Query 036628
Match_columns 254
No_of_seqs 162 out of 1200
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 03:56:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036628hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0542 Predicted exonuclease 100.0 7.4E-40 1.6E-44 288.5 9.5 162 8-169 51-257 (280)
2 PTZ00315 2'-phosphotransferase 100.0 4.1E-31 8.9E-36 258.1 16.7 164 6-169 49-268 (582)
3 PRK07748 sporulation inhibitor 99.9 6.6E-27 1.4E-31 203.6 13.0 149 14-166 5-190 (207)
4 COG5018 KapD Inhibitor of the 99.9 1.2E-26 2.5E-31 194.6 5.1 151 11-164 2-193 (210)
5 PRK06722 exonuclease; Provisio 99.9 5.5E-25 1.2E-29 200.1 15.5 138 10-154 2-179 (281)
6 cd06133 ERI-1_3'hExo_like DEDD 99.9 1.4E-23 3E-28 175.6 13.1 134 15-153 1-176 (176)
7 smart00479 EXOIII exonuclease 99.9 8.1E-22 1.8E-26 163.1 14.7 131 14-156 1-167 (169)
8 PRK06807 DNA polymerase III su 99.9 2.6E-21 5.7E-26 178.7 14.8 134 8-156 3-172 (313)
9 cd06131 DNA_pol_III_epsilon_Ec 99.9 7.6E-21 1.6E-25 158.7 13.6 127 15-152 1-166 (167)
10 PRK08517 DNA polymerase III su 99.8 1.7E-20 3.7E-25 169.0 14.8 129 14-156 69-231 (257)
11 TIGR01406 dnaQ_proteo DNA poly 99.8 2.2E-20 4.8E-25 165.1 14.6 134 14-157 1-173 (225)
12 PRK06063 DNA polymerase III su 99.8 1.5E-20 3.3E-25 173.6 13.7 131 13-156 15-179 (313)
13 cd06130 DNA_pol_III_epsilon_li 99.8 2.2E-20 4.8E-25 153.5 12.8 119 15-150 1-155 (156)
14 PRK06195 DNA polymerase III su 99.8 5.6E-20 1.2E-24 169.4 13.9 127 14-157 2-165 (309)
15 PRK05711 DNA polymerase III su 99.8 1.2E-19 2.6E-24 162.0 15.5 138 13-161 4-181 (240)
16 PRK09145 DNA polymerase III su 99.8 5.2E-20 1.1E-24 159.4 12.7 127 13-154 29-199 (202)
17 PRK05168 ribonuclease T; Provi 99.8 9.2E-20 2E-24 159.5 14.2 141 13-156 17-201 (211)
18 PRK07740 hypothetical protein; 99.8 1.4E-19 3.1E-24 161.7 14.2 135 9-157 53-227 (244)
19 PRK07942 DNA polymerase III su 99.8 1.6E-19 3.6E-24 160.1 14.1 138 13-157 6-181 (232)
20 cd06134 RNaseT DEDDh 3'-5' exo 99.8 2E-19 4.4E-24 154.7 13.9 138 15-155 7-188 (189)
21 TIGR00573 dnaq exonuclease, DN 99.8 6.5E-19 1.4E-23 154.5 14.6 136 13-160 7-181 (217)
22 COG2176 PolC DNA polymerase II 99.8 2.7E-20 5.8E-25 190.5 6.3 142 8-163 414-593 (1444)
23 PRK07883 hypothetical protein; 99.8 4.6E-19 9.9E-24 175.0 14.6 132 14-159 16-185 (557)
24 PRK07247 DNA polymerase III su 99.8 1.4E-18 3E-23 150.7 15.7 128 10-157 2-170 (195)
25 TIGR01298 RNaseT ribonuclease 99.8 1E-18 2.2E-23 151.8 13.5 140 14-156 9-192 (200)
26 PRK06310 DNA polymerase III su 99.8 1.6E-18 3.4E-23 155.5 14.8 133 13-156 7-174 (250)
27 cd06127 DEDDh DEDDh 3'-5' exon 99.8 7.7E-19 1.7E-23 141.9 10.2 121 16-149 1-158 (159)
28 cd06135 Orn DEDDh 3'-5' exonuc 99.8 4E-18 8.8E-23 144.6 11.8 132 15-155 1-171 (173)
29 PRK07246 bifunctional ATP-depe 99.8 6.6E-18 1.4E-22 173.2 15.7 131 12-158 6-172 (820)
30 PRK08074 bifunctional ATP-depe 99.8 6E-18 1.3E-22 175.6 15.0 131 13-157 3-170 (928)
31 PRK06309 DNA polymerase III su 99.8 7E-18 1.5E-22 149.5 12.7 128 13-156 2-166 (232)
32 TIGR01405 polC_Gram_pos DNA po 99.8 5.4E-18 1.2E-22 178.7 14.1 133 14-160 191-359 (1213)
33 cd06136 TREX1_2 DEDDh 3'-5' ex 99.8 9.2E-18 2E-22 142.9 12.6 131 15-151 1-176 (177)
34 PRK09146 DNA polymerase III su 99.8 1.6E-17 3.6E-22 148.1 14.6 128 14-156 48-227 (239)
35 TIGR01407 dinG_rel DnaQ family 99.7 2.2E-17 4.8E-22 170.0 15.9 129 14-156 1-165 (850)
36 PRK05601 DNA polymerase III su 99.7 5.2E-17 1.1E-21 152.1 15.5 130 14-156 47-249 (377)
37 cd06138 ExoI_N N-terminal DEDD 99.7 9E-17 1.9E-21 137.3 11.2 125 16-149 1-182 (183)
38 PF00929 RNase_T: Exonuclease; 99.7 1.6E-17 3.4E-22 134.4 4.7 125 16-149 1-164 (164)
39 PRK09182 DNA polymerase III su 99.7 1.8E-15 3.8E-20 138.9 13.9 138 12-161 36-206 (294)
40 PRK07983 exodeoxyribonuclease 99.6 4.3E-15 9.3E-20 131.0 13.8 122 15-155 2-153 (219)
41 PRK00448 polC DNA polymerase I 99.6 1.7E-15 3.7E-20 161.8 12.1 132 14-159 420-587 (1437)
42 PRK05359 oligoribonuclease; Pr 99.6 5.8E-15 1.3E-19 126.5 12.2 133 12-155 2-174 (181)
43 COG0847 DnaQ DNA polymerase II 99.6 1.6E-14 3.4E-19 127.7 14.3 131 13-155 13-181 (243)
44 PRK11779 sbcB exonuclease I; P 99.5 1.3E-13 2.9E-18 133.8 16.1 137 11-155 4-197 (476)
45 cd06137 DEDDh_RNase DEDDh 3'-5 99.5 4.4E-14 9.5E-19 118.5 7.8 112 16-150 1-161 (161)
46 cd06144 REX4_like DEDDh 3'-5' 99.5 2.2E-13 4.9E-18 113.1 9.1 114 16-150 1-152 (152)
47 PF06839 zf-GRF: GRF zinc fing 99.4 4.7E-14 1E-18 94.8 2.7 44 208-254 1-44 (45)
48 cd06149 ISG20 DEDDh 3'-5' exon 99.4 1.3E-12 2.7E-17 109.4 8.5 114 16-150 1-157 (157)
49 cd06145 REX1_like DEDDh 3'-5' 99.3 4.6E-12 9.9E-17 105.2 8.5 110 16-150 1-150 (150)
50 PHA02570 dexA exonuclease; Pro 99.3 1.8E-11 3.8E-16 107.5 9.5 136 16-156 4-199 (220)
51 cd06125 DnaQ_like_exo DnaQ-lik 99.0 3.2E-09 7E-14 81.9 9.8 94 16-148 1-94 (96)
52 COG1949 Orn Oligoribonuclease 98.4 2.3E-06 5.1E-11 72.2 9.5 136 9-155 2-177 (184)
53 PF13482 RNase_H_2: RNase_H su 98.4 1.8E-06 4E-11 71.5 8.7 102 16-131 1-116 (164)
54 cd05160 DEDDy_DNA_polB_exo DED 98.1 6.4E-05 1.4E-09 64.4 13.3 79 16-100 2-106 (199)
55 KOG1956 DNA topoisomerase III 97.9 6.7E-06 1.4E-10 81.6 3.0 42 206-252 717-758 (758)
56 cd05782 DNA_polB_like1_exo Unc 97.7 0.0003 6.6E-09 61.6 10.3 94 30-129 49-168 (208)
57 cd05781 DNA_polB_B3_exo DEDDy 97.6 0.00054 1.2E-08 59.0 10.2 81 14-101 4-92 (188)
58 KOG3242 Oligoribonuclease (3'- 97.6 0.00037 8E-09 59.7 8.6 55 11-67 24-84 (208)
59 cd05780 DNA_polB_Kod1_like_exo 97.4 0.0061 1.3E-07 52.5 14.1 80 14-101 4-100 (195)
60 KOG0304 mRNA deadenylase subun 97.3 0.00088 1.9E-08 59.1 7.6 137 14-154 25-237 (239)
61 PF04857 CAF1: CAF1 family rib 97.3 0.006 1.3E-07 55.1 12.9 134 14-151 23-262 (262)
62 TIGR03491 RecB family nuclease 97.2 0.0021 4.6E-08 62.5 9.4 109 13-133 284-412 (457)
63 COG3359 Predicted exonuclease 97.2 0.0062 1.3E-07 54.9 11.4 132 12-155 97-268 (278)
64 PF10108 DNA_pol_B_exo2: Predi 97.0 0.013 2.8E-07 51.7 12.3 124 30-160 7-177 (209)
65 PRK05755 DNA polymerase I; Pro 96.7 0.0058 1.3E-07 64.1 8.8 126 13-155 315-468 (880)
66 COG2925 SbcB Exonuclease I [DN 96.3 0.02 4.3E-07 54.7 8.6 133 13-152 9-197 (475)
67 cd05783 DNA_polB_B1_exo DEDDy 95.7 0.26 5.7E-06 43.0 12.4 76 14-99 6-113 (204)
68 cd05779 DNA_polB_epsilon_exo D 95.1 0.3 6.4E-06 42.8 10.7 81 14-101 3-117 (204)
69 cd06139 DNA_polA_I_Ecoli_like_ 94.6 0.23 5E-06 41.5 8.5 126 14-156 6-170 (193)
70 cd05785 DNA_polB_like2_exo Unc 94.3 0.58 1.3E-05 40.9 10.6 79 14-101 10-102 (207)
71 cd06143 PAN2_exo DEDDh 3'-5' e 93.2 1.4 3E-05 37.9 10.7 66 74-149 102-173 (174)
72 COG5228 POP2 mRNA deadenylase 92.7 0.16 3.5E-06 45.4 4.2 152 14-168 43-265 (299)
73 cd05777 DNA_polB_delta_exo DED 91.8 2.2 4.8E-05 37.6 10.6 81 14-99 8-113 (230)
74 KOG2249 3'-5' exonuclease [Rep 90.7 4.8 0.0001 36.9 11.6 35 121-155 230-265 (280)
75 PF03104 DNA_pol_B_exo1: DNA p 88.8 2.9 6.2E-05 37.8 8.9 85 11-100 155-265 (325)
76 cd05784 DNA_polB_II_exo DEDDy 85.8 9.2 0.0002 33.0 9.9 74 14-100 4-94 (193)
77 KOG1798 DNA polymerase epsilon 85.4 3.9 8.5E-05 45.4 8.6 149 14-169 247-466 (2173)
78 smart00486 POLBc DNA polymeras 83.9 10 0.00022 35.8 10.2 83 14-100 4-112 (471)
79 PHA02563 DNA polymerase; Provi 83.5 8.5 0.00018 39.4 9.8 84 7-99 6-91 (630)
80 PTZ00166 DNA polymerase delta 82.5 6.9 0.00015 42.4 9.2 79 14-99 265-372 (1054)
81 PF01396 zf-C4_Topoisom: Topoi 82.1 1.4 3.1E-05 28.4 2.5 27 220-253 11-37 (39)
82 PF01612 DNA_pol_A_exo1: 3'-5' 75.6 35 0.00077 27.4 9.6 122 15-155 22-174 (176)
83 KOG4793 Three prime repair exo 69.2 3.4 7.5E-05 38.0 2.2 69 83-155 209-290 (318)
84 TIGR01685 MDP-1 magnesium-depe 68.9 14 0.00031 31.4 5.9 63 14-81 3-70 (174)
85 cd06129 RNaseD_like DEDDy 3'-5 67.6 67 0.0015 26.3 10.8 122 13-153 13-160 (161)
86 PRK05762 DNA polymerase II; Re 66.5 40 0.00087 35.3 9.7 76 13-100 155-246 (786)
87 PHA02528 43 DNA polymerase; Pr 64.4 48 0.001 35.4 9.8 82 13-99 106-221 (881)
88 cd06146 mut-7_like_exo DEDDy 3 64.1 92 0.002 26.5 10.1 131 12-154 21-193 (193)
89 KOG2248 3'-5' exonuclease [Rep 63.9 39 0.00085 32.5 8.3 131 11-160 214-379 (380)
90 KOG4793 Three prime repair exo 61.6 7 0.00015 36.1 2.7 26 75-101 122-148 (318)
91 PRK10829 ribonuclease D; Provi 56.4 1.9E+02 0.0041 27.7 11.6 122 14-155 23-169 (373)
92 COG0349 Rnd Ribonuclease D [Tr 52.3 2.2E+02 0.0048 27.3 11.2 123 14-155 18-165 (361)
93 PF13017 Maelstrom: piRNA path 49.8 22 0.00048 31.2 3.8 24 32-56 8-31 (213)
94 PRK06319 DNA topoisomerase I/S 48.9 12 0.00026 39.7 2.3 36 207-252 696-731 (860)
95 TIGR01056 topB DNA topoisomera 44.9 15 0.00032 37.8 2.3 38 209-252 613-652 (660)
96 PF10902 DUF2693: Protein of u 43.4 22 0.00048 26.9 2.4 38 5-43 41-78 (83)
97 COG0417 PolB DNA polymerase el 42.5 1.2E+02 0.0026 31.9 8.5 83 13-101 154-255 (792)
98 cd05778 DNA_polB_zeta_exo inac 38.5 2.8E+02 0.006 24.4 10.0 31 13-43 4-37 (231)
99 PF00370 FGGY_N: FGGY family o 35.1 45 0.00098 29.0 3.5 28 14-54 1-28 (245)
100 KOG1294 Apurinic/apyrimidinic 32.7 25 0.00053 33.3 1.5 21 217-237 299-319 (335)
101 PRK07726 DNA topoisomerase III 31.1 28 0.00062 35.7 1.8 16 231-252 629-644 (658)
102 PF12377 DuffyBP_N: Duffy bind 30.9 21 0.00045 25.4 0.5 27 12-39 20-48 (66)
103 PF07846 Metallothio_Cad: Meta 30.5 30 0.00064 19.4 1.0 17 210-229 1-17 (21)
104 PHA02524 43A DNA polymerase su 25.6 5.4E+02 0.012 25.8 9.5 37 58-99 184-223 (498)
105 TIGR01388 rnd ribonuclease D. 25.5 5.8E+02 0.013 24.1 12.2 124 13-155 18-165 (367)
106 COG3218 ABC-type uncharacteriz 24.5 92 0.002 27.5 3.5 46 11-56 122-170 (205)
107 COG1070 XylB Sugar (pentulose 23.7 98 0.0021 30.4 4.0 30 11-52 2-31 (502)
108 PF03413 PepSY: Peptidase prop 22.9 83 0.0018 20.9 2.4 14 39-52 50-63 (64)
109 PF05325 DUF730: Protein of un 22.6 68 0.0015 25.2 2.1 44 208-252 21-65 (122)
110 PHA03036 DNA polymerase; Provi 22.0 1E+03 0.022 26.2 11.2 36 9-44 156-193 (1004)
111 PF14574 DUF4445: Domain of un 20.6 2E+02 0.0043 28.0 5.3 31 14-56 2-32 (412)
No 1
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=7.4e-40 Score=288.49 Aligned_cols=162 Identities=38% Similarity=0.671 Sum_probs=141.0
Q ss_pred CCCCCCeEEEEEEeecCCC-CC-CCCCcEEEEceEEEEc-CCCeEEEEEEEe----------------------------
Q 036628 8 KLQDFDYFVVVDFEATCDK-KI-PHPQEIIEFPSVIVSG-VTGQITVCFQIY---------------------------- 56 (254)
Q Consensus 8 ~~q~~~~fvViDlEtTg~~-~~-~~~~EIIEIgAV~vD~-~~g~iv~~F~~~---------------------------- 56 (254)
.+|+|||++||||||||++ +. .+.+|||||+||++|. ++++|.++||+|
T Consensus 51 ~~q~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~ 130 (280)
T KOG0542|consen 51 LSQPFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAP 130 (280)
T ss_pred ccCccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCC
Confidence 4589999999999999999 44 3689999999996665 556666699999
Q ss_pred ----ehhhHHHHhhhcCCC--CCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC--CC-C---cccHH
Q 036628 57 ----ALFLHDNWQQHMGVT--PTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK--GD-V---RCNLK 124 (254)
Q Consensus 57 ----vl~~f~~wl~~~gi~--~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~--~~-~---~~~L~ 124 (254)
|+.+|..||.+.++. +++++|||||+|||..||+.||++++|.+|.||++|||+|+.|.. ++ . ..+|.
T Consensus 131 ~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mL 210 (280)
T KOG0542|consen 131 TFPQVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGML 210 (280)
T ss_pred CHHHHHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHH
Confidence 578999999987654 379999999999999999999999999999999999999999988 33 2 24678
Q ss_pred HHhcCCCCCCCCchHHHHHHHHHHHHHHHHcCCccCcC--cccccCC
Q 036628 125 EAVELGWHGRVHCGLDDSMNIARLLAVIMQRGFKFSIT--KSLTTPQ 169 (254)
Q Consensus 125 ~~l~i~~eG~~HrALdDA~ntA~l~~~ll~~g~~f~~~--~~~~~~~ 169 (254)
+++|++++|++|+|||||+|+|+|+.+|+++|++|+|| .++...+
T Consensus 211 e~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~~~~~~q 257 (280)
T KOG0542|consen 211 EHYGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELCDLWERQ 257 (280)
T ss_pred HHhCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhhhhcccC
Confidence 88999999999999999999999999999999999999 4444443
No 2
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.97 E-value=4.1e-31 Score=258.14 Aligned_cols=164 Identities=33% Similarity=0.510 Sum_probs=135.3
Q ss_pred CcCCCCCCeEEEEEEeecCCC-CCCCCCcEEEEceEEEEcCCCeEEEEEEEe----------------------------
Q 036628 6 PQKLQDFDYFVVVDFEATCDK-KIPHPQEIIEFPSVIVSGVTGQITVCFQIY---------------------------- 56 (254)
Q Consensus 6 ~~~~q~~~~fvViDlEtTg~~-~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~---------------------------- 56 (254)
+...|+|++||||||||||.+ .....+||||||||+||.++|+|+++|++|
T Consensus 49 ~~~~q~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap 128 (582)
T PTZ00315 49 EIAPQPFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRAD 128 (582)
T ss_pred ccccCCCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCC
Confidence 457899999999999999987 223568999999999998899999999999
Q ss_pred ----ehhhHHHHhhhcCCC----CCCeEEEEcCcccHHHHHHHHHHHcC-CCCCCCCchhhhhHHHhcC-----------
Q 036628 57 ----ALFLHDNWQQHMGVT----PTNFAVVTWSDWDCQVMLESECRFKN-IPKPSYFNRWINLRVPFSK----------- 116 (254)
Q Consensus 57 ----vl~~f~~wl~~~gi~----~~~~~~vt~g~fD~~~fL~~e~~~~g-i~~P~~~~~~iDlr~~f~~----------- 116 (254)
|+++|.+|+++.+.. +++++|+|||+||+..||.++|+..+ ..+|.++..|+|+++.|..
T Consensus 129 ~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~ 208 (582)
T PTZ00315 129 PFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGG 208 (582)
T ss_pred CHHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccc
Confidence 356778888765422 35689999999998789999998543 2445567899998655433
Q ss_pred -------CCCcccHHHHhcCCCCCCCCchHHHHHHHHHHHHHHHHcCCccCcCcccccCC
Q 036628 117 -------GDVRCNLKEAVELGWHGRVHCGLDDSMNIARLLAVIMQRGFKFSITKSLTTPQ 169 (254)
Q Consensus 117 -------~~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~~~ll~~g~~f~~~~~~~~~~ 169 (254)
.+.+.+|.+.+|++++|++|||+|||+|||+|+.+|+++|+.|.+|..++..+
T Consensus 209 ~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~~~~ 268 (582)
T PTZ00315 209 GATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFR 268 (582)
T ss_pred ccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCChhh
Confidence 13356677888999999999999999999999999999999999999887764
No 3
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.94 E-value=6.6e-27 Score=203.58 Aligned_cols=149 Identities=24% Similarity=0.360 Sum_probs=114.5
Q ss_pred eEEEEEEeecCCC--CCC--CCCcEEEEceEEEEcCCCeEEEEEEEeehhhH----HHHhhh-cCCC-------------
Q 036628 14 YFVVVDFEATCDK--KIP--HPQEIIEFPSVIVSGVTGQITVCFQIYALFLH----DNWQQH-MGVT------------- 71 (254)
Q Consensus 14 ~fvViDlEtTg~~--~~~--~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~~f----~~wl~~-~gi~------------- 71 (254)
.|||||+||||.+ .++ ..+||||||||+|+ +|+++++|++||.|.. ..+..+ +||.
T Consensus 5 ~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~--~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ev 82 (207)
T PRK07748 5 QFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVV--GCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEEL 82 (207)
T ss_pred eEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEe--cCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHH
Confidence 6999999999976 222 25899999999997 6789999999954321 111111 2221
Q ss_pred --------CC-CeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccHHHHhcCCCCCCCC
Q 036628 72 --------PT-NFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNLKEAVELGWHGRVH 136 (254)
Q Consensus 72 --------~~-~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L~~~l~i~~eG~~H 136 (254)
++ +..+++|++|| ..||.++|+++|++.| +...|+|+...++. .+.+.++.+.+|++.+|++|
T Consensus 83 l~~f~~~~~~~~~~iv~~~~fD-~~fL~~~~~~~~~~~~-~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~~~~~H 160 (207)
T PRK07748 83 VEKLAEYDKRCKPTIVTWGNMD-MKVLKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHH 160 (207)
T ss_pred HHHHHHHhCcCCeEEEEECHHH-HHHHHHHHHHcCCCCc-ccccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCCCCCCc
Confidence 12 46899999999 6899999999999877 45789998776543 24466788899999888999
Q ss_pred chHHHHHHHHHHHHHHHHcCCccCcCcccc
Q 036628 137 CGLDDSMNIARLLAVIMQRGFKFSITKSLT 166 (254)
Q Consensus 137 rALdDA~ntA~l~~~ll~~g~~f~~~~~~~ 166 (254)
||++||++||+|+.+|++++..+...+..+
T Consensus 161 ~Al~DA~~ta~l~~~l~~~~~~~~~~~~~~ 190 (207)
T PRK07748 161 CALDDAMTTYNIFKLVEKDKEYLVKPEPPT 190 (207)
T ss_pred ChHHHHHHHHHHHHHHHhCcceeecCCCCc
Confidence 999999999999999999987766555443
No 4
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.93 E-value=1.2e-26 Score=194.62 Aligned_cols=151 Identities=25% Similarity=0.397 Sum_probs=123.2
Q ss_pred CCCeEEEEEEeecCCC--CCCCCCcEEEEceEEEEcCCCeEEEEEEEe--------------------------------
Q 036628 11 DFDYFVVVDFEATCDK--KIPHPQEIIEFPSVIVSGVTGQITVCFQIY-------------------------------- 56 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~--~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~-------------------------------- 56 (254)
+..+++|||||+||.+ ..+...|||||+|.+|+....+++|+||+|
T Consensus 2 ~~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~ 81 (210)
T COG5018 2 TTNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSM 81 (210)
T ss_pred CCceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHH
Confidence 4578999999999998 345789999999999998889999999999
Q ss_pred ehhhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCC-CCchhhhhHHHhcC--CCC-cccH---HHHhcC
Q 036628 57 ALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPS-YFNRWINLRVPFSK--GDV-RCNL---KEAVEL 129 (254)
Q Consensus 57 vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~-~~~~~iDlr~~f~~--~~~-~~~L---~~~l~i 129 (254)
|+.+|..||.++.- ..+-++++||+|||+ .|+++|+.+++. |. +-..++||+..|.. +.. +.+| .+..|+
T Consensus 82 v~E~f~r~L~~h~P-r~~~~wa~wG~~Dm~-~l~q~~~~~~~~-p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~ 158 (210)
T COG5018 82 VFEDFIRKLNEHDP-RKNSTWATWGNMDMK-VLKQNCMFNHIP-PFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGD 158 (210)
T ss_pred HHHHHHHHHHhcCc-ccCCccccccchhHH-HHHHHHHhcCCC-CccccCccchHHHHHHHHhcCCccccHHHHHHHhcc
Confidence 35677778877542 233489999999965 577889999997 43 33489999999988 332 3455 455678
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHcCCccCcCcc
Q 036628 130 GWHGRVHCGLDDSMNIARLLAVIMQRGFKFSITKS 164 (254)
Q Consensus 130 ~~eG~~HrALdDA~ntA~l~~~ll~~g~~f~~~~~ 164 (254)
.++|++|||||||+|++||+..+..+.+.|+++..
T Consensus 159 sf~G~~HraldDArn~~rl~klv~~~~~~~e~~~~ 193 (210)
T COG5018 159 SFTGTHHRALDDARNAYRLFKLVEQDKQYLEKPKP 193 (210)
T ss_pred ccCCchhhhHHHHHHHHHHHHHHcchhhhccCCCC
Confidence 99999999999999999999999999999987765
No 5
>PRK06722 exonuclease; Provisional
Probab=99.93 E-value=5.5e-25 Score=200.14 Aligned_cols=138 Identities=22% Similarity=0.317 Sum_probs=110.7
Q ss_pred CCCCeEEEEEEeecCCCC-CCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------h
Q 036628 10 QDFDYFVVVDFEATCDKK-IPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------L 58 (254)
Q Consensus 10 q~~~~fvViDlEtTg~~~-~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l 58 (254)
+.-+.||||||||||... +...+||||||||+|+..+++++++|++|| +
T Consensus 2 ~~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl 81 (281)
T PRK06722 2 ENATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQII 81 (281)
T ss_pred CCCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHH
Confidence 345789999999996541 235689999999999854458999999993 4
Q ss_pred hhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCC-chhhhhHHHh----cC----CCCcccHHHHhcC
Q 036628 59 FLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYF-NRWINLRVPF----SK----GDVRCNLKEAVEL 129 (254)
Q Consensus 59 ~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~-~~~iDlr~~f----~~----~~~~~~L~~~l~i 129 (254)
.+|.+|+++ +..+|+|+.|| ..||..+|++.|++.|.+. .+|+|+++.+ +. ...+.+|.+++|+
T Consensus 82 ~ef~~fig~------~~lvahna~FD-~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL 154 (281)
T PRK06722 82 EKFIQFIGE------DSIFVTWGKED-YRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGL 154 (281)
T ss_pred HHHHHHHCC------CcEEEEEeHHH-HHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCC
Confidence 566666643 46899999999 7899999999999888543 4689987643 22 2347788899999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHH
Q 036628 130 GWHGRVHCGLDDSMNIARLLAVIMQ 154 (254)
Q Consensus 130 ~~eG~~HrALdDA~ntA~l~~~ll~ 154 (254)
+++|++|||++||++||+|+.+|++
T Consensus 155 ~~~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 155 IWEGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCCCCcCcHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999984
No 6
>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=99.91 E-value=1.4e-23 Score=175.62 Aligned_cols=134 Identities=39% Similarity=0.631 Sum_probs=105.4
Q ss_pred EEEEEEeecCCCCC---CCCCcEEEEceEEEEcCCCeEEEEEEEee--------------------------------hh
Q 036628 15 FVVVDFEATCDKKI---PHPQEIIEFPSVIVSGVTGQITVCFQIYA--------------------------------LF 59 (254)
Q Consensus 15 fvViDlEtTg~~~~---~~~~EIIEIgAV~vD~~~g~iv~~F~~~v--------------------------------l~ 59 (254)
|||||+||||.... ...+||||||||++|..+++++++|++|+ +.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 79999999998721 23589999999999976667899999993 35
Q ss_pred hHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCC-CCCCCchhhhhHHHhcC--C----CCcccHHHHhcCCCC
Q 036628 60 LHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIP-KPSYFNRWINLRVPFSK--G----DVRCNLKEAVELGWH 132 (254)
Q Consensus 60 ~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~-~P~~~~~~iDlr~~f~~--~----~~~~~L~~~l~i~~e 132 (254)
+|.+|++... +..+|+|+.|| ..+|.+++.+.+.. .|+++..|+|++++++. + ..+.+|.+++|++.+
T Consensus 81 ~~~~~l~~~~----~~~~v~~~~~d-~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 155 (176)
T cd06133 81 EFLEWLGKNG----KYAFVTWGDWD-LKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFE 155 (176)
T ss_pred HHHHHHHhCC----CeEEEeecHhh-HHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCC
Confidence 6666665421 37899999999 55666666665543 45678899999998876 2 335668888999998
Q ss_pred CCCCchHHHHHHHHHHHHHHH
Q 036628 133 GRVHCGLDDSMNIARLLAVIM 153 (254)
Q Consensus 133 G~~HrALdDA~ntA~l~~~ll 153 (254)
|++|+||+||++||+|+.+|+
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 156 GRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHhC
Confidence 899999999999999999874
No 7
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.88 E-value=8.1e-22 Score=163.14 Aligned_cols=131 Identities=29% Similarity=0.312 Sum_probs=106.6
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh------------------------------hhHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL------------------------------FLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl------------------------------~~f~~ 63 (254)
+||+||+||||.+ +..+||||||||++|. ++++++|+.|+. .+|.+
T Consensus 1 ~~v~~D~Ettg~~--~~~~~Iieig~v~~~~--~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~ 76 (169)
T smart00479 1 TLVVIDCETTGLD--PGKDEIIEIAAVDVDG--GRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLE 76 (169)
T ss_pred CEEEEEeeCCCCC--CCCCeEEEEEEEEEEC--CEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHH
Confidence 5899999999987 5578999999999984 568899999942 34555
Q ss_pred HhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-----CCCcccHHHHhcCCCCCCCCc
Q 036628 64 WQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-----GDVRCNLKEAVELGWHGRVHC 137 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-----~~~~~~L~~~l~i~~eG~~Hr 137 (254)
|+++ ...+++|+ +|| ..+|++++.+.++..|.. ..|+|+..++.. ..++.+|+++++++..+++|+
T Consensus 77 ~l~~------~~~v~~n~~~fD-~~~L~~~~~~~~~~~~~~-~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~ 148 (169)
T smart00479 77 FLKG------KILVAGNALNFD-LRFLKLEHPRLGIKDPPK-NPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHR 148 (169)
T ss_pred HhcC------CEEEEeCCHHHh-HHHHHHHHHHhCCCCCcC-CCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcC
Confidence 5542 45788888 999 789999999999987743 568888666554 345678889999998887899
Q ss_pred hHHHHHHHHHHHHHHHHcC
Q 036628 138 GLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 138 ALdDA~ntA~l~~~ll~~g 156 (254)
|++||++|++|+.+|++++
T Consensus 149 A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 149 ALDDARATAKLFKKLVERL 167 (169)
T ss_pred cHHHHHHHHHHHHHHHHHh
Confidence 9999999999999998874
No 8
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=2.6e-21 Score=178.67 Aligned_cols=134 Identities=22% Similarity=0.273 Sum_probs=110.3
Q ss_pred CCCCCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------
Q 036628 8 KLQDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------ 57 (254)
Q Consensus 8 ~~q~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------ 57 (254)
..+-++.|||||+||||.+ +..+||||||||+++ +|+++++|++++
T Consensus 3 ~~~~~~~~Vv~DlETTGl~--p~~~eIIEIgaV~v~--~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~ev 78 (313)
T PRK06807 3 NISLPLDYVVIDFETTGFN--PYNDKIIQVAAVKYR--NHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEV 78 (313)
T ss_pred CcCCCCCEEEEEEECCCCC--CCCCeEEEEEEEEEE--CCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHH
Confidence 3456889999999999987 667899999999997 789999999993
Q ss_pred hhhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHH----HhcC--CCCcccHHHHhcCCC
Q 036628 58 LFLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRV----PFSK--GDVRCNLKEAVELGW 131 (254)
Q Consensus 58 l~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~----~f~~--~~~~~~L~~~l~i~~ 131 (254)
+++|.+|++ ++..++||++|| ..||.+++.+.|++.| ...++|... .++. ++++.+|++++|++.
T Consensus 79 l~~f~~fl~------~~~lVaHNa~FD-~~fL~~~~~~~gl~~~--~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~ 149 (313)
T PRK06807 79 LPLFLAFLH------TNVIVAHNASFD-MRFLKSNVNMLGLPEP--KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL 149 (313)
T ss_pred HHHHHHHHc------CCeEEEEcHHHH-HHHHHHHHHHcCCCCC--CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC
Confidence 345566664 356899999999 6899999999999766 345777543 4443 566788999999997
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHcC
Q 036628 132 HGRVHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 132 eG~~HrALdDA~ntA~l~~~ll~~g 156 (254)
++|+|++||++||+|+.+|....
T Consensus 150 --~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 150 --SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred --CCcChHHHHHHHHHHHHHHHHhh
Confidence 79999999999999999999874
No 9
>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=99.86 E-value=7.6e-21 Score=158.72 Aligned_cols=127 Identities=20% Similarity=0.188 Sum_probs=97.6
Q ss_pred EEEEEEeecCCCCCC-CCCcEEEEceEEEEcCCCeE-EEEEEEee------------------------------hhhHH
Q 036628 15 FVVVDFEATCDKKIP-HPQEIIEFPSVIVSGVTGQI-TVCFQIYA------------------------------LFLHD 62 (254)
Q Consensus 15 fvViDlEtTg~~~~~-~~~EIIEIgAV~vD~~~g~i-v~~F~~~v------------------------------l~~f~ 62 (254)
||+||+||||++ + ..++|||||||+++ .+.+ .++|+.|+ +.+|.
T Consensus 1 ~v~~D~ETTGl~--~~~~~~iieig~v~v~--~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~ 76 (167)
T cd06131 1 QIVLDTETTGLD--PREGHRIIEIGCVELI--NRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76 (167)
T ss_pred CEEEEeeCCCCC--CCCCCeEEEEEEEEEE--CCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHH
Confidence 699999999986 4 46799999999997 3444 46899883 34455
Q ss_pred HHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCC-CCchhhhhHHH----hcC-CCCcccHHHHhcCCCCC-CC
Q 036628 63 NWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPS-YFNRWINLRVP----FSK-GDVRCNLKEAVELGWHG-RV 135 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~-~~~~~iDlr~~----f~~-~~~~~~L~~~l~i~~eG-~~ 135 (254)
+|+++ ...+++|++|| ..||.++++++++..+. ....|+|..++ ++. .+++.++.++++++.++ .+
T Consensus 77 ~~l~~------~~lv~hn~~fD-~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~ 149 (167)
T cd06131 77 DFIRG------AELVIHNASFD-VGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTL 149 (167)
T ss_pred HHHCC------CeEEEeChHHh-HHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCC
Confidence 55542 45788999999 78999999998876542 23577886544 332 45677889999998875 48
Q ss_pred CchHHHHHHHHHHHHHH
Q 036628 136 HCGLDDSMNIARLLAVI 152 (254)
Q Consensus 136 HrALdDA~ntA~l~~~l 152 (254)
|+|++||++||+|+.+|
T Consensus 150 H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 150 HGALLDAELLAEVYLEL 166 (167)
T ss_pred CChHHHHHHHHHHHHHh
Confidence 99999999999999876
No 10
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.85 E-value=1.7e-20 Score=168.95 Aligned_cols=129 Identities=19% Similarity=0.212 Sum_probs=103.0
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee-----------------------------hhhHHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA-----------------------------LFLHDNW 64 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v-----------------------------l~~f~~w 64 (254)
.|||||+||||.. +..++|||||||+++ +|+++++|++|+ +.+|..|
T Consensus 69 ~~vv~DiETTG~~--~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~f 144 (257)
T PRK08517 69 VFCFVDIETNGSK--PKKHQIIEIGAVKVK--NGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLF 144 (257)
T ss_pred CEEEEEEeCCCCC--CCCCeEEEEEEEEEE--CCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHHH
Confidence 4999999999976 566799999999996 689999999993 4556666
Q ss_pred hhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhh---hHHH-hcC-CCCcccHHHHhcCCCCCCCCchH
Q 036628 65 QQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWIN---LRVP-FSK-GDVRCNLKEAVELGWHGRVHCGL 139 (254)
Q Consensus 65 l~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iD---lr~~-f~~-~~~~~~L~~~l~i~~eG~~HrAL 139 (254)
++ +...++++++|| ..||.+++++.|+... .+.++| +.+. +.. ++.+.+|++.+|++.+ ++|||+
T Consensus 145 l~------~~v~VaHNa~FD-~~fL~~~l~r~g~~~~--~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~HrAl 214 (257)
T PRK08517 145 LG------DSVFVAHNVNFD-YNFISRSLEEIGLGPL--LNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VHHRAY 214 (257)
T ss_pred HC------CCeEEEECHHHH-HHHHHHHHHHcCCCCC--CCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CCCChH
Confidence 64 356788899999 8899999999887542 344444 4332 333 5667889999999876 799999
Q ss_pred HHHHHHHHHHHHHHHcC
Q 036628 140 DDSMNIARLLAVIMQRG 156 (254)
Q Consensus 140 dDA~ntA~l~~~ll~~g 156 (254)
+||++||+|+..++++.
T Consensus 215 ~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 215 ADALAAYEIFKICLLNL 231 (257)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999999764
No 11
>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=99.85 E-value=2.2e-20 Score=165.08 Aligned_cols=134 Identities=17% Similarity=0.112 Sum_probs=102.7
Q ss_pred eEEEEEEeecCCCCCCC-CCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHH
Q 036628 14 YFVVVDFEATCDKKIPH-PQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHD 62 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~-~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~ 62 (254)
.+||||+||||++ +. .++|||||||.++. ...+.++|+.|+ +.+|.
T Consensus 1 r~vvlD~ETTGl~--p~~~d~IIEIgav~~~~-~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~ 77 (225)
T TIGR01406 1 RQIILDTETTGLD--PKGGHRIVEIGAVELVN-RMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFL 77 (225)
T ss_pred CEEEEEeeCCCcC--CCCCCeEEEEEEEEEEC-CcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHH
Confidence 4899999999987 44 38999999998862 233458999993 34566
Q ss_pred HHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCC--CCCchhhhhH----HHhcC-CCCcccHHHHhcCCCCCC-
Q 036628 63 NWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKP--SYFNRWINLR----VPFSK-GDVRCNLKEAVELGWHGR- 134 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P--~~~~~~iDlr----~~f~~-~~~~~~L~~~l~i~~eG~- 134 (254)
+|++. ...++||++|| ..||..++++.|..++ ..+..|+|.. ..|+. .+.+..|++.+|++..++
T Consensus 78 ~fi~~------~~lVaHNa~FD-~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~ 150 (225)
T TIGR01406 78 DFIGG------SELVIHNAAFD-VGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRT 150 (225)
T ss_pred HHhCC------CEEEEEecHHH-HHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCC
Confidence 66653 45788999999 7899999999985333 2335788853 34544 566788899999988764
Q ss_pred CCchHHHHHHHHHHHHHHHHcCC
Q 036628 135 VHCGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 135 ~HrALdDA~ntA~l~~~ll~~g~ 157 (254)
+|+|++||++||+|+.+|.....
T Consensus 151 ~H~Al~DA~~~a~v~~~l~~~~~ 173 (225)
T TIGR01406 151 LHGALLDAHLLAEVYLALTGGQE 173 (225)
T ss_pred CcCHHHHHHHHHHHHHHHHcCCc
Confidence 79999999999999999987543
No 12
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.84 E-value=1.5e-20 Score=173.60 Aligned_cols=131 Identities=17% Similarity=0.103 Sum_probs=105.3
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh----------------------------hhHHHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL----------------------------FLHDNW 64 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl----------------------------~~f~~w 64 (254)
..|||||+||||++ +..++|||||||++| .+|+++++|++|+. .+|.+|
T Consensus 15 ~~fvvlD~ETTGl~--p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~ 91 (313)
T PRK06063 15 RGWAVVDVETSGFR--PGQARIISLAVLGLD-ADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91 (313)
T ss_pred CCEEEEEEECCCCC--CCCCEEEEEEEEEEE-CCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 56999999999987 666899999999998 47899999999942 233334
Q ss_pred hhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHH----HhcC--CCCcccHHHHhcCCCCCCCCch
Q 036628 65 QQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRV----PFSK--GDVRCNLKEAVELGWHGRVHCG 138 (254)
Q Consensus 65 l~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~----~f~~--~~~~~~L~~~l~i~~eG~~HrA 138 (254)
++ ++..++||+.|| ..||.+++++.++..| .+.++|... .+.. ++++.+|++++|++.. ++|+|
T Consensus 92 l~------~~~lVaHNa~FD-~~fL~~~~~r~g~~~~--~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~-~~H~A 161 (313)
T PRK06063 92 LR------GRTLVAHNVAFD-YSFLAAEAERAGAELP--VDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQ-RPHDA 161 (313)
T ss_pred cC------CCEEEEeCHHHH-HHHHHHHHHHcCCCCC--CCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCC-CCCCc
Confidence 42 467889999999 7899999999999877 234566433 3333 5678899999999864 79999
Q ss_pred HHHHHHHHHHHHHHHHcC
Q 036628 139 LDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 139 LdDA~ntA~l~~~ll~~g 156 (254)
++||+.||+|+.+++++.
T Consensus 162 l~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 162 LDDARVLAGILRPSLERA 179 (313)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999998773
No 13
>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=99.84 E-value=2.2e-20 Score=153.48 Aligned_cols=119 Identities=18% Similarity=0.237 Sum_probs=96.1
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHHH
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDNW 64 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~w 64 (254)
||+||+||||. ..++|||||||+++ +|+++++|+.|+ +.+|.+|
T Consensus 1 ~v~~D~Ettg~----~~~~ii~ig~v~~~--~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~ 74 (156)
T cd06130 1 FVAIDFETANA----DRASACSIGLVKVR--DGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPF 74 (156)
T ss_pred CEEEEEeCCCC----CCCceEEEEEEEEE--CCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHH
Confidence 69999999974 36899999999997 689999999993 3455556
Q ss_pred hhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccHHHHhcCCCCCCCCch
Q 036628 65 QQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNLKEAVELGWHGRVHCG 138 (254)
Q Consensus 65 l~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L~~~l~i~~eG~~HrA 138 (254)
+++ +..++++++|| ..||++++++.|+..|. ..++|+...++. ++++.+|.+++|++.. +|+|
T Consensus 75 l~~------~~lv~hn~~fD-~~~l~~~~~~~g~~~~~--~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~H~A 143 (156)
T cd06130 75 LGG------SLVVAHNASFD-RSVLRAALEAYGLPPPP--YQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--HHDA 143 (156)
T ss_pred hCC------CEEEEeChHHh-HHHHHHHHHHcCCCCCC--CCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--CcCc
Confidence 642 45666677999 78999999999998763 467887665544 3557788999999886 9999
Q ss_pred HHHHHHHHHHHH
Q 036628 139 LDDSMNIARLLA 150 (254)
Q Consensus 139 LdDA~ntA~l~~ 150 (254)
++||++||+|+.
T Consensus 144 l~Da~~ta~l~~ 155 (156)
T cd06130 144 LEDARACAEILL 155 (156)
T ss_pred hHHHHHHHHHHh
Confidence 999999999985
No 14
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.83 E-value=5.6e-20 Score=169.37 Aligned_cols=127 Identities=20% Similarity=0.268 Sum_probs=102.8
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeehh-------------------------------hHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYALF-------------------------------LHD 62 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~-------------------------------~f~ 62 (254)
.|||||+||||. ..++|||||||+++ +|+++++|++|+.| +|.
T Consensus 2 ~~vviD~ETTg~----~~d~IieIgav~v~--~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~ 75 (309)
T PRK06195 2 NFVAIDFETANE----KRNSPCSIGIVVVK--DGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIK 75 (309)
T ss_pred cEEEEEEeCCCC----CCCceEEEEEEEEE--CCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHH
Confidence 599999999964 46899999999996 78999999999533 333
Q ss_pred HHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC--CCCcccHHHHhcCCCCCCCC
Q 036628 63 NWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK--GDVRCNLKEAVELGWHGRVH 136 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~--~~~~~~L~~~l~i~~eG~~H 136 (254)
+|++ ++..++||++|| ..||.++++++++..|. ..|+|. +..|+. ++++.+|++++|+++ .+|
T Consensus 76 ~fl~------~~~lVaHNa~FD-~~fL~~~~~r~~~~~~~--~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~--~~H 144 (309)
T PRK06195 76 HYFN------NNLVIAHNASFD-ISVLRKTLELYNIPMPS--FEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF--KHH 144 (309)
T ss_pred HHhC------CCEEEEECcHHH-HHHHHHHHHHhCCCCCC--CCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC--ccc
Confidence 3332 467899999999 78999999999998773 367775 444554 566888999999985 599
Q ss_pred chHHHHHHHHHHHHHHHHcCC
Q 036628 137 CGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 137 rALdDA~ntA~l~~~ll~~g~ 157 (254)
+|++||++||+|+.+|+++..
T Consensus 145 ~Al~DA~ata~l~~~l~~~~~ 165 (309)
T PRK06195 145 DALADAMACSNILLNISKELN 165 (309)
T ss_pred CCHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999998743
No 15
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.83 E-value=1.2e-19 Score=161.97 Aligned_cols=138 Identities=16% Similarity=0.143 Sum_probs=106.1
Q ss_pred CeEEEEEEeecCCCCCCC-CCcEEEEceEEEEcCCCeE-EEEEEEee------------------------------hhh
Q 036628 13 DYFVVVDFEATCDKKIPH-PQEIIEFPSVIVSGVTGQI-TVCFQIYA------------------------------LFL 60 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~-~~EIIEIgAV~vD~~~g~i-v~~F~~~v------------------------------l~~ 60 (254)
..|||||+||||++ +. .++|||||||.++ ++.+ .++|+.|+ +.+
T Consensus 4 ~r~vvlDtETTGld--p~~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~ 79 (240)
T PRK05711 4 MRQIVLDTETTGLN--QREGHRIIEIGAVELI--NRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADE 79 (240)
T ss_pred CeEEEEEeeCCCcC--CCCCCeEEEEEEEEEE--CCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 36999999999987 44 6899999999996 4554 46899993 345
Q ss_pred HHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCC--Cchhhhh----HHHhcC-CCCcccHHHHhcCCCCC
Q 036628 61 HDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSY--FNRWINL----RVPFSK-GDVRCNLKEAVELGWHG 133 (254)
Q Consensus 61 f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~--~~~~iDl----r~~f~~-~~~~~~L~~~l~i~~eG 133 (254)
|.+|++. ...++||++|| ..||.+++++.|..+|.. +..++|. |..|+. ++.+..|++.++++..+
T Consensus 80 f~~fi~~------~~lVaHNa~FD-~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~ 152 (240)
T PRK05711 80 FLDFIRG------AELIIHNAPFD-IGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSH 152 (240)
T ss_pred HHHHhCC------CEEEEEccHHh-HHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCC
Confidence 5556543 34688999999 689999999998766632 3457775 445555 56678899999998765
Q ss_pred C-CCchHHHHHHHHHHHHHHHHcCCccCc
Q 036628 134 R-VHCGLDDSMNIARLLAVIMQRGFKFSI 161 (254)
Q Consensus 134 ~-~HrALdDA~ntA~l~~~ll~~g~~f~~ 161 (254)
+ +|+||.||+.||+|+.+|+.....|..
T Consensus 153 r~~H~AL~DA~~~A~v~~~l~~~~~~l~~ 181 (240)
T PRK05711 153 RTLHGALLDAEILAEVYLAMTGGQTSLGF 181 (240)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCccccccc
Confidence 4 699999999999999999876554443
No 16
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.83 E-value=5.2e-20 Score=159.45 Aligned_cols=127 Identities=20% Similarity=0.227 Sum_probs=96.6
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEE--EEEEEee------------------------------hhh
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQIT--VCFQIYA------------------------------LFL 60 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv--~~F~~~v------------------------------l~~ 60 (254)
+.|||||+||||.+ +..++|||||||++| .++++ ++|+.|+ +.+
T Consensus 29 ~~~vviD~ETTGl~--~~~d~IieIgaV~~~--~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 29 DEWVALDCETTGLD--PRRAEIVSIAAVKIR--GNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CCEEEEEeECCCCC--CCCCceEEEEEEEEE--CCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 47999999999986 667899999999997 34543 6899983 345
Q ss_pred HHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHH-cCCCCCCCCchhhhhHHHhc--------C---CCCcccHHHHhc
Q 036628 61 HDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRF-KNIPKPSYFNRWINLRVPFS--------K---GDVRCNLKEAVE 128 (254)
Q Consensus 61 f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~-~gi~~P~~~~~~iDlr~~f~--------~---~~~~~~L~~~l~ 128 (254)
|.+|++ +...++++..|| ..||.+++++ .+..+| ..++|+..++. . ++++.++++.+|
T Consensus 105 ~~~~i~------~~~lv~hn~~fD-~~fL~~~~~~~~~~~~~---~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~g 174 (202)
T PRK09145 105 LLAFIG------NRPLVGYYLEFD-VAMLNRYVRPLLGIPLP---NPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLD 174 (202)
T ss_pred HHHHHc------CCeEEEeCHHHH-HHHHHHHHHHhcCCCCC---CCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcC
Confidence 556664 244566677999 7899999986 466554 35677765442 1 245677889999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHH
Q 036628 129 LGWHGRVHCGLDDSMNIARLLAVIMQ 154 (254)
Q Consensus 129 i~~eG~~HrALdDA~ntA~l~~~ll~ 154 (254)
++.. .+|+|++||++||+|+.+|++
T Consensus 175 i~~~-~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 175 LPVL-GRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCC-CCCCcHHHHHHHHHHHHHHHh
Confidence 9886 479999999999999999875
No 17
>PRK05168 ribonuclease T; Provisional
Probab=99.83 E-value=9.2e-20 Score=159.49 Aligned_cols=141 Identities=13% Similarity=0.097 Sum_probs=103.2
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEc-CCCeE--EEEEEEeeh-------------------------------
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSG-VTGQI--TVCFQIYAL------------------------------- 58 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~-~~g~i--v~~F~~~vl------------------------------- 58 (254)
.+|||||+||||++ +..++|||||||+|.. .+|++ +++|++|+.
T Consensus 17 ~~~vv~D~ETTGl~--~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~ 94 (211)
T PRK05168 17 FLPVVIDVETAGFN--AKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKE 94 (211)
T ss_pred CceEEEEeeCCCCC--CCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChHH
Confidence 35899999999987 5678999999999852 24653 589999942
Q ss_pred --hhHHHHhhhcC---CCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCC-chhhhhHHHhcC---CCCcccHHHHhcC
Q 036628 59 --FLHDNWQQHMG---VTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYF-NRWINLRVPFSK---GDVRCNLKEAVEL 129 (254)
Q Consensus 59 --~~f~~wl~~~g---i~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~-~~~iDlr~~f~~---~~~~~~L~~~l~i 129 (254)
.++.+|+.+.- ..++...++|+.+|| ..||.+++++.++..+.+. .+++|...+.+. ...+.++++.+++
T Consensus 95 ~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD-~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~~~L~~l~~~~gl 173 (211)
T PRK05168 95 ALHEIFKMVRKGIKASGCNRAILVAHNAHFD-LSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQTVLAKACQAAGI 173 (211)
T ss_pred HHHHHHHHHHHHHHhcccCCceEEEeccHHh-HHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCCCCHHHHHHHCCC
Confidence 23334443210 011346777789999 7899999999987533222 257887666554 2346778888999
Q ss_pred CCCC-CCCchHHHHHHHHHHHHHHHHcC
Q 036628 130 GWHG-RVHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 130 ~~eG-~~HrALdDA~ntA~l~~~ll~~g 156 (254)
++++ .+|+|++||++||+|+.+|+++.
T Consensus 174 ~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 174 EFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 8754 69999999999999999999874
No 18
>PRK07740 hypothetical protein; Provisional
Probab=99.82 E-value=1.4e-19 Score=161.69 Aligned_cols=135 Identities=19% Similarity=0.187 Sum_probs=103.0
Q ss_pred CCCCC--eEEEEEEeecCCCCCCC-CCcEEEEceEEEEcCCCeE-EEEEEEee---------------------------
Q 036628 9 LQDFD--YFVVVDFEATCDKKIPH-PQEIIEFPSVIVSGVTGQI-TVCFQIYA--------------------------- 57 (254)
Q Consensus 9 ~q~~~--~fvViDlEtTg~~~~~~-~~EIIEIgAV~vD~~~g~i-v~~F~~~v--------------------------- 57 (254)
.+++. .|||||+||||.+ |. .+||||||||++| ++++ .++|+.++
T Consensus 53 ~~~~~~~~~vv~D~ETTGl~--p~~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~ 128 (244)
T PRK07740 53 DIPLTDLPFVVFDLETTGFS--PQQGDEILSIGAVKTK--GGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPL 128 (244)
T ss_pred CCCccCCCEEEEEEeCCCCC--CCCCCeEEEEEEEEEE--CCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCH
Confidence 34545 5999999999986 44 3899999999997 5676 89999992
Q ss_pred ---hhhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccHHHHhc
Q 036628 58 ---LFLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNLKEAVE 128 (254)
Q Consensus 58 ---l~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L~~~l~ 128 (254)
+.+|.+|++ ++..+++|+.|| ..||..++.+... .| +...++|+..+++. .+++.++++++|
T Consensus 129 ~evl~~f~~fi~------~~~lVahna~fD-~~fL~~~~~~~~~-~~-~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~g 199 (244)
T PRK07740 129 AEVLHRFYAFIG------AGVLVAHHAGHD-KAFLRHALWRTYR-QP-FTHRLIDTMFLTKLLAHERDFPTLDDALAYYG 199 (244)
T ss_pred HHHHHHHHHHhC------CCEEEEeCHHHH-HHHHHHHHHHhcC-CC-cCCCeechHHHHHHHcCCCCCCCHHHHHHHCC
Confidence 345555654 356788899999 7899988766432 23 44678887665543 344677888999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHcCC
Q 036628 129 LGWHGRVHCGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 129 i~~eG~~HrALdDA~ntA~l~~~ll~~g~ 157 (254)
++.+| +|+|++||++||+|+.+++.+..
T Consensus 200 i~~~~-~H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 200 IPIPR-RHHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred cCCCC-CCCcHHHHHHHHHHHHHHHHHHH
Confidence 99875 68999999999999999987743
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.82 E-value=1.6e-19 Score=160.08 Aligned_cols=138 Identities=19% Similarity=0.147 Sum_probs=102.4
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee-------------------------------hhhH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA-------------------------------LFLH 61 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v-------------------------------l~~f 61 (254)
..|||||+||||++ +..++|||||+|++| .+|+++++|+.|+ +.+|
T Consensus 6 ~~~vv~D~ETTGl~--p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 6 GPLAAFDLETTGVD--PETARIVTAALVVVD-ADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred CcEEEEEeccCCCC--CCCCeeEEEEEEEEe-CCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 36999999999987 667899999999998 4588889999883 2233
Q ss_pred HHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhc--C-CCCcccHHHHhcCCCCCC
Q 036628 62 DNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFS--K-GDVRCNLKEAVELGWHGR 134 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~--~-~~~~~~L~~~l~i~~eG~ 134 (254)
..++.+. +..+...+++|++|| ..||+++++++|+..+ .-..++|. +...+ . ++++.+|++++|++.+ .
T Consensus 83 ~~~l~~~-~~~~~~lVahNa~FD-~~fL~~~~~r~~~~~~-~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~-~ 158 (232)
T PRK07942 83 ADALREA-WARGVPVVVFNAPYD-LTVLDRELRRHGLPSL-VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD-N 158 (232)
T ss_pred HHHHHHH-hhcCCEEEEeCcHhh-HHHHHHHHHHcCCCCc-cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC-C
Confidence 3344321 112456788999999 7899999999997533 11233442 22222 2 4567889999999986 5
Q ss_pred CCchHHHHHHHHHHHHHHHHcCC
Q 036628 135 VHCGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 135 ~HrALdDA~ntA~l~~~ll~~g~ 157 (254)
+|+|++||++||+|+.+|+++..
T Consensus 159 aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 159 AHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCChHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999988644
No 20
>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=99.82 E-value=2e-19 Score=154.67 Aligned_cols=138 Identities=18% Similarity=0.116 Sum_probs=100.7
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEc-CCCe--EEEEEEEeehh--------------------------------
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSG-VTGQ--ITVCFQIYALF-------------------------------- 59 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~-~~g~--iv~~F~~~vl~-------------------------------- 59 (254)
+||||+||||.+ +..++|||||||+|+. ++|. ++++|++|+.+
T Consensus 7 ~vv~D~ETTGl~--~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 7 PVVVDVETGGFN--PQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred eEEEEecCCCCC--CCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 789999999987 6678999999999962 2454 47899998432
Q ss_pred -hHHHHhhhcC---CCCCCeEEEEcCcccHHHHHHHHHHHcCCC-CCCCCchhhhhHHHhcC---CCCcccHHHHhcCCC
Q 036628 60 -LHDNWQQHMG---VTPTNFAVVTWSDWDCQVMLESECRFKNIP-KPSYFNRWINLRVPFSK---GDVRCNLKEAVELGW 131 (254)
Q Consensus 60 -~f~~wl~~~g---i~~~~~~~vt~g~fD~~~fL~~e~~~~gi~-~P~~~~~~iDlr~~f~~---~~~~~~L~~~l~i~~ 131 (254)
+|.+|+.+.- ..++...++|+++|| ..||++++++.++. .|..-..++|+..+.+. ...+.++++++|+++
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna~FD-~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~~~L~~l~~~~gi~~ 163 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNAHFD-LGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAGIEF 163 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecchhh-HHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCCCcHHHHHHHCCCCC
Confidence 2233332210 012356788899999 78999999999983 33212356887665544 334677889999987
Q ss_pred C-CCCCchHHHHHHHHHHHHHHHHc
Q 036628 132 H-GRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 132 e-G~~HrALdDA~ntA~l~~~ll~~ 155 (254)
+ .++|+|++||+.||+|+.+|+++
T Consensus 164 ~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 164 DNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHHh
Confidence 4 47899999999999999999875
No 21
>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=99.80 E-value=6.5e-19 Score=154.48 Aligned_cols=136 Identities=19% Similarity=0.120 Sum_probs=101.1
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHD 62 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~ 62 (254)
..|||||+||||.+ +..+ |||||||+++ ..+.++++|++|+ +++|.
T Consensus 7 ~~fvv~D~ETTGl~--~~~~-IIeIgav~v~-~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 7 DTETTGDNETTGLY--AGHD-IIEIGAVEII-NRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred cCEEEEEecCCCCC--CCCC-EEEEEEEEEE-CCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 47999999999986 4455 9999999976 3456789999992 34566
Q ss_pred HHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC----CCCcccHHHHhcCCCCC-
Q 036628 63 NWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK----GDVRCNLKEAVELGWHG- 133 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~----~~~~~~L~~~l~i~~eG- 133 (254)
+|++ +...+++|++|| ..||.+++++.+...| ....++|+ +..++. ++.+.+|.+++|++...
T Consensus 83 ~~~~------~~~lVaHNa~FD-~~fL~~~~~r~~~~~~-~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~ 154 (217)
T TIGR00573 83 DYIR------GAELVIHNASFD-VGFLNYEFSKLYKVEP-KTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHR 154 (217)
T ss_pred HHhC------CCEEEEeccHHH-HHHHHHHHHHhcCCCC-CccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCc
Confidence 6664 256788899999 7899999988765432 12344553 223333 33467888999997643
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCccC
Q 036628 134 RVHCGLDDSMNIARLLAVIMQRGFKFS 160 (254)
Q Consensus 134 ~~HrALdDA~ntA~l~~~ll~~g~~f~ 160 (254)
.+|+|++||+.||+|+.+|+++..+..
T Consensus 155 ~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 155 ALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred ccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 589999999999999999999865544
No 22
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.80 E-value=2.7e-20 Score=190.50 Aligned_cols=142 Identities=23% Similarity=0.233 Sum_probs=118.6
Q ss_pred CCCCCC--eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe-----------------------------
Q 036628 8 KLQDFD--YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY----------------------------- 56 (254)
Q Consensus 8 ~~q~~~--~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~----------------------------- 56 (254)
..+..+ .|||+|+||||++ +..+||||||||++ ++|+++++|+.|
T Consensus 414 ~d~~l~datyVVfDiETTGLs--~~~d~iIE~aAvKi--kng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~ 489 (1444)
T COG2176 414 DDQKLDDATYVVFDIETTGLS--PVYDEIIEIAAVKI--KNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIE 489 (1444)
T ss_pred cccccccccEEEEEeecCCcC--cccchhhhheeeee--eCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHH
Confidence 344444 3999999999998 78899999999999 799999999999
Q ss_pred -ehhhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC--CCCcccHHHHhcC
Q 036628 57 -ALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK--GDVRCNLKEAVEL 129 (254)
Q Consensus 57 -vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~--~~~~~~L~~~l~i 129 (254)
|+.+|.+|+++ ...++||++|| ..||+..+.+.++.. +-+..||. |.+|+. ++++.+|++.|++
T Consensus 490 ~vL~kf~~~~~d------~IlVAHNasFD-~gFl~~~~~k~~~~~--~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v 560 (1444)
T COG2176 490 EVLEKFREFIGD------SILVAHNASFD-MGFLNTNYEKYGLEP--LTNPVIDTLELARALNPEFKSHRLGTLCKKLGV 560 (1444)
T ss_pred HHHHHHHHHhcC------cEEEeccCccc-hhHHHHHHHHhCCcc--ccCchhhHHHHHHHhChhhhhcchHHHHHHhCc
Confidence 57788888874 57888999999 589999999988753 44566774 667877 7888999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHcCCccCcCc
Q 036628 130 GWHGRVHCGLDDSMNIARLLAVIMQRGFKFSITK 163 (254)
Q Consensus 130 ~~eG~~HrALdDA~ntA~l~~~ll~~g~~f~~~~ 163 (254)
.++ +||||.+||.+||+|+..|+++..+..++.
T Consensus 561 ~le-~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~ 593 (1444)
T COG2176 561 ELE-RHHRADYDAEATAKVFFVFLKDLKEKGITN 593 (1444)
T ss_pred cHH-HhhhhhhhHHHHHHHHHHHHHHHHHhchhh
Confidence 985 999999999999999999988755555443
No 23
>PRK07883 hypothetical protein; Validated
Probab=99.80 E-value=4.6e-19 Score=174.96 Aligned_cols=132 Identities=20% Similarity=0.190 Sum_probs=106.7
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~ 63 (254)
.|||||+||||.+ +..++|||||||+++ +|+++++|+.|+ +.+|.+
T Consensus 16 ~~Vv~D~ETTGl~--p~~~~IIEIgaV~v~--~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~ 91 (557)
T PRK07883 16 TFVVVDLETTGGS--PAGDAITEIGAVKVR--GGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLE 91 (557)
T ss_pred CEEEEEEecCCCC--CCCCeEEEEEEEEEE--CCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHH
Confidence 7999999999986 667899999999996 788999999993 345555
Q ss_pred HhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhH----HHhcC----CCCcccHHHHhcCCCCCCC
Q 036628 64 WQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLR----VPFSK----GDVRCNLKEAVELGWHGRV 135 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr----~~f~~----~~~~~~L~~~l~i~~eG~~ 135 (254)
|++ +...++||++|| ..||..+|+++|++.|. ..++|.. ..++. ++++.+|.+++|++.+ .+
T Consensus 92 fl~------~~~lVaHNa~FD-~~fL~~~~~r~g~~~~~--~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~-~~ 161 (557)
T PRK07883 92 FAR------GAVLVAHNAPFD-IGFLRAAAARCGYPWPG--PPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT-PT 161 (557)
T ss_pred Hhc------CCEEEEeCcHHH-HHHHHHHHHHcCCCCCC--CCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC-CC
Confidence 664 356777899999 78999999999998762 4667763 34442 4567889999999976 58
Q ss_pred CchHHHHHHHHHHHHHHHHcCCcc
Q 036628 136 HCGLDDSMNIARLLAVIMQRGFKF 159 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~g~~f 159 (254)
|+|++||++||+|+.+++++....
T Consensus 162 H~Al~DA~ata~l~~~l~~~~~~~ 185 (557)
T PRK07883 162 HRALDDARATVDVLHGLIERLGNL 185 (557)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999998875443
No 24
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.80 E-value=1.4e-18 Score=150.70 Aligned_cols=128 Identities=14% Similarity=0.154 Sum_probs=95.5
Q ss_pred CCCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe------------------------------ehh
Q 036628 10 QDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY------------------------------ALF 59 (254)
Q Consensus 10 q~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~------------------------------vl~ 59 (254)
...+.|||||+||||.+ ..+||||||||+++ .|+++++|++| |++
T Consensus 2 ~~~~~~vvlD~EtTGl~---~~~eIIeIgaV~v~--~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~ 76 (195)
T PRK07247 2 KRLETYIAFDLEFNTVN---GVSHIIQVSAVKYD--DHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLA 76 (195)
T ss_pred CcCCeEEEEEeeCCCCC---CCCeEEEEEEEEEE--CCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHH
Confidence 45779999999999986 35799999999996 68889999999 345
Q ss_pred hHHHHhhhcCCCCCCeEEEEcCc-ccHHHHHHHHHHHcCCCCCCCCchhhhh-HHHh-------cC--CCCcccHHHHhc
Q 036628 60 LHDNWQQHMGVTPTNFAVVTWSD-WDCQVMLESECRFKNIPKPSYFNRWINL-RVPF-------SK--GDVRCNLKEAVE 128 (254)
Q Consensus 60 ~f~~wl~~~gi~~~~~~~vt~g~-fD~~~fL~~e~~~~gi~~P~~~~~~iDl-r~~f-------~~--~~~~~~L~~~l~ 128 (254)
+|.+|+++ ...++++.. || ..||.. .|+.++.. .++|+ +..+ +. ++++.+|+++||
T Consensus 77 ~f~~f~~~------~~lVaHNa~~fD-~~fL~~----~g~~~~~~--~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~g 143 (195)
T PRK07247 77 AFKEFVGE------LPLIGYNAQKSD-LPILAE----NGLDLSDQ--YQVDLYDEAFERRSSDLNGIANLKLQTVADFLG 143 (195)
T ss_pred HHHHHHCC------CeEEEEeCcHhH-HHHHHH----cCCCcCCC--ceeehHHHHHHhhccccCCCCCCCHHHHHHhcC
Confidence 67777753 346677776 89 678864 46554321 22332 1121 22 466889999999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHcCC
Q 036628 129 LGWHGRVHCGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 129 i~~eG~~HrALdDA~ntA~l~~~ll~~g~ 157 (254)
++. .+|||++||++||+|+.+|++.+.
T Consensus 144 i~~--~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 144 IKG--RGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CCC--CCcCCHHHHHHHHHHHHHHHhhcc
Confidence 984 589999999999999999998753
No 25
>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=99.79 E-value=1e-18 Score=151.79 Aligned_cols=140 Identities=14% Similarity=0.100 Sum_probs=100.7
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEc-CCCeE--EEEEEEeeh--------------------------------
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSG-VTGQI--TVCFQIYAL-------------------------------- 58 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~-~~g~i--v~~F~~~vl-------------------------------- 58 (254)
.+||||+||||.+ +..++|||||||+|.. .+|++ .++|++++.
T Consensus 9 ~~vv~D~ETTGl~--~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~~ 86 (200)
T TIGR01298 9 LPVVVDVETGGFN--AKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYEA 86 (200)
T ss_pred eeEEEEeeCCCCC--CCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHHH
Confidence 4899999999987 5678999999999852 35666 367998832
Q ss_pred -hhHHHHhhhcC---CCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCC-CchhhhhHHHhcC---CCCcccHHHHhcCC
Q 036628 59 -FLHDNWQQHMG---VTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSY-FNRWINLRVPFSK---GDVRCNLKEAVELG 130 (254)
Q Consensus 59 -~~f~~wl~~~g---i~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~-~~~~iDlr~~f~~---~~~~~~L~~~l~i~ 130 (254)
.++..|+.+.- ..++...++|+.+|| ..||.+++++.++....+ -..++|..++.+. .+.+.++++.+|++
T Consensus 87 ~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD-~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~~~L~~l~~~~gi~ 165 (200)
T TIGR01298 87 LHEIFKVVRKAMKASGCQRAILVGHNANFD-LGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAGXD 165 (200)
T ss_pred HHHHHHHHHHHHHhcccCCCEEEEECchhh-HHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCcccHHHHHHHcCCC
Confidence 22333332110 012456788999999 789999999988742111 1246776555443 34567788999998
Q ss_pred CC-CCCCchHHHHHHHHHHHHHHHHcC
Q 036628 131 WH-GRVHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 131 ~e-G~~HrALdDA~ntA~l~~~ll~~g 156 (254)
.+ -++|||++||+.||+|+.+|+++.
T Consensus 166 ~~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 166 FDSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred ccccchhhhHHhHHHHHHHHHHHHHHH
Confidence 64 369999999999999999999874
No 26
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.79 E-value=1.6e-18 Score=155.52 Aligned_cols=133 Identities=14% Similarity=0.105 Sum_probs=105.4
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHD 62 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~ 62 (254)
..|||||+||||.+ +..++|||||+|+++ .++++++|+.++ +.++.
T Consensus 7 ~~~v~~D~ETTGl~--~~~d~IIEIa~v~v~--~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 7 TEFVCLDCETTGLD--VKKDRIIEFAAIRFT--FDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred CcEEEEEEeCCCCC--CCCCeEEEEEEEEEE--CCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 46999999999986 667899999999997 467889999993 23445
Q ss_pred HHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-----CCCcccHHHHhcCCCCCCCCc
Q 036628 63 NWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-----GDVRCNLKEAVELGWHGRVHC 137 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-----~~~~~~L~~~l~i~~eG~~Hr 137 (254)
+|+++ ..+.+.++.+|| ..||.+++.+.|++.+..-..++|...+.+. ++++..|.+++|++.+ .+|+
T Consensus 83 ~fl~~-----~~~lvghn~~FD-~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~-~aH~ 155 (250)
T PRK06310 83 GFFKE-----GDYIVGHSVGFD-LQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYD-GNHR 155 (250)
T ss_pred HHhCC-----CCEEEEECHHHH-HHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCC-CCcC
Confidence 55532 256777888999 7899999999999876333577887655443 3556778889999876 5899
Q ss_pred hHHHHHHHHHHHHHHHHcC
Q 036628 138 GLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 138 ALdDA~ntA~l~~~ll~~g 156 (254)
|++||+.||+|+..|+++.
T Consensus 156 Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 156 AMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred hHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999764
No 27
>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=99.78 E-value=7.7e-19 Score=141.94 Aligned_cols=121 Identities=26% Similarity=0.236 Sum_probs=94.0
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh------------------------------hhHHHHh
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL------------------------------FLHDNWQ 65 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl------------------------------~~f~~wl 65 (254)
|+||+||||.. +..+||||||+|++|. +++++++|+.|+. .++.+|+
T Consensus 1 v~~D~Ettg~~--~~~~~iiei~~v~~~~-~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l 77 (159)
T cd06127 1 VVFDTETTGLD--PKKDRIIEIGAVKVDG-GIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL 77 (159)
T ss_pred CeEEeeCCCcC--CCCCeEEEEEEEEEEC-CcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 68999999986 6689999999999984 3688999999942 3334444
Q ss_pred hhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccH-HHHhcCCCCCCCCch
Q 036628 66 QHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNL-KEAVELGWHGRVHCG 138 (254)
Q Consensus 66 ~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L-~~~l~i~~eG~~HrA 138 (254)
+ +...+++|+.|| ..+|++++.+++. +.+...|+|+..+++. ++++..+ .++++++. +++|+|
T Consensus 78 ~------~~~~v~~n~~fD-~~~l~~~~~~~~~--~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~H~A 147 (159)
T cd06127 78 G------GRVLVAHNASFD-LRFLNRELRRLGG--PPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPL-EGAHRA 147 (159)
T ss_pred C------CCEEEEeCcHhh-HHHHHHHHHHhCC--CCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCC-CCCCCc
Confidence 3 256777788999 7899999999883 3356789999887665 2334444 67788865 589999
Q ss_pred HHHHHHHHHHH
Q 036628 139 LDDSMNIARLL 149 (254)
Q Consensus 139 LdDA~ntA~l~ 149 (254)
++||++|++|+
T Consensus 148 l~Da~~t~~l~ 158 (159)
T cd06127 148 LADALATAELL 158 (159)
T ss_pred HHHHHHHHHHh
Confidence 99999999987
No 28
>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=99.76 E-value=4e-18 Score=144.60 Aligned_cols=132 Identities=14% Similarity=0.045 Sum_probs=89.6
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeehh-----------------------------------
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYALF----------------------------------- 59 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~----------------------------------- 59 (254)
+|+||+||||++ |..++|||||||++|..+++++++|+.++.+
T Consensus 1 lv~iD~ETTGl~--p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLD--PEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQA 78 (173)
T ss_pred CEEEEEecCCCC--CCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHH
Confidence 589999999987 6779999999999997677889999999532
Q ss_pred --hHHHHhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-CCCcccHHHHhcCCCCCCC
Q 036628 60 --LHDNWQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-GDVRCNLKEAVELGWHGRV 135 (254)
Q Consensus 60 --~f~~wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~~~~~L~~~l~i~~eG~~ 135 (254)
+|.+|+++.. ..+...+++++ +|| ..||++++++.+. + +.++.+|++.+... .....++.+ ++++ .+..
T Consensus 79 l~~~~~f~~~~~-~~~~~~lvgh~~~FD-~~fL~~~~~~~~~--~-~~~~~~D~~~l~~l~~~l~p~~~~-~~~~-~~~~ 151 (173)
T cd06135 79 EAELLEFIKKYV-PKGKSPLAGNSVHQD-RRFLDKYMPELEE--Y-LHYRILDVSSIKELARRWYPEIYR-KAPK-KKGT 151 (173)
T ss_pred HHHHHHHHHHhc-CCCCCceeecchhhC-HHHHHHHHHHHhc--c-CCcchhhHHHHHHHHHHhCcHhhh-cCCC-CCCC
Confidence 2223332210 01134566655 999 7899999988773 2 44556786553211 000011111 3444 4678
Q ss_pred CchHHHHHHHHHHHHHHHHc
Q 036628 136 HCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~ 155 (254)
||||+||+.+++++..+++.
T Consensus 152 HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 152 HRALDDIRESIAELKYYREN 171 (173)
T ss_pred cchHHHHHHHHHHHHHHHHH
Confidence 99999999999999988763
No 29
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.76 E-value=6.6e-18 Score=173.21 Aligned_cols=131 Identities=18% Similarity=0.215 Sum_probs=105.2
Q ss_pred CCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhH
Q 036628 12 FDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLH 61 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f 61 (254)
...|||||+||||.+ + .+||||||||+++ +|+++++|++|+ +++|
T Consensus 6 ~~~~vvvD~ETTGl~--~-~d~IIeIgaV~v~--~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~ 80 (820)
T PRK07246 6 LRKYAVVDLEATGAG--P-NASIIQVGIVIIE--GGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHI 80 (820)
T ss_pred CCCEEEEEEecCCcC--C-CCeEEEEEEEEEE--CCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHH
Confidence 367999999999986 3 4899999999995 789999999993 3455
Q ss_pred HHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC--CCCcccHHHHhcCCCCCCC
Q 036628 62 DNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK--GDVRCNLKEAVELGWHGRV 135 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~--~~~~~~L~~~l~i~~eG~~ 135 (254)
.+|++ +...++||.+|| ..||.+++.+.|+.++ ..++|. +..|+. ++++.+|++++|++.+ ++
T Consensus 81 ~~~l~------~~~lVaHN~~FD-~~fL~~~~~~~g~~~~---~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~-~~ 149 (820)
T PRK07246 81 YDLIE------DCIFVAHNVKFD-ANLLAEALFLEGYELR---TPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLA-DA 149 (820)
T ss_pred HHHhC------CCEEEEECcHHH-HHHHHHHHHHcCCCCC---CCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-CC
Confidence 55554 356788899999 7899999988887654 234553 445665 6778999999999875 79
Q ss_pred CchHHHHHHHHHHHHHHHHcCCc
Q 036628 136 HCGLDDSMNIARLLAVIMQRGFK 158 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~g~~ 158 (254)
|+|++||++||+|+.+|+++...
T Consensus 150 H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 150 HTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999987543
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.76 E-value=6e-18 Score=175.60 Aligned_cols=131 Identities=21% Similarity=0.239 Sum_probs=105.7
Q ss_pred CeEEEEEEeecCCCCCCC-CCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhH
Q 036628 13 DYFVVVDFEATCDKKIPH-PQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLH 61 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~-~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f 61 (254)
+.|||||+||||.+ +. .+||||||||+++ +|+++++|++|+ +++|
T Consensus 3 ~~~vvvD~ETTG~~--p~~~d~IIeigav~v~--~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l 78 (928)
T PRK08074 3 KRFVVVDLETTGNS--PKKGDKIIQIAAVVVE--DGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEI 78 (928)
T ss_pred CCEEEEEEeCCCCC--CCCCCcEEEEEEEEEE--CCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHH
Confidence 57999999999975 33 4799999999995 789999999993 2344
Q ss_pred HHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC--CCCcccHHHHhcCCCCCCC
Q 036628 62 DNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK--GDVRCNLKEAVELGWHGRV 135 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~--~~~~~~L~~~l~i~~eG~~ 135 (254)
.+|++ +...++||+.|| ..||++++.+.|++.+ ...++|. +..|+. ++++.+|.++++++.+ ++
T Consensus 79 ~~~l~------~~~~VaHN~~FD-~~fL~~~~~~~g~~~~--~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~-~~ 148 (928)
T PRK08074 79 VELLE------GAYFVAHNVHFD-LNFLNEELERAGYTEI--HCPKLDTVELARILLPTAESYKLRDLSEELGLEHD-QP 148 (928)
T ss_pred HHHhC------CCeEEEEChHHH-HHHHHHHHHHcCCCCC--CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCC-CC
Confidence 44443 356778899999 7899999999998654 3466775 445665 6778899999999874 89
Q ss_pred CchHHHHHHHHHHHHHHHHcCC
Q 036628 136 HCGLDDSMNIARLLAVIMQRGF 157 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~g~ 157 (254)
|+|++||++||+|+.+|+++..
T Consensus 149 H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 149 HRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred CChHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999998754
No 31
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.76 E-value=7e-18 Score=149.55 Aligned_cols=128 Identities=20% Similarity=0.242 Sum_probs=98.8
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHD 62 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~ 62 (254)
..+||||+||||++ +..++||||||| | +++.++|++++ +++|.
T Consensus 2 ~~~vv~D~ETTGl~--~~~d~IIeig~v--~---~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~ 74 (232)
T PRK06309 2 PALIFYDTETTGTQ--IDKDRIIEIAAY--N---GVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFI 74 (232)
T ss_pred CcEEEEEeeCCCCC--CCCCEEEEEEEE--c---CccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 35999999999987 667899999995 3 24567899882 34566
Q ss_pred HHhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccHHHHhcCCCCCCC
Q 036628 63 NWQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNLKEAVELGWHGRV 135 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L~~~l~i~~eG~~ 135 (254)
+|+++ ....+++|+ +|| ..||.+++++.++..|. ..++|..++++. .+++..|.+.++++. +.+
T Consensus 75 ~fi~~-----~~~lVaHN~~~FD-~~~L~~e~~r~g~~~~~--~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~-~~a 145 (232)
T PRK06309 75 EFCGT-----DNILVAHNNDAFD-FPLLRKECRRHGLEPPT--LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEE-NQA 145 (232)
T ss_pred HHHcC-----CCEEEEeCCHHHH-HHHHHHHHHHcCCCCCC--CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCC-CCC
Confidence 66642 245667774 799 78999999999998763 577887655442 345677888899886 479
Q ss_pred CchHHHHHHHHHHHHHHHHcC
Q 036628 136 HCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~g 156 (254)
|+|++||..||+|+.+|+++.
T Consensus 146 H~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 146 HRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCcHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999764
No 32
>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=99.76 E-value=5.4e-18 Score=178.71 Aligned_cols=133 Identities=21% Similarity=0.225 Sum_probs=108.5
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe------------------------------ehhhHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY------------------------------ALFLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~------------------------------vl~~f~~ 63 (254)
.|||||+||||++ +..++|||||||+++ +|+++++|+.| |+++|.+
T Consensus 191 ~~VVfDiETTGL~--~~~d~IIEIGAVkv~--~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~ 266 (1213)
T TIGR01405 191 TYVVFDIETTGLS--PQYDEIIEFGAVKVK--NGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKE 266 (1213)
T ss_pred cEEEEEeEecCCC--CCCCeEEEEEEEEEE--CCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHH
Confidence 6999999999987 678999999999996 68999999999 3456677
Q ss_pred HhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHh----cC--CCCcccHHHHhcCCCCCCCCc
Q 036628 64 WQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPF----SK--GDVRCNLKEAVELGWHGRVHC 137 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f----~~--~~~~~~L~~~l~i~~eG~~Hr 137 (254)
|++. ...++||+.|| ..||++++++++++. +...++|+..+. +. ++++.+|++++|++.++ +||
T Consensus 267 fl~~------~iLVaHNa~FD-~~fL~~~~~r~g~~~--~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~-~Hr 336 (1213)
T TIGR01405 267 FFKD------SILVAHNASFD-IGFLNTNFEKVGLEP--LENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD-HHR 336 (1213)
T ss_pred HhCC------CeEEEEChHHH-HHHHHHHHHHcCCCc--cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-CcC
Confidence 7753 56788899999 789999999999852 345678764443 33 56678899999999875 999
Q ss_pred hHHHHHHHHHHHHHHHHcCCccC
Q 036628 138 GLDDSMNIARLLAVIMQRGFKFS 160 (254)
Q Consensus 138 ALdDA~ntA~l~~~ll~~g~~f~ 160 (254)
|++||.+||+|+.+|+++..+..
T Consensus 337 Al~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 337 ADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999998754443
No 33
>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=99.76 E-value=9.2e-18 Score=142.91 Aligned_cols=131 Identities=16% Similarity=0.055 Sum_probs=92.6
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEcCC-----------CeEEEEEEEeehh------------------------
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSGVT-----------GQITVCFQIYALF------------------------ 59 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~-----------g~iv~~F~~~vl~------------------------ 59 (254)
|||||+||||++ .+..++|||||||+|+... .+++++|++++.+
T Consensus 1 ~vv~D~ETTGl~-~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~ 79 (177)
T cd06136 1 FVFLDLETTGLP-KHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAP 79 (177)
T ss_pred CeEEeeecCCCC-CCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCC
Confidence 799999999985 1357899999999997321 1367899999321
Q ss_pred -------hHHHHhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-CCCcccHHH-HhcC
Q 036628 60 -------LHDNWQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-GDVRCNLKE-AVEL 129 (254)
Q Consensus 60 -------~f~~wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~~~~~L~~-~l~i 129 (254)
.+.+|++.. .+....++||+ +|| ..||++++++.|+..| .-..++|...+++. ..++..|.+ ++|+
T Consensus 80 ~~~~~~~~l~~f~~~~--~~~~~lVaHNa~~FD-~~fL~~~~~r~~~~~~-~~~~~iDtl~l~r~~~~~L~~l~~~~~~~ 155 (177)
T cd06136 80 FDSDTANLIKLFLRRQ--PKPICLVAHNGNRFD-FPILRSELERLGTKLP-DDILCVDSLPAFRELDQSLGSLYKRLFGQ 155 (177)
T ss_pred ccHHHHHHHHHHHHhc--CCCCEEEEcCCcccC-HHHHHHHHHHcCCCCC-CCCEEEEeHHHHhhhHhhHHHHHHHHhCC
Confidence 122233210 11235788898 899 7899999999998876 23355676555554 224566755 4888
Q ss_pred CCCCCCCchHHHHHHHHHHHHH
Q 036628 130 GWHGRVHCGLDDSMNIARLLAV 151 (254)
Q Consensus 130 ~~eG~~HrALdDA~ntA~l~~~ 151 (254)
+.. .+|+|++||..||+++.+
T Consensus 156 ~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 EPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred Ccc-cccchHHHHHHHHHHHhh
Confidence 864 689999999999999864
No 34
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.75 E-value=1.6e-17 Score=148.14 Aligned_cols=128 Identities=17% Similarity=0.072 Sum_probs=95.4
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeE--EEEEEEeeh------------------------------hhH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQI--TVCFQIYAL------------------------------FLH 61 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~i--v~~F~~~vl------------------------------~~f 61 (254)
.|+|||+||||.+ +..++|||||||+++ .+++ .++|+.++. .+|
T Consensus 48 ~~vviD~ETTGl~--p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l 123 (239)
T PRK09146 48 PFVALDFETTGLD--AEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDEL 123 (239)
T ss_pred CEEEEEeECCCCC--CCCCcEEEEEEEEEE--CCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHH
Confidence 5999999999987 677999999999996 4555 478998832 333
Q ss_pred HHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHc-CCCCCCCCchhhhhHHH----hcC---------------CCCcc
Q 036628 62 DNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFK-NIPKPSYFNRWINLRVP----FSK---------------GDVRC 121 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~-gi~~P~~~~~~iDlr~~----f~~---------------~~~~~ 121 (254)
.++++ ++..++|+..|| ..||++++++. +..++ ..++|..++ ++. .+++.
T Consensus 124 ~~~~~------~~~lVaHna~FD-~~fL~~~l~~~~~~~~~---~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~ 193 (239)
T PRK09146 124 LEALA------GKVVVVHYRRIE-RDFLDQALRNRIGEGIE---FPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLA 193 (239)
T ss_pred HHHhC------CCEEEEECHHHH-HHHHHHHHHHhcCCCCC---CceechHHHHHHHcccccccccchhccCCCCCCCHH
Confidence 33432 357888999999 89999999864 33332 245664332 211 12456
Q ss_pred cHHHHhcCCCCCCCCchHHHHHHHHHHHHHHHHcC
Q 036628 122 NLKEAVELGWHGRVHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 122 ~L~~~l~i~~eG~~HrALdDA~ntA~l~~~ll~~g 156 (254)
++.+++|++.. .+|+|++||+.||+|+..+++..
T Consensus 194 ~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 194 DSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred HHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Confidence 78889999864 68999999999999999999875
No 35
>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=99.74 E-value=2.2e-17 Score=170.01 Aligned_cols=129 Identities=21% Similarity=0.209 Sum_probs=102.7
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~ 63 (254)
.|||||+||||.+ +..+||||||||+++ +|+++++|+.|+ ++++.+
T Consensus 1 ~~vvvD~ETTG~~--~~~~~IIeig~v~v~--~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~ 76 (850)
T TIGR01407 1 RYAVVDLETTGTQ--LSFDKIIQIGIVVVE--DGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYD 76 (850)
T ss_pred CEEEEEEECCCCC--CCCCeEEEEEEEEEE--CCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHH
Confidence 3899999999986 667999999999995 789999999993 234444
Q ss_pred HhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhh---h-HHHhcC--CCCcccHHHHhcCCCCCCCCc
Q 036628 64 WQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWIN---L-RVPFSK--GDVRCNLKEAVELGWHGRVHC 137 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iD---l-r~~f~~--~~~~~~L~~~l~i~~eG~~Hr 137 (254)
|++ +...++||.+|| ..||.+++++.|++.. ...++| + +..++. ++++.+|++++|++.+ ++|+
T Consensus 77 ~l~------~~~~VahN~~fD-~~fL~~~~~~~g~~~~--~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~~H~ 146 (850)
T TIGR01407 77 LLE------DGIFVAHNVHFD-LNFLAKALKDCGYEPL--PKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-NPHR 146 (850)
T ss_pred HhC------CCEEEEeCcHHH-HHHHHHHHHHcCCCCC--CCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-CCCC
Confidence 443 356777889999 7899999999998632 234455 4 334444 6778899999999875 6999
Q ss_pred hHHHHHHHHHHHHHHHHcC
Q 036628 138 GLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 138 ALdDA~ntA~l~~~ll~~g 156 (254)
|++||++||+|+.+|+++.
T Consensus 147 Al~DA~ata~l~~~l~~~~ 165 (850)
T TIGR01407 147 ADSDAQATAELLLLLFEKM 165 (850)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 9999999999999998764
No 36
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.74 E-value=5.2e-17 Score=152.08 Aligned_cols=130 Identities=18% Similarity=0.190 Sum_probs=101.4
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee----------------------------hhhHHHHh
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA----------------------------LFLHDNWQ 65 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v----------------------------l~~f~~wl 65 (254)
.||||||||||++ +..++|||||||+++ .+|+++++|++|+ +++|.+|+
T Consensus 47 ~fVvlDiETTGLd--p~~drIIeIgAV~i~-~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~fL 123 (377)
T PRK05601 47 PFVAVSIQTSGIH--PSTSRLITIDAVTLT-ADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLI 123 (377)
T ss_pred CEEEEEEECCCCC--CCCCeEEEEEEEEEE-cCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHHh
Confidence 5999999999987 778999999999997 4789999999993 44555566
Q ss_pred hhcCCCCCCeEEEEcCcccHHHHHHHHHHHcC----------------------------CCCCCCCchhhhh----HHH
Q 036628 66 QHMGVTPTNFAVVTWSDWDCQVMLESECRFKN----------------------------IPKPSYFNRWINL----RVP 113 (254)
Q Consensus 66 ~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~g----------------------------i~~P~~~~~~iDl----r~~ 113 (254)
+ +...++|+..|| +.||.+++++.. ++.| +.++|. |+.
T Consensus 124 ~------g~vLVaHNA~FD-~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p---~~~iDTL~LARrl 193 (377)
T PRK05601 124 D------GRTLILHNAPRT-WGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKP---VVIVDTLATARRQ 193 (377)
T ss_pred C------CCEEEEECcHHH-HHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCC---CCEEEhHHHHHHH
Confidence 4 357899999999 789999987641 2222 345663 556
Q ss_pred hcC--CCCcccHHHHhcCCC---------CCCCCchH--HHHHHHHHHHHHHHHcC
Q 036628 114 FSK--GDVRCNLKEAVELGW---------HGRVHCGL--DDSMNIARLLAVIMQRG 156 (254)
Q Consensus 114 f~~--~~~~~~L~~~l~i~~---------eG~~HrAL--dDA~ntA~l~~~ll~~g 156 (254)
++. ++++.+|+++||++. -...|++| |||+.+|+|+.++.+.+
T Consensus 194 ~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~~ 249 (377)
T PRK05601 194 GVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRASG 249 (377)
T ss_pred cCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhccC
Confidence 655 688999999999976 13678988 79999999999874443
No 37
>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=99.70 E-value=9e-17 Score=137.31 Aligned_cols=125 Identities=15% Similarity=0.115 Sum_probs=87.3
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh---------------------------------hhHH
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL---------------------------------FLHD 62 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl---------------------------------~~f~ 62 (254)
++||+||||++ +..++|||||||++|. +++++++|+.++. ++|.
T Consensus 1 ~~~D~ETTGl~--~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~ 77 (183)
T cd06138 1 LFYDYETFGLN--PSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIH 77 (183)
T ss_pred CEEEeecCCCC--CCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHH
Confidence 58999999987 6678999999999973 4466689999942 2222
Q ss_pred HHhhhcCCCCCCeEEEEc-CcccHHHHHHHHHHHcCCCCCC--C--Cchh---hhhHHH-h---c-----------C-CC
Q 036628 63 NWQQHMGVTPTNFAVVTW-SDWDCQVMLESECRFKNIPKPS--Y--FNRW---INLRVP-F---S-----------K-GD 118 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt~-g~fD~~~fL~~e~~~~gi~~P~--~--~~~~---iDlr~~-f---~-----------~-~~ 118 (254)
.|+++ .+...++++ .+|| ..||++++++.++..+. + .+.+ +++.+. + + . ++
T Consensus 78 ~~~~~----~~~~lVahn~~~FD-~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~ 152 (183)
T cd06138 78 RLFNT----PGTCIVGYNNIRFD-DEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSF 152 (183)
T ss_pred HHHcc----CCCcEEeeCchhhH-HHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcch
Confidence 33321 123556666 5899 78999999999875321 1 1122 344332 2 1 1 34
Q ss_pred CcccHHHHhcCCCCCCCCchHHHHHHHHHHH
Q 036628 119 VRCNLKEAVELGWHGRVHCGLDDSMNIARLL 149 (254)
Q Consensus 119 ~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~ 149 (254)
++.+|++++|++. ..+|+|++||+.||+|+
T Consensus 153 ~L~~l~~~~gi~~-~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 153 KLEDLAQANGIEH-SNAHDALSDVEATIALA 182 (183)
T ss_pred hHHHHHHHCCCCc-cccccHHHHHHHHHHHh
Confidence 5778899999987 47999999999999986
No 38
>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=99.69 E-value=1.6e-17 Score=134.38 Aligned_cols=125 Identities=25% Similarity=0.267 Sum_probs=89.8
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee--------------------------------hhhHHH
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA--------------------------------LFLHDN 63 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v--------------------------------l~~f~~ 63 (254)
||||+||||.+ +..++|||||+|+++....+++++|++|+ +.+|.+
T Consensus 1 v~~D~Ettg~~--~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLD--PRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSST--TTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCC--CCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhh
Confidence 79999999987 56799999999999966555889999993 345566
Q ss_pred HhhhcCCCCCCeEEEE-cCcccHHHHHHHHHHHc-CCCCC---CCCchhhhhHHHhcC--CCCcccHHHHhcCCCCCCCC
Q 036628 64 WQQHMGVTPTNFAVVT-WSDWDCQVMLESECRFK-NIPKP---SYFNRWINLRVPFSK--GDVRCNLKEAVELGWHGRVH 136 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt-~g~fD~~~fL~~e~~~~-gi~~P---~~~~~~iDlr~~f~~--~~~~~~L~~~l~i~~eG~~H 136 (254)
|+.+. ..+|. +..|| ..+|...+.+. +...| .+++.....+..++. ..++..|++.++++..+++|
T Consensus 79 ~~~~~------~~~v~~n~~fd-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~H 151 (164)
T PF00929_consen 79 FLKKN------DILVGHNASFD-IGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTAH 151 (164)
T ss_dssp HHHHH------TEEEETTCCHE-EESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTTT
T ss_pred hhhcc------cccccccccch-hhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCCc
Confidence 66532 35555 56888 56777777665 34333 123332223444444 34567889999999888899
Q ss_pred chHHHHHHHHHHH
Q 036628 137 CGLDDSMNIARLL 149 (254)
Q Consensus 137 rALdDA~ntA~l~ 149 (254)
+|++||++||+|+
T Consensus 152 ~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 152 DALDDARATAELF 164 (164)
T ss_dssp SHHHHHHHHHHHH
T ss_pred ChHHHHHHHhCcC
Confidence 9999999999986
No 39
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.65 E-value=1.8e-15 Score=138.91 Aligned_cols=138 Identities=20% Similarity=0.173 Sum_probs=95.3
Q ss_pred CCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcC-CC---eEEEEEEEeehh---------------------------h
Q 036628 12 FDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGV-TG---QITVCFQIYALF---------------------------L 60 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~-~g---~iv~~F~~~vl~---------------------------~ 60 (254)
-..+||||+||||++ +..++|||||+|+++.. +| +++++|+.|+-+ .
T Consensus 36 ~~~~vvlD~ETTGLd--~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~~ 113 (294)
T PRK09182 36 VRLGVILDTETTGLD--PRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA 113 (294)
T ss_pred CCeEEEEEeeCCCCC--CCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHHH
Confidence 357999999999987 67799999999999732 34 457899999421 2
Q ss_pred HHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC--CCCcccHHHHhcCCCCCCCCch
Q 036628 61 HDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK--GDVRCNLKEAVELGWHGRVHCG 138 (254)
Q Consensus 61 f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~--~~~~~~L~~~l~i~~eG~~HrA 138 (254)
+.+|++ ..+.+++||+.|| +.||++.+....- .+ +..+...+...... ++++.+|++++|. . ..+|||
T Consensus 114 l~~fl~-----~~~vlVAHNA~FD-~~fL~~~~~~~~~-~~-~~ct~~~i~~~~~~~~~~kL~~La~~~g~-~-~~aHrA 183 (294)
T PRK09182 114 VDALIA-----PADLIIAHNAGFD-RPFLERFSPVFAT-KP-WACSVSEIDWSARGFEGTKLGYLAGQAGF-F-HEGHRA 183 (294)
T ss_pred HHHHhc-----CCCEEEEeCHHHH-HHHHHHHHHhccC-Cc-ccccHHHHhhccccCCCCCHHHHHHHcCC-C-CCCcCh
Confidence 222322 2356788999999 8899877654321 23 23232223221222 5678889999994 3 368999
Q ss_pred HHHHHHHHHHHHHHHHcCCccCc
Q 036628 139 LDDSMNIARLLAVIMQRGFKFSI 161 (254)
Q Consensus 139 LdDA~ntA~l~~~ll~~g~~f~~ 161 (254)
++||+.|++|+..++........
T Consensus 184 l~Da~Ata~ll~~~l~~~~~~~l 206 (294)
T PRK09182 184 VDDCQALLELLARPLPETGQPPL 206 (294)
T ss_pred HHHHHHHHHHHHHHHhhcCCcCH
Confidence 99999999999988876543343
No 40
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.63 E-value=4.3e-15 Score=131.03 Aligned_cols=122 Identities=21% Similarity=0.168 Sum_probs=88.8
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeehhhH--HHHhhh-cCC------------------CCC
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYALFLH--DNWQQH-MGV------------------TPT 73 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~~f--~~wl~~-~gi------------------~~~ 73 (254)
++|||+||||.+ .+|||||+|.|. +|+++++|++|+.+.- .....+ +|| .++
T Consensus 2 ~~vlD~ETTGl~-----~~IieIg~v~v~--~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~~~~ 74 (219)
T PRK07983 2 LRVIDTETCGLQ-----GGIVEIASVDVI--DGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGS 74 (219)
T ss_pred eEEEEEECCCCC-----CCCEEEEEEEEE--CCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHHHcCC
Confidence 899999999975 249999999984 7899999999953311 000000 122 134
Q ss_pred CeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC-CCCcccHHHHhcCCC----CCCCCchHHHHHH
Q 036628 74 NFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK-GDVRCNLKEAVELGW----HGRVHCGLDDSMN 144 (254)
Q Consensus 74 ~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~-~~~~~~L~~~l~i~~----eG~~HrALdDA~n 144 (254)
...++||.+|| +.||.. . ...|+|. |..++. .+.+.+|++.++++. ...+|||++||+.
T Consensus 75 ~~lVaHNa~FD-~~~L~~------~-----~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~a 142 (219)
T PRK07983 75 EWYVAHNASFD-RRVLPE------M-----PGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYI 142 (219)
T ss_pred CEEEEeCcHhh-HHHHhC------c-----CCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHH
Confidence 67899999999 788852 1 1345664 456665 566778999999854 2479999999999
Q ss_pred HHHHHHHHHHc
Q 036628 145 IARLLAVIMQR 155 (254)
Q Consensus 145 tA~l~~~ll~~ 155 (254)
||.|+.+|++.
T Consensus 143 ta~ll~~l~~~ 153 (219)
T PRK07983 143 TAALLIDIMNT 153 (219)
T ss_pred HHHHHHHHHHH
Confidence 99999999975
No 41
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.62 E-value=1.7e-15 Score=161.85 Aligned_cols=132 Identities=19% Similarity=0.167 Sum_probs=105.3
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~ 63 (254)
.|||+|+||||.+ +..++|||||||+++ +|+++++|+.|+ +.+|.+
T Consensus 420 ~~VVfDLETTGL~--~~~deIIEIgAV~V~--~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~~ 495 (1437)
T PRK00448 420 TYVVFDVETTGLS--AVYDEIIEIGAVKIK--NGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKE 495 (1437)
T ss_pred cEEEEEhhhcCCC--CchhhhheeeeEEEe--CCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHHHH
Confidence 5999999999987 678999999999996 789999999993 234444
Q ss_pred HhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHH----hcC--CCCcccHHHHhcCCCCCCCCc
Q 036628 64 WQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVP----FSK--GDVRCNLKEAVELGWHGRVHC 137 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~----f~~--~~~~~~L~~~l~i~~eG~~Hr 137 (254)
|++ +...++||+.|| ..||+.++++.|++.+ ...++|.-.+ ++. .+++.+|++.+|+..+ .+||
T Consensus 496 fig------g~vLVAHNa~FD-~~fL~~~l~rlgl~~l--~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~-~~Hr 565 (1437)
T PRK00448 496 FCG------DSILVAHNASFD-VGFINTNYEKLGLEKI--KNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELE-HHHR 565 (1437)
T ss_pred HhC------CCEEEEeCcccc-HHHHHHHHHHcCCccc--cccceeHHHHHHHHcCccccccHHHHHHHcCCCCC-CCcC
Confidence 443 357889999999 7899999999988543 4466775433 333 4567789999999886 4799
Q ss_pred hHHHHHHHHHHHHHHHHcCCcc
Q 036628 138 GLDDSMNIARLLAVIMQRGFKF 159 (254)
Q Consensus 138 ALdDA~ntA~l~~~ll~~g~~f 159 (254)
|++||++||+|+.+|+++....
T Consensus 566 Al~DA~aTa~lf~~ll~~l~~~ 587 (1437)
T PRK00448 566 ADYDAEATAYLLIKFLKDLKEK 587 (1437)
T ss_pred hHHHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999998875433
No 42
>PRK05359 oligoribonuclease; Provisional
Probab=99.61 E-value=5.8e-15 Score=126.51 Aligned_cols=133 Identities=14% Similarity=0.017 Sum_probs=86.9
Q ss_pred CCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEE-EEEEEee---------------------------------
Q 036628 12 FDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQIT-VCFQIYA--------------------------------- 57 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv-~~F~~~v--------------------------------- 57 (254)
.+.|||||+||||++ |..++|||||||++|. +.+++ +.|+.++
T Consensus 2 ~~~~vvlD~ETTGLd--p~~d~IieIgaV~~~~-~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 2 EDNLIWIDLEMTGLD--PERDRIIEIATIVTDA-DLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred CCcEEEEEeecCCCC--CCCCeEEEEEEEEEcC-CceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 467999999999987 7789999999999973 33444 5577763
Q ss_pred ----hhhHHHHhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-CCCcccHHHHhcCCC
Q 036628 58 ----LFLHDNWQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-GDVRCNLKEAVELGW 131 (254)
Q Consensus 58 ----l~~f~~wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~~~~~L~~~l~i~~ 131 (254)
+.+|.+|++..-. .+...+|+++ .|| ..||++.+.+.+..+ -++++|+.++... .....++ .++++.
T Consensus 79 ~~e~~~~~l~fl~~~~~-~~~~~l~g~~v~FD-~~FL~~~~~~~~~~l---~~~~~Dv~tl~~l~r~~~P~~--~~~~~~ 151 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVP-AGKSPLCGNSIGQD-RRFLARYMPELEAYF---HYRNLDVSTLKELARRWKPEI--LNGFKK 151 (181)
T ss_pred HHHHHHHHHHHHHHhcC-CCCCceeecchhhC-HHHHHHHHHHhcccC---CCcccchhHHHHHHHHhChhh--hhCCCC
Confidence 2333334432111 1234567765 999 789999987766543 3456675433211 0001112 346665
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHc
Q 036628 132 HGRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 132 eG~~HrALdDA~ntA~l~~~ll~~ 155 (254)
+ ..|||++||+.+.+.+....+.
T Consensus 152 ~-~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 152 Q-GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred c-CCcccHHHHHHHHHHHHHHHHH
Confidence 5 4799999999999998887765
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.60 E-value=1.6e-14 Score=127.71 Aligned_cols=131 Identities=22% Similarity=0.241 Sum_probs=102.4
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEE-EEEeeh------------------------------hhH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVC-FQIYAL------------------------------FLH 61 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~-F~~~vl------------------------------~~f 61 (254)
..+||||+||||.+ +..++|||||||.+ .++++++. |+.|+- ++|
T Consensus 13 ~~~vv~D~ETtg~~--~~~~~iieIgav~~--~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~ 88 (243)
T COG0847 13 TRFVVIDLETTGLN--PKKDRIIEIGAVTL--EDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEF 88 (243)
T ss_pred CcEEEEecccCCCC--CCCCceEEEEeEEE--ECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHH
Confidence 47999999999986 56899999999999 47888855 999932 333
Q ss_pred HHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC--CCCcccHHHHhcCCCC-CC
Q 036628 62 DNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK--GDVRCNLKEAVELGWH-GR 134 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~--~~~~~~L~~~l~i~~e-G~ 134 (254)
.+|+.. ....++|+..|| ..||..++.+.++..+ ...++|. |..++. .+.+..|++.+|++.. ..
T Consensus 89 ~~~i~~-----~~~~Vahna~fD-~~fl~~~~~~~~~~~~--~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~ 160 (243)
T COG0847 89 LDFIGG-----LRLLVAHNAAFD-VGFLRVESERLGIEIP--GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFH 160 (243)
T ss_pred HHHHCC-----CCeEEEEchhhc-HHHHHHHHHHcCCCcc--cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcC
Confidence 344432 157888999999 7899999999999876 3344443 445555 4557789999999743 36
Q ss_pred CCchHHHHHHHHHHHHHHHHc
Q 036628 135 VHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 135 ~HrALdDA~ntA~l~~~ll~~ 155 (254)
+|+|+.||..+|.++..+...
T Consensus 161 ~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 161 PHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CcchHHHHHHHHHHHHHHHhc
Confidence 799999999999999999885
No 44
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.55 E-value=1.3e-13 Score=133.78 Aligned_cols=137 Identities=11% Similarity=0.015 Sum_probs=94.3
Q ss_pred CCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeehh-------------------------------
Q 036628 11 DFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYALF------------------------------- 59 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~------------------------------- 59 (254)
.-..|||+|+||||.+ |..++|||||||++|.....+.+.|+.|+.+
T Consensus 4 ~~~~fvv~D~ETTGLd--P~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 4 MQPTFLWHDYETFGAN--PALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred CCCcEEEEEEECCCCC--CCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 3456999999999987 7789999999999984333555779988322
Q ss_pred --hHHHHhhhcCCCCCCeEEEEc-CcccHHHHHHHHHHHcCCCC-------CCCCchhhhhHH-Hhc-------------
Q 036628 60 --LHDNWQQHMGVTPTNFAVVTW-SDWDCQVMLESECRFKNIPK-------PSYFNRWINLRV-PFS------------- 115 (254)
Q Consensus 60 --~f~~wl~~~gi~~~~~~~vt~-g~fD~~~fL~~e~~~~gi~~-------P~~~~~~iDlr~-~f~------------- 115 (254)
++.+++.. .+.+.+.++ .+|| ..||++++.++.+.. +......+|+.. .+.
T Consensus 82 ~~~i~~~l~~----~~~~lVGhNni~FD-~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~ 156 (476)
T PRK11779 82 AARIHAEFSQ----PGTCILGYNNIRFD-DEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENED 156 (476)
T ss_pred HHHHHHHHhc----CCCEEEEeCchhhc-HHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCccccc
Confidence 12222210 134555555 4799 789998887665431 000114466533 332
Q ss_pred --CCCCcccHHHHhcCCCCCCCCchHHHHHHHHHHHHHHHHc
Q 036628 116 --KGDVRCNLKEAVELGWHGRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 116 --~~~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~~~ll~~ 155 (254)
.++++.+|.+++|++. +.+|+|++||+.|+.|+..|.++
T Consensus 157 g~~s~rLe~L~~~~gI~~-~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 157 GLPSFKLEHLTKANGIEH-ENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCCcHHHHHHHcCCCC-CCCCCcHHHHHHHHHHHHHHHHh
Confidence 1356788999999986 47999999999999999988876
No 45
>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=99.50 E-value=4.4e-14 Score=118.48 Aligned_cols=112 Identities=17% Similarity=0.138 Sum_probs=78.4
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh-------------------------------------
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL------------------------------------- 58 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl------------------------------------- 58 (254)
||||+||||.+ +..++|||||||.+ ++|+++ |++|+.
T Consensus 1 v~lD~EttGl~--~~~d~ii~Ig~V~v--~~g~i~--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~ 74 (161)
T cd06137 1 VALDCEMVGLA--DGDSEVVRISAVDV--LTGEVL--IDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAAR 74 (161)
T ss_pred CEEEeeeeeEc--CCCCEEEEEEEEEc--CCCeEE--EeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHH
Confidence 68999999987 56789999999999 578875 888831
Q ss_pred hhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC---------CCCcccHHHH-hc
Q 036628 59 FLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK---------GDVRCNLKEA-VE 128 (254)
Q Consensus 59 ~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~---------~~~~~~L~~~-l~ 128 (254)
++|.+|++ ++...+.|+..|| ..||+.. ...++|...+++. ++++.+|++. +|
T Consensus 75 ~~~~~~i~-----~~~vlVgHn~~fD-~~fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~ 137 (161)
T cd06137 75 AALWKFID-----PDTILVGHSLQND-LDALRMI-----------HTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLG 137 (161)
T ss_pred HHHHHhcC-----CCcEEEeccHHHH-HHHHhCc-----------CCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCC
Confidence 12333332 1256777889999 6899631 1245676555543 1335566765 68
Q ss_pred CCCC--CCCCchHHHHHHHHHHHH
Q 036628 129 LGWH--GRVHCGLDDSMNIARLLA 150 (254)
Q Consensus 129 i~~e--G~~HrALdDA~ntA~l~~ 150 (254)
++.. ..+|+|++||++||+|+.
T Consensus 138 ~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 138 LKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred chhcCCCCCCCcHHHHHHHHHHhC
Confidence 7652 368999999999999873
No 46
>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=99.46 E-value=2.2e-13 Score=113.07 Aligned_cols=114 Identities=16% Similarity=0.154 Sum_probs=75.3
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHHHh
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDNWQ 65 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~wl 65 (254)
||||+||||.+ +. ++++||++|.+....|+++ |++|+ ++++.+|+
T Consensus 1 v~lD~EttGl~--~~-~~~~~i~~v~~v~~~~~~~--~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l 75 (152)
T cd06144 1 VALDCEMVGVG--PD-GSESALARVSIVNEDGNVV--YDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL 75 (152)
T ss_pred CEEEEEeeccc--CC-CCEEEEEEEEEEeCCCCEE--EEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHh
Confidence 68999999986 32 3788887664332355554 88883 34555555
Q ss_pred hhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhH------HHhc-CCCCcccHHHH-hcCCCCCCCCc
Q 036628 66 QHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLR------VPFS-KGDVRCNLKEA-VELGWHGRVHC 137 (254)
Q Consensus 66 ~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr------~~f~-~~~~~~~L~~~-l~i~~eG~~Hr 137 (254)
+ ++..++||..|| ..||. +..|. ..++|.. ..+. .++++.+|++. +|++..+.+|+
T Consensus 76 ~------~~vlVgHn~~fD-~~~L~-------~~~~~--~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~ 139 (152)
T cd06144 76 K------GRILVGHALKND-LKVLK-------LDHPK--KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHS 139 (152)
T ss_pred C------CCEEEEcCcHHH-HHHhc-------CcCCC--ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcC
Confidence 4 356788899999 67886 22231 2334432 2221 14556677776 69887657999
Q ss_pred hHHHHHHHHHHHH
Q 036628 138 GLDDSMNIARLLA 150 (254)
Q Consensus 138 ALdDA~ntA~l~~ 150 (254)
|++||++||+|++
T Consensus 140 Al~DA~at~~l~~ 152 (152)
T cd06144 140 SVEDARAAMRLYR 152 (152)
T ss_pred cHHHHHHHHHHhC
Confidence 9999999999974
No 47
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.44 E-value=4.7e-14 Score=94.84 Aligned_cols=44 Identities=30% Similarity=0.716 Sum_probs=39.9
Q ss_pred eeeecCcccccceeccCCCCCCCceeecCCCCCCCCCccccccccCC
Q 036628 208 RYCFCGAKSFKKIIRKPGPKCGSFFFGCGNLTPNKGACCNYFHSATA 254 (254)
Q Consensus 208 ~~c~cg~~~~~~~~~~~gp~~g~~f~~c~~~~~~~~~~c~~f~w~~~ 254 (254)
|+|.||..+.+.+++|.|+|+||.||+|+++.. +.|+||+|+|.
T Consensus 1 p~C~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~---~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKCPCGEPAVRRTSKKTGPNPGRRFYKCPNYKD---KGCNFFQWEDE 44 (45)
T ss_pred CCCCCCCEeEEEEEeCCCCCCCCcceECCCCCC---CCcCCEEeccC
Confidence 589999999999999899999999999998744 67999999983
No 48
>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=99.39 E-value=1.3e-12 Score=109.43 Aligned_cols=114 Identities=14% Similarity=0.062 Sum_probs=77.3
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------------------hhhHHHHh
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------------------LFLHDNWQ 65 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------------------l~~f~~wl 65 (254)
||||+||||.+......||++|++|.+ +|+++ |++|| ++++.+++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~---~g~~~--~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l 75 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNY---HGDVL--YDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL 75 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeC---CCCEE--EEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc
Confidence 689999999971112478888888876 46665 88883 34444454
Q ss_pred hhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhh------HHH--hcC--CCCcccHHHHh---cCCCC
Q 036628 66 QHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINL------RVP--FSK--GDVRCNLKEAV---ELGWH 132 (254)
Q Consensus 66 ~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDl------r~~--f~~--~~~~~~L~~~l---~i~~e 132 (254)
+ ++..++|+..|| ..||..+ .|. ..++|+ ++. |+. ++++..|++.+ +++..
T Consensus 76 ~------~~vlV~Hn~~~D-~~~l~~~-------~~~--~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~ 139 (157)
T cd06149 76 K------GKVVVGHAIHND-FKALKYF-------HPK--HMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVG 139 (157)
T ss_pred C------CCEEEEeCcHHH-HHHhccc-------CCC--cCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCC
Confidence 3 467888899999 5788743 121 112332 222 443 46677888888 56654
Q ss_pred CCCCchHHHHHHHHHHHH
Q 036628 133 GRVHCGLDDSMNIARLLA 150 (254)
Q Consensus 133 G~~HrALdDA~ntA~l~~ 150 (254)
++.|+|+.||++||+|++
T Consensus 140 ~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 140 RQGHSSVEDARATMELYK 157 (157)
T ss_pred CCCcCcHHHHHHHHHHhC
Confidence 578999999999999873
No 49
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.33 E-value=4.6e-12 Score=105.22 Aligned_cols=110 Identities=15% Similarity=0.055 Sum_probs=76.9
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee-------------------------------hhhHHHH
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA-------------------------------LFLHDNW 64 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v-------------------------------l~~f~~w 64 (254)
+++|.||||.. ..+|||||++|.+ +|++ .|++|+ +++|.+|
T Consensus 1 ~~iD~E~~g~~---~g~ei~~i~~v~~---~~~~--~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~f 72 (150)
T cd06145 1 FALDCEMCYTT---DGLELTRVTVVDE---NGKV--VLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSL 72 (150)
T ss_pred CEEeeeeeeec---CCCEEEEEEEEeC---CCCE--EEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHH
Confidence 58999999986 2399999999976 3444 488883 2355555
Q ss_pred hhhcCCCCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC------CCCcccHHHHh-cCCC--CCCC
Q 036628 65 QQHMGVTPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK------GDVRCNLKEAV-ELGW--HGRV 135 (254)
Q Consensus 65 l~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~------~~~~~~L~~~l-~i~~--eG~~ 135 (254)
++. +...+.|+.+|| ..||+.. ..+++|...+++. ++++.+|++.+ ++.. .+.+
T Consensus 73 l~~-----~~vlVgHn~~fD-~~fL~~~-----------~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~ 135 (150)
T cd06145 73 ISP-----DTILVGHSLEND-LKALKLI-----------HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGG 135 (150)
T ss_pred hCC-----CCEEEEcChHHH-HHHhhcc-----------CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCC
Confidence 531 356777899999 6788631 1346776666554 24567788765 5433 2478
Q ss_pred CchHHHHHHHHHHHH
Q 036628 136 HCGLDDSMNIARLLA 150 (254)
Q Consensus 136 HrALdDA~ntA~l~~ 150 (254)
|||++||+.||+|+.
T Consensus 136 H~Al~DA~~t~~l~~ 150 (150)
T cd06145 136 HDSVEDARAALELVK 150 (150)
T ss_pred CCcHHHHHHHHHHhC
Confidence 999999999999873
No 50
>PHA02570 dexA exonuclease; Provisional
Probab=99.28 E-value=1.8e-11 Score=107.48 Aligned_cols=136 Identities=13% Similarity=0.084 Sum_probs=95.0
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe---------------------------------------
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY--------------------------------------- 56 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~--------------------------------------- 56 (254)
+|||+||.|.. ...-||+||||.+|..++ ++.+|+.+
T Consensus 4 lMIDlETmG~~---p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L 79 (220)
T PHA02570 4 FIIDFETFGNT---PDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNL 79 (220)
T ss_pred EEEEeeccCCC---CCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhc
Confidence 79999999864 678999999999998766 67888754
Q ss_pred -----------ehhhHHHHhhhcCCCCCCeEEEEcC-cccHHHHHHHHHHHc----C--CCCCCCCchhhhhHHHhcCC-
Q 036628 57 -----------ALFLHDNWQQHMGVTPTNFAVVTWS-DWDCQVMLESECRFK----N--IPKPSYFNRWINLRVPFSKG- 117 (254)
Q Consensus 57 -----------vl~~f~~wl~~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~----g--i~~P~~~~~~iDlr~~f~~~- 117 (254)
++.+|.+|+.+++.......+-++| +|| ..+|+..+++. + ++.||.|.+..|+|+.....
T Consensus 80 ~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD-~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~~ 158 (220)
T PHA02570 80 KPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFD-FPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEATL 158 (220)
T ss_pred cCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccC-HHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhhh
Confidence 2467777887765332223344444 799 78999999887 7 78899898889999976541
Q ss_pred -CCcccHHHHhcCCCCC-CCCchHHHHHHHHHHHHHHHHcC
Q 036628 118 -DVRCNLKEAVELGWHG-RVHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 118 -~~~~~L~~~l~i~~eG-~~HrALdDA~ntA~l~~~ll~~g 156 (254)
.+-.+++..-.=..+| .+|.||.||-+=|..+..-.+.-
T Consensus 159 l~r~~~~cp~~~g~l~gfv~H~sihDcakd~lml~y~~rya 199 (220)
T PHA02570 159 LTRGMTTCPLPKGTLDGFVAHDSIHDCAKDILMLIYAKRYA 199 (220)
T ss_pred ccCCcccCCCcCccccchhhcccHHHHHHHHHHHHHHHHHh
Confidence 1111222211111245 79999999998887766655553
No 51
>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=99.00 E-value=3.2e-09 Score=81.87 Aligned_cols=94 Identities=21% Similarity=0.210 Sum_probs=70.9
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeehhhHHHHhhhcCCCCCCeEEEEcCcccHHHHHHHHHHH
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVMLESECRF 95 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL~~e~~~ 95 (254)
+++|+||||.+ +..+||++|++...+ +++ +|... |.+|+++.. ....+.++++|| ..||+++|++
T Consensus 1 ~~~DiEt~~~~--~~~~~i~~i~~~~~~--~~~---~~~~~----f~~~l~~~~---~~v~V~hn~~fD-~~fL~~~~~~ 65 (96)
T cd06125 1 IAIDTEATGLD--GAVHEIIEIALADVN--PED---TAVID----LKDILRDKP---LAILVGHNGSFD-LPFLNNRCAE 65 (96)
T ss_pred CEEEEECCCCC--CCCCcEEEEEEEEcc--CCC---EEEeh----HHHHHhhCC---CCEEEEeCcHHh-HHHHHHHHHH
Confidence 57999999987 678999999998653 122 23322 888998632 123444456999 6899999999
Q ss_pred cCCCCCCCCchhhhhHHHhcCCCCcccHHHHhcCCCCCCCCchHHHHHHHHHH
Q 036628 96 KNIPKPSYFNRWINLRVPFSKGDVRCNLKEAVELGWHGRVHCGLDDSMNIARL 148 (254)
Q Consensus 96 ~gi~~P~~~~~~iDlr~~f~~~~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l 148 (254)
++++.|.+...++|+.++ |+.||+++.+|
T Consensus 66 ~~~~~p~~~~~~lDT~~l------------------------~~~~~~~~~~~ 94 (96)
T cd06125 66 LGLKYPLLAGSWIDTIKL------------------------AADDVENTLQI 94 (96)
T ss_pred cCCCCCCcCCcEEEehHH------------------------hhhhHHHHHHh
Confidence 999988667788998753 89999988876
No 52
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.39 E-value=2.3e-06 Score=72.19 Aligned_cols=136 Identities=17% Similarity=0.159 Sum_probs=80.2
Q ss_pred CCCCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe-------ehhhHHHHhhh-c---CC-------
Q 036628 9 LQDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY-------ALFLHDNWQQH-M---GV------- 70 (254)
Q Consensus 9 ~q~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~-------vl~~f~~wl~~-~---gi------- 70 (254)
.+..+++|=||+|+||++ +..+.||||++++-|. +..++++=-.+ ++...++|..+ + |+
T Consensus 2 ~~~~~nLiWIDlEMTGLd--~~~drIIEiA~iVTD~-~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S 78 (184)
T COG1949 2 SANKNNLIWIDLEMTGLD--PERDRIIEIATIVTDA-NLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKAS 78 (184)
T ss_pred CCcCCceEEEeeeeccCC--cCcceEEEEEEEEecC-cccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHh
Confidence 357889999999999997 8889999999999994 45554432222 34555666643 1 21
Q ss_pred -------------------CCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCC-CchhhhhHHHhcC-CCCcccHHHHhc
Q 036628 71 -------------------TPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSY-FNRWINLRVPFSK-GDVRCNLKEAVE 128 (254)
Q Consensus 71 -------------------~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~-~~~~iDlr~~f~~-~~~~~~L~~~l~ 128 (254)
..+...++.|+ .-| ++||.++.=.. -.| ..+++|+.++--. +.-...+.. +
T Consensus 79 ~~t~~~aE~~~l~flkkwvp~~~spicGNSI~qD-RrFl~r~MP~L----e~yfHYR~lDVSTlKELa~RW~P~i~~--~ 151 (184)
T COG1949 79 TVTEAEAEAQTLDFLKKWVPKGVSPICGNSIAQD-RRFLFRYMPKL----EAYFHYRYLDVSTLKELARRWNPEILA--G 151 (184)
T ss_pred hccHHHHHHHHHHHHHHhCCCCCCCCccchhhHH-HHHHHHHhhhH----HHHhhhHhhhHHHHHHHHHhhCcHhhh--c
Confidence 12334566665 468 78886543111 112 3477786553211 000011111 2
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHc
Q 036628 129 LGWHGRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 129 i~~eG~~HrALdDA~ntA~l~~~ll~~ 155 (254)
...+..|+||+|.+---.=++...+.
T Consensus 152 -~~K~~~H~Al~DI~ESI~EL~~YR~~ 177 (184)
T COG1949 152 -FKKGGTHRALDDIRESIAELRYYREH 177 (184)
T ss_pred -cccccchhHHHHHHHHHHHHHHHHHH
Confidence 23567999999998755555544443
No 53
>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=98.38 E-value=1.8e-06 Score=71.48 Aligned_cols=102 Identities=14% Similarity=0.060 Sum_probs=52.6
Q ss_pred EEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEeeh---------hhHHHHhhhcCCCCCCeEEEEcC-cccH
Q 036628 16 VVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYAL---------FLHDNWQQHMGVTPTNFAVVTWS-DWDC 85 (254)
Q Consensus 16 vViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl---------~~f~~wl~~~gi~~~~~~~vt~g-~fD~ 85 (254)
|++|+||||+. +..+.|+-||++.+|...... |..+.. .++.+++.+. +.++..+| .||
T Consensus 1 l~~DIET~Gl~--~~~~~i~liG~~~~~~~~~~~---~~~~~~~~~~ee~~~~~~~~~l~~~-----~~iv~yng~~FD- 69 (164)
T PF13482_consen 1 LFFDIETTGLS--PDNDTIYLIGVADFDDDEIIT---FIQWFAEDPDEEEIILEFFELLDEA-----DNIVTYNGKNFD- 69 (164)
T ss_dssp --EEEEESS-G--G-G---EEEEEEE-ETTTTE----EEEE-GGGHHHHHHHHH--HHHHTT-------EEESSTTTTH-
T ss_pred CcEEecCCCCC--CCCCCEEEEEEEEeCCCceEE---eeHhhccCcHHHHHHHHHHHHHhcC-----CeEEEEeCcccC-
Confidence 68999999987 556789999999998533332 655532 2222445442 23333354 899
Q ss_pred HHHHHHHHHHcCCCCCCCCchhhhhHHHhcC----CCCcccHHHHhcCCC
Q 036628 86 QVMLESECRFKNIPKPSYFNRWINLRVPFSK----GDVRCNLKEAVELGW 131 (254)
Q Consensus 86 ~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~----~~~~~~L~~~l~i~~ 131 (254)
..+|++-+.+++++. -..++||.+...+ ++++.++++.+|+.+
T Consensus 70 ~p~L~~~~~~~~~~~---~~~~iDl~~~~~~~~~~~~~Lk~ve~~lg~~~ 116 (164)
T PF13482_consen 70 IPFLKRRAKRYGLPP---PFNHIDLLKIIKKHFLESYSLKNVEKFLGIER 116 (164)
T ss_dssp HHHHHHHH-HHHH-----GGGEEEHHHHHT-TTSCCTT--SHHH------
T ss_pred HHHHHHHHHHcCCCc---ccchhhHHHHHHhccCCCCCHHHHhhhccccc
Confidence 789998886666653 4577999887765 446678888888755
No 54
>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=98.14 E-value=6.4e-05 Score=64.40 Aligned_cols=79 Identities=15% Similarity=0.063 Sum_probs=54.3
Q ss_pred EEEEEeecCCCC--CCCCCcEEEEceEEEEcCCCeEE-EEEE--E---------------e-----ehhhHHHHhhhcCC
Q 036628 16 VVVDFEATCDKK--IPHPQEIIEFPSVIVSGVTGQIT-VCFQ--I---------------Y-----ALFLHDNWQQHMGV 70 (254)
Q Consensus 16 vViDlEtTg~~~--~~~~~EIIEIgAV~vD~~~g~iv-~~F~--~---------------~-----vl~~f~~wl~~~gi 70 (254)
+++|+|||+..+ .+..+|||+||++.. .+|+.. -.+. . + .+.+|.+++++..
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~--~~g~~~~~~~~~~~~~~~~~~i~~~~v~~~~~E~~lL~~f~~~i~~~d- 78 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADS--FDGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREYD- 78 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEe--eCCceeeEEEeecccCCcCCCCCCceEEEeCCHHHHHHHHHHHHHhcC-
Confidence 689999999743 356799999999887 234432 1111 0 1 3678888887632
Q ss_pred CCCCeEEEEcC-cccHHHHHHHHHHHcCCCC
Q 036628 71 TPTNFAVVTWS-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 71 ~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~ 100 (254)
-+.++.+|+ .|| ..||...++..|++.
T Consensus 79 --pdiivg~N~~~FD-~~~L~~R~~~~~~~~ 106 (199)
T cd05160 79 --PDILTGYNIDDFD-LPYLLKRAEALGIKL 106 (199)
T ss_pred --CCEEEEeccCCCc-HHHHHHHHHHhCCCc
Confidence 234555577 799 689998899988876
No 55
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=97.90 E-value=6.7e-06 Score=81.59 Aligned_cols=42 Identities=31% Similarity=0.649 Sum_probs=37.3
Q ss_pred ceeeeecCcccccceeccCCCCCCCceeecCCCCCCCCCcccccccc
Q 036628 206 EFRYCFCGAKSFKKIIRKPGPKCGSFFFGCGNLTPNKGACCNYFHSA 252 (254)
Q Consensus 206 ~~~~c~cg~~~~~~~~~~~gp~~g~~f~~c~~~~~~~~~~c~~f~w~ 252 (254)
....|.||-++..++|.|.|||-||.||.|..- +.|+||.|+
T Consensus 717 ~~~~c~c~~ra~~l~v~k~~~nrGR~f~sc~~~-----k~c~ff~w~ 758 (758)
T KOG1956|consen 717 EEVTCGCGTRAVKLLVAKTEPNRGRKFYSCLPE-----KSCNFFAWE 758 (758)
T ss_pred cccccCCcchhhhhhhhccCccCCCCCcccCCC-----CCcceEeeC
Confidence 347999999999999999999999999999742 449999996
No 56
>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=97.72 E-value=0.0003 Score=61.55 Aligned_cols=94 Identities=12% Similarity=0.128 Sum_probs=62.9
Q ss_pred CCCcEEEEceEEEEcCCCeEE-EEEEEe----ehhhHHHHhhhcCCCCCCeEEEE-cC-cccHHHHHHHHHHHcCCCCCC
Q 036628 30 HPQEIIEFPSVIVSGVTGQIT-VCFQIY----ALFLHDNWQQHMGVTPTNFAVVT-WS-DWDCQVMLESECRFKNIPKPS 102 (254)
Q Consensus 30 ~~~EIIEIgAV~vD~~~g~iv-~~F~~~----vl~~f~~wl~~~gi~~~~~~~vt-~g-~fD~~~fL~~e~~~~gi~~P~ 102 (254)
..+.||-||++..+..++.+. -..... .+.+|.+++++. .. .+|+ || .|| ..+|..-+..+|++.|.
T Consensus 49 ~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~----~p-~lv~yNg~~FD-lP~L~~Ra~~~gi~~p~ 122 (208)
T cd05782 49 PFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKK----NP-RLVSFNGRGFD-LPVLHLRALIHGVSAPA 122 (208)
T ss_pred ccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHh----CC-EEEecCCCcCC-HHHHHHHHHHhCCCCcc
Confidence 478999999999864344321 111111 467888888764 13 5777 45 699 68999889999998885
Q ss_pred CCc--------------hhhhhHHHhcC-----CCCcccHHHHhcC
Q 036628 103 YFN--------------RWINLRVPFSK-----GDVRCNLKEAVEL 129 (254)
Q Consensus 103 ~~~--------------~~iDlr~~f~~-----~~~~~~L~~~l~i 129 (254)
++. +.+||-..++. ++++..+++++|+
T Consensus 123 ~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG~ 168 (208)
T cd05782 123 YFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGI 168 (208)
T ss_pred ccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCC
Confidence 442 26887666554 3446677788887
No 57
>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=97.62 E-value=0.00054 Score=59.02 Aligned_cols=81 Identities=12% Similarity=0.096 Sum_probs=55.0
Q ss_pred eEEEEEEeecCCCC--CCCCCcEEEEceEEEEcCCCeEEEEEEEe----ehhhHHHHhhhcCCCCCCeEEEEcC--cccH
Q 036628 14 YFVVVDFEATCDKK--IPHPQEIIEFPSVIVSGVTGQITVCFQIY----ALFLHDNWQQHMGVTPTNFAVVTWS--DWDC 85 (254)
Q Consensus 14 ~fvViDlEtTg~~~--~~~~~EIIEIgAV~vD~~~g~iv~~F~~~----vl~~f~~wl~~~gi~~~~~~~vt~g--~fD~ 85 (254)
..+.+|+||++..+ ++..+.||-||++..|. ..++. ..+.- .+.+|.+++.+.. .-++++|. .||
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g-~~~~~-~~~~~~E~~lL~~F~~~i~~~d----Pd~i~gyN~~~FD- 76 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNG-DVEFI-LAEGLDDRKIIREFVKYVKEYD----PDIIVGYNSNAFD- 76 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCC-CEEEE-EecCCCHHHHHHHHHHHHHHcC----CCEEEecCCCcCc-
Confidence 46899999996543 34578999999977542 11221 11001 4678888998742 23677864 699
Q ss_pred HHHHHHHHHHcCCCCC
Q 036628 86 QVMLESECRFKNIPKP 101 (254)
Q Consensus 86 ~~fL~~e~~~~gi~~P 101 (254)
..+|..-|+.+|+.++
T Consensus 77 lpyl~~Ra~~~gi~~~ 92 (188)
T cd05781 77 WPYLVERARVLGVKLD 92 (188)
T ss_pred HHHHHHHHHHhCCCcc
Confidence 6799888999998765
No 58
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=97.60 E-value=0.00037 Score=59.67 Aligned_cols=55 Identities=20% Similarity=0.189 Sum_probs=40.7
Q ss_pred CCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe------ehhhHHHHhhh
Q 036628 11 DFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY------ALFLHDNWQQH 67 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~------vl~~f~~wl~~ 67 (254)
-++.+|=||+|+||++ ...+.||||++++-|..-..+.+-+... ++....+|..+
T Consensus 24 l~q~lVWiD~EMTGLd--vekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~e 84 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLD--VEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIE 84 (208)
T ss_pred ccCceEEEeeeccccc--cccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHH
Confidence 3567999999999997 5689999999999985444444445444 45666777755
No 59
>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=97.42 E-value=0.0061 Score=52.51 Aligned_cols=80 Identities=11% Similarity=0.086 Sum_probs=53.6
Q ss_pred eEEEEEEeecCCCC--CCCCCcEEEEceEEEEcCCCeEEEEEE--------Ee-----ehhhHHHHhhhcCCCCCCeEEE
Q 036628 14 YFVVVDFEATCDKK--IPHPQEIIEFPSVIVSGVTGQITVCFQ--------IY-----ALFLHDNWQQHMGVTPTNFAVV 78 (254)
Q Consensus 14 ~fvViDlEtTg~~~--~~~~~EIIEIgAV~vD~~~g~iv~~F~--------~~-----vl~~f~~wl~~~gi~~~~~~~v 78 (254)
..+.||+|||+..+ .+..++||.||.+.. ..++++ .+. .+ .+.+|.+++.+.. .-+++
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~~~~-~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~d----pdiiv 76 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGNKVI-TWKKFDLPFVEVVKTEKEMIKRFIEIVKEKD----PDVIY 76 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCceEE-EecCCCCCeEEEeCCHHHHHHHHHHHHHHcC----CCEEE
Confidence 46889999996543 346799999998663 233332 221 12 3567888887632 22566
Q ss_pred Ec-C-cccHHHHHHHHHHHcCCCCC
Q 036628 79 TW-S-DWDCQVMLESECRFKNIPKP 101 (254)
Q Consensus 79 t~-g-~fD~~~fL~~e~~~~gi~~P 101 (254)
+| | .|| ..+|..-+..+|+++|
T Consensus 77 gyN~~~FD-~pyL~~R~~~~gi~~~ 100 (195)
T cd05780 77 TYNGDNFD-FPYLKKRAEKLGIELD 100 (195)
T ss_pred ecCCCCCc-HHHHHHHHHHhCCCCc
Confidence 65 4 699 6799888899999866
No 60
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.31 E-value=0.00088 Score=59.14 Aligned_cols=137 Identities=18% Similarity=0.161 Sum_probs=90.6
Q ss_pred eEEEEEEeecCCC-C------------------CCCCCcEEEEceEEEEcCCCeEEE----E----EEEeeh------hh
Q 036628 14 YFVVVDFEATCDK-K------------------IPHPQEIIEFPSVIVSGVTGQITV----C----FQIYAL------FL 60 (254)
Q Consensus 14 ~fvViDlEtTg~~-~------------------~~~~~EIIEIgAV~vD~~~g~iv~----~----F~~~vl------~~ 60 (254)
.||.+|.|.-|.- + +.+.-.+|++|.-+.| ++|++-+ + |+.|-+ .+
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd-~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~~ 103 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSD-EKGNLPDCGTDTWQFNFSDFNLEKDMYAQD 103 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeec-cCCCCCCCCCceeEEecccCCchhhccchh
Confidence 4888888865432 1 1145679999999999 4565543 3 343411 12
Q ss_pred HHHHhhhcCC-------------------------CCCCeEEEE-cCcccHHHHHHHHHHHcCCCCCC-----------C
Q 036628 61 HDNWQQHMGV-------------------------TPTNFAVVT-WSDWDCQVMLESECRFKNIPKPS-----------Y 103 (254)
Q Consensus 61 f~~wl~~~gi-------------------------~~~~~~~vt-~g~fD~~~fL~~e~~~~gi~~P~-----------~ 103 (254)
-.++|+++|| .+++..||| .|.+| ..+|-+-+.. -++|. +
T Consensus 104 SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YD-fgYLlK~Lt~--~~LP~~~~eF~~~v~~~ 180 (239)
T KOG0304|consen 104 SIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYD-FGYLLKILTG--KPLPETEEEFFEIVRQL 180 (239)
T ss_pred hHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccch-HHHHHHHHcC--CCCcchHHHHHHHHHHH
Confidence 2344444433 145788999 68999 6777665544 44452 2
Q ss_pred CchhhhhHHHhcC--C----CCcccHHHHhcCCCCCCCCchHHHHHHHHHHHHHHHH
Q 036628 104 FNRWINLRVPFSK--G----DVRCNLKEAVELGWHGRVHCGLDDSMNIARLLAVIMQ 154 (254)
Q Consensus 104 ~~~~iDlr~~f~~--~----~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~~~ll~ 154 (254)
|....|++.+..- + +.+..+++.|+++-.|..|.|=.|++.||+++.+|.+
T Consensus 181 fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 181 FPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred cchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 3455677766543 2 2245678889998899999999999999999999875
No 61
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=97.28 E-value=0.006 Score=55.09 Aligned_cols=134 Identities=21% Similarity=0.280 Sum_probs=75.2
Q ss_pred eEEEEEEeecCCC-CCC------------------CCCcEEEEceEEEEcCCCeEEEEEEEe-------------ehh--
Q 036628 14 YFVVVDFEATCDK-KIP------------------HPQEIIEFPSVIVSGVTGQITVCFQIY-------------ALF-- 59 (254)
Q Consensus 14 ~fvViDlEtTg~~-~~~------------------~~~EIIEIgAV~vD~~~g~iv~~F~~~-------------vl~-- 59 (254)
.||.||+|.||.. ... ..--||+||...+..++++....|..+ .-.
T Consensus 23 ~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~s 102 (262)
T PF04857_consen 23 DFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQASS 102 (262)
T ss_dssp SEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHHH
T ss_pred CEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecchh
Confidence 4999999999997 221 456799999999933566664443333 101
Q ss_pred ---------hHHHHhhh-------------------cCC-----CCCCeEEEEcCcccHHHHHHHHHHHcCCCCCCCCch
Q 036628 60 ---------LHDNWQQH-------------------MGV-----TPTNFAVVTWSDWDCQVMLESECRFKNIPKPSYFNR 106 (254)
Q Consensus 60 ---------~f~~wl~~-------------------~gi-----~~~~~~~vt~g~fD~~~fL~~e~~~~gi~~P~~~~~ 106 (254)
.|.+|+.+ .++ ..+..+|.|+|-.|+ .+|-+.+ .| ++|.-...
T Consensus 103 l~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl-~~l~~~f--~~-~LP~t~~e 178 (262)
T PF04857_consen 103 LQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDL-MYLYKKF--IG-PLPETLEE 178 (262)
T ss_dssp HHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHH-HHHHHHH--TT-S--SSHHH
T ss_pred HHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHH-HHHHHHh--cC-CCCCCHHH
Confidence 22222211 111 122456666899994 5665533 34 77855444
Q ss_pred hhh-hHHHhcC-----------C---CCcccHHHHhcCCC-----------------------CCC-CCchHHHHHHHHH
Q 036628 107 WIN-LRVPFSK-----------G---DVRCNLKEAVELGW-----------------------HGR-VHCGLDDSMNIAR 147 (254)
Q Consensus 107 ~iD-lr~~f~~-----------~---~~~~~L~~~l~i~~-----------------------eG~-~HrALdDA~ntA~ 147 (254)
|.. ++..|+. . ..+..|.+.++..- .|. .|.|=.||..|+.
T Consensus 179 F~~~~~~~FP~i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~ 258 (262)
T PF04857_consen 179 FKELLRELFPRIYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGC 258 (262)
T ss_dssp HHHHHHHHSSSEEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHHH
T ss_pred HHHHHHHHCcccccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHHH
Confidence 433 2444443 1 12345556665432 344 9999999999999
Q ss_pred HHHH
Q 036628 148 LLAV 151 (254)
Q Consensus 148 l~~~ 151 (254)
++.+
T Consensus 259 ~F~~ 262 (262)
T PF04857_consen 259 VFIK 262 (262)
T ss_dssp HHHH
T ss_pred HHcC
Confidence 9864
No 62
>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=97.17 E-value=0.0021 Score=62.54 Aligned_cols=109 Identities=11% Similarity=0.174 Sum_probs=77.7
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe----------ehhhHHHHhhhcCCCCCCeEEEEcCc
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY----------ALFLHDNWQQHMGVTPTNFAVVTWSD 82 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~----------vl~~f~~wl~~~gi~~~~~~~vt~g~ 82 (254)
...+.|||||+ |+..-.--||++..| .++..++|+.| ++.+|.+|+... .+..++|++.
T Consensus 284 ~~~~ffDiEt~-----P~~~~~yL~G~~~~~--~~~~~~~~~~fla~~~~~E~~~~~~f~~~l~~~----~~~~i~hY~~ 352 (457)
T TIGR03491 284 PGELIFDIESD-----PDENLDYLHGFLVVD--KGQENEKYRPFLAEDPNTEELAWQQFLQLLQSY----PDAPIYHYGE 352 (457)
T ss_pred CccEEEEecCC-----CCCCCceEEEEEEec--CCCCCcceeeeecCCchHHHHHHHHHHHHHHHC----CCCeEEeeCH
Confidence 45788999999 455677899997764 34333458877 467899998763 2458999999
Q ss_pred ccHHHHHHHHHHHcCCCCC---CCCchhhhhHHHhcC-------CCCcccHHHHhcCCCCC
Q 036628 83 WDCQVMLESECRFKNIPKP---SYFNRWINLRVPFSK-------GDVRCNLKEAVELGWHG 133 (254)
Q Consensus 83 fD~~~fL~~e~~~~gi~~P---~~~~~~iDlr~~f~~-------~~~~~~L~~~l~i~~eG 133 (254)
+- ...|++-+.+++..-. .+..+++||-...+. ++.+.+++..+|.++..
T Consensus 353 ~e-~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~~~~ 412 (457)
T TIGR03491 353 TE-KDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFEWRQ 412 (457)
T ss_pred HH-HHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCcccCC
Confidence 98 7789888888887521 234578888654443 46677788888887653
No 63
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.16 E-value=0.0062 Score=54.87 Aligned_cols=132 Identities=11% Similarity=0.065 Sum_probs=74.6
Q ss_pred CCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee-hhh-----HHHHhhhcCCCCCCeEEEE-cC-cc
Q 036628 12 FDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA-LFL-----HDNWQQHMGVTPTNFAVVT-WS-DW 83 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v-l~~-----f~~wl~~~gi~~~~~~~vt-~g-~f 83 (254)
=++++-||+||||++ ...+-|+=.|...+. .+++.- =+.+. -++ +..|+..- +-..+|| || .|
T Consensus 97 ~e~~~FFDiETTGL~--~ag~~I~~~g~a~~~--~~~~~V-rq~~lp~p~~E~avle~fl~~~----~~~~lvsfNGkaF 167 (278)
T COG3359 97 AEDVAFFDIETTGLD--RAGNTITLVGGARGV--DDTMHV-RQHFLPAPEEEVAVLENFLHDP----DFNMLVSFNGKAF 167 (278)
T ss_pred ccceEEEeeeccccC--CCCCeEEEEEEEEcc--CceEEE-EeecCCCcchhhHHHHHHhcCC----CcceEEEecCccc
Confidence 456999999999997 355667666665552 222211 12221 112 34455431 2237888 66 69
Q ss_pred cHHHHHHHHHHHcCCCCCCCCchhhhh----HHHhcC---CCCcccHHHHhcCCC----C--------------------
Q 036628 84 DCQVMLESECRFKNIPKPSYFNRWINL----RVPFSK---GDVRCNLKEAVELGW----H-------------------- 132 (254)
Q Consensus 84 D~~~fL~~e~~~~gi~~P~~~~~~iDl----r~~f~~---~~~~~~L~~~l~i~~----e-------------------- 132 (254)
| ..|+++ +.+..+++. .-+..+|| |.+... +..+.+..+.||+.- .
T Consensus 168 D-~PfikR-~v~~~~el~-l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll 244 (278)
T COG3359 168 D-IPFIKR-MVRDRLELS-LEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREEDTDGYDGPELYRLYRRYGDPGLL 244 (278)
T ss_pred C-cHHHHH-HHhcccccC-ccccchhhhhhhhhhhhccCCCCChhhHHHHhCccccccCCCcchHHHHHHHHHcCCHHHH
Confidence 9 789995 556666653 22345776 444432 333455666666511 1
Q ss_pred -CCCCchHHHHHHHHHHHHHHHHc
Q 036628 133 -GRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 133 -G~~HrALdDA~ntA~l~~~ll~~ 155 (254)
|--|.--.|..|++.|+..+.++
T Consensus 245 ~~l~~hN~eDvlnL~~i~~h~~~~ 268 (278)
T COG3359 245 DGLVLHNREDVLNLPTIIKHVSKK 268 (278)
T ss_pred HHHHHccHHHHHhHHHHHHHHHHH
Confidence 11233346888888888877654
No 64
>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=97.05 E-value=0.013 Score=51.69 Aligned_cols=124 Identities=17% Similarity=0.112 Sum_probs=81.8
Q ss_pred CCCcEEEEceEEEEcCCCeE-EEEEEEe------ehhhHHHHhhhcCCCCCCeEEEE-cC-cccHHHHHHHHHHHcCCCC
Q 036628 30 HPQEIIEFPSVIVSGVTGQI-TVCFQIY------ALFLHDNWQQHMGVTPTNFAVVT-WS-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 30 ~~~EIIEIgAV~vD~~~g~i-v~~F~~~------vl~~f~~wl~~~gi~~~~~~~vt-~g-~fD~~~fL~~e~~~~gi~~ 100 (254)
..+.||-|+++.++ ..++. +.+|..- .+.+|.+.++++. -.+|+ || .|| ..+|..-...+|++.
T Consensus 7 ~f~kIV~Is~~~~~-~~~~~~v~s~~~~~~~E~~lL~~F~~~~~~~~-----p~LVs~NG~~FD-lP~L~~Ral~~gi~~ 79 (209)
T PF10108_consen 7 PFHKIVCISVVYAD-DDGQFKVKSLGGPDDDEKELLQDFFDLVEKYN-----PQLVSFNGRGFD-LPVLCRRALIHGISA 79 (209)
T ss_pred cCCCeEEEEEEEEe-cCCcEEEEeccCCCCCHHHHHHHHHHHHHhCC-----CeEEecCCccCC-HHHHHHHHHHhCCCC
Confidence 46899999999887 33443 4444322 4677888887532 25677 45 699 679998899999999
Q ss_pred CCCCc---------------hhhhhHHHhcC-C----CCcccHHHHhcCCCC--------------CC----CCchHHHH
Q 036628 101 PSYFN---------------RWINLRVPFSK-G----DVRCNLKEAVELGWH--------------GR----VHCGLDDS 142 (254)
Q Consensus 101 P~~~~---------------~~iDlr~~f~~-~----~~~~~L~~~l~i~~e--------------G~----~HrALdDA 142 (254)
|.++. +.+||...+.. + ..+..|+..+|++-. |+ ..=-..|+
T Consensus 80 p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DV 159 (209)
T PF10108_consen 80 PRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDV 159 (209)
T ss_pred chhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 86542 35777776655 2 224456777887421 11 11125799
Q ss_pred HHHHHHHHHHHHcCCccC
Q 036628 143 MNIARLLAVIMQRGFKFS 160 (254)
Q Consensus 143 ~ntA~l~~~ll~~g~~f~ 160 (254)
+||+.|+.++..--..++
T Consensus 160 l~T~~lylR~~~~~G~l~ 177 (209)
T PF10108_consen 160 LNTYLLYLRFELLRGRLS 177 (209)
T ss_pred HHHHHHHHHHHHhhCCCC
Confidence 999999999977533344
No 65
>PRK05755 DNA polymerase I; Provisional
Probab=96.73 E-value=0.0058 Score=64.10 Aligned_cols=126 Identities=15% Similarity=0.038 Sum_probs=78.3
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCe--EEEEEEE--eehhhHHHHhhhcCCCCCCeEEEEcCcccHHHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQ--ITVCFQI--YALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVM 88 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~--iv~~F~~--~vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~f 88 (254)
..++++|+|||+.+ +...+|+.|+. ..+ +|. .++..+. .+++.+.+++++.. -..+.|++.|| ..+
T Consensus 315 ~~~~a~DtEt~~l~--~~~~~i~~i~l-s~~--~g~~~~ip~~~i~~~~l~~l~~~L~d~~----v~kV~HNakfD-l~~ 384 (880)
T PRK05755 315 AGLFAFDTETTSLD--PMQAELVGLSF-AVE--PGEAAYIPLDQLDREVLAALKPLLEDPA----IKKVGQNLKYD-LHV 384 (880)
T ss_pred cCeEEEEeccCCCC--cccccEEEEEE-EeC--CCcEEEEecccccHHHHHHHHHHHhCCC----CcEEEeccHhH-HHH
Confidence 35899999999986 67788999875 332 332 2222111 24566777887532 23688899999 567
Q ss_pred HHHHHHHcCCCCCCCCchhhhhHHHhcC-----CCCcccHHHH-hcCCC------------------CCCCCchHHHHHH
Q 036628 89 LESECRFKNIPKPSYFNRWINLRVPFSK-----GDVRCNLKEA-VELGW------------------HGRVHCGLDDSMN 144 (254)
Q Consensus 89 L~~e~~~~gi~~P~~~~~~iDlr~~f~~-----~~~~~~L~~~-l~i~~------------------eG~~HrALdDA~n 144 (254)
|.+ .|+.++ ..++|.+..... ++.+.+|.+. ++... +...|.|..|+..
T Consensus 385 L~~----~gi~~~---~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~ 457 (880)
T PRK05755 385 LAR----YGIELR---GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADV 457 (880)
T ss_pred HHh----CCCCcC---CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHH
Confidence 763 477764 345665443222 2333444433 23321 1134789999999
Q ss_pred HHHHHHHHHHc
Q 036628 145 IARLLAVIMQR 155 (254)
Q Consensus 145 tA~l~~~ll~~ 155 (254)
+.+|+..|.+.
T Consensus 458 ~~~L~~~L~~~ 468 (880)
T PRK05755 458 TLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHH
Confidence 99999988775
No 66
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=96.31 E-value=0.02 Score=54.65 Aligned_cols=133 Identities=15% Similarity=0.190 Sum_probs=80.6
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee------------------h-----------hhHHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------------L-----------FLHDN 63 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v------------------l-----------~~f~~ 63 (254)
-.|.+.|.||.|.. |..++.-+|++|.-|..-+.|.+--..|. - .+|..
T Consensus 9 ~tF~~yDYETfG~~--Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 9 PTFLFYDYETFGVH--PALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred CcEEEEehhhcCCC--cccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 36899999999986 78899999999999975555544444441 1 22322
Q ss_pred HhhhcCCCCCCeEEEEcC--cccHHHHHHHHHHHcCCCCCCCCchh---------hhh-HHHhcC---C-----------
Q 036628 64 WQQHMGVTPTNFAVVTWS--DWDCQVMLESECRFKNIPKPSYFNRW---------INL-RVPFSK---G----------- 117 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g--~fD~~~fL~~e~~~~gi~~P~~~~~~---------iDl-r~~f~~---~----------- 117 (254)
-+.. .+..-+.+++.+. +|| ..+-++-+=++=++ | |-..| +|+ |..|.. |
T Consensus 87 ~I~~-~ls~P~Tcv~GYNniRFD-DEvtRy~fyRNF~D-P-Ya~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~p 162 (475)
T COG2925 87 RIHA-ELTQPNTCVLGYNNIRFD-DEVTRYIFYRNFYD-P-YAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLP 162 (475)
T ss_pred HHHH-HhCCCCeeeecccccccc-hHHHHHHHHHhcCc-h-hhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCc
Confidence 2221 1112345666633 677 66666555555554 3 33332 332 444443 1
Q ss_pred -CCcccHHHHhcCCCCCCCCchHHHHHHHHHHHHHH
Q 036628 118 -DVRCNLKEAVELGWHGRVHCGLDDSMNIARLLAVI 152 (254)
Q Consensus 118 -~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~~~l 152 (254)
-++..|..+-|+.. +++|.|+.|+++|-.+...+
T Consensus 163 SFkLEhLt~ANgieH-~nAHdAmsDVyATIamAklv 197 (475)
T COG2925 163 SFKLEHLTKANGIEH-SNAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred chhhHHHhhcccccc-chhhHHHHHHHHHHHHHHHH
Confidence 12345666777875 68999999999876665544
No 67
>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=95.69 E-value=0.26 Score=42.98 Aligned_cols=76 Identities=16% Similarity=0.213 Sum_probs=49.9
Q ss_pred eEEEEEEeecCCC--CCCC----CCcEEEEceEEEEcCCC--eEE--E---------------EEEEe-----ehhhHHH
Q 036628 14 YFVVVDFEATCDK--KIPH----PQEIIEFPSVIVSGVTG--QIT--V---------------CFQIY-----ALFLHDN 63 (254)
Q Consensus 14 ~fvViDlEtTg~~--~~~~----~~EIIEIgAV~vD~~~g--~iv--~---------------~F~~~-----vl~~f~~ 63 (254)
..+.||+||++.. +.|. .++||.|+.+ + .++ ++. . .+..| .+.+|.+
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~-~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~ 82 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--G-SDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFK 82 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--C-CCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHH
Confidence 5789999999643 2332 2689999874 2 112 111 0 13333 4678888
Q ss_pred HhhhcCCCCCCeEEEEcC--cccHHHHHHHHHHHcCCC
Q 036628 64 WQQHMGVTPTNFAVVTWS--DWDCQVMLESECRFKNIP 99 (254)
Q Consensus 64 wl~~~gi~~~~~~~vt~g--~fD~~~fL~~e~~~~gi~ 99 (254)
++.+. + .+++|. .|| ..+|..-++.+|++
T Consensus 83 ~i~~~-----~-~iig~N~~~FD-lpyl~~R~~~~gi~ 113 (204)
T cd05783 83 IISEY-----P-IVLTFNGDNFD-LPYLYNRALKLGIP 113 (204)
T ss_pred HHhcC-----C-EEEEeCCCCcC-HHHHHHHHHHhCCC
Confidence 88753 2 677864 699 67999889999987
No 68
>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=95.08 E-value=0.3 Score=42.75 Aligned_cols=81 Identities=16% Similarity=0.197 Sum_probs=54.1
Q ss_pred eEEEEEEeecCCC-C--CCCCCcEEEEceEEEEcCCCeEE----------E------------EEEEe-------ehhhH
Q 036628 14 YFVVVDFEATCDK-K--IPHPQEIIEFPSVIVSGVTGQIT----------V------------CFQIY-------ALFLH 61 (254)
Q Consensus 14 ~fvViDlEtTg~~-~--~~~~~EIIEIgAV~vD~~~g~iv----------~------------~F~~~-------vl~~f 61 (254)
..+.+|+|+++.+ + ++..++||.|+.+.- .+|..+ . .+..+ .+.+|
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~--~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f 80 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMID--GQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEe--cCCEEEecccccccccccccccCCCCCCCceEEecCCCHHHHHHHH
Confidence 3689999998754 3 346799999998753 234321 0 12222 36788
Q ss_pred HHHhhhcCCCCCCeEEEEcC--cccHHHHHHHHHHHcCCCCC
Q 036628 62 DNWQQHMGVTPTNFAVVTWS--DWDCQVMLESECRFKNIPKP 101 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g--~fD~~~fL~~e~~~~gi~~P 101 (254)
.+|+.+.. .-++++|. .|| ..+|..-++.+|+.+.
T Consensus 81 ~~~i~~~~----Pd~i~gyN~~~FD-~pyl~~R~~~~~~~~~ 117 (204)
T cd05779 81 FEHIREVK----PHIIVTYNGDFFD-WPFVEARAAIHGLSME 117 (204)
T ss_pred HHHHHHhC----CCEEEecCccccC-HHHHHHHHHHhCCCch
Confidence 88888742 23677764 699 6799888899998754
No 69
>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=94.62 E-value=0.23 Score=41.45 Aligned_cols=126 Identities=13% Similarity=0.028 Sum_probs=69.6
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEE----EE--E-E--Ee--ehhhHHHHhhhcCCCCCCeEEEEcCc
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQIT----VC--F-Q--IY--ALFLHDNWQQHMGVTPTNFAVVTWSD 82 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv----~~--F-~--~~--vl~~f~~wl~~~gi~~~~~~~vt~g~ 82 (254)
.++++|+|+|+.. +...+|+.++... ..++.. .. + . .. ++..+.+++++.+ ...++++..
T Consensus 6 ~~~a~d~e~~~~~--~~~~~i~~l~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~----~~~v~hn~k 76 (193)
T cd06139 6 KVFAFDTETTSLD--PMQAELVGISFAV---EPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPS----IKKVGQNLK 76 (193)
T ss_pred CeEEEEeecCCCC--cCCCeEEEEEEEc---CCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCC----CcEEeeccH
Confidence 4789999999875 4467888777542 123221 00 0 0 01 2334667776421 246888999
Q ss_pred ccHHHHHHHHHHHcCCCCCCCCchhhhhHHHh----cC--CCCcccHHHH-hcCC----------------CCC-----C
Q 036628 83 WDCQVMLESECRFKNIPKPSYFNRWINLRVPF----SK--GDVRCNLKEA-VELG----------------WHG-----R 134 (254)
Q Consensus 83 fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f----~~--~~~~~~L~~~-l~i~----------------~eG-----~ 134 (254)
|| ..+|. ..|+.++ ..++|+.... +. ++.+..|.+. ++.. ++. .
T Consensus 77 ~d-~~~l~----~~gi~~~---~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~~~~ 148 (193)
T cd06139 77 FD-LHVLA----NHGIELR---GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPLEKA 148 (193)
T ss_pred HH-HHHHH----HCCCCCC---CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCHHHH
Confidence 99 56774 4577765 2346654432 21 1122233332 2211 110 1
Q ss_pred CCchHHHHHHHHHHHHHHHHcC
Q 036628 135 VHCGLDDSMNIARLLAVIMQRG 156 (254)
Q Consensus 135 ~HrALdDA~ntA~l~~~ll~~g 156 (254)
.|.|..||..+.+|+..|.+..
T Consensus 149 ~~ya~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 149 AEYAAEDADITLRLYELLKPKL 170 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 2358888999999988887764
No 70
>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=94.32 E-value=0.58 Score=40.89 Aligned_cols=79 Identities=13% Similarity=-0.036 Sum_probs=52.2
Q ss_pred eEEEEEEeecCCCC------CCCCCcEEEEceEEEEcCCCeEEEEEE-Ee-----ehhhHHHHhhhcCCCCCCeEEEEc-
Q 036628 14 YFVVVDFEATCDKK------IPHPQEIIEFPSVIVSGVTGQITVCFQ-IY-----ALFLHDNWQQHMGVTPTNFAVVTW- 80 (254)
Q Consensus 14 ~fvViDlEtTg~~~------~~~~~EIIEIgAV~vD~~~g~iv~~F~-~~-----vl~~f~~wl~~~gi~~~~~~~vt~- 80 (254)
..+.||+|++...+ .+..++||-||...- ...+.+ +. .. .+.+|.+++.+.. .-++++|
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~--~~~~~~--~~~~~~~E~~lL~~f~~~i~~~d----Pdii~g~N 81 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN--RGWEEV--LHAEDAAEKELLEELVAIIRERD----PDVIEGHN 81 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC--CCceee--eccCCCCHHHHHHHHHHHHHHhC----CCEEeccC
Confidence 47899999987642 124588999997522 221221 21 12 4678888888642 2366665
Q ss_pred C-cccHHHHHHHHHHHcCCCCC
Q 036628 81 S-DWDCQVMLESECRFKNIPKP 101 (254)
Q Consensus 81 g-~fD~~~fL~~e~~~~gi~~P 101 (254)
+ .|| ..+|.+-|+.+|++.+
T Consensus 82 ~~~FD-~pyl~~R~~~~~~~~~ 102 (207)
T cd05785 82 IFRFD-LPYLRRRCRRHGVPLA 102 (207)
T ss_pred CcccC-HHHHHHHHHHhCCCcc
Confidence 4 699 6799999999998874
No 71
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=93.21 E-value=1.4 Score=37.89 Aligned_cols=66 Identities=20% Similarity=0.171 Sum_probs=41.2
Q ss_pred CeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-CCC---cccHH-HHhcCCCCCCCCchHHHHHHHHH
Q 036628 74 NFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-GDV---RCNLK-EAVELGWHGRVHCGLDDSMNIAR 147 (254)
Q Consensus 74 ~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~~---~~~L~-~~l~i~~eG~~HrALdDA~ntA~ 147 (254)
+.++|..+ ..| ++..++..|. ..-+|...+|+. ..+ +..|+ +.|+.+.+...|+.+.||+++.+
T Consensus 102 ~tILVGHsL~nD--------L~aL~l~hp~--~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~HdSvEDArAam~ 171 (174)
T cd06143 102 GCIFVGHGLAKD--------FRVINIQVPK--EQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSETHDSIEDARTALK 171 (174)
T ss_pred CCEEEeccchhH--------HHHhcCcCCC--cceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCCcCcHHHHHHHHH
Confidence 34555554 455 2333555552 245777777776 222 33443 45777665568999999999998
Q ss_pred HH
Q 036628 148 LL 149 (254)
Q Consensus 148 l~ 149 (254)
|+
T Consensus 172 Ly 173 (174)
T cd06143 172 LY 173 (174)
T ss_pred Hh
Confidence 86
No 72
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=92.65 E-value=0.16 Score=45.35 Aligned_cols=152 Identities=20% Similarity=0.192 Sum_probs=88.2
Q ss_pred eEEEEEEeecCCCCC-------------------CCCCcEEEEceEEEEcCCCeE--EEEEEEe----------e-----
Q 036628 14 YFVVVDFEATCDKKI-------------------PHPQEIIEFPSVIVSGVTGQI--TVCFQIY----------A----- 57 (254)
Q Consensus 14 ~fvViDlEtTg~~~~-------------------~~~~EIIEIgAV~vD~~~g~i--v~~F~~~----------v----- 57 (254)
++|-+|.|.-|.-.. .+.-.||++|.-+-|.+.++- ..+++.= +
T Consensus 43 n~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ESie 122 (299)
T COG5228 43 NHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIE 122 (299)
T ss_pred CceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhhcchHHHH
Confidence 467788887665411 145679999999999544332 2333321 1
Q ss_pred ------------------hhhHHHHhhhcCCC-CCCeEEEE-cCcccHHHHHHHHHHHcCCCCCC-----------CCch
Q 036628 58 ------------------LFLHDNWQQHMGVT-PTNFAVVT-WSDWDCQVMLESECRFKNIPKPS-----------YFNR 106 (254)
Q Consensus 58 ------------------l~~f~~wl~~~gi~-~~~~~~vt-~g~fD~~~fL~~e~~~~gi~~P~-----------~~~~ 106 (254)
..+|.+-|-..|+. .++..|+| .+.+| ..+|-+. .-+.++|. ||-.
T Consensus 123 LL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfHsaYD-fgyLiki--lt~~plP~~~EdFy~~l~~yfP~ 199 (299)
T COG5228 123 LLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYD-FGYLIKI--LTNDPLPNNKEDFYWWLHQYFPN 199 (299)
T ss_pred HHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEeecchh-HHHHHHH--HhcCCCCccHHHHHHHHHHHCcc
Confidence 11222222223332 35677888 46799 6778654 34566663 2334
Q ss_pred hhhhHHHhcC-CCCcccH---HHHhcCCCCCCCCchHHHHHHHHHHHHHHHHcCCccCcCcccccC
Q 036628 107 WINLRVPFSK-GDVRCNL---KEAVELGWHGRVHCGLDDSMNIARLLAVIMQRGFKFSITKSLTTP 168 (254)
Q Consensus 107 ~iDlr~~f~~-~~~~~~L---~~~l~i~~eG~~HrALdDA~ntA~l~~~ll~~g~~f~~~~~~~~~ 168 (254)
+.|++-+++. .+...+| +.-|++...|.+|.|=.||+.||+.+-+.......=.+.++|...
T Consensus 200 fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~sig~~ll~~ 265 (299)
T COG5228 200 FYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQSLLML 265 (299)
T ss_pred ccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheecccccHHHHHH
Confidence 4556555544 1212233 344677778999999999999999987665554444444444443
No 73
>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=91.84 E-value=2.2 Score=37.56 Aligned_cols=81 Identities=15% Similarity=0.252 Sum_probs=49.8
Q ss_pred eEEEEEEeecCCCC---CCCCCcEEEEceEEEEcCCCeE--EEEEE-------------Ee-----ehhhHHHHhhhcCC
Q 036628 14 YFVVVDFEATCDKK---IPHPQEIIEFPSVIVSGVTGQI--TVCFQ-------------IY-----ALFLHDNWQQHMGV 70 (254)
Q Consensus 14 ~fvViDlEtTg~~~---~~~~~EIIEIgAV~vD~~~g~i--v~~F~-------------~~-----vl~~f~~wl~~~gi 70 (254)
..+.+|+|++...+ +|..++||-|+.+.-....... -.-|. .| .+.+|.+++.+..
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~E~eLL~~f~~~i~~~D- 86 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD- 86 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCCCCEEEEECCHHHHHHHHHHHHHhcC-
Confidence 46899999987652 3467899999998652111011 01111 11 3567777777532
Q ss_pred CCCCeEEEE-cC-cccHHHHHHHHHHHcCCC
Q 036628 71 TPTNFAVVT-WS-DWDCQVMLESECRFKNIP 99 (254)
Q Consensus 71 ~~~~~~~vt-~g-~fD~~~fL~~e~~~~gi~ 99 (254)
-+ ++++ |+ .|| ..+|.+-++..|++
T Consensus 87 --PD-ii~GyN~~~FD-l~yL~~R~~~l~i~ 113 (230)
T cd05777 87 --PD-IITGYNICNFD-LPYLLERAKALKLN 113 (230)
T ss_pred --CC-EEEEecCCCCC-HHHHHHHHHHhCCc
Confidence 13 4555 44 699 67888778888775
No 74
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=90.69 E-value=4.8 Score=36.88 Aligned_cols=35 Identities=14% Similarity=0.135 Sum_probs=25.9
Q ss_pred ccHHH-HhcCCCCCCCCchHHHHHHHHHHHHHHHHc
Q 036628 121 CNLKE-AVELGWHGRVHCGLDDSMNIARLLAVIMQR 155 (254)
Q Consensus 121 ~~L~~-~l~i~~eG~~HrALdDA~ntA~l~~~ll~~ 155 (254)
..|.+ .||++..--.|+.+.||++|.+|+..+-.+
T Consensus 230 K~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 230 KKLTEALLGKDIQVGEHSSVEDARATMELYKRVKVQ 265 (280)
T ss_pred HHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHHH
Confidence 34444 577755434699999999999999987655
No 75
>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=88.79 E-value=2.9 Score=37.84 Aligned_cols=85 Identities=14% Similarity=0.067 Sum_probs=53.5
Q ss_pred CCCeEEEEEEeecCCCC---CCCCCcEEEEceEEEEcC-CCeEEEEEEEe--------------------ehhhHHHHhh
Q 036628 11 DFDYFVVVDFEATCDKK---IPHPQEIIEFPSVIVSGV-TGQITVCFQIY--------------------ALFLHDNWQQ 66 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~~---~~~~~EIIEIgAV~vD~~-~g~iv~~F~~~--------------------vl~~f~~wl~ 66 (254)
+-=..+.+|+||....+ .+..+||+-|+.++.+.. .....+.+-.+ .|.+|.+++.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~ 234 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSIEDNVEVIYFDSEKELLEAFLDIIQ 234 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCTTCTTEEEEESSHHHHHHHHHHHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCCCCCcEEEEECCHHHHHHHHHHHHH
Confidence 33468899999987763 356799999999876421 00011111111 2567788887
Q ss_pred hcCCCCCCeEEEEc-C-cccHHHHHHHHHHHcCCCC
Q 036628 67 HMGVTPTNFAVVTW-S-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 67 ~~gi~~~~~~~vt~-g-~fD~~~fL~~e~~~~gi~~ 100 (254)
+.. -+ ++++| + .|| ..+|..-++..|++.
T Consensus 235 ~~d---PD-ii~GyN~~~fD-~~yl~~R~~~l~~~~ 265 (325)
T PF03104_consen 235 EYD---PD-IITGYNIDGFD-LPYLIERAKKLGIDM 265 (325)
T ss_dssp HHS----S-EEEESSTTTTH-HHHHHHHHHHTTTCT
T ss_pred hcC---Cc-EEEEecccCCC-HHHHHHHHHHhCccc
Confidence 643 12 55555 4 599 678888888888764
No 76
>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=85.79 E-value=9.2 Score=33.00 Aligned_cols=74 Identities=14% Similarity=0.246 Sum_probs=45.5
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEE----------EEEEEe-----ehhhHHHHhhhcCCCCCCeEEE
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQIT----------VCFQIY-----ALFLHDNWQQHMGVTPTNFAVV 78 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv----------~~F~~~-----vl~~f~~wl~~~gi~~~~~~~v 78 (254)
..+.||+|+++. .+|+-||. .|.+...++ .....+ .+.+|.+++.+.. -+ +++
T Consensus 4 ~~~~fDIE~~~~------~~i~~i~~--~~~~~~~i~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~d---PD-vi~ 71 (193)
T cd05784 4 KVVSLDIETSMD------GELYSIGL--YGEGQERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYD---PD-III 71 (193)
T ss_pred cEEEEEeecCCC------CCEEEEEe--ecCCCCEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHhhC---CC-EEE
Confidence 468899999853 27888775 222222111 012223 4678888887642 12 455
Q ss_pred E-cC-cccHHHHHHHHHHHcCCCC
Q 036628 79 T-WS-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 79 t-~g-~fD~~~fL~~e~~~~gi~~ 100 (254)
+ |+ .|| ..+|.+-++..|++.
T Consensus 72 g~N~~~FD-~~yl~~R~~~~~i~~ 94 (193)
T cd05784 72 GWNVINFD-LRLLQRRAEAHGLPL 94 (193)
T ss_pred ECCCcCcC-HHHHHHHHHHhCCCc
Confidence 5 44 699 578888888888875
No 77
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=85.36 E-value=3.9 Score=45.42 Aligned_cols=149 Identities=16% Similarity=0.196 Sum_probs=85.4
Q ss_pred eEEEEEEeecCCC-CCC--CCCcEEEEceEEEEcCC-----CeEE----EEE------------EEe-------ehhhHH
Q 036628 14 YFVVVDFEATCDK-KIP--HPQEIIEFPSVIVSGVT-----GQIT----VCF------------QIY-------ALFLHD 62 (254)
Q Consensus 14 ~fvViDlEtTg~~-~~~--~~~EIIEIgAV~vD~~~-----g~iv----~~F------------~~~-------vl~~f~ 62 (254)
..++||+|||-+. ..| ..++|.=|. +.+|.+. .+|| +-| ..+ .+.+|.
T Consensus 247 ~VlAFDIETtKlPLKFPDae~DqIMMIS-YMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv~Ll~RfF 325 (2173)
T KOG1798|consen 247 RVLAFDIETTKLPLKFPDAESDQIMMIS-YMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEVGLLQRFF 325 (2173)
T ss_pred eEEEEeeecccCCCCCCCcccceEEEEE-EEecCceEEEechhhhccchhhcccCCccccccceEEecCCcHHHHHHHHH
Confidence 4789999999887 555 467787774 4666431 2222 222 222 234444
Q ss_pred HHhhhcCCCCCCeEEEE-cCc-ccHHHHHHHHHHHcCCCCCCCCc--------------hhhhhHHHhcC-CCCc---cc
Q 036628 63 NWQQHMGVTPTNFAVVT-WSD-WDCQVMLESECRFKNIPKPSYFN--------------RWINLRVPFSK-GDVR---CN 122 (254)
Q Consensus 63 ~wl~~~gi~~~~~~~vt-~g~-fD~~~fL~~e~~~~gi~~P~~~~--------------~~iDlr~~f~~-~~~~---~~ 122 (254)
+-+.+. +..++|| ||+ || +.|+++-+..+|+++-.-.. .++|-=+..+. +|.+ .+
T Consensus 326 eHiq~~----kP~iivTyNGDFFD-WPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqg 400 (2173)
T KOG1798|consen 326 EHIQEV----KPTIIVTYNGDFFD-WPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQG 400 (2173)
T ss_pred HHHHhc----CCcEEEEecCcccc-chhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCcccc
Confidence 444432 3457888 776 79 99999999999998752111 11221111111 2211 12
Q ss_pred HHH----Hhc-------------CCCCCCCCc---hHHHHHHHHHHHHHHHHcCCccCcCcccccCC
Q 036628 123 LKE----AVE-------------LGWHGRVHC---GLDDSMNIARLLAVIMQRGFKFSITKSLTTPQ 169 (254)
Q Consensus 123 L~~----~l~-------------i~~eG~~Hr---ALdDA~ntA~l~~~ll~~g~~f~~~~~~~~~~ 169 (254)
|+. .|| +..|-.+|- ...||.+|--|+++...- +.|.....+...|
T Consensus 401 LKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP-FIFsLctIIPl~P 466 (2173)
T KOG1798|consen 401 LKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP-FIFSLCTIIPLNP 466 (2173)
T ss_pred hhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh-HHhhhhhccccCh
Confidence 322 233 233333444 489999999999988766 6777777766554
No 78
>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=83.93 E-value=10 Score=35.81 Aligned_cols=83 Identities=18% Similarity=0.203 Sum_probs=50.0
Q ss_pred eEEEEEEeecCCCC-CC--C--CCcEEEEceEEEEcCCC--eEEEE-------------EEEe-----ehhhHHHHhhhc
Q 036628 14 YFVVVDFEATCDKK-IP--H--PQEIIEFPSVIVSGVTG--QITVC-------------FQIY-----ALFLHDNWQQHM 68 (254)
Q Consensus 14 ~fvViDlEtTg~~~-~~--~--~~EIIEIgAV~vD~~~g--~iv~~-------------F~~~-----vl~~f~~wl~~~ 68 (254)
..+++|+||+...+ .| . .++||.|+.+.-+.... ..... .+.+ .+.+|.+++.+.
T Consensus 4 ~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~ 83 (471)
T smart00486 4 KILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEIDGVEVYEFNNEKELLKAFLEFIKKY 83 (471)
T ss_pred eEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCCCCeEEecCCHHHHHHHHHHHHHHh
Confidence 47899999987642 22 2 57999999988764321 00001 1111 245666666653
Q ss_pred CCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCC
Q 036628 69 GVTPTNFAVVTWS-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 69 gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~ 100 (254)
. .+.++.+|+ .|| ..+|...+...++..
T Consensus 84 d---pdii~g~N~~~FD-~~~i~~R~~~~~~~~ 112 (471)
T smart00486 84 D---PDIIYGHNISNFD-LPYIISRLEKLKIKP 112 (471)
T ss_pred C---CCEEEeecCCCCC-HHHHHHHHHHcCCCC
Confidence 2 245555566 599 678877777766643
No 79
>PHA02563 DNA polymerase; Provisional
Probab=83.52 E-value=8.5 Score=39.40 Aligned_cols=84 Identities=10% Similarity=-0.015 Sum_probs=52.2
Q ss_pred cCCCCCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe-ehhhHHHHhhhcCCCCCC-eEEEEcCccc
Q 036628 7 QKLQDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY-ALFLHDNWQQHMGVTPTN-FAVVTWSDWD 84 (254)
Q Consensus 7 ~~~q~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~-vl~~f~~wl~~~gi~~~~-~~~vt~g~fD 84 (254)
+.++.-..++..||||+..+ ...+...+-.+| +++..+|..- ...+|..|+........+ .+.+||+.||
T Consensus 6 k~k~~~~~~~~~DfET~t~~-----~~~~~~~~~~~d---~~~~~s~~~~~~~~~f~~~i~~~~~k~~~~~vYfHN~~FD 77 (630)
T PHA02563 6 KKKHKPRKILACDFETTTIN-----KDCRRWFWGEID---VEDFPSYYGGNSFDEFLQWIEDTTYKETECIIYFHNLKFD 77 (630)
T ss_pred ccccccceEEEEEEEecccC-----CcceeeeeeEec---cceeceeeccccHHHHHHHHhhccccccceEEEEecCCcc
Confidence 34445667999999999765 333333333443 4443444222 367888888732222222 4788999999
Q ss_pred HHHHHHHHHHHcCCC
Q 036628 85 CQVMLESECRFKNIP 99 (254)
Q Consensus 85 ~~~fL~~e~~~~gi~ 99 (254)
..||-+.+.+++.+
T Consensus 78 -~~Fil~~L~~~~~~ 91 (630)
T PHA02563 78 -GSFILKWLLRNGFN 91 (630)
T ss_pred -HHHHHHHHHhhccc
Confidence 78998888776643
No 80
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=82.47 E-value=6.9 Score=42.35 Aligned_cols=79 Identities=14% Similarity=0.238 Sum_probs=48.7
Q ss_pred eEEEEEEeecCCCC--CC--CCCcEEEEceEEEEcCCCeEEEEEEE------------------e-----ehhhHHHHhh
Q 036628 14 YFVVVDFEATCDKK--IP--HPQEIIEFPSVIVSGVTGQITVCFQI------------------Y-----ALFLHDNWQQ 66 (254)
Q Consensus 14 ~fvViDlEtTg~~~--~~--~~~EIIEIgAV~vD~~~g~iv~~F~~------------------~-----vl~~f~~wl~ 66 (254)
..+.||+||++.++ .| ..++||.|+.+... .|.-.+.+.+ + .|.+|.+++.
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~--~g~~~~~~~r~vftl~~c~~i~g~~V~~f~sE~eLL~~f~~~I~ 342 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTN--QGDEEEPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVI 342 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEee--CCCccCCcceEEEecCccccCCCceEEEeCCHHHHHHHHHHHHH
Confidence 48899999987542 23 57999999998653 2221111111 1 2456777776
Q ss_pred hcCCCCCCeEEEEc-C-cccHHHHHHHHHHHcCCC
Q 036628 67 HMGVTPTNFAVVTW-S-DWDCQVMLESECRFKNIP 99 (254)
Q Consensus 67 ~~gi~~~~~~~vt~-g-~fD~~~fL~~e~~~~gi~ 99 (254)
+.. -+ ++++| + .|| +.+|..-++..|+.
T Consensus 343 ~~D---PD-II~GYNi~~FD-lpYL~~Ra~~l~i~ 372 (1054)
T PTZ00166 343 AVD---PD-FLTGYNIINFD-LPYLLNRAKALKLN 372 (1054)
T ss_pred hcC---CC-EEEecCCcCCc-HHHHHHHHHHhCCC
Confidence 532 13 55554 4 699 67887777776665
No 81
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=82.10 E-value=1.4 Score=28.38 Aligned_cols=27 Identities=30% Similarity=0.684 Sum_probs=19.1
Q ss_pred eeccCCCCCCCceeecCCCCCCCCCccccccccC
Q 036628 220 IIRKPGPKCGSFFFGCGNLTPNKGACCNYFHSAT 253 (254)
Q Consensus 220 ~~~~~gp~~g~~f~~c~~~~~~~~~~c~~f~w~~ 253 (254)
+|.+.|..- .||||.+++ .|.|-+|..
T Consensus 11 lv~r~~k~g--~F~~Cs~yP-----~C~~~~~~~ 37 (39)
T PF01396_consen 11 LVLRRGKKG--KFLGCSNYP-----ECKYTEPLP 37 (39)
T ss_pred eEEEECCCC--CEEECCCCC-----CcCCeEeCC
Confidence 444545543 999999883 499998864
No 82
>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=75.65 E-value=35 Score=27.40 Aligned_cols=122 Identities=15% Similarity=0.085 Sum_probs=60.0
Q ss_pred EEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe--------ehhhHHHHhhhcCCCCCCeEEEEcCcccHH
Q 036628 15 FVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY--------ALFLHDNWQQHMGVTPTNFAVVTWSDWDCQ 86 (254)
Q Consensus 15 fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~--------vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~ 86 (254)
.+.||+||++.........| ..+-+- +++ ..|-.. +...+.+++++.. -..+.++..+| .
T Consensus 22 ~~a~D~E~~~~~~~~~~~~~---~~iq~~--~~~--~~~i~~~~~~~~~~~~~~l~~ll~~~~----i~kv~~n~~~D-~ 89 (176)
T PF01612_consen 22 VLAFDTETTGLDPYSYNPKI---ALIQLA--TGE--GCYIIDPIDLGDNWILDALKELLEDPN----IIKVGHNAKFD-L 89 (176)
T ss_dssp EEEEEEEEETSTSTTSSEEE---EEEEEE--ESC--EEEEECGTTSTTTTHHHHHHHHHTTTT----SEEEESSHHHH-H
T ss_pred eEEEEEEECCCCccccCCeE---EEEEEe--cCC--CceeeeeccccccchHHHHHHHHhCCC----ccEEEEEEech-H
Confidence 89999999987611122222 222221 121 111111 1345566666422 13455677999 5
Q ss_pred HHHHHHHHHcCCCCCCCCchhhhh--HHHhcC---CCCcccHHH-Hhc-C--CC---CCCCC--c---------hHHHHH
Q 036628 87 VMLESECRFKNIPKPSYFNRWINL--RVPFSK---GDVRCNLKE-AVE-L--GW---HGRVH--C---------GLDDSM 143 (254)
Q Consensus 87 ~fL~~e~~~~gi~~P~~~~~~iDl--r~~f~~---~~~~~~L~~-~l~-i--~~---eG~~H--r---------ALdDA~ 143 (254)
..|.+. .|+.+..+ +|+ ...... ++.+.+|.+ +++ + +. .+... + |-.||.
T Consensus 90 ~~L~~~---~~i~~~~~----~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~ 162 (176)
T PF01612_consen 90 KWLYRS---FGIDLKNV----FDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAV 162 (176)
T ss_dssp HHHHHH---HTS--SSE----EEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHH
T ss_pred HHHHHH---hccccCCc----cchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHH
Confidence 667654 67776533 444 111222 233444533 445 2 11 11111 2 556999
Q ss_pred HHHHHHHHHHHc
Q 036628 144 NIARLLAVIMQR 155 (254)
Q Consensus 144 ntA~l~~~ll~~ 155 (254)
.+.+|+..|.++
T Consensus 163 ~~~~l~~~l~~~ 174 (176)
T PF01612_consen 163 VTFRLYEKLKPQ 174 (176)
T ss_dssp THHHHHHHHHHH
T ss_pred HHHHHHHHHHHh
Confidence 999998888764
No 83
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=69.16 E-value=3.4 Score=38.04 Aligned_cols=69 Identities=12% Similarity=0.050 Sum_probs=48.3
Q ss_pred ccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC-------------CCCcccHHHHhcCCCCCCCCchHHHHHHHHHHH
Q 036628 83 WDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK-------------GDVRCNLKEAVELGWHGRVHCGLDDSMNIARLL 149 (254)
Q Consensus 83 fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-------------~~~~~~L~~~l~i~~eG~~HrALdDA~ntA~l~ 149 (254)
+| .+|..+++.+.+-+.+ ..|.-++.+|.. .+.+..|..++...-++.+|||+.|...+.+++
T Consensus 209 ~~-fqf~~~ellR~~deqa---~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~ 284 (318)
T KOG4793|consen 209 FI-FQFRINELLRWSDEQA---RPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLLLSKVF 284 (318)
T ss_pred HH-HHHHHHHHHhhHhhcC---CCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhccccchhhhHH
Confidence 66 5788888888776654 235666666642 111334555666666789999999999999999
Q ss_pred HHHHHc
Q 036628 150 AVIMQR 155 (254)
Q Consensus 150 ~~ll~~ 155 (254)
+++-.+
T Consensus 285 q~~~id 290 (318)
T KOG4793|consen 285 QKLTID 290 (318)
T ss_pred HHhhhh
Confidence 987554
No 84
>TIGR01685 MDP-1 magnesium-dependent phosphatase-1. This model represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterized as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues.
Probab=68.94 E-value=14 Score=31.40 Aligned_cols=63 Identities=14% Similarity=0.032 Sum_probs=37.6
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEee-----hhhHHHHhhhcCCCCCCeEEEEcC
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA-----LFLHDNWQQHMGVTPTNFAVVTWS 81 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~v-----l~~f~~wl~~~gi~~~~~~~vt~g 81 (254)
.+||||++.|-|. ++..+|---+.-.+|..+|-|++....-+ ..++.++|.+.|+ +.+++|+.
T Consensus 3 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~pGv~elL~~Lk~~G~---~l~I~Sn~ 70 (174)
T TIGR01685 3 RVIVFDLDGTLWD--HYMISLLGGPFKPVKQNNSIIIDKSGTEVTLIKEVRDVLQTLKDAGT---YLATASWN 70 (174)
T ss_pred cEEEEeCCCCCcC--cccccccCCCceeccCCCCeEEeCCCCEEEEcccHHHHHHHHHHCCC---EEEEEeCC
Confidence 5899999999886 22222222233345555555554443321 3566777776553 57899977
No 85
>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=67.65 E-value=67 Score=26.28 Aligned_cols=122 Identities=11% Similarity=0.005 Sum_probs=65.8
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe----ehhhHHHHhhhcCCCCCCeE-EEEcCcccHHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY----ALFLHDNWQQHMGVTPTNFA-VVTWSDWDCQV 87 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~----vl~~f~~wl~~~gi~~~~~~-~vt~g~fD~~~ 87 (254)
...|.||+|+.........--+|+|+.- ++ .+--|+.. ..+.+.+++++. +.. +.++...| ..
T Consensus 13 ~~~ig~D~E~~~~~~~~~~~~liQl~~~-----~~-~~~l~d~~~~~~~~~~L~~lL~d~-----~i~Kvg~~~k~D-~~ 80 (161)
T cd06129 13 GDVIAFDMEWPPGRRYYGEVALIQLCVS-----EE-KCYLFDPLSLSVDWQGLKMLLENP-----SIVKALHGIEGD-LW 80 (161)
T ss_pred CCEEEEECCccCCCCCCCceEEEEEEEC-----CC-CEEEEecccCccCHHHHHHHhCCC-----CEEEEEeccHHH-HH
Confidence 3578999999976522233557777431 01 11222222 234556677642 333 55667888 44
Q ss_pred HHHHHHHHcCCCCCCCCchhhhhHHHhcC-CC----CcccHHH-HhcC---------CCCCC------CCchHHHHHHHH
Q 036628 88 MLESECRFKNIPKPSYFNRWINLRVPFSK-GD----VRCNLKE-AVEL---------GWHGR------VHCGLDDSMNIA 146 (254)
Q Consensus 88 fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~----~~~~L~~-~l~i---------~~eG~------~HrALdDA~ntA 146 (254)
.|.+ ..|+.+. ..+|++..... +. .+..|.+ ++|. +|..+ -|=|..||..+.
T Consensus 81 ~L~~---~~gi~~~----~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~ 153 (161)
T cd06129 81 KLLR---DFGEKLQ----RLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALL 153 (161)
T ss_pred HHHH---HcCCCcc----cHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHH
Confidence 5542 3566543 34777664443 21 1223333 3343 44332 455889999999
Q ss_pred HHHHHHH
Q 036628 147 RLLAVIM 153 (254)
Q Consensus 147 ~l~~~ll 153 (254)
+|+.+|.
T Consensus 154 ~l~~~l~ 160 (161)
T cd06129 154 IIYTKLR 160 (161)
T ss_pred HHHHHHh
Confidence 9988875
No 86
>PRK05762 DNA polymerase II; Reviewed
Probab=66.53 E-value=40 Score=35.33 Aligned_cols=76 Identities=20% Similarity=0.326 Sum_probs=45.6
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEce-------EE-EEcCCCeEEEEE-EEe-----ehhhHHHHhhhcCCCCCCeEEE
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPS-------VI-VSGVTGQITVCF-QIY-----ALFLHDNWQQHMGVTPTNFAVV 78 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgA-------V~-vD~~~g~iv~~F-~~~-----vl~~f~~wl~~~gi~~~~~~~v 78 (254)
=..+.||+|+++. .+|+.|+. |+ +...+.. .+.| ..+ .+.+|.+++.+.. --+++
T Consensus 155 lrvlsfDIE~~~~------~~i~sI~~~~~~~~~vi~ig~~~~~-~~~~v~~~~sE~~LL~~F~~~i~~~D----PDIIv 223 (786)
T PRK05762 155 LKVVSLDIETSNK------GELYSIGLEGCGQRPVIMLGPPNGE-ALDFLEYVADEKALLEKFNAWFAEHD----PDVII 223 (786)
T ss_pred CeEEEEEEEEcCC------CceEEeeecCCCCCeEEEEECCCCC-CcceEEEcCCHHHHHHHHHHHHHhcC----CCEEE
Confidence 3689999999863 25666663 22 2111111 1122 122 3678888888742 22566
Q ss_pred Ec-C-cccHHHHHHHHHHHcCCCC
Q 036628 79 TW-S-DWDCQVMLESECRFKNIPK 100 (254)
Q Consensus 79 t~-g-~fD~~~fL~~e~~~~gi~~ 100 (254)
+| + .|| ..+|.+-++.+|+++
T Consensus 224 GyNi~~FD-lpyL~~Ra~~lgi~~ 246 (786)
T PRK05762 224 GWNVVQFD-LRLLQERAERYGIPL 246 (786)
T ss_pred EeCCCCCc-HHHHHHHHHHhCCCc
Confidence 65 4 699 678888888899875
No 87
>PHA02528 43 DNA polymerase; Provisional
Probab=64.36 E-value=48 Score=35.40 Aligned_cols=82 Identities=15% Similarity=0.174 Sum_probs=46.8
Q ss_pred CeEEEEEEeecCCCCCC--C--CCcEEEEceE--------EEEcC-------CCe-----EEE--EEEEe-----ehhhH
Q 036628 13 DYFVVVDFEATCDKKIP--H--PQEIIEFPSV--------IVSGV-------TGQ-----ITV--CFQIY-----ALFLH 61 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~--~--~~EIIEIgAV--------~vD~~-------~g~-----iv~--~F~~~-----vl~~f 61 (254)
=..+.||+||+...+.| . .++||.||.. ++... .|. +.+ .+..+ .+.+|
T Consensus 106 lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F 185 (881)
T PHA02528 106 IRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEY 185 (881)
T ss_pred ccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHH
Confidence 35899999998644434 2 4589999971 12100 011 111 11112 36788
Q ss_pred HHHhhhcCCCCCCeEEEEcC--cccHHHHHHHHHH-HcCCC
Q 036628 62 DNWQQHMGVTPTNFAVVTWS--DWDCQVMLESECR-FKNIP 99 (254)
Q Consensus 62 ~~wl~~~gi~~~~~~~vt~g--~fD~~~fL~~e~~-~~gi~ 99 (254)
.+|+.+.. .-+++.|. .|| ..+|..-++ ..|+.
T Consensus 186 ~~~i~~~D----PDII~GyNi~~FD-lpYL~~Ra~~~lg~~ 221 (881)
T PHA02528 186 INFWEENT----PVIFTGWNVELFD-VPYIINRIKNILGEK 221 (881)
T ss_pred HHHHHHhC----CcEEEecCCccCC-HHHHHHHHHHHcCcc
Confidence 88887642 23666664 699 567766665 34544
No 88
>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=64.05 E-value=92 Score=26.54 Aligned_cols=131 Identities=11% Similarity=0.055 Sum_probs=66.5
Q ss_pred CCeEEEEEEeecCCCCC--CCCCcEEEEceEEEEcCCCeEEEEEEEeehh-----hHHHHhhhcCCCCCCeE-EEEcCcc
Q 036628 12 FDYFVVVDFEATCDKKI--PHPQEIIEFPSVIVSGVTGQITVCFQIYALF-----LHDNWQQHMGVTPTNFA-VVTWSDW 83 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~--~~~~EIIEIgAV~vD~~~g~iv~~F~~~vl~-----~f~~wl~~~gi~~~~~~-~vt~g~f 83 (254)
-...|.||+|++..... ...--+|+|.. .+ . +--|+.+.+. .+..++.+ -+.+.+.. +.++...
T Consensus 21 ~~~vig~D~Ew~~~~~~~~~~~v~LiQiat-----~~-~-~~lid~~~~~~~~~~~~~~~L~~-ll~d~~i~KVg~~~~~ 92 (193)
T cd06146 21 AGRVVGIDSEWKPSFLGDSDPRVAILQLAT-----ED-E-VFLLDLLALENLESEDWDRLLKR-LFEDPDVLKLGFGFKQ 92 (193)
T ss_pred cCCEEEEECccCCCccCCCCCCceEEEEec-----CC-C-EEEEEchhccccchHHHHHHHHH-HhCCCCeeEEEechHH
Confidence 34579999999866521 23456888863 11 1 1122222111 22222321 00122333 5567789
Q ss_pred cHHHHHHHHHHHcCCCC--CCCCchhhhhHHHhcC-C------------CC---cccHHHH-hcC---------CCCCC-
Q 036628 84 DCQVMLESECRFKNIPK--PSYFNRWINLRVPFSK-G------------DV---RCNLKEA-VEL---------GWHGR- 134 (254)
Q Consensus 84 D~~~fL~~e~~~~gi~~--P~~~~~~iDlr~~f~~-~------------~~---~~~L~~~-l~i---------~~eG~- 134 (254)
| ..+|.+.+ |+.. +......+|++..+.. . .. +..|++. +|. +|+.+
T Consensus 93 D-~~~L~~~~---~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rp 168 (193)
T cd06146 93 D-LKALSASY---PALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRP 168 (193)
T ss_pred H-HHHHHHhc---CccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCC
Confidence 9 56776543 3321 1123566787665432 0 11 2233332 332 44332
Q ss_pred -----CCchHHHHHHHHHHHHHHHH
Q 036628 135 -----VHCGLDDSMNIARLLAVIMQ 154 (254)
Q Consensus 135 -----~HrALdDA~ntA~l~~~ll~ 154 (254)
-+=|..||..+.+|+.+|.+
T Consensus 169 Ls~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 169 LREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34588999999999998863
No 89
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=63.94 E-value=39 Score=32.55 Aligned_cols=131 Identities=18% Similarity=0.169 Sum_probs=74.8
Q ss_pred CCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEE-----------e-------------ehhhHHHHhh
Q 036628 11 DFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQI-----------Y-------------ALFLHDNWQQ 66 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~-----------~-------------vl~~f~~wl~ 66 (254)
...+.+++|-|+...+ ...|+..+++|=+|. ..+.|+|-- | .+....+.|.
T Consensus 214 ~~~~i~AlDCEm~~te---~g~el~RVt~VD~~~--~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~ 288 (380)
T KOG2248|consen 214 KSPNIFALDCEMVVTE---NGLELTRVTAVDRDG--KVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELL 288 (380)
T ss_pred CCCCeEEEEeeeeeec---cceeeEEeeeeeccC--cEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHH
Confidence 3456899999997655 347899999876642 223333321 2 0122222222
Q ss_pred hcCCCCCCeEEEEcC-cccHHHHHHHHHHHcCCCCCCCCchhhhhHHHhcC--C-CC-cc---cHHH-HhcCCC-CC-CC
Q 036628 67 HMGVTPTNFAVVTWS-DWDCQVMLESECRFKNIPKPSYFNRWINLRVPFSK--G-DV-RC---NLKE-AVELGW-HG-RV 135 (254)
Q Consensus 67 ~~gi~~~~~~~vt~g-~fD~~~fL~~e~~~~gi~~P~~~~~~iDlr~~f~~--~-~~-~~---~L~~-~l~i~~-eG-~~ 135 (254)
+ +.+.+.++|..| .-|+ +-|+ +. ....||...+|.. + +. +. .|++ +|+... +| ..
T Consensus 289 ~--~~~~~TILVGHSLenDL-~aLK-------l~----H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~ 354 (380)
T KOG2248|consen 289 E--LISKNTILVGHSLENDL-KALK-------LD----HPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGG 354 (380)
T ss_pred h--hcCcCcEEEeechhhHH-HHHh-------hh----CCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCC
Confidence 2 123456777766 5673 3343 11 2345777777766 3 12 22 2332 444322 33 35
Q ss_pred CchHHHHHHHHHHHHHHHHcCCccC
Q 036628 136 HCGLDDSMNIARLLAVIMQRGFKFS 160 (254)
Q Consensus 136 HrALdDA~ntA~l~~~ll~~g~~f~ 160 (254)
|....||+++.+|+...+..+..+.
T Consensus 355 HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 355 HDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred CccHHHHHHHHHHHHHHHhcccccC
Confidence 9999999999999998888766543
No 90
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=61.62 E-value=7 Score=36.07 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=22.3
Q ss_pred eEEEEcC-cccHHHHHHHHHHHcCCCCC
Q 036628 75 FAVVTWS-DWDCQVMLESECRFKNIPKP 101 (254)
Q Consensus 75 ~~~vt~g-~fD~~~fL~~e~~~~gi~~P 101 (254)
+.++|+| .+| ..+|..+++.-|+..|
T Consensus 122 CLVaHng~~~d-fpil~qela~lg~~lp 148 (318)
T KOG4793|consen 122 CLVAHNGNEYD-FPILAQELAGLGYSLP 148 (318)
T ss_pred eEEeecCCccc-cHHHHHHHHhcCccch
Confidence 5678888 588 6799999999999988
No 91
>PRK10829 ribonuclease D; Provisional
Probab=56.37 E-value=1.9e+02 Score=27.70 Aligned_cols=122 Identities=12% Similarity=0.105 Sum_probs=65.7
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEc----eEEEEcCCCeEEEEEEEeehhhHHHHhhhcCCCCCCeEEEEcCcccHHHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFP----SVIVSGVTGQITVCFQIYALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVML 89 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIg----AV~vD~~~g~iv~~F~~~vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL 89 (254)
..|.||.|+.........--+|+|+ +.+||+-. .-.+..+.+.+.+.++ .-+.|.+++|+ .+|
T Consensus 23 ~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~--------~~d~~~L~~ll~~~~i----vKV~H~~~~Dl-~~l 89 (373)
T PRK10829 23 PAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLG--------ITDWSPFKALLRDPQV----TKFLHAGSEDL-EVF 89 (373)
T ss_pred CeEEEecccccCccCCCceeEEEEecCCceEEEecCC--------ccchHHHHHHHcCCCe----EEEEeChHhHH-HHH
Confidence 4789999998765211223456663 22333211 0013445556654321 23678899994 556
Q ss_pred HHHHHHcCCCCCCCCchhhhhHHHhcC-CCC-ccc---HH-HHhcC---------CCCCC------CCchHHHHHHHHHH
Q 036628 90 ESECRFKNIPKPSYFNRWINLRVPFSK-GDV-RCN---LK-EAVEL---------GWHGR------VHCGLDDSMNIARL 148 (254)
Q Consensus 90 ~~e~~~~gi~~P~~~~~~iDlr~~f~~-~~~-~~~---L~-~~l~i---------~~eG~------~HrALdDA~ntA~l 148 (254)
.+ ..|+... ..+|++..... |.. ..+ |. +++|+ +|.-+ .+=|.+|+..+..|
T Consensus 90 ~~---~~g~~p~----~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l 162 (373)
T PRK10829 90 LN---AFGELPQ----PLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPI 162 (373)
T ss_pred HH---HcCCCcC----CeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 43 4566432 44666654433 322 223 32 34554 33222 23389999999998
Q ss_pred HHHHHHc
Q 036628 149 LAVIMQR 155 (254)
Q Consensus 149 ~~~ll~~ 155 (254)
+.+|.+.
T Consensus 163 ~~~L~~~ 169 (373)
T PRK10829 163 AAKLMAE 169 (373)
T ss_pred HHHHHHH
Confidence 8887664
No 92
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=52.32 E-value=2.2e+02 Score=27.31 Aligned_cols=123 Identities=15% Similarity=0.203 Sum_probs=68.0
Q ss_pred eEEEEEEeecCCCCCCCCCc--EEEEc----eEEEEcCCCeEEEEEEEeehhhHHHHhhhcCCCCCCeEEEEcCcccHHH
Q 036628 14 YFVVVDFEATCDKKIPHPQE--IIEFP----SVIVSGVTGQITVCFQIYALFLHDNWQQHMGVTPTNFAVVTWSDWDCQV 87 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~E--IIEIg----AV~vD~~~g~iv~~F~~~vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~ 87 (254)
.+|.||.|+.+.. ++..+ +|+|. +.+||...+ .+-.+-|...+....+ .-+.|.++||+.
T Consensus 18 ~~iAiDTEf~r~~--t~~p~LcLIQi~~~e~~~lIdpl~~-------~~d~~~l~~Ll~d~~v----~KIfHaa~~DL~- 83 (361)
T COG0349 18 KAIAIDTEFMRLR--TYYPRLCLIQISDGEGASLIDPLAG-------ILDLPPLVALLADPNV----VKIFHAARFDLE- 83 (361)
T ss_pred CceEEeccccccc--ccCCceEEEEEecCCCceEeccccc-------ccccchHHHHhcCCce----eeeeccccccHH-
Confidence 4899999999886 44444 55553 344443322 1224667777765443 248999999954
Q ss_pred HHHHHHHHcCCCCCCCCchhhhhHHHhcC-C--CCcccHH-HHhcC---------CCCCC------CCchHHHHHHHHHH
Q 036628 88 MLESECRFKNIPKPSYFNRWINLRVPFSK-G--DVRCNLK-EAVEL---------GWHGR------VHCGLDDSMNIARL 148 (254)
Q Consensus 88 fL~~e~~~~gi~~P~~~~~~iDlr~~f~~-~--~~~~~L~-~~l~i---------~~eG~------~HrALdDA~ntA~l 148 (254)
+|.+.+ |+...+.|.+.|= ..+.. + +.+.+|. +.+|+ +|--+ .-=|..|+.++..|
T Consensus 84 ~l~~~~---g~~p~plfdTqiA--a~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l 158 (361)
T COG0349 84 VLLNLF---GLLPTPLFDTQIA--AKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPL 158 (361)
T ss_pred HHHHhc---CCCCCchhHHHHH--HHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHH
Confidence 454332 5543334433322 12323 2 2233343 34454 22111 11268899999999
Q ss_pred HHHHHHc
Q 036628 149 LAVIMQR 155 (254)
Q Consensus 149 ~~~ll~~ 155 (254)
..+|.+.
T Consensus 159 ~~~L~~~ 165 (361)
T COG0349 159 YDKLTEE 165 (361)
T ss_pred HHHHHHH
Confidence 8887665
No 93
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=49.85 E-value=22 Score=31.18 Aligned_cols=24 Identities=21% Similarity=0.141 Sum_probs=21.2
Q ss_pred CcEEEEceEEEEcCCCeEEEEEEEe
Q 036628 32 QEIIEFPSVIVSGVTGQITVCFQIY 56 (254)
Q Consensus 32 ~EIIEIgAV~vD~~~g~iv~~F~~~ 56 (254)
---.|||++.+..++| |++.||++
T Consensus 8 y~PaEiai~~fSL~~G-I~~~~H~~ 31 (213)
T PF13017_consen 8 YVPAEIAICKFSLKEG-IIDSFHTF 31 (213)
T ss_pred EEeEEEEEEEEecCCc-cchhhhcc
Confidence 3468999999999887 89999999
No 94
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=48.86 E-value=12 Score=39.68 Aligned_cols=36 Identities=14% Similarity=0.487 Sum_probs=23.5
Q ss_pred eeeeecCcccccceeccCCCCCCCceeecCCCCCCCCCcccccccc
Q 036628 207 FRYCFCGAKSFKKIIRKPGPKCGSFFFGCGNLTPNKGACCNYFHSA 252 (254)
Q Consensus 207 ~~~c~cg~~~~~~~~~~~gp~~g~~f~~c~~~~~~~~~~c~~f~w~ 252 (254)
+|-|.||-. ++.+-|. -|+.||+|++++ .|.|..|.
T Consensus 696 CP~~~C~g~----l~~r~gr-~G~~f~~Cs~yp-----~C~~~~~~ 731 (860)
T PRK06319 696 CPAIGCTGH----IVKRRSR-FNKMFYSCSEYP-----ACSVIGNS 731 (860)
T ss_pred CCCcCCCCc----EEEEecC-CCCeeeccCCCC-----CCceeecc
Confidence 455668743 3334454 377899999873 48888664
No 95
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=44.89 E-value=15 Score=37.77 Aligned_cols=38 Identities=13% Similarity=0.317 Sum_probs=24.9
Q ss_pred eeecCcccccceeccCCCCCCCceeecCCCCCCCC--Ccccccccc
Q 036628 209 YCFCGAKSFKKIIRKPGPKCGSFFFGCGNLTPNKG--ACCNYFHSA 252 (254)
Q Consensus 209 ~c~cg~~~~~~~~~~~gp~~g~~f~~c~~~~~~~~--~~c~~f~w~ 252 (254)
.|-||-. ++++ -|.+ |+ |.+|++++.-.+ .+|+|=.|.
T Consensus 613 ~cpcg~~---l~~~-~~~~-g~-f~~c~~~p~C~~~~~~c~~~~~~ 652 (660)
T TIGR01056 613 PVSCGGI---AKCP-AKDN-GR-LIDCKKFPECTEYGNGCEFTIPK 652 (660)
T ss_pred cCCCCCc---eeee-ecCC-Ce-eecCCCCCCccCcCCCCeEEccH
Confidence 4558853 2333 3544 54 999999865543 689998885
No 96
>PF10902 DUF2693: Protein of unknown function (DUF2693); InterPro: IPR024401 This family of proteins is found in bacteria and bacteriophages. Its function is unknown.
Probab=43.36 E-value=22 Score=26.92 Aligned_cols=38 Identities=11% Similarity=0.094 Sum_probs=30.0
Q ss_pred CCcCCCCCCeEEEEEEeecCCCCCCCCCcEEEEceEEEE
Q 036628 5 LPQKLQDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVS 43 (254)
Q Consensus 5 ~~~~~q~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD 43 (254)
.|.+.+......++|+|+.++. .-..+.+|+|+-+.++
T Consensus 41 ~~~rkes~~s~~yfDve~~~WR-SFk~dnLIsV~gl~~~ 78 (83)
T PF10902_consen 41 KPERKESTTSVRYFDVEKKGWR-SFKIDNLISVNGLKIE 78 (83)
T ss_pred CccccCCcceEEEEEeccCcee-eeeheeEEEECCcChH
Confidence 3446778888999999999996 4456889999987763
No 97
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=42.48 E-value=1.2e+02 Score=31.89 Aligned_cols=83 Identities=19% Similarity=0.171 Sum_probs=52.7
Q ss_pred CeEEEEEEeecCCC-CCC--CCCcEEEEceEEEEcCCCeE-------EEEEEEe-------ehhhHHHHhhhcCCCCCCe
Q 036628 13 DYFVVVDFEATCDK-KIP--HPQEIIEFPSVIVSGVTGQI-------TVCFQIY-------ALFLHDNWQQHMGVTPTNF 75 (254)
Q Consensus 13 ~~fvViDlEtTg~~-~~~--~~~EIIEIgAV~vD~~~g~i-------v~~F~~~-------vl~~f~~wl~~~gi~~~~~ 75 (254)
-..+++|+|+.... ..+ ..+.|+.|+...-. .++.+ ...|... .+.+|.+|+.+.+ .-
T Consensus 154 l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~-~~~~~~~~~~~~~~~~~v~~~~~e~e~l~~~~~~i~~~d----Pd 228 (792)
T COG0417 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEA-EGGLIEVFIYTSGEGFSVEVVISEAELLERFVELIREYD----PD 228 (792)
T ss_pred ceEEEEEEEEecCCCCCCCccCCceEEEEEEecc-CCCccccccccCCCCceeEEecCHHHHHHHHHHHHHhcC----CC
Confidence 35799999999876 222 36778888776542 22211 1112211 4678888887643 23
Q ss_pred EEEE-cC-cccHHHHHHHHHHHcCCCCC
Q 036628 76 AVVT-WS-DWDCQVMLESECRFKNIPKP 101 (254)
Q Consensus 76 ~~vt-~g-~fD~~~fL~~e~~~~gi~~P 101 (254)
++++ ++ +|| ..+|..-+...|++..
T Consensus 229 VIvgyn~~~fd-~pyl~~Ra~~lgi~~~ 255 (792)
T COG0417 229 VIVGYNGDNFD-WPYLAERAERLGIPLR 255 (792)
T ss_pred EEEeccCCcCC-hHHHHHHHHHhCCCcc
Confidence 5666 55 499 7899888889988765
No 98
>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=38.46 E-value=2.8e+02 Score=24.39 Aligned_cols=31 Identities=10% Similarity=-0.025 Sum_probs=22.8
Q ss_pred CeEEEEEEeecCCC-C--CCCCCcEEEEceEEEE
Q 036628 13 DYFVVVDFEATCDK-K--IPHPQEIIEFPSVIVS 43 (254)
Q Consensus 13 ~~fvViDlEtTg~~-~--~~~~~EIIEIgAV~vD 43 (254)
=..+.+|+|+.... . +|..++||.|..++-+
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~ 37 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDD 37 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEec
Confidence 35678999997544 2 3567899999988654
No 99
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=35.09 E-value=45 Score=29.00 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=21.5
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEE
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQ 54 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~ 54 (254)
||++||+=||+.+ ++++| ++|+++.+-+
T Consensus 1 y~lgiDiGTts~K------------~~l~d-~~g~iv~~~~ 28 (245)
T PF00370_consen 1 YYLGIDIGTTSVK------------AVLFD-EDGKIVASAS 28 (245)
T ss_dssp EEEEEEECSSEEE------------EEEEE-TTSCEEEEEE
T ss_pred CEEEEEEcccceE------------EEEEe-CCCCEEEEEE
Confidence 6899999999754 67888 7787765543
No 100
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]
Probab=32.73 E-value=25 Score=33.31 Aligned_cols=21 Identities=33% Similarity=0.698 Sum_probs=18.6
Q ss_pred ccceeccCCCCCCCceeecCC
Q 036628 217 FKKIIRKPGPKCGSFFFGCGN 237 (254)
Q Consensus 217 ~~~~~~~~gp~~g~~f~~c~~ 237 (254)
.-.+|++||||-||.||=|+.
T Consensus 299 dy~~Vsk~~~n~~r~~~Ic~r 319 (335)
T KOG1294|consen 299 DYILVSKPGPNNGRRFYICSR 319 (335)
T ss_pred eEEEecCcCCCCCceeeeecC
Confidence 345999999999999999976
No 101
>PRK07726 DNA topoisomerase III; Provisional
Probab=31.12 E-value=28 Score=35.69 Aligned_cols=16 Identities=13% Similarity=0.326 Sum_probs=10.9
Q ss_pred ceeecCCCCCCCCCcccccccc
Q 036628 231 FFFGCGNLTPNKGACCNYFHSA 252 (254)
Q Consensus 231 ~f~~c~~~~~~~~~~c~~f~w~ 252 (254)
.||||.|++ |.+++|.
T Consensus 629 ~f~~Cs~~~------~~~~~~~ 644 (658)
T PRK07726 629 KMLVCQDRE------CGKRKNV 644 (658)
T ss_pred eeEecCCCc------ccccccc
Confidence 499999842 5555773
No 102
>PF12377 DuffyBP_N: Duffy binding protein N terminal ; InterPro: IPR021032 This entry represents the N terminus of the Duffy-antigen binding protein and is thought to bind to the human erythrocytes Duffy blood group determinant. These domains are found in eukaryotic proteins and are approximately 70 amino acids in length [].
Probab=30.93 E-value=21 Score=25.36 Aligned_cols=27 Identities=19% Similarity=0.557 Sum_probs=17.9
Q ss_pred CCeEEEEEEeecCCCCCC--CCCcEEEEce
Q 036628 12 FDYFVVVDFEATCDKKIP--HPQEIIEFPS 39 (254)
Q Consensus 12 ~~~fvViDlEtTg~~~~~--~~~EIIEIgA 39 (254)
-.++|++|.||++-. -| -.+.++||++
T Consensus 20 ~~nlvmldyd~s~ng-hp~g~~dnvle~~t 48 (66)
T PF12377_consen 20 CNNLVMLDYDTSSNG-HPAGTIDNVLEFVT 48 (66)
T ss_pred ccceEEEEeeccCCC-CcCchhhhHHHhhh
Confidence 357999999998754 12 2455666654
No 103
>PF07846 Metallothio_Cad: Metallothionein family; InterPro: IPR012484 The sequence making up family 7 of the metallothionein superfamily are found repeated in metallothionein proteins expressed by two Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess []. Some of the metallothioneins found in this family (for example, Q8T6B3 from SWISSPROT) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes []. Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit. ; GO: 0046870 cadmium ion binding
Probab=30.47 E-value=30 Score=19.37 Aligned_cols=17 Identities=29% Similarity=0.737 Sum_probs=12.4
Q ss_pred eecCcccccceeccCCCCCC
Q 036628 210 CFCGAKSFKKIIRKPGPKCG 229 (254)
Q Consensus 210 c~cg~~~~~~~~~~~gp~~g 229 (254)
|-||+.++-.-. .||.|
T Consensus 1 CccG~naK~cC~---DPnsG 17 (21)
T PF07846_consen 1 CCCGVNAKPCCT---DPNSG 17 (21)
T ss_pred CccCCCCccccc---CCCCc
Confidence 678888877654 67776
No 104
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=25.55 E-value=5.4e+02 Score=25.78 Aligned_cols=37 Identities=11% Similarity=0.037 Sum_probs=23.6
Q ss_pred hhhHHHHhhhcCCCCCCeEEEEcC--cccHHHHHHHHHH-HcCCC
Q 036628 58 LFLHDNWQQHMGVTPTNFAVVTWS--DWDCQVMLESECR-FKNIP 99 (254)
Q Consensus 58 l~~f~~wl~~~gi~~~~~~~vt~g--~fD~~~fL~~e~~-~~gi~ 99 (254)
|.+|.+|+.+.. --++.+|. +|| ..+|..-++ ..|+.
T Consensus 184 L~~F~~~i~~~D----PDIItGYNi~nFD-lPYL~~Ra~~~lGi~ 223 (498)
T PHA02524 184 LLNYIQLWKANT----PDLVFGWNSEGFD-IPYIITRITNILGEK 223 (498)
T ss_pred HHHHHHHHHHhC----CCEEEeCCCcccC-HHHHHHHHHHHhCCc
Confidence 567888887642 22566664 699 567766664 46663
No 105
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=25.46 E-value=5.8e+02 Score=24.12 Aligned_cols=124 Identities=14% Similarity=0.084 Sum_probs=62.5
Q ss_pred CeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe---ehhhHHHHhhhcCCCCCCeEEEEcCcccHHHHH
Q 036628 13 DYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY---ALFLHDNWQQHMGVTPTNFAVVTWSDWDCQVML 89 (254)
Q Consensus 13 ~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~---vl~~f~~wl~~~gi~~~~~~~vt~g~fD~~~fL 89 (254)
...|.||.|++........--+|+|+. +..+--|..+ .+..+.+++.+.+ -..+.++...| ..+|
T Consensus 18 ~~~ia~DtE~~~~~~y~~~l~LiQia~-------~~~~~liD~~~~~~~~~L~~lL~d~~----i~KV~h~~k~D-l~~L 85 (367)
T TIGR01388 18 FPFVALDTEFVRERTFWPQLGLIQVAD-------GEQLALIDPLVIIDWSPLKELLRDES----VVKVLHAASED-LEVF 85 (367)
T ss_pred CCEEEEeccccCCCCCCCcceEEEEee-------CCeEEEEeCCCcccHHHHHHHHCCCC----ceEEEeecHHH-HHHH
Confidence 358999999987652111234555532 1111122222 2455666776432 12467788899 4556
Q ss_pred HHHHHHcCCCCCCCCchhhhhHHHhcC-C----CCcccHH-HHhcCCCC-CC-----CCc---------hHHHHHHHHHH
Q 036628 90 ESECRFKNIPKPSYFNRWINLRVPFSK-G----DVRCNLK-EAVELGWH-GR-----VHC---------GLDDSMNIARL 148 (254)
Q Consensus 90 ~~e~~~~gi~~P~~~~~~iDlr~~f~~-~----~~~~~L~-~~l~i~~e-G~-----~Hr---------ALdDA~ntA~l 148 (254)
.+ .+...| ...+|++..... + ....+|. +++|+... +. ..+ |..||..+..|
T Consensus 86 ~~----~~~~~~---~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L 158 (367)
T TIGR01388 86 LN----LFGELP---QPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158 (367)
T ss_pred HH----HhCCCC---CCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 43 233344 234666553221 1 1123343 34555321 10 022 67888888888
Q ss_pred HHHHHHc
Q 036628 149 LAVIMQR 155 (254)
Q Consensus 149 ~~~ll~~ 155 (254)
+..|.++
T Consensus 159 ~~~L~~~ 165 (367)
T TIGR01388 159 YAKLMER 165 (367)
T ss_pred HHHHHHH
Confidence 8877654
No 106
>COG3218 ABC-type uncharacterized transport system, auxiliary component [General function prediction only]
Probab=24.46 E-value=92 Score=27.49 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=32.3
Q ss_pred CCCeEEEEEEeecCCC-CCCCCCcEEEEceEEEEcCCCeEEEE--EEEe
Q 036628 11 DFDYFVVVDFEATCDK-KIPHPQEIIEFPSVIVSGVTGQITVC--FQIY 56 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~-~~~~~~EIIEIgAV~vD~~~g~iv~~--F~~~ 56 (254)
.-||-+..|+-+=... ..+.+.-.|||-+.+++.++|+++.. |..-
T Consensus 122 ~aDy~l~~dlr~FE~~y~~~~~~A~Iei~v~Ll~~~n~~v~A~r~F~a~ 170 (205)
T COG3218 122 AADYQLILDLRAFEIQYVTGAPTAVIEISVRLLNDRNGTVRASRVFRAS 170 (205)
T ss_pred eeeeeeeehhhhhhhhccCCCceEEEEEEEEEeccCCCcEEEEEEEEEe
Confidence 3567777776554333 33566789999999999999998643 5544
No 107
>COG1070 XylB Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=23.69 E-value=98 Score=30.44 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=21.4
Q ss_pred CCCeEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEE
Q 036628 11 DFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVC 52 (254)
Q Consensus 11 ~~~~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~ 52 (254)
..+++++||+=||+.+ ||++|...++++++
T Consensus 2 ~~~~~lgIDiGTt~~K------------avl~d~~~~~~~~~ 31 (502)
T COG1070 2 MMKYVLGIDIGTTSVK------------AVLFDEDGGEVVAT 31 (502)
T ss_pred CccEEEEEEcCCCcEE------------EEEEeCCCCeEEEE
Confidence 4679999999999876 66777443555443
No 108
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=22.91 E-value=83 Score=20.90 Aligned_cols=14 Identities=36% Similarity=0.449 Sum_probs=9.5
Q ss_pred eEEEEcCCCeEEEE
Q 036628 39 SVIVSGVTGQITVC 52 (254)
Q Consensus 39 AV~vD~~~g~iv~~ 52 (254)
-|.||+.+|+|++.
T Consensus 50 ~v~VDa~tG~Il~~ 63 (64)
T PF03413_consen 50 EVYVDAYTGEILSS 63 (64)
T ss_dssp EEEEETTT--EEEE
T ss_pred EEEEECCCCeEEEe
Confidence 35699999999875
No 109
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=22.60 E-value=68 Score=25.16 Aligned_cols=44 Identities=25% Similarity=0.486 Sum_probs=28.2
Q ss_pred eeeecCcccccceeccCCCCCCCceeecCCC-CCCCCCcccccccc
Q 036628 208 RYCFCGAKSFKKIIRKPGPKCGSFFFGCGNL-TPNKGACCNYFHSA 252 (254)
Q Consensus 208 ~~c~cg~~~~~~~~~~~gp~~g~~f~~c~~~-~~~~~~~c~~f~w~ 252 (254)
.-|.|..+....+-+.| -..|+.||+|.-- ..+-|..|.|=.|-
T Consensus 21 ie~dcnakvvvats~dp-vts~klyfscpyeisdg~g~~~gfkrww 65 (122)
T PF05325_consen 21 IECDCNAKVVVATSRDP-VTSGKLYFSCPYEISDGPGRGCGFKRWW 65 (122)
T ss_pred eeccCCceEEEEeccCC-cccceeeecCccccccCCCCCccceeEE
Confidence 46788776555443333 3579999999422 33356789998873
No 110
>PHA03036 DNA polymerase; Provisional
Probab=22.05 E-value=1e+03 Score=26.17 Aligned_cols=36 Identities=17% Similarity=0.275 Sum_probs=25.9
Q ss_pred CCCCCeEEEEEEeecCCCCCC--CCCcEEEEceEEEEc
Q 036628 9 LQDFDYFVVVDFEATCDKKIP--HPQEIIEFPSVIVSG 44 (254)
Q Consensus 9 ~q~~~~fvViDlEtTg~~~~~--~~~EIIEIgAV~vD~ 44 (254)
..---.|+-||+|+-.....| ..+-||.|....+|.
T Consensus 156 ~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~ 193 (1004)
T PHA03036 156 FDIPRSYLFLDIECHFDKKFPSVFINPVSHISCCYIDL 193 (1004)
T ss_pred ccCcceeEEEEEEeccCCCCCCcccCcceEEEEEEEec
Confidence 334456999999998543333 568899999877774
No 111
>PF14574 DUF4445: Domain of unknown function (DUF4445); PDB: 3ZYY_X.
Probab=20.58 E-value=2e+02 Score=28.03 Aligned_cols=31 Identities=23% Similarity=0.319 Sum_probs=24.4
Q ss_pred eEEEEEEeecCCCCCCCCCcEEEEceEEEEcCCCeEEEEEEEe
Q 036628 14 YFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIY 56 (254)
Q Consensus 14 ~fvViDlEtTg~~~~~~~~EIIEIgAV~vD~~~g~iv~~F~~~ 56 (254)
+=++||+=||. |.+.++|.++|+++++.+.+
T Consensus 2 ~GiAvDiGTTt------------i~~~L~dl~~G~~l~~~s~~ 32 (412)
T PF14574_consen 2 YGIAVDIGTTT------------IAAYLVDLETGEVLATASFL 32 (412)
T ss_dssp EEEEEEE-SSE------------EEEEEEETTT--EEEEEEEE
T ss_pred EEEEEEcchhh------------eeeEEEECCCCCEEEeeccc
Confidence 34789999994 67899999999999999998
Done!