Query psy5651
Match_columns 843
No_of_seqs 410 out of 1683
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 23:10:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5651.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5651hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04845 PurA: PurA ssDNA and 100.0 2E-62 4.3E-67 495.9 8.2 198 309-506 4-211 (218)
2 KOG3074|consensus 100.0 2.5E-57 5.3E-62 460.1 14.1 197 309-506 25-232 (263)
3 PRK10829 ribonuclease D; Provi 100.0 2.2E-42 4.8E-47 379.8 27.0 241 18-285 2-258 (373)
4 COG0349 Rnd Ribonuclease D [Tr 100.0 4.8E-40 1.1E-44 356.4 23.1 238 22-285 1-254 (361)
5 TIGR01388 rnd ribonuclease D. 100.0 2.8E-38 6.1E-43 346.9 26.1 238 21-285 1-254 (367)
6 PF04845 PurA: PurA ssDNA and 100.0 2E-36 4.3E-41 307.1 1.9 141 297-444 71-218 (218)
7 KOG3074|consensus 100.0 6.6E-32 1.4E-36 275.1 10.4 141 302-448 97-243 (263)
8 KOG2206|consensus 100.0 2.7E-30 5.9E-35 289.5 13.1 253 8-287 181-453 (687)
9 cd06129 RNaseD_like DEDDy 3'-5 100.0 3.1E-29 6.8E-34 244.8 17.3 157 28-206 2-161 (161)
10 cd06148 Egl_like_exo DEDDy 3'- 100.0 1.8E-29 4E-34 254.9 15.3 190 31-224 3-193 (197)
11 cd06146 mut-7_like_exo DEDDy 3 100.0 3.4E-28 7.3E-33 245.4 18.4 177 19-205 1-192 (193)
12 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 9.8E-27 2.1E-31 227.1 18.1 163 23-205 2-169 (170)
13 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 8.4E-26 1.8E-30 217.4 18.4 170 19-209 1-176 (176)
14 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 2E-21 4.3E-26 188.9 21.0 173 28-224 2-176 (178)
15 smart00474 35EXOc 3'-5' exonuc 99.8 1.5E-18 3.2E-23 165.6 19.4 167 20-208 2-171 (172)
16 smart00712 PUR DNA/RNA-binding 99.8 1.1E-19 2.4E-24 154.7 7.1 63 382-445 1-63 (63)
17 cd06147 Rrp6p_like_exo DEDDy 3 99.8 1.3E-17 2.8E-22 167.0 19.9 173 16-212 2-176 (192)
18 PRK05755 DNA polymerase I; Pro 99.7 9.2E-17 2E-21 194.3 21.8 186 18-222 295-483 (880)
19 cd06140 DNA_polA_I_Bacillus_li 99.7 8.6E-16 1.9E-20 150.6 16.6 162 38-219 3-167 (178)
20 cd09018 DEDDy_polA_RNaseD_like 99.7 1.4E-15 2.9E-20 143.7 15.0 146 40-205 1-149 (150)
21 cd00007 35EXOc 3'-5' exonuclea 99.7 1.9E-15 4E-20 141.6 14.9 151 40-207 2-154 (155)
22 cd06139 DNA_polA_I_Ecoli_like_ 99.6 1.6E-14 3.5E-19 142.1 17.6 170 36-219 3-182 (193)
23 PRK14975 bifunctional 3'-5' ex 99.6 4.7E-15 1E-19 171.6 13.2 151 19-219 3-161 (553)
24 smart00712 PUR DNA/RNA-binding 99.5 6.2E-15 1.3E-19 125.8 2.9 62 309-370 2-63 (63)
25 KOG2207|consensus 99.3 1.2E-12 2.6E-17 149.6 7.2 180 17-209 390-586 (617)
26 TIGR00593 pola DNA polymerase 99.3 4.4E-11 9.5E-16 145.2 18.9 178 19-219 304-488 (887)
27 COG0749 PolA DNA polymerase I 99.3 2.5E-11 5.5E-16 140.4 14.8 184 21-219 5-192 (593)
28 cd06128 DNA_polA_exo DEDDy 3'- 98.9 5.9E-08 1.3E-12 93.3 15.1 132 53-205 17-150 (151)
29 KOG2405|consensus 97.9 6.9E-07 1.5E-11 98.7 -4.2 150 43-196 63-215 (458)
30 KOG4373|consensus 97.8 6.8E-05 1.5E-09 82.1 8.2 131 52-201 145-281 (319)
31 KOG2405|consensus 97.4 1.7E-05 3.7E-10 88.0 -2.8 168 51-225 208-379 (458)
32 cd06125 DnaQ_like_exo DnaQ-lik 97.3 0.00067 1.5E-08 62.0 6.9 73 41-125 1-83 (96)
33 PRK07942 DNA polymerase III su 97.2 0.0069 1.5E-07 63.8 14.1 85 94-212 94-184 (232)
34 PRK06063 DNA polymerase III su 97.1 0.0096 2.1E-07 65.6 14.9 139 38-213 15-184 (313)
35 PRK07740 hypothetical protein; 97.1 0.014 3.1E-07 62.0 15.3 96 83-215 133-233 (244)
36 TIGR01298 RNaseT ribonuclease 97.1 0.01 2.2E-07 61.1 13.7 85 94-214 106-198 (200)
37 PF11680 DUF3276: Protein of u 97.1 0.00095 2.1E-08 64.6 5.7 67 379-445 8-82 (124)
38 cd06131 DNA_pol_III_epsilon_Ec 96.8 0.0096 2.1E-07 58.3 10.5 87 82-204 72-166 (167)
39 PRK06310 DNA polymerase III su 96.7 0.034 7.4E-07 59.4 14.8 135 35-208 4-174 (250)
40 smart00479 EXOIII exonuclease 96.7 0.087 1.9E-06 50.9 15.9 91 82-209 71-168 (169)
41 PRK05168 ribonuclease T; Provi 96.7 0.05 1.1E-06 56.5 15.1 86 93-214 114-207 (211)
42 PRK05711 DNA polymerase III su 96.6 0.046 9.9E-07 58.4 14.5 88 83-206 78-174 (240)
43 TIGR01406 dnaQ_proteo DNA poly 96.6 0.038 8.3E-07 58.1 13.7 88 83-206 74-170 (225)
44 COG2176 PolC DNA polymerase II 96.5 0.0088 1.9E-07 74.5 9.2 158 35-231 418-612 (1444)
45 cd06144 REX4_like DEDDh 3'-5' 96.5 0.012 2.6E-07 57.7 8.6 84 82-202 68-152 (152)
46 PRK06309 DNA polymerase III su 96.5 0.12 2.5E-06 54.6 16.4 133 39-209 3-167 (232)
47 TIGR00573 dnaq exonuclease, DN 96.4 0.048 1E-06 56.7 13.0 95 83-210 79-179 (217)
48 PRK06807 DNA polymerase III su 96.3 0.077 1.7E-06 58.7 14.9 89 83-209 80-173 (313)
49 PRK09146 DNA polymerase III su 96.3 0.1 2.2E-06 55.6 15.2 147 36-209 45-228 (239)
50 PRK07883 hypothetical protein; 96.3 0.066 1.4E-06 63.5 14.8 144 33-213 10-187 (557)
51 PRK06195 DNA polymerase III su 96.3 0.11 2.3E-06 57.2 15.3 91 83-211 72-167 (309)
52 TIGR01405 polC_Gram_pos DNA po 96.2 0.086 1.9E-06 67.5 15.9 143 36-215 188-362 (1213)
53 cd06130 DNA_pol_III_epsilon_li 96.1 0.14 3.1E-06 49.2 13.9 65 82-158 68-137 (156)
54 cd06137 DEDDh_RNase DEDDh 3'-5 96.1 0.065 1.4E-06 53.2 11.6 64 84-159 76-140 (161)
55 PRK07246 bifunctional ATP-depe 96.0 0.14 3E-06 63.5 16.4 138 37-213 6-175 (820)
56 cd06145 REX1_like DEDDh 3'-5' 96.0 0.069 1.5E-06 52.6 11.0 61 83-158 67-128 (150)
57 PRK08517 DNA polymerase III su 96.0 0.23 4.9E-06 53.6 15.7 134 36-209 66-232 (257)
58 PRK05601 DNA polymerase III su 95.9 0.1 2.2E-06 59.2 13.3 143 35-204 43-245 (377)
59 PRK09145 DNA polymerase III su 95.9 0.23 5E-06 51.0 14.7 143 28-205 19-198 (202)
60 cd06134 RNaseT DEDDh 3'-5' exo 95.9 0.22 4.7E-06 50.9 14.3 78 94-207 103-188 (189)
61 cd06149 ISG20 DEDDh 3'-5' exon 95.4 0.15 3.2E-06 50.7 10.7 65 82-159 68-136 (157)
62 cd05160 DEDDy_DNA_polB_exo DED 95.4 0.29 6.2E-06 49.6 13.1 99 82-201 67-198 (199)
63 PRK08074 bifunctional ATP-depe 95.2 0.34 7.4E-06 60.8 15.5 137 38-212 3-173 (928)
64 TIGR01407 dinG_rel DnaQ family 95.1 0.45 9.7E-06 59.1 16.3 92 83-211 72-168 (850)
65 smart00341 HRDC Helicase and R 95.0 0.03 6.4E-07 48.8 4.2 48 236-286 2-50 (81)
66 cd06127 DEDDh DEDDh 3'-5' exon 94.8 0.52 1.1E-05 44.2 12.2 83 82-201 70-158 (159)
67 PF13482 RNase_H_2: RNase_H su 94.3 0.063 1.4E-06 52.4 5.0 150 41-204 1-163 (164)
68 PRK09182 DNA polymerase III su 94.3 0.75 1.6E-05 50.7 13.7 87 82-206 111-199 (294)
69 KOG2249|consensus 94.1 0.31 6.7E-06 53.0 9.9 134 39-211 106-269 (280)
70 PRK00448 polC DNA polymerase I 93.6 0.82 1.8E-05 59.9 14.2 88 93-215 499-591 (1437)
71 cd05780 DNA_polB_Kod1_like_exo 93.6 0.86 1.9E-05 46.7 11.8 104 82-204 60-195 (195)
72 PRK07983 exodeoxyribonuclease 93.1 1.8 3.9E-05 45.8 13.5 80 94-208 75-154 (219)
73 PF00570 HRDC: HRDC domain Blo 92.8 0.054 1.2E-06 45.9 1.5 47 238-287 1-48 (68)
74 PRK11779 sbcB exonuclease I; P 91.5 4.8 0.0001 47.4 15.7 98 83-207 83-197 (476)
75 PRK07247 DNA polymerase III su 90.9 5.7 0.00012 41.3 14.0 93 82-209 75-170 (195)
76 PF11680 DUF3276: Protein of u 90.6 0.15 3.2E-06 49.8 2.0 31 455-485 13-44 (124)
77 cd06136 TREX1_2 DEDDh 3'-5' ex 90.3 4.9 0.00011 40.6 12.7 80 83-202 86-175 (177)
78 cd06133 ERI-1_3'hExo_like DEDD 90.3 7.8 0.00017 37.9 13.8 89 82-204 79-175 (176)
79 cd05781 DNA_polB_B3_exo DEDDy 89.8 6.5 0.00014 40.4 13.2 151 39-204 4-188 (188)
80 cd06143 PAN2_exo DEDDh 3'-5' e 88.8 1.1 2.3E-05 46.3 6.6 76 85-201 95-173 (174)
81 cd05785 DNA_polB_like2_exo Unc 88.4 4.7 0.0001 42.2 11.2 150 39-201 10-206 (207)
82 cd05782 DNA_polB_like1_exo Unc 87.8 4.4 9.5E-05 42.4 10.6 135 51-202 48-207 (208)
83 PRK06722 exonuclease; Provisio 87.2 13 0.00029 41.0 14.3 163 82-295 81-262 (281)
84 COG0847 DnaQ DNA polymerase II 84.6 15 0.00032 38.5 12.6 90 84-207 87-181 (243)
85 PRK07748 sporulation inhibitor 84.5 5.6 0.00012 41.2 9.3 92 82-208 83-180 (207)
86 cd06138 ExoI_N N-terminal DEDD 81.1 11 0.00024 38.3 9.7 75 83-159 74-165 (183)
87 PF10108 DNA_pol_B_exo2: Predi 80.4 24 0.00052 37.6 12.1 108 80-205 39-170 (209)
88 KOG3657|consensus 77.1 4.9 0.00011 49.8 6.6 106 94-210 242-385 (1075)
89 PF09281 Taq-exonuc: Taq polym 71.0 13 0.00028 37.1 6.7 68 102-208 70-138 (138)
90 TIGR01389 recQ ATP-dependent D 70.5 4.5 9.7E-05 48.2 4.2 47 238-287 521-568 (591)
91 KOG1275|consensus 63.4 4.8 0.0001 50.3 2.5 101 88-231 1009-1110(1118)
92 PTZ00315 2'-phosphotransferase 62.3 1.5E+02 0.0034 36.2 14.5 100 82-205 134-252 (582)
93 cd05784 DNA_polB_II_exo DEDDy 61.9 62 0.0013 33.7 10.0 55 144-202 138-193 (193)
94 PF00929 RNase_T: Exonuclease; 55.3 3.2 6.9E-05 38.9 -0.6 84 83-201 74-164 (164)
95 cd05776 DNA_polB_alpha_exo ina 54.5 25 0.00054 37.4 5.8 96 90-204 96-226 (234)
96 KOG2206|consensus 48.1 8.4 0.00018 46.3 1.2 29 273-301 397-428 (687)
97 cd05783 DNA_polB_B1_exo DEDDy 41.4 4.4E+02 0.0096 27.6 14.1 103 81-202 76-202 (204)
98 cd05779 DNA_polB_epsilon_exo D 39.5 4.5E+02 0.0098 27.7 12.2 50 145-202 154-204 (204)
99 cd06135 Orn DEDDh 3'-5' exonuc 36.3 1.8E+02 0.0039 29.4 8.4 40 83-122 80-127 (173)
100 KOG2248|consensus 35.0 1E+02 0.0022 35.8 7.1 63 83-159 285-348 (380)
101 PRK05359 oligoribonuclease; Pr 33.3 2.2E+02 0.0047 29.3 8.5 18 38-55 3-21 (181)
102 COG3359 Predicted exonuclease 32.9 7.4E+02 0.016 27.7 12.6 158 40-210 100-271 (278)
103 PRK05762 DNA polymerase II; Re 32.4 5.6E+02 0.012 32.4 13.4 108 82-204 207-348 (786)
104 PF04857 CAF1: CAF1 family rib 22.7 1.2E+02 0.0026 32.8 4.7 55 91-157 147-216 (262)
No 1
>PF04845 PurA: PurA ssDNA and RNA-binding protein; InterPro: IPR006628 The Pur protein family consists of four known members in humans and is strongly conserved throughout evolution. Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. Pur-alpha has a modular structure with alternating three basic aromatic class I and two acidic leucine-rich class II repeats in the central region of the protein []. In addition to its involved in basic cellular function, Pur-alpha, has been implicated in the development of blood cells and cells of the central nervous system; it has also been implicated in the inhibition of oncogenic transformation and along with Pur-beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. JC virus causes opportunistic infections in the brains of certain HIV-1-infected individuals [].; PDB: 3K44_A.
Probab=100.00 E-value=2e-62 Score=495.95 Aligned_cols=198 Identities=36% Similarity=0.596 Sum_probs=122.5
Q ss_pred ccchhhHHhhhhhHhhhhccCCccceEEeeecCCccceeEEEecchHHHHHHHHHHHHHHhcC-CC--CCCCCCcc--cc
Q psy5651 309 IDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAHQN-TP--RHRYRDTH--TI 383 (843)
Q Consensus 309 L~Sk~L~~l~Kr~y~DlKeN~RGrFlkI~E~~~~g~rs~I~ls~~~~~efrd~L~~lie~y~~-~~--~~~~~~~~--~l 383 (843)
|+||+|+.++||||+|+|||.||||+||+|++++|++|+|+||+++|+||||||++|+|+|++ +| ++.+++++ .|
T Consensus 4 Lask~l~iq~KrfYlDVkqN~RGrfiKiaE~~~~g~ksri~lsm~~A~efrd~L~~f~~~ya~l~p~n~~~~~~~~~~~l 83 (218)
T PF04845_consen 4 LASKMLQIQNKRFYLDVKQNRRGRFIKIAEVGAGGRKSRITLSMSAAAEFRDHLGDFIEFYAQLGPSNPENLPDEGRSEL 83 (218)
T ss_dssp EEEEEEEETTEEEEEEEEEETTEEEEEEEEE-TT--EEEEEEEHHHHHHHHHHHHHHHHHHHCS-S--SS---TT---EC
T ss_pred hhhhheEecceEEEEEecccCcceeEEEeeccCCCCcceEEEechhHHHHHHHHHHHHHHHhccCCCCccccccccccee
Confidence 999999999999999999999999999999999999999999999999999999999999999 65 55666665 99
Q ss_pred ccceeeecccEEEEeccCCCcceEEEEEecccCC--CCCceEEEcccCHHHHHHHHHHHHHHhCCCCC---CCCCCCCce
Q psy5651 384 KSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVG--GKLSSIAFPAQDLGPIIGLISDLQQEHSCPED---EDGAPEGNY 458 (843)
Q Consensus 384 ~Se~i~ve~KrFyfDlkeN~RGrFLRISE~~~r~--~~Rs~I~IPa~g~~~Frd~L~~l~ee~~~~~~---~~~lp~s~~ 458 (843)
+||.|++|+|+||||||||+|||||||||..++| |.|+||+|||+|+.+|+|||.+|+++||++++ .++||+|++
T Consensus 84 kSe~i~~e~r~yylDLKEN~RGrfLRisq~~~~~~~~~R~qIaiPa~G~~ef~~al~~lid~~g~~~~~~~~~~Lpes~~ 163 (218)
T PF04845_consen 84 KSEKINVENRRYYLDLKENSRGRFLRISQTVSRGPRGRRSQIAIPAQGMIEFRDALTDLIDEFGEDDEEDEQGELPESKS 163 (218)
T ss_dssp EEEEEEETTEEEEEEEEEETTEEEEEEEEEETTT----EEEEEEEGGGHHHHHHHHHHHHHHH-----------------
T ss_pred eehheeeccceEEEEcccccCcceEEEEEeeccCCCCCccEEEEehHHHHHHHHHHHHHHHHhcCcccccccccCCCCcE
Confidence 9999999999999999999999999999998877 89999999999999999999999999999762 335999999
Q ss_pred eeeeceEEEEEcCCCCceeEEEEeeecCCCCceeEEeeccccccCCcc
Q psy5651 459 MRCNNKRFFFNVSKNGKGTFMRISEISTPSKVLTNIGIKSNIKTDTNI 506 (843)
Q Consensus 459 ~r~d~K~fyFD~g~N~rG~fLRISEv~~~~r~~~~i~~~~~~~~~~~~ 506 (843)
+++|||+||||+|+|+||+|||||||++++|+.|+||.++|++|-+-+
T Consensus 164 lrvdnK~FyFD~g~N~rG~fLrISEv~~~~Rs~ItIP~~~w~~Fr~~~ 211 (218)
T PF04845_consen 164 LRVDNKRFYFDVGSNRRGVFLRISEVKSNFRSAITIPESAWSRFRDIF 211 (218)
T ss_dssp ------------------------------------------------
T ss_pred EEECCeEEEEECCCCCCeeEEEecccCCCCCceeeCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999997744
No 2
>KOG3074|consensus
Probab=100.00 E-value=2.5e-57 Score=460.15 Aligned_cols=197 Identities=33% Similarity=0.551 Sum_probs=185.6
Q ss_pred ccchhhHHhhhhhHhhhhccCCccceEEeeecCCccceeEEEecchHHHHHHHHHHHHHHhcC-CC----CCCCCCcccc
Q psy5651 309 IDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAHQN-TP----RHRYRDTHTI 383 (843)
Q Consensus 309 L~Sk~L~~l~Kr~y~DlKeN~RGrFlkI~E~~~~g~rs~I~ls~~~~~efrd~L~~lie~y~~-~~----~~~~~~~~~l 383 (843)
|+||.|++++||||+|+|||+|||||||+|++.+++ |+|+||+++|+||+|+|++|+++|++ +| .++++++..|
T Consensus 25 Lask~l~iq~KrfYlDvkqN~rGRflKIaE~g~~~~-Sri~ls~s~aaef~d~l~~f~~~ya~lg~~~~~~~~~~ee~~l 103 (263)
T KOG3074|consen 25 LASKRLQIQHKRFYLDVKQNPRGRFLKIAEVGAGGR-SRIILSLSVAAEFRDILNDFIEHYAQLGPPPPELAAPSEEHEL 103 (263)
T ss_pred HhhhhhhhhhheEEEEeccCCCcceEEEEEeccCCc-ceEEEehhhHHHHHHHHHHHHHHHHhcCCCCcccccchhhhhH
Confidence 999999999999999999999999999999997654 99999999999999999999999999 65 2456677899
Q ss_pred ccceeeecccEEEEeccCCCcceEEEEEecccCCC-CCce---EEEcccCHHHHHHHHHHHHHHhCCCCCCCCCCCCcee
Q psy5651 384 KSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGG-KLSS---IAFPAQDLGPIIGLISDLQQEHSCPEDEDGAPEGNYM 459 (843)
Q Consensus 384 ~Se~i~ve~KrFyfDlkeN~RGrFLRISE~~~r~~-~Rs~---I~IPa~g~~~Frd~L~~l~ee~~~~~~~~~lp~s~~~ 459 (843)
+|+.++.|+|+||||||||.|||||||+|+..+++ .|+| |++|+|||++|||+|.+|+++||++|+.+++|++.++
T Consensus 104 kSe~L~~d~RkfY~DLKEN~RGRFLRI~qt~~rg~~~~~Q~~tIalPaqG~aEfrdaLaelle~~G~~~~gqelpeg~~~ 183 (263)
T KOG3074|consen 104 KSEELQRDNRKFYLDLKENQRGRFLRISQTPMRGRQTRTQVQTIALPAQGIAEFRDALAELLEDFGEGDEGQELPEGTSI 183 (263)
T ss_pred HHHHHhhcCceEEEEcccccccceEEeeecccCCCCccccccceeccchhHHHHHHHHHHHHHHhCCccccCCCCCCCeE
Confidence 99999999999999999999999999999987766 6777 9999999999999999999999999876889999999
Q ss_pred eeeceEEEEEcCCCCceeEEEEeeecC--CCCceeEEeeccccccCCcc
Q psy5651 460 RCNNKRFFFNVSKNGKGTFMRISEIST--PSKVLTNIGIKSNIKTDTNI 506 (843)
Q Consensus 460 r~d~K~fyFD~g~N~rG~fLRISEv~~--~~r~~~~i~~~~~~~~~~~~ 506 (843)
.||||+||||+|+|+||.|+|||||++ ++|+.||+|.++|.+|.+.+
T Consensus 184 tvDnk~F~Fd~G~N~~G~f~riSEVk~n~~yRnsITvP~k~w~~F~~~f 232 (263)
T KOG3074|consen 184 TVDNKRFLFDVGKNKRGVFVRISEVKSNGSYRNSITVPFKAWKRFGEVF 232 (263)
T ss_pred EEecceeEEecCCCCccceEEEEEecCCCCcccceeeehhHhhhhhhHH
Confidence 999999999999999999999999998 89999999999999999875
No 3
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=2.2e-42 Score=379.84 Aligned_cols=241 Identities=18% Similarity=0.206 Sum_probs=218.7
Q ss_pred CcEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceE
Q psy5651 18 RTNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILK 96 (843)
Q Consensus 18 ~~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlK 96 (843)
.|.+|+|+++|+++++.+..++.+|+||||++. +|++++|||||++.+ ++|+||++++. ++++|+++|+|++++|
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~-~~~LiD~l~~~---d~~~L~~ll~~~~ivK 77 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGE-QLSLIDPLGIT---DWSPFKALLRDPQVTK 77 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecCC-ceEEEecCCcc---chHHHHHHHcCCCeEE
Confidence 478999999999999999999999999999999 999999999999754 79999999875 4789999999999999
Q ss_pred EEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCc
Q psy5651 97 VIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPH 175 (843)
Q Consensus 97 VgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~S 175 (843)
|+|+|++|+++|++.+|+.+.++||||+|+++||.+. ++||+.|+++| |+.++ |+ ++.+
T Consensus 78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~-----------~~gl~~Lv~~~lgv~ld--K~-------~~~s 137 (373)
T PRK10829 78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPL-----------SCGFASMVEEYTGVTLD--KS-------ESRT 137 (373)
T ss_pred EEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCc-----------cccHHHHHHHHhCCccC--cc-------cccC
Confidence 9999999999998999999999999999999998753 48999999999 99998 53 6889
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHHH------------hhhcccCC-CCCChHhhHHH
Q psy5651 176 IWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIYE------------TLFNHVVP-LNIRKRRQFRQ 242 (843)
Q Consensus 176 DW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~e------------~~y~~v~~-~~L~~r~l~~L 242 (843)
||..||||++|+.|||.||+||+.||+.|.++|.+.|+.+|+.+||.. ..|.++++ |.+++++++++
T Consensus 138 DW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~lavl 217 (373)
T PRK10829 138 DWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACL 217 (373)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHhccccCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999999962 35677776 78999999999
Q ss_pred HHHHHHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhh
Q psy5651 243 NQLRRWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKL 285 (843)
Q Consensus 243 ~eL~~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~ 285 (843)
++|++|||..|+. +.|++||+. ++.|+......|.+..++
T Consensus 218 ~~L~~WRe~~Ar~~d~p~~~Vl~---d~~L~~lA~~~P~~~~~L 258 (373)
T PRK10829 218 QLLADWRLRKARERDLAVNFVVR---EEHLWQVARYMPGSLGEL 258 (373)
T ss_pred HHHHHHHHHHHHHhCCCcceecC---hHHHHHHHHhCCCCHHHH
Confidence 9999999999986 799999995 668888666788775544
No 4
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-40 Score=356.42 Aligned_cols=238 Identities=24% Similarity=0.317 Sum_probs=211.8
Q ss_pred ecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEec
Q psy5651 22 ITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHG 100 (843)
Q Consensus 22 IdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHd 100 (843)
|++.+.+++++..+.+++.||+||||.++ +|++++||||++.+++ +++||+.... .++++|..+|.|++|+||||+
T Consensus 1 i~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~-~~lIdpl~~~--~d~~~l~~Ll~d~~v~KIfHa 77 (361)
T COG0349 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEG-ASLIDPLAGI--LDLPPLVALLADPNVVKIFHA 77 (361)
T ss_pred CCchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCC-ceEecccccc--cccchHHHHhcCCceeeeecc
Confidence 45677899999999999999999999999 9999999999997764 9999998742 257899999999999999999
Q ss_pred ccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCC
Q psy5651 101 AFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKT 179 (843)
Q Consensus 101 aK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~ 179 (843)
+++|+.+|++.+|+.|.++||||+|+.++|.+. ++||++||+++ |++++ |+ +|.+||.+
T Consensus 78 a~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-----------~~gl~~Lv~~ll~v~ld--K~-------~q~SDW~~ 137 (361)
T COG0349 78 ARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-----------SHGLADLVEELLGVELD--KS-------EQRSDWLA 137 (361)
T ss_pred ccccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-----------cccHHHHHHHHhCCccc--cc-------cccccccc
Confidence 999999999999999999999999999999864 59999999999 99998 53 78999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHH------------HhhhcccC-CCCCChHhhHHHHHHH
Q psy5651 180 RPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIY------------ETLFNHVV-PLNIRKRRQFRQNQLR 246 (843)
Q Consensus 180 RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~------------e~~y~~v~-~~~L~~r~l~~L~eL~ 246 (843)
||||++|++|||.||.||+.||+.|.++|.+.|+..|++++|. +..|.+++ .|.+++++++++++|+
T Consensus 138 RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a~~~~p~~la~l~~La 217 (361)
T COG0349 138 RPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKIAHSLDPRELAVLRELA 217 (361)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhhhhcCChHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999997 23455555 4778999999999999
Q ss_pred HHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhh
Q psy5651 247 RWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKL 285 (843)
Q Consensus 247 ~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~ 285 (843)
+|||..|++ +.|++||+. ++.+|......|....++
T Consensus 218 ~wRe~~Ar~rd~~~~~vl~---de~i~~~a~~~P~~~~~l 254 (361)
T COG0349 218 AWREREARERDLARNFVLK---DEALWELARYTPKNLKEL 254 (361)
T ss_pred HHHHHHHHHhccccccccc---hhHHHHHHHhCCCCHHHH
Confidence 999999987 599999995 778998555555554443
No 5
>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=100.00 E-value=2.8e-38 Score=346.88 Aligned_cols=238 Identities=22% Similarity=0.284 Sum_probs=213.1
Q ss_pred EecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEe
Q psy5651 21 LITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIH 99 (843)
Q Consensus 21 lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgH 99 (843)
||+|+++|+++++.+..++.+||||||++. +|++++|||||++.+ .+|+||+..+. +++.|.++|+|+++.||+|
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~~-~~~liD~~~~~---~~~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGE-QLALIDPLVII---DWSPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeCC-eEEEEeCCCcc---cHHHHHHHHCCCCceEEEe
Confidence 588999999999999999999999999998 999999999999765 89999998764 4789999999999999999
Q ss_pred cccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCC
Q psy5651 100 GAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWK 178 (843)
Q Consensus 100 daK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~ 178 (843)
|+++|+++|++.+|..+.++||||+|+|+|+++. ++||+.|+++| |+.++ |+ ++.++|.
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~-----------~~~l~~Lv~~~Lg~~l~--K~-------~~~sdW~ 136 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGM-----------SMGYAKLVQEVLGVELD--KS-------ESRTDWL 136 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCC-----------CccHHHHHHHHcCCCCC--cc-------cccccCC
Confidence 9999999998878888888999999999999864 47999999999 98876 42 5689999
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHHH------------hhhcccCC-CCCChHhhHHHHHH
Q psy5651 179 TRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIYE------------TLFNHVVP-LNIRKRRQFRQNQL 245 (843)
Q Consensus 179 ~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~e------------~~y~~v~~-~~L~~r~l~~L~eL 245 (843)
.|||+++|+.||+.||++|+.||+.|.++|.+.|+..|+.+||.. ..|.++++ |.+++++++++++|
T Consensus 137 ~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~~~l~~~~l~~l~~L 216 (367)
T TIGR01388 137 ARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQAL 216 (367)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhcccccCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999982 34666765 78999999999999
Q ss_pred HHHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhh
Q psy5651 246 RRWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKL 285 (843)
Q Consensus 246 ~~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~ 285 (843)
++|||..|+. +.|++||+. ++.++......|.+..++
T Consensus 217 ~~wRe~~A~~~d~p~~~il~---d~~l~~lA~~~P~~~~~l 254 (367)
T TIGR01388 217 AAWREREARERDLPRNFVLK---EEALWELARQAPGNLTEL 254 (367)
T ss_pred HHHHHHHHHHcCCCcceeeC---HHHHHHHHHhCCCCHHHH
Confidence 9999999987 699999995 678888777777765553
No 6
>PF04845 PurA: PurA ssDNA and RNA-binding protein; InterPro: IPR006628 The Pur protein family consists of four known members in humans and is strongly conserved throughout evolution. Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. Pur-alpha has a modular structure with alternating three basic aromatic class I and two acidic leucine-rich class II repeats in the central region of the protein []. In addition to its involved in basic cellular function, Pur-alpha, has been implicated in the development of blood cells and cells of the central nervous system; it has also been implicated in the inhibition of oncogenic transformation and along with Pur-beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. JC virus causes opportunistic infections in the brains of certain HIV-1-infected individuals [].; PDB: 3K44_A.
Probab=100.00 E-value=2e-36 Score=307.12 Aligned_cols=141 Identities=22% Similarity=0.398 Sum_probs=60.1
Q ss_pred hhccCcccccccccchhhHHhhhhhHhhhhccCCccceEEeeecC-C--ccceeEEEecchHHHHHHHHHHHHHHhcCCC
Q psy5651 297 EKESANEERIEVIDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNM-D--QTRNQIHISMSVVGHLRDHLNALLTAHQNTP 373 (843)
Q Consensus 297 ~~es~~~~~~g~L~Sk~L~~l~Kr~y~DlKeN~RGrFlkI~E~~~-~--g~rs~I~ls~~~~~efrd~L~~lie~y~~~~ 373 (843)
+-|++|.+.+..|.|+.|..++|+||+|||||+|||||+|+|..+ + |++++|+||++|+.||+|+|.+|||+||++.
T Consensus 71 n~~~~~~~~~~~lkSe~i~~e~r~yylDLKEN~RGrfLRisq~~~~~~~~~R~qIaiPa~G~~ef~~al~~lid~~g~~~ 150 (218)
T PF04845_consen 71 NPENLPDEGRSELKSEKINVENRRYYLDLKENSRGRFLRISQTVSRGPRGRRSQIAIPAQGMIEFRDALTDLIDEFGEDD 150 (218)
T ss_dssp -SS---TT---ECEEEEEEETTEEEEEEEEEETTEEEEEEEEEETTT----EEEEEEEGGGHHHHHHHHHHHHHHH----
T ss_pred CcccccccccceeeehheeeccceEEEEcccccCcceEEEEEeeccCCCCCccEEEEehHHHHHHHHHHHHHHHHhcCcc
Confidence 344445555668999999999999999999999999999999975 3 6899999999999999999999999999843
Q ss_pred ----CCCCCCccccccceeeecccEEEEeccCCCcceEEEEEecccCCCCCceEEEcccCHHHHHHHHHHHHHHh
Q psy5651 374 ----RHRYRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGLISDLQQEH 444 (843)
Q Consensus 374 ----~~~~~~~~~l~Se~i~ve~KrFyfDlkeN~RGrFLRISE~~~r~~~Rs~I~IPa~g~~~Frd~L~~l~ee~ 444 (843)
+.++|+ |+++++|||+||||+|+|+||+||||||+ +++.|++|+||+++|.+||++|++|+++|
T Consensus 151 ~~~~~~~Lpe-----s~~lrvdnK~FyFD~g~N~rG~fLrISEv--~~~~Rs~ItIP~~~w~~Fr~~~~~~~e~M 218 (218)
T PF04845_consen 151 EEDEQGELPE-----SKSLRVDNKRFYFDVGSNRRGVFLRISEV--KSNFRSAITIPESAWSRFRDIFNEYAEEM 218 (218)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccccccCCC-----CcEEEECCeEEEEECCCCCCeeEEEeccc--CCCCCceeeCCHHHHHHHHHHHHHHHhcC
Confidence 234444 89999999999999999999999999999 46789999999999999999999999886
No 7
>KOG3074|consensus
Probab=99.97 E-value=6.6e-32 Score=275.15 Aligned_cols=141 Identities=25% Similarity=0.403 Sum_probs=126.8
Q ss_pred cccccccccchhhHHhhhhhHhhhhccCCccceEEeeecCCc--ccee---EEEecchHHHHHHHHHHHHHHhcCCCC-C
Q psy5651 302 NEERIEVIDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQ--TRNQ---IHISMSVVGHLRDHLNALLTAHQNTPR-H 375 (843)
Q Consensus 302 ~~~~~g~L~Sk~L~~l~Kr~y~DlKeN~RGrFlkI~E~~~~g--~rs~---I~ls~~~~~efrd~L~~lie~y~~~~~-~ 375 (843)
|.+. +.|.|++|..++++||+|||||+|||||+|+|+..+| +++| |+||++|++||||+|.+|+|.||.++. .
T Consensus 97 ~~ee-~~lkSe~L~~d~RkfY~DLKEN~RGRFLRI~qt~~rg~~~~~Q~~tIalPaqG~aEfrdaLaelle~~G~~~~gq 175 (263)
T KOG3074|consen 97 PSEE-HELKSEELQRDNRKFYLDLKENQRGRFLRISQTPMRGRQTRTQVQTIALPAQGIAEFRDALAELLEDFGEGDEGQ 175 (263)
T ss_pred chhh-hhHHHHHHhhcCceEEEEcccccccceEEeeecccCCCCccccccceeccchhHHHHHHHHHHHHHHhCCccccC
Confidence 3444 7799999999999999999999999999999986544 3566 999999999999999999999998553 5
Q ss_pred CCCCccccccceeeecccEEEEeccCCCcceEEEEEecccCCCCCceEEEcccCHHHHHHHHHHHHHHhCCCC
Q psy5651 376 RYRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGLISDLQQEHSCPE 448 (843)
Q Consensus 376 ~~~~~~~l~Se~i~ve~KrFyfDlkeN~RGrFLRISE~~~r~~~Rs~I~IPa~g~~~Frd~L~~l~ee~~~~~ 448 (843)
++|+ ..++.||||+||||+|+|.||.|+||||+.+.+++|++|+||.++|..|+++|++|+++++..-
T Consensus 176 elpe-----g~~~tvDnk~F~Fd~G~N~~G~f~riSEVk~n~~yRnsITvP~k~w~~F~~~f~~y~e~mk~~~ 243 (263)
T KOG3074|consen 176 ELPE-----GTSITVDNKRFLFDVGKNKRGVFVRISEVKSNGSYRNSITVPFKAWKRFGEVFGKYSEEMKKIS 243 (263)
T ss_pred CCCC-----CCeEEEecceeEEecCCCCccceEEEEEecCCCCcccceeeehhHhhhhhhHHHHHHHHHHHhh
Confidence 5665 7899999999999999999999999999987778999999999999999999999999998653
No 8
>KOG2206|consensus
Probab=99.96 E-value=2.7e-30 Score=289.53 Aligned_cols=253 Identities=23% Similarity=0.287 Sum_probs=208.1
Q ss_pred CcccccccCC-CcEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHH
Q psy5651 8 QNNLLRTLMN-RTNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKL 85 (843)
Q Consensus 8 ~~~l~~~~~~-~~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~L 85 (843)
+|..+.++.. .+.||++..+|.++.+.|.....+|+|+|++.+ +|.|-.||+||+|.+ +.|+||...+.+ ..+.|
T Consensus 181 ~~~~~~~le~T~~~~I~t~~el~~l~~~l~~~~Efavdlehhsyrsf~gltclmqISTr~-ed~iIDt~~l~~--~i~~l 257 (687)
T KOG2206|consen 181 EPRKSSPLEITPKVWICTLGELEALPEILDSVIEFAVDLEHHSYRSFLGLTCLMQISTRT-EDFIIDTFKLRD--HIGIL 257 (687)
T ss_pred cccCCCcccccCceeeechHHHHHHHHHHhhhhhhhhhccccchhhhcCceeEEEeeccc-hhheehhHHHHH--HHHHh
Confidence 4444444444 578999999999999999999999999999999 999999999999987 799999988754 45689
Q ss_pred HHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccc
Q psy5651 86 HEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKK 164 (843)
Q Consensus 86 keLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd 164 (843)
+++|.||.++||+|++..|+.||+++||+++.|+|||..|+.+|+.+. +||++|.+.| |+..+ |
T Consensus 258 ~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L~~~r------------~sL~~ll~~~~~v~~n--k- 322 (687)
T KOG2206|consen 258 NEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGLPR------------PSLAYLLECVCGVLTN--K- 322 (687)
T ss_pred hhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHHHHhCCCc------------ccHHHHHHHHHhhhhh--h-
Confidence 999999999999999999999999999999999999999999998864 8999999999 98766 3
Q ss_pred cccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-HHH----HHHHHHHh---------hhcccC
Q psy5651 165 NIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQN-RLL----LDNLIYET---------LFNHVV 230 (843)
Q Consensus 165 ~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~-~~L----feEEc~e~---------~y~~v~ 230 (843)
++|.+||+.|||+++|..||..|++||+.+|+.|+..|.+.+. ... ..+.|... -|.++.
T Consensus 323 ------~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~~~~~~~~~~d~c~~~~~k~~~~~~sy~~v~ 396 (687)
T KOG2206|consen 323 ------KYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDMCTNGYKKKTFCTKSYLEVE 396 (687)
T ss_pred ------hhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcccccccchhhhhhhcceecccCCCcchHhHH
Confidence 3789999999999999999999999999999999988876541 111 12333311 112221
Q ss_pred C--CCCChHhhHHHHHHHHHHHHHhhhc-CCcCceecccCccchhhhhhCCCchhhhhhh
Q psy5651 231 P--LNIRKRRQFRQNQLRRWRKDLMSSK-RPYPYIEEVNSNEYIWRNDYNVPLANAKLLN 287 (843)
Q Consensus 231 ~--~~L~~r~l~~L~eL~~WRe~~Ar~~-~pr~~I~~~n~~~~l~~~q~~vP~~~~~~i~ 287 (843)
. .++.++++.+++.|++||+-.||++ .+++||+ |+..+....--.|.+-..++.
T Consensus 397 ~~q~~ln~~q~~~l~~L~~wRd~iARaeDES~~yVl---pN~~ll~l~e~~P~~v~gl~~ 453 (687)
T KOG2206|consen 397 DIQSRLNSSQLDVLRALLRWRDFIARAEDESVHYVL---PNDQLLKLAEERPDTVDGLLG 453 (687)
T ss_pred HHHhccchhHHHHHHHHHHHHHHHHhhccCCCceec---ccHHHHHHHHHCCccHHHHHH
Confidence 1 3488999999999999999999975 9999999 567777655555655555443
No 9
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.96 E-value=3.1e-29 Score=244.84 Aligned_cols=157 Identities=29% Similarity=0.425 Sum_probs=141.9
Q ss_pred HHHHHHHHh-cCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccH
Q psy5651 28 AQSAMATIL-NESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDA 105 (843)
Q Consensus 28 LaelLe~Lk-~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL 105 (843)
|+++++++. ..+.+|+|+||.+. ++.|++|++|||++++.+|+||+..++. .+..|+++|+|+++.||+|++++|+
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~--~~~~L~~lL~d~~i~Kvg~~~k~D~ 79 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSV--DWQGLKMLLENPSIVKALHGIEGDL 79 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCcc--CHHHHHHHhCCCCEEEEEeccHHHH
Confidence 678899999 99999999999988 7889999999998745899999988753 4678999999999999999999999
Q ss_pred HHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCH
Q psy5651 106 GGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTS 184 (843)
Q Consensus 106 ~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSe 184 (843)
..|++.+|+.+.++|||++|+|+++++. +.||++|+++| |..++ |. .+.+||..||||+
T Consensus 80 ~~L~~~~gi~~~~~~D~~~aa~ll~~~~-----------~~~L~~l~~~~lg~~l~--K~-------~~~s~W~~rpLt~ 139 (161)
T cd06129 80 WKLLRDFGEKLQRLFDTTIAANLKGLPE-----------RWSLASLVEHFLGKTLD--KS-------ISCADWSYRPLTE 139 (161)
T ss_pred HHHHHHcCCCcccHhHHHHHHHHhCCCC-----------CchHHHHHHHHhCCCCC--cc-------ceeccCCCCCCCH
Confidence 9998789999999999999999998753 37999999999 98886 42 6789999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy5651 185 DMLLYAAADVESLLALFHRMTK 206 (843)
Q Consensus 185 eQL~YAA~DA~~LL~Lyd~L~~ 206 (843)
+|+.|||.||++++.||+.|++
T Consensus 140 ~qi~YAa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 140 DQKLYAAADVYALLIIYTKLRN 161 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999863
No 10
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.96 E-value=1.8e-29 Score=254.85 Aligned_cols=190 Identities=37% Similarity=0.578 Sum_probs=156.4
Q ss_pred HHHHHhcCCeEEEEeeeeCCCcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhh
Q psy5651 31 AMATILNESKVGLDLEGMDLGVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLS 110 (843)
Q Consensus 31 lLe~Lk~s~~IALDtE~~~~ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r 110 (843)
+++.+.+++.+|+|+||.+.+.+|++|++|||+.++++|+||+..++...+...|+++|+++++.||+||+++|+.+|++
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~ 82 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYH 82 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHH
Confidence 56778889999999999888668999999999874589999999876333568899999999999999999999999988
Q ss_pred hcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHH
Q psy5651 111 NFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLY 189 (843)
Q Consensus 111 ~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~Y 189 (843)
.+|+.+.++|||++|+|+|+++..|... ....+||++++++| |.+++.. +..+..+.++.++|..||||++|+.|
T Consensus 83 ~~gi~~~~~fDt~iA~~lL~~~~~~~~~---~~~~~~L~~l~~~~l~~~~~k~-~~~~~~~~~~~s~W~~RPLt~~ql~Y 158 (197)
T cd06148 83 QYGIKLNNVFDTQVADALLQEQETGGFN---PDRVISLVQLLDKYLYISISLK-EDVKKLMREDPKFWALRPLTEDMIRY 158 (197)
T ss_pred hcCccccceeeHHHHHHHHHHHhcCCcc---ccccccHHHHHHHhhCCChHHH-HHHHHHHhcCchhhhcCCCCHHHHHH
Confidence 9999999999999999999886432110 11246999999999 9887521 11111123678999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHHHh
Q psy5651 190 AAADVESLLALFHRMTKEYALKQNRLLLDNLIYET 224 (843)
Q Consensus 190 AA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~e~ 224 (843)
||.||++|+.||+.|...|.+......+++.|.++
T Consensus 159 Aa~Dv~~Ll~l~~~l~~~l~~~~~~~~~~~~~~~~ 193 (197)
T cd06148 159 AALDVLCLLPLYYAMLDALISKFLKAVFKYLNTER 193 (197)
T ss_pred HHHHHHhHHHHHHHHHHHhhhhHHHHHHHHhhhhh
Confidence 99999999999999999999877777777776553
No 11
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.96 E-value=3.4e-28 Score=245.39 Aligned_cols=177 Identities=27% Similarity=0.382 Sum_probs=146.8
Q ss_pred cEEecCHHHHHHHHHH--HhcCCeEEEEeeeeCC-C--cCceEEEEEEEEeCCeEEEEeCCCCCc---ccchHHHHHhhc
Q psy5651 19 TNLITDVQEAQSAMAT--ILNESKVGLDLEGMDL-G--VDGKVSLVSLALQNGKIFIFDVYSCPL---IMFDGKLHEVLE 90 (843)
Q Consensus 19 ~~lIdT~eeLaelLe~--Lk~s~~IALDtE~~~~-t--y~gkL~LIQIAT~dgqvyLID~laL~~---~~dLs~LkeLLE 90 (843)
+.+|++++++++++++ +...+.+|+|+||.+. . ..+++|++|||+.+ .+|+||+..++. ......|+++|+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~-~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATED-EVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecCC-CEEEEEchhccccchHHHHHHHHHHhC
Confidence 4689999999999999 8899999999999877 3 37899999999865 899999987752 223467999999
Q ss_pred CCCceEEEecccccHHHHhhhcCCc------cCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCcccc
Q psy5651 91 SDRILKVIHGAFGDAGGLLSNFNIR------LKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFK 163 (843)
Q Consensus 91 DpsIlKVgHdaK~DL~~L~r~~GI~------L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~K 163 (843)
||+|+||||++++|+..|++++|+. +.++|||+.+++.+.....+..-.......+||++|++++ |.+++ |
T Consensus 80 d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~--K 157 (193)
T cd06146 80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLD--K 157 (193)
T ss_pred CCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcC--c
Confidence 9999999999999999999999974 5789999998888764321100000011368999999999 98887 4
Q ss_pred ccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 164 KNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 164 d~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
. .++|||..||||++|+.|||.||++++.||+.|.
T Consensus 158 ~-------~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 158 S-------EQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred c-------cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3 6789999999999999999999999999999985
No 12
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.95 E-value=9.8e-27 Score=227.09 Aligned_cols=163 Identities=28% Similarity=0.408 Sum_probs=144.3
Q ss_pred cCHHHHHHHHHHHh-cCCeEEEEeeeeCC-C--cCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEE
Q psy5651 23 TDVQEAQSAMATIL-NESKVGLDLEGMDL-G--VDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVI 98 (843)
Q Consensus 23 dT~eeLaelLe~Lk-~s~~IALDtE~~~~-t--y~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVg 98 (843)
+++++++++++.+. ....+|+|+||.+. . +.+++|++|+|+.+ .+|+||+..++. ....|.++|+++++.||+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~-~~~l~~~~~~~~--~~~~l~~ll~~~~i~kv~ 78 (170)
T cd06141 2 DSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATES-RCLLFQLAHMDK--LPPSLKQLLEDPSILKVG 78 (170)
T ss_pred CCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecCC-cEEEEEhhhhhc--ccHHHHHHhcCCCeeEEE
Confidence 57888999999998 99999999999887 4 78899999999765 899999987642 457799999999999999
Q ss_pred ecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccC
Q psy5651 99 HGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIW 177 (843)
Q Consensus 99 HdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW 177 (843)
||+++|+..|++.+|+.+.++|||++|+|++++.. .+.||++|++.| |..++..| ..+.+||
T Consensus 79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~----------~~~~l~~l~~~~l~~~~~k~k-------~~~~s~W 141 (170)
T cd06141 79 VGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRR----------KLVSLARLVEEVLGLPLSKPK-------KVRCSNW 141 (170)
T ss_pred eeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCc----------CCccHHHHHHHHcCcccCCCC-------CcccCCC
Confidence 99999999998799999999999999999999853 136999999999 98887222 2678999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 178 KTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 178 ~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
..|||+++|++|||.||++++.||+.|.
T Consensus 142 ~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 142 EARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999885
No 13
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.94 E-value=8.4e-26 Score=217.42 Aligned_cols=170 Identities=29% Similarity=0.400 Sum_probs=147.2
Q ss_pred cEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-C--cCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCce
Q psy5651 19 TNLITDVQEAQSAMATILNESKVGLDLEGMDL-G--VDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRIL 95 (843)
Q Consensus 19 ~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-t--y~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIl 95 (843)
|++|++.+++.++++.+...+.+|+|+|+.+. . ..+.++++|+++.+ .+|++|+...+....+..|+++|+||++.
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~-~~~i~~~~~~~~~~~~~~l~~ll~~~~i~ 79 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYSYNPKIALIQLATGE-GCYIIDPIDLGDNWILDALKELLEDPNII 79 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESC-EEEEECGTTSTTTTHHHHHHHHHTTTTSE
T ss_pred CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccccCCeEEEEEEecCC-CceeeeeccccccchHHHHHHHHhCCCcc
Confidence 67899999999999999999999999999988 4 67899999999864 78998887665322368899999999999
Q ss_pred EEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-C-CCCccccccccccccCC
Q psy5651 96 KVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-K-ISPNNFKKNIQNLYREN 173 (843)
Q Consensus 96 KVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-G-v~Ld~~Kd~vK~~~keq 173 (843)
||+||+++|+.+|++.+|+.+.++|||++|++++++.. ++||++|+.+| | ...+ + +.+
T Consensus 80 kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~-----------~~~L~~L~~~~l~~~~~~--~-------~~~ 139 (176)
T PF01612_consen 80 KVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTR-----------SYSLKDLAEEYLGNIDLD--K-------KEQ 139 (176)
T ss_dssp EEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTST-----------TSSHHHHHHHHHSEEE-G--H-------CCT
T ss_pred EEEEEEechHHHHHHHhccccCCccchhhhhhcccccc-----------cccHHHHHHHHhhhccCc--H-------HHh
Confidence 99999999999998889999999999999999999864 38999999999 8 3333 2 267
Q ss_pred CccCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 174 PHIWK-TRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 174 ~SDW~-~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
.++|. .|||+++|+.|||.||+++++||+.|.++|+
T Consensus 140 ~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 140 MSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp TSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred hccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 89999 9999999999999999999999999999874
No 14
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.88 E-value=2e-21 Score=188.95 Aligned_cols=173 Identities=27% Similarity=0.374 Sum_probs=145.3
Q ss_pred HHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHH
Q psy5651 28 AQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAG 106 (843)
Q Consensus 28 LaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~ 106 (843)
|+++++.+...+.+|+|+|+.+. ++.+.++++|+++. +++|+||+... .....|+++|+|+++.||+||++.|+.
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~~i~~~~~---~~~~~l~~ll~~~~i~kv~~d~K~~~~ 77 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVYLIDPLAI---GDLSPLKELLADPNIVKVFHAAREDLE 77 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeC-CCEEEEeCCCc---ccHHHHHHHHcCCCceEEEeccHHHHH
Confidence 45566556556689999988666 55789999999976 46899986532 145678999999999999999999999
Q ss_pred HHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHH
Q psy5651 107 GLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSD 185 (843)
Q Consensus 107 ~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSee 185 (843)
.|++++|+...++|||++|+|+|+|+. +++|++++++| |..+. ++ ...++|..|||+.+
T Consensus 78 ~L~~~~gi~~~~~~D~~laayLl~p~~-----------~~~l~~l~~~~l~~~~~--~~-------~~~~~w~~~~l~~~ 137 (178)
T cd06142 78 LLKRDFGILPQNLFDTQIAARLLGLGD-----------SVGLAALVEELLGVELD--KG-------EQRSDWSKRPLTDE 137 (178)
T ss_pred HHHHHcCCCCCCcccHHHHHHHhCCCc-----------cccHHHHHHHHhCCCCC--cc-------cccccCCCCCCCHH
Confidence 997777999555899999999999864 36999999999 87643 21 35678999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHHHh
Q psy5651 186 MLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIYET 224 (843)
Q Consensus 186 QL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~e~ 224 (843)
|..||+.||.++++|++.|.++|.+.|...++.+||+..
T Consensus 138 ~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~~~~ 176 (178)
T cd06142 138 QLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECELL 176 (178)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHh
Confidence 999999999999999999999999999999999999865
No 15
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.81 E-value=1.5e-18 Score=165.59 Aligned_cols=167 Identities=32% Similarity=0.447 Sum_probs=134.4
Q ss_pred EEecCHHHHHHHHHHHh-cCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEE
Q psy5651 20 NLITDVQEAQSAMATIL-NESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKV 97 (843)
Q Consensus 20 ~lIdT~eeLaelLe~Lk-~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKV 97 (843)
.+|++.+++.++++.+. ..+.+|+|+|+.+. .+.+.++++|++..++.+|+++..... .....|.++|+++.+.||
T Consensus 2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~--~~~~~l~~~l~~~~~~kv 79 (172)
T smart00474 2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALG--DDLEILKDLLEDETITKV 79 (172)
T ss_pred EEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccch--hhHHHHHHHhcCCCceEE
Confidence 57888888888777776 56699999998766 567899999999643355665543222 124568999999999999
Q ss_pred EecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCcc
Q psy5651 98 IHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHI 176 (843)
Q Consensus 98 gHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SD 176 (843)
+||++.|+.+|.+ +|+.+.++|||++|+|+++|+. ..++|+++++.| |...+ +. .+.++
T Consensus 80 ~~d~k~~~~~L~~-~gi~~~~~~D~~laayll~p~~----------~~~~l~~l~~~~l~~~~~--~~-------~~~~~ 139 (172)
T smart00474 80 GHNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGP----------SKHGLATLLKEYLGVELD--KE-------EQKSD 139 (172)
T ss_pred EechHHHHHHHHH-CCCcccchhHHHHHHHHHcCCC----------CcCCHHHHHHHHhCCCCC--cc-------cCccc
Confidence 9999999999964 9999998999999999999864 136999999999 86643 11 22358
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 177 WKTRPLTSDMLLYAAADVESLLALFHRMTKEY 208 (843)
Q Consensus 177 W~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rL 208 (843)
|..+||..+|..||+.||+++++|++.|.++|
T Consensus 140 ~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 140 WGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 88889999999999999999999999999876
No 16
>smart00712 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Probab=99.79 E-value=1.1e-19 Score=154.73 Aligned_cols=63 Identities=29% Similarity=0.508 Sum_probs=57.7
Q ss_pred ccccceeeecccEEEEeccCCCcceEEEEEecccCCCCCceEEEcccCHHHHHHHHHHHHHHhC
Q psy5651 382 TIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGLISDLQQEHS 445 (843)
Q Consensus 382 ~l~Se~i~ve~KrFyfDlkeN~RGrFLRISE~~~r~~~Rs~I~IPa~g~~~Frd~L~~l~ee~~ 445 (843)
+|+|+.|++|+|+||||||+|+||+||||||+.+ ++.|++|+||++||.+|+++|.+++++|+
T Consensus 1 el~Sk~l~~~~k~fyfDvk~N~rG~fLrIsE~~~-~~~r~~I~lp~~~~~~F~~~l~~~~~~~~ 63 (63)
T smart00712 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEVKN-NGGRSSITVPEQGAAEFRDALNKLIEKYG 63 (63)
T ss_pred CCcccEEEeCCcEEEEEecccCCccEEEEEEecC-CCCceEEEEEHHHHHHHHHHHHHHHHhhC
Confidence 4679999999999999999999999999999943 23499999999999999999999999885
No 17
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.78 E-value=1.3e-17 Score=166.95 Aligned_cols=173 Identities=25% Similarity=0.371 Sum_probs=140.5
Q ss_pred CCCcEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCc
Q psy5651 16 MNRTNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRI 94 (843)
Q Consensus 16 ~~~~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsI 94 (843)
++++.++++.+++..+++.+...+.+++|+|+.+. ++.+.++++|++..+ .+|+||+... ......|.++|+++++
T Consensus 2 ~~~~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~-~~~~i~~l~~--~~~~~~L~~~L~~~~i 78 (192)
T cd06147 2 ETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTRE-EDYIVDTLKL--RDDMHILNEVFTDPNI 78 (192)
T ss_pred CCCcEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCC-CcEEEEeccc--ccchHHHHHHhcCCCc
Confidence 35688997778888877777556689999987665 667899999999765 4888874222 1234568999999999
Q ss_pred eEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCC
Q psy5651 95 LKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYREN 173 (843)
Q Consensus 95 lKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq 173 (843)
.||+||++.|+.+|.+.+|+.+.++|||++|+|+|+|+ + ++|+.|+++| +..+. | +.+
T Consensus 79 ~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~-----------~~l~~l~~~yl~~~~~--k-------~~~ 137 (192)
T cd06147 79 LKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R-----------HSLAYLLQKYCNVDAD--K-------KYQ 137 (192)
T ss_pred eEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c-----------ccHHHHHHHHhCCCcc--h-------hhh
Confidence 99999999999999547899988889999999999985 3 4999999999 76542 2 135
Q ss_pred CccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5651 174 PHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQ 212 (843)
Q Consensus 174 ~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G 212 (843)
.++|..+||+.+|..||+.||.++++|++.|..+|+++.
T Consensus 138 ~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 138 LADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred ccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 677888898999999999999999999999999998543
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=99.73 E-value=9.2e-17 Score=194.26 Aligned_cols=186 Identities=21% Similarity=0.196 Sum_probs=151.0
Q ss_pred CcEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceE
Q psy5651 18 RTNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILK 96 (843)
Q Consensus 18 ~~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlK 96 (843)
.|.+|+++++|.++++.+...+.+|+|+|+.+. ++.++++++|+++.++.+|++|+..++. ..++.|.++|+++.+.|
T Consensus 295 ~~~~I~~~~~L~~~l~~l~~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~-~~l~~l~~~L~d~~v~k 373 (880)
T PRK05755 295 DYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDR-EVLAALKPLLEDPAIKK 373 (880)
T ss_pred ceEEeCCHHHHHHHHHHhhccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccH-HHHHHHHHHHhCCCCcE
Confidence 578899999999999999888999999999998 8999999999998876689998754432 25678999999999999
Q ss_pred EEecccccHHHHhhhcCCccCc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCC
Q psy5651 97 VIHGAFGDAGGLLSNFNIRLKN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENP 174 (843)
Q Consensus 97 VgHdaK~DL~~L~r~~GI~L~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~ 174 (843)
|+||+++|+.+|+ .+|+.+.+ +|||++|+|+++++. ++||++|+++| |..+..+.+..+ ..
T Consensus 374 V~HNakfDl~~L~-~~gi~~~~~~~DT~iAa~Ll~~~~-----------~~~L~~L~~~ylg~~~~~~~~~~g-----k~ 436 (880)
T PRK05755 374 VGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGR-----------RHGLDSLAERYLGHKTISFEEVAG-----KQ 436 (880)
T ss_pred EEeccHhHHHHHH-hCCCCcCCCcccHHHHHHHcCCCC-----------CCCHHHHHHHHhCCCccchHHhcC-----CC
Confidence 9999999999995 57988754 999999999999864 38999999999 877532221111 12
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHH
Q psy5651 175 HIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIY 222 (843)
Q Consensus 175 SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~ 222 (843)
.+|..+|+ +.|..||+.||.+++.||+.|.++|.+.+...++.++++
T Consensus 437 ~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~eiE 483 (880)
T PRK05755 437 LTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIE 483 (880)
T ss_pred CCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhh
Confidence 34555687 689999999999999999999999987655555555544
No 19
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.68 E-value=8.6e-16 Score=150.55 Aligned_cols=162 Identities=19% Similarity=0.143 Sum_probs=126.1
Q ss_pred CCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCcc
Q psy5651 38 ESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRL 116 (843)
Q Consensus 38 s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L 116 (843)
.+.+++|+|+.+. ++.+++++++++..+ ++|++|+... ....+.|+++|+++++.|++||++.|++.| ..+|+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~ 78 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGG-GAYYIPLELA--LLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIEL 78 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEEEEeccch--HHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcC
Confidence 4568999999888 678899999999765 6888884321 013456899999999999999999999999 5689988
Q ss_pred Cc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHH
Q psy5651 117 KN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADV 194 (843)
Q Consensus 117 ~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA 194 (843)
.+ +|||++|+|||+|+.+ +++|++++.+| +.++....+.. + .. .+| .++..+++..||+.||
T Consensus 79 ~~~~fDt~laaYLL~p~~~----------~~~l~~l~~~yl~~~~~~~~~~~-~---~~-~~~-~~~~~~~~~~y~~~~a 142 (178)
T cd06140 79 AGVAFDTMLAAYLLDPTRS----------SYDLADLAKRYLGRELPSDEEVY-G---KG-AKF-AVPDEEVLAEHLARKA 142 (178)
T ss_pred CCcchhHHHHHHHcCCCCC----------CCCHHHHHHHHcCCCCcchHHhc-C---CC-CCc-ccCCHHHHHHHHHHHH
Confidence 76 7999999999999752 47999999999 87654211100 0 00 113 2455677899999999
Q ss_pred HHHHHHHHHHHHHHHhhhcHHHHHH
Q psy5651 195 ESLLALFHRMTKEYALKQNRLLLDN 219 (843)
Q Consensus 195 ~~LL~Lyd~L~~rLee~G~~~LfeE 219 (843)
.+++.|++.|.++|.+.++..+|++
T Consensus 143 ~~l~~l~~~l~~~L~~~~l~~L~~~ 167 (178)
T cd06140 143 AAIARLAPKLEEELEENEQLELYYE 167 (178)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 9999999999999998888887754
No 20
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.66 E-value=1.4e-15 Score=143.68 Aligned_cols=146 Identities=24% Similarity=0.322 Sum_probs=112.6
Q ss_pred eEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCc
Q psy5651 40 KVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKN 118 (843)
Q Consensus 40 ~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~n 118 (843)
.+++|+|+.+. ++.++++++|+++.++.+|++|+... ......|.++|+|+++.||+||++.|+.+| ...|+...+
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~--~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L-~~~~~~~~~ 77 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHD--YLALELLKPLLEDEKALKVGQNLKYDRGIL-LNYFIELRG 77 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCc--ccCHHHHHHHhcCCCCceeeecHHHHHHHH-HHcCCccCC
Confidence 37899987666 55789999999976545888885431 112567899999999999999999999999 456766554
Q ss_pred -eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHH
Q psy5651 119 -VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVES 196 (843)
Q Consensus 119 -VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~ 196 (843)
+|||++|+|+|+|+.. +++|++|+++| +..+... +... .+.|..+|++.+|..||+.||.+
T Consensus 78 ~~~D~~laayLl~p~~~----------~~~l~~l~~~~l~~~~~~~-~~~~------~~~~~~~~~~~~~~~ya~~~a~~ 140 (150)
T cd09018 78 IAFDTMLEAYILNSVAG----------RWDMDSLVERWLGHKLIKF-ESIA------GKLWFNQPLTEEQGRYAAEDADV 140 (150)
T ss_pred cchhHHHHHHHhCCCCC----------CCCHHHHHHHHhCCCcccH-HHhc------CCCCcccCCHHHHHHHHHHHHHH
Confidence 8999999999998640 25999999999 8764311 1010 12386688899999999999999
Q ss_pred HHHHHHHHH
Q psy5651 197 LLALFHRMT 205 (843)
Q Consensus 197 LL~Lyd~L~ 205 (843)
++.|++.|.
T Consensus 141 l~~L~~~l~ 149 (150)
T cd09018 141 TLQIHLKLW 149 (150)
T ss_pred HHHHHHHhc
Confidence 999999875
No 21
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.66 E-value=1.9e-15 Score=141.64 Aligned_cols=151 Identities=29% Similarity=0.290 Sum_probs=111.4
Q ss_pred eEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCc
Q psy5651 40 KVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKN 118 (843)
Q Consensus 40 ~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~n 118 (843)
.+|+|+|+.+. ++.++++++|+++. +++++++... ......+.|.++|+++.+.||+||+++|+.+|.+.++..+.+
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~i~~~~-~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~ 79 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAYIPDEL-ELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGN 79 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEEEEcCC-CHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCC
Confidence 57899988666 56789999999976 3355554322 111245668999999999999999999999996544444456
Q ss_pred eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHH
Q psy5651 119 VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESL 197 (843)
Q Consensus 119 VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~L 197 (843)
+|||++|+|+++++.. +++|++|+++| +.......+ ..+ .... |..+|++.+|..||+.||.++
T Consensus 80 ~~D~~~~ayll~~~~~----------~~~l~~l~~~~l~~~~~~~~~-~~~---~~~~-~~~~~~~~~~~~y~~~da~~~ 144 (155)
T cd00007 80 IFDTMLAAYLLNPGEG----------SHSLDDLAKEYLGIELDKDEQ-IYG---KGAK-TFARPLSEELLEYAAEDADAL 144 (155)
T ss_pred cccHHHHHHHhCCCCC----------cCCHHHHHHHHcCCCCccHHH-Hhc---CCCC-ccccCCHHHHHHHHHHhHHHH
Confidence 8999999999998641 36999999999 765431111 111 0001 435888999999999999999
Q ss_pred HHHHHHHHHH
Q psy5651 198 LALFHRMTKE 207 (843)
Q Consensus 198 L~Lyd~L~~r 207 (843)
++|++.|.++
T Consensus 145 ~~l~~~l~~~ 154 (155)
T cd00007 145 LRLYEKLLEE 154 (155)
T ss_pred HHHHHHHHhh
Confidence 9999999865
No 22
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.62 E-value=1.6e-14 Score=142.07 Aligned_cols=170 Identities=22% Similarity=0.242 Sum_probs=126.8
Q ss_pred hcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCC------CCcccchHHHHHhhcCCCceEEEecccccHHHH
Q psy5651 36 LNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYS------CPLIMFDGKLHEVLESDRILKVIHGAFGDAGGL 108 (843)
Q Consensus 36 k~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~la------L~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L 108 (843)
.+.+.+|+|+|..+. ++.++++.++++..++..+++++.. .........|.++|++..+.+|+||+++|+.+|
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 356789999998777 7788999999997655577776542 111123445889999988899999999999999
Q ss_pred hhhcCCccCc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHH
Q psy5651 109 LSNFNIRLKN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDM 186 (843)
Q Consensus 109 ~r~~GI~L~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQ 186 (843)
..+|+.+.+ +|||++++|+++++.. .++|++++++| |.....+.+..+. ..+..+|...|+ ..+
T Consensus 83 -~~~gi~~~~~~~Dt~l~a~ll~p~~~----------~~~l~~l~~~~l~~~~~~~~~~~~k--~~~~~~~~~~~~-~~~ 148 (193)
T cd06139 83 -ANHGIELRGPAFDTMLASYLLNPGRR----------RHGLDDLAERYLGHKTISFEDLVGK--GKKQITFDQVPL-EKA 148 (193)
T ss_pred -HHCCCCCCCCcccHHHHHHHhCCCCC----------CCCHHHHHHHHhCCCCccHHHHcCC--CcCcCCccccCH-HHH
Confidence 568888766 8999999999998641 36999999999 7653211111110 123455665566 678
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-hhcHHHHHH
Q psy5651 187 LLYAAADVESLLALFHRMTKEYAL-KQNRLLLDN 219 (843)
Q Consensus 187 L~YAA~DA~~LL~Lyd~L~~rLee-~G~~~LfeE 219 (843)
..||+.|+.++++|++.|.++|.+ .++..+|++
T Consensus 149 ~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~ 182 (193)
T cd06139 149 AEYAAEDADITLRLYELLKPKLKEEPGLLELYEE 182 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 999999999999999999999987 666666643
No 23
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.60 E-value=4.7e-15 Score=171.55 Aligned_cols=151 Identities=18% Similarity=0.122 Sum_probs=125.3
Q ss_pred cEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEE
Q psy5651 19 TNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKV 97 (843)
Q Consensus 19 ~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKV 97 (843)
+.+|++.++|..+++.+...+.+++|+|+.+. + .+|++|++.. +..|++|+... +.+ +
T Consensus 3 ~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~-~~~~liDpl~~-----l~~---~--------- 61 (553)
T PRK14975 3 MKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEE-EPRWVWASTAA-----LYP---R--------- 61 (553)
T ss_pred ceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCC-CceEEECchHH-----hHH---H---------
Confidence 57899999999999999999999999999987 5 8999999954 58999997531 221 1
Q ss_pred EecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCcc
Q psy5651 98 IHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHI 176 (843)
Q Consensus 98 gHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SD 176 (843)
| ..+|+.+.++||||+|+|+|+++.. . .++||+.++++| ++.++ |. ++.+|
T Consensus 62 ----------L-~~~Gv~~~~~fDT~LAa~lL~~~~~-~-------~~~~l~~la~~~l~~~l~--k~-------~~~sd 113 (553)
T PRK14975 62 ----------L-LAAGVRVERCHDLMLASQLLLGSEG-R-------AGSSLSAAAARALGEGLD--KP-------PQTSA 113 (553)
T ss_pred ----------H-HHCCCccCCCchHHHHHHHcCCCCC-c-------CCCCHHHHHHHHhCCCCC--Ch-------hhhcc
Confidence 4 3569998899999999999998641 0 147999999999 98887 32 45689
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh------hcHHHHHH
Q psy5651 177 WKTRPLTSDMLLYAAADVESLLALFHRMTKEYALK------QNRLLLDN 219 (843)
Q Consensus 177 W~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~------G~~~LfeE 219 (843)
|. |||+++|+.||+.||.+++.||+.|.++|.+. |+..|+.+
T Consensus 114 w~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~~ 161 (553)
T PRK14975 114 LS-DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLAA 161 (553)
T ss_pred cc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHHH
Confidence 96 99999999999999999999999999999876 67766544
No 24
>smart00712 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Probab=99.51 E-value=6.2e-15 Score=125.84 Aligned_cols=62 Identities=32% Similarity=0.568 Sum_probs=59.3
Q ss_pred ccchhhHHhhhhhHhhhhccCCccceEEeeecCCccceeEEEecchHHHHHHHHHHHHHHhc
Q psy5651 309 IDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAHQ 370 (843)
Q Consensus 309 L~Sk~L~~l~Kr~y~DlKeN~RGrFlkI~E~~~~g~rs~I~ls~~~~~efrd~L~~lie~y~ 370 (843)
|.|+.|+.++|+||+|+|+|+||+||+|+|+..++++++|+||++++.+|+|+|++++|+|+
T Consensus 2 l~Sk~l~~~~k~fyfDvk~N~rG~fLrIsE~~~~~~r~~I~lp~~~~~~F~~~l~~~~~~~~ 63 (63)
T smart00712 2 LASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGRSSITVPEQGAAEFRDALNKLIEKYG 63 (63)
T ss_pred CcccEEEeCCcEEEEEecccCCccEEEEEEecCCCCceEEEEEHHHHHHHHHHHHHHHHhhC
Confidence 68999999999999999999999999999998777799999999999999999999999985
No 25
>KOG2207|consensus
Probab=99.34 E-value=1.2e-12 Score=149.57 Aligned_cols=180 Identities=22% Similarity=0.285 Sum_probs=132.8
Q ss_pred CCcEEecCHHHHHHHH-HHHhcC-CeEEEEeeeeCC--CcCceEEEEEEEEeCCeEEEEeCCCCCcccc--h-HHHHHhh
Q psy5651 17 NRTNLITDVQEAQSAM-ATILNE-SKVGLDLEGMDL--GVDGKVSLVSLALQNGKIFIFDVYSCPLIMF--D-GKLHEVL 89 (843)
Q Consensus 17 ~~~~lIdT~eeLaelL-e~Lk~s-~~IALDtE~~~~--ty~gkL~LIQIAT~dgqvyLID~laL~~~~d--L-s~LkeLL 89 (843)
..+.+|+++.++..++ +.+... -.||+|.||.+. ....++|++|++..+ .+||+|+.++..... + ..+..+|
T Consensus 390 ~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~-~v~Lidc~~l~~~~se~w~~~~s~if 468 (617)
T KOG2207|consen 390 ESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKD-CVYLIDCVKLENLASEIWHLLLSQIF 468 (617)
T ss_pred cceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcC-eEEEeehHHhhhchHHHHHHHHHHHc
Confidence 3678899999998887 345444 679999999887 456789999999865 899999987653211 2 3467799
Q ss_pred cCCCceEEEecccccHHHHhhhcC-----CccC---c-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCC
Q psy5651 90 ESDRILKVIHGAFGDAGGLLSNFN-----IRLK---N-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISP 159 (843)
Q Consensus 90 EDpsIlKVgHdaK~DL~~L~r~~G-----I~L~---n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~L 159 (843)
+++++.|||++.++|++++++..+ +.+. + .-++-++..+.+-... ..+-....-+|+.|...+ |..+
T Consensus 469 ~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~---i~n~~~~~~~L~~Lt~~llg~~l 545 (617)
T KOG2207|consen 469 ESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLS---IENLNEATKGLADLTDCLLGKKL 545 (617)
T ss_pred cCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccch---hhhhcchhhhhhhhhHHHhhhhc
Confidence 999999999999999999975322 2221 2 2234444444332210 000011246788899888 9888
Q ss_pred ccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 160 NNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 160 d~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
+ |. +|+++|..|||+..|+.|||.||..+..+|..+.....
T Consensus 546 n--Kt-------eqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 546 N--KT-------EQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred c--cc-------cccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 7 43 78999999999999999999999999999999987766
No 26
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.31 E-value=4.4e-11 Score=145.24 Aligned_cols=178 Identities=18% Similarity=0.071 Sum_probs=128.1
Q ss_pred cEEecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeC-CeEEEEeCCC---CCcccchHHHHHhhcCCC
Q psy5651 19 TNLITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQN-GKIFIFDVYS---CPLIMFDGKLHEVLESDR 93 (843)
Q Consensus 19 ~~lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~d-gqvyLID~la---L~~~~dLs~LkeLLEDps 93 (843)
+..+.+.+++.++++. ...+.+++ .+. +..+.+.++.+++.+ +.+|+++... +........|+++|+|+.
T Consensus 304 ~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 378 (887)
T TIGR00593 304 AKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQ 378 (887)
T ss_pred ceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCC
Confidence 4567677888887765 44456777 233 456778889998764 4577776431 111123456999999999
Q ss_pred ceEEEecccccHHHHhhhcCCccCc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCcccccccccccc
Q psy5651 94 ILKVIHGAFGDAGGLLSNFNIRLKN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYR 171 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r~~GI~L~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~k 171 (843)
+.||+||+++|+.+| ..+|+.+.+ +|||++|+|||+++. .++|++|+.+| +.....+.+.. +
T Consensus 379 ~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt~la~yll~~~~-----------~~~l~~la~~yl~~~~~~~~~~~-~--- 442 (887)
T TIGR00593 379 IKKIGHDAKFLMHLL-KREGIELGGVIFDTMLAAYLLDPAQ-----------VSTLDTLARRYLVEELILDEKIG-G--- 442 (887)
T ss_pred CcEEEeeHHHHHHHH-HhCCCCCCCcchhHHHHHHHcCCCC-----------CCCHHHHHHHHcCcccccHHHhc-c---
Confidence 999999999999999 569998876 899999999999864 36999999999 75543222110 1
Q ss_pred CCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHH
Q psy5651 172 ENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDN 219 (843)
Q Consensus 172 eq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeE 219 (843)
.. ..|...|+ +.+..||+.||.++++||..|.++|.+.+...+|.+
T Consensus 443 ~~-~~~~~~~~-~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~ 488 (887)
T TIGR00593 443 KL-AKFAFPPL-EEATEYLARRAAATKRLAEELLKELDENKLLSLYRE 488 (887)
T ss_pred CC-CCcccccH-HHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHH
Confidence 00 12222233 556799999999999999999999987777777654
No 27
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.29 E-value=2.5e-11 Score=140.44 Aligned_cols=184 Identities=21% Similarity=0.188 Sum_probs=137.6
Q ss_pred EecCHHHHHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEEEeCCeEEEEeCCCCC-cccchHHHHHhhcCCCceEEE
Q psy5651 21 LITDVQEAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCP-LIMFDGKLHEVLESDRILKVI 98 (843)
Q Consensus 21 lIdT~eeLaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT~dgqvyLID~laL~-~~~dLs~LkeLLEDpsIlKVg 98 (843)
.+.+.+.+..++..+...+.+|+|+|..+. +..+.+.++.++..+ ++++++....+ .......|++||+++...||+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~ 83 (593)
T COG0749 5 TITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEE-EAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVG 83 (593)
T ss_pred hhhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccc-cceeEeeccchhhhhhHHHHHHHhhCcccchhc
Confidence 345566677888777766669999999988 767778888888766 56666655411 112568899999999999999
Q ss_pred ecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccC
Q psy5651 99 HGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIW 177 (843)
Q Consensus 99 HdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW 177 (843)
||++.|.+.| +.+|+.....|||++|+|+++|+. +.+++++|+++| +.....+++..+. ..+.-++
T Consensus 84 ~~~K~d~~~l-~~~Gi~~~~~~DtmlasYll~~~~----------~~~~~~~l~~r~l~~~~~~~~~i~~k--g~~~~~~ 150 (593)
T COG0749 84 QNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGA----------GAHNLDDLAKRYLGLETITFEDIAGK--GKKQLTF 150 (593)
T ss_pred cccchhHHHH-HHcCCcccchHHHHHHHhccCcCc----------CcCCHHHHHHHhcCCccchhHHhhcc--ccccCcc
Confidence 9999999999 568865345899999999999975 258999999999 7766554442111 1222445
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-HHHHHH
Q psy5651 178 KTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQN-RLLLDN 219 (843)
Q Consensus 178 ~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~-~~LfeE 219 (843)
..-|+ +....||+.||..+++|++.|..+|.+... ..+|.+
T Consensus 151 ~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~ 192 (593)
T COG0749 151 ADVKL-EKATEYAAEDADATLRLESILEPELLKTPVLLELYEE 192 (593)
T ss_pred ccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHH
Confidence 55556 556899999999999999999998876665 555543
No 28
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.86 E-value=5.9e-08 Score=93.33 Aligned_cols=132 Identities=20% Similarity=0.198 Sum_probs=90.4
Q ss_pred CceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCc-eechHHHHHHcCC
Q psy5651 53 DGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKN-VYDTQCAFTALQL 131 (843)
Q Consensus 53 ~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~n-VFDTQLAAyLLgp 131 (843)
.+.+..+.+++.+ ++|++++.. . . ....|.++|+++.+.|++||+|.++.+| ..+|+.+.+ +|||++|+|||+|
T Consensus 17 ~~~~~glal~~~~-~~~yi~~~~-~-~-~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~p 91 (151)
T cd06128 17 SANLVGLAFAIEG-VAAYIPVAH-D-Y-ALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLDP 91 (151)
T ss_pred cCcEEEEEEEcCC-CeEEEeCCC-C-c-CHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcCC
Confidence 4667778888655 477776321 1 0 2356889999999999999999999999 678998887 6999999999999
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 132 SDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 132 ~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
+. ++.++++|+++| +.....+.+.. + .. .....-|+ .+...|++..+.++++|++.|.
T Consensus 92 ~~----------~~~~l~~la~~yl~~~~~~~~~~~-g---kg-~~~~~~~~-~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 92 VA----------GRHDMDSLAERWLKEKTITFEEIA-G---KG-LTFNQIAL-EEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CC----------CCCCHHHHHHHHcCCCCccHHHHc-C---CC-CChhhcCH-HHHHHHHHHHHHHHHHHHHHhh
Confidence 65 124999999999 76521111110 1 10 00010112 2234588888888999998875
No 29
>KOG2405|consensus
Probab=97.90 E-value=6.9e-07 Score=98.67 Aligned_cols=150 Identities=27% Similarity=0.420 Sum_probs=109.5
Q ss_pred EEeeeeCCCcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceech
Q psy5651 43 LDLEGMDLGVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDT 122 (843)
Q Consensus 43 LDtE~~~~ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDT 122 (843)
+..|+.....+|++|++|+++.- .+|++|++.++..++...+..+++|.+|.||.|+|+.-++.+.+.||+.++++|||
T Consensus 63 ~~~e~a~~~~~~~l~~~q~~~~~-~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~ 141 (458)
T KOG2405|consen 63 VAAEGANVCRHGKLCWLQVATNC-RVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDT 141 (458)
T ss_pred ccccCccccccCcchhHHHHHHH-HHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhh
Confidence 55566555677899999999764 78999999888776778889999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCCCcccCCCCCCCCCH-HHHHHHhCCCCccccccccc--cccCCCccCCCCCCCHHHHHHHHHHHHH
Q psy5651 123 QCAFTALQLSDPRLLSQDLVPHTIGL-NDLLKFYKISPNNFKKNIQN--LYRENPHIWKTRPLTSDMLLYAAADVES 196 (843)
Q Consensus 123 QLAAyLLgp~~sG~~lp~~~~~s~SL-a~LveryGv~Ld~~Kd~vK~--~~keq~SDW~~RPLSeeQL~YAA~DA~~ 196 (843)
|+|.-+-...+.|.-+|+.- ..+ +.|.+++.+.+.......+. +..+....|-.||-++..+.-.+..+.|
T Consensus 142 q~~d~~q~~~e~g~~~~n~~---~~~q~sl~kh~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 142 QVADVLQFSMETGGYLPNCI---TTLQESLIKHLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred hhhhhhhhcccccccCCccc---cchHHHHHHHHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 99876655544565554322 223 45666663332211111111 1123467799999999988887777776
No 30
>KOG4373|consensus
Probab=97.76 E-value=6.8e-05 Score=82.06 Aligned_cols=131 Identities=18% Similarity=0.146 Sum_probs=94.9
Q ss_pred cCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhh-hcCCccCceechHHH-HHHc
Q psy5651 52 VDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLS-NFNIRLKNVYDTQCA-FTAL 129 (843)
Q Consensus 52 y~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r-~~GI~L~nVFDTQLA-AyLL 129 (843)
..|....+||++.+..++++.+..... ..+.|+.+|+|++.+.||.+..+|..-|.+ .|++.+..+.|+-.- .-.+
T Consensus 145 ~~P~~~~lqlcV~en~C~I~ql~~~~~--IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~ 222 (319)
T KOG4373|consen 145 SDPPPDTLQLCVGENRCLIIQLIHCKR--IPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSL 222 (319)
T ss_pred cCCCcchhhhhhcccceeeEEeecccc--chHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhh
Confidence 345678899999877888886655442 467888999999999999999999999877 788888777776542 1222
Q ss_pred CCCCCCcccCCCCCCCCCHHHHHHHh----CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 130 QLSDPRLLSQDLVPHTIGLNDLLKFY----KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 130 gp~~sG~~lp~~~~~s~SLa~Lvery----Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
+. .. .+-+...|++.+ |..+. ++ ..-+.+||...||+.+|+.||+.||+....|+
T Consensus 223 g~-----~~-----~~~s~e~i~~~~~~~~~~~v~--l~-----~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 223 GG-----SM-----PNDSFEEIVSETLGYYGKDVR--LD-----KEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cc-----Cc-----cCccHHHHHHHHhhccccccc--cC-----hhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 22 11 123455555544 41111 11 12468999999999999999999999999999
No 31
>KOG2405|consensus
Probab=97.38 E-value=1.7e-05 Score=87.97 Aligned_cols=168 Identities=24% Similarity=0.244 Sum_probs=105.7
Q ss_pred CcCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcC
Q psy5651 51 GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQ 130 (843)
Q Consensus 51 ty~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLg 130 (843)
...+.+.++++|+.. +.|++|...-+.....+..+..|+...+ |. |++.+.+.|...|+..+.+++|||+|+.++.
T Consensus 208 ~~~~e~~~m~ia~~n-~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~sLve 283 (458)
T KOG2405|consen 208 ILALEATYMNIADGN-EIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIASSLVE 283 (458)
T ss_pred hhhhhhhhhhhcccc-hhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHHHHhh
Confidence 344555668888654 8999998754322122346667777664 55 9999999999999999999999999999998
Q ss_pred CCCCCcccCCCCCCCCCHHHHHH--Hh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 131 LSDPRLLSQDLVPHTIGLNDLLK--FY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKE 207 (843)
Q Consensus 131 p~~sG~~lp~~~~~s~SLa~Lve--ry-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~r 207 (843)
+.+-|..+|... -++.-.|.. .| +..... ++++.+........|..||.++...+-++.||++|+...+.|.+.
T Consensus 284 ~~e~grr~p~~~--lIsft~Lq~~~~y~~~s~~~-~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~ 360 (458)
T KOG2405|consen 284 PSEYGRRHPTSI--LISFTCLQTYIFYIKASGLI-FEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAV 360 (458)
T ss_pred hHHhcccCCccc--eeeeEeccccceeehhhhhh-HHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhh
Confidence 865343332111 111111111 11 211110 111222122334579999999999999999999999977766554
Q ss_pred HHhhh-cHHHHHHHHHHhh
Q psy5651 208 YALKQ-NRLLLDNLIYETL 225 (843)
Q Consensus 208 Lee~G-~~~LfeEEc~e~~ 225 (843)
.-.+- +...++.+|.+..
T Consensus 361 ~l~HL~~rp~~e~ecie~~ 379 (458)
T KOG2405|consen 361 CLSHLTRRPYTEPECIELV 379 (458)
T ss_pred ChHhhccCCccccchhhhc
Confidence 43211 1344566776543
No 32
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=97.28 E-value=0.00067 Score=62.01 Aligned_cols=73 Identities=21% Similarity=0.196 Sum_probs=56.1
Q ss_pred EEEEeeeeCC-CcCceEEEEEEEEe-CCeEEEEeCCCCCcccchHHHHHhhcCCC-ceEEEecccccHHHHhhhc---CC
Q psy5651 41 VGLDLEGMDL-GVDGKVSLVSLALQ-NGKIFIFDVYSCPLIMFDGKLHEVLESDR-ILKVIHGAFGDAGGLLSNF---NI 114 (843)
Q Consensus 41 IALDtE~~~~-ty~gkL~LIQIAT~-dgqvyLID~laL~~~~dLs~LkeLLEDps-IlKVgHdaK~DL~~L~r~~---GI 114 (843)
+++|+|+.+. ++.+.++++|++.. ++..|++| +.+++.+.. ...|+||+..|+..|.+.+ |.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~ 68 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID------------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGL 68 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCC
Confidence 4799999998 88899999999875 35667766 666787766 6789999999998776543 33
Q ss_pred c----cCceechHHH
Q psy5651 115 R----LKNVYDTQCA 125 (843)
Q Consensus 115 ~----L~nVFDTQLA 125 (843)
. ....+||+.+
T Consensus 69 ~~p~~~~~~lDT~~l 83 (96)
T cd06125 69 KYPLLAGSWIDTIKL 83 (96)
T ss_pred CCCCcCCcEEEehHH
Confidence 2 2348999987
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.19 E-value=0.0069 Score=63.83 Aligned_cols=85 Identities=18% Similarity=0.117 Sum_probs=59.9
Q ss_pred ceEEEecccccHHHHhhh---cCCcc---CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccccccc
Q psy5651 94 ILKVIHGAFGDAGGLLSN---FNIRL---KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQ 167 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r~---~GI~L---~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK 167 (843)
.+-|+||+.+|+.+|.+. +|... ..++||...+..+.+... .+++|++|+++||++...
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~---------~~~~L~~l~~~~gi~~~~------ 158 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK---------GKRTLTALCEHYGVRLDN------ 158 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC---------CCCCHHHHHHHcCCCCCC------
Confidence 456999999999887543 45431 348999988776654221 247999999999876530
Q ss_pred ccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5651 168 NLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQ 212 (843)
Q Consensus 168 ~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G 212 (843)
.. =|..||..+..|+..|..+..+.+
T Consensus 159 ------aH-------------~Al~Da~ata~l~~~l~~~~~~l~ 184 (232)
T PRK07942 159 ------AH-------------EATADALAAARVAWALARRFPELA 184 (232)
T ss_pred ------CC-------------ChHHHHHHHHHHHHHHHHHHHHhh
Confidence 11 178999999999999987765433
No 34
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.11 E-value=0.0096 Score=65.60 Aligned_cols=139 Identities=15% Similarity=0.128 Sum_probs=89.6
Q ss_pred CCeEEEEeeeeCC-CcCceEEEEEEEE-e-CCe-----EEEEeCCC---------CCc---------ccchHHHHHhhcC
Q psy5651 38 ESKVGLDLEGMDL-GVDGKVSLVSLAL-Q-NGK-----IFIFDVYS---------CPL---------IMFDGKLHEVLES 91 (843)
Q Consensus 38 s~~IALDtE~~~~-ty~gkL~LIQIAT-~-dgq-----vyLID~la---------L~~---------~~dLs~LkeLLED 91 (843)
.+.+++|+|+.+. +...+++-|.+.. . ++. ..++++.. +.. ...+..|.+++.+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~l~~ 94 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHHHHcCC
Confidence 4679999999988 5545544333321 1 222 23454421 110 0123456666665
Q ss_pred CCceEEEecccccHHHHhhh---cCCcc--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccccc
Q psy5651 92 DRILKVIHGAFGDAGGLLSN---FNIRL--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNI 166 (843)
Q Consensus 92 psIlKVgHdaK~DL~~L~r~---~GI~L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~v 166 (843)
-+-|+||+.+|+.+|.+. +|..+ ...+||+..+..+.++. .+++|++|+++||++..
T Consensus 95 --~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~----------~~~kL~~l~~~~gi~~~------ 156 (313)
T PRK06063 95 --RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGL----------PNLRLETLAAHWGVPQQ------ 156 (313)
T ss_pred --CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCC----------CCCCHHHHHHHcCCCCC------
Confidence 356999999999988653 45543 24899998888776542 25899999999986532
Q ss_pred cccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5651 167 QNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQN 213 (843)
Q Consensus 167 K~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~ 213 (843)
+. +-|..||.++..|+..+.+++.+.+.
T Consensus 157 ------~~-------------H~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 157 ------RP-------------HDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred ------CC-------------CCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 11 12778999999999999888876554
No 35
>PRK07740 hypothetical protein; Provisional
Probab=97.07 E-value=0.014 Score=61.97 Aligned_cols=96 Identities=18% Similarity=0.101 Sum_probs=68.5
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhh----cCCccC-ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSN----FNIRLK-NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKI 157 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~----~GI~L~-nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv 157 (843)
..|.+++.+ -.-|+|++..|..+|.+. ++..+. .++||+..+..+.+.. .+++|++|++.||+
T Consensus 133 ~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~----------~~~sL~~l~~~~gi 200 (244)
T PRK07740 133 HRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHER----------DFPTLDDALAYYGI 200 (244)
T ss_pred HHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCC----------CCCCHHHHHHHCCc
Confidence 344445544 356899999999887542 344443 4899999888776542 25899999988887
Q ss_pred CCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHH
Q psy5651 158 SPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRL 215 (843)
Q Consensus 158 ~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~ 215 (843)
+... . +-|..||..+..|+..+..++.+.|...
T Consensus 201 ~~~~------------~-------------H~Al~Da~ata~l~~~ll~~~~~~~~~~ 233 (244)
T PRK07740 201 PIPR------------R-------------HHALGDALMTAKLWAILLVEAQQRGITT 233 (244)
T ss_pred CCCC------------C-------------CCcHHHHHHHHHHHHHHHHHHHHcCCcC
Confidence 6530 0 1177899999999999999988766544
No 36
>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=97.07 E-value=0.01 Score=61.15 Aligned_cols=85 Identities=16% Similarity=0.043 Sum_probs=61.7
Q ss_pred ceEEEecccccHHHHhhh---cCCc---c--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccccc
Q psy5651 94 ILKVIHGAFGDAGGLLSN---FNIR---L--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKN 165 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r~---~GI~---L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~ 165 (843)
-.-|+||+.+|+.+|.+. +|.. . ..+.||...+..+.+ ..+|+.++++||++...
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-------------~~~L~~l~~~~gi~~~~---- 168 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-------------QTVLAKACQAAGXDFDS---- 168 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-------------cccHHHHHHHcCCCccc----
Confidence 457999999999988643 3432 1 237999988876543 25799999988865420
Q ss_pred ccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcH
Q psy5651 166 IQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNR 214 (843)
Q Consensus 166 vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~ 214 (843)
.+.+=|..||..+..|+..|..++.+.+.+
T Consensus 169 -------------------~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 169 -------------------TQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred -------------------cchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 112337899999999999999999876654
No 37
>PF11680 DUF3276: Protein of unknown function (DUF3276); InterPro: IPR021694 This bacterial family of proteins has no known function. ; PDB: 3NM7_C 3N8B_A.
Probab=97.06 E-value=0.00095 Score=64.61 Aligned_cols=67 Identities=24% Similarity=0.386 Sum_probs=54.0
Q ss_pred CccccccceeeecccEEEEeccCCCcc-eEEEEEecccC--C-C----CCceEEEcccCHHHHHHHHHHHHHHhC
Q psy5651 379 DTHTIKSEVLIKDTRRYFLDLKDNGRA-RFVTISQLLPV--G-G----KLSSIAFPAQDLGPIIGLISDLQQEHS 445 (843)
Q Consensus 379 ~~~~l~Se~i~ve~KrFyfDlkeN~RG-rFLRISE~~~r--~-~----~Rs~I~IPa~g~~~Frd~L~~l~ee~~ 445 (843)
+.++|.|+.+..++|.||||||+|..| .||-|+|-... + | .|..|.|=.+-+..|.+.|.+.++...
T Consensus 8 ~r~eifSk~v~agkRtYFFDVK~~r~gD~yLtItESKk~~~~~g~~~f~khkI~LYkEDf~~F~~~L~e~i~~i~ 82 (124)
T PF11680_consen 8 DREEIFSKVVKAGKRTYFFDVKENRKGDYYLTITESKKFTDGDGSFSFEKHKIFLYKEDFEKFLEGLDEAIDFIK 82 (124)
T ss_dssp -TTEEEEEE--SSSEEEEEEEEE-TTS-EEEEEEEEEE-TTS-----EEEEEEEEEGGGHHHHHHHHHHHHHHHH
T ss_pred ccceeeeeeeecCCeeEEEEeecccCCCEEEEEEeecccCCCCcceeeeeeEEEEeHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999999997 68999998622 1 2 589999999999999999999887654
No 38
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.80 E-value=0.0096 Score=58.35 Aligned_cols=87 Identities=22% Similarity=0.209 Sum_probs=58.7
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhh---cCCc-----cCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSN---FNIR-----LKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~GI~-----L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
...|.+++.+. ..|+||+.+|+.+|.+. +|.. +..++||+..+..+.+.. +++|+++++
T Consensus 72 ~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~-----------~~~L~~l~~ 138 (167)
T cd06131 72 ADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK-----------PNSLDALCK 138 (167)
T ss_pred HHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC-----------CCCHHHHHH
Confidence 34566666653 35899999999888643 2332 124899997776655432 479999999
Q ss_pred HhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 154 FYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 154 ryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
+||++... .+ .+-|..||.++..|+..|
T Consensus 139 ~~~i~~~~----------~~-------------~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 RFGIDNSH----------RT-------------LHGALLDAELLAEVYLEL 166 (167)
T ss_pred HCCCCCCC----------CC-------------CCChHHHHHHHHHHHHHh
Confidence 99865430 00 123789999999988765
No 39
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.74 E-value=0.034 Score=59.38 Aligned_cols=135 Identities=16% Similarity=0.129 Sum_probs=84.8
Q ss_pred HhcCCeEEEEeeeeCC-CcCceEEEEEEEE---eCC-----eEEEEeCCC-CCc----------c---------cchHHH
Q psy5651 35 ILNESKVGLDLEGMDL-GVDGKVSLVSLAL---QNG-----KIFIFDVYS-CPL----------I---------MFDGKL 85 (843)
Q Consensus 35 Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT---~dg-----qvyLID~la-L~~----------~---------~dLs~L 85 (843)
++....+.+|+|+.+. +...++ +|||. ..+ ...++.+.. ++. + .....+
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~I--IEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDRI--IEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCeE--EEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 3456789999999987 544443 34432 111 223455431 110 0 112345
Q ss_pred HHhhcCCCceEEEecccccHHHHhhh---cCCcc----CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCC
Q psy5651 86 HEVLESDRILKVIHGAFGDAGGLLSN---FNIRL----KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKIS 158 (843)
Q Consensus 86 keLLEDpsIlKVgHdaK~DL~~L~r~---~GI~L----~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~ 158 (843)
.+++.+.. .-|+|++.+|..+|.+. +|+.. ..++||+-.++.++... +++|++|++.||++
T Consensus 82 ~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~-----------~~~L~~l~~~~g~~ 149 (250)
T PRK06310 82 KGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSP-----------NNSLEALAVHFNVP 149 (250)
T ss_pred HHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCC-----------CCCHHHHHHHCCCC
Confidence 55665533 56999999999888643 45543 24899998887764321 48999999988765
Q ss_pred CccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 159 PNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEY 208 (843)
Q Consensus 159 Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rL 208 (843)
... . +=|..||.++..|+..+..++
T Consensus 150 ~~~------------a-------------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 150 YDG------------N-------------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CCC------------C-------------cChHHHHHHHHHHHHHHHHhc
Confidence 430 0 127799999999999887665
No 40
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.67 E-value=0.087 Score=50.91 Aligned_cols=91 Identities=21% Similarity=0.117 Sum_probs=63.5
Q ss_pred hHHHHHhhcCCCceEEEecc-cccHHHHhhh---cCCccC---ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHH
Q psy5651 82 DGKLHEVLESDRILKVIHGA-FGDAGGLLSN---FNIRLK---NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKF 154 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHda-K~DL~~L~r~---~GI~L~---nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lver 154 (843)
...|..++.+. ..|+|++ ++|+.+|.+. +|+... ..+||+..++.+.++. +++|++|++.
T Consensus 71 ~~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~-----------~~~L~~l~~~ 137 (169)
T smart00479 71 LEELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR-----------KYSLKKLAER 137 (169)
T ss_pred HHHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC-----------CCCHHHHHHH
Confidence 45667777654 3467777 9999988653 444322 3799988887765432 5899999999
Q ss_pred hCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 155 YKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 155 yGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
||.+.. . . .+.|..||..+.+|+..+.+++.
T Consensus 138 ~~~~~~-----------~-~------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 138 LGLEVI-----------G-R------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCCCCC-----------C-C------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 975432 0 0 14488999999999999877653
No 41
>PRK05168 ribonuclease T; Provisional
Probab=96.66 E-value=0.05 Score=56.55 Aligned_cols=86 Identities=19% Similarity=0.131 Sum_probs=61.2
Q ss_pred CceEEEecccccHHHHhh---hcCCc---c--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccc
Q psy5651 93 RILKVIHGAFGDAGGLLS---NFNIR---L--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKK 164 (843)
Q Consensus 93 sIlKVgHdaK~DL~~L~r---~~GI~---L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd 164 (843)
+.+-|+|++.+|+..|.+ .+|+. . ..++||...+..+.+ ..+|+.++++||++...
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-------------~~~L~~l~~~~gl~~~~--- 177 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-------------QTVLAKACQAAGIEFDN--- 177 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-------------CCCHHHHHHHCCCCCCC---
Confidence 456899999999988754 34542 1 247999887766532 25799999998876431
Q ss_pred cccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcH
Q psy5651 165 NIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNR 214 (843)
Q Consensus 165 ~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~ 214 (843)
... +=|..||..+.+|+..|..++.+.|.+
T Consensus 178 -------~~~-------------H~Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 178 -------KEA-------------HSALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred -------CCC-------------CChHHHHHHHHHHHHHHHHHHHHccCC
Confidence 011 127899999999999999998766654
No 42
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.60 E-value=0.046 Score=58.37 Aligned_cols=88 Identities=22% Similarity=0.174 Sum_probs=60.3
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhh---cCCcc------CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSN---FNIRL------KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~GI~L------~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
..|.+++.+. ..|+||+.+|+..|.+. +|..+ ..++||...++.+.|+. +++|++|++
T Consensus 78 ~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~-----------~~~L~aL~~ 144 (240)
T PRK05711 78 DEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK-----------RNSLDALCK 144 (240)
T ss_pred HHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC-----------CCCHHHHHH
Confidence 3455566553 35899999999887643 34222 34899998887776643 479999999
Q ss_pred HhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 154 FYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTK 206 (843)
Q Consensus 154 ryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~ 206 (843)
+||++.. . .+. +-|..||..+..+|..|..
T Consensus 145 ~~gi~~~--~--------r~~-------------H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 145 RYGIDNS--H--------RTL-------------HGALLDAEILAEVYLAMTG 174 (240)
T ss_pred HCCCCCC--C--------CCC-------------CCHHHHHHHHHHHHHHHHC
Confidence 9986432 0 011 2278999999999988753
No 43
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.58 E-value=0.038 Score=58.13 Aligned_cols=88 Identities=22% Similarity=0.200 Sum_probs=61.3
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhh---cC--Cc-c---CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSN---FN--IR-L---KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~G--I~-L---~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
..|.+++.+. .-|+||+.+|+.+|.+. +| +. + ..++||...++.+.|+. +++|++|++
T Consensus 74 ~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~-----------~~~L~~L~~ 140 (225)
T TIGR01406 74 DEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ-----------RNSLDALCK 140 (225)
T ss_pred HHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC-----------CCCHHHHHH
Confidence 4555666653 35899999999988643 45 22 1 35899999887766543 479999999
Q ss_pred HhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 154 FYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTK 206 (843)
Q Consensus 154 ryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~ 206 (843)
+||++... .+. +=|..||..+..||..|..
T Consensus 141 ~~gi~~~~----------r~~-------------H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 RFKVDNSH----------RTL-------------HGALLDAHLLAEVYLALTG 170 (225)
T ss_pred hcCCCCCC----------CCC-------------cCHHHHHHHHHHHHHHHHc
Confidence 99865420 011 2278999999999987753
No 44
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=96.48 E-value=0.0088 Score=74.54 Aligned_cols=158 Identities=24% Similarity=0.233 Sum_probs=110.3
Q ss_pred HhcCCeEEEEeeeeCC-CcCceEEEEEEEE---eCCe-----EEEEeCCC-CC-------------------cccchHHH
Q psy5651 35 ILNESKVGLDLEGMDL-GVDGKVSLVSLAL---QNGK-----IFIFDVYS-CP-------------------LIMFDGKL 85 (843)
Q Consensus 35 Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT---~dgq-----vyLID~la-L~-------------------~~~dLs~L 85 (843)
|..+..+.+|+|+.++ +.+.. ++|+|. ..|+ -++++|.. ++ ....+..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~--iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf 495 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDE--IIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKF 495 (1444)
T ss_pred cccccEEEEEeecCCcCcccch--hhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHH
Confidence 5567789999999998 66655 355553 1222 13444431 11 01235667
Q ss_pred HHhhcCCCceEEEecccccHHHHhhh---cCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCc
Q psy5651 86 HEVLESDRILKVIHGAFGDAGGLLSN---FNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPN 160 (843)
Q Consensus 86 keLLEDpsIlKVgHdaK~DL~~L~r~---~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld 160 (843)
++++.|. +-|-||+.+|+-.|... +|+.+. ++.||.-.|+.|.|.. ++|+|..||++||+.+.
T Consensus 496 ~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~----------ksh~Lg~l~kk~~v~le 563 (1444)
T COG2176 496 REFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEF----------KSHRLGTLCKKLGVELE 563 (1444)
T ss_pred HHHhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhh----------hhcchHHHHHHhCccHH
Confidence 7788763 46999999999888653 556543 4999999999999875 37999999999976553
Q ss_pred cccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHH---HHHHHHhhhcccCC
Q psy5651 161 NFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLL---DNLIYETLFNHVVP 231 (843)
Q Consensus 161 ~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~Lf---eEEc~e~~y~~v~~ 231 (843)
+.+-|--||.++.+++-.+.+.+.+.|...+- ...|.+..|.+.+|
T Consensus 564 -------------------------~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l~eln~~l~~~~~ykr~r~ 612 (1444)
T COG2176 564 -------------------------RHHRADYDAEATAKVFFVFLKDLKEKGITNLSELNDKLSSEDLYKRLRP 612 (1444)
T ss_pred -------------------------HhhhhhhhHHHHHHHHHHHHHHHHHhchhhHHHHhHhhhhhHHHhhccc
Confidence 22336679999999999999999988765432 22455677877776
No 45
>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=96.47 E-value=0.012 Score=57.73 Aligned_cols=84 Identities=20% Similarity=0.180 Sum_probs=54.5
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCc
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPN 160 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld 160 (843)
+..|.+++.+ .+ -|+|++.+|+.+|. .+.....++||.....+..+.. ..+++|++|+++| |++..
T Consensus 68 ~~~l~~~l~~-~v-lVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~~~~~~---------~~~~sL~~l~~~~lgi~~~ 134 (152)
T cd06144 68 QKKVAELLKG-RI-LVGHALKNDLKVLK--LDHPKKLIRDTSKYKPLRKTAK---------GKSPSLKKLAKQLLGLDIQ 134 (152)
T ss_pred HHHHHHHhCC-CE-EEEcCcHHHHHHhc--CcCCCccEEEeEEeeccccccC---------CCChhHHHHHHHHcCcccC
Confidence 4567777775 44 59999999999994 3333335889876444333210 1268999999987 86543
Q ss_pred cccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5651 161 NFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202 (843)
Q Consensus 161 ~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd 202 (843)
. .. +=|..||..+..||+
T Consensus 135 --~---------~~-------------H~Al~DA~at~~l~~ 152 (152)
T cd06144 135 --E---------GE-------------HSSVEDARAAMRLYR 152 (152)
T ss_pred --C---------CC-------------cCcHHHHHHHHHHhC
Confidence 0 01 116789998888873
No 46
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.46 E-value=0.12 Score=54.55 Aligned_cols=133 Identities=17% Similarity=0.094 Sum_probs=82.9
Q ss_pred CeEEEEeeeeCC-CcCceEEEEEEEEeC---C--eEEEEeCCC-CC----------cc---------cchHHHHHhhcCC
Q psy5651 39 SKVGLDLEGMDL-GVDGKVSLVSLALQN---G--KIFIFDVYS-CP----------LI---------MFDGKLHEVLESD 92 (843)
Q Consensus 39 ~~IALDtE~~~~-ty~gkL~LIQIAT~d---g--qvyLID~la-L~----------~~---------~dLs~LkeLLEDp 92 (843)
..+.+|+|+.+. +..+++ +|+|.-+ + -..++++.. ++ ++ .....+.+++.+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~I--Ieig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRI--IEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTD 80 (232)
T ss_pred cEEEEEeeCCCCCCCCCEE--EEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHcCC
Confidence 358899999987 444543 4444211 1 223555532 11 00 0123445555443
Q ss_pred CceEEEec-ccccHHHHhh---hcCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccccc
Q psy5651 93 RILKVIHG-AFGDAGGLLS---NFNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNI 166 (843)
Q Consensus 93 sIlKVgHd-aK~DL~~L~r---~~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~v 166 (843)
..-|+|| +.+|+..|.+ .+|+... ..+||+-.+..+.++. ..++|++|++.||++.. .
T Consensus 81 -~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~----------~~~~L~~l~~~~~~~~~--~--- 144 (232)
T PRK06309 81 -NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDL----------PKHNLQYLRQVYGFEEN--Q--- 144 (232)
T ss_pred -CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCC----------CCCCHHHHHHHcCCCCC--C---
Confidence 4569999 5899998864 3455432 4899998887765532 14799999999875432 0
Q ss_pred cccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 167 QNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 167 K~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
.. =|..||.++..|+..+..++.
T Consensus 145 -------aH-------------~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 145 -------AH-------------RALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -------CC-------------CcHHHHHHHHHHHHHHHHHHH
Confidence 11 177999999999999887775
No 47
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.40 E-value=0.048 Score=56.72 Aligned_cols=95 Identities=25% Similarity=0.179 Sum_probs=62.6
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhhc---CCc--c-CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSNF---NIR--L-KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYK 156 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~~---GI~--L-~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryG 156 (843)
..|.+++.+ -.-|+||+.+|+.+|.+.+ +.. + ..++||...+..+.+... ..+++|+.|+++||
T Consensus 79 ~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~--------~~~~~L~~l~~~~g 148 (217)
T TIGR00573 79 EDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFP--------GKRNTLDALCKRYE 148 (217)
T ss_pred HHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCC--------CCCCCHHHHHHHcC
Confidence 455566654 3468999999999987653 221 2 237899876665543221 12579999999987
Q ss_pred CCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5651 157 ISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYAL 210 (843)
Q Consensus 157 v~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee 210 (843)
++... ... +=|..||.++..|+..+..+..+
T Consensus 149 l~~~~----------~~~-------------H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 149 ITNSH----------RAL-------------HGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred CCCCC----------ccc-------------CCHHHHHHHHHHHHHHHHhcchh
Confidence 54320 011 12789999999999999877664
No 48
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.35 E-value=0.077 Score=58.71 Aligned_cols=89 Identities=20% Similarity=0.118 Sum_probs=63.0
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhh---cCCc-cC-ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSN---FNIR-LK-NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKI 157 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~GI~-L~-nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv 157 (843)
..|.+++.+. .-|+|++.+|+..|.+. +|+. +. ..+||+..+..+.++. .+++|++|++.||+
T Consensus 80 ~~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~----------~~~kL~~L~~~lgi 147 (313)
T PRK06807 80 PLFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHA----------PNHKLETLKRMLGI 147 (313)
T ss_pred HHHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCC----------CCCCHHHHHHHcCC
Confidence 4455566543 24999999999998754 4553 33 3899998777665532 25799999998875
Q ss_pred CCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 158 SPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 158 ~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
+.+ .+=|..||.++..|+..+.....
T Consensus 148 ~~~--------------------------~H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 148 RLS--------------------------SHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred CCC--------------------------CcChHHHHHHHHHHHHHHHHhhh
Confidence 431 01277899999999999988774
No 49
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.33 E-value=0.1 Score=55.57 Aligned_cols=147 Identities=18% Similarity=0.108 Sum_probs=85.4
Q ss_pred hcCCeEEEEeeeeCC-CcCceEEEEEEE-EeCCe-------EEEEeCCC-CC----------cc---------cchHHHH
Q psy5651 36 LNESKVGLDLEGMDL-GVDGKVSLVSLA-LQNGK-------IFIFDVYS-CP----------LI---------MFDGKLH 86 (843)
Q Consensus 36 k~s~~IALDtE~~~~-ty~gkL~LIQIA-T~dgq-------vyLID~la-L~----------~~---------~dLs~Lk 86 (843)
...+.+++|+|+.+. +..++++-+... ..++. .+++++.. ++ .+ ..+..|.
T Consensus 45 ~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~l~ 124 (239)
T PRK09146 45 SEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELL 124 (239)
T ss_pred ccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 345679999999988 555553322221 12222 24555421 11 00 1123444
Q ss_pred HhhcCCCceEEEecccccHHHHhhh----cCCccC-ceechHHHHHHcCCCCCCccc---CCCCCCCCCHHHHHHHhCCC
Q psy5651 87 EVLESDRILKVIHGAFGDAGGLLSN----FNIRLK-NVYDTQCAFTALQLSDPRLLS---QDLVPHTIGLNDLLKFYKIS 158 (843)
Q Consensus 87 eLLEDpsIlKVgHdaK~DL~~L~r~----~GI~L~-nVFDTQLAAyLLgp~~sG~~l---p~~~~~s~SLa~LveryGv~ 158 (843)
+.+.+ -.-|+|++..|..+|.+. +|..+. .++||...+..+.+...+... +.+...+++|++++++||++
T Consensus 125 ~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~ 202 (239)
T PRK09146 125 EALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLP 202 (239)
T ss_pred HHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCC
Confidence 44443 356899999999988653 344443 489999988766442100000 01111368899999999865
Q ss_pred CccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 159 PNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 159 Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
.. +. +-|..||.++..|+..+..++.
T Consensus 203 ~~------------~~-------------H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 203 AY------------SP-------------HHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CC------------CC-------------CCcHHHHHHHHHHHHHHHHHHc
Confidence 42 11 1277899999999988877764
No 50
>PRK07883 hypothetical protein; Validated
Probab=96.28 E-value=0.066 Score=63.50 Aligned_cols=144 Identities=14% Similarity=0.095 Sum_probs=91.1
Q ss_pred HHHhcCCeEEEEeeeeCC-CcCceEEEEEEEE---eCCe-----EEEEeCCC-----------CCcc---------cchH
Q psy5651 33 ATILNESKVGLDLEGMDL-GVDGKVSLVSLAL---QNGK-----IFIFDVYS-----------CPLI---------MFDG 83 (843)
Q Consensus 33 e~Lk~s~~IALDtE~~~~-ty~gkL~LIQIAT---~dgq-----vyLID~la-----------L~~~---------~dLs 83 (843)
..+.+...+.+|+|+.+. +....+ +||+. .++. ..+|++.. +..+ ..+.
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p~~~~I--IEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~ 87 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSPAGDAI--TEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLP 87 (557)
T ss_pred CCCcCCCEEEEEEecCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 445667889999999987 444443 33332 2222 23454421 1100 1234
Q ss_pred HHHHhhcCCCceEEEecccccHHHHhh---hcCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCC
Q psy5651 84 KLHEVLESDRILKVIHGAFGDAGGLLS---NFNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKIS 158 (843)
Q Consensus 84 ~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~ 158 (843)
.|.+++.+ ..-|+||+.+|+..|.+ .+|+... ..+||+..+.-+.+.. + ..+++|++|++.||++
T Consensus 88 ~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~-~-------~~~~~L~~L~~~~gi~ 157 (557)
T PRK07883 88 AFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRD-E-------APNVRLSTLARLFGAT 157 (557)
T ss_pred HHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccC-C-------CCCCCHHHHHHHCCcc
Confidence 55566664 35689999999998864 3566543 3889987665544321 0 1368999999988865
Q ss_pred CccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5651 159 PNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQN 213 (843)
Q Consensus 159 Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~ 213 (843)
... . +-|..||.++..|+..+..++.+.|.
T Consensus 158 ~~~------------~-------------H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 158 TTP------------T-------------HRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred cCC------------C-------------CCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 430 1 22889999999999999999975544
No 51
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.25 E-value=0.11 Score=57.17 Aligned_cols=91 Identities=20% Similarity=0.124 Sum_probs=62.9
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhh---hcCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLS---NFNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKI 157 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv 157 (843)
..|.+++.+ -+-|+||+.+|+..|.+ .+|.... ..+||+..+.-+-++. .+++|+.|++.||+
T Consensus 72 ~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~----------~~~~L~~L~~~~gi 139 (309)
T PRK06195 72 EKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNI----------DNARLNTVNNFLGY 139 (309)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCC----------CcCCHHHHHHHcCC
Confidence 455556654 45699999999988854 3455433 3899987666554432 25899999999975
Q ss_pred CCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5651 158 SPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALK 211 (843)
Q Consensus 158 ~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~ 211 (843)
+.. . +-|..||..+..|+..|..++...
T Consensus 140 ~~~-------------~-------------H~Al~DA~ata~l~~~l~~~~~~~ 167 (309)
T PRK06195 140 EFK-------------H-------------HDALADAMACSNILLNISKELNSK 167 (309)
T ss_pred CCc-------------c-------------cCCHHHHHHHHHHHHHHHHHhccC
Confidence 421 0 227789999999988887777543
No 52
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.17 E-value=0.086 Score=67.55 Aligned_cols=143 Identities=20% Similarity=0.174 Sum_probs=95.5
Q ss_pred hcCCeEEEEeeeeCC-CcCceEEEEEEE-EeCCeE-----EEEeCCC-CC-------------------cccchHHHHHh
Q psy5651 36 LNESKVGLDLEGMDL-GVDGKVSLVSLA-LQNGKI-----FIFDVYS-CP-------------------LIMFDGKLHEV 88 (843)
Q Consensus 36 k~s~~IALDtE~~~~-ty~gkL~LIQIA-T~dgqv-----yLID~la-L~-------------------~~~dLs~LkeL 88 (843)
.....+.+|+|+.+. +...++.-+... ..++.+ .+|.|.. ++ ....+..|.++
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 556889999999988 555554322221 122222 2343321 11 01134566667
Q ss_pred hcCCCceEEEecccccHHHHhh---hcCCcc--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccc
Q psy5651 89 LESDRILKVIHGAFGDAGGLLS---NFNIRL--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFK 163 (843)
Q Consensus 89 LEDpsIlKVgHdaK~DL~~L~r---~~GI~L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~K 163 (843)
+.+ -.-|+||+.+|+..|.+ .+|..+ ..++||+..++.+.++. .+++|+.|+++||++...
T Consensus 268 l~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~----------k~~kL~~Lak~lgi~~~~-- 333 (1213)
T TIGR01405 268 FKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEY----------KSHRLGNICKKLGVDLDD-- 333 (1213)
T ss_pred hCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccC----------CCCCHHHHHHHcCCCCCC--
Confidence 765 35699999999998864 346543 34899999998887643 268999999999865530
Q ss_pred ccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHH
Q psy5651 164 KNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRL 215 (843)
Q Consensus 164 d~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~ 215 (843)
.+-|..||.++..|+..|.+++.+.+...
T Consensus 334 -----------------------~HrAl~DA~aTa~I~~~ll~~l~~~~i~~ 362 (1213)
T TIGR01405 334 -----------------------HHRADYDAEATAKVFKVMVEQLKEKGITN 362 (1213)
T ss_pred -----------------------CcCHHHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 13388999999999999999998776543
No 53
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=96.14 E-value=0.14 Score=49.19 Aligned_cols=65 Identities=17% Similarity=0.020 Sum_probs=46.1
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhh---hcCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhC
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLS---NFNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYK 156 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryG 156 (843)
+..|..++.+ ..-|+||+.+|..+|.+ .+|+... ..+||+..+..+.++. .+++|+.|++.||
T Consensus 68 ~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~----------~~~~L~~l~~~~g 135 (156)
T cd06130 68 WPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLL----------PNHKLNTVAEHLG 135 (156)
T ss_pred HHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccC----------CCCCHHHHHHHcC
Confidence 3456677776 35699999999998864 3455433 3899998777665432 2589999999887
Q ss_pred CC
Q psy5651 157 IS 158 (843)
Q Consensus 157 v~ 158 (843)
.+
T Consensus 136 ~~ 137 (156)
T cd06130 136 IE 137 (156)
T ss_pred CC
Confidence 54
No 54
>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=96.11 E-value=0.065 Score=53.20 Aligned_cols=64 Identities=17% Similarity=0.135 Sum_probs=44.2
Q ss_pred HHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCC
Q psy5651 84 KLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISP 159 (843)
Q Consensus 84 ~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~L 159 (843)
.|.+++.+.. +-|+|++.+|+.+|.. . ...+.||...+..+.+...+ ..+++|+.|+++| |.+.
T Consensus 76 ~~~~~i~~~~-vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~~~~~~~~~~-------~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 76 ALWKFIDPDT-ILVGHSLQNDLDALRM-I---HTRVVDTAILTREAVKGPLA-------KRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred HHHHhcCCCc-EEEeccHHHHHHHHhC-c---CCCeeEehhhhhhccCCCcC-------CCCccHHHHHHHHCCchh
Confidence 4555665433 4699999999999943 1 23488999988877653200 0258999999987 8654
No 55
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.03 E-value=0.14 Score=63.45 Aligned_cols=138 Identities=17% Similarity=0.140 Sum_probs=89.8
Q ss_pred cCCeEEEEeeeeCCCcCceEEEEEEEE---eCCeE-----EEEeCCC-CC----------c---------ccchHHHHHh
Q psy5651 37 NESKVGLDLEGMDLGVDGKVSLVSLAL---QNGKI-----FIFDVYS-CP----------L---------IMFDGKLHEV 88 (843)
Q Consensus 37 ~s~~IALDtE~~~~ty~gkL~LIQIAT---~dgqv-----yLID~la-L~----------~---------~~dLs~LkeL 88 (843)
....+++|+|+.+....++ ++||+. .++++ .+|.|.. ++ . ...+..|.++
T Consensus 6 ~~~~vvvD~ETTGl~~~d~--IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNAS--IIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCCe--EEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 3567999999988732333 455543 23322 2344421 11 0 0123456666
Q ss_pred hcCCCceEEEecccccHHHHhhh---cCCccCc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccc
Q psy5651 89 LESDRILKVIHGAFGDAGGLLSN---FNIRLKN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKK 164 (843)
Q Consensus 89 LEDpsIlKVgHdaK~DL~~L~r~---~GI~L~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd 164 (843)
+.+ -+-|+||+.+|+..|.+. .|..+.+ .+||...+..+-+.. .+++|++|++.||++.. .
T Consensus 84 l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~----------~~~~L~~L~~~lgl~~~--~- 148 (820)
T PRK07246 84 IED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTL----------EKYSLSHLSRELNIDLA--D- 148 (820)
T ss_pred hCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCC----------CCCCHHHHHHHcCCCCC--C-
Confidence 765 346999999999988653 3665543 799998887776542 25899999998886543 0
Q ss_pred cccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5651 165 NIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQN 213 (843)
Q Consensus 165 ~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~ 213 (843)
. +=|..||.++..|+..|.+++.+.+.
T Consensus 149 ---------~-------------H~Al~DA~ata~L~~~l~~~l~~l~~ 175 (820)
T PRK07246 149 ---------A-------------HTAIADARATAELFLKLLQKIESLPK 175 (820)
T ss_pred ---------C-------------CCHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 0 12789999999999999988875443
No 56
>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=95.98 E-value=0.069 Score=52.57 Aligned_cols=61 Identities=23% Similarity=0.165 Sum_probs=41.5
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KIS 158 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~ 158 (843)
..+.+++.+ +.+-|+|++.+|+.+|.. . ...+.||...+..+.+.. .+++|..|+++| +..
T Consensus 67 ~~~~~fl~~-~~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~~----------~~~~L~~L~~~~~~~~ 128 (150)
T cd06145 67 KKLLSLISP-DTILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGPP----------YKPSLKNLAKKYLGRD 128 (150)
T ss_pred HHHHHHhCC-CCEEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCCC----------CChhHHHHHHHHCCcc
Confidence 355566652 345799999999999943 2 234899987655443321 258999999998 643
No 57
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.96 E-value=0.23 Score=53.62 Aligned_cols=134 Identities=15% Similarity=0.054 Sum_probs=83.2
Q ss_pred hcCCeEEEEeeeeCC-CcCceEEEEEEEE---eCCeE-----EEEeCCCCCc-------------------ccchHHHHH
Q psy5651 36 LNESKVGLDLEGMDL-GVDGKVSLVSLAL---QNGKI-----FIFDVYSCPL-------------------IMFDGKLHE 87 (843)
Q Consensus 36 k~s~~IALDtE~~~~-ty~gkL~LIQIAT---~dgqv-----yLID~laL~~-------------------~~dLs~Lke 87 (843)
.....+.+|+|+.+. +..+++ ++|+. .+++. .++.+..++. ...+..|.+
T Consensus 66 ~~~~~vv~DiETTG~~~~~~~I--IEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~ 143 (257)
T PRK08517 66 KDQVFCFVDIETNGSKPKKHQI--IEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRL 143 (257)
T ss_pred CCCCEEEEEEeCCCCCCCCCeE--EEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHH
Confidence 445679999999987 554443 33332 23321 2444322110 012455666
Q ss_pred hhcCCCceEEEecccccHHHHhh---hcCCcc--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccc
Q psy5651 88 VLESDRILKVIHGAFGDAGGLLS---NFNIRL--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNF 162 (843)
Q Consensus 88 LLEDpsIlKVgHdaK~DL~~L~r---~~GI~L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~ 162 (843)
++.+. ..|+||+.+|..+|.+ .+|..+ ...+||.-.+..+-+. ..++|++|++.||++..
T Consensus 144 fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~-----------~~~~L~~L~~~lgi~~~-- 208 (257)
T PRK08517 144 FLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-----------PRYGLSFLKELLGIEIE-- 208 (257)
T ss_pred HHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC-----------CCCCHHHHHHHcCcCCC--
Confidence 77653 4789999999998854 455543 2378887655443222 14899999998886543
Q ss_pred cccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 163 KKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 163 Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
. . +=|..||.++.+|+..+..++.
T Consensus 209 ~----------~-------------HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 209 V----------H-------------HRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred C----------C-------------CChHHHHHHHHHHHHHHHHHhH
Confidence 1 1 1177899999999999987775
No 58
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=95.93 E-value=0.1 Score=59.20 Aligned_cols=143 Identities=11% Similarity=0.130 Sum_probs=86.5
Q ss_pred HhcCCeEEEEeeeeCC-CcCceEEEEEEE---Ee-CC-----eEEEEeCCC---------CCc---------ccchHHHH
Q psy5651 35 ILNESKVGLDLEGMDL-GVDGKVSLVSLA---LQ-NG-----KIFIFDVYS---------CPL---------IMFDGKLH 86 (843)
Q Consensus 35 Lk~s~~IALDtE~~~~-ty~gkL~LIQIA---T~-dg-----qvyLID~la---------L~~---------~~dLs~Lk 86 (843)
+...+.++||+|+.++ +...+ +|+|+ .. ++ ...+|++.. +.. ...+..|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~dr--IIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSR--LITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCe--EEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 4556899999999998 65554 33332 11 22 223454432 100 01345566
Q ss_pred HhhcCCCceEEEecccccHHHHhhhc-------------------------------CCccC-ceechHHHHHHcCCCCC
Q psy5651 87 EVLESDRILKVIHGAFGDAGGLLSNF-------------------------------NIRLK-NVYDTQCAFTALQLSDP 134 (843)
Q Consensus 87 eLLEDpsIlKVgHdaK~DL~~L~r~~-------------------------------GI~L~-nVFDTQLAAyLLgp~~s 134 (843)
+++.+. +.|+||+.+|+..|.+.+ ++.+. .++||.-.++.+.+..
T Consensus 121 ~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l- 197 (377)
T PRK05601 121 RLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVAL- 197 (377)
T ss_pred HHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCC-
Confidence 777653 569999999999876532 22333 3899999888887653
Q ss_pred CcccCCCCCCCCCHHHHHHHhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 135 RLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 135 G~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
.++.|..|+++||++.+.-.. . .++.+ +| .. ..+..|+..|..||..+
T Consensus 198 ---------~~~rL~~La~~lGi~~p~~~A---~---~~Ra~---~p--~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 198 ---------DDIRIRGVAHTLGLDAPAAEA---S---VERAQ---VP--HR--QLCREETLLVARLYFAL 245 (377)
T ss_pred ---------CCCCHHHHHHHhCCCCCchhh---h---hhhhc---CC--hh--hhhhHHHHHHHHHHHHh
Confidence 269999999999877642110 0 01111 11 11 22446999999999776
No 59
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.87 E-value=0.23 Score=50.98 Aligned_cols=143 Identities=16% Similarity=0.075 Sum_probs=81.9
Q ss_pred HHHHHHHHhcCCeEEEEeeeeCC-CcCceEEEEEEE---EeCCe-------EEEEeCCC-CC----------c-------
Q psy5651 28 AQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLA---LQNGK-------IFIFDVYS-CP----------L------- 78 (843)
Q Consensus 28 LaelLe~Lk~s~~IALDtE~~~~-ty~gkL~LIQIA---T~dgq-------vyLID~la-L~----------~------- 78 (843)
+..+.+.......+++|+|+.+. +..+.+ ++|+ +.++. .++|++.. ++ .
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~~~d~I--ieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~ 96 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDPRRAEI--VSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGL 96 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCCCCCce--EEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCC
Confidence 33444444456789999999987 544543 3333 22221 13444431 10 0
Q ss_pred --ccchHHHHHhhcCCCceEEEecccccHHHHhhh----cCCccCc-eechHHHHHH-cCCCCCCcccCCCCCCCCCHHH
Q psy5651 79 --IMFDGKLHEVLESDRILKVIHGAFGDAGGLLSN----FNIRLKN-VYDTQCAFTA-LQLSDPRLLSQDLVPHTIGLND 150 (843)
Q Consensus 79 --~~dLs~LkeLLEDpsIlKVgHdaK~DL~~L~r~----~GI~L~n-VFDTQLAAyL-Lgp~~sG~~lp~~~~~s~SLa~ 150 (843)
...+..|.+++.+ -..|+|++.+|...|.+. +|..+.. .+|+.-..+- ..... |. ...+++|++
T Consensus 97 ~~~~vl~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~-----~~-~~~~~~L~~ 168 (202)
T PRK09145 97 SEEEALRQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHL-----PD-AYIDLRFDA 168 (202)
T ss_pred CHHHHHHHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccC-----CC-cccCCCHHH
Confidence 0123455666665 346999999999888643 3555443 7898643321 11110 00 112589999
Q ss_pred HHHHhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 151 LLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 151 LveryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
+++.||++.. . .. =|..||.++..||..|.
T Consensus 169 l~~~~gi~~~--~----------~H-------------~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 169 ILKHLDLPVL--G----------RH-------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred HHHHcCCCCC--C----------CC-------------CcHHHHHHHHHHHHHHH
Confidence 9999986542 0 11 16789999999998774
No 60
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=95.85 E-value=0.22 Score=50.92 Aligned_cols=78 Identities=21% Similarity=0.120 Sum_probs=55.2
Q ss_pred ceEEEecccccHHHHhh---hcCCc-----cCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccccc
Q psy5651 94 ILKVIHGAFGDAGGLLS---NFNIR-----LKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKN 165 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r---~~GI~-----L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~ 165 (843)
.+-|+||+.+|+..|.+ .+|+. +..++||...+..+.+ ..+|++++++||++.+.
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-------------~~~L~~l~~~~gi~~~~---- 165 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-------------QTVLAKACQAAGIEFDN---- 165 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-------------CCcHHHHHHHCCCCCCC----
Confidence 46799999999988764 35551 1237999998877643 25799999999876431
Q ss_pred ccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 166 IQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKE 207 (843)
Q Consensus 166 vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~r 207 (843)
.+. +=|..||..+..|+..|.++
T Consensus 166 ------~~~-------------H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 166 ------KEA-------------HSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred ------CCC-------------cChHHHHHHHHHHHHHHHHh
Confidence 011 12778999999998887653
No 61
>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=95.36 E-value=0.15 Score=50.73 Aligned_cols=65 Identities=15% Similarity=0.060 Sum_probs=39.7
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHH---HHcCCCCCCcccCCCCCCCCCHHHHHHHh-CC
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAF---TALQLSDPRLLSQDLVPHTIGLNDLLKFY-KI 157 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAA---yLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv 157 (843)
...|.+++.+ -+-|+|++.+|+.+|... .....+.||.... .....+. ...++|..|+++| +.
T Consensus 68 ~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~---------~~~~~L~~L~~~~~~~ 134 (157)
T cd06149 68 QKEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPE---------NCRVSLKVLAKRLLHR 134 (157)
T ss_pred HHHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcc---------cCChhHHHHHHHHcCh
Confidence 4556666754 357999999999998432 2223477885421 1111111 1358999999999 54
Q ss_pred CC
Q psy5651 158 SP 159 (843)
Q Consensus 158 ~L 159 (843)
.+
T Consensus 135 ~i 136 (157)
T cd06149 135 DI 136 (157)
T ss_pred hh
Confidence 33
No 62
>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=95.36 E-value=0.29 Score=49.59 Aligned_cols=99 Identities=16% Similarity=0.165 Sum_probs=63.1
Q ss_pred hHHHHHhhcC--CCceEEEecc-cccHHHHhh---hcCCccC----------------------c--eechHHHHHHcCC
Q psy5651 82 DGKLHEVLES--DRILKVIHGA-FGDAGGLLS---NFNIRLK----------------------N--VYDTQCAFTALQL 131 (843)
Q Consensus 82 Ls~LkeLLED--psIlKVgHda-K~DL~~L~r---~~GI~L~----------------------n--VFDTQLAAyLLgp 131 (843)
+..|.+++.+ |++ -||||. .+|+..|.. .+|+.+. + ++|+...+.-..+
T Consensus 67 L~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~ 145 (199)
T cd05160 67 LKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK 145 (199)
T ss_pred HHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC
Confidence 4455555554 554 699999 789988764 3565541 2 6898877765433
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCcc--CCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 132 SDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHI--WKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 132 ~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SD--W~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
. .+++|+++++++ +..-..+. . ....+ |.. -....++|...||...++|+
T Consensus 146 -l----------~sy~L~~v~~~~l~~~k~~~~----~---~~~~~~~~~~--~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 146 -L----------KSYTLDAVAEELLGEGKEKVD----G---EIIEDAEWEE--DPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred -c----------ccCCHHHHHHHHhCCCCCcCC----H---HHHhhccCcc--hHHHHHHHHHHHHHHHHHhh
Confidence 1 368999999998 54322111 1 11122 322 22577999999999999886
No 63
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.16 E-value=0.34 Score=60.78 Aligned_cols=137 Identities=20% Similarity=0.162 Sum_probs=88.3
Q ss_pred CCeEEEEeeeeCC-CcCceEEEEEEEE---eCCeE-----EEEeCCC-CC----------c---------ccchHHHHHh
Q psy5651 38 ESKVGLDLEGMDL-GVDGKVSLVSLAL---QNGKI-----FIFDVYS-CP----------L---------IMFDGKLHEV 88 (843)
Q Consensus 38 s~~IALDtE~~~~-ty~gkL~LIQIAT---~dgqv-----yLID~la-L~----------~---------~~dLs~LkeL 88 (843)
...+++|+|+.+. +..+ -.+|||+. .++++ .+|.+.. ++ . ......|.++
T Consensus 3 ~~~vvvD~ETTG~~p~~~-d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKG-DKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCC-CcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 3578999999876 3322 23455553 23322 2444431 11 0 0123456667
Q ss_pred hcCCCceEEEecccccHHHHhhh---cCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccc
Q psy5651 89 LESDRILKVIHGAFGDAGGLLSN---FNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFK 163 (843)
Q Consensus 89 LEDpsIlKVgHdaK~DL~~L~r~---~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~K 163 (843)
+.+ ..-|+||+.+|+.+|.+. .|..+. ..+||.-.+..+-|.. .+++|++|++.||++.+ .
T Consensus 82 l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~----------~~~~L~~l~~~l~i~~~--~ 147 (928)
T PRK08074 82 LEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTA----------ESYKLRDLSEELGLEHD--Q 147 (928)
T ss_pred hCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCC----------CCCCHHHHHHhCCCCCC--C
Confidence 764 356999999999998643 465432 4899988877776542 25899999999876543 1
Q ss_pred ccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5651 164 KNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQ 212 (843)
Q Consensus 164 d~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G 212 (843)
. +=|..||.++..|+..|.+++.+..
T Consensus 148 ----------~-------------H~Al~DA~ata~l~~~l~~~~~~l~ 173 (928)
T PRK08074 148 ----------P-------------HRADSDAEVTAELFLQLLNKLERLP 173 (928)
T ss_pred ----------C-------------CChHHHHHHHHHHHHHHHHHHHhcC
Confidence 1 1177899999999999999887543
No 64
>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=95.14 E-value=0.45 Score=59.12 Aligned_cols=92 Identities=16% Similarity=0.150 Sum_probs=66.4
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhh---hcCCcc--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLS---NFNIRL--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKI 157 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI~L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv 157 (843)
..|.+++.+ . .-|+||+.+|+.+|.+ .+|..+ ...+||...+..+.+.. .+++|++|++.||+
T Consensus 72 ~~l~~~l~~-~-~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~----------~~~~L~~l~~~~gi 139 (850)
T TIGR01407 72 QEIYDLLED-G-IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTE----------ESYQLSELSEALGL 139 (850)
T ss_pred HHHHHHhCC-C-EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCC----------CCCCHHHHHHHCCC
Confidence 455566654 3 4699999999998864 356552 34899998887776543 25899999999976
Q ss_pred CCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5651 158 SPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALK 211 (843)
Q Consensus 158 ~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~ 211 (843)
+.+ . . +=|..||.++..|+..|..++.+.
T Consensus 140 ~~~--~----------~-------------H~Al~DA~ata~l~~~l~~~~~~l 168 (850)
T TIGR01407 140 THE--N----------P-------------HRADSDAQATAELLLLLFEKMEKL 168 (850)
T ss_pred CCC--C----------C-------------CChHHHHHHHHHHHHHHHHHHHhc
Confidence 543 0 1 127789999999999998888643
No 65
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=95.03 E-value=0.03 Score=48.83 Aligned_cols=48 Identities=21% Similarity=0.403 Sum_probs=38.8
Q ss_pred hHhhHHHHHHHHHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhhh
Q psy5651 236 KRRQFRQNQLRRWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKLL 286 (843)
Q Consensus 236 ~r~l~~L~eL~~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~i 286 (843)
+++++++++|+.||+..|+. +.|+++|+. +..|+......|.+...++
T Consensus 2 ~~~~~~~~~L~~wR~~~A~~~~~~~~~I~~---~~~L~~ia~~~P~~~~~L~ 50 (81)
T smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLP---DETLIKMAAALPTNVSELL 50 (81)
T ss_pred hHHHHHHHHHHHHHHHHHHHcCCCCeEEEC---HHHHHHHHHHCCCCHHHHh
Confidence 46789999999999999987 699999995 6688887777777655543
No 66
>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=94.80 E-value=0.52 Score=44.20 Aligned_cols=83 Identities=22% Similarity=0.025 Sum_probs=54.0
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhhcC-----CccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHH-HHHh
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSNFN-----IRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDL-LKFY 155 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~~G-----I~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~L-very 155 (843)
...+.+++.+ ...|+|++.+|..+|.+.+. ......+||+..+..+.+.. ..+++..+ ++.+
T Consensus 70 ~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~----------~~~~l~~~~~~~~ 137 (159)
T cd06127 70 LPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGL----------RSHRLGLLLAERY 137 (159)
T ss_pred HHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCC----------CcCchHHHHHHHc
Confidence 4556667776 46799999999999865433 22335899997776655432 24677777 5555
Q ss_pred CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 156 KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 156 Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
|.... + .+-|..||.++..|+
T Consensus 138 ~~~~~------------~-------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 138 GIPLE------------G-------------AHRALADALATAELL 158 (159)
T ss_pred CCCCC------------C-------------CCCcHHHHHHHHHHh
Confidence 53221 1 123778999888876
No 67
>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=94.33 E-value=0.063 Score=52.42 Aligned_cols=150 Identities=15% Similarity=0.113 Sum_probs=70.2
Q ss_pred EEEEeeeeCC-CcCceEEEEEEEEe-CCe-EEEEeCCCCCcccchHHHH---HhhcCCCceEEEecccccHHHHhhhc--
Q psy5651 41 VGLDLEGMDL-GVDGKVSLVSLALQ-NGK-IFIFDVYSCPLIMFDGKLH---EVLESDRILKVIHGAFGDAGGLLSNF-- 112 (843)
Q Consensus 41 IALDtE~~~~-ty~gkL~LIQIAT~-dgq-vyLID~laL~~~~dLs~Lk---eLLEDpsIlKVgHdaK~DL~~L~r~~-- 112 (843)
+.+|.|+.++ +..+.+.++.++.. +++ .++.+...-+.. ....+. ..+.+.......|+..+|...|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~-ee~~~~~~~~~l~~~~~iv~yng~~FD~p~L~~~~~~ 79 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPD-EEEIILEFFELLDEADNIVTYNGKNFDIPFLKRRAKR 79 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHH-HHHHHHH--HHHHTT--EEESSTTTTHHHHHHHHH-H
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcH-HHHHHHHHHHHHhcCCeEEEEeCcccCHHHHHHHHHH
Confidence 4689999988 65667778888752 222 223332211111 112222 45666665555555678999887644
Q ss_pred -CCc-cCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccccccccccCCCccCC---CCCCCHHHH
Q psy5651 113 -NIR-LKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWK---TRPLTSDML 187 (843)
Q Consensus 113 -GI~-L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq~SDW~---~RPLSeeQL 187 (843)
++. ..+.+|++..++-... .+++|..+...+|..... ++..+...-.....|. .+...+..+
T Consensus 80 ~~~~~~~~~iDl~~~~~~~~~------------~~~~Lk~ve~~lg~~~~~-~~~~G~~~~~~~~~~~~~~~~~~~~~i~ 146 (164)
T PF13482_consen 80 YGLPPPFNHIDLLKIIKKHFL------------ESYSLKNVEKFLGIERRD-DDISGSESVKLYKEYLETGDPEALEEIL 146 (164)
T ss_dssp HHH--GGGEEEHHHHHT-TTS------------CCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHH
T ss_pred cCCCcccchhhHHHHHHhccC------------CCCCHHHHhhhccccccc-CCCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 333 3458999987643222 257888888877554331 0000000000001111 012448889
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy5651 188 LYAAADVESLLALFHRM 204 (843)
Q Consensus 188 ~YAA~DA~~LL~Lyd~L 204 (843)
.|...|+..+.+|++.|
T Consensus 147 ~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 147 EYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999999876
No 68
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=94.28 E-value=0.75 Score=50.70 Aligned_cols=87 Identities=15% Similarity=-0.048 Sum_probs=53.5
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhhcCCccC--ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCC
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLK--NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISP 159 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~--nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~L 159 (843)
.+.+.+++++.. +-|+||+.+|..+|.+.+ .... ...+++.......++. .+++|++|+.+|| ..
T Consensus 111 ~~~l~~fl~~~~-vlVAHNA~FD~~fL~~~~-~~~~~~~~~ct~~~i~~~~~~~----------~~~kL~~La~~~g-~~ 177 (294)
T PRK09182 111 PAAVDALIAPAD-LIIAHNAGFDRPFLERFS-PVFATKPWACSVSEIDWSARGF----------EGTKLGYLAGQAG-FF 177 (294)
T ss_pred HHHHHHHhcCCC-EEEEeCHHHHHHHHHHHH-HhccCCcccccHHHHhhccccC----------CCCCHHHHHHHcC-CC
Confidence 356777777643 569999999999995532 2222 2456554322211111 3689999999987 21
Q ss_pred ccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 160 NNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTK 206 (843)
Q Consensus 160 d~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~ 206 (843)
. + . +=|..||.++..|+..+..
T Consensus 178 ~---~---------a-------------HrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 178 H---E---------G-------------HRAVDDCQALLELLARPLP 199 (294)
T ss_pred C---C---------C-------------cChHHHHHHHHHHHHHHHh
Confidence 1 0 0 1278999999888775443
No 69
>KOG2249|consensus
Probab=94.09 E-value=0.31 Score=53.05 Aligned_cols=134 Identities=21% Similarity=0.302 Sum_probs=81.7
Q ss_pred CeEEEEeeeeCCCcCce---EEEEEEEEeCCeEEEEeCCCCCc--------------------c----cchHHHHHhhcC
Q psy5651 39 SKVGLDLEGMDLGVDGK---VSLVSLALQNGKIFIFDVYSCPL--------------------I----MFDGKLHEVLES 91 (843)
Q Consensus 39 ~~IALDtE~~~~ty~gk---L~LIQIAT~dgqvyLID~laL~~--------------------~----~dLs~LkeLLED 91 (843)
..||+|||.++.+..|. ++-+.|-..-|+ .++|-...+. . ..-..+.++|.+
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~-VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGH-VVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCc-EeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC
Confidence 37999999998854444 444555444333 3445432110 0 012345567775
Q ss_pred CCceEEEecccccHHHHhhhcCCccCc-eechHHHHHHcCC-CCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccc
Q psy5651 92 DRILKVIHGAFGDAGGLLSNFNIRLKN-VYDTQCAFTALQL-SDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQN 168 (843)
Q Consensus 92 psIlKVgHdaK~DL~~L~r~~GI~L~n-VFDTQLAAyLLgp-~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~ 168 (843)
-+.|||+.++|+.+|+-.+ |.. +-||.----|... .. ....||..|.+.+ |.++. .+
T Consensus 185 --RIlVGHaLhnDl~~L~l~h---p~s~iRDTs~~~pl~k~~~~---------~~tpSLK~Lt~~~Lg~~IQ------~G 244 (280)
T KOG2249|consen 185 --RILVGHALHNDLQALKLEH---PRSMIRDTSKYPPLMKLLSK---------KATPSLKKLTEALLGKDIQ------VG 244 (280)
T ss_pred --CEEeccccccHHHHHhhhC---chhhhcccccCchHHHHhhc---------cCCccHHHHHHHHhchhhh------cc
Confidence 3569999999999995433 333 6788764444331 11 1258999999998 86553 11
Q ss_pred cccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5651 169 LYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALK 211 (843)
Q Consensus 169 ~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~ 211 (843)
++. ..+||.+..+||.....+-++.
T Consensus 245 ---eHs---------------SvEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 245 ---EHS---------------SVEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred ---ccC---------------cHHHHHHHHHHHHHHHHHHHHH
Confidence 211 3489999999999887666543
No 70
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.59 E-value=0.82 Score=59.89 Aligned_cols=88 Identities=23% Similarity=0.147 Sum_probs=66.4
Q ss_pred CceEEEecccccHHHHh---hhcCCc-cC-ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCcccccccc
Q psy5651 93 RILKVIHGAFGDAGGLL---SNFNIR-LK-NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQ 167 (843)
Q Consensus 93 sIlKVgHdaK~DL~~L~---r~~GI~-L~-nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK 167 (843)
....|.|++.+|+..|. ..+|+. +. ..+||+-.++.+.+.. ..++|+.|+++||+....
T Consensus 499 g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~----------k~~kL~~LAk~lGL~~~~------ 562 (1437)
T PRK00448 499 DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPEL----------KSHRLNTLAKKFGVELEH------ 562 (1437)
T ss_pred CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCcc----------ccccHHHHHHHcCCCCCC------
Confidence 35679999999997763 346663 33 4899999888877643 268999999999865530
Q ss_pred ccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHH
Q psy5651 168 NLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRL 215 (843)
Q Consensus 168 ~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~ 215 (843)
. +-|..||.++..|+..|..++.+.|...
T Consensus 563 ----~---------------HrAl~DA~aTa~lf~~ll~~l~~~gi~~ 591 (1437)
T PRK00448 563 ----H---------------HRADYDAEATAYLLIKFLKDLKEKGITN 591 (1437)
T ss_pred ----C---------------cChHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 1 2378999999999999999998766544
No 71
>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=93.57 E-value=0.86 Score=46.67 Aligned_cols=104 Identities=12% Similarity=0.078 Sum_probs=65.0
Q ss_pred hHHHHHhhcC--CCceEEEeccc-ccHHHHhhh---cCCccC----------------------c--eechHHHHHHcCC
Q psy5651 82 DGKLHEVLES--DRILKVIHGAF-GDAGGLLSN---FNIRLK----------------------N--VYDTQCAFTALQL 131 (843)
Q Consensus 82 Ls~LkeLLED--psIlKVgHdaK-~DL~~L~r~---~GI~L~----------------------n--VFDTQLAAyLLgp 131 (843)
+..+..++.. |++ -|+||.. +|+..|..+ +|+.+. + .+|+...+.-.-
T Consensus 60 L~~F~~~i~~~dpdi-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~- 137 (195)
T cd05780 60 IKRFIEIVKEKDPDV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL- 137 (195)
T ss_pred HHHHHHHHHHcCCCE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC-
Confidence 4556666665 775 5899976 699887643 455421 2 678877664321
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 132 SDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPH-IWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 132 ~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~S-DW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
. ..+++|.++++++ |..-.++.. .+.. -|...+--...++|+..||..+++|...|
T Consensus 138 ~----------l~sy~L~~v~~~~Lg~~k~d~~~-------~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 138 N----------LTRYTLERVYEELFGIEKEDVPG-------EEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred C----------CCcCcHHHHHHHHhCCCCCcCCH-------HHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 1 1368999999988 865332210 1111 23333233677999999999999998653
No 72
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=93.06 E-value=1.8 Score=45.75 Aligned_cols=80 Identities=18% Similarity=-0.108 Sum_probs=55.4
Q ss_pred ceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccccccccccCC
Q psy5651 94 ILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYREN 173 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq 173 (843)
-.-|+||+.+|...|.. + ....+||.-.+..+.|+. .++++.|++.||...+.... .
T Consensus 75 ~~lVaHNa~FD~~~L~~-~---~~~~idTl~lar~l~p~~-----------~~~l~~L~~~~~l~~~~~~~-------~- 131 (219)
T PRK07983 75 EWYVAHNASFDRRVLPE-M---PGEWICTMKLARRLWPGI-----------KYSNMALYKSRKLNVQTPPG-------L- 131 (219)
T ss_pred CEEEEeCcHhhHHHHhC-c---CCCcEeHHHHHHHHccCC-----------CCCHHHHHHHcCCCCCCCCC-------C-
Confidence 45799999999999842 2 235899999888776643 37899999888654320000 0
Q ss_pred CccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 174 PHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEY 208 (843)
Q Consensus 174 ~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rL 208 (843)
..+=|..||.++..|+..+.+..
T Consensus 132 ------------~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 132 ------------HHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred ------------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 01338899999999998886543
No 73
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=92.78 E-value=0.054 Score=45.91 Aligned_cols=47 Identities=21% Similarity=0.318 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhhhh
Q psy5651 238 RQFRQNQLRRWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKLLN 287 (843)
Q Consensus 238 ~l~~L~eL~~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~i~ 287 (843)
|+.++++|+.||++.|+. +.|+++|+. +..|.......|.+..++..
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~---~~~L~~ia~~~P~s~~~L~~ 48 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILS---DEALLEIAKRLPTSIEELLQ 48 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS----HHHHHHHHHH--SSHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccC---HHHHHHHHHhCCCCHHHHHH
Confidence 467889999999999987 599999994 56777755557777666554
No 74
>PRK11779 sbcB exonuclease I; Provisional
Probab=91.53 E-value=4.8 Score=47.42 Aligned_cols=98 Identities=17% Similarity=0.080 Sum_probs=58.7
Q ss_pred HHHHHhhcCCCceEEEec-ccccHHHHhhhcCC---cc--------C---ceechHHHHHHcCCCCCCcccCCC--CCCC
Q psy5651 83 GKLHEVLESDRILKVIHG-AFGDAGGLLSNFNI---RL--------K---NVYDTQCAFTALQLSDPRLLSQDL--VPHT 145 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHd-aK~DL~~L~r~~GI---~L--------~---nVFDTQLAAyLLgp~~sG~~lp~~--~~~s 145 (843)
..+.+.|..+..+-|||+ +.+|...|.+.+.. .+ . .++|+.-+++.+.+.. ...|.. ...+
T Consensus 83 ~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~--i~~P~~~~g~~s 160 (476)
T PRK11779 83 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEG--INWPENEDGLPS 160 (476)
T ss_pred HHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhcccc--ccCcccccCCCC
Confidence 345556654555679997 68999887553311 10 1 1346666665554421 011100 1136
Q ss_pred CCHHHHHHHhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 146 IGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKE 207 (843)
Q Consensus 146 ~SLa~LveryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~r 207 (843)
+.|++|++.||++.. +.. =|..||.++..|+..+..+
T Consensus 161 ~rLe~L~~~~gI~~~------------~AH-------------dALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKANGIEHE------------NAH-------------DAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHcCCCCC------------CCC-------------CcHHHHHHHHHHHHHHHHh
Confidence 999999999986543 111 1778999999999988865
No 75
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=90.92 E-value=5.7 Score=41.33 Aligned_cols=93 Identities=13% Similarity=0.031 Sum_probs=57.2
Q ss_pred hHHHHHhhcCCCceEEEeccc-ccHHHHhhhcCCccCc--eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCC
Q psy5651 82 DGKLHEVLESDRILKVIHGAF-GDAGGLLSNFNIRLKN--VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKIS 158 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK-~DL~~L~r~~GI~L~n--VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~ 158 (843)
+..|.+++.+. ..|+|++. .|+.+| ...|..+.+ ..||.-.++...... .| ...+++|..|+++||++
T Consensus 75 l~~f~~f~~~~--~lVaHNa~~fD~~fL-~~~g~~~~~~~~idt~~~~~~~~~~~----~~--~~~~~~L~~La~~~gi~ 145 (195)
T PRK07247 75 LAAFKEFVGEL--PLIGYNAQKSDLPIL-AENGLDLSDQYQVDLYDEAFERRSSD----LN--GIANLKLQTVADFLGIK 145 (195)
T ss_pred HHHHHHHHCCC--eEEEEeCcHhHHHHH-HHcCCCcCCCceeehHHHHHHhhccc----cC--CCCCCCHHHHHHhcCCC
Confidence 45666677654 36999996 899999 457776554 356542222111000 00 01358999999998764
Q ss_pred CccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 159 PNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYA 209 (843)
Q Consensus 159 Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLe 209 (843)
.. . +=|..||..+..|+..|...-.
T Consensus 146 ~~-----------~---------------HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 146 GR-----------G---------------HNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CC-----------C---------------cCCHHHHHHHHHHHHHHHhhcc
Confidence 21 0 1166899999999988865444
No 76
>PF11680 DUF3276: Protein of unknown function (DUF3276); InterPro: IPR021694 This bacterial family of proteins has no known function. ; PDB: 3NM7_C 3N8B_A.
Probab=90.59 E-value=0.15 Score=49.79 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=25.8
Q ss_pred CCceeeeeceEEEEEcCCCCce-eEEEEeeec
Q psy5651 455 EGNYMRCNNKRFFFNVSKNGKG-TFMRISEIS 485 (843)
Q Consensus 455 ~s~~~r~d~K~fyFD~g~N~rG-~fLRISEv~ 485 (843)
-|+.++++.++|||||.+|..| .||-|+|.+
T Consensus 13 fSk~v~agkRtYFFDVK~~r~gD~yLtItESK 44 (124)
T PF11680_consen 13 FSKVVKAGKRTYFFDVKENRKGDYYLTITESK 44 (124)
T ss_dssp EEEE--SSSEEEEEEEEE-TTS-EEEEEEEEE
T ss_pred eeeeeecCCeeEEEEeecccCCCEEEEEEeec
Confidence 5899999999999999999997 689999987
No 77
>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=90.34 E-value=4.9 Score=40.63 Aligned_cols=80 Identities=28% Similarity=0.203 Sum_probs=51.7
Q ss_pred HHHHHhhcC--CCceEEEecc-cccHHHHhh---hcCCccC---ceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 83 GKLHEVLES--DRILKVIHGA-FGDAGGLLS---NFNIRLK---NVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 83 s~LkeLLED--psIlKVgHda-K~DL~~L~r---~~GI~L~---nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
+.|.+++.. ...+-|+||+ .+|+..|.+ .+|..+. .++||...+..+. . +|++|++
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~--------------~-~L~~l~~ 150 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD--------------Q-SLGSLYK 150 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH--------------h-hHHHHHH
Confidence 345555543 2356799998 899998854 3455432 2679987766542 1 7999998
Q ss_pred Hh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5651 154 FY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202 (843)
Q Consensus 154 ry-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd 202 (843)
++ |++... .+-|..||..+.+++-
T Consensus 151 ~~~~~~~~~-------------------------~H~A~~Da~at~~v~~ 175 (177)
T cd06136 151 RLFGQEPKN-------------------------SHTAEGDVLALLKCAL 175 (177)
T ss_pred HHhCCCccc-------------------------ccchHHHHHHHHHHHh
Confidence 74 765430 1227789988877653
No 78
>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=90.28 E-value=7.8 Score=37.93 Aligned_cols=89 Identities=15% Similarity=0.176 Sum_probs=54.3
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhh---hcCC-----ccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLS---NFNI-----RLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI-----~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
+..|.+++.+..-..+.|.+..|...+.+ .++. .....+|++..+..+.+.. ..++|+++++
T Consensus 79 l~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~----------~~~~L~~l~~ 148 (176)
T cd06133 79 LKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK----------KRTGLSKALE 148 (176)
T ss_pred HHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC----------CCCCHHHHHH
Confidence 45677778774112345556788665433 2333 1234889997776554321 2589999999
Q ss_pred HhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 154 FYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 154 ryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
.||++.. . + .+-|-.||.++..|+..|
T Consensus 149 ~~gi~~~--~---------~-------------~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 YLGLEFE--G---------R-------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred HCCCCCC--C---------C-------------CcCcHHHHHHHHHHHHHh
Confidence 8876543 0 0 122678999998888765
No 79
>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=89.77 E-value=6.5 Score=40.42 Aligned_cols=151 Identities=15% Similarity=0.127 Sum_probs=81.9
Q ss_pred CeEEEEeeeeCC-C----cCceEEEEEEEEeCCeEEEEeCCCCCcccchHHHHHhhcC--CCceEEEeccc-ccHHHHhh
Q psy5651 39 SKVGLDLEGMDL-G----VDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLES--DRILKVIHGAF-GDAGGLLS 110 (843)
Q Consensus 39 ~~IALDtE~~~~-t----y~gkL~LIQIAT~dgqvyLID~laL~~~~dLs~LkeLLED--psIlKVgHdaK-~DL~~L~r 110 (843)
..+++|.|..+. + -.+.+..|.++..++...++-.........+..+.+++.. |++ -++||.. +|+..|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEecCCCcCcHHHHHH
Confidence 468999999743 2 2245666666654444444422112222345555565554 554 4688854 88877653
Q ss_pred ---hcCCccC--------------------c--eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCC-Cccccc
Q psy5651 111 ---NFNIRLK--------------------N--VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKIS-PNNFKK 164 (843)
Q Consensus 111 ---~~GI~L~--------------------n--VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~-Ld~~Kd 164 (843)
.+|+.+. + .+|+.-...-... ..+++|+++++.+|.. .+. |.
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~-----------l~~y~L~~Va~~Lg~~k~~~-k~ 150 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE-----------VKVKTLENVAEYLGVMKKSE-RV 150 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC-----------CCCCCHHHHHHHHCCCcccc-cc
Confidence 3554331 1 5666655432211 1368999999866653 110 11
Q ss_pred cccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 165 NIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 165 ~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
.... .+-..-|...--.....+|+..|+..++.|+..+
T Consensus 151 ~~~~--~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 151 LIEW--YRIYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCCH--HHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 0000 0001224332133778999999999999998753
No 80
>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=88.80 E-value=1.1 Score=46.29 Aligned_cols=76 Identities=22% Similarity=0.210 Sum_probs=49.6
Q ss_pred HHHhhcCCCceEEEecccccHHHHhhhcCCc-c-CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCcc
Q psy5651 85 LHEVLESDRILKVIHGAFGDAGGLLSNFNIR-L-KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNN 161 (843)
Q Consensus 85 LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~-L-~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~ 161 (843)
|.+++ +++.+-|||+..+|+.+|. +. | ..+.||.+... + +.. +..||..|+++| |..+.
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL~----l~hp~~~viDTa~l~~-~-~~~----------r~~sLk~La~~~L~~~IQ- 156 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVIN----IQVPKEQVIDTVELFH-L-PGQ----------RKLSLRFLAWYLLGEKIQ- 156 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHhc----CcCCCcceEEcHHhcc-C-CCC----------CChhHHHHHHHHcCCccc-
Confidence 44444 4555679999999999992 32 2 35899975321 1 111 258999999999 86553
Q ss_pred ccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 162 FKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 162 ~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
..-.| ..+||.+.+.||
T Consensus 157 ----------~~~Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 157 ----------SETHD-------------SIEDARTALKLY 173 (174)
T ss_pred ----------CCCcC-------------cHHHHHHHHHHh
Confidence 10111 357899988888
No 81
>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=88.37 E-value=4.7 Score=42.17 Aligned_cols=150 Identities=20% Similarity=0.305 Sum_probs=80.9
Q ss_pred CeEEEEeeeeCC-C-c-----CceEEEEEEEEeCCe--EEEEeCCCCCcccchHHHHHhhcC--CCceEEEecc-cccHH
Q psy5651 39 SKVGLDLEGMDL-G-V-----DGKVSLVSLALQNGK--IFIFDVYSCPLIMFDGKLHEVLES--DRILKVIHGA-FGDAG 106 (843)
Q Consensus 39 ~~IALDtE~~~~-t-y-----~gkL~LIQIAT~dgq--vyLID~laL~~~~dLs~LkeLLED--psIlKVgHda-K~DL~ 106 (843)
..+++|.|.... + + .+.-..+|||...+. ..++..........+..+.+++.+ |++ -||||. .+|+.
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD~p 88 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDV-IEGHNIFRFDLP 88 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-EeccCCcccCHH
Confidence 568999998654 2 2 123457777764221 122211111222234555555554 664 479998 78998
Q ss_pred HHhh---hcCCcc------------------------------Cc--eechHHHHHHcCCCCCCcccCCCCCCCCCHHHH
Q psy5651 107 GLLS---NFNIRL------------------------------KN--VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDL 151 (843)
Q Consensus 107 ~L~r---~~GI~L------------------------------~n--VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~L 151 (843)
.|.. .+|+.+ .| ++|+..+..-.+... +...+++|.++
T Consensus 89 yl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~-------~~l~sysL~~V 161 (207)
T cd05785 89 YLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSS-------RDLPSYGLKAV 161 (207)
T ss_pred HHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccc-------cCCCCCCHHHH
Confidence 7653 345443 11 378877655332211 01136899999
Q ss_pred HHHhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 152 LKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 152 veryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
++.||..... |..... .+=..-|...+ +...+|+..||..++.|+
T Consensus 162 a~~~g~~~~~-k~d~~~--~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 162 AKHFGLASPD-RTYIDG--RQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred HHHhcccCCC-cCCCCH--HHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 9988642210 100000 00012254442 678999999999998875
No 82
>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=87.82 E-value=4.4 Score=42.35 Aligned_cols=135 Identities=14% Similarity=0.053 Sum_probs=77.2
Q ss_pred CcCceEEEEEEEEe---CCeEEEEeCCCCCcccchHHHHHhhcCCCceEEEecc-cccHHHHhh---hcCCccCc-----
Q psy5651 51 GVDGKVSLVSLALQ---NGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGA-FGDAGGLLS---NFNIRLKN----- 118 (843)
Q Consensus 51 ty~gkL~LIQIAT~---dgqvyLID~laL~~~~dLs~LkeLLEDpsIlKVgHda-K~DL~~L~r---~~GI~L~n----- 118 (843)
...+++..|.++.. ++..-+......+....+..+..++++....-|+||. .+|+..|.. .+|+.+..
T Consensus 48 ~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~ 127 (208)
T cd05782 48 LPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLG 127 (208)
T ss_pred cccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcc
Confidence 44567777877763 3332222222122223456666666652335689998 589988764 35663221
Q ss_pred -------------eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCCCccccccccccccCCCccCCCCCCCHH
Q psy5651 119 -------------VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSD 185 (843)
Q Consensus 119 -------------VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSee 185 (843)
.+|++-+..-.+. ..+.+|..+++.+|.+- |..+.+ .+-..-|...++ +.
T Consensus 128 ~~~~~y~~r~~~~h~DL~~~~~~~~~-----------~~~~~L~~va~~lG~~~---K~d~~G--~~v~~~y~~g~~-~~ 190 (208)
T cd05782 128 NKDWNYRNRYSERHLDLMDLLAFYGA-----------RARASLDLLAKLLGIPG---KMDVDG--SQVWELYAEGKL-DE 190 (208)
T ss_pred cchhhccCcCCCCcccHHHHHhccCc-----------cCCCCHHHHHHHhCCCC---CcCCCH--HHHHHHHHcCCh-HH
Confidence 5677766543221 13689999988777632 221111 011123554443 67
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy5651 186 MLLYAAADVESLLALFH 202 (843)
Q Consensus 186 QL~YAA~DA~~LL~Lyd 202 (843)
-.+|+..||..++.||.
T Consensus 191 I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 191 IAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 79999999999998874
No 83
>PRK06722 exonuclease; Provisional
Probab=87.24 E-value=13 Score=41.00 Aligned_cols=163 Identities=15% Similarity=0.173 Sum_probs=88.2
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhh---cCCccCc-----eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHH
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSN---FNIRLKN-----VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLK 153 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~GI~L~n-----VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lve 153 (843)
+..|.+++.+.. -|+|++..|...|.+. +|+.... .+|++-.++-+-+.. ..+.++|++|++
T Consensus 81 l~ef~~fig~~~--lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l--------~~~~~sL~~l~~ 150 (281)
T PRK06722 81 IEKFIQFIGEDS--IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEEL--------FEHTPSLQSAVE 150 (281)
T ss_pred HHHHHHHHCCCc--EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhh--------ccCCCCHHHHHH
Confidence 345666676533 3667789999888653 5654322 367764333221110 112478999999
Q ss_pred HhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHhh----hcHHHHHHHHHHhhhc
Q psy5651 154 FYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKE--YALK----QNRLLLDNLIYETLFN 227 (843)
Q Consensus 154 ryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~r--Lee~----G~~~LfeEEc~e~~y~ 227 (843)
.||++.. .+. +=|..||..+..|+..|..+ |.+. +...++
T Consensus 151 ~lgL~~~-----------g~~-------------HrAL~DA~~TA~L~l~l~~~~~l~~~~~~~~~~~~~---------- 196 (281)
T PRK06722 151 QLGLIWE-----------GKQ-------------HRALADAENTANILLKAYSERDITKRYKRHGELELV---------- 196 (281)
T ss_pred HCCCCCC-----------CCC-------------cCcHHHHHHHHHHHHHHhcccchHHHhcCCCCHHHH----------
Confidence 9986643 001 11668999998888877532 2211 111111
Q ss_pred ccCCCCCChHhhHHHHHHHHHHHHHhhh--cCCcCceecccCccchhh---hhhCCCchhhhhhhccccchhh
Q psy5651 228 HVVPLNIRKRRQFRQNQLRRWRKDLMSS--KRPYPYIEEVNSNEYIWR---NDYNVPLANAKLLNNPINRMFH 295 (843)
Q Consensus 228 ~v~~~~L~~r~l~~L~eL~~WRe~~Ar~--~~pr~~I~~~n~~~~l~~---~q~~vP~~~~~~i~~~~D~~~~ 295 (843)
+...|.+.. -..+.+|=....+. .+|..|--..||+ -|. .+|-+-....+|+.+.+-...+
T Consensus 197 --~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (281)
T PRK06722 197 --KNGKLTEKA---KKKMRKWVFKEMRKNTERPFVWSTFESSD--TWESITERYYISESTIELLKKHFRTAVR 262 (281)
T ss_pred --hhhhhhhcc---HHHHHHHHHHHHhhccCCCcchhhccccc--ccccchheeeecchHHHHHHHHHHHHHH
Confidence 001122111 13345665555554 3888886655543 353 4777766667888777754433
No 84
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=84.62 E-value=15 Score=38.47 Aligned_cols=90 Identities=23% Similarity=0.160 Sum_probs=62.5
Q ss_pred HHHHhhcCCCceEEEecccccHHHHhh---hcCCcc--CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHhCCC
Q psy5651 84 KLHEVLESDRILKVIHGAFGDAGGLLS---NFNIRL--KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKIS 158 (843)
Q Consensus 84 ~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~GI~L--~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~LveryGv~ 158 (843)
.+.+++.+. -.-|+||+..|+..|.. .+|..+ ..+.||...+....++. ...+|+.|+.++|++
T Consensus 87 ~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~----------~~~~L~~l~~~~gi~ 155 (243)
T COG0847 87 EFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGF----------DRSSLDALAERLGID 155 (243)
T ss_pred HHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCC----------ccchHHHHHHHcCCC
Confidence 344555553 45699999999998854 344443 23789999888887762 158999999988876
Q ss_pred CccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 159 PNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKE 207 (843)
Q Consensus 159 Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~r 207 (843)
... ... +-|..|+..+..+|..+...
T Consensus 156 ~~~----------~~~-------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 156 RNP----------FHP-------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCC----------cCC-------------cchHHHHHHHHHHHHHHHhc
Confidence 320 000 22778999999999888774
No 85
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=84.48 E-value=5.6 Score=41.17 Aligned_cols=92 Identities=15% Similarity=0.092 Sum_probs=59.0
Q ss_pred hHHHHHhhcCCCceEEEecccccHHHHhhh---cCCcc---CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh
Q psy5651 82 DGKLHEVLESDRILKVIHGAFGDAGGLLSN---FNIRL---KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY 155 (843)
Q Consensus 82 Ls~LkeLLEDpsIlKVgHdaK~DL~~L~r~---~GI~L---~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery 155 (843)
+..|.+++.+.... ++|++..|+..|.+. +|+.. ....|++.....+.+.. ..++|++++++|
T Consensus 83 l~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~----------~~~~L~~~~~~~ 151 (207)
T PRK07748 83 VEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGER----------NQTGLWKAIEEY 151 (207)
T ss_pred HHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcC----------CCCCHHHHHHHc
Confidence 45677777763333 446678999888653 46543 23778887655443221 248999999999
Q ss_pred CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 156 KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEY 208 (843)
Q Consensus 156 Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rL 208 (843)
|++.. .+. +-|..||..+..|+..|....
T Consensus 152 gi~~~-----------~~~-------------H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 152 GKEGT-----------GKH-------------HCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CCCCC-----------CCC-------------cChHHHHHHHHHHHHHHHhCc
Confidence 86532 000 227789999999998877553
No 86
>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=81.09 E-value=11 Score=38.25 Aligned_cols=75 Identities=16% Similarity=0.023 Sum_probs=40.9
Q ss_pred HHHHHhhcCCCceEEEec-ccccHHHHhhh---cCCcc--------CceechHHHHHH---cCCCCCCcccCCC--CCCC
Q psy5651 83 GKLHEVLESDRILKVIHG-AFGDAGGLLSN---FNIRL--------KNVYDTQCAFTA---LQLSDPRLLSQDL--VPHT 145 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHd-aK~DL~~L~r~---~GI~L--------~nVFDTQLAAyL---Lgp~~sG~~lp~~--~~~s 145 (843)
..+.+++..+...-|+|+ +.+|...|.+. +|..+ ...+||.-.+.+ +.+.. ...|.. ...+
T Consensus 74 ~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~--~~~~~~~~~~~~ 151 (183)
T cd06138 74 AKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDG--IVWPKNDDGKPS 151 (183)
T ss_pred HHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhh--ccCccccCCCcc
Confidence 345556654444468886 78999988653 33321 124577654443 32310 000000 0135
Q ss_pred CCHHHHHHHhCCCC
Q psy5651 146 IGLNDLLKFYKISP 159 (843)
Q Consensus 146 ~SLa~LveryGv~L 159 (843)
++|++|+++||++.
T Consensus 152 ~~L~~l~~~~gi~~ 165 (183)
T cd06138 152 FKLEDLAQANGIEH 165 (183)
T ss_pred hhHHHHHHHCCCCc
Confidence 88999999998654
No 87
>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=80.45 E-value=24 Score=37.61 Aligned_cols=108 Identities=15% Similarity=0.154 Sum_probs=68.7
Q ss_pred cchHHHHHhhcCCCceEEEeccc-ccHHHHhh---hcCCccCc-------------------eechHHHHHHcCCCCCCc
Q psy5651 80 MFDGKLHEVLESDRILKVIHGAF-GDAGGLLS---NFNIRLKN-------------------VYDTQCAFTALQLSDPRL 136 (843)
Q Consensus 80 ~dLs~LkeLLEDpsIlKVgHdaK-~DL~~L~r---~~GI~L~n-------------------VFDTQLAAyLLgp~~sG~ 136 (843)
..+..+...++.....-|+||.+ +|+-.|.. .+|+.++. -+||+-....-+.
T Consensus 39 ~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~----- 113 (209)
T PF10108_consen 39 ELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGA----- 113 (209)
T ss_pred HHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCc-----
Confidence 34667777787656667999976 89987754 46777543 2466544322221
Q ss_pred ccCCCCCCCCCHHHHHHHhCCCCccccccccccccCC-CccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 137 LSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYREN-PHIWKTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 137 ~lp~~~~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq-~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
.+..||+.||.-+|++- |....| .+ ..-|..-.+ ++-..|+..||..+..||-.+.
T Consensus 114 ------~~~~sLd~la~~lgiPg---K~~idG---s~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 114 ------KARTSLDELAALLGIPG---KDDIDG---SQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred ------cccCCHHHHHHHcCCCC---CCCCCH---HHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 13589999998888763 321111 11 112434444 5678999999999999998875
No 88
>KOG3657|consensus
Probab=77.15 E-value=4.9 Score=49.82 Aligned_cols=106 Identities=21% Similarity=0.212 Sum_probs=62.4
Q ss_pred ceEEEecccccHHHHhhhcCCccCc--eechHHHHHHcC----CCCCCcc---------------cCCCC---------C
Q psy5651 94 ILKVIHGAFGDAGGLLSNFNIRLKN--VYDTQCAFTALQ----LSDPRLL---------------SQDLV---------P 143 (843)
Q Consensus 94 IlKVgHdaK~DL~~L~r~~GI~L~n--VFDTQLAAyLLg----p~~sG~~---------------lp~~~---------~ 143 (843)
-+.||||..+|-.-+...|.+.-.. +.|||-.+-... .++ ..+ -|++. .
T Consensus 242 ~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qr-plw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~S 320 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQR-PLWFKARKAKSAMYDSETNPSISDYDNPWLGRS 320 (1075)
T ss_pred ceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccc-hhHhhhhhhhhhhhhcccCCchhhhhhhhhhhh
Confidence 5679999999999988889877554 679997654321 111 000 00000 0
Q ss_pred CCCCHHHHHHHh-CCC-CccccccccccccCCCccCCCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5651 144 HTIGLNDLLKFY-KIS-PNNFKKNIQNLYRENPHIWKTRPLT------SDMLLYAAADVESLLALFHRMTKEYAL 210 (843)
Q Consensus 144 ~s~SLa~Lvery-Gv~-Ld~~Kd~vK~~~keq~SDW~~RPLS------eeQL~YAA~DA~~LL~Lyd~L~~rLee 210 (843)
+--||.++...| |.+ ++ |+ .+.+|..-++. .+.+.|+|.|+++..++|..+.....+
T Consensus 321 S~NSL~dVhk~~c~~~~Ld--Kt--------~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 321 SLNSLVDVHKFHCGIDALD--KT--------PRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hhHHHHHHHHhhCCCCccc--cc--------hHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 012344555555 554 55 21 12222222211 345789999999999999988877764
No 89
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=71.04 E-value=13 Score=37.07 Aligned_cols=68 Identities=13% Similarity=0.044 Sum_probs=41.5
Q ss_pred cccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCC
Q psy5651 102 FGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTR 180 (843)
Q Consensus 102 K~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~R 180 (843)
..|+.++...-|+.+.+--|-++.+|||+|.. -.-+.++++| |- +|...
T Consensus 70 AK~LAv~a~~~G~~v~PGDDPlLlAYLlDPsN------------t~p~~varRY~~~------------------~W~~d 119 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPGDDPLLLAYLLDPSN------------TNPEGVARRYLGG------------------EWPED 119 (138)
T ss_dssp HHHHHHHHHHTT----B---HHHHHHHH-TT--------------SHHHHHHHH-TS---------------------SS
T ss_pred HHHHHHHHHhcCcccCCCCCcchhhhhcCccC------------CChHHHHHHhcCC------------------CCCcc
Confidence 35676665778998888889999999999864 4667788898 52 34332
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 181 PLTSDMLLYAAADVESLLALFHRMTKEY 208 (843)
Q Consensus 181 PLSeeQL~YAA~DA~~LL~Lyd~L~~rL 208 (843)
|+..+....+|++.|..+|
T Consensus 120 ---------A~~RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 120 ---------AATRALATARLLRALPPRL 138 (138)
T ss_dssp ---------HHHHHHHHHHHHHHHHHHT
T ss_pred ---------HHHHHHHHHHHHHHhhhcC
Confidence 6677777788888887764
No 90
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=70.52 E-value=4.5 Score=48.21 Aligned_cols=47 Identities=19% Similarity=0.134 Sum_probs=37.4
Q ss_pred hhHHHHHHHHHHHHHhhh-cCCcCceecccCccchhhhhhCCCchhhhhhh
Q psy5651 238 RQFRQNQLRRWRKDLMSS-KRPYPYIEEVNSNEYIWRNDYNVPLANAKLLN 287 (843)
Q Consensus 238 ~l~~L~eL~~WRe~~Ar~-~~pr~~I~~~n~~~~l~~~q~~vP~~~~~~i~ 287 (843)
..+.+++|++||++.|++ +.|+.+|+. +..|+......|.+..+++.
T Consensus 521 ~~~l~~~L~~wR~~~A~~~~~p~~~If~---d~~L~~ia~~~P~~~~~l~~ 568 (591)
T TIGR01389 521 DNALFEALRELRKEQADEQNVPPYVIFS---DSTLREMAEKRPATLNALLK 568 (591)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCeEEEC---HHHHHHHHHHCCCCHHHHhC
Confidence 348899999999999977 599999995 66888877777777665543
No 91
>KOG1275|consensus
Probab=63.38 E-value=4.8 Score=50.31 Aligned_cols=101 Identities=17% Similarity=0.210 Sum_probs=65.4
Q ss_pred hhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccc
Q psy5651 88 VLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNI 166 (843)
Q Consensus 88 LLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~v 166 (843)
+|-+-.+.-|||+...|..++ . .-+....++||-+.. +++.+ +-+||..|+-++ |..+.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI-N-i~Vp~~QiiDTv~lf-~~~s~-----------R~LSLrfLa~~lLg~~IQ------ 1068 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI-N-IHVPEEQIIDTVTLF-RLGSQ-----------RMLSLRFLAWELLGETIQ------ 1068 (1118)
T ss_pred HHHHcCcEEEcccccccceEE-E-EecChhhheeeeEEE-ecccc-----------cEEEHHHHHHHHhcchhh------
Confidence 677889999999999999877 2 223323399997643 23322 258999999988 86543
Q ss_pred cccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHHHhhhcccCC
Q psy5651 167 QNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLIYETLFNHVVP 231 (843)
Q Consensus 167 K~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~~rLee~G~~~LfeEEc~e~~y~~v~~ 231 (843)
....| ...||++.|.||+... +|.++|. |++++. .+|...++
T Consensus 1069 -----~~~HD-------------SIeDA~taLkLYk~Yl-~lkeq~~---~~~~l~-niye~gr~ 1110 (1118)
T KOG1275|consen 1069 -----MEAHD-------------SIEDARTALKLYKKYL-KLKEQGK---LESELR-NIYECGRP 1110 (1118)
T ss_pred -----ccccc-------------cHHHHHHHHHHHHHHH-HHHHhhH---HHHHHH-HHhhcCcc
Confidence 11122 3579999999999885 4554443 334433 45554443
No 92
>PTZ00315 2'-phosphotransferase; Provisional
Probab=62.27 E-value=1.5e+02 Score=36.18 Aligned_cols=100 Identities=10% Similarity=-0.015 Sum_probs=56.1
Q ss_pred hHHHHHhhcCCCc--------eEEEecccccHH-HHhhh------cCCccCc--eechH--HHHHHcCCCCCCcccCCCC
Q psy5651 82 DGKLHEVLESDRI--------LKVIHGAFGDAG-GLLSN------FNIRLKN--VYDTQ--CAFTALQLSDPRLLSQDLV 142 (843)
Q Consensus 82 Ls~LkeLLEDpsI--------lKVgHdaK~DL~-~L~r~------~GI~L~n--VFDTQ--LAAyLLgp~~sG~~lp~~~ 142 (843)
+..|.++|.+... ..|.|++.+|+. .|.+. .|+.+.. ..|++ ++.+++.....++..+...
T Consensus 134 l~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 134 YCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccccc
Confidence 4566677776531 357899999985 55332 3554432 55664 3443332100000001111
Q ss_pred CCCCCHHHHHHHhCCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5651 143 PHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMT 205 (843)
Q Consensus 143 ~~s~SLa~LveryGv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L~ 205 (843)
..+++|.++++.+|++.. + +. +=|-.||..+.+|+..|.
T Consensus 214 ~~~~~L~~al~~lgL~~e-------G----r~-------------HrAlDDA~ntA~L~~~Ll 252 (582)
T PTZ00315 214 LGPSDMPDMLQMLGLPLQ-------G----RH-------------HSGIDDCRNIAAVLCELL 252 (582)
T ss_pred cCCcCHHHHHHHCCCCCC-------C----CC-------------cCcHHHHHHHHHHHHHHH
Confidence 235899999999886543 0 00 115688999888887765
No 93
>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=61.92 E-value=62 Score=33.67 Aligned_cols=55 Identities=11% Similarity=0.161 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5651 144 HTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202 (843)
Q Consensus 144 ~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd 202 (843)
.+++|+++++++ |..-......... .+=..-|...| ....+|+..||...++|++
T Consensus 138 ~sy~L~~Va~~~Lg~~K~~~~~~~~~--~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 138 ESFSLENVAQELLGEGKLIHDVDDRG--AEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred CcCCHHHHHHHHhCCCccccCcccCH--HHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 369999999988 7432111000000 00011243333 5679999999999999874
No 94
>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=55.28 E-value=3.2 Score=38.88 Aligned_cols=84 Identities=26% Similarity=0.281 Sum_probs=48.8
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhh---hc-CCcc---CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLS---NF-NIRL---KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY 155 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r---~~-GI~L---~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery 155 (843)
..+.+++.. ....|+|++..|..++.+ .+ +... ..++|+......+.+.. ...+|.+|++.|
T Consensus 74 ~~~~~~~~~-~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~l~~l~~~~ 142 (164)
T PF00929_consen 74 DEFEEFLKK-NDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNR----------KKYSLDDLAEYF 142 (164)
T ss_dssp HHHHHHHHH-HTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHH----------HHHSHHHHHHHT
T ss_pred Hhhhhhhhc-ccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhcc----------ccCCHHHHHHHc
Confidence 345566653 246789998888755432 12 2221 23677766555443321 136899999999
Q ss_pred CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy5651 156 KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201 (843)
Q Consensus 156 Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Ly 201 (843)
+.+.. .... =|..||..+..||
T Consensus 143 ~~~~~-----------~~~H-------------~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 143 GIPFD-----------GTAH-------------DALDDARATAELF 164 (164)
T ss_dssp TSSST-----------STTT-------------SHHHHHHHHHHHH
T ss_pred CCCCC-----------CCCc-------------ChHHHHHHHhCcC
Confidence 65433 0011 1788999988875
No 95
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=54.48 E-value=25 Score=37.36 Aligned_cols=96 Identities=20% Similarity=0.206 Sum_probs=56.4
Q ss_pred cCCCceEEEecc-cccHHHHhhh---cCCc---------------------------cCc--eechHHHHHHcCCCCCCc
Q psy5651 90 ESDRILKVIHGA-FGDAGGLLSN---FNIR---------------------------LKN--VYDTQCAFTALQLSDPRL 136 (843)
Q Consensus 90 EDpsIlKVgHda-K~DL~~L~r~---~GI~---------------------------L~n--VFDTQLAAyLLgp~~sG~ 136 (843)
.||++. +|||. .+|+..|.++ +|+. +.| ++|+...+.-+-.
T Consensus 96 ~DPDii-vG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~----- 169 (234)
T cd05776 96 IDPDVL-VGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIR----- 169 (234)
T ss_pred cCCCEE-EeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHHHHHHhC-----
Confidence 368864 89999 6788876532 2322 112 4566666544321
Q ss_pred ccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCC-CCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 137 LSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKT-RPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 137 ~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~-RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
..+++|.++++.+ |..-.++.. . .-..-|.. ..+ ..-++|...||.+.++|...|
T Consensus 170 ------~~sY~L~~va~~~Lg~~k~di~~--~----~i~~~~~~~~~l-~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 170 ------CKSYDLTELSQQVLGIERQDIDP--E----EILNMYNDSESL-LKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred ------CCCCChHHHHHHHhCcCcccCCH--H----HHHHHHhCHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 1368999999988 753222210 0 00112332 111 455889999999999998876
No 96
>KOG2206|consensus
Probab=48.14 E-value=8.4 Score=46.35 Aligned_cols=29 Identities=14% Similarity=0.007 Sum_probs=25.2
Q ss_pred hhhhCCCchhh---hhhhccccchhhhhhccC
Q psy5651 273 RNDYNVPLANA---KLLNNPINRMFHKEKESA 301 (843)
Q Consensus 273 ~~q~~vP~~~~---~~i~~~~D~~~~~~~es~ 301 (843)
..|++.++.+. ++|.+|||.+|+.|||||
T Consensus 397 ~~q~~ln~~q~~~l~~L~~wRd~iARaeDES~ 428 (687)
T KOG2206|consen 397 DIQSRLNSSQLDVLRALLRWRDFIARAEDESV 428 (687)
T ss_pred HHHhccchhHHHHHHHHHHHHHHHHhhccCCC
Confidence 46888888887 566899999999999999
No 97
>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=41.41 E-value=4.4e+02 Score=27.64 Aligned_cols=103 Identities=16% Similarity=0.094 Sum_probs=58.0
Q ss_pred chHHHHHhhcCCCceEEEeccc-ccHHHHhh---hcCCc--------------cCc--eechHHHHHH--cC-CCCCCcc
Q psy5651 81 FDGKLHEVLESDRILKVIHGAF-GDAGGLLS---NFNIR--------------LKN--VYDTQCAFTA--LQ-LSDPRLL 137 (843)
Q Consensus 81 dLs~LkeLLEDpsIlKVgHdaK-~DL~~L~r---~~GI~--------------L~n--VFDTQLAAyL--Lg-p~~sG~~ 137 (843)
.+..+.+++.+.. .-|+||.. +|+..|.. .+|+. ..+ .+|+.-.... +. ... |.
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~-~~- 152 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAF-GN- 152 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhh-cc-
Confidence 3566667777664 45678765 78877653 45665 112 5676553221 10 000 00
Q ss_pred cCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5651 138 SQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202 (843)
Q Consensus 138 lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd 202 (843)
...+++|.++++.+ |..-... . . ..|... .+.-.+|+..||...+.|..
T Consensus 153 ----~~~~~~L~~Va~~~lg~~K~~~----~----~--~i~~~~--~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 ----KYREYTLDAVAKALLGEGKVEL----E----K--NISELN--LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ----ccccCcHHHHHHHhcCCCcccC----C----c--hhhhhc--HHHHHHhhHHHHHHHHHHhc
Confidence 11368999999988 6421111 0 0 112111 26679999999999988864
No 98
>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=39.51 E-value=4.5e+02 Score=27.71 Aligned_cols=50 Identities=16% Similarity=0.280 Sum_probs=32.2
Q ss_pred CCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5651 145 TIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202 (843)
Q Consensus 145 s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd 202 (843)
+++|..+++.+ |..-..+. . ..=..-|...| +.-.+|+..||..++.||.
T Consensus 154 sysLd~Va~~~Lg~~K~~~~----~--~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 154 SQGLKAVTKAKLGYDPVELD----P--EDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred CccHHHHHHHHhCCCcCcCC----H--HHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 58999999987 75321110 0 00011355544 5779999999999999983
No 99
>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=36.27 E-value=1.8e+02 Score=29.38 Aligned_cols=40 Identities=15% Similarity=0.086 Sum_probs=24.8
Q ss_pred HHHHHhhcC----CCceEEEecccccHHHHhhhc---CCccCc-eech
Q psy5651 83 GKLHEVLES----DRILKVIHGAFGDAGGLLSNF---NIRLKN-VYDT 122 (843)
Q Consensus 83 s~LkeLLED----psIlKVgHdaK~DL~~L~r~~---GI~L~n-VFDT 122 (843)
..|.+++.+ ....-|+|++.+|+.+|.+.+ |....+ ..|+
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~ 127 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDV 127 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhH
Confidence 345555553 245678999999999886543 433333 5565
No 100
>KOG2248|consensus
Probab=35.01 E-value=1e+02 Score=35.77 Aligned_cols=63 Identities=24% Similarity=0.222 Sum_probs=39.9
Q ss_pred HHHHHhhcCCCceEEEecccccHHHHhhhcCCccCceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCC
Q psy5651 83 GKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISP 159 (843)
Q Consensus 83 s~LkeLLEDpsIlKVgHdaK~DL~~L~r~~GI~L~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~L 159 (843)
..|.+++ +++-+-|||+.-.||.+|.-.| ..+.||.+. +.+.. |. .+...+|..|++.| |..+
T Consensus 285 ~~l~~~~-~~~TILVGHSLenDL~aLKl~H----~~ViDTa~l---f~~~~-g~-----~~~k~sLk~L~~~~L~~~I 348 (380)
T KOG2248|consen 285 KELLELI-SKNTILVGHSLENDLKALKLDH----PSVIDTAVL---FKHPT-GP-----YPFKSSLKNLAKSYLGKLI 348 (380)
T ss_pred HHHHhhc-CcCcEEEeechhhHHHHHhhhC----CceeeeeEE---EecCC-CC-----ccchHHHHHHHHHHHHHHH
Confidence 3456644 4555679999999999995433 347899842 22222 21 01246799999998 7443
No 101
>PRK05359 oligoribonuclease; Provisional
Probab=33.27 E-value=2.2e+02 Score=29.29 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=14.1
Q ss_pred CCeEEEEeeeeCC-CcCce
Q psy5651 38 ESKVGLDLEGMDL-GVDGK 55 (843)
Q Consensus 38 s~~IALDtE~~~~-ty~gk 55 (843)
...+++|+|..++ +...+
T Consensus 3 ~~~vvlD~ETTGLdp~~d~ 21 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDR 21 (181)
T ss_pred CcEEEEEeecCCCCCCCCe
Confidence 4679999999998 65554
No 102
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=32.86 E-value=7.4e+02 Score=27.73 Aligned_cols=158 Identities=16% Similarity=0.099 Sum_probs=86.4
Q ss_pred eEEEEeeeeCCCcCc-eEEEEEEEEeCCeEEEEeCCCCCc-ccchHHHHHhhcCCCc-eEEE-ecccccHHHHh----hh
Q psy5651 40 KVGLDLEGMDLGVDG-KVSLVSLALQNGKIFIFDVYSCPL-IMFDGKLHEVLESDRI-LKVI-HGAFGDAGGLL----SN 111 (843)
Q Consensus 40 ~IALDtE~~~~ty~g-kL~LIQIAT~dgqvyLID~laL~~-~~dLs~LkeLLEDpsI-lKVg-HdaK~DL~~L~----r~ 111 (843)
..-+|+|+.+++..| .+.++..+...+....|--.-++. ......|..++.+++. ..|. -+.++|.-.++ ..
T Consensus 100 ~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~~~ 179 (278)
T COG3359 100 VAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVRDR 179 (278)
T ss_pred eEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHHHhcc
Confidence 788999999983344 566666665433444443222221 1123456667777732 2344 45568988886 22
Q ss_pred cCCccCc-eechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCcc-ccccccccccCCCccCCCCC---CCHH
Q psy5651 112 FNIRLKN-VYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNN-FKKNIQNLYRENPHIWKTRP---LTSD 185 (843)
Q Consensus 112 ~GI~L~n-VFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~-~Kd~vK~~~keq~SDW~~RP---LSee 185 (843)
+...+.. -||++..++-|.... + -.-+|.. ++++ |+.-.. ..+... ..-.-.|.+-+ |-..
T Consensus 180 ~el~l~~~H~DL~h~~RRlwk~~----l-----~~c~Lk~-VEr~LGi~R~edtdG~~~---p~lyr~~~~~~dp~ll~~ 246 (278)
T COG3359 180 LELSLEFGHFDLYHPSRRLWKHL----L-----PRCGLKT-VERILGIRREEDTDGYDG---PELYRLYRRYGDPGLLDG 246 (278)
T ss_pred cccCccccchhhhhhhhhhhhcc----C-----CCCChhh-HHHHhCccccccCCCcch---HHHHHHHHHcCCHHHHHH
Confidence 4444443 899999998887321 1 1245654 4445 754321 000000 00011122211 1144
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5651 186 MLLYAAADVESLLALFHRMTKEYAL 210 (843)
Q Consensus 186 QL~YAA~DA~~LL~Lyd~L~~rLee 210 (843)
.+.|-..|+.-|..|+..+.+.+.+
T Consensus 247 l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 247 LVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred HHHccHHHHHhHHHHHHHHHHHHHH
Confidence 5677788999999999988887764
No 103
>PRK05762 DNA polymerase II; Reviewed
Probab=32.40 E-value=5.6e+02 Score=32.37 Aligned_cols=108 Identities=13% Similarity=0.080 Sum_probs=58.6
Q ss_pred hHHHHHhhc--CCCceEEEeccc-ccHHHHhh---hcCCcc-------------------------Cc--eechHHHHHH
Q psy5651 82 DGKLHEVLE--SDRILKVIHGAF-GDAGGLLS---NFNIRL-------------------------KN--VYDTQCAFTA 128 (843)
Q Consensus 82 Ls~LkeLLE--DpsIlKVgHdaK-~DL~~L~r---~~GI~L-------------------------~n--VFDTQLAAyL 128 (843)
+..|..++. ||++ -+|||.. +|+..|.+ .+|+.+ .| ++|+.....-
T Consensus 207 L~~F~~~i~~~DPDI-IvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~ 285 (786)
T PRK05762 207 LEKFNAWFAEHDPDV-IIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKS 285 (786)
T ss_pred HHHHHHHHHhcCCCE-EEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHH
Confidence 444444444 4775 4899965 79987764 345432 11 4566655443
Q ss_pred cCCCCCCcccCCCCCCCCCHHHHHHHh-CCCCccccccccccccCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5651 129 LQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204 (843)
Q Consensus 129 Lgp~~sG~~lp~~~~~s~SLa~Lvery-Gv~Ld~~Kd~vK~~~keq~SDW~~RPLSeeQL~YAA~DA~~LL~Lyd~L 204 (843)
.... ..+++|+.+++++ |..-... +.... ..+=..-|... .+...+|...||...+.|+..+
T Consensus 286 ~~~~----------l~sysL~~Va~~~Lg~~K~~~-d~~~~-~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 286 ATWV----------FDSFSLEYVSQRLLGEGKAID-DPYDR-MDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred hhcc----------CCCCCHHHHHHHHhCCCeecc-Ccccc-HHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 2111 1368999999988 6321100 00000 00001123322 1567899999999999999843
No 104
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=22.70 E-value=1.2e+02 Score=32.78 Aligned_cols=55 Identities=22% Similarity=0.152 Sum_probs=38.1
Q ss_pred CCCceEEEecccccHHHHhhhc-CCcc--------------CceechHHHHHHcCCCCCCcccCCCCCCCCCHHHHHHHh
Q psy5651 91 SDRILKVIHGAFGDAGGLLSNF-NIRL--------------KNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFY 155 (843)
Q Consensus 91 DpsIlKVgHdaK~DL~~L~r~~-GI~L--------------~nVFDTQLAAyLLgp~~sG~~lp~~~~~s~SLa~Lvery 155 (843)
+.+++.|+||+-.|+-.|++.+ |-.| +.++||-..+..+... ..+|+.|.+.+
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~------------~~~L~~l~~~l 214 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECPGK------------STSLQELAEEL 214 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS-------------SSHHHHHHHT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcccc------------ccCHHHHHHHh
Confidence 3447899999999998876543 3111 2488999988766521 46899999988
Q ss_pred CC
Q psy5651 156 KI 157 (843)
Q Consensus 156 Gv 157 (843)
+.
T Consensus 215 ~~ 216 (262)
T PF04857_consen 215 GI 216 (262)
T ss_dssp TS
T ss_pred CC
Confidence 44
Done!