||.|||.||+|||. -|++||.+|..|||+.||+||++++..||+++ ...+.|
T Consensus 639 k~ek--Dp~kr~vldGRQLAlKisANSvYGFTGAt-vGkLPCleIS~SVT~yGR~MI~~TK~~Ve~~y~~~ngy~~da~V 715 (1066)
T KOG0969|consen 639 KKEK--DPFKRAVLDGRQLALKISANSVYGFTGAT-VGKLPCLEISQSVTAYGRQMIEKTKKLVEEKYTIKNGYSHDAVV 715 (1066)
T ss_pred Hhcc--CHHHHhhhcchhhheeecccccccccccc-cCccceeeechhhHHHHHHHHHHHHHHHHHHhhhccCCccccEE
Confidence 9876 68999999999999999999999999996 59999999999999999999999999999853 567999
Q ss_pred EEeccceeEEEC
Q 000502 1448 IYGDTDRYTVCI 1459 (1459)
Q Consensus 1448 IYGDTDSlFV~l 1459 (1459)
|||||||+||.+
T Consensus 716 iYGDTDSVMv~F 727 (1066)
T KOG0969|consen 716 IYGDTDSVMVKF 727 (1066)
T ss_pred EecCCceEEEec
Confidence 999999999964
No 4
>PHA02528 43 DNA polymerase; Provisional
Probab=100.00 E-value=8.2e-78 Score=758.87 Aligned_cols=446 Identities=20% Similarity=0.272 Sum_probs=346.3
Q ss_pred CCceEEEEEEEeCcCCCCCCCCC--CCcEEEEEEEeecCCCceEEEEEEEecCC-Cccc-ccc---CCCCCcEEEEeCCH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPR--YDSINVVALAFENDSDHAVEIYVLLYCKS-ESHQ-RSL---VGIPDCKVFVCSKE 1027 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe--~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~~-~~~---~~i~g~~V~~f~SE 1027 (1459)
+.|++++|||||.+++ .||+|+ .|+|++|++. +.... .+.++..+.. .... ... ....++.+..|.+|
T Consensus 104 p~lrv~s~DIE~~~~~-gfP~p~~~~d~IisIsl~--~~~~~--~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE 178 (881)
T PHA02528 104 SKIRIANLDIEVTAED-GFPDPEEAKYEIDAITHY--DSIDD--RFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTE 178 (881)
T ss_pred CCccEEEEEEEECCCC-CCCCcccCCCcEEEEEEe--cCCCC--EEEEEEecCcccccccCCcccccccCCeeEEEcCCH
Confidence 6799999999997754 499999 6799999984 22222 2222322211 1110 111 11235677889999
Q ss_pred HHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHH-hCCCCccCCCCCCccccccCCCccccccccccccccchhhH
Q 000502 1028 IHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH-LGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVA 1106 (1459)
Q Consensus 1028 kELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~-LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~ 1106 (1459)
++||.+|+++|+++|||||+|||+++||||||++||+. +|+++..++++.+.... +
T Consensus 179 ~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~----------~------------- 235 (881)
T PHA02528 179 REMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKE----------R------------- 235 (881)
T ss_pred HHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCccccccccccccccc----------c-------------
Confidence 99999999999999999999999999999999999996 68776444443221100 0
Q ss_pred HhhhhhhhhhccccccccccceeecCeEEeehHHHHhh--ccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhH
Q 000502 1107 ESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRG--EVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRA 1184 (1459)
Q Consensus 1107 g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rk--elKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~ 1184 (1459)
...+.||+.+ ..+.|.||+++|+|.++|+ ..++++|+|++||+++||++|+++++++|.+||.++
T Consensus 236 --------~~~~~~g~~~-~~~~i~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d---- 302 (881)
T PHA02528 236 --------TIENMYGREE-IAYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETD---- 302 (881)
T ss_pred --------cccccccccc-eeEEEcceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcC----
Confidence 0113355433 3578999999999999997 357999999999999999999999999999999865
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhh-hHHHHHHHhhhCCEEeeCCCCCccccccc
Q 000502 1185 RYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYR-VESMLLRLAHTQNYLAISPGNHQVASQPA 1263 (1459)
Q Consensus 1185 r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~r-VESlLlr~ak~~nfllpsPs~~qv~~q~a 1263 (1459)
..++++||++||.|+++|+.++++++++.|+|+++|+++.+|++ |.+ +++++++.++++||++|+... ...+ .
T Consensus 303 ~~~l~~Ynl~Da~Lv~~L~~kl~ll~~~~e~ArltGi~l~~v~s---q~~~~~~lll~~~~r~g~viP~~~~--~~~~-~ 376 (881)
T PHA02528 303 HQKYIEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFS---PIKTWDAIIFNSLKEEKIVIPENKS--HKKQ-K 376 (881)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHhcc---hHhHHHHHHHHHHHHcCcccCCccc--cCCC-C
Confidence 35799999999999999999999999999999999999999953 444 468999999999999976532 2222 2
Q ss_pred cccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCc
Q 000502 1264 MECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGV 1343 (1459)
Q Consensus 1264 ~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv 1343 (1459)
+ .||+||||++|||+ ||+||||+||||||||+|||||+|+++..... ...+.. ........+.+.++|||.
T Consensus 377 y-~Gg~V~eP~pGlY~-~VvVLDF~SLYPSIIiayNIcp~Tlv~~~~~~--~~~~~~-----~~~~~~~~~~~~~~p~G~ 447 (881)
T PHA02528 377 Y-AGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVA--PVHEYI-----NKTAPRPSDEYSCSPNGW 447 (881)
T ss_pred C-CCcEEecCCCCccc-ceEEEeccccChHHHHHhCCChhhcccccccc--cccccc-----ccccCCCCCceeEcCCCC
Confidence 3 48999999999998 69999999999999999999999999754311 001110 011111235577899999
Q ss_pred eecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCch-------------------------------------------
Q 000502 1344 MYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQ------------------------------------------- 1380 (1459)
Q Consensus 1344 ~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d------------------------------------------- 1380 (1459)
+|++ .++||||+||++|+++|+++|+.||+++.+.
T Consensus 448 ~F~k--~~~GiLP~iL~~Ll~~R~~~Kk~Mk~~~~~~~~~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 525 (881)
T PHA02528 448 MYRK--DIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIKTILEDLNDSVDTPIDVDYYFDFSDEFKAELKTLTKSSLK 525 (881)
T ss_pred eEeC--CCCeehHHHHHHHHHHHHHHHHHHHhccccccccccccccccccccccccccccccchhhhhhhhcccchhhhh
Confidence 9975 5899999999999999999999998765321
Q ss_pred ------HHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHH----HHhhc--CCCCcEEE
Q 000502 1381 ------QILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAIS----FVNEN--EKWKAKVI 1448 (1459)
Q Consensus 1381 ------~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~----~Ie~~--~~~GakVI 1448 (1459)
+.++++||.+|+|+||+|||+|||+|+. .+||||.++|++||++||++|+.+++ ++++. ..++++||
T Consensus 526 ~~~~~~~~~~~~~d~~Q~A~KI~~NS~YG~lG~~-~~r~y~~~~A~aiT~~Gr~~I~~i~~~~~e~l~~~~~~~g~~~VI 604 (881)
T PHA02528 526 ALLEECEKEIALCNTIQMARKILINSLYGALGNE-HFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDYVI 604 (881)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHhhhhhccCc-CccCCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhcccCCcEEE
Confidence 1456899999999999999999999986 47999999999999999998875554 44331 12347999
Q ss_pred EeccceeEEEC
Q 000502 1449 YGDTDRYTVCI 1459 (1459)
Q Consensus 1449 YGDTDSlFV~l 1459 (1459)
||||||+||++
T Consensus 605 YGDTDSvfV~~ 615 (881)
T PHA02528 605 YGDTDSIYVNL 615 (881)
T ss_pred EEcCCeeEEEe
Confidence 99999999985
No 5
>PHA03036 DNA polymerase; Provisional
Probab=100.00 E-value=8.6e-76 Score=734.08 Aligned_cols=460 Identities=17% Similarity=0.248 Sum_probs=355.0
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc----ccc------ccC---CCCCcEEE
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES----HQR------SLV---GIPDCKVF 1022 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~----~~~------~~~---~i~g~~V~ 1022 (1459)
+++.|||||||.. .++||+|..|||.+|++|+.... +....++++.....+ ..+ .+. ...+..+.
T Consensus 159 ~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~~~-~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (1004)
T PHA03036 159 PRSYLFLDIECHF-DKKFPSVFINPVSHISCCYIDLS-GKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKEL 236 (1004)
T ss_pred cceeEEEEEEecc-CCCCCCcccCcceEEEEEEEecC-CCeeEEEEeccccccccccccceeeeeeccccccccCCceee
Confidence 4789999999986 67899999999999998765432 224555666543211 111 122 23678999
Q ss_pred EeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC--ccCCCCCCccccccCCCccccccccccccc
Q 000502 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL--LNDISRTPLESKIAAGDSEISERGITDNML 1100 (1459)
Q Consensus 1023 ~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l--~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l 1100 (1459)
.|.+|++|| .|++.+++.|||||+|||+++||||||.+|++.|.... +..++|..... ..+.++++.
T Consensus 237 ~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~------~~v~~r~~~---- 305 (1004)
T PHA03036 237 ILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVH------LCIYERNLS---- 305 (1004)
T ss_pred ecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHhccCceeeccCCCccccc------ceeeccccc----
Confidence 999999988 67999999999999999999999999999999984421 11233322111 011111110
Q ss_pred cchhhHHhhhhhhhhhccccccccc--ccee-ecCeEEeehHHHHhhccCCCCCCHHHHHHHHh----------------
Q 000502 1101 AEPVVAESLLAKDAIIEDEWGRTHA--SGLH-VGGRIVLNVWRLMRGEVKLNMYTVEAVAETVL---------------- 1161 (1459)
Q Consensus 1101 ~~p~~~g~~~~k~s~~~~~~G~~~~--s~i~-I~GRivIDLwrv~rkelKL~sYSLEnVA~~vL---------------- 1161 (1459)
+....|.... ..+. +.||+++|||.++|+.++|++|||++|++++|
T Consensus 306 ---------------s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~ 370 (1004)
T PHA03036 306 ---------------SHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNNEVTF 370 (1004)
T ss_pred ---------------cccccCccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCceeEE
Confidence 0111222111 2233 58999999999999999999999999999977
Q ss_pred -c--------------------------C------------------------------------CCCCCChhhhHHHHh
Q 000502 1162 -R--------------------------R------------------------------------KIPSIPFRVLTKWFA 1178 (1459)
Q Consensus 1162 -g--------------------------e------------------------------------kkpd~s~k~Ltk~y~ 1178 (1459)
| + +|.|++..+|.+.|+
T Consensus 371 ~g~~~~~~~~~~~~f~~vl~t~ny~~i~~~~~~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~KdDV~~~~i~~~~~ 450 (1004)
T PHA03036 371 IGDNTTDAKGKASIFSEVLSTGNYVTINDDDICKILDKDIIENSFTVKVICKNNYIPGDTYTLSFGKDDVDLSDMYKNYN 450 (1004)
T ss_pred ccCcccccccchhhhhhhhcccceeeecccchhhhcccccccccceeeeecccccccccceeecccccCCCHHHHHHHhC
Confidence 4 4 678888889988886
Q ss_pred cCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCcc
Q 000502 1179 SGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQV 1258 (1459)
Q Consensus 1179 sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv 1258 (1459)
. ..|.+++.||++|+.|+++|+++++++.+..++|+.+++|...++..|+|.+|+++|+|.|.++|+++|...+.
T Consensus 451 ~---~~r~rla~YClkDa~L~l~L~~~l~~~~~v~~~a~~~~lp~~~~i~~~~s~~i~~qllr~~~~~~~i~p~~~~~-- 525 (1004)
T PHA03036 451 L---EIALEMARYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYRASTLIKGPLLKLLLEEKTILVRSETK-- 525 (1004)
T ss_pred h---hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhheEeeeeccccccHHHHHHHHCCcccccCCCC--
Confidence 3 46889999999999999999999999999999999999999999999999999999999999999998732211
Q ss_pred ccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCC-----C-cccCCCchhhccc
Q 000502 1259 ASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLG-----V-SSFRPDLHVLRDL 1332 (1459)
Q Consensus 1259 ~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~G-----v-~~~~~d~~~l~~L 1332 (1459)
....|+ ||+||||++|||.+||+||||+||||||||||||||+|+++...+....... + ..+. ++ +.
T Consensus 526 -~~~~Ye-Ga~VlEP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~~~~~~~i~~~~i~~~~p-~~----dy 598 (1004)
T PHA03036 526 -NKFPYE-GGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKYP-YP----RY 598 (1004)
T ss_pred -ccCCcC-ceEEecCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccccccccccccccccccCC-Cc----cc
Confidence 111344 8999999999999899999999999999999999999999764321100000 0 0010 00 00
Q ss_pred CcccccCCCC---c--eecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccc
Q 000502 1333 KDELLIPPNG---V--MYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAA 1407 (1459)
Q Consensus 1333 kd~i~isPng---v--~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA 1407 (1459)
..+.+.|++ + .|+.+++++||||++|++|+++|+++|+.||+.+ ++.++++||++|+|+|++|||+|||||+
T Consensus 599 -~~v~~~~~~~~~v~~~~vf~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~~~--d~~e~~~lD~rQlAlKI~aNS~YG~~G~ 675 (1004)
T PHA03036 599 -IYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKEAT--SSVEKAIYDSMQYTYKIVANSVYGLMGF 675 (1004)
T ss_pred -eeeeccCCcccccccceeecCCCCcChHHHHHHHHHHHHHHHHHHhhCC--ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence 112234432 2 4555678999999999999999999999999876 4567899999999999999999999998
Q ss_pred cccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhc-----------------------------------CCCCcEEEEecc
Q 000502 1408 GFSGRMPCAELADSIVQCGRSTLEKAISFVNEN-----------------------------------EKWKAKVIYGDT 1452 (1459)
Q Consensus 1408 ~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~-----------------------------------~~~GakVIYGDT 1452 (1459)
. +|||||.++|++||++||++|++++++|++. ..+|++||||||
T Consensus 676 ~-~~rly~~~iA~sVTa~GR~mI~~tk~~Ve~~~~~~~~~~l~~~p~~~f~~~~r~~~~~~~~~l~~~~~~g~kVIYGDT 754 (1004)
T PHA03036 676 R-NSALYSYASAKSCTAIGRNMIKYLNSVLNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDT 754 (1004)
T ss_pred c-CccccCHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhccccccccccccccccccccccccccCCcEEEEEec
Confidence 6 5899999999999999999999999887531 237999999999
Q ss_pred ceeEEEC
Q 000502 1453 DRYTVCI 1459 (1459)
Q Consensus 1453 DSlFV~l 1459 (1459)
||+||.+
T Consensus 755 DSVFV~~ 761 (1004)
T PHA03036 755 DSVFLEI 761 (1004)
T ss_pred CeeEEEc
Confidence 9999974
No 6
>PRK05762 DNA polymerase II; Reviewed
Probab=100.00 E-value=3.9e-74 Score=727.46 Aligned_cols=462 Identities=22% Similarity=0.291 Sum_probs=366.2
Q ss_pred CCCChhHHHHHhhhcCCCcc---ccccccceeecCCCccccceecchhhhhcccccCCCCCCCCCCcccccccccccccC
Q 000502 838 FSPPSVDSVHKWLLHDDKGA---SGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNGVTAIMHNEGHIAE 914 (1459)
Q Consensus 838 ~sp~s~~~v~~wL~~~~~~~---~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~~~~~~~~~~~~~~ 914 (1459)
.++-.+..+.+-|+..++++ +|..+.||++|+++.+++|+.+.... + +++.++ +.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~i~EaDI~~~~R~lid~~i~~~~w~~~~~~~-~------~~~~~~---------~~------ 142 (786)
T PRK05762 85 RQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGEVEQ-Y------TTDGVL---------RN------ 142 (786)
T ss_pred ccHHHHHHHHHHHHHcCCeEEECCCChhHhheeeCCCCCcEEEEEEeec-c------ccceeE---------Ee------
Confidence 55666777788888888865 89999999999999999999875321 0 122111 11
Q ss_pred CCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc
Q 000502 915 PNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH 994 (1459)
Q Consensus 915 ~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~ 994 (1459)
.++. | .. +..|++++++|||||... ++|.+|++.- ..+.
T Consensus 143 -----------~~i~-~--------~~----------~~~p~lrvlsfDIE~~~~---------~~i~sI~~~~--~~~~ 181 (786)
T PRK05762 143 -----------ARLK-P--------AP----------DYRPPLKVVSLDIETSNK---------GELYSIGLEG--CGQR 181 (786)
T ss_pred -----------ccee-e--------CC----------CCCCCCeEEEEEEEEcCC---------CceEEeeecC--CCCC
Confidence 0111 0 00 012569999999999753 2588888752 1111
Q ss_pred eEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCC
Q 000502 995 AVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDI 1074 (1459)
Q Consensus 995 ~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~L 1074 (1459)
.+ ++.+... +..+..|..|.+|++||.+|+++|+++|||||+|||+.+||||||.+||+.||+.+ .+
T Consensus 182 --~v--i~ig~~~-------~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~--~~ 248 (786)
T PRK05762 182 --PV--IMLGPPN-------GEALDFLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RL 248 (786)
T ss_pred --eE--EEEECCC-------CCCcceEEEcCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCc--cc
Confidence 22 2223211 00112377899999999999999999999999999999999999999999999986 58
Q ss_pred CCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhcc-CCCCCCH
Q 000502 1075 SRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEV-KLNMYTV 1153 (1459)
Q Consensus 1075 SR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkel-KL~sYSL 1153 (1459)
||.+.....+ . ..+......+.+.||++||+|+++|+.. ++.+|+|
T Consensus 249 GR~~~~~~~~--~-------------------------------~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 249 GRDGSELEWR--E-------------------------------HPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred CcCCCccccc--c-------------------------------CCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 8865431110 0 0001112346899999999999999875 9999999
Q ss_pred HHHHHHHhcCCCCCCC----hhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccC
Q 000502 1154 EAVAETVLRRKIPSIP----FRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSR 1229 (1459)
Q Consensus 1154 EnVA~~vLgekkpd~s----~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsR 1229 (1459)
++||+++||++|+..+ +++|.++|.++ +.++++||++||.++++|+.++++++.+.|+|+++|+++.+|.
T Consensus 296 ~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~----~~~l~~Y~l~Da~lt~~L~~kl~ll~~~~ela~l~g~~~~~v~-- 369 (786)
T PRK05762 296 EYVSQRLLGEGKAIDDPYDRMDEIDRRFAED----KPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVG-- 369 (786)
T ss_pred HHHHHHHhCCCeeccCccccHHHHHHHHhhh----HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCHHHhC--
Confidence 9999999999886543 47889999843 6789999999999999999999999999999999999999985
Q ss_pred CchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCcccccccccc
Q 000502 1230 GSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKI 1309 (1459)
Q Consensus 1230 GSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~ 1309 (1459)
|++.++|++|+++|+++||++|+.... .. ..+ .||+|++|++|||++ |++|||+|||||||++|||||+|+++..
T Consensus 370 ~~~~~~e~lll~~~~~~g~v~P~~~~~--~~-~~y-~Gg~V~~p~~G~y~~-V~~lDF~SLYPSIi~~~Ni~p~T~~~~~ 444 (786)
T PRK05762 370 GSVAAFEHLYLPRAHRAGYVAPNLGER--PG-EAS-PGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGL 444 (786)
T ss_pred ccHHhHHHHHHHHHHHCCEeCCCcccc--cc-ccc-CccEEecCCCCCcCc-eEEEEchhhhHHHHHHhCcCccceecCC
Confidence 777788999999999999999864322 11 223 479999999999986 9999999999999999999999998532
Q ss_pred CCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHH
Q 000502 1310 LPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNA 1389 (1459)
Q Consensus 1310 ~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDa 1389 (1459)
... ..+...+|+|.+|++ ++||||++|++|+++|+++|+.||+ +
T Consensus 445 ~~~--------------------~~~~~~~~~~~~f~k---~~gilp~~l~~l~~~R~~~K~~~~~-------------~ 488 (786)
T PRK05762 445 AQP--------------------PEESVAGFLGARFSR---EKHFLPEIVERLWEGRDEAKREMNK-------------P 488 (786)
T ss_pred CCC--------------------CcccccCCCCccccc---cCcchHHHHHHHHHHHHHHHHHHHH-------------H
Confidence 110 012245788999964 8999999999999999999999985 6
Q ss_pred HHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1390 RQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1390 rQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
+|+|+|++|||+|||+|+++ +||||.++|++||++||++|++|++++++ +|++||||||||+||++
T Consensus 489 ~q~a~Ki~~Ns~YG~~g~~~-~r~~~~~~A~~it~~Gr~~l~~~~~~~~~---~g~~viYgDTDSifv~~ 554 (786)
T PRK05762 489 LSQAIKIIMNAFYGVLGSSG-CRFFDPRLASSITMRGHEIMKQTRELIEA---QGYQVIYGDTDSTFVWL 554 (786)
T ss_pred HHHHHHhhhhhccccccccc-ccccChHHHHHHHHhHHHHHHHHHHHHHH---CCCEEEeecCCceEEEc
Confidence 89999999999999999864 69999999999999999999999999987 69999999999999974
No 7
>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=1.2e-71 Score=726.29 Aligned_cols=483 Identities=24% Similarity=0.322 Sum_probs=389.8
Q ss_pred ccccccccceeecCCCccccceecchhhhhcccccCCCCCCCCCCcccccccccccccCCCcccccccccccccCCCCCC
Q 000502 856 GASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRS 935 (1459)
Q Consensus 856 ~~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~ 935 (1459)
..|..+..||+++..+.+.+|..+.....+...+.|+|..|..|....++.
T Consensus 446 ~~n~g~~erfll~rki~gp~WL~i~~p~~~~~~~~S~c~yEga~v~~p~v~----------------------------- 496 (1172)
T TIGR00592 446 GSNTGNLERFLLLRKIKGPCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVE----------------------------- 496 (1172)
T ss_pred ccCHHHHHHHHhcCCCCCCceEEeCCCcccCcCCccccceEEEEecCcccc-----------------------------
Confidence 347777788999999999999999877665544567777555554331100
Q ss_pred CCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCC-------CceEEE-EEEEecC-C
Q 000502 936 KPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDS-------DHAVEI-YVLLYCK-S 1006 (1459)
Q Consensus 936 ~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~-------d~~~ei-~vLv~~~-~ 1006 (1459)
.|+. ...|++++|||.|++ ++|....++|+||+..+.... ...... .+..... .
T Consensus 497 -------~g~~-----~~~pPl~vLdFsi~S-----lyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~ 559 (1172)
T TIGR00592 497 -------KGLD-----KTPPPLVVLDFSMKS-----LNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKD 559 (1172)
T ss_pred -------cccc-----CCCCCeEEEEeeeEE-----ecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCC
Confidence 0110 113679999999993 589999999999998876642 111111 1111111 0
Q ss_pred Cc---c-ccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCcccc
Q 000502 1007 ES---H-QRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082 (1459)
Q Consensus 1007 ~~---~-~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~ 1082 (1459)
.. . .....++.+..|..+.+|++||.+|+..++.+|||+++|||+.+|||+||.+||+.+++..|.++||.+...
T Consensus 560 ~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~- 638 (1172)
T TIGR00592 560 CSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSP- 638 (1172)
T ss_pred CCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCC-
Confidence 00 0 001223445679999999999999999999999999999999999999999999999999888888764221
Q ss_pred ccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhc
Q 000502 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLR 1162 (1459)
Q Consensus 1083 ~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLg 1162 (1459)
.+|.. ....+.||+++|+|..++..+++.+|+|++||.++||
T Consensus 639 ------------------------------------~~~~~--~~~~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~ 680 (1172)
T TIGR00592 639 ------------------------------------KFGRR--FGERTCGRMICDVEISAKELIRCKSYDLSELVQQILK 680 (1172)
T ss_pred ------------------------------------Ccccc--ccceECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhC
Confidence 01111 1235899999999999999999999999999999999
Q ss_pred CCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHH
Q 000502 1163 RKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRL 1242 (1459)
Q Consensus 1163 ekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ 1242 (1459)
+++.++++..|.++|..+. .+.+++.||++|+.++++|+.++++++++.++|+++|.++..++.+|+|.|+|++|+++
T Consensus 681 ~~k~~~~~~~i~~~~~~~~--~~~~~~~y~~~Da~l~~~L~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~ 758 (1172)
T TIGR00592 681 TERKVIPIDNINNMYSESS--SLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHA 758 (1172)
T ss_pred CCCcccCHHHHHHHHhCcH--HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHH
Confidence 9999999999999998543 48899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhCCEEeeCCCCCcc---------------ccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCcccccccc
Q 000502 1243 AHTQNYLAISPGNHQV---------------ASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLG 1307 (1459)
Q Consensus 1243 ak~~nfllpsPs~~qv---------------~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg 1307 (1459)
++++||++|.+..... ....+.+.||+|++|++|||++||++|||+|||||||++|||||+|+++
T Consensus 759 ~~~~~~i~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~t~~~ 838 (1172)
T TIGR00592 759 FYENNYIVPDKQIFRKQQKLGDEDEEIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQ 838 (1172)
T ss_pred HHhCCEEccCccccccccccccccccccccccccccCcCCCeEecCCCCcccCCEEEEEcCCccHHHHHHhCcCccccCC
Confidence 9999999987532100 0012345699999999999999999999999999999999999999985
Q ss_pred ccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHH
Q 000502 1308 KILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIF 1387 (1459)
Q Consensus 1308 ~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iL 1387 (1459)
..... .+ | .+...+.++||||++|++|++.|+++|+.||+ + .++.++++|
T Consensus 839 ~~~~~----------------------~~---~---~~~~~~~~~Gilp~il~~L~~~R~~~K~~mk~-~-~~~~~~~~~ 888 (1172)
T TIGR00592 839 KVDED----------------------EL---P---ELPDSELEMGILPRELRKLVERRKEVKKLMKQ-D-LNPDLRLQY 888 (1172)
T ss_pred CCcch----------------------hc---c---cCCcccccCcchHHHHHHHHHHHHHHHHHhhc-C-CCHHHHHHH
Confidence 42110 01 0 12234579999999999999999999999998 3 367889999
Q ss_pred HHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1388 NARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1388 DarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
|.||+|+|++|||+|||+|+. .|||||.++|++||++||++|++|++++++ +|++|||||||||||.+
T Consensus 889 d~~Q~AlKi~aNS~YG~lG~~-~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~---~g~~VIYGDTDSv~v~~ 956 (1172)
T TIGR00592 889 DIRQKALKLTANSMYGCLGYS-KSRFYAKPLAALVTAKGREILEHTRQLVEE---MNLEVIYGDTDSIMINT 956 (1172)
T ss_pred HHHHHHHHHhhhccccccccc-cccccChHHHHHHHHHHHHHHHHHHHHHHH---cCCEEEEecCCeEEEEc
Confidence 999999999999999999986 479999999999999999999999999986 69999999999999973
No 8
>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=3.5e-70 Score=649.35 Aligned_cols=458 Identities=33% Similarity=0.511 Sum_probs=374.7
Q ss_pred CceEEEEEEEeCcCCCCCCCCC--CCcEEEEEEEeecCCCceE-EEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPR--YDSINVVALAFENDSDHAV-EIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFS 1032 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe--~DpI~~Is~~v~~d~d~~~-ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~ 1032 (1459)
++++++|||||.+.++.||+|. .|+|++|++...+...... ...++... ....+.+..++.|.+|++||.
T Consensus 2 ~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~E~~lL~ 74 (471)
T smart00486 2 PLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLG-------TCKEIDGVEVYEFNNEKELLK 74 (471)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEec-------CcCCCCCCeEEecCCHHHHHH
Confidence 4689999999987766799998 7999999999877653221 12222221 123345578899999999999
Q ss_pred HHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhh
Q 000502 1033 HFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAK 1112 (1459)
Q Consensus 1033 aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k 1112 (1459)
+|+++|+..|||||+|||+.+|||+||++|+..+++.....+||........... ...
T Consensus 75 ~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~-----~~~----------------- 132 (471)
T smart00486 75 AFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKK-----PLF----------------- 132 (471)
T ss_pred HHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCccccc-----Ccc-----------------
Confidence 9999999999999999999999999999999999998755678866431110000 000
Q ss_pred hhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHH
Q 000502 1113 DAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYV 1192 (1459)
Q Consensus 1113 ~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~Yc 1192 (1459)
..... .....+.+.||+++|+|..+++.+++.+|+|++||+++||+++++++++++.++|..+ ...+.++++||
T Consensus 133 ---~~~~~--~~~~~~~~~g~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~-~~~~~~~~~Y~ 206 (471)
T smart00486 133 ---GSKSF--GKTIKVKIKGRLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLN-YKLRDELLEYC 206 (471)
T ss_pred ---ccccc--cccceeEeccEEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcC-HHHHHHHHHHH
Confidence 00000 1233578999999999999999999999999999999999999999999999999976 34578899999
Q ss_pred HHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCccc------ccccccc
Q 000502 1193 VGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVA------SQPAMEC 1266 (1459)
Q Consensus 1193 lkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv~------~q~a~E~ 1266 (1459)
++|+.++++|+.++++++...++|+++|+++..++.+|++++||+++++.++..|+++|++...... .+.....
T Consensus 207 ~~D~~l~~~l~~~l~~~~~~~~~s~~~~~~~~~~~~~g~~~~v~~~l~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~y~ 286 (471)
T smart00486 207 IQDAVLTLKLFNKLNVIPLIIELARIAGIPQRRTLYYGSQIRVESLLLREAKKNNYILPSKSLIDFKGSEPELKKKAKYP 286 (471)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHHHhcCcHHHHHHHHHHHHhhCCEEeccchhccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999976543321 1123344
Q ss_pred CCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceec
Q 000502 1267 LPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYV 1346 (1459)
Q Consensus 1267 GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FV 1346 (1459)
||+|++|.+|+|.+||++|||+|||||||++||+||+|+++....... +..+ . ..........+++..|+
T Consensus 287 gg~v~~p~~g~~~~~v~~lDf~SlYPsii~~~nl~~~t~~~~~~~~~~-------~~~~--~-~~~~~~~~~~~~~~~~~ 356 (471)
T smart00486 287 GGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGRGENSGE-------LFLD--V-EDLLTIKYEKPEGYHFV 356 (471)
T ss_pred ccEEecCCCCcccCceEEeehhhccHHHHHHhCCCCcccccccccccc-------cCCC--h-hhcceeeecCCCcceee
Confidence 789999999999999999999999999999999999999975432110 0000 0 11111134578889999
Q ss_pred CCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHH
Q 000502 1347 PPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCG 1426 (1459)
Q Consensus 1347 k~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~G 1426 (1459)
++.+++|+||++|+++++.|.++|+.||+.+.+...++.+||.+|+|+|++|||+|||+|+.. +||||.++|++||++|
T Consensus 357 ~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~~~~~~~~~~~d~~q~a~K~~~Ns~yG~~g~~~-~~~~~~~~a~~iT~~g 435 (471)
T smart00486 357 KKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGFTN-SRLYCKPLAASVTALG 435 (471)
T ss_pred cCCCCCeehHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccccccccccc-ccCccHHHHHHHHHHH
Confidence 888889999999999999999999999987755556899999999999999999999999865 5999999999999999
Q ss_pred HHHHHHHHHHHhhcCC-CCcEEEEeccceeEEEC
Q 000502 1427 RSTLEKAISFVNENEK-WKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1427 Re~Le~Ai~~Ie~~~~-~GakVIYGDTDSlFV~l 1459 (1459)
|.+|+.+++++++... +|++|||||||||||..
T Consensus 436 r~~l~~~~~~i~~~~~~~~~~viYgDTDSi~v~~ 469 (471)
T smart00486 436 REILEKTKELIEKNGYPPGFKVIYGDTDSIFVTK 469 (471)
T ss_pred HHHHHHHHHHHHHhCCCCCeEEEEecCceEEEec
Confidence 9999999999998522 46999999999999974
No 9
>PRK05761 DNA polymerase I; Reviewed
Probab=100.00 E-value=2.8e-69 Score=680.01 Aligned_cols=460 Identities=18% Similarity=0.187 Sum_probs=352.2
Q ss_pred eccCCceEEeecCCCCCChhHHHHHhhhcC--CCccccccccceeecCCCccccceecchhhhhcccccCCCCCCCCCCc
Q 000502 824 YLNDGSCLYMLRPPFSPPSVDSVHKWLLHD--DKGASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNG 901 (1459)
Q Consensus 824 y~~d~s~~~~lt~~~sp~s~~~v~~wL~~~--~~~~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~ 901 (1459)
|.-....+++++. ..|-.+..+.+-+.+. -++.++....||++|+++.+++|+.+.....+..... +..++.+..
T Consensus 91 ~~~~~~~~~kI~~-~~p~~v~~~r~~~~~~~~~~EaDI~f~~RyliD~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 167 (787)
T PRK05761 91 LRDKKVKVTKIVV-KDPLAVRRLRLSVRDIPRAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESVEPEI--LVEEIKKAF 167 (787)
T ss_pred cCCCcceEEEEEE-CCHHHHHHHHHHHHhhhhheeCCCChHHheEEeCCCCCCceEEeccccccccccc--ccccccccc
Confidence 3334688999999 8888888888877654 2355899999999999999999999966433222111 222222211
Q ss_pred ccccccccccccCCCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCC-CCCCCCCCCc
Q 000502 902 VTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRG-DLRPDPRYDS 980 (1459)
Q Consensus 902 ~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg-~lfPDPe~Dp 980 (1459)
... |. -. .....+ ..+..|++++++|||||.+.. +.+|+
T Consensus 168 ~~~--~~---------------------~~---~~~~~l---------~~~~~P~lk~lsfDIE~~~~~~g~~P~----- 207 (787)
T PRK05761 168 KDE--RK---------------------LA---EDWLPI---------FEAPIPKIKRIAIDIEVYTPAKGRIPD----- 207 (787)
T ss_pred hhh--hh---------------------hh---hhhhhh---------ccCCCCCcceEEEEEEeccCcCCCCCC-----
Confidence 100 00 00 000000 012346799999999997652 34555
Q ss_pred EEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHH
Q 000502 981 INVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 981 I~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLi 1060 (1459)
.+|++||.+|+++|+++||||+ ||+.+||||||.
T Consensus 208 --------------------------------------------~~E~eLL~~f~~~i~~~dPdi~--yN~~~FDlPYL~ 241 (787)
T PRK05761 208 --------------------------------------------DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLY 241 (787)
T ss_pred --------------------------------------------CCHHHHHHHHHHHHHhcCCEEE--EcCCcchHHHHH
Confidence 3799999999999999999986 999999999999
Q ss_pred HHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeehHH
Q 000502 1061 ERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWR 1140 (1459)
Q Consensus 1061 eRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwr 1140 (1459)
+||+.+|+... .++|. +| .|+.++|++.
T Consensus 242 ~Ra~~lgi~~~-~~~~~------------------------------------------~~---------~~~~~iDl~~ 269 (787)
T PRK05761 242 NRALKLGIPKE-EIPIE------------------------------------------PG---------RAGIHIDLYK 269 (787)
T ss_pred HHHHHhCCCch-hcccc------------------------------------------cC---------CCceEEechh
Confidence 99999998652 12221 01 1223466665
Q ss_pred HHhh----------ccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHH--Hhccc
Q 000502 1141 LMRG----------EVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIM--NQLDM 1208 (1459)
Q Consensus 1141 v~rk----------elKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll--~kL~i 1208 (1459)
.++. .+++.+|+|++||+++||++|.+++ ..|.+ .++.++++||++||.|+++|+ .+..+
T Consensus 270 ~~~~~~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~-~~i~~-------~~~~~l~~Y~l~Da~l~~~L~~f~~~~~ 341 (787)
T PRK05761 270 FFQNKAVRSYAFYGKYRHREARLDAVGRALLGISKVELE-TNISE-------LDLEELAEYNFRDAEITLKLTFFNNELV 341 (787)
T ss_pred heeecceeeeeccceeecccCChHHHHHHHhCCCccccc-ccccc-------cCHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 5542 2466799999999999999999887 45543 247889999999999999985 57778
Q ss_pred chhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCC----Cc-cc----cccccccCCeeeeccCCccc
Q 000502 1209 INRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGN----HQ-VA----SQPAMECLPLVMEPESGFYA 1279 (1459)
Q Consensus 1209 I~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~----~q-v~----~q~a~E~GglVmEP~sGfY~ 1279 (1459)
++...+|||++|+|+..|...|++.+|+++++++|+++|+++|+... .. .. .......||+|++|++|+|+
T Consensus 342 l~~~~elarit~lpl~~v~r~~~g~~i~~~l~~~a~~~~~liP~~~~~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G~y~ 421 (787)
T PRK05761 342 LKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFF 421 (787)
T ss_pred HHHHHHHHHHHCcCHHHHhccCHHHHHHHHHHHHHHhCCEeCCCCccccccccccccccccccCCcCCcEEeccCCCcee
Confidence 99999999999999999954455789999999999999999997543 11 00 01123448999999999999
Q ss_pred CCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHH
Q 000502 1280 DPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLL 1359 (1459)
Q Consensus 1280 nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL 1359 (1459)
+ |++|||+|||||||++|||||+|+++..+.... .....+.|..|+ ..++||+|.+|
T Consensus 422 ~-V~vlDF~SLYPSIi~~~Ni~p~T~~~~~~~~~~--------------------~~~~~~~~~~~~--~~~~gl~~~il 478 (787)
T PRK05761 422 N-VYVLDFASLYPSIIVKWNLSPETVRIPECKCHY--------------------DDEVPELGHSVC--DDRPGLTSVLV 478 (787)
T ss_pred e-EEEeeecccchHHHHHhCCChhhccCccccccc--------------------cCCCCCCCceee--cCCCCchHHHH
Confidence 7 999999999999999999999999864321100 000112344454 57899999999
Q ss_pred HHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 000502 1360 EEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNE 1439 (1459)
Q Consensus 1360 ~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~ 1439 (1459)
+.|++.|+++|+.||+.++.++.++++||++|+|+|++|||+|||||+.. +||||.++|++||++||++|++|++++++
T Consensus 479 ~~l~~~R~~~k~~~~~~~~~~~~~~~~ld~~Q~AlKi~~NS~YGy~G~~~-~r~~~~~~A~~IT~~GR~~l~~t~~~ie~ 557 (787)
T PRK05761 479 GLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAEN-FKLYRIEVAESITALGREILLSTKKKAEE 557 (787)
T ss_pred HHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHhheeeeecccccccccC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999987665678899999999999999999999999864 79999999999999999999999999987
Q ss_pred cCCCCcEEEEeccceeEEEC
Q 000502 1440 NEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1440 ~~~~GakVIYGDTDSlFV~l 1459 (1459)
+|++||||||||+||..
T Consensus 558 ---~g~~VIYGDTDSvfv~~ 574 (787)
T PRK05761 558 ---LGLKVLYGDTDSLFVWG 574 (787)
T ss_pred ---cCCEEEEEeCceEEEEC
Confidence 69999999999999973
No 10
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.6e-68 Score=673.96 Aligned_cols=490 Identities=27% Similarity=0.384 Sum_probs=394.5
Q ss_pred ccCCceEEeecCCCCCChhHHHHHhhhc---CC---CccccccccceeecCCCccccceecchhhhhcccccCCCCCCCC
Q 000502 825 LNDGSCLYMLRPPFSPPSVDSVHKWLLH---DD---KGASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPD 898 (1459)
Q Consensus 825 ~~d~s~~~~lt~~~sp~s~~~v~~wL~~---~~---~~~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~ 898 (1459)
......+.++.. ..|-.+..+.+-... .. ++.++-...|+++|+++-.+.|+++...-....+...
T Consensus 72 ~~~~~~~~~i~~-~~p~~v~~~r~~~~~~~~~~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~~~~~~~~~~~~------- 143 (792)
T COG0417 72 LGREVEVLKIYA-RDPQAVRKLREKVKRELEGVVDIFEADIPFAMRYLIDKGIRPMVWVSVDVEDIGSIHSLF------- 143 (792)
T ss_pred cCCcccceeeEe-cCHHHHHHHHHHHhhhhhccceEeecCCCcchheeeecCCCCceEEEeeeccccchhhcc-------
Confidence 333334444443 333345555554442 12 2348888999999999999999988643221000000
Q ss_pred CCcccccccccccccCCCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCC
Q 000502 899 LNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRY 978 (1459)
Q Consensus 899 ~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~ 978 (1459)
+ .......+.|++|+|||++.+++..+|++..
T Consensus 144 -----------------------------~-------------------~~~~~~~p~l~~la~DiE~~~~~~~~~~~~~ 175 (792)
T COG0417 144 -----------------------------L-------------------EHREDVRPPLRVLAFDIETLSEPGKFPDGEK 175 (792)
T ss_pred -----------------------------c-------------------ccccCcCCCceEEEEEEEEecCCCCCCCccC
Confidence 0 0011234679999999999999999999999
Q ss_pred CcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHH
Q 000502 979 DSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGF 1058 (1459)
Q Consensus 979 DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpY 1058 (1459)
|+|.+|+++...++... . ........+..|..+.+|.+||.+|+++++.+|||||+|||+++|||||
T Consensus 176 d~~~~i~~~~~~~~~~~--------~-----~~~~~~~~~~~v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~py 242 (792)
T COG0417 176 DPIIMISYAIEAEGGLI--------E-----VFIYTSGEGFSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPY 242 (792)
T ss_pred CceEEEEEEeccCCCcc--------c-----cccccCCCCceeEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHH
Confidence 99999999987765432 0 0011223345599999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeeh
Q 000502 1059 LAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNV 1138 (1459)
Q Consensus 1059 LieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDL 1138 (1459)
|.+||+.||+.+. +||.+...... ...+. ...||+++|+
T Consensus 243 l~~Ra~~lgi~~~--~gr~~~~~~~~--------------------------------~~~~~-------~~~Gr~~iDl 281 (792)
T COG0417 243 LAERAERLGIPLR--LGRDGSELRVR--------------------------------KSGFS-------SQVGRLHIDL 281 (792)
T ss_pred HHHHHHHhCCCcc--cccccccccee--------------------------------ecccc-------cccceEEEec
Confidence 9999999999985 78765432110 00111 1129999999
Q ss_pred HHHHh-hccCCCCCCHHHHHHHHhcCCC-CCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHH
Q 000502 1139 WRLMR-GEVKLNMYTVEAVAETVLRRKI-PSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELA 1216 (1459)
Q Consensus 1139 wrv~r-kelKL~sYSLEnVA~~vLgekk-pd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElA 1216 (1459)
|..++ +.+++.+|+|++|+..+|++.+ .++++..+.+++.... ....+.+.||+.|+.|+++++.+.++++...|+|
T Consensus 282 ~~~~~~~~~~~~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~l~~~~~~~~~~l~~~~e~s 360 (792)
T COG0417 282 YPALRRRPLNLKSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWA-DSKLRLLLYNLSDADLVLRILLKNELLPLLIELS 360 (792)
T ss_pred HHHHhhhhcccccccHHHHHHHhcccccccccCccchhhccccCc-cchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 99999 6999999999999999999877 8888888777666443 2356899999999999999999999999999999
Q ss_pred HHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccCCeeeeccCCcccCCeEEeeccccchhHHh
Q 000502 1217 RVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMI 1296 (1459)
Q Consensus 1217 Rl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMI 1296 (1459)
+++|+++.++..+|++.++|++++++|+++|+++|++...... ..+.||+||+|++|+|+| |+||||+|||||||+
T Consensus 361 ~vsg~~~~~~~~~~~~~~~~~~l~~~a~~~~~~iP~~~~~~~~---~~~~Gg~V~~P~~Gly~~-V~vLDF~SLYPSII~ 436 (792)
T COG0417 361 RVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIPNKEERPER---KKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIII 436 (792)
T ss_pred HHhCCCHHHHcccchhHHHHHHHHHHHhhcCEeccCccccchh---hhcCCCEEccCCccccCc-EEEEEccccChHHHH
Confidence 9999999999999999999999999999999999876543221 234589999999999998 999999999999999
Q ss_pred hcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhh
Q 000502 1297 AYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKL 1376 (1459)
Q Consensus 1297 AyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~ 1376 (1459)
+|||||+|+.+.... ...+++|..+..++.++|++|++|++|++.|.++|+.||+.
T Consensus 437 ~~Ni~p~T~~~~~~~------------------------~~~~~~~~~~~~~~~~~G~lp~il~~L~~~R~~~K~~~k~~ 492 (792)
T COG0417 437 KYNISPDTLVEEDCS------------------------DDYSPPGVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKE 492 (792)
T ss_pred HhCCCcceecCCCcc------------------------ccccCCCCcccccccCCCchHHHHHHHHHHHHHHHHHhccc
Confidence 999999999854321 12356677777778999999999999999999999999987
Q ss_pred CCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeE
Q 000502 1377 APSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYT 1456 (1459)
Q Consensus 1377 ~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlF 1456 (1459)
+++ .++++||.+|+|+|++|||+|||+|+.. +||||.++|++||++||++|..|++++++ .|++||||||||+|
T Consensus 493 ~~~--~e~~~~d~rQ~AlKvl~NS~YGy~G~~~-~rf~~~e~a~~VT~~gR~ii~~t~~~ae~---~G~~ViyGDTDSlf 566 (792)
T COG0417 493 KDP--SERKLLDGRQLALKVLANSFYGYLGYSN-SRFYCIECAESVTAFGREILRETKELAEE---MGLRVIYGDTDSLF 566 (792)
T ss_pred CCh--HHHHHHHHHHHHHHHHHhhccccccccC-CccCCHHHHHHHHHHHHHHHHHHHHHHHH---cCCEEEEECCceeE
Confidence 743 4899999999999999999999999864 59999999999999999999999999997 69999999999999
Q ss_pred EEC
Q 000502 1457 VCI 1459 (1459)
Q Consensus 1457 V~l 1459 (1459)
|.+
T Consensus 567 v~~ 569 (792)
T COG0417 567 VTL 569 (792)
T ss_pred EEc
Confidence 974
No 11
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=100.00 E-value=3.2e-60 Score=590.74 Aligned_cols=453 Identities=17% Similarity=0.197 Sum_probs=316.0
Q ss_pred CcEEEEEEEeecCCCce---EEEEEEEecCC--CccccccC----CCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEec
Q 000502 979 DSINVVALAFENDSDHA---VEIYVLLYCKS--ESHQRSLV----GIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGW 1049 (1459)
Q Consensus 979 DpI~~Is~~v~~d~d~~---~ei~vLv~~~~--~~~~~~~~----~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGY 1049 (1459)
-+|..|++.+.+..... ....++....- .+..-.++ -+..+++..|.+|.+||.+|+..|++. .|||.-|
T Consensus 274 ~eitsislv~~~~~~~~~~~~~r~v~yn~~~~~~~~p~~~~~~~~~~t~~~~~~c~~e~~~l~~fl~~~~~~-v~vlyv~ 352 (1545)
T PHA03334 274 GEITSISLVYCTTKPKGPKKKKRYVFYNAALVEGPEPLHLDSSYDVVTRIEFVACADELEMLLAFLNRLRKS-VNVLYVY 352 (1545)
T ss_pred cceeEEEEEEeccccccccccceEEEEchhhcCCCCcccccccccceeeeEEEEeccHHHHHHHHHHHHHhh-ccEEEEe
Confidence 47888888876654221 12333333211 10100111 123568899999999999999999983 6799999
Q ss_pred cCCCccHHHHHHHHHHhCCCCc-----cC--------CCCCCccccccCCCccccccccccccccc---hhhHHhhhh--
Q 000502 1050 DIQGGSLGFLAERAAHLGIGLL-----ND--------ISRTPLESKIAAGDSEISERGITDNMLAE---PVVAESLLA-- 1111 (1459)
Q Consensus 1050 NI~~FDLpYLieRAk~LGi~l~-----~~--------LSR~~~~~~~~~~~~~f~~k~~~~~~l~~---p~~~g~~~~-- 1111 (1459)
|.+ ||+..|..|.+.|..... .. +|+.+.... ..--| ..+++.. .++++....
T Consensus 353 n~~-fdv~vi~~rl~~y~~~~~~~~~~~~l~~~~~~~~s~~~~~~~---~~~~f-----~~~~~~s~y~~ll~~~~~~~~ 423 (1545)
T PHA03334 353 NAE-FDVQVIQSRLNYYAFKQRPHPLTKALMEAWEAFLSKDPQLVP---AQLLF-----GSDILNSNYLELLDVIESHKA 423 (1545)
T ss_pred ccc-ccHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHhccCCccCC---ceeEe-----hhhHHHHHHHHHHHHHHHHHH
Confidence 996 999999999998754221 11 222211100 00001 1111110 111111000
Q ss_pred ----------------------hhhhhccccccc----cccceeecCeEEeehHHHHhh---ccCCCCCCHHHHHHHHhc
Q 000502 1112 ----------------------KDAIIEDEWGRT----HASGLHVGGRIVLNVWRLMRG---EVKLNMYTVEAVAETVLR 1162 (1459)
Q Consensus 1112 ----------------------k~s~~~~~~G~~----~~s~i~I~GRivIDLwrv~rk---elKL~sYSLEnVA~~vLg 1162 (1459)
++.+ ..|..+ -.+.+.+.||++||||+++++ +++|.+|||++||+++||
T Consensus 424 ~~~~~~~~~~~~~~~~~~~~~~r~~v--~~f~~n~~~~~~~kv~~~GrviiDMy~Vc~~K~~~~kL~sYkLNTVA~~~Lg 501 (1545)
T PHA03334 424 QFKATCRKAAARKEEIGSYMKTRDTV--QDFNDNDKKYLNSTSHGFGAHIIDLMRVCNTKSIKAKCSSRKLDTVARLIIS 501 (1545)
T ss_pred HhhhHHHHHHHHHHHhhhHHHHHHHH--HhhcccccccccceeeeccEEEEehHHHHhhcccccCccCCcHHHHHHHHHh
Confidence 0000 112111 124689999999999999998 599999999999999999
Q ss_pred CCC-----------CCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCC-
Q 000502 1163 RKI-----------PSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRG- 1230 (1459)
Q Consensus 1163 ekk-----------pd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRG- 1230 (1459)
+.| +|++|++|.++|..|+ ..|++++.||++|+.|+++|++++..+...+|++|+++.+....++||
T Consensus 502 eqKp~k~~~k~~K~eDV~YkeI~~lf~~g~-e~RaRla~YCLkDA~LvlrLlkkl~~h~e~~eraRvT~~id~~~l~RG~ 580 (1545)
T PHA03334 502 KSKPHKNPPKIGKMDDVKYTEMDGMFTAGG-AALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRATYNIDYVAHGRGV 580 (1545)
T ss_pred cccccccccccCcccCCCHHHHHHHHhcCh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCceeecccce
Confidence 988 8999999999998875 579999999999999999999999999999999999987765555555
Q ss_pred -------chhhhHHHHHHHhh-hCCEEee---------CCCCCcc--ccccccccCCeeeeccCCc-----ccCCeEEee
Q 000502 1231 -------SQYRVESMLLRLAH-TQNYLAI---------SPGNHQV--ASQPAMECLPLVMEPESGF-----YADPVVVLD 1286 (1459)
Q Consensus 1231 -------Sq~rVESlLlr~ak-~~nfllp---------sPs~~qv--~~q~a~E~GglVmEP~sGf-----Y~nPVvVLD 1286 (1459)
||+||.+++++.|+ +.|+++| .|..... .....| .||+|++|++|| |.+||+|||
T Consensus 581 v~fdG~vQQIKV~s~lL~kA~~~~~~~ia~~~i~~s~ilP~~~~~~~~~~~~Y-eGAtVLEP~~Gf~~~~~Y~~PVaVLD 659 (1545)
T PHA03334 581 MNFCGFVQSTKSVEVPLLKARLRIGIFVATGRIAESLCMPEKYARDCRQKIKL-KGGYVFAPLTGLTFAGPYQGTELTLD 659 (1545)
T ss_pred ecccCccchhhHHHHHHHHHHHhcCcccccccccccccCCccccccccccccc-CCeEeecCCCCccccccCCCcEEEEE
Confidence 99999998888888 6777763 1322111 112234 389999999999 567999999
Q ss_pred ccccchhHHhhcCccccccccccCCCc-cccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHH
Q 000502 1287 FQSLYPSMMIAYNLCFCTCLGKILPSK-ENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILST 1365 (1459)
Q Consensus 1287 FqSLYPSIMIAyNICyST~vg~~~~~~-~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~ 1365 (1459)
|+||||||||+|||||||++....... .+..|.....++.+ +.....-..+.-.+..+++.....|++|++|++||+.
T Consensus 660 FASLYPSIIiahNLCYeTLV~~~c~~~~~~~~~~d~~k~p~g-y~~~~~vy~V~~~~~~~P~~~rf~SiLp~LL~eLL~~ 738 (1545)
T PHA03334 660 FASLYPSNMCDANISPEAIVDPDCTARVRGWVVFDWKKIDRG-FGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSM 738 (1545)
T ss_pred ccccchHHHHHhCCCcccccCccchhhhccccccccccCCcc-cCccccceeeccccCcCCCcceecchHHHHHHHHHHH
Confidence 999999999999999999996532111 11112111111111 1000000000001111333344568999999999999
Q ss_pred HHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCc
Q 000502 1366 RIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKA 1445 (1459)
Q Consensus 1366 R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~Ga 1445 (1459)
|+++|+.||+.+ |+.++.+||++|+|+|++|||+|||+|+ ++|.+||++||++|++++++|++ ..|+
T Consensus 739 RK~~Kk~MKk~k--Dp~er~iLD~rQlALKVtANSvYGytG~---------~cA~lVTa~GRemI~~t~~~IE~--e~G~ 805 (1545)
T PHA03334 739 RTEYKGAMKQAK--DPKLKSYHNQLQNEMKICANSHYGVAPH---------ACQHLITTLGRHKIKLVEEFIKK--EPGM 805 (1545)
T ss_pred HHHHHHHHhhCC--CHHHHHHHHHHHHHHHHHHHhhcCcchh---------HHHHHHHHHHHHHHHHHHHHHHH--hCCC
Confidence 999999999866 4668999999999999999999999863 36889999999999999999983 3799
Q ss_pred EEEEeccceeEEEC
Q 000502 1446 KVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1446 kVIYGDTDSlFV~l 1459 (1459)
+||||||||+||.+
T Consensus 806 ~VIYGDTDSVfV~~ 819 (1545)
T PHA03334 806 TVNYGDTDSVMFQL 819 (1545)
T ss_pred EEEEEeCCceEEEe
Confidence 99999999999974
No 12
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=5.5e-61 Score=583.13 Aligned_cols=489 Identities=25% Similarity=0.336 Sum_probs=377.7
Q ss_pred cccccccceeecCCCccccceecchhhhhcccccCCCCCCCCCCcccccccccccccCCCcccccccccccccCCCCCCC
Q 000502 857 ASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSK 936 (1459)
Q Consensus 857 ~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~ 936 (1459)
.|..+.+||++.+-+-+=.|..+++.. -.....|||.+|+.|.--+.+-..
T Consensus 469 t~tn~lE~fll~rKimGPCWlkv~~~s-~~~~~~SwCk~Ev~v~sP~nI~~~---------------------------- 519 (1429)
T KOG0970|consen 469 TNTNPLERFLLSRKIMGPCWLKVKGYS-DPPRNASWCKVEVTVKSPQNITVV---------------------------- 519 (1429)
T ss_pred cCccHHHHHHHhccccCceEEEeecCC-CCCCCccceeeEEEecCCcceEEe----------------------------
Confidence 356667788888888899999999887 445567888877776654322222
Q ss_pred CCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc-------e-EEEEEEEecCCC-
Q 000502 937 PTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH-------A-VEIYVLLYCKSE- 1007 (1459)
Q Consensus 937 ~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~-------~-~ei~vLv~~~~~- 1007 (1459)
-. .....|+|++|++-|.+.- -|.-.+.+|.+|+.-+...-+. . ...++++.....
T Consensus 520 ----~~-------~~a~~Ppl~llsL~i~T~~----N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~ 584 (1429)
T KOG0970|consen 520 ----CS-------KKAPPPPLTLLSLNIRTSM----NPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGT 584 (1429)
T ss_pred ----ec-------CCCCCCCeeEEEeeeeehh----ccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCC
Confidence 00 0023577999999998842 1223346888888654432211 1 112233332210
Q ss_pred cccc---ccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCcccccc
Q 000502 1008 SHQR---SLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIA 1084 (1459)
Q Consensus 1008 ~~~~---~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~ 1084 (1459)
.-+. .+..-....|..+.+|+.||..|+..++..|||||+|||+.+|.+..|..|+..+++..|.+|||.+....
T Consensus 585 ~fP~g~~ela~~k~~~v~~~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~-- 662 (1429)
T KOG0970|consen 585 SFPLGLKELAKQKLSKVVLHNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWP-- 662 (1429)
T ss_pred cCCchHHHHHHhccCceEEecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccc--
Confidence 0000 00000123588999999999999999999999999999999999999999999999999999998754311
Q ss_pred CCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhc-cCCCCCCHHHHHHHHhcC
Q 000502 1085 AGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE-VKLNMYTVEAVAETVLRR 1163 (1459)
Q Consensus 1085 ~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke-lKL~sYSLEnVA~~vLge 1163 (1459)
.+++ ..+.||. ...+.||+++|+ ..+.++ .+..+|+|.++++.+|+.
T Consensus 663 --------~kfg-------------------~~s~~~e----~~~~aGRl~CD~-~~~a~~lik~~S~~LseL~q~~l~~ 710 (1429)
T KOG0970|consen 663 --------PKFG-------------------RSSSFGE----FFIIAGRLMCDL-NLAARELIKAQSYSLSELSQQILKE 710 (1429)
T ss_pred --------cccC-------------------Ccccccc----cccccceEEeeh-HHHHHhhhccccccHHHHHHHHHhh
Confidence 0011 0112332 234899999999 655555 677999999999999998
Q ss_pred CCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHh
Q 000502 1164 KIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLA 1243 (1459)
Q Consensus 1164 kkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~a 1243 (1459)
....+...++.++|..+.. +-.+++.+++|+.+.++|+.++++++.+.+|..++|.-+...+.+|...|+|.+||++.
T Consensus 711 eR~~i~~~~i~~~y~~s~~--L~~ll~~~~~d~~~~l~i~~~l~~LpLs~qlTnIaGni~~RTL~G~RAeRnEylLLH~F 788 (1429)
T KOG0970|consen 711 ERKEINANEIPKMYEDSKS--LTYLLEHTITDAELILQIMFRLNALPLSKQLTNIAGNIWARTLQGGRAERNEYLLLHEF 788 (1429)
T ss_pred hcccCCHhHhhhhccChHH--HHHHHHHHhHHHHHHHHHHHHhccchHHHHHHHHHhHHHHHHhhccchhhhhHHHHHHH
Confidence 8888888999999987754 67789999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCEEeeCCC---CCc--------------cccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccc
Q 000502 1244 HTQNYLAISPG---NHQ--------------VASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCL 1306 (1459)
Q Consensus 1244 k~~nfllpsPs---~~q--------------v~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~v 1306 (1459)
+++|||+|... +.+ -+..++.+.||||+||+.|||++.|++|||+|||||||+.|||||+|+-
T Consensus 789 ~~~~fIvPDK~~ssk~~~d~d~~~eg~d~~~~~KKk~kYaGGLVlePkkGlYe~~VLllDFNSLYPSIIQEyNICFTTv~ 868 (1429)
T KOG0970|consen 789 YKNGFIVPDKQNSSKAQKDADETEEGADEPSKGKKKAKYAGGLVLEPKKGLYEKYVLLLDFNSLYPSIIQEYNICFTTVD 868 (1429)
T ss_pred HHCCccCCCccchhhhhhhhhhhhccccccccccccccccCceeeccccchhhheeEEEEccccchHHHHHhhheeeecc
Confidence 99999997422 000 0123356679999999999999999999999999999999999999974
Q ss_pred cccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHH
Q 000502 1307 GKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRI 1386 (1459)
Q Consensus 1307 g~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~i 1386 (1459)
.. +.+.+.+..+ | .+....||||++|+.|++.|+.||+.||+.. ++.++..
T Consensus 869 ~~--------------~~d~Dqlp~l-------P------~s~~~~GiLPr~l~~LVerRk~VK~lMK~~~--tp~~~~q 919 (1429)
T KOG0970|consen 869 RF--------------SVDSDQLPRL-------P------SSSSEQGILPRLLENLVERRKEVKKLMKQEL--TPEKRKQ 919 (1429)
T ss_pred cc--------------ccCcccCCCC-------C------CccccCCccHHHHHHHHHHHHHHHHHHhcCC--CHHHHHh
Confidence 21 1111111111 1 1236899999999999999999999999853 5678899
Q ss_pred HHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEE
Q 000502 1387 FNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1387 LDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~ 1458 (1459)
||+||+|||++||||||++|.. .+|||...+|+.||..||++|.++++++++ .|.+|||||||||||+
T Consensus 920 ~DIRQqALKLTANSMYGCLGf~-~SRFyAkpLAaLVT~KGReiLm~Tk~Lve~---mnl~VIYGDTDSvMIn 987 (1429)
T KOG0970|consen 920 LDIRQQALKLTANSMYGCLGFV-NSRFYAKPLAALVTYKGREILMNTKDLVEK---MNLEVIYGDTDSVMIN 987 (1429)
T ss_pred hhHHHHHHhhhhccchhhcccc-cchhhhhhHHHHHhhhhHHHHHHHHHHHHh---cCeEEEEcCCceEEee
Confidence 9999999999999999999975 359999999999999999999999999986 7999999999999986
No 13
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=100.00 E-value=3.2e-58 Score=547.76 Aligned_cols=400 Identities=18% Similarity=0.269 Sum_probs=294.1
Q ss_pred CCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCCC--cEEEEEEEeecCCCceEEEEEEEecCCCcc-
Q 000502 933 GRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYD--SINVVALAFENDSDHAVEIYVLLYCKSESH- 1009 (1459)
Q Consensus 933 ~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~D--pI~~Is~~v~~d~d~~~ei~vLv~~~~~~~- 1009 (1459)
+++.+.++++. |++....+. ..++++.+|||+.+. .||+|... +|.+|+..-..+++..+.++.++.+..++.
T Consensus 84 ~~~~~~yi~~~-y~~~~~~d~-~~i~~~~~DIEv~~~--~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~~~~ 159 (498)
T PHA02524 84 DDYGISYISDT-YRGVIDFDR-DDVVIDVVDIEVTAP--EFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLVKDVGHWDP 159 (498)
T ss_pred hHHHHHHHHHh-cCCccccch-hhceEEEEEEEecCC--CCCChhhcCCceEEEEeeecccCCccEEEEeccccccCCCc
Confidence 44545555543 443333332 458999999999663 59999986 666666543333344455554432222222
Q ss_pred -cc--ccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHH-hCCCCccCCCCCCccccccC
Q 000502 1010 -QR--SLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH-LGIGLLNDISRTPLESKIAA 1085 (1459)
Q Consensus 1010 -~~--~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~-LGi~l~~~LSR~~~~~~~~~ 1085 (1459)
.. ....++++.|..|++|++||.+|+++|+++|||||+|||+.+||||||++||+. ||+.....++|.+.....
T Consensus 160 ~~~~~~~~~~~~v~v~~f~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~-- 237 (498)
T PHA02524 160 KKSVLEKYILDNVVYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSK-- 237 (498)
T ss_pred ccccccccccCCeEEEEeCCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccc--
Confidence 11 123367899999999999999999999999999999999999999999999975 898643333332211000
Q ss_pred CCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhc--cCCCCCCHHHHHHHHhcC
Q 000502 1086 GDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE--VKLNMYTVEAVAETVLRR 1163 (1459)
Q Consensus 1086 ~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke--lKL~sYSLEnVA~~vLge 1163 (1459)
.+...+|.. ..+.|.||++||+|.++|+. .+|.+|+|++||+++||+
T Consensus 238 -----------------------------~s~~~~G~~--~~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~ 286 (498)
T PHA02524 238 -----------------------------TITNLYGEK--IIYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGYREVKA 286 (498)
T ss_pred -----------------------------cceeecCce--eEEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHHHhcCC
Confidence 011234432 24789999999999999986 799999999999999999
Q ss_pred CCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHh
Q 000502 1164 KIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLA 1243 (1459)
Q Consensus 1164 kkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~a 1243 (1459)
.|.++.. .+.++|.++ +.++++||++||.|+++|..++.+++...++|+++|+|+..|+ |+...++++|+++|
T Consensus 287 ~K~d~~~-~I~~l~~~d----~~rla~YclkDa~L~~~L~~~~~ll~~~~~larvtglpl~~v~--~qikv~~~lllr~~ 359 (498)
T PHA02524 287 DKLDYEG-PINKFRKAD----HQRYVDYCVRDTDIILLIDGRRCFIDLILSLSYYAKIRFDDVL--GTIKVWDSIIFNSL 359 (498)
T ss_pred ccccchh-hHHHHhcCc----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHhc--cHHHHHHHHHHHHH
Confidence 9988753 578888754 5689999999999999999889999999999999999999995 44455678999999
Q ss_pred hhCCEEeeCCCCCccccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccC
Q 000502 1244 HTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFR 1323 (1459)
Q Consensus 1244 k~~nfllpsPs~~qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~ 1323 (1459)
+++|+++|+..... ...++ ||+|++|++|+|++ |+||||+||||||||+|||||+|+++...+... ..+.
T Consensus 360 ~~~g~viP~~~~~~---~~~Y~-GA~V~eP~~GlY~~-VivLDFaSLYPSII~a~NIsPeTl~~~~~~~~~-----~~~~ 429 (498)
T PHA02524 360 VESNVVIPAMKASP---KQSFP-GAYVKEPVPGGYRY-GLSFDLTSLYPSILRLLNISPEMIAGMFSPARL-----EDYI 429 (498)
T ss_pred HHCCEecCCCCCCC---CCccC-CeEEecCCCccccC-eEEEEccccCHHHHHHhCCCHHHhhccccccch-----hhhc
Confidence 99999998643221 12344 89999999999997 678999999999999999999999875432110 0000
Q ss_pred CCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHH
Q 000502 1324 PDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNAR 1390 (1459)
Q Consensus 1324 ~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDar 1390 (1459)
...-....+++..+|||.+|++ .++||||++|++||+.|+++|+.||++.......+++|..|
T Consensus 430 --~~~~~~~~~~~~~~P~G~~F~K--~~~GilP~iLe~Ll~~RK~~Kk~M~~a~~~~~~~~~~~~~~ 492 (498)
T PHA02524 430 --NKVAPKPSDQFSCAPNGMMYKK--GVVGVLPNETEKVFLQRKSEKKMMLAAIRNQEAIKKILASR 492 (498)
T ss_pred --cccCCCCCcceEECCCCCEEec--CCCcccHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHhh
Confidence 0000011367889999999986 77999999999999999999999998765433333444433
No 14
>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=2e-54 Score=517.49 Aligned_cols=229 Identities=64% Similarity=1.033 Sum_probs=196.5
Q ss_pred CchhhhHHHHHHHhhhCCEEeeCCCCCccccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCcccccccccc
Q 000502 1230 GSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKI 1309 (1459)
Q Consensus 1230 GSq~rVESlLlr~ak~~nfllpsPs~~qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~ 1309 (1459)
|||+|||++|+|.|+++||++|+++..++..++++++||+||||++|||++||+||||+||||||||+|||||||+++..
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 89999999999999999999999986667778888899999999999999999999999999999999999999999865
Q ss_pred CCCcc--cc--CCCcc-cCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHH
Q 000502 1310 LPSKE--NT--LGVSS-FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILH 1384 (1459)
Q Consensus 1310 ~~~~~--n~--~Gv~~-~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~ 1384 (1459)
.+... +. .+... ...+........+.+.++|||.+|+++++++||||++|++|++.|+++|+.||+.++ ++.++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~-~~~~~ 159 (451)
T cd05534 81 EELNGGGKFGFLGVKLYLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKD-DKKLQ 159 (451)
T ss_pred cccccccccccccccccccccccccccCCCcEEECCCcceeecCCCCCCchHHHHHHHHHHHHHHHHHHhhCCC-CHHHH
Confidence 43211 00 00000 000011112234567889999999998899999999999999999999999998764 35788
Q ss_pred HHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1385 RIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1385 ~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
++||++|+|+|++|||+|||+|+.|+|||||.++|++||++||++|++|++++++...+|++||||||||+||.+
T Consensus 160 ~~ld~~Q~AlKi~~NS~YGy~G~~~~gr~~~~~iA~~IT~~GR~~l~~~~~~ie~~~~~g~~VIYGDTDSvfv~~ 234 (451)
T cd05534 160 RILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLL 234 (451)
T ss_pred HHHHHHHHHHHHHhhccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEeecccceeEec
Confidence 999999999999999999999998889999999999999999999999999999855689999999999999974
No 15
>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=7.4e-45 Score=429.34 Aligned_cols=173 Identities=42% Similarity=0.716 Sum_probs=154.4
Q ss_pred CCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceec
Q 000502 1267 LPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYV 1346 (1459)
Q Consensus 1267 GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FV 1346 (1459)
||+||+|++|||++||++|||+|||||||++|||||+|+++..... . .+ .+++..+|+|..|+
T Consensus 5 Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~---~-------~~-------~~~~~~~p~~~~f~ 67 (393)
T cd05533 5 GATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAK---K-------LP-------PEDYIKTPNGDYFV 67 (393)
T ss_pred CeEeccCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCcccc---c-------CC-------CcceEECCCCceee
Confidence 7999999999999999999999999999999999999999753211 0 00 13456789999999
Q ss_pred CCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHH
Q 000502 1347 PPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCG 1426 (1459)
Q Consensus 1347 k~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~G 1426 (1459)
++++++||||++|++|++.|+++|++||+.+ |+.++++||++|+|+|++|||+|||+|+++ |||||.++|++||++|
T Consensus 68 ~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~--d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~-~r~~~~~~A~~iT~~G 144 (393)
T cd05533 68 KSSVRKGLLPEILEELLAARKRAKKDLKEET--DPFKKAVLDGRQLALKISANSVYGFTGATV-GKLPCLEISSSVTSFG 144 (393)
T ss_pred cCCCCCCchHHHHHHHHHHHHHHHHHHhhCC--CHHHHHHHHHHHHhhheeeeeccccccccc-CCccchHHHHHHHHhH
Confidence 9889999999999999999999999999854 567899999999999999999999999874 8999999999999999
Q ss_pred HHHHHHHHHHHhhc------CCCCcEEEEeccceeEEEC
Q 000502 1427 RSTLEKAISFVNEN------EKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1427 Re~Le~Ai~~Ie~~------~~~GakVIYGDTDSlFV~l 1459 (1459)
|++|+.|++++++. ..||++||||||||+||.+
T Consensus 145 R~~l~~~~~~ie~~~~~~~g~~~~~~VIYGDTDSvfv~~ 183 (393)
T cd05533 145 RQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMVKF 183 (393)
T ss_pred HHHHHHHHHHHHHhhcccccCCCceEEEecCCCceEEEc
Confidence 99999999999974 2358999999999999974
No 16
>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=2.7e-45 Score=442.12 Aligned_cols=218 Identities=42% Similarity=0.609 Sum_probs=170.0
Q ss_pred CchhhhHHHHHHHhhhCCEEeeCCCCC-----ccccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccc
Q 000502 1230 GSQYRVESMLLRLAHTQNYLAISPGNH-----QVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCT 1304 (1459)
Q Consensus 1230 GSq~rVESlLlr~ak~~nfllpsPs~~-----qv~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST 1304 (1459)
|||++||++|++.|+++||++|++... ....+.+...||+|++|++|||++++.||||+||||||||+|||||+|
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 899999999999999999999975433 011223344589999999999999555899999999999999999999
Q ss_pred ccccc-CCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHH
Q 000502 1305 CLGKI-LPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQIL 1383 (1459)
Q Consensus 1305 ~vg~~-~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l 1383 (1459)
+++.. ..... +. .....+....+...+++..|+++..++||||++|+++|+.|+++|+.|++.+++. .+
T Consensus 81 ~~~~~~~~~~~----~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~gilp~~l~~~l~~R~~~K~~~~~~~~~~-~~ 150 (466)
T PF00136_consen 81 IVDDDECKDNE----VS-----PDIKYDYGPFIVGSPVGVRFVKKGVRPGILPEILEELLEKRKEIKKLMKKAKDPD-EE 150 (466)
T ss_dssp BTCTTHCSSEE----EH-----TTCCCCTCEEEECSCCSEEEESSTCSHHHHHHHHHHHHHHHHHHHHHHHHCCHHH-HH
T ss_pred Eecchhhhccc----cc-----ccccccccceeecCCceeeecccCcccccChHHHHHHHHHHHHHhhhhhhhccch-hh
Confidence 99864 11100 00 0000001112334667789999999999999999999999999999999876332 24
Q ss_pred HHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1384 HRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1384 ~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
+.+||++|+|+|++|||+|||+|+.+ +||||.++|++||++||++|+.|++++++. .+|++||||||||+||.+
T Consensus 151 ~~~~d~~Q~a~Ki~~NS~YG~~g~~~-~r~~~~~~a~~iT~~GR~~i~~~~~~~~~~-~~g~~viYgDTDSv~v~~ 224 (466)
T PF00136_consen 151 YAILDARQLALKIIANSFYGYLGAKN-SRFYCKEIAEAITATGREIIKKAIEIIEEM-EFGFEVIYGDTDSVFVQF 224 (466)
T ss_dssp HHHHHHHHHHHHHHHTTHHHHHTSTT-STT--HHHHHHHHHHHHHHHHHHHHHHHHH-SCTEEEEEEETTEEEEEC
T ss_pred HHHHHHHHHhhcccceeeEeecCccc-cchhhhhhhheehhhhHhhHHHHHHHHHhh-cccceEEEEcccceEEec
Confidence 89999999999999999999999875 699999999999999999999999999984 359999999999999975
No 17
>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=6e-42 Score=395.75 Aligned_cols=165 Identities=42% Similarity=0.618 Sum_probs=145.6
Q ss_pred cCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCcee
Q 000502 1266 CLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMY 1345 (1459)
Q Consensus 1266 ~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~F 1345 (1459)
.||+|++|++|+|+ ||++|||+|||||||++|||||+|+++...... . + .+-+..|
T Consensus 4 ~Gg~V~~P~~G~~~-~V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~~----------~---------~----~~~~~~~ 59 (323)
T cd00145 4 EGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAA----------P---------E----DYIGVGF 59 (323)
T ss_pred CCcEEecCcccccC-ceEEeecCCccHHHHHHhCCCcccccccccccC----------c---------c----cccCccc
Confidence 48999999999997 699999999999999999999999986432110 0 0 0114567
Q ss_pred cCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHH
Q 000502 1346 VPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQC 1425 (1459)
Q Consensus 1346 Vk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~ 1425 (1459)
+.+++++||+|.+|++|++.|+++|+.||+.++ ++.++++||.+|+|+|++|||+|||+|+.+ +||||.++|++||++
T Consensus 60 ~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~-~~~~~~~~d~~Q~AlKi~~NS~YG~~G~~~-~r~~~~~~A~~IT~~ 137 (323)
T cd00145 60 RSPKDRKGLLPRILEELLNFRDEAKKRMKAAKL-APEERVLYDNRQQALKVLANSFYGYLGAKF-FRFYDPEVAASITSF 137 (323)
T ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhhCcC-CHHHHHHHHHHhhhhheeeecceeeccccc-ccCCChHHHHHHHHH
Confidence 777899999999999999999999999998764 467899999999999999999999999975 599999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1426 GRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1426 GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
||++|++|++++++ +|++||||||||+||.+
T Consensus 138 GR~~l~~~~~~ie~---~g~~VIYGDTDSifv~~ 168 (323)
T cd00145 138 GREIIQDTIALVEE---HGARVIYGDTDSIFVSL 168 (323)
T ss_pred HHHHHHHHHHHHHH---cCCEEEEECCCceEEEe
Confidence 99999999999987 59999999999999974
No 18
>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=100.00 E-value=1.1e-40 Score=368.96 Aligned_cols=222 Identities=42% Similarity=0.750 Sum_probs=188.1
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceE----EEEEEEecCCCccc---cccCCCCCcEEEEeCCH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAV----EIYVLLYCKSESHQ---RSLVGIPDCKVFVCSKE 1027 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~----ei~vLv~~~~~~~~---~~~~~i~g~~V~~f~SE 1027 (1459)
|+|++|++||||.+++++||||+.|||++|+|+++++..... ..+++++....... .....+.++.|..|++|
T Consensus 2 ~~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E 81 (231)
T cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVESE 81 (231)
T ss_pred CceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCCH
Confidence 679999999999999999999999999999999988765322 23455554322111 11234567899999999
Q ss_pred HHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCc-cCCCCCCccccccCCCccccccccccccccchhhH
Q 000502 1028 IHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLL-NDISRTPLESKIAAGDSEISERGITDNMLAEPVVA 1106 (1459)
Q Consensus 1028 kELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~-~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~ 1106 (1459)
++||.+|+++|+.+|||||+|||+++||||||++||+.+++..+ .+|||.+...... +
T Consensus 82 ~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~-----~---------------- 140 (231)
T cd05778 82 LELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGK-----F---------------- 140 (231)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCccc-----c----------------
Confidence 99999999999999999999999999999999999999999876 7899986543210 0
Q ss_pred HhhhhhhhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHH
Q 000502 1107 ESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARY 1186 (1459)
Q Consensus 1107 g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~ 1186 (1459)
....+.||.++.+.+.|.||+++|+|+++|++++|.+|||++||+++||++||++++++|++||.+++...|+
T Consensus 141 -------~~~~~~~g~~~~~~~~i~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~ 213 (231)
T cd05778 141 -------GDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERW 213 (231)
T ss_pred -------cccccccccccCCceEEeeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhH
Confidence 0012458888888899999999999999999999999999999999999999999999999999988878899
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 000502 1187 RCVEYVVGRAKLNLEIMN 1204 (1459)
Q Consensus 1187 rvl~YclkDa~Lvl~Ll~ 1204 (1459)
++++||++|+.++++|++
T Consensus 214 ~v~~Y~l~d~~l~l~Ll~ 231 (231)
T cd05778 214 RVLEYYLKRVRLNLEILD 231 (231)
T ss_pred HHHHHHHHHHHHHHHhhC
Confidence 999999999999999974
No 19
>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=1.1e-41 Score=403.51 Aligned_cols=163 Identities=34% Similarity=0.551 Sum_probs=144.4
Q ss_pred cCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCcee
Q 000502 1266 CLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMY 1345 (1459)
Q Consensus 1266 ~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~F 1345 (1459)
.||+|+||++|||++||++|||+|||||||++|||||+|+++....... +....|
T Consensus 9 ~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~~-------------------------~~~~~~ 63 (400)
T cd05532 9 AGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDED-------------------------DEEPPL 63 (400)
T ss_pred CCceeecCCCCcccCceEEEeccccchHHHHHhcCChhhcccccccccC-------------------------Cccccc
Confidence 3899999999999999999999999999999999999999875321100 000235
Q ss_pred cCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHH
Q 000502 1346 VPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQC 1425 (1459)
Q Consensus 1346 Vk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~ 1425 (1459)
+.+++++||||++|++|+++|.++|+.||+.+ |+.++++||++|+|+|++|||+|||+|+.. +||||.++|++||++
T Consensus 64 ~~~~~~~Gilp~~l~~l~~~R~~~K~~~k~~~--d~~~~~~~d~~Q~alKi~~NS~YG~~g~~~-~r~~~~~~A~~iT~~ 140 (400)
T cd05532 64 PPSDQEKGILPRIIRKLVERRRQVKKLMKSEK--DPDKKAQLDIRQLALKLTANSMYGCLGFSY-SRFYAKPLAALITSK 140 (400)
T ss_pred cccccCCCchHHHHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHHHHHHHHHhhccccccccc-ccccChHHHHHHHHH
Confidence 55678999999999999999999999999876 567899999999999999999999999865 699999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1426 GRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1426 GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
||++|+.|++++++ .|++||||||||+||.+
T Consensus 141 GR~~l~~~~~~~e~---~g~~ViYgDTDSifv~~ 171 (400)
T cd05532 141 GREILQKTKDLVEK---MNLEVIYGDTDSIMINT 171 (400)
T ss_pred HHHHHHHHHHHHHH---cCCEEEEeCCCeEEEec
Confidence 99999999999987 49999999999999973
No 20
>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=1.7e-41 Score=398.23 Aligned_cols=163 Identities=37% Similarity=0.567 Sum_probs=144.6
Q ss_pred CCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceec
Q 000502 1267 LPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYV 1346 (1459)
Q Consensus 1267 GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FV 1346 (1459)
||+|++|++|||++ |++|||+|||||||++|||||+|+++..... .....++|..|.
T Consensus 6 Gg~V~~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~~----------------------~~~~~~~~~~f~ 62 (371)
T cd05536 6 GGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCED----------------------CDVEPQVGHKFR 62 (371)
T ss_pred ceEEeCCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCccc----------------------cccCCCCCcEEe
Confidence 89999999999996 9999999999999999999999998643211 011234788887
Q ss_pred CCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHH
Q 000502 1347 PPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCG 1426 (1459)
Q Consensus 1347 k~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~G 1426 (1459)
+ .++||+|++|++|+++|+++|+.||+.+++ +.++++||++|+|+|++|||+|||+|+. +|||||.++|++||++|
T Consensus 63 ~--~~~Gilp~il~~ll~~R~~~K~~mk~~~~~-~~~~~~~d~~Q~AlKi~~NS~YG~~g~~-~~r~~~~~~A~~iT~~G 138 (371)
T cd05536 63 K--DPPGFIPSVLEDLLEERRRIKEKMKKLDPE-SEEYKLLDERQRAIKILANSFYGYMGWA-NARWYCKECAEAVTAWG 138 (371)
T ss_pred c--CCCCchHHHHHHHHHHHHHHHHHHhhCCCc-HHHHHHHHHHHHHHHHHHhccccccccc-cccCCCHHHHHHHHHHH
Confidence 4 689999999999999999999999987653 4678999999999999999999999986 58999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1427 RSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1427 Re~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
|++|+.|++++++ .|++||||||||+||.+
T Consensus 139 R~~l~~~~~~i~~---~g~~VIYgDTDSvfv~~ 168 (371)
T cd05536 139 REYIKTTIKIAEE---KGFKVIYGDTDSLFVKI 168 (371)
T ss_pred HHHHHHHHHHHHH---cCCEEEEEcCcccEEee
Confidence 9999999999987 59999999999999974
No 21
>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=2.7e-40 Score=386.98 Aligned_cols=165 Identities=28% Similarity=0.426 Sum_probs=139.9
Q ss_pred cCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCcee
Q 000502 1266 CLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMY 1345 (1459)
Q Consensus 1266 ~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~F 1345 (1459)
.||+||+|++|||++ |++|||+|||||||++|||||+|+++..... ....+...+..|
T Consensus 14 ~Gg~V~~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~~~~~---------------------~~~~~p~~~~~~ 71 (372)
T cd05530 14 RGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCEC---------------------KTNEVPEVGHWV 71 (372)
T ss_pred CCCEeecCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccCcccc---------------------cceecCCCCceE
Confidence 489999999999998 9999999999999999999999998642110 011122233334
Q ss_pred cCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHH
Q 000502 1346 VPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQC 1425 (1459)
Q Consensus 1346 Vk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~ 1425 (1459)
+ .+++||+|++|++|++.|.++|+.|++....++.++++||++|+|+|++|||+|||+|+. ++||||.++|++||++
T Consensus 72 ~--~~~~Gilp~il~~L~~~R~~~~k~~~k~~~~d~~~~~~ld~~Q~alKi~~NS~YG~~g~~-~~~~~~~~~A~~it~~ 148 (372)
T cd05530 72 C--KKRPGITSQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAE-NFPLYCPPVAESTTAL 148 (372)
T ss_pred E--ecCCCccHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHhccccccccc-cCCCCcHHHHHHHHHH
Confidence 3 478999999999999999998776665443357789999999999999999999999985 4799999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCcEEEEeccceeEEE
Q 000502 1426 GRSTLEKAISFVNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1426 GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~ 1458 (1459)
||++|++|++++++ +|++||||||||+||.
T Consensus 149 GR~~l~~~~~~~~~---~g~~VIYGDTDSvfv~ 178 (372)
T cd05530 149 GRYIITSTIKKARE---LGLKVLYGDTDSLFLW 178 (372)
T ss_pred HHHHHHHHHHHHHH---CCcEEEEEeccceEEe
Confidence 99999999999976 6999999999999996
No 22
>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=1.1e-38 Score=374.12 Aligned_cols=153 Identities=27% Similarity=0.417 Sum_probs=134.1
Q ss_pred CCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceec
Q 000502 1267 LPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYV 1346 (1459)
Q Consensus 1267 GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FV 1346 (1459)
||+||||++|||++ |++|||+|||||||++|||||+|++...... ..+....+|+|.+|+
T Consensus 5 Gg~V~eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~~~~-------------------~~~~~~~~~~~~~f~ 64 (371)
T cd05537 5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAP-------------------DPEDLIPGFLGARFS 64 (371)
T ss_pred CcEEeCCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCCCCC-------------------CccccccCCCCCeEe
Confidence 89999999999996 9999999999999999999999987532110 012345678899998
Q ss_pred CCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHH
Q 000502 1347 PPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCG 1426 (1459)
Q Consensus 1347 k~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~G 1426 (1459)
+ ++||||++|++|+++|+++|+.|++ .+|+|+|++|||+|||+|+. .+||||.++|++||++|
T Consensus 65 ~---~~Gilp~~l~~l~~~R~~~K~~~~~-------------~~q~AlKi~~Ns~YG~~g~~-~~r~~~~~~A~~iT~~G 127 (371)
T cd05537 65 R---EKHILPDLIARLWAARDEAKREKNA-------------PLSQAIKIIMNSFYGVLGST-GCRFFDPRLASSITLRG 127 (371)
T ss_pred c---CCCchHHHHHHHHHHHHHHHHhccH-------------HHHHhHhhheecceeecccc-cccccChHHHHHHHHHH
Confidence 5 3599999999999999999987642 47999999999999999986 58999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1427 RSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1427 Re~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
|++|+.|++++++ +|++||||||||+||++
T Consensus 128 R~~l~~~~~~~e~---~g~~ViYgDTDSvfV~~ 157 (371)
T cd05537 128 HEIMKQTRAWIEQ---QGYQVIYGDTDSTFVWL 157 (371)
T ss_pred HHHHHHHHHHHHH---cCCEEEEecCCceEEec
Confidence 9999999999987 69999999999999974
No 23
>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=100.00 E-value=4.5e-37 Score=339.67 Aligned_cols=224 Identities=20% Similarity=0.352 Sum_probs=185.1
Q ss_pred CCCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCce-EEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHH
Q 000502 954 GEQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHA-VEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFS 1032 (1459)
Q Consensus 954 ~~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~-~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~ 1032 (1459)
.|++++|+|||||.++++.||+|+.|+|++|++++..+++.. ....+++.. .+..+.++.|..|++|++||.
T Consensus 4 ~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~-------~~~~~~~~~v~~~~~E~eLL~ 76 (230)
T cd05777 4 IAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLK-------TCAPIVGAQVFSFETEEELLL 76 (230)
T ss_pred CCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeC-------CCCCCCCCEEEEECCHHHHHH
Confidence 467999999999999888899999999999999988665421 122233322 123456789999999999999
Q ss_pred HHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhh
Q 000502 1033 HFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAK 1112 (1459)
Q Consensus 1033 aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k 1112 (1459)
+|+++|+++|||||+|||+++||||||.+||+.+|+..+..+||.+...... .. .
T Consensus 77 ~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~-~~-----~------------------- 131 (230)
T cd05777 77 AWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTI-KD-----T------------------- 131 (230)
T ss_pred HHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeE-eC-----C-------------------
Confidence 9999999999999999999999999999999999999877899976432110 00 0
Q ss_pred hhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHH
Q 000502 1113 DAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYV 1192 (1459)
Q Consensus 1113 ~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~Yc 1192 (1459)
......||.+..+.+.|.||+++|+|++++++++|++|+|++||+++||++|+++++++|.+||..++ ..++++++||
T Consensus 132 -~~~~~~~g~~~~~~~~i~GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~-~~~~~l~~Y~ 209 (230)
T cd05777 132 -TFSSKQMGTRETKEINIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNP-ETRRRLAVYC 209 (230)
T ss_pred -cccccccccccceEEEEcCEEeeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCH-hHhHHHHHhh
Confidence 00123577665667899999999999999999999999999999999999999999999999997554 4578999999
Q ss_pred HHHHHHHHHHHHhcccchh
Q 000502 1193 VGRAKLNLEIMNQLDMINR 1211 (1459)
Q Consensus 1193 lkDa~Lvl~Ll~kL~iI~~ 1211 (1459)
++||.++++|+++++++..
T Consensus 210 ~~Da~l~l~L~~kl~~~~~ 228 (230)
T cd05777 210 LKDAYLPLRLLDKLMCLVN 228 (230)
T ss_pred HHHHHHHHHHHHHHhhHcc
Confidence 9999999999999987654
No 24
>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=3.7e-38 Score=367.52 Aligned_cols=155 Identities=30% Similarity=0.459 Sum_probs=134.3
Q ss_pred cCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCcee
Q 000502 1266 CLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMY 1345 (1459)
Q Consensus 1266 ~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~F 1345 (1459)
.||+|++|++|+|++ |++|||+|||||||++|||||+|+++...... . ..+.+..|
T Consensus 6 ~Gg~V~~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~~~~~~--------------------~---~~~~~~~~ 61 (352)
T cd05531 6 RGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCECR--------------------D---HVYLGHRI 61 (352)
T ss_pred CCcEEecCCCCccCc-eEEEEccccchHHHHHhCCChhhccccCcccc--------------------c---CCCCCceE
Confidence 489999999999987 99999999999999999999999985421110 0 01334344
Q ss_pred cCCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHH
Q 000502 1346 VPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQC 1425 (1459)
Q Consensus 1346 Vk~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~ 1425 (1459)
+ .+++||+|++|++|+++|.++|+.||+.+. .|++|+|+|++|||+|||||+. ++||+|.++|++||++
T Consensus 62 ~--~~~~gilp~~l~~l~~~R~~~K~~~k~~~~--------~d~~q~AlKi~~NS~YGylG~~-~~~f~~~~~A~~vT~~ 130 (352)
T cd05531 62 C--LKRRGFLPEVLEPLLERRLEYKRLKKEEDP--------YAGRQKALKWILVTSFGYLGYK-NAKFGRIEVHEAITAY 130 (352)
T ss_pred e--cCCCCchHHHHHHHHHHHHHHHHHhhcCCC--------chHHHhhheeeeeccccccccc-ccccCChHHHHHHHHH
Confidence 3 579999999999999999999999997542 2899999999999999999985 3699999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCcEEEEeccceeEEE
Q 000502 1426 GRSTLEKAISFVNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1426 GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~ 1458 (1459)
||++|++|++++++ +|++||||||||+||.
T Consensus 131 GR~~L~~~~~~~e~---~g~~VIygDTDSvfv~ 160 (352)
T cd05531 131 GRKILLRAKEIAEE---MGFRVLHGIVDSLWIQ 160 (352)
T ss_pred HHHHHHHHHHHHHH---cCCEEEEEccccceee
Confidence 99999999999986 7999999999999996
No 25
>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=9.7e-38 Score=363.25 Aligned_cols=141 Identities=27% Similarity=0.392 Sum_probs=130.8
Q ss_pred CCeeeeccCCcccCCeEEeeccccchhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceec
Q 000502 1267 LPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYV 1346 (1459)
Q Consensus 1267 GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FV 1346 (1459)
||+|++|++|+|++ |++|||+|||||||++|||||+
T Consensus 5 GG~v~~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~------------------------------------------- 40 (347)
T cd05538 5 GGYAYVFITGVLGP-IVHADVASLYPSIMLAYRICPA------------------------------------------- 40 (347)
T ss_pred CceEcccCCcCcCc-eEEEEcccchHHHHHHhCCCCC-------------------------------------------
Confidence 79999999999996 9999999999999999999973
Q ss_pred CCCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHH
Q 000502 1347 PPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCG 1426 (1459)
Q Consensus 1347 k~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~G 1426 (1459)
..+.||+|++|++|++.|.++|+.||+.+ ++.++.+||.+|+|+|++|||+|||||+. ++||||.++|++||++|
T Consensus 41 --~~~~Gilp~il~~Ll~~R~~~K~~~k~~~--~~~~~~~~d~~Q~AlKi~~NS~YG~lG~~-~~r~~~~~~A~~iT~~G 115 (347)
T cd05538 41 --RDSLGIFLALLKYLVELRLAAKESARAAA--RPAERDAFKAKQAAFKVLINSFYGYLGTG-LHAFSDPEAAAEVTRLG 115 (347)
T ss_pred --CCCCcccHHHHHHHHHHHHHHHHHHhcCC--ChHHHHHHHHHHHHHhhhhhhchhhhcCC-CCCCCCHHHHHHHHHHH
Confidence 13579999999999999999999999766 46778999999999999999999999985 58999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1427 RSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1427 Re~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
|++|+++++++++ +|++||||||||+||.+
T Consensus 116 R~~L~~~~~~~e~---~g~~VIygDTDSi~v~~ 145 (347)
T cd05538 116 RELLKLMIRWLRR---RGATPVEVDTDGIYFIP 145 (347)
T ss_pred HHHHHHHHHHHHH---CCCEEEEEcCCeeEEEe
Confidence 9999999999986 79999999999999963
No 26
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-36 Score=375.77 Aligned_cols=447 Identities=16% Similarity=0.167 Sum_probs=328.1
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC--c--cccccCCCCCcEEEEeCCHHHH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE--S--HQRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~--~--~~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
+..++|.|||||....-+|||++.|+|.||+|.+...|-.+....++ +++. . ++++ +-..-..|...++|.+|
T Consensus 244 adp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiV--s~DIedfEYTPKp-E~eG~F~v~Ne~dEv~L 320 (2173)
T KOG1798|consen 244 ADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIV--SEDIEDFEYTPKP-EYEGPFCVFNEPDEVGL 320 (2173)
T ss_pred CCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhh--ccchhhcccCCcc-ccccceEEecCCcHHHH
Confidence 45799999999999899999999999999999987654221111111 1110 0 1111 11122577888999999
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhh
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLL 1110 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~ 1110 (1459)
|.+|++.|++..|.||+.||++-|||||+..||+.+|+++..++|-.+..
T Consensus 321 l~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~------------------------------ 370 (2173)
T KOG1798|consen 321 LQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDS------------------------------ 370 (2173)
T ss_pred HHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecc------------------------------
Confidence 99999999999999999999999999999999999999987776632210
Q ss_pred hhhhhhccccccccccceeecCeEEeehHHHHhhc--cCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHH
Q 000502 1111 AKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE--VKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRC 1188 (1459)
Q Consensus 1111 ~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke--lKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rv 1188 (1459)
++. +.-+-.+++|.++++|++ +.-.+-.|..|.+.-||..-..++++.+.++..+.|+ ++
T Consensus 371 ------~gE--------yks~~c~HmDcfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ----~l 432 (2173)
T KOG1798|consen 371 ------QGE--------YKSPFCIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQ----TL 432 (2173)
T ss_pred ------ccc--------ccccceeehhhhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCch----hh
Confidence 111 222446899999999987 4556889999999999999999999999999988874 78
Q ss_pred HHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEeeCCCCCc--------ccc
Q 000502 1189 VEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQ--------VAS 1260 (1459)
Q Consensus 1189 l~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllpsPs~~q--------v~~ 1260 (1459)
+.|.+.|+..++-|+.+. +++.++.|+.++.+...+||..||+...|++|+-+|...|.++|+..... .-+
T Consensus 433 asYSVSDAVATYyLYMkY-VhPFIFsLctIIPl~PDevLRKGSGTLCE~LLmVeA~~~NIv~PNK~~e~~~~f~dGhlle 511 (2173)
T KOG1798|consen 433 ASYSVSDAVATYYLYMKY-VHPFIFSLCTIIPLNPDEVLRKGSGTLCEALLMVEAYHANIVFPNKHTEDPEKFYDGHLLE 511 (2173)
T ss_pred hhcchHHHHHHHHHHHHH-hhhHHhhhhhccccChHHHHhcCcchHHHHHHHHHHHhcCeecCCcCccchhhhccCeeee
Confidence 999999999999999998 79999999999999999999999999999999999999999998632210 011
Q ss_pred ccccccCCeeeeccCCcc--------------------------------------------------------------
Q 000502 1261 QPAMECLPLVMEPESGFY-------------------------------------------------------------- 1278 (1459)
Q Consensus 1261 q~a~E~GglVmEP~sGfY-------------------------------------------------------------- 1278 (1459)
...| -||-|=--++|+|
T Consensus 512 SETY-VGGHVE~LesGVFRSDip~~F~~dp~a~~eLi~~l~~~L~~~l~vE~k~~vd~v~nfeEv~~~I~~kL~~lrd~p 590 (2173)
T KOG1798|consen 512 SETY-VGGHVECLESGVFRSDIPTEFRMDPSAYEELIDELGETLDFALTVENKVRVDEVTNFEEVKDEILEKLEELRDVP 590 (2173)
T ss_pred eeee-echhhhhHhcccccccCcccccCCHHHHHHHHHHHHHHHHHHHhhhcccchhhhcCHHHHHHHHHHHHHHhcCCC
Confidence 1112 2555555556654
Q ss_pred ---cCCe-EEeeccccchhHHhhcCccccccccccC--CCccccCCCc-------------------cc----------C
Q 000502 1279 ---ADPV-VVLDFQSLYPSMMIAYNLCFCTCLGKIL--PSKENTLGVS-------------------SF----------R 1323 (1459)
Q Consensus 1279 ---~nPV-vVLDFqSLYPSIMIAyNICyST~vg~~~--~~~~n~~Gv~-------------------~~----------~ 1323 (1459)
+.|. ..||.++|||+||++..|-|..++.... .+.-|+.|-+ .| .
T Consensus 591 ~R~E~PlIYHLDVaaMYPNIilTNRLQP~siv~E~~C~~CDfN~P~ktC~Rkm~W~WRGe~~pa~r~EY~~I~~qlesE~ 670 (2173)
T KOG1798|consen 591 IREEGPLIYHLDVAAMYPNIILTNRLQPDSIVDEEICAACDFNKPGKTCKRKMEWAWRGEYFPAKRSEYHRIKKQLESES 670 (2173)
T ss_pred ccccCCeEEEEehhhccCceeeecCCCCcccccHhhhccCCCCCCCcchhhhheeeeeeeEecCcchHHHHHHHHHHhcc
Confidence 3354 5899999999999999999999886421 1122222110 00 0
Q ss_pred CC-------chhhccc-------------Cc-------ccccCCCCcee-cCCCCcCCChHHHHHHHHHHHHHHHHHHHh
Q 000502 1324 PD-------LHVLRDL-------------KD-------ELLIPPNGVMY-VPPKVRKGVLPRLLEEILSTRIMVKQAIKK 1375 (1459)
Q Consensus 1324 ~d-------~~~l~~L-------------kd-------~i~isPngv~F-Vk~~vrkGILP~mL~eLL~~R~~vKk~MKk 1375 (1459)
++ ...+.+| ++ .+.+++--.+= .-+.....+.-..++.+-++|.++|..-|.
T Consensus 671 f~~~~~~~~~k~F~~L~~~eq~~~~kkRl~~Ysrk~Y~rv~~~~i~eRet~ICqRENpFYVdTVrsFRDRRYeyK~L~K~ 750 (2173)
T KOG1798|consen 671 FPAGAPFSPSKSFHELSREEQAAKLKKRLKDYSRKVYHRVKDTEIEERETTICQRENPFYVDTVRSFRDRRYEYKGLHKV 750 (2173)
T ss_pred CCCCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHhHhcccchhhhhcchhhccCchhhhhHHHhhhhhhHHHHHHHH
Confidence 00 0001111 00 01111100000 001234456678889999999999988776
Q ss_pred hCCc--------h-------HHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhc
Q 000502 1376 LAPS--------Q-------QILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNEN 1440 (1459)
Q Consensus 1376 ~~~~--------d-------~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~Ie~~ 1440 (1459)
.++. + +.+--+||..|+|-|+|.||+|||... .++|||..|+|.-++.+|-.+|+.|.++||..
T Consensus 751 wkg~ls~a~~sg~~a~i~eak~mvVlYdSLQLAHKcILNSFYGYVMR-KGsRWYSMEMAGIvc~TGAnIIq~AR~lVEri 829 (2173)
T KOG1798|consen 751 WKGKLSAAKASGDLARIKEAKKMVVLYDSLQLAHKCILNSFYGYVMR-KGSRWYSMEMAGIVCLTGANIIQMARELVERI 829 (2173)
T ss_pred HHHHHhhhhccCchhhHHhhhheEEehHhHHHHHHHHHhhhhhhhhc-cccchheeehhheeeccchHHHHHHHHHHHHh
Confidence 5321 1 111236999999999999999999874 46799999999999999999999999999974
Q ss_pred CCCCcEEEEeccceeEEEC
Q 000502 1441 EKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1441 ~~~GakVIYGDTDSlFV~l 1459 (1459)
.+.+-=|||+||..|
T Consensus 830 ----GrPLELDTDGIWCil 844 (2173)
T KOG1798|consen 830 ----GRPLELDTDGIWCIL 844 (2173)
T ss_pred ----CCCeeccCCceEEec
Confidence 677889999999865
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=99.97 E-value=2.3e-34 Score=377.15 Aligned_cols=385 Identities=21% Similarity=0.222 Sum_probs=279.7
Q ss_pred CCCceEEEEEEEeCcCC--CC--CCCCCCCcEEEEEEE----eecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeC
Q 000502 954 GEQLTLLSIEVQAESRG--DL--RPDPRYDSINVVALA----FENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCS 1025 (1459)
Q Consensus 954 ~~~LtiLSIEIet~srg--~l--fPDPe~DpI~~Is~~----v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~ 1025 (1459)
.|++++++|||+|.++. +. +|+|..|+|++|++. +...+.......++ .....+.++.|+.|+.|.
T Consensus 195 ~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~v~~~~ 268 (1172)
T TIGR00592 195 DPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESEPEARVV------TWKKPDKPTTGSYVESVS 268 (1172)
T ss_pred CCcccccccccccccccccccCcccccccccccccccccccccccccCCCccchhh------hccCccccCCCccceecc
Confidence 36789999999987643 23 367778999999853 11111111011111 113456778889999999
Q ss_pred CHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHH-------------HHHHhCCCCccCCCCCCccccccCCCccccc
Q 000502 1026 KEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAE-------------RAAHLGIGLLNDISRTPLESKIAAGDSEISE 1092 (1459)
Q Consensus 1026 SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLie-------------RAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~ 1092 (1459)
+|++||.+|+++|+++|||||+|||+.+||||||.+ |++.+|.-. .+||..... .+.
T Consensus 269 ~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~~~~~~~~~da~~dr~~~~G~~~--lfGr~~~~~-------s~~- 338 (1172)
T TIGR00592 269 EEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKLGVVL--LFGRDVDHV-------SPC- 338 (1172)
T ss_pred chHHHHhhHHHHHhhcCcchhcccccccCccceecCCceEEeeHHhhhHHhhCCCeEE--EecccCCce-------eEE-
Confidence 999999999999999999999999999999999999 566665533 466621100 000
Q ss_pred cccccccccchhhHHhhhhhhhhhccccc-cccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChh
Q 000502 1093 RGITDNMLAEPVVAESLLAKDAIIEDEWG-RTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFR 1171 (1459)
Q Consensus 1093 k~~~~~~l~~p~~~g~~~~k~s~~~~~~G-~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k 1171 (1459)
....| .+....+.+.||+.+|+|..+++.+++.+|+||.|++++||.++.+++++
T Consensus 339 ------------------------~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~k~dv~~k 394 (1172)
T TIGR00592 339 ------------------------VQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAK 394 (1172)
T ss_pred ------------------------EEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcCcCceeeE
Confidence 01122 11234468899999999999999999999999999999999999999999
Q ss_pred hhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEee
Q 000502 1172 VLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAI 1251 (1459)
Q Consensus 1172 ~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllp 1251 (1459)
.+.+.|..+... +++.||.+|+.+++.|+.++..+.... +++.|.+|..|+.-+.+..++.++.|.++..+++.+
T Consensus 395 ~I~~~~~~~~~~---~~v~y~~~~lkv~y~l~~~~~~l~~l~--~~~~g~~~~~vf~~n~g~~erfll~rki~gp~WL~i 469 (1172)
T TIGR00592 395 PIAKKYEFEAPD---IDAPYSSEYLEVTYELGKEFAPMEALP--SDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAV 469 (1172)
T ss_pred EehhhccCCCCc---cCCcCCcceEEEEEccCccchhhhhhh--hhccCCcchheeccCHHHHHHHHhcCCCCCCceEEe
Confidence 999999877542 578999999999999987765555443 466788888886655556677788899999999987
Q ss_pred C-CCCCcc--ccccccccCCeeeec--cCCcccC--CeEEeecc--ccchhHHhhcCccccccccccCCCccccCCCccc
Q 000502 1252 S-PGNHQV--ASQPAMECLPLVMEP--ESGFYAD--PVVVLDFQ--SLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSF 1322 (1459)
Q Consensus 1252 s-Ps~~qv--~~q~a~E~GglVmEP--~sGfY~n--PVvVLDFq--SLYPSIMIAyNICyST~vg~~~~~~~n~~Gv~~~ 1322 (1459)
. |..... .....+| |++|++| .+|+|.+ ||++|||+ |||||||+++|||++|++...... .+
T Consensus 470 ~~p~~~~~~~~S~c~yE-ga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~----d~---- 540 (1172)
T TIGR00592 470 KGPDELEYPRRSWCKYE-GGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFAL----DK---- 540 (1172)
T ss_pred CCCcccCcCCccccceE-EEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeecccc----cC----
Confidence 4 332111 1123455 6899999 9999998 89999999 999999999999998876432110 00
Q ss_pred CCCchhhcccCcccccCC-CCceecC-------CCCcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHh
Q 000502 1323 RPDLHVLRDLKDELLIPP-NGVMYVP-------PKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLAL 1394 (1459)
Q Consensus 1323 ~~d~~~l~~Lkd~i~isP-ngv~FVk-------~~vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlAL 1394 (1459)
.++. +...+.+ .+..|.. ...++|++|..|+.++++|.++|+.|+....-|+.+...||.+|.++
T Consensus 541 -~~~~------~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdl 613 (1172)
T TIGR00592 541 -PPPE------PPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRAL 613 (1172)
T ss_pred -CCCC------CccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccH
Confidence 0000 0000111 1112211 12578999999999999999999999988765666777899999999
Q ss_pred hheee
Q 000502 1395 KLIAN 1399 (1459)
Q Consensus 1395 KIiAN 1399 (1459)
|+++|
T Consensus 614 kvl~n 618 (1172)
T TIGR00592 614 KVLAN 618 (1172)
T ss_pred HHHHH
Confidence 99999
No 28
>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=99.97 E-value=3.5e-30 Score=278.30 Aligned_cols=195 Identities=27% Similarity=0.418 Sum_probs=159.6
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
|++++++|||||.+.++ ||+|..|+|++|++..... . . ++.+.. .. ...|..|.+|++||.+|
T Consensus 1 p~l~i~~fDIEt~~~~g-~p~~~~d~Ii~Is~~~~~~--~--~--~~~~~~-------~~---~~~v~~~~~E~~lL~~F 63 (195)
T cd05780 1 EDLKILSFDIEVLNHEG-EPNPEKDPIIMISFADEGG--N--K--VITWKK-------FD---LPFVEVVKTEKEMIKRF 63 (195)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCcEEEEEEecCCC--c--e--EEEecC-------CC---CCeEEEeCCHHHHHHHH
Confidence 46899999999987654 8999999999999876332 1 1 122211 11 12577899999999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhh
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDA 1114 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s 1114 (1459)
+++|+++|||||+|||+.+||||||.+||..+|++. .+||.+.....
T Consensus 64 ~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~--~~~r~~~~~~~------------------------------- 110 (195)
T cd05780 64 IEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--DLGRDGSEIKI------------------------------- 110 (195)
T ss_pred HHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCC--ccccCCCceeE-------------------------------
Confidence 999999999999999999999999999999999984 57775422110
Q ss_pred hhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHH
Q 000502 1115 IIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVG 1194 (1459)
Q Consensus 1115 ~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~Yclk 1194 (1459)
..+|.. ....+.||+++|+|+++++.+++++|+|++||+++||.+|+++++++|.+||.+++ .+.++++||++
T Consensus 111 ---~~~g~~--~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~--~~~~l~~Y~~~ 183 (195)
T cd05780 111 ---QRGGFN--NASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE--NLERLFRYSME 183 (195)
T ss_pred ---eeccee--eeeccCCeEEEeHHHHHHhhCCCCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCC--chHHHHHHhHH
Confidence 112222 23578999999999999999999999999999999999999999999999999875 47899999999
Q ss_pred HHHHHHHHHHhc
Q 000502 1195 RAKLNLEIMNQL 1206 (1459)
Q Consensus 1195 Da~Lvl~Ll~kL 1206 (1459)
|+.++++|++++
T Consensus 184 D~~lt~~L~~~~ 195 (195)
T cd05780 184 DAKYTYEIGKEF 195 (195)
T ss_pred HHHHHHHHHhhC
Confidence 999999998864
No 29
>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=99.96 E-value=1.1e-28 Score=268.75 Aligned_cols=200 Identities=16% Similarity=0.163 Sum_probs=152.0
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCC-cEEEEeCCHHHHHHHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPD-CKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g-~~V~~f~SEkELL~aF 1034 (1459)
++++|+|||||.++++.||+|+.|+|++|++.+...+.......++........-..+..+++ +.|..|.+|++||.+|
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 378999999998777789999999999999998664421100000000000000001112222 4677899999999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhh
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDA 1114 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s 1114 (1459)
+++|+++|||||+|||+.+||||||.+||+.+|+.+...+||..
T Consensus 81 ~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~------------------------------------ 124 (204)
T cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRK------------------------------------ 124 (204)
T ss_pred HHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEe------------------------------------
Confidence 99999999999999999999999999999999987643333210
Q ss_pred hhccccccccccceeecCeEEeehHHHHhhccC--CCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHH
Q 000502 1115 IIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVK--LNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYV 1192 (1459)
Q Consensus 1115 ~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelK--L~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~Yc 1192 (1459)
..++ .+.+.||+++|+|.++++... ..+|+|++||+++||++|.++++.+|.++|+.++ .++++||
T Consensus 125 ---~~~~-----~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~----~~l~~Y~ 192 (204)
T cd05779 125 ---DSEG-----EYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP----QTLASYS 192 (204)
T ss_pred ---cCCC-----eEEeccEEEEEhHHHHHHhhcCCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc----HHHHhcc
Confidence 0011 245789999999999998644 4699999999999999999999999999998764 4799999
Q ss_pred HHHHHHHHHHH
Q 000502 1193 VGRAKLNLEIM 1203 (1459)
Q Consensus 1193 lkDa~Lvl~Ll 1203 (1459)
++||.+++.|+
T Consensus 193 ~~D~~~T~~l~ 203 (204)
T cd05779 193 VSDAVATYYLY 203 (204)
T ss_pred HHHHHHHHHHh
Confidence 99999999986
No 30
>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=99.96 E-value=3.3e-28 Score=261.99 Aligned_cols=184 Identities=24% Similarity=0.400 Sum_probs=149.6
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
|+|++++|||||.++. .||+|+.|+|++|+++..++ . .++ + . ..+.+|++||.+|
T Consensus 1 p~l~~l~fDIEt~~~~-gfp~~~~d~Ii~Is~~~~~g-~--~~~--~-~------------------~~~~~E~~lL~~F 55 (188)
T cd05781 1 PDLKTLAFDIEVYSKY-GTPNPRRDPIIVISLATSNG-D--VEF--I-L------------------AEGLDDRKIIREF 55 (188)
T ss_pred CCceEEEEEEEecCCC-CCCCCCCCCEEEEEEEeCCC-C--EEE--E-E------------------ecCCCHHHHHHHH
Confidence 5689999999998654 59999999999999986432 1 111 1 1 1236999999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhh
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDA 1114 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s 1114 (1459)
+++|+++|||||+|||+.+||||||.+||+.+|+.+ .+||......
T Consensus 56 ~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~--~~gr~~~~~~-------------------------------- 101 (188)
T cd05781 56 VKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL--DVGRRGGSEP-------------------------------- 101 (188)
T ss_pred HHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCc--ccccCCCccc--------------------------------
Confidence 999999999999999999999999999999999986 4666432100
Q ss_pred hhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcC----CCCCCChhhhHHHHhcCChhHHHHHHH
Q 000502 1115 IIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRR----KIPSIPFRVLTKWFASGPGRARYRCVE 1190 (1459)
Q Consensus 1115 ~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLge----kkpd~s~k~Ltk~y~sg~~~~r~rvl~ 1190 (1459)
....|| .+.+.||++||+|.++++..++.+|+|++||++ ||. .+++++++++.++|.++. .+.++++
T Consensus 102 -~~~~~~-----~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~~-Lg~~k~~~k~~~~~~~i~~~~~~~~--~~~~l~~ 172 (188)
T cd05781 102 -STGVYG-----HYSITGRLNVDLYDFAEEIPEVKVKTLENVAEY-LGVMKKSERVLIEWYRIYEYWDDEK--KRDILLK 172 (188)
T ss_pred -ccCCcc-----eEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHHH-HCCCccccccCCCHHHHHHHHcCcc--cHHHHHH
Confidence 011233 368999999999999999999999999999985 775 467899999999998642 3789999
Q ss_pred HHHHHHHHHHHHHHhc
Q 000502 1191 YVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1191 YclkDa~Lvl~Ll~kL 1206 (1459)
||++|+.++++|++++
T Consensus 173 Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 173 YNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHHHHHHHHHHhhC
Confidence 9999999999998764
No 31
>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=99.96 E-value=8.9e-29 Score=283.04 Aligned_cols=258 Identities=21% Similarity=0.278 Sum_probs=189.5
Q ss_pred eccCCceEEeecCCCCCChhHHHHHhhhcCCC---ccccccccceeecCCCccccceecchhhhhcccccCCCCCCCCCC
Q 000502 824 YLNDGSCLYMLRPPFSPPSVDSVHKWLLHDDK---GASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLN 900 (1459)
Q Consensus 824 y~~d~s~~~~lt~~~sp~s~~~v~~wL~~~~~---~~~~~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~ 900 (1459)
|...+..++++++ .+|-.+..+.+-|...+. +.++....||++|+++.+++|+.+.+.......+.++|+.|++|+
T Consensus 63 y~~~~~~~lkV~~-~~~~~~~~~~~~l~~~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~~~~~~~~s~~~~e~~~~ 141 (325)
T PF03104_consen 63 YDGKEEPFLKVYF-SSPRDVRKLRDNLKKTFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPSKPVKDRVSWCDIEFSVD 141 (325)
T ss_dssp ETTEEEEEEEEEE-SSTTHHHHHHHHHHHTEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTECHHHHHTCTCSCECECC
T ss_pred CCCCCceEEEEEE-CcHHHHHHHHHHHHhccchhhccCCCHHHheeeecCcccceeeecccccccccccccccccccccc
Confidence 4444445888988 888888888888886433 448999999999999999999999999666788889999999998
Q ss_pred cccccccccccccCCCcccccccccccccCCCCCCCCCCCccCCcCCCCCCCCCCCceEEEEEEEeCcCCCCCCCCCCCc
Q 000502 901 GVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYDS 980 (1459)
Q Consensus 901 ~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~~~~~~~~~~~~LtiLSIEIet~srg~lfPDPe~Dp 980 (1459)
..++..+. ... ..|++++|+|||||.++++.||+|..|+
T Consensus 142 ~~~~~~~~------------------------~~~-----------------~~p~l~i~s~DIe~~~~~~~~P~~~~d~ 180 (325)
T PF03104_consen 142 YSNLKPLP------------------------DES-----------------IPPPLRILSFDIETYSNDGKFPDPEKDE 180 (325)
T ss_dssp HHHHECHT------------------------SSS-----------------SGGGSEEEEEEEEECSSSSSS-TTTTSE
T ss_pred cccccccc------------------------ccc-----------------cccccceeEEEEEEccccCCCCCCCCCe
Confidence 87555444 000 0156999999999999888899999999
Q ss_pred EEEEEEEeecCCC-ceEEEEEEEecCCCccccccCCCC-CcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHH
Q 000502 981 INVVALAFENDSD-HAVEIYVLLYCKSESHQRSLVGIP-DCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGF 1058 (1459)
Q Consensus 981 I~~Is~~v~~d~d-~~~ei~vLv~~~~~~~~~~~~~i~-g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpY 1058 (1459)
|.+|++.+++.+. ......++++. .+.... +..|..|++|++||.+|+++|+++|||||+|||+++|||||
T Consensus 181 I~~Is~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~dPDii~GyN~~~fD~~y 253 (325)
T PF03104_consen 181 IIMISYVVYRNGSSEPYRRKVFTLG-------SCDSIEDNVEVIYFDSEKELLEAFLDIIQEYDPDIITGYNIDGFDLPY 253 (325)
T ss_dssp EEEEEEEEEETTEEETTEEEEEECS-------CSCCTTCTTEEEEESSHHHHHHHHHHHHHHHS-SEEEESSTTTTHHHH
T ss_pred EEEEEEEEEeccccCCCceEEEEec-------CCCCCCCCcEEEEECCHHHHHHHHHHHHHhcCCcEEEEecccCCCHHH
Confidence 9999999886641 11112222222 122233 68999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecCeEEeeh
Q 000502 1059 LAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNV 1138 (1459)
Q Consensus 1059 LieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDL 1138 (1459)
|++||+.+|++.....++...... + +...+ .....||......+.++||++||+
T Consensus 254 l~~R~~~l~~~~~~~~~~~~~~~~-~-----~~~~~--------------------~~~~~~~~~~~~~~~~~Gr~~~D~ 307 (325)
T PF03104_consen 254 LIERAKKLGIDMFDLNGRRWSRFG-R-----LKRKK--------------------WPSSANGSRKFSRIDIPGRLVLDL 307 (325)
T ss_dssp HHHHHHHTTTCTHHSTTSTTTEEE-E-----EEEEE--------------------SEECTCCCTTEEEEEETTSEEEEH
T ss_pred HHHHHHHhCcccccccccccccee-E-----Eeecc--------------------cccccCCCcceeEEEECCChHhHH
Confidence 999999999987544443221100 0 00000 001124445556789999999999
Q ss_pred HHHHhhccCCCCCCHHHH
Q 000502 1139 WRLMRGEVKLNMYTVEAV 1156 (1459)
Q Consensus 1139 wrv~rkelKL~sYSLEnV 1156 (1459)
|+++|+.++|.+|+|++|
T Consensus 308 ~~~~~~~~~l~sY~L~~V 325 (325)
T PF03104_consen 308 YRLARKDYKLDSYSLDNV 325 (325)
T ss_dssp HHHHHHHS--SS-SHHHH
T ss_pred HHHHHhhCCCCCCCCCCC
Confidence 999999999999999997
No 32
>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=99.95 E-value=5e-27 Score=256.47 Aligned_cols=192 Identities=21% Similarity=0.243 Sum_probs=148.5
Q ss_pred CCCceEEEEEEEeCcCCCCC---CCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHH
Q 000502 954 GEQLTLLSIEVQAESRGDLR---PDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 954 ~~~LtiLSIEIet~srg~lf---PDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
.|.|++|+|||||.+.++.+ |++..|+|++|++...... ..+ + . ..+.+|++|
T Consensus 6 ~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~---~~~--~-~------------------~~~~~E~~l 61 (207)
T cd05785 6 FDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGW---EEV--L-H------------------AEDAAEKEL 61 (207)
T ss_pred CCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCc---eee--e-c------------------cCCCCHHHH
Confidence 36799999999998876544 5566799999998643321 011 1 0 025799999
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhh
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLL 1110 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~ 1110 (1459)
|.+|+++|+++|||||+|||+.+||||||.+||+.+|+.. .+||.+........ ..
T Consensus 62 L~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~--~~~r~~~~~~~~~~-------~~--------------- 117 (207)
T cd05785 62 LEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPL--AIGRDGSIPRQRPS-------RF--------------- 117 (207)
T ss_pred HHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCc--ccccCCCcceEeec-------cc---------------
Confidence 9999999999999999999999999999999999999986 47776433211000 00
Q ss_pred hhhhhhccccccccccceeecCeEEeehHHHHhh----ccCCCCCCHHHHHHHH--hcCCCCCCChhhhHHHHhcCChhH
Q 000502 1111 AKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRG----EVKLNMYTVEAVAETV--LRRKIPSIPFRVLTKWFASGPGRA 1184 (1459)
Q Consensus 1111 ~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rk----elKL~sYSLEnVA~~v--Lgekkpd~s~k~Ltk~y~sg~~~~ 1184 (1459)
...++......+.|.||+++|+|.++++ .++|.+|+|++||+++ +++++.++++++|.++|+++
T Consensus 118 ------~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~---- 187 (207)
T cd05785 118 ------RFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSD---- 187 (207)
T ss_pred ------cccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcC----
Confidence 0001111224578999999999999996 5789999999999997 67788999999999999876
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 000502 1185 RYRCVEYVVGRAKLNLEIM 1203 (1459)
Q Consensus 1185 r~rvl~YclkDa~Lvl~Ll 1203 (1459)
..++++||++||.++++|.
T Consensus 188 ~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 188 PARLLAYALDDVRETEGLA 206 (207)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 3589999999999999875
No 33
>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=99.95 E-value=1e-26 Score=251.45 Aligned_cols=188 Identities=20% Similarity=0.308 Sum_probs=146.5
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
|++++++|||||.+.+ +|.+|++.... .. . +++.+.. ....+..|..|.+|++||.+|
T Consensus 1 p~l~~~~fDIE~~~~~---------~i~~i~~~~~~--~~---~-i~~~~~~-------~~~~~~~v~~~~~E~~lL~~f 58 (193)
T cd05784 1 PKLKVVSLDIETSMDG---------ELYSIGLYGEG--QE---R-VLMVGDP-------EDDAPDNIEWFADEKSLLLAL 58 (193)
T ss_pred CCccEEEEEeecCCCC---------CEEEEEeecCC--CC---E-EEEECCC-------CCCCCCEEEEECCHHHHHHHH
Confidence 5689999999996532 78888764322 11 1 2222221 122367899999999999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhh
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDA 1114 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s 1114 (1459)
+++|+++|||||+|||+++||||||.+||+.+|+.. .+||.+......
T Consensus 59 ~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~--~~gR~~~~~~~~------------------------------ 106 (193)
T cd05784 59 IAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSPLNWR------------------------------ 106 (193)
T ss_pred HHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCc--ccccCCCccccc------------------------------
Confidence 999999999999999999999999999999999986 578865421100
Q ss_pred hhccccccccccceeecCeEEeehHHHHhh-ccCCCCCCHHHHHHHHhcCCCCCC----ChhhhHHHHhcCChhHHHHHH
Q 000502 1115 IIEDEWGRTHASGLHVGGRIVLNVWRLMRG-EVKLNMYTVEAVAETVLRRKIPSI----PFRVLTKWFASGPGRARYRCV 1189 (1459)
Q Consensus 1115 ~~~~~~G~~~~s~i~I~GRivIDLwrv~rk-elKL~sYSLEnVA~~vLgekkpd~----s~k~Ltk~y~sg~~~~r~rvl 1189 (1459)
..|......+.+.||+++|+|.++|+ .+++.+|+|++||+++||++|.++ ++++|.++|.+++ .+++
T Consensus 107 ----~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~----~~l~ 178 (193)
T cd05784 107 ----QSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK----LALA 178 (193)
T ss_pred ----cCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH----HHHH
Confidence 00111233578999999999999987 589999999999999999987765 3679999998653 4899
Q ss_pred HHHHHHHHHHHHHHH
Q 000502 1190 EYVVGRAKLNLEIMN 1204 (1459)
Q Consensus 1190 ~YclkDa~Lvl~Ll~ 1204 (1459)
+||++||.|+++|++
T Consensus 179 ~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 179 RYNLQDCELVWRIFE 193 (193)
T ss_pred HHHHHHHHHHHHHhC
Confidence 999999999999974
No 34
>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=99.95 E-value=2.3e-27 Score=263.39 Aligned_cols=220 Identities=17% Similarity=0.232 Sum_probs=168.0
Q ss_pred CCceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc-------e--EEEEEEEecCCC---c-cccccCCCCCcEE
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH-------A--VEIYVLLYCKSE---S-HQRSLVGIPDCKV 1021 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~-------~--~ei~vLv~~~~~---~-~~~~~~~i~g~~V 1021 (1459)
|+|+++||-+-|--. +.-.+.+|.+|++.+.++-.. . ...+.++..... + .........+..|
T Consensus 1 Ppl~v~sls~~T~~n----~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v 76 (234)
T cd05776 1 PPLTVMSLSIKTVLN----SKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKV 76 (234)
T ss_pred CCeEEEEEEeEEEec----CcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcE
Confidence 579999999998431 122358999999988764311 0 112222222111 0 0001111234679
Q ss_pred EEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCcccccccccccccc
Q 000502 1022 FVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLA 1101 (1459)
Q Consensus 1022 ~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~ 1101 (1459)
..|++|++||.+|+.+|+.+|||||+|||+++|||+||.+||+.+|++.|.++||.+...... + .
T Consensus 77 ~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~--------~-~------ 141 (234)
T cd05776 77 RIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPK--------K-K------ 141 (234)
T ss_pred EEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCcc--------c-c------
Confidence 999999999999999999999999999999999999999999999999888888875321100 0 0
Q ss_pred chhhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCC
Q 000502 1102 EPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGP 1181 (1459)
Q Consensus 1102 ~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~ 1181 (1459)
....| .....+.||+++|+|..+|+.+++.+|+|++||+++||++++++++++|.++|.+
T Consensus 142 --------------~~~~~----~~~~~~~GRl~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~-- 201 (234)
T cd05776 142 --------------GGGKF----GERELTAGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-- 201 (234)
T ss_pred --------------ccccc----cccccccCchhhccHHHHHHHhCCCCCChHHHHHHHhCcCcccCCHHHHHHHHhC--
Confidence 00111 1235789999999999999999999999999999999999999999999999987
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcccchhHH
Q 000502 1182 GRARYRCVEYVVGRAKLNLEIMNQLDMINRTS 1213 (1459)
Q Consensus 1182 ~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ 1213 (1459)
...+.++++||++||.++++|+.++++++.+.
T Consensus 202 ~~~l~~l~~y~~~Da~l~~~L~~kl~il~Ltk 233 (234)
T cd05776 202 SESLLKLLEHTEKDAYLILQLMFKLNILPLTK 233 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCC
Confidence 45688999999999999999999999998763
No 35
>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=99.95 E-value=1.2e-26 Score=249.91 Aligned_cols=198 Identities=27% Similarity=0.392 Sum_probs=154.2
Q ss_pred EEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHH
Q 000502 959 LLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKIL 1038 (1459)
Q Consensus 959 iLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlI 1038 (1459)
+++|||||.+.+ .||+|..|+|++|++....++.. .+..+...... ....++.+..|..|++|++||.+|+++|
T Consensus 1 v~~~DIEt~~~~-~~p~~~~d~Ii~I~~~~~~~g~~--~~~~~~~~~~~---~~~~~i~~~~v~~~~~E~~lL~~f~~~i 74 (199)
T cd05160 1 VLSFDIETTPPV-GGPEPDRDPIICITYADSFDGVK--VVFLLKTSTVG---DDIEFIDGIEVEYFADEKELLKRFFDII 74 (199)
T ss_pred CccEEEeecCCC-CCcCCCCCCEEEEEEEEeeCCce--eeEEEeecccC---CcCCCCCCceEEEeCCHHHHHHHHHHHH
Confidence 468889987754 48999999999999988644332 22222111110 0111566789999999999999999999
Q ss_pred hhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhcc
Q 000502 1039 CSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIED 1118 (1459)
Q Consensus 1039 r~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~ 1118 (1459)
+.+|||||+|||+++||||||.+||+.+|+..+..++|...... .
T Consensus 75 ~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~-----------------------------------~ 119 (199)
T cd05160 75 REYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEK-----------------------------------S 119 (199)
T ss_pred HhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCc-----------------------------------c
Confidence 99999999999999999999999999999987422333211100 0
Q ss_pred ccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHH
Q 000502 1119 EWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKL 1198 (1459)
Q Consensus 1119 ~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~L 1198 (1459)
......+.+.||+++|+|+.+|+..++++|+|++||+++||.+|++++++.+.+|+.. ..+.++++||++||.+
T Consensus 120 ---~~~~~~~~~~gr~~~D~~~~~r~~~~l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~---~~~~~~~~Y~~~D~~~ 193 (199)
T cd05160 120 ---SGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWE---EDPERLIEYNLKDAEL 193 (199)
T ss_pred ---CCcccceeeeccEeeehHHHHHHhcCcccCCHHHHHHHHhCCCCCcCCHHHHhhccCc---chHHHHHHHHHHHHHH
Confidence 0112346799999999999999999999999999999999999999999999986332 3478999999999999
Q ss_pred HHHHH
Q 000502 1199 NLEIM 1203 (1459)
Q Consensus 1199 vl~Ll 1203 (1459)
+++|+
T Consensus 194 ~~~l~ 198 (199)
T cd05160 194 TLQIL 198 (199)
T ss_pred HHHhh
Confidence 99986
No 36
>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=99.92 E-value=3.4e-24 Score=233.75 Aligned_cols=190 Identities=22% Similarity=0.272 Sum_probs=141.1
Q ss_pred CCCceEEEEEEEeCcCC-CCCCCCCC--CcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHH
Q 000502 954 GEQLTLLSIEVQAESRG-DLRPDPRY--DSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 954 ~~~LtiLSIEIet~srg-~lfPDPe~--DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
.|+|++|+|||||.+.. +.||+|+. |+|++|++.- +++ . ...+++. .............+..|..|.+|++|
T Consensus 2 ~P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~-~~~--~-~~v~~~~-~~~~~~~~~~~~~~~~v~~~~~E~~l 76 (204)
T cd05783 2 IPKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAG-SDG--L-KRVLVLK-REGVEGLEGLLPEGAEVEFFDSEKEL 76 (204)
T ss_pred CCCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcC-CCC--C-cEEEEEe-cCCcccccccCCCCCeEEecCCHHHH
Confidence 36799999999998753 67999998 7887777642 122 1 1222222 11100001112345789999999999
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhh
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLL 1110 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~ 1110 (1459)
|.+|+++|+++ |+|+|||+.+||||||.+||+++|+... +.+
T Consensus 77 L~~F~~~i~~~--~~iig~N~~~FDlpyl~~R~~~~gi~~~----~~~-------------------------------- 118 (204)
T cd05783 77 IREAFKIISEY--PIVLTFNGDNFDLPYLYNRALKLGIPKE----EIP-------------------------------- 118 (204)
T ss_pred HHHHHHHHhcC--CEEEEeCCCCcCHHHHHHHHHHhCCChh----hCc--------------------------------
Confidence 99999999987 5899999999999999999999998641 000
Q ss_pred hhhhhhccccccccccceeecCeEEeehHHHHhhc--------cCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCCh
Q 000502 1111 AKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE--------VKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPG 1182 (1459)
Q Consensus 1111 ~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke--------lKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~ 1182 (1459)
-.||+ ..+.+.||+++|+|++++.. .++.+|+|++||+++||.+|.+++ .++.++
T Consensus 119 -------~~~~~---~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va~~~lg~~K~~~~-~~i~~~------ 181 (204)
T cd05783 119 -------IYLKR---DYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREYTLDAVAKALLGEGKVELE-KNISEL------ 181 (204)
T ss_pred -------eeecC---CceeccCcEEeECHHHhhccchhhhhhccccccCcHHHHHHHhcCCCcccCC-chhhhh------
Confidence 01232 13568999999999988752 267999999999999999999997 556655
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 000502 1183 RARYRCVEYVVGRAKLNLEIMN 1204 (1459)
Q Consensus 1183 ~~r~rvl~YclkDa~Lvl~Ll~ 1204 (1459)
++.++++||++||.++++|++
T Consensus 182 -~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 182 -NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred -cHHHHHHhhHHHHHHHHHHhc
Confidence 367899999999999999875
No 37
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=99.92 E-value=4.8e-26 Score=272.01 Aligned_cols=144 Identities=28% Similarity=0.510 Sum_probs=110.5
Q ss_pred eeccCCCCCCC-----CcccccccCcc--------cCCccEEEEEeeCCCCCEEEEEEcCccceEeeeCCCCcccccccc
Q 000502 19 DHYMAPPIPGY-----DICYSSLQGGK--------VNEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADIPVQLRQED 85 (1459)
Q Consensus 19 D~y~rpP~p~~-----d~~f~~ld~~~--------~~~~PVIRIFGvT~~G~SVClHVHGf~PYFYV~~p~~f~~~~~~~ 85 (1459)
..|.|||+|.+ ++.|||+|.+. .+.+||||+||+|.+|+|||||||||+|||||++|.+|.+++
T Consensus 58 ~~w~Rp~~p~~~p~~~~i~fqq~~~e~y~~~~~~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g~~~e~--- 134 (1066)
T KOG0969|consen 58 SRWARPALPALDPIKNDIEFQQIDIEFYVENGSGTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNGFGPEH--- 134 (1066)
T ss_pred ccccCCCCCccCcccccceEEEeehhhhccCCCcccCCCceEEEeeeccCCCeEEEEEecccceEEecCCCCCCHHH---
Confidence 44999999986 46899999653 357899999999999999999999999999999999999887
Q ss_pred hhHHHHHHHHHHHHHHh----------cCC----CCCCCeeeeEEEE-----Eeccc----CCccc-----CCCCCcccc
Q 000502 86 DGYMHAISLALEKALKV----------KGS----AGSKRQHVHECSL-----VRAKK----GGAVF-----DKSLQPHES 137 (1459)
Q Consensus 86 ~~~i~~L~~~Ln~al~~----------~~~----~~~~~~~V~~v~l-----V~~~~----~G~v~-----~~~~q~YES 137 (1459)
|..++++|+..+.. +.+ .+..++...++.+ +.+.+ +|+.. .-.+++|||
T Consensus 135 ---i~~~~~~l~~~~~~~av~~ve~~~k~~l~~~~g~~k~~f~kit~~lP~~~~~~r~~lergv~~~~~~~~~~~~~yEs 211 (1066)
T KOG0969|consen 135 ---IGKFQQALDVKVTAHAVDHVEVVSKESLYGYQGDTKQPFLKITVTLPRMVAAARRLLERGVFISGKGEKVGFTTYES 211 (1066)
T ss_pred ---HHHHHHHHHHHHHHhHHHHHHHHhhhhhheecCCCCceeEEEecccHHHHHHhHHHHHhcccccccCcceeeeEecC
Confidence 66777777654431 000 1112344444443 22222 45222 125789999
Q ss_pred ChhhhhhhhhccCcccceeEEeCCcccccCC
Q 000502 138 HIPFLLQFLVDYNLYGMGHLHLSKLKFRHPV 168 (1459)
Q Consensus 138 nIpf~LRFMID~nI~Gm~WI~lp~~kfR~p~ 168 (1459)
||+|++|||+|++|+||+||++|+++|+...
T Consensus 212 Ni~f~lrfmvd~~iVG~~wi~lp~gk~~~~~ 242 (1066)
T KOG0969|consen 212 NIDFVLRFMVDCDIVGMNWIELPAGKYRIRD 242 (1066)
T ss_pred CccEEEEEEecCccccceeEEeccchheecc
Confidence 9999999999999999999999999999886
No 38
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=99.89 E-value=3.7e-23 Score=268.89 Aligned_cols=146 Identities=25% Similarity=0.412 Sum_probs=108.2
Q ss_pred CceEEEEEEeeec------cCCCCCCCCcccccccCcccCCccEEEEEeeCCCCCEEEEEEcCccceEeeeCCCCccccc
Q 000502 9 NIFSVRIVSIDHY------MAPPIPGYDICYSSLQGGKVNEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADIPVQLR 82 (1459)
Q Consensus 9 ~~~~Vriv~iD~y------~rpP~p~~d~~f~~ld~~~~~~~PVIRIFGvT~~G~SVClHVHGf~PYFYV~~p~~f~~~~ 82 (1459)
+.+..|++|+||| ...|.+.++ +...+.+|||||||+|++|+|||||||||+|||||++|++|.+++
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~pvIRlFGvTe~G~SV~v~V~gF~PYFYV~~p~~~~~~~ 112 (1054)
T PTZ00166 40 KDLVFFQLDADYTEKDDKSQGNPHNTVS-------GVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPED 112 (1054)
T ss_pred CCceEEEEeeeccccccccccCccccCC-------CccCCCceEEEEEEecCCCCEEEEEEeCCceEEEEecCCCCCHHH
Confidence 3455666666665 444444333 333467899999999999999999999999999999999998655
Q ss_pred ccchhHHHHHHHHHHHHHHhcCCCCCCCeeeeEEEEEeccc-------------------------------CCccc---
Q 000502 83 QEDDGYMHAISLALEKALKVKGSAGSKRQHVHECSLVRAKK-------------------------------GGAVF--- 128 (1459)
Q Consensus 83 ~~~~~~i~~L~~~Ln~al~~~~~~~~~~~~V~~v~lV~~~~-------------------------------~G~v~--- 128 (1459)
+..|+..|+..+......+.....|..|++|.+++ .|..+
T Consensus 113 ------~~~~~~~L~~~l~~~~~~~~~~~~V~~VeiV~k~sl~gY~~~~~~~flKIt~~~P~~v~klR~~Le~g~~~~~~ 186 (1054)
T PTZ00166 113 ------SQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGG 186 (1054)
T ss_pred ------HHHHHHHHHHHHhhcccccccCCceEEEEEEEeeeeceeCCCCceeEEEEEEcCHHHHHHHHHHHHcCCccccc
Confidence 66788888877654221112234678888877644 23221
Q ss_pred ----CCCCCccccChhhhhhhhhccCcccceeEEeCCcccccC
Q 000502 129 ----DKSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKLKFRHP 167 (1459)
Q Consensus 129 ----~~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~kfR~p 167 (1459)
...+++|||||||++|||||+||.||+||++++++|...
T Consensus 187 ~~~~~~~~~vyEsnI~f~lRFmID~~I~g~~Wi~i~~~~~~~~ 229 (1054)
T PTZ00166 187 GWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIR 229 (1054)
T ss_pred ccccccccceeecCCCHHHHHHhccCCCceeEEEecCcceeec
Confidence 134789999999999999999999999999999998643
No 39
>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=99.84 E-value=9.7e-21 Score=228.62 Aligned_cols=105 Identities=20% Similarity=0.196 Sum_probs=90.7
Q ss_pred CcCCChHHHHHHHHHHHHHHHHHHHhhCC--------ch-------HHHHHHHHHHHHHhhheeeeecccccccccCcCC
Q 000502 1350 VRKGVLPRLLEEILSTRIMVKQAIKKLAP--------SQ-------QILHRIFNARQLALKLIANVTYGYTAAGFSGRMP 1414 (1459)
Q Consensus 1350 vrkGILP~mL~eLL~~R~~vKk~MKk~~~--------~d-------~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmp 1414 (1459)
...++....++.+.+.|..+|...|..++ ++ +.+-.+||++|+|+|+++||+|||+|+. .+|||
T Consensus 219 rEn~Fyvdtvr~FrdrRy~yK~~~k~~k~~~~~~~~~~~~~~~~~a~~~~~lyDs~Q~A~KiIlNSfYGYlG~~-gsRwY 297 (621)
T cd05535 219 RENPFYVDTVRAFRDRRYEYKGLHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRK-GSRWY 297 (621)
T ss_pred ccCCcHHhhHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccCcC-CcccC
Confidence 45688899999999999999998876543 11 1344689999999999999999999975 46999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEEC
Q 000502 1415 CAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1415 c~eIAdSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~l 1459 (1459)
+.++|++||.+||++|+.|++++++ .|..| |||||||||.|
T Consensus 298 s~emA~~VT~~GreIIk~tr~lvE~---~G~~V-egDTDsI~~~l 338 (621)
T cd05535 298 SMEMAGIVCYTGANIIQMARELVEQ---IGRPL-ELDTDGIWCIL 338 (621)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHh---cCCEE-EEecCeeEEEc
Confidence 9999999999999999999999986 57877 79999999974
No 40
>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=99.78 E-value=4.8e-18 Score=186.18 Aligned_cols=166 Identities=13% Similarity=0.098 Sum_probs=129.0
Q ss_pred CCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEec
Q 000502 970 GDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGW 1049 (1459)
Q Consensus 970 g~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGY 1049 (1459)
|.-|+.+..++|++||+...+..+....+ .. ..+.+|++||.+|+++|++++| +|+||
T Consensus 42 ~~~~l~~~~~~Iv~Is~~~~~~~~~~~~~----~~-----------------~~~~~E~elL~~F~~~i~~~~p-~lv~y 99 (208)
T cd05782 42 GSDFLPLPFHKVVSISALYRDDDGGFLKV----RT-----------------LDGADEKELLEDFFQLIEKKNP-RLVSF 99 (208)
T ss_pred CCCCCccccCceEEEEEEEEecCCCeEEE----ee-----------------cCCCCHHHHHHHHHHHHHHhCC-EEEec
Confidence 34478888999999999876332221111 01 1246899999999999999988 89999
Q ss_pred cCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhcccccccccccee
Q 000502 1050 DIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLH 1129 (1459)
Q Consensus 1050 NI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~ 1129 (1459)
|+.+||||||..||..||+.....+++... ...|+ ..
T Consensus 100 Ng~~FDlP~L~~Ra~~~gi~~p~~~~~~~~-------------------------------------~~~y~------~r 136 (208)
T cd05782 100 NGRGFDLPVLHLRALIHGVSAPAYFDLGNK-------------------------------------DWNYR------NR 136 (208)
T ss_pred CCCcCCHHHHHHHHHHhCCCCccccCcccc-------------------------------------hhhcc------Cc
Confidence 999999999999999999975322222100 00121 12
Q ss_pred ecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHH
Q 000502 1130 VGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMN 1204 (1459)
Q Consensus 1130 I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~ 1204 (1459)
+.|| ++|+|.+++...++.+|+|++||+.+...+|.++++.++.++|..|+ +.++++||++|+..+..|+.
T Consensus 137 ~~~~-h~DL~~~~~~~~~~~~~~L~~va~~lG~~~K~d~~G~~v~~~y~~g~---~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 137 YSER-HLDLMDLLAFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGK---LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred CCCC-cccHHHHHhccCccCCCCHHHHHHHhCCCCCcCCCHHHHHHHHHcCC---hHHHHHHHHHHHHHHHHHHh
Confidence 4678 99999999987778999999999876556899999999999999875 78999999999999999875
No 41
>PHA02563 DNA polymerase; Provisional
Probab=99.62 E-value=4.2e-15 Score=183.75 Aligned_cols=347 Identities=16% Similarity=0.179 Sum_probs=185.8
Q ss_pred HHHHHHHHh----hcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhH
Q 000502 1031 FSHFIKILC----SFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVA 1106 (1459)
Q Consensus 1031 L~aFidlIr----~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~ 1106 (1459)
+..|+++|. +.+.=+|.-|| -+||-.||+.-..+++.+...++. +++.. .
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN-~~FD~~Fil~~L~~~~~~~~~e~~-~~~~~------------~------------ 103 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHN-LKFDGSFILKWLLRNGFNWILELR-VRSSK------------N------------ 103 (630)
T ss_pred HHHHHHHHhhccccccceEEEEec-CCccHHHHHHHHHhhccccccccc-ccCcc------------c------------
Confidence 336666666 22334777899 899999999988888865432211 11100 0
Q ss_pred HhhhhhhhhhccccccccccceeecCeEE--eehHHHHhhccCCCCCCHHHHHHHH-hcCCCCCCCh--hhhHHHHhcCC
Q 000502 1107 ESLLAKDAIIEDEWGRTHASGLHVGGRIV--LNVWRLMRGEVKLNMYTVEAVAETV-LRRKIPSIPF--RVLTKWFASGP 1181 (1459)
Q Consensus 1107 g~~~~k~s~~~~~~G~~~~s~i~I~GRiv--IDLwrv~rkelKL~sYSLEnVA~~v-Lgekkpd~s~--k~Ltk~y~sg~ 1181 (1459)
+ ...+...||+. .+-+..++..+.+-.-+|+.++..+ +...+.++++ ..-..++-..-
T Consensus 104 -------------~----~~~i~~~g~~~~i~~~~~~f~DS~~llp~~L~~l~~~F~~~~~k~~~d~~~~~~~~y~~~~~ 166 (630)
T PHA02563 104 -------------F----DTTIFINGRWYTITDSFMKFRDSLKLLPFSLEKLKKDFGLTILKKDIDLNKERPVGYEFTTF 166 (630)
T ss_pred -------------c----cceEeeCCEEEEEEEEEEEEEehHhhhhHHHHHHHHHhCcccccCCcCccccccccceeccc
Confidence 0 00122233321 0111223334555567888888877 3333333322 11100000000
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCccccccccCCc-hhhhHHHHHHHhhhCCEEeeCCCCCcccc
Q 000502 1182 GRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGS-QYRVESMLLRLAHTQNYLAISPGNHQVAS 1260 (1459)
Q Consensus 1182 ~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGS-q~rVESlLlr~ak~~nfllpsPs~~qv~~ 1260 (1459)
...+...++|+.+|+.++..++... .+.+ ..-++-+| ..++.-.++...+....-+|.++..-...
T Consensus 167 ~~~~~e~~~Yl~~D~~il~~~~~i~--------~~~~-----f~~~TisS~a~~ifk~~~~~~~~~~~~~p~l~~~~~~f 233 (630)
T PHA02563 167 EKLDPEELEYIHNDCVIIAGMLDIH--------FSEG-----FTRFTTGSDAMTVYKELYQKIKIKYTHFPILDLGFDDF 233 (630)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHH--------HHhc-----cccCCcchHHHHHHHHHHhhcccccccCCCCCchHHHH
Confidence 0124578999999998777765432 1111 11222233 23344333321111111124443321111
Q ss_pred ccccccCCeee---eccCCcccCCeEEeeccccchhHHhhcCccccccc-cccCCCcccc---------CCCccc--CCC
Q 000502 1261 QPAMECLPLVM---EPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCL-GKILPSKENT---------LGVSSF--RPD 1325 (1459)
Q Consensus 1261 q~a~E~GglVm---EP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST~v-g~~~~~~~n~---------~Gv~~~--~~d 1325 (1459)
-+....||.|+ ++..|+|.+ +.++|++|||||+|..+++|+.+-. -...+..... .|+... ..+
T Consensus 234 Ir~sY~GGr~~~~~~~~~~~~~~-~~~yDvnSlYPsaM~~~~~P~g~p~~~~~k~~~~~~~~~~i~~~~~~f~~~ev~~p 312 (630)
T PHA02563 234 IRKFYRGGRTWYNPKYIGKLIEE-GYVYDVNSLYPYVMYNAKLPYGEPFYEKGKPAELKPDPLYIYNYGALFKLKKGYVP 312 (630)
T ss_pred HHHheeCceeecccccccccccc-ccccccccccHHHHhhccCCCCCceeeccCcccccccccccccceEEEEEEEccCC
Confidence 11123478998 899999986 7899999999999999999997632 1111100000 010000 000
Q ss_pred ch----hhcccC-cccccCC--------------------------------------CCceecCCCCcCCChHHHHHHH
Q 000502 1326 LH----VLRDLK-DELLIPP--------------------------------------NGVMYVPPKVRKGVLPRLLEEI 1362 (1459)
Q Consensus 1326 ~~----~l~~Lk-d~i~isP--------------------------------------ngv~FVk~~vrkGILP~mL~eL 1362 (1459)
.. .+.... +.-.+-| .|+.|- ...+++.+.++.+
T Consensus 313 ~~~~i~Ik~~~~~~~~~i~p~g~~~g~~~~~E~~~~~~~~i~le~~ik~y~~~~i~v~~Gy~fe---~~~~~FkeyI~~l 389 (630)
T PHA02563 313 DDMLIQIKSNLDFNGRLVLKVGIVKYVNSGNEYVDLNLNNLDLELEITHYDAFNEEVESGVVFE---CETGLFRDFIDHF 389 (630)
T ss_pred CccccceeccccCCCceeeecccEeeEecCceEEEEEeceEEHHHhhhccceeEEEEEEEEEEc---ccCchHHHHHHHH
Confidence 00 000000 0000000 233342 2368888999999
Q ss_pred HHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeeccccccccc--CcCCC---------------------HHHH
Q 000502 1363 LSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFS--GRMPC---------------------AELA 1419 (1459)
Q Consensus 1363 L~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fS--GRmpc---------------------~eIA 1419 (1459)
.+.|...|+. . ..++..|+++||.||-+|..-. ++.++ +.+|
T Consensus 390 Y~iK~~~K~~----~-----------~~~~i~KLlLNSLYGKfg~~p~~~~~~~~l~~~~~l~~~~~~~~~~~~~yv~iA 454 (630)
T PHA02563 390 YEIKTNSKGA----K-----------KQNMLAKLMLNSLYGKFALNPDNTGKVPYLDDNGRLDLISNGEENKEPNYIPIA 454 (630)
T ss_pred HHHHhccccC----c-----------cHHHHHHHHHhcccchhhcCccccCceeeecccceeeeecCCccccccccchHH
Confidence 8888654331 1 1246899999999999986422 12221 4599
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCcEEEEeccceeEEE
Q 000502 1420 DSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1420 dSIT~~GRe~Le~Ai~~Ie~~~~~GakVIYGDTDSlFV~ 1458 (1459)
++||+.||.+|..++..+++. |+||||||+||.
T Consensus 455 a~ITa~aR~~m~~~~~~~~~~------v~Y~DTDSi~v~ 487 (630)
T PHA02563 455 AFITARARSNLLSALQYLYEK------FIYCDTDSIHLE 487 (630)
T ss_pred HHHHHHHHHHHHHHHHHhhcc------EEEECCceEEEe
Confidence 999999999999999988652 999999999985
No 42
>PHA02523 43B DNA polymerase subunit B; Provisional
Probab=99.58 E-value=1.8e-15 Score=173.49 Aligned_cols=75 Identities=24% Similarity=0.231 Sum_probs=61.9
Q ss_pred HHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHH----HHhh-cCCCCcE-EEEeccceeEE
Q 000502 1384 HRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAIS----FVNE-NEKWKAK-VIYGDTDRYTV 1457 (1459)
Q Consensus 1384 ~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~----~Ie~-~~~~Gak-VIYGDTDSlFV 1457 (1459)
.+.++.+|.|+|+++||+|||+|+. .+||||.++|++||++||++|+.+.. ++++ ....|++ ||||||||+||
T Consensus 36 ~a~~~~~q~AiKIlmNSfYGylG~~-~~R~yd~e~A~aVT~~Gre~Ik~i~~~~ney~~~l~~t~G~~~VIYgDTDSifv 114 (391)
T PHA02523 36 EQKRNTNQLNRKILINSLYGALGNN-WFRYFDLRNAEAITTYGQLAIRWIERKLNEYINELVKTTGVDYVCYIDTDSVYL 114 (391)
T ss_pred HHHHhcchHHHHHHHHhhhhhhcCC-CceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcceEEEecCCeeEE
Confidence 4567899999999999999999985 47999999999999999999994443 2222 1236996 99999999999
Q ss_pred EC
Q 000502 1458 CI 1459 (1459)
Q Consensus 1458 ~l 1459 (1459)
.+
T Consensus 115 ~~ 116 (391)
T PHA02523 115 NM 116 (391)
T ss_pred Ee
Confidence 75
No 43
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=99.29 E-value=2.5e-12 Score=160.43 Aligned_cols=169 Identities=30% Similarity=0.465 Sum_probs=118.5
Q ss_pred CCCCCCC-CCceEEEEEEeeeccCCCCCCCCcccccccC-c---ccCCccEEEEEeeCCCCCEEEEEEcCccceEeeeCC
Q 000502 1 MADSQPD-SNIFSVRIVSIDHYMAPPIPGYDICYSSLQG-G---KVNEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCA 75 (1459)
Q Consensus 1 ~~~~~~~-~~~~~Vriv~iD~y~rpP~p~~d~~f~~ld~-~---~~~~~PVIRIFGvT~~G~SVClHVHGf~PYFYV~~p 75 (1459)
|+|-|.. ...-.+++..++++.+|=.|..|......+. . .....||+|+||..+.|+.||||+||.+||+||.+.
T Consensus 1 ~~dlq~~~~~~dt~~~s~~s~~lsp~~~k~d~~~~~n~t~~es~t~q~tqv~~v~~a~~~g~~~~~~s~g~l~~i~~k~d 80 (1488)
T KOG0968|consen 1 MSDLQNDTIQSDTFSISYISWELSPCDPKYDFVGKDNPTANESPTTQPTQVIRVFGANEEGETVCCFSHGVLPYIYVKYD 80 (1488)
T ss_pred CcccccCcccccccccccccccccCCCcccccccCCCcccccCcccCCCccceecccccccceeeeeecccchhhhhhhh
Confidence 4444444 3344566777788888776654422211110 0 112346999999999999999999999999999988
Q ss_pred CCcccccccchhHHHHHHHHHHHHHHhcC--CCCCCCe---eeeEEEEEeccc---------------------------
Q 000502 76 DIPVQLRQEDDGYMHAISLALEKALKVKG--SAGSKRQ---HVHECSLVRAKK--------------------------- 123 (1459)
Q Consensus 76 ~~f~~~~~~~~~~i~~L~~~Ln~al~~~~--~~~~~~~---~V~~v~lV~~~~--------------------------- 123 (1459)
.-.+......-+++.+++..||-++.... +....+. .|..+++|++.+
T Consensus 81 ~~~t~t~l~~~d~~aqi~k~le~a~~~~~~a~~esq~~~~~~v~sv~~vk~~p~~~~~~~~s~~~k~~l~~~sck~rl~e 160 (1488)
T KOG0968|consen 81 SFATTTDLEVPDFLAQIQKSLEYALALAARANPESQKPNLNAVQSVQLVKGIPFYGYSFCFSKFLKICLFSPSCKDRLVE 160 (1488)
T ss_pred hhccccccccccHHHHHHHHHHHHHHHHhhcChhhhcchHHHHHHHHhcCCCCccccccchhhHHHHHhcCchhHHHHHH
Confidence 75554332345678888888887766421 1112222 233455554433
Q ss_pred ---CCcccCCCCCccccChhhhhhhhhccCcccceeEEeCCcccccCCC
Q 000502 124 ---GGAVFDKSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKLKFRHPVP 169 (1459)
Q Consensus 124 ---~G~v~~~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~kfR~p~p 169 (1459)
.|++.+..+++||+|+||.++||+|+|++||.||.+....++.++.
T Consensus 161 l~rdg~ipnk~is~~esh~~y~~~r~~d~n~~~~~~ikvds~~~~n~~d 209 (1488)
T KOG0968|consen 161 LFRDGAIPNKVISVYESHLPYLLQRMVDHNLYGCAPIKVDSSIIKNDVD 209 (1488)
T ss_pred HHhcccCCCcccccchhccchhhhhhhhcccccceeeecchhhhcCCcc
Confidence 5888899999999999999999999999999999999998888843
No 44
>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=99.26 E-value=1.9e-10 Score=126.21 Aligned_cols=170 Identities=15% Similarity=0.208 Sum_probs=122.0
Q ss_pred CCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCC
Q 000502 973 RPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQ 1052 (1459)
Q Consensus 973 fPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~ 1052 (1459)
|+......|++|++....+... ..+..+ + + ...+|++||..|.+.|.++.| .++|||+.
T Consensus 3 Fl~~~f~kIV~Is~~~~~~~~~-~~v~s~--~----------~-------~~~~E~~lL~~F~~~~~~~~p-~LVs~NG~ 61 (209)
T PF10108_consen 3 FLPLPFHKIVCISVVYADDDGQ-FKVKSL--G----------G-------PDDDEKELLQDFFDLVEKYNP-QLVSFNGR 61 (209)
T ss_pred CCcccCCCeEEEEEEEEecCCc-EEEEec--c----------C-------CCCCHHHHHHHHHHHHHhCCC-eEEecCCc
Confidence 5566688999999985543221 222211 1 0 113699999999999999998 56899999
Q ss_pred CccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccccccccccceeecC
Q 000502 1053 GGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGG 1132 (1459)
Q Consensus 1053 ~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~~G~~~~s~i~I~G 1132 (1459)
+||+|||..||-.+|+.....+.+.. ..|.. -.+.+.+
T Consensus 62 ~FDlP~L~~Ral~~gi~~p~~~~~~~---------------------------------------k~Wen-Y~~Ry~~-- 99 (209)
T PF10108_consen 62 GFDLPVLCRRALIHGISAPRYLDIGN---------------------------------------KPWEN-YRNRYSE-- 99 (209)
T ss_pred cCCHHHHHHHHHHhCCCCchhhhcCC---------------------------------------CCccc-cccccCc--
Confidence 99999999999999998632222110 01210 0011122
Q ss_pred eEEeehHHHHhhccCCCCCCHHHHHHHHhcC-CCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccch
Q 000502 1133 RIVLNVWRLMRGEVKLNMYTVEAVAETVLRR-KIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMIN 1210 (1459)
Q Consensus 1133 RivIDLwrv~rkelKL~sYSLEnVA~~vLge-kkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~ 1210 (1459)
+ ++|++..+...-.-...+|+.+|..+ |. .|.+++..++.++|.+|. ..++.+||.+||..+..|+.++..+.
T Consensus 100 ~-H~DLmd~l~~~g~~~~~sLd~la~~l-giPgK~~idGs~V~~~y~~g~---i~~I~~YCe~DVl~T~~lylR~~~~~ 173 (209)
T PF10108_consen 100 R-HLDLMDLLSFYGAKARTSLDELAALL-GIPGKDDIDGSQVAELYQEGD---IDEIREYCEKDVLNTYLLYLRFELLR 173 (209)
T ss_pred c-cccHHHHHhccCccccCCHHHHHHHc-CCCCCCCCCHHHHHHHHHcCC---HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3 89999998655455678999999865 44 589999999999998775 77899999999999999998875443
No 45
>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=98.96 E-value=1.7e-10 Score=132.72 Aligned_cols=96 Identities=25% Similarity=0.431 Sum_probs=64.6
Q ss_pred CCCCCEEEEEEcCccceEeeeCCCCcccccccchhHHHHHHHHHHHHHHhcCCCCCCCeeeeEEEEEec-cc----CC--
Q 000502 53 TPAGQKTCLHIHRALPYLYVPCADIPVQLRQEDDGYMHAISLALEKALKVKGSAGSKRQHVHECSLVRA-KK----GG-- 125 (1459)
Q Consensus 53 T~~G~SVClHVHGf~PYFYV~~p~~f~~~~~~~~~~i~~L~~~Ln~al~~~~~~~~~~~~V~~v~lV~~-~~----~G-- 125 (1459)
|++|+|||+|||||.|||||..++..... .+.+.+++.+.. .....+++++.|.+ .. .+
T Consensus 2 t~~g~svcv~v~~f~pyfYv~~~~~~~~~---------~~~~~~~~~~~~-----~~~~~~~~~~~V~r~~~~~~y~~~~ 67 (325)
T PF03104_consen 2 TEDGKSVCVRVHGFRPYFYVLPPESDSPK---------DLEQFIEQLLRK-----KFKIDVFKIEKVKRKKSFYGYDGKE 67 (325)
T ss_dssp ECTSEEEEEEEST--EEEEEEESSGGGHH---------HHTTHEEHHEET-----TEEEEEEEEEEEEEEEESSEETTEE
T ss_pred CCCCCEEEEEEcCCCEEEEEECCCCccHH---------HHHHHHHHHhhh-----ccCCceEEEEEEEeeeeeccCCCCC
Confidence 78999999999999999999988765432 122221111111 22356677777766 33 00
Q ss_pred -----cc-------------cC-CCCCccccChhhhhhhhhccCcccceeEEeCCc
Q 000502 126 -----AV-------------FD-KSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKL 162 (1459)
Q Consensus 126 -----~v-------------~~-~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~ 162 (1459)
+. +. ..+++||+||+|.+|||+|++|.||+|++++..
T Consensus 68 ~~~lkV~~~~~~~~~~~~~~l~~~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~ 123 (325)
T PF03104_consen 68 EPFLKVYFSSPRDVRKLRDNLKKTFFKVYEADIPPLERFLIDRNIRGPGWIKIKNP 123 (325)
T ss_dssp EEEEEEEESSTTHHHHHHHHHHHTEEEEESTSS-HHHHHHHHTTHCTTEEEEEETT
T ss_pred ceEEEEEECcHHHHHHHHHHHHhccchhhccCCCHHHheeeecCcccceeeecccc
Confidence 00 11 357889999999999999999999999999976
No 46
>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=98.92 E-value=6.1e-09 Score=109.22 Aligned_cols=158 Identities=16% Similarity=0.225 Sum_probs=93.0
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHh
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILC 1039 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr 1039 (1459)
+.||||+++ + +|..+.|.+|+++..+++.... ...+... -.+|.+.+..+++.+.
T Consensus 1 l~~DIET~G---l--~~~~~~i~liG~~~~~~~~~~~-~~~~~~~-------------------~~~ee~~~~~~~~~l~ 55 (164)
T PF13482_consen 1 LFFDIETTG---L--SPDNDTIYLIGVADFDDDEIIT-FIQWFAE-------------------DPDEEEIILEFFELLD 55 (164)
T ss_dssp --EEEEESS------GG-G---EEEEEEE-ETTTTE--EEEE-GG-------------------GHHHHHHHHH--HHHH
T ss_pred CcEEecCCC---C--CCCCCCEEEEEEEEeCCCceEE-eeHhhcc-------------------CcHHHHHHHHHHHHHh
Confidence 458999863 3 4555779999999765543221 1111111 0245555556557777
Q ss_pred hcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhccc
Q 000502 1040 SFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDE 1119 (1459)
Q Consensus 1040 ~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~~~ 1119 (1459)
+. +.+++||+.+||+|+|..|++.++++.
T Consensus 56 ~~--~~iv~yng~~FD~p~L~~~~~~~~~~~------------------------------------------------- 84 (164)
T PF13482_consen 56 EA--DNIVTYNGKNFDIPFLKRRAKRYGLPP------------------------------------------------- 84 (164)
T ss_dssp TT----EEESSTTTTHHHHHHHHH-HHHH---------------------------------------------------
T ss_pred cC--CeEEEEeCcccCHHHHHHHHHHcCCCc-------------------------------------------------
Confidence 65 689999999999999999997775431
Q ss_pred cccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCC-CCCChhhhHHHHhc----CChhHHHHHHHHHHH
Q 000502 1120 WGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKI-PSIPFRVLTKWFAS----GPGRARYRCVEYVVG 1194 (1459)
Q Consensus 1120 ~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekk-pd~s~k~Ltk~y~s----g~~~~r~rvl~Yclk 1194 (1459)
...++|+++.+++... .+|+|.+|++.+...+. ++++...+.+||.. ++...+.+++.||..
T Consensus 85 ------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~ 151 (164)
T PF13482_consen 85 ------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNED 151 (164)
T ss_dssp ------------GGGEEEHHHHHT-TTS-CCTT--SHHH-----------HHHHHHHHHH---TTGGTS--HHHHHHHHH
T ss_pred ------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 0126899999976544 99999999999544444 67888888888765 334567899999999
Q ss_pred HHHHHHHHHHhc
Q 000502 1195 RAKLNLEIMNQL 1206 (1459)
Q Consensus 1195 Da~Lvl~Ll~kL 1206 (1459)
|+..+.+|++.|
T Consensus 152 Dv~~~~~L~~~l 163 (164)
T PF13482_consen 152 DVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh
Confidence 999999999876
No 47
>PRK05762 DNA polymerase II; Reviewed
Probab=98.84 E-value=2.1e-09 Score=138.69 Aligned_cols=117 Identities=12% Similarity=0.077 Sum_probs=72.6
Q ss_pred cccccCcc--cCCccEEEEEeeCCCCCEEEEEEcCccceEeeeCCCCcccccccchhHHHHHHHHHHHHHHhcC--CCCC
Q 000502 33 YSSLQGGK--VNEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADIPVQLRQEDDGYMHAISLALEKALKVKG--SAGS 108 (1459)
Q Consensus 33 f~~ld~~~--~~~~PVIRIFGvT~~G~SVClHVHGf~PYFYV~~p~~f~~~~~~~~~~i~~L~~~Ln~al~~~~--~~~~ 108 (1459)
++.||.++ .+..||||+||.|++|.++|+++.||.||||+..+.... ...+..... ..... -..-
T Consensus 6 ~~lL~~~~~~~~~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~~~---------~~~~~~~~~--~~~~~~~l~~~ 74 (786)
T PRK05762 6 GFILTRHYRDTPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERA---------ESLLAGEIG--VRLSPLALKDF 74 (786)
T ss_pred EEEEeeEEEEECCeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchhhh---------HHHHhhccc--ceeeccceecc
Confidence 44455442 345799999999999999999999999999998554211 111111100 00000 0000
Q ss_pred CCeeeeEEEEEeccc----CCcccCCCCCccccChhhhhhhhhccCcccceeEEeC
Q 000502 109 KRQHVHECSLVRAKK----GGAVFDKSLQPHESHIPFLLQFLVDYNLYGMGHLHLS 160 (1459)
Q Consensus 109 ~~~~V~~v~lV~~~~----~G~v~~~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp 160 (1459)
..+.+.++.+-..+. ...+....+.+||++|+|..|||||.+|.||+|+...
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~EaDI~~~~R~lid~~i~~~~w~~~~ 130 (786)
T PRK05762 75 HRRPVLGLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPCVWFSGE 130 (786)
T ss_pred cCCeeeEEEeccHHHHHHHHHHHHHcCCeEEECCCChhHhheeeCCCCCcEEEEEE
Confidence 112333333222111 1122235789999999999999999999999999875
No 48
>PRK05761 DNA polymerase I; Reviewed
Probab=98.32 E-value=4.3e-07 Score=117.34 Aligned_cols=109 Identities=13% Similarity=0.099 Sum_probs=69.0
Q ss_pred cccCcc--cCCccEEEEEeeCCCCCEEEEEEc-CccceEeeeCCCCcccccccchhHHHHHHHHHHHHHHhcCCCCCCCe
Q 000502 35 SLQGGK--VNEVPVIRVYGSTPAGQKTCLHIH-RALPYLYVPCADIPVQLRQEDDGYMHAISLALEKALKVKGSAGSKRQ 111 (1459)
Q Consensus 35 ~ld~~~--~~~~PVIRIFGvT~~G~SVClHVH-Gf~PYFYV~~p~~f~~~~~~~~~~i~~L~~~Ln~al~~~~~~~~~~~ 111 (1459)
.||.++ ..+.|||++||.. .|..+.++.. ||.||||+..+++... .. . +... ..
T Consensus 21 lld~~Y~~~~~~~vi~l~~~~-~~~~~~~~d~~gfkPYfy~~~~~~~~~----------~~---~-~~~~--------~~ 77 (787)
T PRK05761 21 LLSVDYDGKLGKAVVKLYDPE-TGKIYKWYDRTGHKPYFLTDLDPDEID----------KI---P-KILR--------HP 77 (787)
T ss_pred EEEEEEeccCCeeEEEEEecC-CCeEEEEEcCCCCCCeEEecCChHHHH----------hh---h-hhhc--------CC
Confidence 455543 4567999999997 6666666655 6999999987765211 10 0 0000 11
Q ss_pred eeeEEEEEeccc---------------------C-CcccCCCCCccccChhhhhhhhhccCcccceeEEeCCccccc
Q 000502 112 HVHECSLVRAKK---------------------G-GAVFDKSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKLKFRH 166 (1459)
Q Consensus 112 ~V~~v~lV~~~~---------------------~-G~v~~~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~kfR~ 166 (1459)
.+..++++.+.+ . ...+...+.+|||+|+|.+|||+|++|.||+|+.+..++++.
T Consensus 78 ~~~~~e~~~~~~~~~~~~~~~~kI~~~~p~~v~~~r~~~~~~~~~~EaDI~f~~RyliD~~i~~~~~~~~~~~~~~~ 154 (787)
T PRK05761 78 SFDHLEIVEKYDGLRDKKVKVTKIVVKDPLAVRRLRLSVRDIPRAWEADIKYEFRYIYDNGLIPGMPYDVKNGLESV 154 (787)
T ss_pred CeeeEEEEEEEeccCCCcceEEEEEECCHHHHHHHHHHHHhhhhheeCCCChHHheEEeCCCCCCceEEeccccccc
Confidence 233333333322 0 000111268999999999999999999999999998766443
No 49
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.17 E-value=2.8e-05 Score=86.60 Aligned_cols=160 Identities=13% Similarity=0.089 Sum_probs=111.2
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKI 1037 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidl 1037 (1459)
.++.|||||.+ + ++..+.|.+++...-.++.. .+... +.+-+ ..|..+|+.|...
T Consensus 99 ~~~FFDiETTG----L-~~ag~~I~~~g~a~~~~~~~------~Vrq~-------~lp~p-------~~E~avle~fl~~ 153 (278)
T COG3359 99 DVAFFDIETTG----L-DRAGNTITLVGGARGVDDTM------HVRQH-------FLPAP-------EEEVAVLENFLHD 153 (278)
T ss_pred ceEEEeeeccc----c-CCCCCeEEEEEEEEccCceE------EEEee-------cCCCc-------chhhHHHHHHhcC
Confidence 57789999864 2 44678888888775443321 11110 00101 3699999999877
Q ss_pred HhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhhhhhhhhc
Q 000502 1038 LCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIE 1117 (1459)
Q Consensus 1038 Ir~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k~s~~~ 1117 (1459)
+ |..+++.||+..||||||. |+.+..+++.
T Consensus 154 ~---~~~~lvsfNGkaFD~Pfik-R~v~~~~el~---------------------------------------------- 183 (278)
T COG3359 154 P---DFNMLVSFNGKAFDIPFIK-RMVRDRLELS---------------------------------------------- 183 (278)
T ss_pred C---CcceEEEecCcccCcHHHH-HHHhcccccC----------------------------------------------
Confidence 6 6679999999999999999 8776655431
Q ss_pred cccccccccceeecCeEEeehHHHHhhc--cCCCCCCHHHHHHHHhcCCCC----CCChhhhHH-HHhcCChhHHHHHHH
Q 000502 1118 DEWGRTHASGLHVGGRIVLNVWRLMRGE--VKLNMYTVEAVAETVLRRKIP----SIPFRVLTK-WFASGPGRARYRCVE 1190 (1459)
Q Consensus 1118 ~~~G~~~~s~i~I~GRivIDLwrv~rke--lKL~sYSLEnVA~~vLgekkp----d~s~k~Ltk-~y~sg~~~~r~rvl~ 1190 (1459)
.-+-++|+|..+|+- ..|..-+|.+|-+ +||.++. .+..-++.+ |.+.+++.....++.
T Consensus 184 -------------l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~ 249 (278)
T COG3359 184 -------------LEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVL 249 (278)
T ss_pred -------------ccccchhhhhhhhhhhhccCCCCChhhHHH-HhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHH
Confidence 002378999999874 4589999999988 8997543 333334444 445566667888999
Q ss_pred HHHHHHHHHHHHHHhc
Q 000502 1191 YVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1191 YclkDa~Lvl~Ll~kL 1206 (1459)
|+--|+.-...|+.++
T Consensus 250 hN~eDvlnL~~i~~h~ 265 (278)
T COG3359 250 HNREDVLNLPTIIKHV 265 (278)
T ss_pred ccHHHHHhHHHHHHHH
Confidence 9999998877777664
No 50
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=97.70 E-value=5.6e-05 Score=98.48 Aligned_cols=115 Identities=17% Similarity=0.312 Sum_probs=69.9
Q ss_pred CCccEEEEEeeCCCCCEEEEEEcCccceEeeeCCCCcccccccchhHHHHHHH-HHHHHHHhcC----CCCCCCeeeeEE
Q 000502 42 NEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADIPVQLRQEDDGYMHAISL-ALEKALKVKG----SAGSKRQHVHEC 116 (1459)
Q Consensus 42 ~~~PVIRIFGvT~~G~SVClHVHGf~PYFYV~~p~~f~~~~~~~~~~i~~L~~-~Ln~al~~~~----~~~~~~~~V~~v 116 (1459)
...|++|+||.+++|.+|++++-+|.||||+.+++....+. +..... .......... ........+...
T Consensus 6 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (792)
T COG0417 6 DGFPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNSRPEDY------VLKILNRRLDDVLELEEVENVPDPYLGREVEVL 79 (792)
T ss_pred cCceEEEEeeecCCCCEEEEEecCCCCcEEEecCCCcccch------hhhhccccccccceeeeeeeeeccccCCcccce
Confidence 34799999999999999999999999999999997622111 101000 0000000000 000000111112
Q ss_pred EEEecccC------Cc---ccCCCCCccccChhhhhhhhhccCcccceeEEeCCc
Q 000502 117 SLVRAKKG------GA---VFDKSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKL 162 (1459)
Q Consensus 117 ~lV~~~~~------G~---v~~~~~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~ 162 (1459)
.+....+. .. .......+||++|||..|||+|.+|++|.|+.++..
T Consensus 80 ~i~~~~p~~v~~~r~~~~~~~~~~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~~~ 134 (792)
T COG0417 80 KIYARDPQAVRKLREKVKRELEGVVDIFEADIPFAMRYLIDKGIRPMVWVSVDVE 134 (792)
T ss_pred eeEecCHHHHHHHHHHHhhhhhccceEeecCCCcchheeeecCCCCceEEEeeec
Confidence 22222221 11 123467899999999999999999999999999843
No 51
>PHA02735 putative DNA polymerase type B; Provisional
Probab=97.61 E-value=0.00048 Score=81.15 Aligned_cols=135 Identities=17% Similarity=0.118 Sum_probs=78.5
Q ss_pred CHHHHHHHHhcCCC--CCCChhhhH-HHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCcccccccc
Q 000502 1152 TVEAVAETVLRRKI--PSIPFRVLT-KWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLS 1228 (1459)
Q Consensus 1152 SLEnVA~~vLgekk--pd~s~k~Lt-k~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sVls 1228 (1459)
+|++.|...||+.| ..+...... +-|-.+ +...+++|+..|+.|+..|...+ ...|.-.-||+..-++
T Consensus 170 sldna~~ewlge~ka~dgid~~~f~~k~yi~~---n~~dilkyak~da~l~~dl~~e~------~n~~e~ldipmgrp~s 240 (716)
T PHA02735 170 SLDNAAEEWLGENKAKDGIDAGKFDAKEYIKD---NFDDILKYAKIDAELTQDLAIEA------TNEAEELDIPMGRPFS 240 (716)
T ss_pred HHHhHHHHHhccccccccccccccchHHHHhh---hHHHHHHHHhhhHHHHHHHHHHH------hhhHhhcCCccCCCcc
Confidence 79999999999865 223221111 112111 24579999999999999987654 3445555677666555
Q ss_pred CCchhhhHHHHHHHhhhCCEEeeCCCCCcc--ccccccccCCeeeeccCCcccCCeEEeeccccchhHHhhcCccccc
Q 000502 1229 RGSQYRVESMLLRLAHTQNYLAISPGNHQV--ASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCT 1304 (1459)
Q Consensus 1229 RGSq~rVESlLlr~ak~~nfllpsPs~~qv--~~q~a~E~GglVmEP~sGfY~nPVvVLDFqSLYPSIMIAyNICyST 1304 (1459)
.| +..+++|-.-...+ |.-+.... -....|. ||-+=--++|-+-. |+.-|.+|+||+||.. =-.|.|
T Consensus 241 tg--yla~~yl~~~~~ek----p~lg~~~ma~~~wEsYy-GGrfeV~KrgnvGE-v~~pDINSaYPaim~d-lPDpKT 309 (716)
T PHA02735 241 TG--YLAAEYLDANLEEK----PGLGNEAMAKLAWESYA-GGRFEVFKRGNVGE-VAAPDINSAYPAILAD-LPDPKT 309 (716)
T ss_pred cc--hhhHHHHhcccccC----CCCChHHHHHHHHHhhc-CCceEEeccCccce-eeeccccccchHHHHh-CCCCcc
Confidence 43 44455543222211 11111100 0012233 45554456777765 9999999999999987 234555
No 52
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.46 E-value=0.0038 Score=71.35 Aligned_cols=105 Identities=13% Similarity=0.155 Sum_probs=70.1
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCC-Ccc--ccccCCCCCcEEEEeCCHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKS-ESH--QRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~--~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
++.+.||+||.+ + +|..|.|+.|++..-..+ ...+.+..+.... ... .....+|..-.|.-.++..+++..
T Consensus 7 ~~~v~~D~ETTG----l-~~~~d~IIEIa~v~v~~~-~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~ 80 (250)
T PRK06310 7 TEFVCLDCETTG----L-DVKKDRIIEFAAIRFTFD-EVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQ 80 (250)
T ss_pred CcEEEEEEeCCC----C-CCCCCeEEEEEEEEEECC-eEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHH
Confidence 578889999864 2 778899999988755433 2233333333222 111 112334443445566788999999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
|.+++.. .++++|||+. ||+++|.+-+.++|+..
T Consensus 81 ~~~fl~~--~~~lvghn~~-FD~~~L~~~~~r~g~~~ 114 (250)
T PRK06310 81 IKGFFKE--GDYIVGHSVG-FDLQVLSQESERIGETF 114 (250)
T ss_pred HHHHhCC--CCEEEEECHH-HHHHHHHHHHHHcCCCc
Confidence 9998853 3799999984 99999999888877653
No 53
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.37 E-value=0.0033 Score=72.18 Aligned_cols=103 Identities=11% Similarity=0.251 Sum_probs=69.1
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEE-EEEecCCCc-cccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIY-VLLYCKSES-HQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~-vLv~~~~~~-~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
...+.+|+|+++ ++|..|+|+.|++....++. ....+ .++.....+ ....+.||..-.+....+..+.+..|
T Consensus 68 ~~~vv~DiETTG-----~~~~~~~IIEIGAv~v~~g~-i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 68 QVFCFVDIETNG-----SKPKKHQIIEIGAVKVKNGE-IIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CCEEEEEEeCCC-----CCCCCCeEEEEEEEEEECCE-EEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 467788998864 36778899999987665442 22222 233222111 11223444444455667899999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
.+++.. .+++|||+ .||+.+|...+.++|..
T Consensus 142 ~~fl~~---~v~VaHNa-~FD~~fL~~~l~r~g~~ 172 (257)
T PRK08517 142 RLFLGD---SVFVAHNV-NFDYNFISRSLEEIGLG 172 (257)
T ss_pred HHHHCC---CeEEEECH-HHHHHHHHHHHHHcCCC
Confidence 999864 58999999 79999998888777654
No 54
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.36 E-value=0.0025 Score=71.92 Aligned_cols=102 Identities=16% Similarity=0.175 Sum_probs=67.9
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCC-Cc--cccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKS-ES--HQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~--~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
+++.||+||++ + +|..|+|+.|++. .... .+.+..+.... .. ......+|.+-.|.-.++..+.+..|
T Consensus 3 ~~vv~D~ETTG----l-~~~~d~IIeig~v-~~~~---~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~ 73 (232)
T PRK06309 3 ALIFYDTETTG----T-QIDKDRIIEIAAY-NGVT---SESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKF 73 (232)
T ss_pred cEEEEEeeCCC----C-CCCCCEEEEEEEE-cCcc---ccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHH
Confidence 46778888864 2 6788999999973 2211 12222222222 11 11223455545566677899999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
.+++.. .++++|||+..||+++|.+-++++|+..
T Consensus 74 ~~fi~~--~~~lVaHN~~~FD~~~L~~e~~r~g~~~ 107 (232)
T PRK06309 74 IEFCGT--DNILVAHNNDAFDFPLLRKECRRHGLEP 107 (232)
T ss_pred HHHHcC--CCEEEEeCCHHHHHHHHHHHHHHcCCCC
Confidence 999853 4699999988899999998888887653
No 55
>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=97.30 E-value=0.0058 Score=75.48 Aligned_cols=122 Identities=15% Similarity=0.255 Sum_probs=91.8
Q ss_pred CCHHHHHHHHHHHHhhcCCC-EEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccch
Q 000502 1025 SKEIHLFSHFIKILCSFDPD-ILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEP 1103 (1459)
Q Consensus 1025 ~SEkELL~aFidlIr~~DPD-IItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p 1103 (1459)
.+|++++..|++++..+ |+ -|+.|| +|-.++|.+.|.++|.... .
T Consensus 326 ~~E~~~~~~f~~~l~~~-~~~~i~hY~--~~e~~~l~rla~~~~~~~~-~------------------------------ 371 (457)
T TIGR03491 326 NTEELAWQQFLQLLQSY-PDAPIYHYG--ETEKDSLRRLAKRYGTPEA-E------------------------------ 371 (457)
T ss_pred hHHHHHHHHHHHHHHHC-CCCeEEeeC--HHHHHHHHHHHHHcCCCHH-H------------------------------
Confidence 47999999999999887 77 688999 5679999999988875420 0
Q ss_pred hhHHhhhhhhhhhccccccccccceeecCeEEeehHHHHhhc--cCCCCCCHHHHHHHHhcCC--CCCCChhhhHHHHh-
Q 000502 1104 VVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE--VKLNMYTVEAVAETVLRRK--IPSIPFRVLTKWFA- 1178 (1459)
Q Consensus 1104 ~~~g~~~~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke--lKL~sYSLEnVA~~vLgek--kpd~s~k~Ltk~y~- 1178 (1459)
+. .+ . +..+|++.++++. +...||+|++|+..+ |-. .+..+......||.
T Consensus 372 -------~~------~l----------~-~~~vDL~~~vr~~~~~p~~sysLK~v~~~l-g~~~~~~~~~G~~ai~~y~~ 426 (457)
T TIGR03491 372 -------IE------EL----------L-KRFVDIHTIVRRSWILPIESYSLKSIARWL-GFEWRQKEASGAKSLLWYRQ 426 (457)
T ss_pred -------HH------HH----------H-HHheehHHHHHhhEECCCCCCCHHHHHHHh-CcccCCCCCCHHHHHHHHHH
Confidence 00 00 0 1378999999975 566899999999875 542 34577777777774
Q ss_pred ---cCChhHHHHHHHHHHHHHHHHHHHHHh
Q 000502 1179 ---SGPGRARYRCVEYVVGRAKLNLEIMNQ 1205 (1459)
Q Consensus 1179 ---sg~~~~r~rvl~YclkDa~Lvl~Ll~k 1205 (1459)
.++...+..++.||..||..+..|.+.
T Consensus 427 ~~~~~~~~~l~~l~~YN~dD~~At~~l~~w 456 (457)
T TIGR03491 427 WKKTGDRRLLERILRYNEDDCRATWIVADW 456 (457)
T ss_pred HHHhCCHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 455566788999999999999988754
No 56
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.27 E-value=0.0073 Score=71.23 Aligned_cols=104 Identities=13% Similarity=0.105 Sum_probs=66.2
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEE-EEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIY-VLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFI 1035 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~-vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFi 1035 (1459)
...+.||+|+.+ .+|..|+|+.|++...+......+.+ .++............+|..-.|.-.+.-.+++..|.
T Consensus 15 ~~fvvlD~ETTG-----l~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~ 89 (313)
T PRK06063 15 RGWAVVDVETSG-----FRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVA 89 (313)
T ss_pred CCEEEEEEECCC-----CCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHH
Confidence 356678888864 26788999999988654322222333 333221111111223444334445567788999998
Q ss_pred HHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1036 KILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1036 dlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
+++. -++++|||+ .||+++|..-++++|+.
T Consensus 90 ~~l~---~~~lVaHNa-~FD~~fL~~~~~r~g~~ 119 (313)
T PRK06063 90 ELLR---GRTLVAHNV-AFDYSFLAAEAERAGAE 119 (313)
T ss_pred HHcC---CCEEEEeCH-HHHHHHHHHHHHHcCCC
Confidence 8875 369999998 69999998888877653
No 57
>PRK07883 hypothetical protein; Validated
Probab=97.16 E-value=0.0057 Score=77.28 Aligned_cols=104 Identities=16% Similarity=0.245 Sum_probs=71.1
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc-c--ccccCCCCCcEEEEeCCHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES-H--QRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~-~--~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
...+.||+|+.+- +|..|+|+.|++..-+++. +...+..+...... . ...+.||....+.....+.+.+..
T Consensus 15 ~~~Vv~D~ETTGl-----~p~~~~IIEIgaV~v~~g~-iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 15 VTFVVVDLETTGG-----SPAGDAITEIGAVKVRGGE-VLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CCEEEEEEecCCC-----CCCCCeEEEEEEEEEECCE-EEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 4778889998642 6778999999988665442 23333222322211 1 112344544445566789999999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
|.+++. ..+++|||+ .||+++|...++++|++.
T Consensus 89 f~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~g~~~ 121 (557)
T PRK07883 89 FLEFAR---GAVLVAHNA-PFDIGFLRAAAARCGYPW 121 (557)
T ss_pred HHHHhc---CCEEEEeCc-HHHHHHHHHHHHHcCCCC
Confidence 999886 479999999 699999999999987753
No 58
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.03 E-value=0.017 Score=60.54 Aligned_cols=102 Identities=18% Similarity=0.197 Sum_probs=66.8
Q ss_pred EEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-cc--ccccCCCCCcEEEEeCCHHHHHHHHH
Q 000502 959 LLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-SH--QRSLVGIPDCKVFVCSKEIHLFSHFI 1035 (1459)
Q Consensus 959 iLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~~--~~~~~~i~g~~V~~f~SEkELL~aFi 1035 (1459)
.+.||+|+.+ .+|..++|+.|++...+.+. ....+-.+..... .. ...+.||..-.+..-..+.+.+..|.
T Consensus 2 ~v~~D~Ettg-----~~~~~~~Iieig~v~~~~~~-~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~ 75 (169)
T smart00479 2 LVVIDCETTG-----LDPGKDEIIEIAAVDVDGGR-IIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELL 75 (169)
T ss_pred EEEEEeeCCC-----CCCCCCeEEEEEEEEEECCE-eEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 5678888865 25667899999988766543 2233322222211 01 11123443333444568899999999
Q ss_pred HHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1036 KILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1036 dlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
+++.. .++++||...||+.+|..-+.++|+.
T Consensus 76 ~~l~~---~~~v~~n~~~fD~~~L~~~~~~~~~~ 106 (169)
T smart00479 76 EFLKG---KILVAGNALNFDLRFLKLEHPRLGIK 106 (169)
T ss_pred HHhcC---CEEEEeCCHHHhHHHHHHHHHHhCCC
Confidence 99865 46889999889999999888888764
No 59
>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=97.03 E-value=0.011 Score=63.93 Aligned_cols=107 Identities=10% Similarity=0.084 Sum_probs=58.5
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc------------eEEEE-EEEecCCCc--cccccCCCCCcEEEEe
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH------------AVEIY-VLLYCKSES--HQRSLVGIPDCKVFVC 1024 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~------------~~ei~-vLv~~~~~~--~~~~~~~i~g~~V~~f 1024 (1459)
..||+||.+ ++.|..|+|+.|++..-..+.. ....+ .++...... ....+.||.+-.+.--
T Consensus 2 vv~D~ETTG----l~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~ 77 (177)
T cd06136 2 VFLDLETTG----LPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHK 77 (177)
T ss_pred eEEeeecCC----CCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcC
Confidence 357888753 3236789999999875443211 11112 222211110 1111233332222222
Q ss_pred CC-HHHHHHHHHHHHhhcC-CCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1025 SK-EIHLFSHFIKILCSFD-PDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1025 ~S-EkELL~aFidlIr~~D-PDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
.. +.++...+.+++...+ +.+|+|||+..||+++|..-++++|+..
T Consensus 78 ~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~ 125 (177)
T cd06136 78 APFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKL 125 (177)
T ss_pred CCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCC
Confidence 22 2245555555555544 5699999998899999999998887643
No 60
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.94 E-value=0.016 Score=65.59 Aligned_cols=106 Identities=14% Similarity=0.113 Sum_probs=65.3
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecC-CCceEEEEEEEecCCCc---cccccCCCCCcEEEE-eCCHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFEND-SDHAVEIYVLLYCKSES---HQRSLVGIPDCKVFV-CSKEIHLF 1031 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d-~d~~~ei~vLv~~~~~~---~~~~~~~i~g~~V~~-f~SEkELL 1031 (1459)
..++.||+|+.+ -+|..|+|+.|++...+. +. ....+..+.....+ ....+.||..-.+.. =..+.+.|
T Consensus 6 ~~~vv~D~ETTG-----l~p~~d~Iieig~v~v~~~g~-~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl 79 (232)
T PRK07942 6 GPLAAFDLETTG-----VDPETARIVTAALVVVDADGE-VVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVL 79 (232)
T ss_pred CcEEEEEeccCC-----CCCCCCeeEEEEEEEEeCCCc-cccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHH
Confidence 467788999864 278889999999876553 32 22223222222110 011123333222221 12456789
Q ss_pred HHHHHHHhhc--CCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1032 SHFIKILCSF--DPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1032 ~aFidlIr~~--DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
..|...|..+ +-.+|+|||. .||+++|..=++++|+.
T Consensus 80 ~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~ 118 (232)
T PRK07942 80 AEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLP 118 (232)
T ss_pred HHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCC
Confidence 9999988753 4579999999 69999998877777653
No 61
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.83 E-value=0.029 Score=66.10 Aligned_cols=100 Identities=12% Similarity=0.149 Sum_probs=64.9
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC----ccccccCCCCCcEEEEeCCHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE----SHQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~----~~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
..+.||+|+. ++..|.|+.|++....++. ....+..+..... +....+.||..-.|.-..+..+.+..
T Consensus 2 ~~vviD~ETT-------g~~~d~IieIgav~v~~g~-i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 2 NFVAIDFETA-------NEKRNSPCSIGIVVVKDGE-IVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred cEEEEEEeCC-------CCCCCceEEEEEEEEECCE-EEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHH
Confidence 4567777774 2467999999987665442 2333322232221 11112345554456566788889999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
|.+++.. ++++|||+ .||+++|..-++++++.
T Consensus 74 ~~~fl~~---~~lVaHNa-~FD~~fL~~~~~r~~~~ 105 (309)
T PRK06195 74 IKHYFNN---NLVIAHNA-SFDISVLRKTLELYNIP 105 (309)
T ss_pred HHHHhCC---CEEEEECc-HHHHHHHHHHHHHhCCC
Confidence 9988854 79999999 59999998777776653
No 62
>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=96.81 E-value=0.014 Score=60.74 Aligned_cols=98 Identities=12% Similarity=0.147 Sum_probs=62.2
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-c--cccccCCCCCcEEEEeCCHHHHHHHHHH
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-S--HQRSLVGIPDCKVFVCSKEIHLFSHFIK 1036 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~--~~~~~~~i~g~~V~~f~SEkELL~aFid 1036 (1459)
+.+|+|+.+ | ..|+|+.|++...+++. ....+..+..... . ....+.||..-.+..-....+.+..|.+
T Consensus 2 v~~D~Ettg-----~--~~~~ii~ig~v~~~~~~-~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~ 73 (156)
T cd06130 2 VAIDFETAN-----A--DRASACSIGLVKVRDGQ-IVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73 (156)
T ss_pred EEEEEeCCC-----C--CCCceEEEEEEEEECCE-EEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHH
Confidence 457788753 2 25789999988665432 2232322222221 1 1122334433334445567889999999
Q ss_pred HHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1037 ILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1037 lIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
++.. ++++|||+ .||+++|..-++.+|+.
T Consensus 74 ~l~~---~~lv~hn~-~fD~~~l~~~~~~~g~~ 102 (156)
T cd06130 74 FLGG---SLVVAHNA-SFDRSVLRAALEAYGLP 102 (156)
T ss_pred HhCC---CEEEEeCh-HHhHHHHHHHHHHcCCC
Confidence 9875 69999998 69999999888887764
No 63
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.75 E-value=0.016 Score=78.78 Aligned_cols=102 Identities=16% Similarity=0.294 Sum_probs=71.0
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc-c--ccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES-H--QRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~-~--~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
+.+.||+|+.+ .+|..|+|+.|++....++. ..+.+..+...... . ...+.+|..-.+.-..+..+.|..|
T Consensus 191 ~~VVfDiETTG-----L~~~~d~IIEIGAVkv~~g~-iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f 264 (1213)
T TIGR01405 191 TYVVFDIETTG-----LSPQYDEIIEFGAVKVKNGR-IIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKF 264 (1213)
T ss_pred cEEEEEeEecC-----CCCCCCeEEEEEEEEEECCe-EEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 77889999864 26788999999988766543 33333333322211 1 1123344433455567899999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
.+++.. .+++||| ..||++||.+.++++|+.
T Consensus 265 ~~fl~~---~iLVaHN-a~FD~~fL~~~~~r~g~~ 295 (1213)
T TIGR01405 265 KEFFKD---SILVAHN-ASFDIGFLNTNFEKVGLE 295 (1213)
T ss_pred HHHhCC---CeEEEEC-hHHHHHHHHHHHHHcCCC
Confidence 999864 6999999 579999999999888764
No 64
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.70 E-value=0.015 Score=65.50 Aligned_cols=100 Identities=14% Similarity=0.147 Sum_probs=62.6
Q ss_pred EEEEEEEeCcCCCCCCCCCC-CcEEEEEEEeecCCCceEEEEEEEecCC-Cc--cccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 959 LLSIEVQAESRGDLRPDPRY-DSINVVALAFENDSDHAVEIYVLLYCKS-ES--HQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 959 iLSIEIet~srg~lfPDPe~-DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~--~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
.+.+|+||.+ .+|.. |+|+-|++....+...+.+.+..+.... .. ....+.||..-.+.--+...+.+..|
T Consensus 2 ~vvlD~ETTG-----l~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f 76 (225)
T TIGR01406 2 QIILDTETTG-----LDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76 (225)
T ss_pred EEEEEeeCCC-----cCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHH
Confidence 4678888864 26655 8999999773333221222232222221 11 11123344433444456788999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLG 1067 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LG 1067 (1459)
.+++.. .+++|||. .||++||..-+.++|
T Consensus 77 ~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g 105 (225)
T TIGR01406 77 LDFIGG---SELVIHNA-AFDVGFLNYELERLG 105 (225)
T ss_pred HHHhCC---CEEEEEec-HHHHHHHHHHHHHhC
Confidence 999875 47899999 599999998888776
No 65
>PRK07740 hypothetical protein; Provisional
Probab=96.69 E-value=0.047 Score=62.33 Aligned_cols=101 Identities=14% Similarity=0.214 Sum_probs=65.5
Q ss_pred CceEEEEEEEeCcCCCCCCCCCC-CcEEEEEEEeecCCCceEEEEEEEecCC-Ccc--ccccCCCCCcEEEEeCCHHHHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRY-DSINVVALAFENDSDHAVEIYVLLYCKS-ESH--QRSLVGIPDCKVFVCSKEIHLF 1031 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~-DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~--~~~~~~i~g~~V~~f~SEkELL 1031 (1459)
.+.++.||+|+.+ + +|.. |+|+.|++...+++....+.+..+.... ... ...+.||....+.-.....+.+
T Consensus 58 ~~~~vv~D~ETTG----l-~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl 132 (244)
T PRK07740 58 DLPFVVFDLETTG----F-SPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVL 132 (244)
T ss_pred CCCEEEEEEeCCC----C-CCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHH
Confidence 3578888999853 2 5665 8999999887665432123332222222 111 1223455444566677899999
Q ss_pred HHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHH
Q 000502 1032 SHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH 1065 (1459)
Q Consensus 1032 ~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~ 1065 (1459)
..|.+++.. ++++|||+ .||+.+|..-+.+
T Consensus 133 ~~f~~fi~~---~~lVahna-~fD~~fL~~~~~~ 162 (244)
T PRK07740 133 HRFYAFIGA---GVLVAHHA-GHDKAFLRHALWR 162 (244)
T ss_pred HHHHHHhCC---CEEEEeCH-HHHHHHHHHHHHH
Confidence 999998764 69999998 6999998764433
No 66
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.69 E-value=0.02 Score=68.57 Aligned_cols=195 Identities=13% Similarity=0.164 Sum_probs=113.1
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeec-CCCceEEEEE-EEecCCCccccccCCCCCcEEEEeCCHHHHHHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFEN-DSDHAVEIYV-LLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~-d~d~~~ei~v-Lv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
....+.||||+.+ + +|..|.|+.|++.... ++. +.+.+. ++..........+.||..-.+.--.+-.+++..
T Consensus 45 ~~~fVvlDiETTG----L-dp~~drIIeIgAV~i~~~g~-ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 45 AAPFVAVSIQTSG----I-HPSTSRLITIDAVTLTADGE-EVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCEEEEEEECCC----C-CCCCCeEEEEEEEEEEcCCE-EEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHH
Confidence 3578889999864 2 7899999999877443 442 334443 333221111222445544455566788899999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCc-cCCCCCCccccccCCCccccccccccccccchhhHHhhhhh
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLL-NDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAK 1112 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~-~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~~k 1112 (1459)
|.++|... +|++||.. |||+||..-+++.....+ ....|........ +..
T Consensus 119 l~~fL~g~---vLVaHNA~-FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~--------~~~----------------- 169 (377)
T PRK05601 119 LDRLIDGR---TLILHNAP-RTWGFIVSEAKRAMNAAARANRNRNRGNRRGG--------RGR----------------- 169 (377)
T ss_pred HHHHhCCC---EEEEECcH-HHHHHHHHHHHHhhhhhhhccccccccccccc--------ccc-----------------
Confidence 99999854 89999986 999999998877644321 0001110000000 000
Q ss_pred hhhhccccccccccceeecCeEEeehHHHHhhc-cCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHH--H
Q 000502 1113 DAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGE-VKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRC--V 1189 (1459)
Q Consensus 1113 ~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rke-lKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rv--l 1189 (1459)
....+| .+..+ -.+||++.+.|+. ..+.+|+|++||.++ |...|+-. ..+ .|... -
T Consensus 170 ---rr~~~g-----~~p~p-~~~iDTL~LARrl~p~l~~~rL~~La~~l-Gi~~p~~~-A~~----------~Ra~~p~~ 228 (377)
T PRK05601 170 ---RRQRVG-----HIPKP-VVIVDTLATARRQGVALDDIRIRGVAHTL-GLDAPAAE-ASV----------ERAQVPHR 228 (377)
T ss_pred ---cccccC-----CCCCC-CCEEEhHHHHHHHcCCCCCCCHHHHHHHh-CCCCCchh-hhh----------hhhcCChh
Confidence 000111 11122 3579999999986 468999999999984 54443210 000 01111 1
Q ss_pred HHHHHHHHHHHHHHHhc
Q 000502 1190 EYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1190 ~YclkDa~Lvl~Ll~kL 1206 (1459)
..+..|+.++.+|+.++
T Consensus 229 ~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 229 QLCREETLLVARLYFAL 245 (377)
T ss_pred hhhhHHHHHHHHHHHHh
Confidence 22457999999998774
No 67
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.67 E-value=0.016 Score=68.40 Aligned_cols=103 Identities=19% Similarity=0.287 Sum_probs=68.6
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-c--cccccCCCCCcEEEEeCCHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-S--HQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~--~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
...+.||+|+.+ + +|..|+|+.|++...+++ .+.+.+..+..... . ....+.||..-.+.-.....+.+..
T Consensus 8 ~~~Vv~DlETTG----l-~p~~~eIIEIgaV~v~~g-~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~ 81 (313)
T PRK06807 8 LDYVVIDFETTG----F-NPYNDKIIQVAAVKYRNH-ELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPL 81 (313)
T ss_pred CCEEEEEEECCC----C-CCCCCeEEEEEEEEEECC-EEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHH
Confidence 356777888743 2 567899999998766543 23333333332221 1 1122344443345556788999999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
|.+++.. ++|+|||+ .||+++|.+.+.++|+.
T Consensus 82 f~~fl~~---~~lVaHNa-~FD~~fL~~~~~~~gl~ 113 (313)
T PRK06807 82 FLAFLHT---NVIVAHNA-SFDMRFLKSNVNMLGLP 113 (313)
T ss_pred HHHHHcC---CeEEEEcH-HHHHHHHHHHHHHcCCC
Confidence 9999864 57899999 89999999999888764
No 68
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.66 E-value=0.02 Score=65.20 Aligned_cols=167 Identities=11% Similarity=0.052 Sum_probs=102.5
Q ss_pred CCceEEEEEEEeCcCCCCCCCCC-CCcEEEEEEEeecCCCceEEEEEEEecCC-Ccc--ccccCCCCCcEEEEeCCHHHH
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPR-YDSINVVALAFENDSDHAVEIYVLLYCKS-ESH--QRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 955 ~~LtiLSIEIet~srg~lfPDPe-~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~--~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
+.++.+.||+||.+ + +|. .|+|+-|++..-.+...+...+..+.... ... ...+.||..-.+.--+...++
T Consensus 2 ~~~r~vvlDtETTG----l-dp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev 76 (240)
T PRK05711 2 AIMRQIVLDTETTG----L-NQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76 (240)
T ss_pred CCCeEEEEEeeCCC----c-CCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHH
Confidence 34788899999864 2 565 79999999765443322222232222221 111 112334443344555678899
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCCccCCCCCCccccccCCCccccccccccccccchhhHHhhh
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLL 1110 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~ 1110 (1459)
+..|.+++.. ..++|||. .||+++|..-++++|..+ .+..
T Consensus 77 ~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g~~~----~~~~-------------------------------- 116 (240)
T PRK05711 77 ADEFLDFIRG---AELIIHNA-PFDIGFMDYEFALLGRDI----PKTN-------------------------------- 116 (240)
T ss_pred HHHHHHHhCC---CEEEEEcc-HHhHHHHHHHHHHhCCCC----Cccc--------------------------------
Confidence 9999999865 36889999 699999988887776322 1000
Q ss_pred hhhhhhccccccccccceeecCeEEeehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHH
Q 000502 1111 AKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVE 1190 (1459)
Q Consensus 1111 ~k~s~~~~~~G~~~~s~i~I~GRivIDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~ 1190 (1459)
. -..++|++.+.|+.+.-..|+|+++++++ |...... . .-
T Consensus 117 ------------------~--~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~~r---~----------------~H 156 (240)
T PRK05711 117 ------------------T--FCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNSHR---T----------------LH 156 (240)
T ss_pred ------------------c--cCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC---C----------------CC
Confidence 0 01278888888876655678999999875 4211100 0 01
Q ss_pred HHHHHHHHHHHHHHhc
Q 000502 1191 YVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1191 YclkDa~Lvl~Ll~kL 1206 (1459)
-++.|+.++.+++.++
T Consensus 157 ~AL~DA~~~A~v~~~l 172 (240)
T PRK05711 157 GALLDAEILAEVYLAM 172 (240)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 1367888888877654
No 69
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.63 E-value=0.014 Score=61.74 Aligned_cols=100 Identities=14% Similarity=0.158 Sum_probs=62.6
Q ss_pred EEEEEEeCcCCCCCCCC-CCCcEEEEEEEeecCCCceEEEEEEEecCCCc---cccccCCCCCcEEEEeCCHHHHHHHHH
Q 000502 960 LSIEVQAESRGDLRPDP-RYDSINVVALAFENDSDHAVEIYVLLYCKSES---HQRSLVGIPDCKVFVCSKEIHLFSHFI 1035 (1459)
Q Consensus 960 LSIEIet~srg~lfPDP-e~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~---~~~~~~~i~g~~V~~f~SEkELL~aFi 1035 (1459)
+.||+|+.+ .+| ..|+|+.|++..-.++....+.+..+...... ....+.||..-.+.......+.+..|.
T Consensus 2 v~~D~ETTG-----l~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~ 76 (167)
T cd06131 2 IVLDTETTG-----LDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76 (167)
T ss_pred EEEEeeCCC-----CCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHH
Confidence 367888864 366 56899999987544332221222222222211 111223444334555567889999999
Q ss_pred HHHhhcCCCEEEeccCCCccHHHHHHHHHHhCC
Q 000502 1036 KILCSFDPDILMGWDIQGGSLGFLAERAAHLGI 1068 (1459)
Q Consensus 1036 dlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi 1068 (1459)
.++.. .+++|||+ .||+.+|..-+.++|+
T Consensus 77 ~~l~~---~~lv~hn~-~fD~~~l~~~~~~~~~ 105 (167)
T cd06131 77 DFIRG---AELVIHNA-SFDVGFLNAELSLLGL 105 (167)
T ss_pred HHHCC---CeEEEeCh-HHhHHHHHHHHHHhCC
Confidence 98765 46899999 5999999888888765
No 70
>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=96.58 E-value=0.0091 Score=64.86 Aligned_cols=103 Identities=11% Similarity=0.088 Sum_probs=64.3
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEE-EEecCC--Ccc--ccccCCCCCcEEEE-eCCHHHHHHHH
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYV-LLYCKS--ESH--QRSLVGIPDCKVFV-CSKEIHLFSHF 1034 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~v-Lv~~~~--~~~--~~~~~~i~g~~V~~-f~SEkELL~aF 1034 (1459)
.||+||.+ + +|..|+|+.|++...+.+....+.+- ++...+ ... .....||..-.+.. -.++.+++..|
T Consensus 2 ~~D~ETTG----l-~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~ 76 (183)
T cd06138 2 FYDYETFG----L-NPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKI 76 (183)
T ss_pred EEEeecCC----C-CCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 57888864 2 67889999999876544312223222 222111 011 11123443333444 36788999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
..++.+ ...+++|||...||++||..=+.+++..
T Consensus 77 ~~~~~~-~~~~lVahn~~~FD~~fL~~~~~r~~~~ 110 (183)
T cd06138 77 HRLFNT-PGTCIVGYNNIRFDDEFLRFAFYRNLYD 110 (183)
T ss_pred HHHHcc-CCCcEEeeCchhhHHHHHHHHHHHCCCc
Confidence 999875 3468999997789999997777776654
No 71
>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=96.40 E-value=0.019 Score=64.06 Aligned_cols=101 Identities=12% Similarity=-0.026 Sum_probs=64.5
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCC-Ccc--ccccCCCCCcEEEEeCCHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKS-ESH--QRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~--~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
.+.+.||+||.+ .+|..| |+.|++..-.++....+.+..+..+. ... ...+.||..-.+.......+++..
T Consensus 7 ~~fvv~D~ETTG-----l~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 7 DTETTGDNETTG-----LYAGHD-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred cCEEEEEecCCC-----CCCCCC-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 466788999864 367778 99999886333322223332222222 111 112234443345555788899999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLG 1067 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LG 1067 (1459)
|.+++.. ++++|||+ .||+++|..-+.+++
T Consensus 81 ~~~~~~~---~~lVaHNa-~FD~~fL~~~~~r~~ 110 (217)
T TIGR00573 81 FADYIRG---AELVIHNA-SFDVGFLNYEFSKLY 110 (217)
T ss_pred HHHHhCC---CEEEEecc-HHHHHHHHHHHHHhc
Confidence 9998854 68999998 699999988777653
No 72
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.28 E-value=0.061 Score=72.06 Aligned_cols=102 Identities=16% Similarity=0.246 Sum_probs=67.9
Q ss_pred eEEEEEEEeCcCCCCCCCCC-CCcEEEEEEEeecCCCceEEEEEEEecCCCc---cccccCCCCCcEEEEeCCHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPR-YDSINVVALAFENDSDHAVEIYVLLYCKSES---HQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe-~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~---~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
+.+.+|+|+.+ .+|. .|+|+.|+++.-.++. +.+.+..+...... ....+.||..-.|.-.....+.+..
T Consensus 4 ~~vvvD~ETTG-----~~p~~~d~IIeigav~v~~~~-i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~ 77 (928)
T PRK08074 4 RFVVVDLETTG-----NSPKKGDKIIQIAAVVVEDGE-ILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPE 77 (928)
T ss_pred CEEEEEEeCCC-----CCCCCCCcEEEEEEEEEECCE-EEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHH
Confidence 45678888764 2444 3899999998765542 33444333332211 1123445554456666789999999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
|.+++. ..+++|||+. ||+++|..-+.+.|+.
T Consensus 78 l~~~l~---~~~~VaHN~~-FD~~fL~~~~~~~g~~ 109 (928)
T PRK08074 78 IVELLE---GAYFVAHNVH-FDLNFLNEELERAGYT 109 (928)
T ss_pred HHHHhC---CCeEEEEChH-HHHHHHHHHHHHcCCC
Confidence 999985 4689999985 9999998888777654
No 73
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.27 E-value=0.091 Score=59.91 Aligned_cols=102 Identities=9% Similarity=0.083 Sum_probs=66.8
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCce-EEEEEEEecCCC-cc--ccccCCCCCcEEEEeCCHHHHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHA-VEIYVLLYCKSE-SH--QRSLVGIPDCKVFVCSKEIHLF 1031 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~-~ei~vLv~~~~~-~~--~~~~~~i~g~~V~~f~SEkELL 1031 (1459)
....+.||+|+.+ -+|..|+|+.|++..-+.+... .+.+..+...+. .. ...+.||....+.--.+..+.+
T Consensus 46 ~~~~vviD~ETTG-----l~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl 120 (239)
T PRK09146 46 EVPFVALDFETTG-----LDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERIL 120 (239)
T ss_pred cCCEEEEEeECCC-----CCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHH
Confidence 4678889999864 2678899999999866543211 122222222211 11 1123455444455556888899
Q ss_pred HHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHh
Q 000502 1032 SHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHL 1066 (1459)
Q Consensus 1032 ~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~L 1066 (1459)
.+|..++. .++++|||. .||+++|..-++.+
T Consensus 121 ~~l~~~~~---~~~lVaHna-~FD~~fL~~~l~~~ 151 (239)
T PRK09146 121 DELLEALA---GKVVVVHYR-RIERDFLDQALRNR 151 (239)
T ss_pred HHHHHHhC---CCEEEEECH-HHHHHHHHHHHHHh
Confidence 99988874 369999998 59999998888764
No 74
>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=96.23 E-value=0.068 Score=71.01 Aligned_cols=101 Identities=16% Similarity=0.243 Sum_probs=68.0
Q ss_pred EEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc---cccccCCCCCcEEEEeCCHHHHHHHHH
Q 000502 959 LLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES---HQRSLVGIPDCKVFVCSKEIHLFSHFI 1035 (1459)
Q Consensus 959 iLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~---~~~~~~~i~g~~V~~f~SEkELL~aFi 1035 (1459)
.+.+|+|+.+ .+|..|+|+.|++..-+++. +.+.+..+...... ....+.||..-.+...+...+.+..|.
T Consensus 2 ~vvvD~ETTG-----~~~~~~~IIeig~v~v~~~~-i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~ 75 (850)
T TIGR01407 2 YAVVDLETTG-----TQLSFDKIIQIGIVVVEDGE-IVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIY 75 (850)
T ss_pred EEEEEEECCC-----CCCCCCeEEEEEEEEEECCE-EEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHH
Confidence 4568888864 36778999999998765442 33444333332211 112234444334555678899999999
Q ss_pred HHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1036 KILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1036 dlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
+++. -.+++|||+ .||+++|..-++++|+.
T Consensus 76 ~~l~---~~~~VahN~-~fD~~fL~~~~~~~g~~ 105 (850)
T TIGR01407 76 DLLE---DGIFVAHNV-HFDLNFLAKALKDCGYE 105 (850)
T ss_pred HHhC---CCEEEEeCc-HHHHHHHHHHHHHcCCC
Confidence 9875 468999998 59999999888887764
No 75
>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=95.96 E-value=0.03 Score=54.96 Aligned_cols=69 Identities=30% Similarity=0.342 Sum_probs=51.4
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHHHhh
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCS 1040 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidlIr~ 1040 (1459)
.+|+|+.+ .++..++|..|++...+++. .+ + . . |..++++
T Consensus 2 ~~DiEt~~-----~~~~~~~i~~i~~~~~~~~~----~~-~---------------------~-~--------f~~~l~~ 41 (96)
T cd06125 2 AIDTEATG-----LDGAVHEIIEIALADVNPED----TA-V---------------------I-D--------LKDILRD 41 (96)
T ss_pred EEEEECCC-----CCCCCCcEEEEEEEEccCCC----EE-E---------------------e-h--------HHHHHhh
Confidence 67888864 35677899999987543211 00 0 0 1 8888888
Q ss_pred cCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1041 FDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1041 ~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
..|.+++|||. .||++||.++++++++..
T Consensus 42 ~~~~v~V~hn~-~fD~~fL~~~~~~~~~~~ 70 (96)
T cd06125 42 KPLAILVGHNG-SFDLPFLNNRCAELGLKY 70 (96)
T ss_pred CCCCEEEEeCc-HHhHHHHHHHHHHcCCCC
Confidence 88899999999 799999999999987753
No 76
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.58 E-value=0.19 Score=66.69 Aligned_cols=100 Identities=17% Similarity=0.220 Sum_probs=64.8
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-cc--ccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-SH--QRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~~--~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
+.+.+|+|+.+- +| .|+|+.|++..-.++. +...+..+..... .. ...+.||..-.|...+...+.+..|
T Consensus 8 ~~vvvD~ETTGl-----~~-~d~IIeIgaV~v~~g~-i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~ 80 (820)
T PRK07246 8 KYAVVDLEATGA-----GP-NASIIQVGIVIIEGGE-IIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHI 80 (820)
T ss_pred CEEEEEEecCCc-----CC-CCeEEEEEEEEEECCE-EEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHH
Confidence 567788888642 34 4899999988765542 3333332222221 11 1234455544566677889999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGI 1068 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi 1068 (1459)
.+++.. .+++|||+ .||+++|.+-+...|.
T Consensus 81 ~~~l~~---~~lVaHN~-~FD~~fL~~~~~~~g~ 110 (820)
T PRK07246 81 YDLIED---CIFVAHNV-KFDANLLAEALFLEGY 110 (820)
T ss_pred HHHhCC---CEEEEECc-HHHHHHHHHHHHHcCC
Confidence 998864 68999999 5999999665544443
No 77
>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=95.52 E-value=0.03 Score=57.07 Aligned_cols=98 Identities=18% Similarity=0.251 Sum_probs=61.9
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-c--cccccCCCCCcEEEEeCCHHHHHHHHHHH
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-S--HQRSLVGIPDCKVFVCSKEIHLFSHFIKI 1037 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~--~~~~~~~i~g~~V~~f~SEkELL~aFidl 1037 (1459)
.+|+|+.+ .+|..++|+.|+++..+.+-.....+..+..... . ....+.++..-.+..-....+.+.+|.++
T Consensus 2 ~~D~Ettg-----~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~ 76 (159)
T cd06127 2 VFDTETTG-----LDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEF 76 (159)
T ss_pred eEEeeCCC-----cCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHH
Confidence 57888864 2567899999998877654111122212222211 0 01111222212233345677899999988
Q ss_pred HhhcCCCEEEeccCCCccHHHHHHHHHHhC
Q 000502 1038 LCSFDPDILMGWDIQGGSLGFLAERAAHLG 1067 (1459)
Q Consensus 1038 Ir~~DPDIItGYNI~~FDLpYLieRAk~LG 1067 (1459)
+.. ++++|||+ .||+++|...+..++
T Consensus 77 l~~---~~~v~~n~-~fD~~~l~~~~~~~~ 102 (159)
T cd06127 77 LGG---RVLVAHNA-SFDLRFLNRELRRLG 102 (159)
T ss_pred HCC---CEEEEeCc-HhhHHHHHHHHHHhC
Confidence 876 79999999 799999999999987
No 78
>PRK11779 sbcB exonuclease I; Provisional
Probab=95.50 E-value=0.12 Score=64.37 Aligned_cols=104 Identities=12% Similarity=0.010 Sum_probs=63.8
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCce-EEEEEEEecCCC---cc--ccccCCCCCcEEEEe-CCHH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHA-VEIYVLLYCKSE---SH--QRSLVGIPDCKVFVC-SKEI 1028 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~-~ei~vLv~~~~~---~~--~~~~~~i~g~~V~~f-~SEk 1028 (1459)
.++.+.+|+||.+- +|..|.|+.|++..-+.+-.. .+.+.+.+.... +. ...+.||..-.+.-- .+|.
T Consensus 5 ~~~fvv~D~ETTGL-----dP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~ 79 (476)
T PRK11779 5 QPTFLWHDYETFGA-----NPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEA 79 (476)
T ss_pred CCcEEEEEEECCCC-----CCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHH
Confidence 35788899998642 789999999998755443211 122333332211 01 111223322222121 2688
Q ss_pred HHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHH
Q 000502 1029 HLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH 1065 (1459)
Q Consensus 1029 ELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~ 1065 (1459)
+++..|.+++.. .-.+++|||...||+.+|..-+.+
T Consensus 80 e~~~~i~~~l~~-~~~~lVGhNni~FD~eflr~~~~r 115 (476)
T PRK11779 80 EFAARIHAEFSQ-PGTCILGYNNIRFDDEVTRYIFYR 115 (476)
T ss_pred HHHHHHHHHHhc-CCCEEEEeCchhhcHHHHHHHHHh
Confidence 999999998863 236899999889999999776654
No 79
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=95.35 E-value=0.45 Score=52.26 Aligned_cols=104 Identities=18% Similarity=0.214 Sum_probs=60.0
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeec-CCCce---EEEEEEEecC--CC-cc--ccccCCCCCcE-EEEeCCHHH
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFEN-DSDHA---VEIYVLLYCK--SE-SH--QRSLVGIPDCK-VFVCSKEIH 1029 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~-d~d~~---~ei~vLv~~~--~~-~~--~~~~~~i~g~~-V~~f~SEkE 1029 (1459)
+.+|+||.+ .+|+.|.|+.|++.... +.+.. .+.+..+... +. .. ...+.+|.... +..-..+.+
T Consensus 8 vv~D~ETTG-----l~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~ 82 (189)
T cd06134 8 VVVDVETGG-----FNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKE 82 (189)
T ss_pred EEEEecCCC-----CCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHH
Confidence 478888864 37788999999977443 32221 1233222222 11 01 11223443211 112234556
Q ss_pred HHHHHHHHHhhc------CCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1030 LFSHFIKILCSF------DPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1030 LL~aFidlIr~~------DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
-+..|.+.|.++ +=.+++|||+ .||+.||..-++++|+.
T Consensus 83 ~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~ 127 (189)
T cd06134 83 ALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIK 127 (189)
T ss_pred HHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCC
Confidence 677777766643 1258999999 59999999888888763
No 80
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.27 E-value=0.2 Score=55.57 Aligned_cols=93 Identities=19% Similarity=0.278 Sum_probs=59.7
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEE-EEEecCCCc--cccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIY-VLLYCKSES--HQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~-vLv~~~~~~--~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
..+.+|+|+.+ . ++ .|+|+.|++...+++.. ...+ .++...... ....+.||..-.|.--++-.+.|..|
T Consensus 6 ~~vvlD~EtTG----l-~~-~~eIIeIgaV~v~~g~~-~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f 78 (195)
T PRK07247 6 TYIAFDLEFNT----V-NG-VSHIIQVSAVKYDDHKE-VDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAF 78 (195)
T ss_pred eEEEEEeeCCC----C-CC-CCeEEEEEEEEEECCEE-EEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHH
Confidence 45667777753 2 22 57899999886665432 2333 233221111 12234455544566667899999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHH
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLi 1060 (1459)
.+++.. .+++|||...||+.+|.
T Consensus 79 ~~f~~~---~~lVaHNa~~fD~~fL~ 101 (195)
T PRK07247 79 KEFVGE---LPLIGYNAQKSDLPILA 101 (195)
T ss_pred HHHHCC---CeEEEEeCcHhHHHHHH
Confidence 999864 37999999989999984
No 81
>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=95.08 E-value=0.53 Score=49.88 Aligned_cols=104 Identities=13% Similarity=0.138 Sum_probs=64.5
Q ss_pred EEEEEEeCcCCCCCCC---CCCCcEEEEEEEeecCCCc-eEEEEEEEecCCC-cc----ccccCCCCCcEEEEeCCHHHH
Q 000502 960 LSIEVQAESRGDLRPD---PRYDSINVVALAFENDSDH-AVEIYVLLYCKSE-SH----QRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 960 LSIEIet~srg~lfPD---Pe~DpI~~Is~~v~~d~d~-~~ei~vLv~~~~~-~~----~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
+.||+|+.+- .|. +..++|+.|++...+.... ..+.+..+..... .. .....+|..-.+.-.....+.
T Consensus 2 vv~D~Ettg~---~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~v 78 (176)
T cd06133 2 LVIDFEATCW---EGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEV 78 (176)
T ss_pred EEEEeecccc---CCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHH
Confidence 4678888642 111 1248999999887655433 3344422222221 01 112334443345556789999
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCC
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGI 1068 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi 1068 (1459)
+.+|.+++....+.++++|. .||+..|...+..++.
T Consensus 79 l~~~~~~l~~~~~~~~v~~~--~~d~~~l~~~~~~~~~ 114 (176)
T cd06133 79 LKEFLEWLGKNGKYAFVTWG--DWDLKDLLQNQCKYKI 114 (176)
T ss_pred HHHHHHHHHhCCCeEEEeec--HhhHHHHHHHHHHhcC
Confidence 99999999975446777875 6999999988877654
No 82
>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=94.58 E-value=0.11 Score=55.52 Aligned_cols=90 Identities=11% Similarity=0.101 Sum_probs=48.5
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-c-cccccCCCCCcEEEEeCC-------HHHHH
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-S-HQRSLVGIPDCKVFVCSK-------EIHLF 1031 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~-~~~~~~~i~g~~V~~f~S-------EkELL 1031 (1459)
.||+|+.+- +|..|.|+.|++.-..++..... .++..... . ....+.||....+.-..+ -.+.+
T Consensus 2 ~lD~EttGl-----~~~~d~ii~Ig~V~v~~g~i~~~--~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~ 74 (161)
T cd06137 2 ALDCEMVGL-----ADGDSEVVRISAVDVLTGEVLID--SLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAAR 74 (161)
T ss_pred EEEeeeeeE-----cCCCCEEEEEEEEEcCCCeEEEe--ccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHH
Confidence 578887532 56789999999886544322111 12221111 0 111223433222211111 13667
Q ss_pred HHHHHHHhhcCCCEEEeccCCCccHHHHH
Q 000502 1032 SHFIKILCSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 1032 ~aFidlIr~~DPDIItGYNI~~FDLpYLi 1060 (1459)
..|.+++... .||+|||+. ||+.+|.
T Consensus 75 ~~~~~~i~~~--~vlVgHn~~-fD~~fL~ 100 (161)
T cd06137 75 AALWKFIDPD--TILVGHSLQ-NDLDALR 100 (161)
T ss_pred HHHHHhcCCC--cEEEeccHH-HHHHHHh
Confidence 7777777531 599999995 9999983
No 83
>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=94.20 E-value=1.6 Score=48.50 Aligned_cols=105 Identities=14% Similarity=0.141 Sum_probs=58.9
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeec-CCCceE---EEEE-EEecC-CC-cc--ccccCCCCCc-EEEEeCCH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFEN-DSDHAV---EIYV-LLYCK-SE-SH--QRSLVGIPDC-KVFVCSKE 1027 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~-d~d~~~---ei~v-Lv~~~-~~-~~--~~~~~~i~g~-~V~~f~SE 1027 (1459)
.=+.||+||.+ .+|..|+|+-|++..-. +....+ +.+. ++... +. .. ...+.||..- .+.--..+
T Consensus 9 ~~vv~D~ETTG-----l~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 9 LPVVVDVETGG-----FNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred eeEEEEeeCCC-----CCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 44578888864 37788999999876432 222221 1122 22211 10 00 1122344311 12223456
Q ss_pred HHHHHHHHHHHhhc------CCCEEEeccCCCccHHHHHHHHHHhCC
Q 000502 1028 IHLFSHFIKILCSF------DPDILMGWDIQGGSLGFLAERAAHLGI 1068 (1459)
Q Consensus 1028 kELL~aFidlIr~~------DPDIItGYNI~~FDLpYLieRAk~LGi 1068 (1459)
.+.+..|...+.++ +-.+++|||+. ||+.||..=++++|.
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~-FD~~fL~~~~~r~~~ 129 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNAN-FDLGFLNAAVERTSL 129 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECch-hhHHHHHHHHHHhCC
Confidence 66677777766422 33589999995 999999877777765
No 84
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=93.97 E-value=0.19 Score=55.57 Aligned_cols=104 Identities=14% Similarity=0.142 Sum_probs=66.5
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceE-EEEEEEecCCC-cc--ccccCCCCCcEEEEeCCHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAV-EIYVLLYCKSE-SH--QRSLVGIPDCKVFVCSKEIHLFS 1032 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~-ei~vLv~~~~~-~~--~~~~~~i~g~~V~~f~SEkELL~ 1032 (1459)
-..+.||+|+.+ .+|..|+|+.|++...+++.... +.+..+..... .. ...+.+|....+..-.++.+.+.
T Consensus 29 ~~~vviD~ETTG-----l~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~ 103 (202)
T PRK09145 29 DEWVALDCETTG-----LDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALR 103 (202)
T ss_pred CCEEEEEeECCC-----CCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 367788888864 26778999999987665432111 22222222211 11 11223443334555678999999
Q ss_pred HHHHHHhhcCCCEEEeccCCCccHHHHHHHHHH-hCCC
Q 000502 1033 HFIKILCSFDPDILMGWDIQGGSLGFLAERAAH-LGIG 1069 (1459)
Q Consensus 1033 aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~-LGi~ 1069 (1459)
.|.+++.. .+++|||. .||+.+|..-+++ ++..
T Consensus 104 ~~~~~i~~---~~lv~hn~-~fD~~fL~~~~~~~~~~~ 137 (202)
T PRK09145 104 QLLAFIGN---RPLVGYYL-EFDVAMLNRYVRPLLGIP 137 (202)
T ss_pred HHHHHHcC---CeEEEeCH-HHHHHHHHHHHHHhcCCC
Confidence 99999864 57999997 5999999988876 4443
No 85
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=93.81 E-value=0.52 Score=52.39 Aligned_cols=110 Identities=13% Similarity=0.129 Sum_probs=67.0
Q ss_pred ceEEEEEEEeCcCC-CCCCCCCCCcEEEEEEEeecCCCceEEEE-EEEecCCC--c--cccccCCCCCcEEEEeCCHHHH
Q 000502 957 LTLLSIEVQAESRG-DLRPDPRYDSINVVALAFENDSDHAVEIY-VLLYCKSE--S--HQRSLVGIPDCKVFVCSKEIHL 1030 (1459)
Q Consensus 957 LtiLSIEIet~srg-~lfPDPe~DpI~~Is~~v~~d~d~~~ei~-vLv~~~~~--~--~~~~~~~i~g~~V~~f~SEkEL 1030 (1459)
+..+.||+|+++-. ..-|....|+|+.|++..-+++. ..+.+ .++..... . ....+.||..-.|.--.+..+.
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~-i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ev 82 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCE-VEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEEL 82 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCc-ChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHH
Confidence 56777888876421 12343336899999987655442 22222 22221110 0 0112345544455566788999
Q ss_pred HHHHHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1031 FSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1031 L~aFidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
+..|.+++... +.++++| . +||+.+|..-++.+|++.
T Consensus 83 l~~f~~~~~~~-~~~iv~~-~-~fD~~fL~~~~~~~~~~~ 119 (207)
T PRK07748 83 VEKLAEYDKRC-KPTIVTW-G-NMDMKVLKHNCEKAGVPF 119 (207)
T ss_pred HHHHHHHhCcC-CeEEEEE-C-HHHHHHHHHHHHHcCCCC
Confidence 99999998753 3467776 3 699999999998887653
No 86
>PRK06722 exonuclease; Provisional
Probab=93.79 E-value=1.5 Score=51.39 Aligned_cols=106 Identities=13% Similarity=0.177 Sum_probs=63.7
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc-eEEEE-EEEecCCCc--cccccCCCCCcEEEEeCCHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH-AVEIY-VLLYCKSES--HQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~-~~ei~-vLv~~~~~~--~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
+.+.||+|+. +.....+..|+|+.|++..-+++.. +...+ .++...... ....+-||..-.|.--+.-.+.+..
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 HFIVFDIERN--FRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEK 83 (281)
T ss_pred EEEEEEeeCC--CCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 4556666763 2211124458999999886655422 22333 233321111 1123445555556666788899999
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
|.+++... .++++| . .||+++|..=++.+|+.
T Consensus 84 f~~fig~~--~lvahn-a-~FD~~FL~~~l~~~gi~ 115 (281)
T PRK06722 84 FIQFIGED--SIFVTW-G-KEDYRFLSHDCTLHSVE 115 (281)
T ss_pred HHHHHCCC--cEEEEE-e-HHHHHHHHHHHHHcCCC
Confidence 99999642 245555 4 79999999988887764
No 87
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=93.16 E-value=0.55 Score=52.92 Aligned_cols=106 Identities=17% Similarity=0.272 Sum_probs=67.0
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEE-EEEEEecCCCc--cccccCCCCCcEEEEeCCHHHHHHH
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVE-IYVLLYCKSES--HQRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~e-i~vLv~~~~~~--~~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
.+...||+|+.+- +|..|.|+-|+.....++..... ...++...... ....+.+|.+-.+..-+.=.+.+..
T Consensus 13 ~~~vv~D~ETtg~-----~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~ 87 (243)
T COG0847 13 TRFVVIDLETTGL-----NPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPE 87 (243)
T ss_pred CcEEEEecccCCC-----CCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHH
Confidence 4778889998652 56889999999887666533322 22333321110 1111223322222222333788888
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
|.+++... .++++||. .||+++|..++..++...
T Consensus 88 ~~~~i~~~--~~~Vahna-~fD~~fl~~~~~~~~~~~ 121 (243)
T COG0847 88 FLDFIGGL--RLLVAHNA-AFDVGFLRVESERLGIEI 121 (243)
T ss_pred HHHHHCCC--CeEEEEch-hhcHHHHHHHHHHcCCCc
Confidence 88888765 79999995 699999999999987654
No 88
>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=92.97 E-value=1.1 Score=46.99 Aligned_cols=52 Identities=19% Similarity=0.365 Sum_probs=35.1
Q ss_pred CCHHHHHHHHhcCCCCCCChhhh-HHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhc
Q 000502 1151 YTVEAVAETVLRRKIPSIPFRVL-TKWFASGPGRARYRCVEYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1151 YSLEnVA~~vLgekkpd~s~k~L-tk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL 1206 (1459)
++|++++..++| ....+.+.. .+|-...+ .....+.|+..|+..+++|..+|
T Consensus 119 ~~L~~L~~~~l~--~~~~~~~~~~~~~~~~~~--l~~~~~~YAa~D~~~~~~l~~~l 171 (176)
T PF01612_consen 119 YSLKDLAEEYLG--NIDLDKKEQMSDWRKARP--LSEEQIEYAAQDAVVTFRLYEKL 171 (176)
T ss_dssp SSHHHHHHHHHS--EEE-GHCCTTSSTTTSSS---HHHHHHHHHHHHHTHHHHHHHH
T ss_pred ccHHHHHHHHhh--hccCcHHHhhccCCcCCC--ChHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999 112222222 22321333 24567899999999999999886
No 89
>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=92.92 E-value=0.016 Score=71.42 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=29.2
Q ss_pred CcCCChHHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccc
Q 000502 1350 VRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAA 1407 (1459)
Q Consensus 1350 vrkGILP~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA 1407 (1459)
.+.+++++-++.+.+.|...|+..++ .+.-.|+++||.||=+|-
T Consensus 329 ~~~~~F~~~i~~~~~~k~~~k~~~~~--------------~~~i~KL~lNSlyGkf~~ 372 (459)
T PF03175_consen 329 EKGGLFKEYIDKLYELKKNAKKKADK--------------EKSIAKLLLNSLYGKFGQ 372 (459)
T ss_dssp EES-TTHHHHHHHHHHHHH--HHHHH-----------------HHHHHHHHHHHHHS-
T ss_pred cccCchHHHHHHHHHhhhhhccCCch--------------hHHHHHHHHhhhhhhhcc
Confidence 35789999999999888766553221 115789999999998774
No 90
>PRK05168 ribonuclease T; Provisional
Probab=92.34 E-value=0.72 Score=51.61 Aligned_cols=107 Identities=16% Similarity=0.130 Sum_probs=63.9
Q ss_pred ceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeec-CCCce---EEEEE-EEecC-CC--c-cccccCCCCCcE-EEEeCC
Q 000502 957 LTLLSIEVQAESRGDLRPDPRYDSINVVALAFEN-DSDHA---VEIYV-LLYCK-SE--S-HQRSLVGIPDCK-VFVCSK 1026 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~-d~d~~---~ei~v-Lv~~~-~~--~-~~~~~~~i~g~~-V~~f~S 1026 (1459)
++.+.||+||.+ .+|..|+|+.|++..-. +.++. .+.+. ++... +. + ....+.||..-. +..-..
T Consensus 17 ~~~vv~D~ETTG-----l~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~ 91 (211)
T PRK05168 17 FLPVVIDVETAG-----FNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVS 91 (211)
T ss_pred CceEEEEeeCCC-----CCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCC
Confidence 678899999864 36778999999977543 21121 12332 33221 11 0 111223332111 122245
Q ss_pred HHHHHHHHHHHHhhc------CCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1027 EIHLFSHFIKILCSF------DPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1027 EkELL~aFidlIr~~------DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
+.+.+..|.+++.++ +=.+++|||+ .||+.||..-++++|+.
T Consensus 92 ~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~ 139 (211)
T PRK05168 92 EKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLK 139 (211)
T ss_pred hHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCC
Confidence 667777777777642 1259999999 59999999999888763
No 91
>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=91.96 E-value=8.3 Score=47.50 Aligned_cols=214 Identities=16% Similarity=0.205 Sum_probs=114.2
Q ss_pred cchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEee-C----CCCC--cccccc---ccccCCeeeeccCCc
Q 000502 1208 MINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAI-S----PGNH--QVASQP---AMECLPLVMEPESGF 1277 (1459)
Q Consensus 1208 iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfllp-s----Ps~~--qv~~q~---a~E~GglVmEP~sGf 1277 (1459)
.+...+++||.++||+..+-..-..+-++-++-|..++.|+|+= + |+-. +..... ..+....+---.||+
T Consensus 121 wl~~~i~laRY~~IPlgNl~~D~~~f~~Di~yAR~L~~~~~VLW~S~~~~PDlGG~e~Dd~~~~~~~~~~~~~~in~pG~ 200 (396)
T PF08490_consen 121 WLSERIELARYAHIPLGNLPSDNPLFLIDIFYARRLRKNNHVLWWSPSPRPDLGGKEEDDNRLLWDMDELESPEINNPGA 200 (396)
T ss_pred HHHHHHHHHHHcCCCcccCCcchHHHHHHHHHHHHHHHCCeEEeCCCCCCCCCCcchhhhhcccccccccCceEEECCCc
Confidence 45667899999999999885555567788888999999999982 2 2211 111000 011111112235899
Q ss_pred ccCCeEEeeccccc-hhHHhhcCccccccccccCCCccccCCCcccCCCchhhcccCcccccCCCCceecCCCCcCCChH
Q 000502 1278 YADPVVVLDFQSLY-PSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLP 1356 (1459)
Q Consensus 1278 Y~nPVvVLDFqSLY-PSIMIAyNICyST~vg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPngv~FVk~~vrkGILP 1356 (1459)
|.+-.+-||+..|= -+|+.+.-|- .. .+....|+. +....... ... ......|. ....-+
T Consensus 201 Y~~vcvEl~i~~LavnaiL~S~~i~------e~--EG~~~~~~~-~~~~~~~~---~~~---~~~~~~~~----e~~~~~ 261 (396)
T PF08490_consen 201 YRSVCVELDISNLAVNAILQSSLIN------EL--EGSDSAGFN-FDTASDAS---NGS---ANSSSSYD----ESAFCS 261 (396)
T ss_pred cceEEEEEEecceeHHHHHHHhHHh------hh--cCCcccccc-cccccccc---ccc---cccccccc----cccccH
Confidence 99855668887662 2222221110 00 000000000 00000000 000 00011121 111112
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHHHHHhhheeeeecccccccccCcCCCHHHHHHHHHHHHHHHHHHHHH
Q 000502 1357 RLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISF 1436 (1459)
Q Consensus 1357 ~mL~eLL~~R~~vKk~MKk~~~~d~~l~~iLDarQlALKIiANS~YGYtGA~fSGRmpc~eIAdSIT~~GRe~Le~Ai~~ 1436 (1459)
. .+--.|.|+|..+++....+.. .|. +.+.+|-.+... ++.||++.+...|-..=+..+.+-+.-
T Consensus 262 ~---~f~iLr~mv~~w~~d~~~~n~~----AD~-------ll~~f~rWl~sp-~S~LyDPaL~~~v~~LmkK~flqLl~E 326 (396)
T PF08490_consen 262 A---AFRILRSMVKSWLRDALKGNSF----ADS-------LLQHFYRWLSSP-SSLLYDPALHRMVHNLMKKVFLQLLAE 326 (396)
T ss_pred H---HHHHHHHHHHHHHHHHhcCCcc----HHH-------HHHHHHHHHcCC-cccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 2 2333466666666653222211 111 145588888754 458999999999998888887766665
Q ss_pred HhhcCCCCcEEEEeccceeEEE
Q 000502 1437 VNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1437 Ie~~~~~GakVIYGDTDSlFV~ 1458 (1459)
++. .|++|||+|-..|.|.
T Consensus 327 f~r---lG~~VVyA~~~riil~ 345 (396)
T PF08490_consen 327 FRR---LGSKVVYADFNRIILC 345 (396)
T ss_pred HHH---cCCEEEEEcCCEEEEE
Confidence 554 7999999999998874
No 92
>PRK05359 oligoribonuclease; Provisional
Probab=91.79 E-value=0.82 Score=50.10 Aligned_cols=107 Identities=21% Similarity=0.200 Sum_probs=65.5
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceE-EEEEEEecCCCc-----c--cccc---CCCCCcEEEEeCC
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAV-EIYVLLYCKSES-----H--QRSL---VGIPDCKVFVCSK 1026 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~-ei~vLv~~~~~~-----~--~~~~---~~i~g~~V~~f~S 1026 (1459)
+.+.||+|+.+ + ||..|.|+.|++...+.+-... +.+.++...... . .... .||.+-.+..-.+
T Consensus 4 ~~vvlD~ETTG----L-dp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 4 NLIWIDLEMTG----L-DPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred cEEEEEeecCC----C-CCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 45678888754 2 7889999999988765432111 212222221100 0 0011 1333223334457
Q ss_pred HHHHHHHHHHHHhhcC---CCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1027 EIHLFSHFIKILCSFD---PDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1027 EkELL~aFidlIr~~D---PDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
+.+.+..|.+++..+- -.+|+|+|+ .||+.||..-+..++..+
T Consensus 79 ~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l 124 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEAYF 124 (181)
T ss_pred HHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcccC
Confidence 8999999999997532 246899887 599999999988776543
No 93
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.46 E-value=1.9 Score=60.23 Aligned_cols=102 Identities=17% Similarity=0.276 Sum_probs=67.1
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc-c--ccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES-H--QRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~-~--~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
+.+.+|+|+.+ .+|..|.|+.|+......+. ..+.+-.+...... . ...+.+|....+....+..+.|..|
T Consensus 420 ~~VVfDLETTG-----L~~~~deIIEIgAV~V~~G~-iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f 493 (1437)
T PRK00448 420 TYVVFDVETTG-----LSAVYDEIIEIGAVKIKNGE-IIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKF 493 (1437)
T ss_pred cEEEEEhhhcC-----CCCchhhhheeeeEEEeCCe-EeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHH
Confidence 56778888853 26788999999887655442 22333223332211 0 1122344333344556888999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIG 1069 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~ 1069 (1459)
.+++.. .++++||. .||+++|.+.++++|+.
T Consensus 494 ~~figg---~vLVAHNa-~FD~~fL~~~l~rlgl~ 524 (1437)
T PRK00448 494 KEFCGD---SILVAHNA-SFDVGFINTNYEKLGLE 524 (1437)
T ss_pred HHHhCC---CEEEEeCc-cccHHHHHHHHHHcCCc
Confidence 888754 59999999 69999999999888764
No 94
>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=91.17 E-value=1.1 Score=47.45 Aligned_cols=87 Identities=14% Similarity=0.172 Sum_probs=52.7
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCC-c-cccccCCCCCcEEEEe-CCHHHHHHHHHHH
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSE-S-HQRSLVGIPDCKVFVC-SKEIHLFSHFIKI 1037 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~-~-~~~~~~~i~g~~V~~f-~SEkELL~aFidl 1037 (1459)
.+|||+.+-+ +. |+|..|+..-.+ +...++ .++..... + ....+.||..-.|.-- +++.+.+..|.++
T Consensus 2 ~iD~E~~g~~-----~g-~ei~~i~~v~~~-~~~~f~--~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~f 72 (150)
T cd06145 2 ALDCEMCYTT-----DG-LELTRVTVVDEN-GKVVLD--ELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSL 72 (150)
T ss_pred EEeeeeeeec-----CC-CEEEEEEEEeCC-CCEEEE--EeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHH
Confidence 5777776532 22 888888877332 211111 23322111 1 1223455554445555 4899999999999
Q ss_pred HhhcCCCEEEeccCCCccHHHH
Q 000502 1038 LCSFDPDILMGWDIQGGSLGFL 1059 (1459)
Q Consensus 1038 Ir~~DPDIItGYNI~~FDLpYL 1059 (1459)
+..- .+|+|||+. ||+.+|
T Consensus 73 l~~~--~vlVgHn~~-fD~~fL 91 (150)
T cd06145 73 ISPD--TILVGHSLE-NDLKAL 91 (150)
T ss_pred hCCC--CEEEEcChH-HHHHHh
Confidence 9621 499999995 999997
No 95
>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=89.84 E-value=1.1 Score=48.60 Aligned_cols=102 Identities=14% Similarity=0.152 Sum_probs=63.8
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCce-EEEEEEEecCCCc-c---------ccccCCCCCcEEEEeCCHH
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHA-VEIYVLLYCKSES-H---------QRSLVGIPDCKVFVCSKEI 1028 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~-~ei~vLv~~~~~~-~---------~~~~~~i~g~~V~~f~SEk 1028 (1459)
+.||+|+.+- +|..|+|+.|++...+.+... .+.+..+...... . .....+|.+-.+.--.++.
T Consensus 2 v~iD~ETTGl-----~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~ 76 (173)
T cd06135 2 VWIDLEMTGL-----DPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLA 76 (173)
T ss_pred EEEEEecCCC-----CCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHH
Confidence 4678888642 678899999999876543221 1222222222110 0 0011233223344557899
Q ss_pred HHHHHHHHHHhhc---CCCEEEeccCCCccHHHHHHHHHHhC
Q 000502 1029 HLFSHFIKILCSF---DPDILMGWDIQGGSLGFLAERAAHLG 1067 (1459)
Q Consensus 1029 ELL~aFidlIr~~---DPDIItGYNI~~FDLpYLieRAk~LG 1067 (1459)
+.+..|.+++... +-.+|+|+|+ .||+.+|..-+.++|
T Consensus 77 ~vl~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~ 117 (173)
T cd06135 77 QAEAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELE 117 (173)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHh
Confidence 9999999999863 4468889886 699999988777776
No 96
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=89.73 E-value=0.51 Score=62.96 Aligned_cols=103 Identities=17% Similarity=0.271 Sum_probs=66.7
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc---cccccCCCCCcEEEEeCCHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES---HQRSLVGIPDCKVFVCSKEIHLFSHF 1034 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~---~~~~~~~i~g~~V~~f~SEkELL~aF 1034 (1459)
+-+-||||+.+ + .|..|.|+.|+..--..+..+ +.+-.+.....+ ....+.+|.+-.+.--....+.|..|
T Consensus 422 tyVVfDiETTG----L-s~~~d~iIE~aAvKikng~iI-d~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 422 TYVVFDIETTG----L-SPVYDEIIEIAAVKIKNGRII-DKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cEEEEEeecCC----c-CcccchhhhheeeeeeCCcch-HHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 55667888753 2 678898888886644433221 211111111111 11223445444566667888999999
Q ss_pred HHHHhhcCCCEEEeccCCCccHHHHHHHHHHhCCCC
Q 000502 1035 IKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGL 1070 (1459)
Q Consensus 1035 idlIr~~DPDIItGYNI~~FDLpYLieRAk~LGi~l 1070 (1459)
.+++.. .|++.+| -+||+|||..+.+++++..
T Consensus 496 ~~~~~d---~IlVAHN-asFD~gFl~~~~~k~~~~~ 527 (1444)
T COG2176 496 REFIGD---SILVAHN-ASFDMGFLNTNYEKYGLEP 527 (1444)
T ss_pred HHHhcC---cEEEecc-CccchhHHHHHHHHhCCcc
Confidence 988876 5999999 6799999999999988754
No 97
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=85.56 E-value=1.1 Score=60.79 Aligned_cols=51 Identities=8% Similarity=0.071 Sum_probs=40.9
Q ss_pred HHHHHhcccchhHHHHHHHhCccccccccCCchhhhHHHHHHHhhhCCEEe
Q 000502 1200 LEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLA 1250 (1459)
Q Consensus 1200 l~Ll~kL~iI~~t~ElARl~GIpf~sVlsRGSq~rVESlLlr~ak~~nfll 1250 (1459)
...+.....+...++++|.++||+..+=..-.+|-++-++.|..++.|.++
T Consensus 1583 ~h~~a~~~wl~~~i~~SRY~~VPigNl~~D~~~f~iD~~faR~Lrk~~~vL 1633 (2173)
T KOG1798|consen 1583 QHYLASGSWLSHRIKLSRYSHVPIGNLPEDWLTFIIDLFFARKLRKHNHVL 1633 (2173)
T ss_pred HHHHhHHHHHHHHHHHHHhcCCcccCCchHHHHHHHHHHHHHHHHhcCeeE
Confidence 334444456677899999999999987555667889999999999999987
No 98
>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=82.38 E-value=19 Score=38.34 Aligned_cols=54 Identities=20% Similarity=0.265 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhc
Q 000502 1150 MYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1150 sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL 1206 (1459)
..+|.+++..+||.+...-.....+.|-. .+ . ...-+.|+..|+.+.+.|.++|
T Consensus 115 ~~~l~~l~~~~l~~~~~k~k~~~~s~W~~-rp-L-t~~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 115 LVSLARLVEEVLGLPLSKPKKVRCSNWEA-RP-L-SKEQILYAATDAYASLELYRKL 168 (170)
T ss_pred CccHHHHHHHHcCcccCCCCCcccCCCCC-CC-C-CHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999987654211223445533 22 1 2345799999999999999886
No 99
>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=82.37 E-value=4.7 Score=42.69 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=34.4
Q ss_pred cCCCCCcEEEEeCCHHHHHHHHHHHHhhcCCCEEEeccCCCccHHHHH
Q 000502 1013 LVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 1013 ~~~i~g~~V~~f~SEkELL~aFidlIr~~DPDIItGYNI~~FDLpYLi 1060 (1459)
+.||..-.|.-..+..+.+.+|.+++.. .+++|||+ .||+.+|.
T Consensus 50 ihGIt~~~v~~a~~~~~~~~~l~~~l~~---~vlVgHn~-~fD~~~L~ 93 (152)
T cd06144 50 VSGIRPEHLKDAPDFEEVQKKVAELLKG---RILVGHAL-KNDLKVLK 93 (152)
T ss_pred CCCCCHHHHcCCCCHHHHHHHHHHHhCC---CEEEEcCc-HHHHHHhc
Confidence 3455444566677899999999999863 69999999 59999883
No 100
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=82.29 E-value=3.3 Score=48.99 Aligned_cols=97 Identities=18% Similarity=0.190 Sum_probs=50.6
Q ss_pred CceEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeec---CCCc--eEEEEEEEecCCCc-c--ccccCCCCCcEEEEeCCH
Q 000502 956 QLTLLSIEVQAESRGDLRPDPRYDSINVVALAFEN---DSDH--AVEIYVLLYCKSES-H--QRSLVGIPDCKVFVCSKE 1027 (1459)
Q Consensus 956 ~LtiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~---d~d~--~~ei~vLv~~~~~~-~--~~~~~~i~g~~V~~f~SE 1027 (1459)
..+.+.+|+||.+- ||..|.|+.|++.... ++.. ..+.+-.+...... . ...+.||..-.|.--...
T Consensus 36 ~~~~vvlD~ETTGL-----d~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~ 110 (294)
T PRK09182 36 VRLGVILDTETTGL-----DPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTID 110 (294)
T ss_pred CCeEEEEEeeCCCC-----CCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCc
Confidence 34778899998642 7888999999987544 2211 11222222222110 0 111233321111111111
Q ss_pred HHHHHHHHHHHhhcCCCEEEeccCCCccHHHHHHHH
Q 000502 1028 IHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERA 1063 (1459)
Q Consensus 1028 kELL~aFidlIr~~DPDIItGYNI~~FDLpYLieRA 1063 (1459)
.+-+.+| +.. -++|+|||. .||++||...+
T Consensus 111 ~~~l~~f---l~~--~~vlVAHNA-~FD~~fL~~~~ 140 (294)
T PRK09182 111 PAAVDAL---IAP--ADLIIAHNA-GFDRPFLERFS 140 (294)
T ss_pred HHHHHHH---hcC--CCEEEEeCH-HHHHHHHHHHH
Confidence 2223333 433 379999999 69999997544
No 101
>PTZ00315 2'-phosphotransferase; Provisional
Probab=81.44 E-value=72 Score=41.36 Aligned_cols=105 Identities=9% Similarity=0.024 Sum_probs=64.5
Q ss_pred ceEEEEEEEeCcCCCCCCC-CCCCcEEEEEEEeecCCC-ceEEEE-EEEecCCCc--c--ccccCCCCCcEEEEeCCHHH
Q 000502 957 LTLLSIEVQAESRGDLRPD-PRYDSINVVALAFENDSD-HAVEIY-VLLYCKSES--H--QRSLVGIPDCKVFVCSKEIH 1029 (1459)
Q Consensus 957 LtiLSIEIet~srg~lfPD-Pe~DpI~~Is~~v~~d~d-~~~ei~-vLv~~~~~~--~--~~~~~~i~g~~V~~f~SEkE 1029 (1459)
-..+.||+|+.+. .|. ...|+|+-|++...+... .++..+ .++.....+ . -..+.+|....|.--.+-.+
T Consensus 56 d~~IV~DlETTgl---~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~e 132 (582)
T PTZ00315 56 DAYVVLDFEATCE---ADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPV 132 (582)
T ss_pred CeEEEEEEecCCC---CCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHH
Confidence 4556677777442 222 246899999999865222 223334 233321111 1 12344555556666778889
Q ss_pred HHHHHHHHHhhcCC-------CEEEeccCCCccHH-HHHHHHHH
Q 000502 1030 LFSHFIKILCSFDP-------DILMGWDIQGGSLG-FLAERAAH 1065 (1459)
Q Consensus 1030 LL~aFidlIr~~DP-------DIItGYNI~~FDLp-YLieRAk~ 1065 (1459)
.+..|.+++..... .++++.|+ .||+. +|..-++.
T Consensus 133 Vl~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~ 175 (582)
T PTZ00315 133 VYCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRV 175 (582)
T ss_pred HHHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHH
Confidence 99999999987641 47888888 59995 77766663
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=81.08 E-value=77 Score=33.97 Aligned_cols=52 Identities=23% Similarity=0.287 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHhcCCCCCCChhhhHHHHhcC------ChhHHHHHHHHHHHHHHHHHHHHHhc
Q 000502 1150 MYTVEAVAETVLRRKIPSIPFRVLTKWFASG------PGRARYRCVEYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1150 sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg------~~~~r~rvl~YclkDa~Lvl~Ll~kL 1206 (1459)
+++|+++++.+++..+.. +.. ++..+ ..........|+..|+..+.+|+.++
T Consensus 109 ~~~l~~l~~~~l~~~~~~--~~~---~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l 166 (193)
T cd06139 109 RHGLDDLAERYLGHKTIS--FED---LVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELL 166 (193)
T ss_pred CCCHHHHHHHHhCCCCcc--HHH---HcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999999998765322 111 11110 00113456779999999999998886
No 103
>PRK05755 DNA polymerase I; Provisional
Probab=74.26 E-value=37 Score=46.03 Aligned_cols=70 Identities=21% Similarity=0.306 Sum_probs=44.3
Q ss_pred eEEEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCccccccCCCCCcEEEEeCCHHHHHHHHHHH
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKI 1037 (1459)
Q Consensus 958 tiLSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~~~~~~~~i~g~~V~~f~SEkELL~aFidl 1037 (1459)
.++.+|+|+.+ .+|..+.|..|++++.+. . .+.+ . +..+ . .+.+..|.++
T Consensus 316 ~~~a~DtEt~~-----l~~~~~~i~~i~ls~~~g-~----~~~i--p--------~~~i---------~-~~~l~~l~~~ 365 (880)
T PRK05755 316 GLFAFDTETTS-----LDPMQAELVGLSFAVEPG-E----AAYI--P--------LDQL---------D-REVLAALKPL 365 (880)
T ss_pred CeEEEEeccCC-----CCcccccEEEEEEEeCCC-c----EEEE--e--------cccc---------c-HHHHHHHHHH
Confidence 56788887754 256778899998876432 1 1111 1 0000 1 1567777777
Q ss_pred HhhcCCCE-EEeccCCCccHHHHH
Q 000502 1038 LCSFDPDI-LMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 1038 Ir~~DPDI-ItGYNI~~FDLpYLi 1060 (1459)
+. |+++ +++||. .||+.+|.
T Consensus 366 L~--d~~v~kV~HNa-kfDl~~L~ 386 (880)
T PRK05755 366 LE--DPAIKKVGQNL-KYDLHVLA 386 (880)
T ss_pred Hh--CCCCcEEEecc-HhHHHHHH
Confidence 77 4554 789999 69999986
No 104
>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=73.78 E-value=3.2 Score=44.11 Aligned_cols=62 Identities=8% Similarity=0.002 Sum_probs=43.6
Q ss_pred cCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHhCcccccc
Q 000502 1162 RRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSV 1226 (1459)
Q Consensus 1162 gekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL~iI~~t~ElARl~GIpf~sV 1226 (1459)
.-+|.|++-.+ +|.+-.-..-..+.+||++|+.|+..|++..++...+..-|.-+=+|-..|
T Consensus 85 sfgKDDVdL~d---mY~nYnl~~a~em~~YCiHDacLCkyLw~Yy~i~~KidA~astYlLPQsmv 146 (149)
T PF08408_consen 85 SFGKDDVDLSD---MYKNYNLDIALEMARYCIHDACLCKYLWDYYGIETKIDAAASTYLLPQSMV 146 (149)
T ss_pred EecCCCCCHHH---HHHhccHHHHHHHHHHHHhHHHHHHHHHHHcCcceeeeccceeeecchhhe
Confidence 33566765444 555544444567999999999999999999988777766666555555444
No 105
>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=72.05 E-value=8.1 Score=41.34 Aligned_cols=90 Identities=13% Similarity=0.136 Sum_probs=53.9
Q ss_pred EEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCCCc--cccccCCCCCcEEEEeCCHHHHHHHHHHHH
Q 000502 961 SIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSES--HQRSLVGIPDCKVFVCSKEIHLFSHFIKIL 1038 (1459)
Q Consensus 961 SIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~~~--~~~~~~~i~g~~V~~f~SEkELL~aFidlI 1038 (1459)
.||+|+.+- -|.-..++|..|++...+ +... ...++...... ....+.||....+.--.+-.+.+.+|.+++
T Consensus 2 ~~D~EttGl---~~~~~~~~i~~i~~v~~~-g~~~--~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l 75 (157)
T cd06149 2 AIDCEMVGT---GPGGRESELARCSIVNYH-GDVL--YDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL 75 (157)
T ss_pred EEEeEeccc---cCCCCeEEEEEEEEEeCC-CCEE--EEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc
Confidence 578888542 233235777777776532 2211 11233222111 122334554445556678889999999998
Q ss_pred hhcCCCEEEeccCCCccHHHHH
Q 000502 1039 CSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 1039 r~~DPDIItGYNI~~FDLpYLi 1060 (1459)
.. .|++|||. .||+.+|.
T Consensus 76 ~~---~vlV~Hn~-~~D~~~l~ 93 (157)
T cd06149 76 KG---KVVVGHAI-HNDFKALK 93 (157)
T ss_pred CC---CEEEEeCc-HHHHHHhc
Confidence 64 59999998 59998885
No 106
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=71.95 E-value=2.5 Score=43.11 Aligned_cols=99 Identities=20% Similarity=0.298 Sum_probs=58.9
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCc-eEEEE-EEEecCCC--cc--ccccCCCCCcEEEEeCCHHHHHHH
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDH-AVEIY-VLLYCKSE--SH--QRSLVGIPDCKVFVCSKEIHLFSH 1033 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~-~~ei~-vLv~~~~~--~~--~~~~~~i~g~~V~~f~SEkELL~a 1033 (1459)
+.||+|+.+ ++|..+.|+.|++...++... ....+ .++..... .. .....+|....+.......+.+..
T Consensus 1 v~~D~Ettg-----~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTG-----LDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESS-----STTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCC-----CCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHh
Confidence 468888865 355678888888876666543 22222 22222211 00 111222322223334567778888
Q ss_pred HHHHHhhcCCCEEEeccCCCccHHHHHHHHHHh
Q 000502 1034 FIKILCSFDPDILMGWDIQGGSLGFLAERAAHL 1066 (1459)
Q Consensus 1034 FidlIr~~DPDIItGYNI~~FDLpYLieRAk~L 1066 (1459)
|.++++.. .+++||| ..||++++..=..++
T Consensus 76 ~~~~~~~~--~~~v~~n-~~fd~~~l~~~~~~~ 105 (164)
T PF00929_consen 76 FEEFLKKN--DILVGHN-ASFDIGFLRREDKRF 105 (164)
T ss_dssp HHHHHHHH--TEEEETT-CCHEEESSHHHHHHH
T ss_pred hhhhhhcc--ccccccc-ccchhhHHHHhhhhc
Confidence 99999855 5999999 679998886655554
No 107
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=47.75 E-value=62 Score=36.86 Aligned_cols=84 Identities=12% Similarity=0.031 Sum_probs=42.7
Q ss_pred EEEEEEeCcCCCCCCCCCCCcEEEEEEEeecCCCceEEEEEEEecCC-Ccc--ccccCCCCCcEEEEeCCHHHHHHHHHH
Q 000502 960 LSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKS-ESH--QRSLVGIPDCKVFVCSKEIHLFSHFIK 1036 (1459)
Q Consensus 960 LSIEIet~srg~lfPDPe~DpI~~Is~~v~~d~d~~~ei~vLv~~~~-~~~--~~~~~~i~g~~V~~f~SEkELL~aFid 1036 (1459)
..||+||.+- ++. |+.|++.--.++. +.+.+..+.... ... ...+.+|..-.|.-.+.-.+.+..|
T Consensus 3 ~vlD~ETTGl-----~~~---IieIg~v~v~~~~-i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~-- 71 (219)
T PRK07983 3 RVIDTETCGL-----QGG---IVEIASVDVIDGK-IVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHY-- 71 (219)
T ss_pred EEEEEECCCC-----CCC---CEEEEEEEEECCE-EEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHHH--
Confidence 4568887642 332 6666655333332 223332222222 111 1123344333343344455566554
Q ss_pred HHhhcCCCEEEeccCCCccHHHH
Q 000502 1037 ILCSFDPDILMGWDIQGGSLGFL 1059 (1459)
Q Consensus 1037 lIr~~DPDIItGYNI~~FDLpYL 1059 (1459)
..-++|+|||+. ||+.+|
T Consensus 72 ----~~~~~lVaHNa~-FD~~~L 89 (219)
T PRK07983 72 ----YGSEWYVAHNAS-FDRRVL 89 (219)
T ss_pred ----cCCCEEEEeCcH-hhHHHH
Confidence 245799999995 999987
No 108
>cd05767 IgC_MHC_II_alpha Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosom
Probab=38.12 E-value=29 Score=34.31 Aligned_cols=24 Identities=17% Similarity=0.422 Sum_probs=20.3
Q ss_pred cEEEEEeeCCCC----CEEEEEEcCccc
Q 000502 45 PVIRVYGSTPAG----QKTCLHIHRALP 68 (1459)
Q Consensus 45 PVIRIFGvT~~G----~SVClHVHGf~P 68 (1459)
|.|+||...+.+ ..+.||+.||+|
T Consensus 2 P~V~v~~~~~~~~~~~~tL~C~a~gFyP 29 (94)
T cd05767 2 PEVTVFSLKPVELGEPNTLICFVDNFFP 29 (94)
T ss_pred CEEEEEeCCcccCCCCeEEEEEEEEEEC
Confidence 889999997654 479999999987
No 109
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=32.95 E-value=75 Score=35.23 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhc
Q 000502 1149 NMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1149 ~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL 1206 (1459)
..++|.++++.+||.+...- ..++.|-. .+- ...-+.|+..||...+.|+++|
T Consensus 139 ~~~sL~~l~~~~lg~~l~K~--~q~SdW~~-rpL--s~~Qi~YAA~Da~~l~~l~~~L 191 (193)
T cd06146 139 KTKGLADLVQEVLGKPLDKS--EQCSNWER-RPL--REEQILYAALDAYCLLEVFDKL 191 (193)
T ss_pred ccCCHHHHHHHHhCCCcCcc--cccCCCCC-CCC--CHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999765431 24556633 221 2356799999999999999886
No 110
>cd05770 IgC_beta2m Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.
Probab=24.76 E-value=70 Score=31.68 Aligned_cols=25 Identities=28% Similarity=0.420 Sum_probs=19.8
Q ss_pred cEEEEEeeCCC--CC--EEEEEEcCccce
Q 000502 45 PVIRVYGSTPA--GQ--KTCLHIHRALPY 69 (1459)
Q Consensus 45 PVIRIFGvT~~--G~--SVClHVHGf~PY 69 (1459)
|.++||-..+. |+ ...||+.||+|-
T Consensus 2 P~v~v~~~~~~~~g~~~~L~C~a~gFyP~ 30 (93)
T cd05770 2 PKVQVYSRFPAENGKPNVLNCYVTGFHPP 30 (93)
T ss_pred CEEEEEecCCCcCCCceEEEEEEEEEeCC
Confidence 78999977644 33 699999999975
No 111
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=24.46 E-value=2e+02 Score=39.88 Aligned_cols=32 Identities=16% Similarity=0.192 Sum_probs=27.0
Q ss_pred CCccccChhhhhhhhhccCcccceeEEeCCcc
Q 000502 132 LQPHESHIPFLLQFLVDYNLYGMGHLHLSKLK 163 (1459)
Q Consensus 132 ~q~YESnIpf~LRFMID~nI~Gm~WI~lp~~k 163 (1459)
..+|=+|..-+=||+++..|-|=+|+++..-.
T Consensus 464 shvfgt~tn~lE~fll~rKimGPCWlkv~~~s 495 (1429)
T KOG0970|consen 464 SHVFGTNTNPLERFLLSRKIMGPCWLKVKGYS 495 (1429)
T ss_pred HHHhccCccHHHHHHHhccccCceEEEeecCC
Confidence 35677788888899999999999999998533
No 112
>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=23.74 E-value=1.2e+02 Score=32.51 Aligned_cols=66 Identities=12% Similarity=0.078 Sum_probs=44.1
Q ss_pred eehHHHHhhccCCCCCCHHHHHHHHhcCCCCCCChhhhHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHhc
Q 000502 1136 LNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQL 1206 (1459)
Q Consensus 1136 IDLwrv~rkelKL~sYSLEnVA~~vLgekkpd~s~k~Ltk~y~sg~~~~r~rvl~YclkDa~Lvl~Ll~kL 1206 (1459)
+|+....+---...+.+|..++.++||...+. ....+.|- ..|- ...-+.|+..|+...+.|+.+|
T Consensus 94 ~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K--~~~~s~W~-~rpL--t~~qi~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 94 FDTTIAANLKGLPERWSLASLVEHFLGKTLDK--SISCADWS-YRPL--TEDQKLYAAADVYALLIIYTKL 159 (161)
T ss_pred hHHHHHHHHhCCCCCchHHHHHHHHhCCCCCc--cceeccCC-CCCC--CHHHHHHHHHHHHHHHHHHHHH
Confidence 67766544211123679999999999986532 22344553 2332 2456899999999999999886
Done!