Query psy5925
Match_columns 696
No_of_seqs 521 out of 2126
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 21:58:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0968|consensus 100.0 5.4E-90 1.2E-94 776.0 24.9 444 213-691 626-1078(1488)
2 PTZ00166 DNA polymerase delta 100.0 2.7E-75 5.8E-80 700.8 40.0 403 221-692 235-660 (1054)
3 KOG0969|consensus 100.0 5.2E-75 1.1E-79 636.4 19.5 380 242-692 271-667 (1066)
4 KOG0970|consensus 100.0 1.7E-67 3.6E-72 594.9 28.6 431 187-692 467-937 (1429)
5 PHA02528 43 DNA polymerase; Pr 100.0 9.9E-64 2.1E-68 587.5 36.7 371 242-676 103-480 (881)
6 PHA02524 43A DNA polymerase su 100.0 1.5E-60 3.2E-65 525.0 35.1 378 242-684 103-489 (498)
7 TIGR00592 pol2 DNA polymerase 100.0 2.9E-60 6.2E-65 578.9 39.8 424 189-692 447-905 (1172)
8 PHA03036 DNA polymerase; Provi 100.0 3.9E-60 8.5E-65 551.5 33.2 409 242-692 157-672 (1004)
9 PRK05762 DNA polymerase II; Re 100.0 2.1E-59 4.6E-64 553.8 35.1 302 349-692 197-503 (786)
10 smart00486 POLBc DNA polymeras 100.0 3.3E-55 7.1E-60 492.3 39.1 390 243-692 1-414 (471)
11 COG0417 PolB DNA polymerase el 100.0 1.2E-52 2.6E-57 495.7 32.3 359 240-692 149-518 (792)
12 PRK05761 DNA polymerase I; Rev 100.0 8.3E-50 1.8E-54 469.1 26.6 285 353-692 208-523 (787)
13 PHA03334 putative DNA polymera 100.0 6.2E-44 1.3E-48 414.6 26.0 340 345-692 321-775 (1545)
14 cd05778 DNA_polB_zeta_exo inac 100.0 1.7E-41 3.6E-46 347.3 24.7 221 243-499 2-231 (231)
15 cd05777 DNA_polB_delta_exo DED 100.0 2.5E-39 5.3E-44 331.7 25.9 219 241-506 3-228 (230)
16 cd05776 DNA_polB_alpha_exo ina 100.0 1E-35 2.2E-40 305.5 19.9 227 243-509 1-234 (234)
17 cd05534 POLBc_zeta DNA polymer 100.0 1.3E-35 2.9E-40 329.9 12.1 167 525-692 1-179 (451)
18 KOG1798|consensus 100.0 6.6E-33 1.4E-37 319.5 22.6 341 204-602 205-623 (2173)
19 cd05780 DNA_polB_Kod1_like_exo 100.0 3.1E-32 6.7E-37 272.4 24.0 195 243-501 1-195 (195)
20 cd05779 DNA_polB_epsilon_exo D 100.0 6.6E-31 1.4E-35 263.4 22.9 201 244-498 1-203 (204)
21 cd05781 DNA_polB_B3_exo DEDDy 100.0 1.7E-30 3.6E-35 258.1 23.1 184 243-501 1-188 (188)
22 TIGR00592 pol2 DNA polymerase 100.0 4.1E-33 8.8E-38 341.0 -3.6 367 241-675 194-596 (1172)
23 cd05784 DNA_polB_II_exo DEDDy 100.0 1.9E-29 4.1E-34 251.0 22.1 146 347-499 43-193 (193)
24 cd05785 DNA_polB_like2_exo Unc 100.0 3.1E-29 6.7E-34 252.4 21.1 188 241-498 5-206 (207)
25 cd05160 DEDDy_DNA_polB_exo DED 100.0 1.5E-28 3.4E-33 246.3 21.4 198 247-498 1-198 (199)
26 PF03104 DNA_pol_B_exo1: DNA p 99.9 3.4E-27 7.4E-32 253.3 16.9 216 190-451 99-325 (325)
27 cd05783 DNA_polB_B1_exo DEDDy 99.9 2E-26 4.3E-31 231.5 21.2 187 242-499 2-202 (204)
28 PF00136 DNA_pol_B: DNA polyme 99.9 1.6E-28 3.6E-33 276.8 5.7 157 525-692 1-171 (466)
29 cd05533 POLBc_delta DNA polyme 99.9 4.6E-27 9.9E-32 258.1 10.3 114 558-692 1-123 (393)
30 cd05536 POLBc_B3 DNA polymeras 99.9 5.4E-25 1.2E-29 240.1 9.7 107 558-692 2-117 (371)
31 cd05532 POLBc_alpha DNA polyme 99.9 1.4E-24 3.1E-29 239.0 9.0 108 556-692 4-120 (400)
32 cd00145 POLBc DNA polymerase t 99.9 3.4E-24 7.4E-29 230.1 9.8 108 558-692 1-117 (323)
33 KOG0969|consensus 99.9 5.6E-24 1.2E-28 235.5 5.4 145 57-228 510-669 (1066)
34 cd05530 POLBc_B1 DNA polymeras 99.9 3.5E-23 7.5E-28 224.8 10.0 109 557-692 10-128 (372)
35 cd05531 POLBc_B2 DNA polymeras 99.9 4.7E-23 1E-27 223.0 9.1 106 558-692 3-110 (352)
36 cd05537 POLBc_Pol_II DNA polym 99.9 2.6E-22 5.6E-27 218.5 8.9 105 559-692 2-106 (371)
37 KOG0968|consensus 99.9 2.3E-23 5E-28 237.7 0.7 149 60-217 901-1060(1488)
38 cd05782 DNA_polB_like1_exo Unc 99.8 9.6E-20 2.1E-24 183.8 19.0 134 351-499 74-207 (208)
39 PTZ00166 DNA polymerase delta 99.8 4.6E-20 1E-24 223.5 6.8 143 59-228 504-662 (1054)
40 cd05538 POLBc_Pol_II_B DNA pol 99.8 1.3E-19 2.8E-24 195.7 7.6 84 559-692 2-94 (347)
41 cd05534 POLBc_zeta DNA polymer 99.8 1.1E-19 2.3E-24 202.8 6.6 147 68-227 5-180 (451)
42 PHA03036 DNA polymerase; Provi 99.8 2E-19 4.2E-24 211.6 5.8 146 66-228 501-674 (1004)
43 PHA03334 putative DNA polymera 99.7 4.4E-18 9.6E-23 200.1 5.9 162 51-227 575-776 (1545)
44 PHA02524 43A DNA polymerase su 99.7 1.8E-17 3.9E-22 184.0 7.2 118 64-198 347-465 (498)
45 cd05533 POLBc_delta DNA polyme 99.6 7.1E-16 1.5E-20 169.8 6.0 110 94-227 1-124 (393)
46 PF00136 DNA_pol_B: DNA polyme 99.6 1.6E-16 3.6E-21 179.4 -0.3 113 67-198 4-131 (466)
47 PRK05761 DNA polymerase I; Rev 99.6 1.1E-15 2.4E-20 181.1 6.1 74 65-141 364-449 (787)
48 PHA02528 43 DNA polymerase; Pr 99.6 2E-15 4.3E-20 179.4 8.2 74 65-143 348-421 (881)
49 COG0417 PolB DNA polymerase el 99.5 1.4E-14 3E-19 172.5 5.3 133 65-227 375-519 (792)
50 PF10108 DNA_pol_B_exo2: Predi 99.5 1.4E-12 3.1E-17 130.0 18.7 140 353-506 35-174 (209)
51 KOG0970|consensus 99.5 1.8E-14 3.9E-19 166.0 5.4 72 67-140 778-869 (1429)
52 PRK05762 DNA polymerase II; Re 99.5 3.5E-14 7.5E-19 169.3 6.8 69 69-141 375-443 (786)
53 KOG1829|consensus 99.5 7.7E-15 1.7E-19 164.2 0.2 62 1-62 506-569 (580)
54 cd05532 POLBc_alpha DNA polyme 99.4 3.9E-14 8.5E-19 156.5 3.9 105 93-227 5-121 (400)
55 cd00145 POLBc DNA polymerase t 99.4 7E-14 1.5E-18 150.5 5.1 77 94-198 1-77 (323)
56 cd05530 POLBc_B1 DNA polymeras 99.4 2.2E-13 4.8E-18 148.4 3.8 45 94-141 11-55 (372)
57 smart00486 POLBc DNA polymeras 99.3 2.9E-12 6.3E-17 144.2 7.1 113 67-198 247-373 (471)
58 cd05536 POLBc_B3 DNA polymeras 99.3 3.5E-12 7.7E-17 139.7 6.2 76 94-198 2-77 (371)
59 cd05537 POLBc_Pol_II DNA polym 99.3 3.6E-12 7.8E-17 139.3 5.8 45 95-142 2-46 (371)
60 cd05531 POLBc_B2 DNA polymeras 99.2 7.7E-12 1.7E-16 135.9 6.1 45 94-141 3-47 (352)
61 PF13482 RNase_H_2: RNase_H su 98.8 1.6E-08 3.4E-13 98.1 8.3 117 354-501 42-163 (164)
62 cd05538 POLBc_Pol_II_B DNA pol 98.8 2.6E-09 5.7E-14 115.9 3.0 39 95-136 2-40 (347)
63 PHA02563 DNA polymerase; Provi 98.7 2E-07 4.3E-12 107.3 13.4 220 359-601 50-281 (630)
64 COG3359 Predicted exonuclease 98.3 1.7E-05 3.8E-10 79.8 14.9 118 353-501 141-265 (278)
65 PRK06309 DNA polymerase III su 97.7 0.0014 3.1E-08 67.5 16.4 102 349-501 60-162 (232)
66 PRK06310 DNA polymerase III su 97.7 0.0019 4.1E-08 67.4 17.1 165 244-501 6-170 (250)
67 PHA02735 putative DNA polymera 97.7 0.00026 5.5E-09 76.2 10.6 145 430-601 160-311 (716)
68 PRK08517 DNA polymerase III su 97.5 0.0029 6.2E-08 66.3 15.8 163 242-501 65-227 (257)
69 cd06136 TREX1_2 DEDDh 3'-5' ex 97.5 0.0034 7.4E-08 61.9 15.3 93 357-500 83-176 (177)
70 PRK05601 DNA polymerase III su 97.4 0.0018 3.9E-08 70.3 13.6 198 242-501 43-245 (377)
71 PRK06807 DNA polymerase III su 97.4 0.004 8.6E-08 67.1 16.2 161 244-501 7-168 (313)
72 PF03175 DNA_pol_B_2: DNA poly 97.4 0.00011 2.4E-09 83.4 3.9 196 480-691 132-368 (459)
73 smart00479 EXOIII exonuclease 97.4 0.0078 1.7E-07 58.0 16.1 100 352-501 64-163 (169)
74 PRK07883 hypothetical protein; 97.3 0.0042 9E-08 72.1 16.0 141 243-458 13-156 (557)
75 PRK06195 DNA polymerase III su 97.3 0.0048 1E-07 66.4 15.2 136 245-455 1-137 (309)
76 PRK06063 DNA polymerase III su 97.3 0.0072 1.6E-07 65.2 16.4 161 243-501 13-175 (313)
77 TIGR03491 RecB family nuclease 97.3 0.0011 2.5E-08 75.1 10.8 123 353-500 326-456 (457)
78 cd06130 DNA_pol_III_epsilon_li 97.3 0.0064 1.4E-07 58.0 14.1 73 352-455 61-134 (156)
79 cd06131 DNA_pol_III_epsilon_Ec 97.2 0.013 2.7E-07 56.9 15.7 103 351-501 64-166 (167)
80 PRK09146 DNA polymerase III su 97.2 0.0089 1.9E-07 62.0 15.4 165 243-501 45-223 (239)
81 PRK07740 hypothetical protein; 97.2 0.0065 1.4E-07 63.2 14.3 163 243-501 57-222 (244)
82 PRK07942 DNA polymerase III su 97.2 0.017 3.8E-07 59.5 17.1 169 242-501 3-176 (232)
83 TIGR01406 dnaQ_proteo DNA poly 97.1 0.021 4.5E-07 58.6 16.4 102 353-501 67-168 (225)
84 TIGR01405 polC_Gram_pos DNA po 97.1 0.0082 1.8E-07 75.0 15.4 141 244-459 189-330 (1213)
85 PRK09145 DNA polymerase III su 97.1 0.018 4E-07 57.9 15.3 162 245-501 29-197 (202)
86 PRK05711 DNA polymerase III su 97.0 0.012 2.6E-07 61.1 13.1 170 243-501 2-172 (240)
87 TIGR00573 dnaq exonuclease, DN 96.9 0.017 3.7E-07 58.9 14.0 100 352-501 71-173 (217)
88 cd06127 DEDDh DEDDh 3'-5' exon 96.9 0.023 4.9E-07 53.5 13.5 75 352-457 63-138 (159)
89 TIGR01407 dinG_rel DnaQ family 96.8 0.024 5.3E-07 69.3 16.5 135 247-455 2-137 (850)
90 cd06138 ExoI_N N-terminal DEDD 96.8 0.011 2.4E-07 58.5 11.1 44 353-397 67-110 (183)
91 PRK08074 bifunctional ATP-depe 96.8 0.028 6E-07 69.3 16.8 136 246-455 4-141 (928)
92 PRK07748 sporulation inhibitor 96.8 0.043 9.3E-07 55.5 15.5 172 244-501 3-176 (207)
93 PRK05168 ribonuclease T; Provi 96.8 0.11 2.3E-06 52.9 18.1 174 242-501 14-197 (211)
94 cd06134 RNaseT DEDDh 3'-5' exo 96.7 0.081 1.7E-06 52.8 16.8 101 354-501 79-185 (189)
95 PRK07246 bifunctional ATP-depe 96.5 0.041 9E-07 66.8 15.5 138 244-458 6-144 (820)
96 cd06125 DnaQ_like_exo DnaQ-lik 96.3 0.02 4.3E-07 50.7 8.5 35 362-397 35-69 (96)
97 PRK06722 exonuclease; Provisio 96.3 0.16 3.5E-06 53.8 16.2 170 245-501 5-177 (281)
98 PRK11779 sbcB exonuclease I; P 96.2 0.17 3.7E-06 57.5 17.1 179 243-501 4-194 (476)
99 TIGR01298 RNaseT ribonuclease 96.2 0.35 7.6E-06 48.7 17.7 102 353-501 81-188 (200)
100 PF14446 Prok-RING_1: Prokaryo 96.2 0.0024 5.2E-08 49.9 1.5 39 5-48 4-44 (54)
101 PRK07247 DNA polymerase III su 96.1 0.2 4.2E-06 50.4 15.2 94 351-501 67-165 (195)
102 cd06144 REX4_like DEDDh 3'-5' 96.1 0.051 1.1E-06 52.2 10.6 34 350-387 59-92 (152)
103 PF01612 DNA_pol_A_exo1: 3'-5' 95.9 0.12 2.7E-06 49.8 12.6 104 358-501 65-171 (176)
104 cd06133 ERI-1_3'hExo_like DEDD 95.9 0.4 8.7E-06 46.5 16.2 104 351-501 71-175 (176)
105 cd06149 ISG20 DEDDh 3'-5' exon 95.2 0.16 3.4E-06 49.2 10.1 73 351-461 60-137 (157)
106 cd06137 DEDDh_RNase DEDDh 3'-5 93.9 0.25 5.5E-06 47.8 8.4 66 356-460 71-140 (161)
107 COG2176 PolC DNA polymerase II 93.8 0.19 4.1E-06 61.2 8.5 76 349-455 482-558 (1444)
108 PRK09182 DNA polymerase III su 93.4 1.7 3.6E-05 46.6 14.3 32 242-278 34-65 (294)
109 PRK00448 polC DNA polymerase I 93.3 0.89 1.9E-05 58.2 13.8 74 351-455 482-556 (1437)
110 cd06145 REX1_like DEDDh 3'-5' 93.1 0.94 2E-05 43.4 10.7 68 353-459 60-128 (150)
111 COG0847 DnaQ DNA polymerase II 92.0 1.6 3.4E-05 45.1 11.5 166 245-502 13-179 (243)
112 PRK05359 oligoribonuclease; Pr 91.6 1.2 2.7E-05 44.0 9.8 44 352-396 76-122 (181)
113 PHA02563 DNA polymerase; Provi 90.1 0.14 3E-06 60.0 1.5 44 94-138 236-280 (630)
114 cd06146 mut-7_like_exo DEDDy 3 88.8 2 4.3E-05 43.0 8.6 100 370-501 80-191 (193)
115 cd06141 WRN_exo DEDDy 3'-5' ex 87.7 3.9 8.5E-05 39.5 9.8 117 347-501 50-168 (170)
116 cd06135 Orn DEDDh 3'-5' exonuc 87.4 2.2 4.8E-05 41.8 7.9 44 351-395 71-117 (173)
117 PF00628 PHD: PHD-finger; Int 86.7 0.63 1.4E-05 35.8 2.8 39 8-51 1-50 (51)
118 PRK05755 DNA polymerase I; Pro 84.9 16 0.00034 45.3 15.0 106 357-502 357-466 (880)
119 PTZ00315 2'-phosphotransferase 84.8 21 0.00045 41.7 14.9 113 242-392 53-174 (582)
120 cd06139 DNA_polA_I_Ecoli_like_ 83.6 11 0.00024 36.8 10.8 108 354-501 51-166 (193)
121 smart00249 PHD PHD zinc finger 82.6 0.84 1.8E-05 33.6 1.8 30 8-42 1-30 (47)
122 PF08271 TF_Zn_Ribbon: TFIIB z 82.1 1.2 2.7E-05 33.2 2.5 34 7-41 1-34 (43)
123 KOG2114|consensus 81.2 0.46 1E-05 56.1 -0.1 33 19-51 836-880 (933)
124 cd06129 RNaseD_like DEDDy 3'-5 80.9 7.5 0.00016 37.4 8.2 66 431-501 94-159 (161)
125 PF13639 zf-RING_2: Ring finge 73.6 1.5 3.1E-05 32.7 0.7 36 8-49 2-43 (44)
126 cd00007 35EXOc 3'-5' exonuclea 72.8 37 0.00081 31.3 10.4 107 356-501 40-151 (155)
127 PF09723 Zn-ribbon_8: Zinc rib 70.9 2.9 6.2E-05 31.1 1.8 31 27-57 6-40 (42)
128 PF08408 DNA_pol_B_3: DNA poly 70.7 4.5 9.7E-05 38.3 3.3 63 456-521 84-146 (149)
129 PF09723 Zn-ribbon_8: Zinc rib 69.7 3 6.5E-05 31.1 1.6 28 7-34 6-34 (42)
130 KOG0954|consensus 65.8 2.3 4.9E-05 49.7 0.5 48 2-52 267-321 (893)
131 PRK07983 exodeoxyribonuclease 65.0 55 0.0012 33.5 10.4 78 370-501 73-150 (219)
132 PF11793 FANCL_C: FANCL C-term 63.6 2.8 6.1E-05 34.9 0.5 32 8-41 4-37 (70)
133 PRK10829 ribonuclease D; Provi 63.5 31 0.00066 38.3 8.7 101 360-501 64-166 (373)
134 PF00130 C1_1: Phorbol esters/ 63.0 9.8 0.00021 29.3 3.5 40 5-47 10-51 (53)
135 PF12760 Zn_Tnp_IS1595: Transp 62.7 7.7 0.00017 29.4 2.7 31 3-34 15-45 (46)
136 smart00109 C1 Protein kinase C 60.8 3.7 8E-05 30.7 0.7 35 5-43 10-44 (49)
137 cd00029 C1 Protein kinase C co 60.5 5 0.00011 30.3 1.4 36 5-43 10-45 (50)
138 TIGR02605 CxxC_CxxC_SSSS putat 60.1 5.7 0.00012 30.7 1.7 31 27-57 6-40 (52)
139 PF00929 RNase_T: Exonuclease; 59.9 6 0.00013 36.9 2.1 39 352-393 66-104 (164)
140 COG4416 Com Mu-like prophage p 58.9 2.1 4.7E-05 33.3 -0.9 31 25-55 3-36 (60)
141 TIGR02605 CxxC_CxxC_SSSS putat 58.2 6.6 0.00014 30.3 1.7 28 7-34 6-34 (52)
142 COG3364 Zn-ribbon containing p 55.3 4.3 9.4E-05 35.9 0.3 31 27-57 3-34 (112)
143 PRK00398 rpoP DNA-directed RNA 54.7 8.5 0.00019 29.1 1.8 26 26-51 3-29 (46)
144 PF13831 PHD_2: PHD-finger; PD 54.2 5.4 0.00012 28.7 0.6 18 25-42 3-20 (36)
145 smart00834 CxxC_CXXC_SSSS Puta 54.1 8.2 0.00018 28.0 1.6 25 27-51 6-34 (41)
146 PF08746 zf-RING-like: RING-li 54.1 5 0.00011 30.1 0.4 24 26-49 11-43 (43)
147 KOG0955|consensus 53.3 7.2 0.00016 48.3 1.8 46 8-56 221-273 (1051)
148 cd00162 RING RING-finger (Real 52.1 5.9 0.00013 28.4 0.5 36 9-51 2-43 (45)
149 COG2051 RPS27A Ribosomal prote 52.0 9.7 0.00021 31.2 1.7 28 8-36 21-48 (67)
150 PF08792 A2L_zn_ribbon: A2L zi 51.7 15 0.00032 26.0 2.4 28 7-36 4-31 (33)
151 PF03107 C1_2: C1 domain; Int 51.1 11 0.00023 25.9 1.6 30 7-41 1-30 (30)
152 cd05778 DNA_polB_zeta_exo inac 50.5 5.3 0.00011 41.2 0.0 33 312-344 79-111 (231)
153 COG1439 Predicted nucleic acid 49.6 7.8 0.00017 38.1 1.0 27 27-56 140-166 (177)
154 COG1545 Predicted nucleic-acid 49.1 9.6 0.00021 36.2 1.5 25 26-53 29-53 (140)
155 PRK04023 DNA polymerase II lar 48.9 9.6 0.00021 46.6 1.8 42 6-55 626-675 (1121)
156 smart00474 35EXOc 3'-5' exonuc 47.3 1.3E+02 0.0028 28.2 9.2 101 360-501 65-167 (172)
157 PF03175 DNA_pol_B_2: DNA poly 47.3 5.6 0.00012 45.2 -0.4 33 94-129 204-236 (459)
158 KOG4323|consensus 45.1 7.6 0.00017 43.7 0.2 51 9-62 171-234 (464)
159 PRK00415 rps27e 30S ribosomal 44.9 15 0.00032 29.6 1.7 28 8-36 13-40 (59)
160 PF05191 ADK_lid: Adenylate ki 44.0 18 0.00039 26.1 2.0 25 27-51 2-29 (36)
161 PF14319 Zn_Tnp_IS91: Transpos 43.1 18 0.00039 32.9 2.3 32 25-57 41-74 (111)
162 COG3357 Predicted transcriptio 42.6 12 0.00026 32.6 1.0 24 27-50 59-83 (97)
163 PF14569 zf-UDP: Zinc-binding 42.0 12 0.00025 31.7 0.8 52 4-56 7-64 (80)
164 PF11781 RRN7: RNA polymerase 41.4 20 0.00044 25.8 1.9 29 5-36 5-35 (36)
165 PF12172 DUF35_N: Rubredoxin-l 40.9 15 0.00033 26.3 1.2 23 25-50 10-32 (37)
166 PF01667 Ribosomal_S27e: Ribos 40.4 17 0.00036 28.9 1.4 28 8-36 9-36 (55)
167 cd05776 DNA_polB_alpha_exo ina 40.2 12 0.00025 38.7 0.7 32 312-343 80-111 (234)
168 PF13717 zinc_ribbon_4: zinc-r 38.9 18 0.00039 26.0 1.3 10 28-37 4-13 (36)
169 PF03337 Pox_F12L: Poxvirus F1 38.8 7.5E+02 0.016 29.5 16.9 86 349-458 248-341 (651)
170 PF15135 UPF0515: Uncharacteri 38.5 13 0.00027 38.4 0.6 54 3-56 109-168 (278)
171 PF09538 FYDLN_acid: Protein o 38.0 17 0.00037 33.0 1.3 32 25-56 8-39 (108)
172 PRK00564 hypA hydrogenase nick 38.0 17 0.00036 33.4 1.3 36 25-62 70-105 (117)
173 PF03604 DNA_RNApol_7kD: DNA d 37.7 22 0.00047 25.0 1.5 25 7-34 1-25 (32)
174 PF09845 DUF2072: Zn-ribbon co 36.1 15 0.00032 34.4 0.6 28 27-54 2-30 (131)
175 TIGR03826 YvyF flagellar opero 36.0 13 0.00028 35.2 0.3 28 26-55 3-30 (137)
176 PLN02638 cellulose synthase A 36.0 21 0.00046 44.3 2.0 49 4-57 15-73 (1079)
177 PLN00209 ribosomal protein S27 35.3 29 0.00062 30.0 2.2 29 8-37 38-66 (86)
178 PF12861 zf-Apc11: Anaphase-pr 35.2 14 0.0003 32.0 0.3 44 7-51 22-79 (85)
179 smart00184 RING Ring finger. E 34.8 16 0.00034 25.1 0.4 22 28-49 12-39 (39)
180 PTZ00083 40S ribosomal protein 34.4 32 0.00069 29.7 2.3 29 8-37 37-65 (85)
181 PF13832 zf-HC5HC2H_2: PHD-zin 34.1 20 0.00043 32.2 1.1 31 6-43 55-87 (110)
182 PF08490 DUF1744: Domain of un 34.0 53 0.0011 36.8 4.6 83 503-585 121-213 (396)
183 PLN02400 cellulose synthase 33.7 25 0.00053 43.8 2.1 49 4-57 34-92 (1085)
184 TIGR00593 pola DNA polymerase 33.5 1.9E+02 0.004 36.1 9.6 108 357-501 365-473 (887)
185 TIGR02300 FYDLN_acid conserved 33.5 23 0.0005 32.9 1.4 31 25-55 8-38 (129)
186 PF14445 Prok-RING_2: Prokaryo 33.3 5 0.00011 30.9 -2.4 42 6-52 7-50 (57)
187 PRK12380 hydrogenase nickel in 33.1 28 0.0006 31.8 1.9 36 24-62 68-103 (113)
188 KOG0320|consensus 32.9 12 0.00026 36.8 -0.6 49 7-68 132-186 (187)
189 cd05777 DNA_polB_delta_exo DED 32.5 17 0.00038 37.2 0.5 32 313-344 70-101 (230)
190 PF03104 DNA_pol_B_exo1: DNA p 32.5 13 0.00027 39.7 -0.5 33 312-344 220-252 (325)
191 COG1107 Archaea-specific RecJ- 32.1 27 0.00059 40.4 1.9 47 6-54 53-106 (715)
192 PLN02189 cellulose synthase 32.1 25 0.00054 43.5 1.8 48 5-57 33-90 (1040)
193 KOG4299|consensus 32.0 17 0.00037 42.1 0.4 43 8-55 255-308 (613)
194 smart00659 RPOLCX RNA polymera 31.2 29 0.00064 26.2 1.4 25 27-51 3-27 (44)
195 COG2251 Predicted nuclease (Re 30.7 63 0.0014 36.4 4.4 71 430-501 388-466 (474)
196 cd05535 POLBc_epsilon DNA poly 30.4 27 0.00058 40.9 1.6 26 577-602 92-117 (621)
197 PRK03681 hypA hydrogenase nick 30.1 32 0.0007 31.4 1.8 47 13-62 58-104 (114)
198 PF15446 zf-PHD-like: PHD/FYVE 29.6 29 0.00062 33.9 1.4 35 25-59 16-67 (175)
199 PF07295 DUF1451: Protein of u 29.5 36 0.00079 32.6 2.1 32 25-56 111-143 (146)
200 PF07649 C1_3: C1-like domain; 29.3 21 0.00046 24.3 0.3 30 7-41 1-30 (30)
201 COG1096 Predicted RNA-binding 29.2 21 0.00046 35.4 0.5 30 27-57 150-179 (188)
202 PHA02929 N1R/p28-like protein; 28.7 34 0.00073 35.5 1.8 47 5-51 173-224 (238)
203 PLN02436 cellulose synthase A 28.2 33 0.00071 42.7 1.8 48 5-57 35-92 (1094)
204 KOG0193|consensus 27.9 27 0.00058 40.7 1.0 36 7-47 187-226 (678)
205 PRK14890 putative Zn-ribbon RN 27.6 52 0.0011 26.5 2.3 41 8-50 9-55 (59)
206 KOG3005|consensus 27.5 19 0.00042 37.6 -0.2 44 8-55 184-244 (276)
207 cd05535 POLBc_epsilon DNA poly 27.1 32 0.0007 40.2 1.5 27 115-141 92-118 (621)
208 PF10080 DUF2318: Predicted me 26.2 43 0.00093 30.1 1.8 37 8-47 37-75 (102)
209 PF12678 zf-rbx1: RING-H2 zinc 26.2 25 0.00053 29.4 0.3 20 30-49 48-72 (73)
210 PRK14892 putative transcriptio 25.9 45 0.00097 29.8 1.9 59 24-86 19-82 (99)
211 cd06143 PAN2_exo DEDDh 3'-5' e 25.8 2.6E+02 0.0056 27.7 7.3 49 429-498 125-173 (174)
212 COG1997 RPL43A Ribosomal prote 25.7 54 0.0012 28.5 2.2 36 5-42 34-69 (89)
213 KOG1706|consensus 25.5 77 0.0017 34.0 3.7 43 71-113 159-210 (412)
214 KOG0825|consensus 25.1 37 0.00081 40.4 1.5 43 6-53 215-267 (1134)
215 PF01155 HypA: Hydrogenase exp 24.4 30 0.00065 31.5 0.5 39 14-54 59-97 (113)
216 PRK12495 hypothetical protein; 24.3 44 0.00096 34.0 1.7 28 6-37 42-69 (226)
217 PLN02915 cellulose synthase A 24.1 38 0.00083 42.0 1.5 48 5-57 14-71 (1044)
218 smart00154 ZnF_AN1 AN1-like Zi 23.8 36 0.00079 24.9 0.7 22 9-36 1-22 (39)
219 KOG4793|consensus 23.6 90 0.0019 32.9 3.8 44 354-399 105-148 (318)
220 KOG4628|consensus 23.3 45 0.00098 36.5 1.7 40 7-51 230-275 (348)
221 KOG0827|consensus 23.1 18 0.0004 39.5 -1.3 45 8-56 6-59 (465)
222 PHA03328 nuclear egress lamina 23.1 28 0.00061 37.2 0.0 67 10-77 86-168 (316)
223 PF10122 Mu-like_Com: Mu-like 22.9 22 0.00048 27.7 -0.5 31 26-56 4-37 (51)
224 PF08274 PhnA_Zn_Ribbon: PhnA 22.8 44 0.00096 23.2 1.0 23 9-34 5-27 (30)
225 KOG3507|consensus 22.8 45 0.00096 26.8 1.1 25 7-34 21-45 (62)
226 KOG4718|consensus 22.7 31 0.00066 34.9 0.2 37 8-51 183-224 (235)
227 PF14354 Lar_restr_allev: Rest 22.4 66 0.0014 25.5 2.1 27 8-34 5-37 (61)
228 PRK12496 hypothetical protein; 22.4 48 0.001 32.3 1.5 30 27-57 128-157 (164)
229 TIGR00373 conserved hypothetic 22.4 34 0.00073 33.2 0.4 29 4-35 107-137 (158)
230 PRK11032 hypothetical protein; 22.2 61 0.0013 31.5 2.2 34 25-58 123-157 (160)
231 COG5194 APC11 Component of SCF 22.2 25 0.00053 30.0 -0.5 20 31-50 53-77 (88)
232 COG2995 PqiA Uncharacterized p 22.1 77 0.0017 35.1 3.1 59 23-82 15-76 (418)
233 PRK14714 DNA polymerase II lar 21.8 48 0.001 41.9 1.6 42 7-56 668-722 (1337)
234 PF10367 Vps39_2: Vacuolar sor 21.8 65 0.0014 28.3 2.2 31 6-42 78-108 (109)
235 cd00350 rubredoxin_like Rubred 21.8 66 0.0014 22.5 1.7 26 27-53 2-27 (33)
236 PF13771 zf-HC5HC2H: PHD-like 21.4 58 0.0013 27.9 1.7 35 5-46 35-71 (90)
237 KOG3657|consensus 21.3 1.5E+02 0.0033 35.9 5.5 60 445-509 322-385 (1075)
238 cd07162 NR_DBD_PXR DNA-binding 20.8 27 0.00059 30.3 -0.5 30 8-40 1-30 (87)
239 PF13719 zinc_ribbon_5: zinc-r 20.6 57 0.0012 23.5 1.2 29 8-37 4-36 (37)
240 TIGR00155 pqiA_fam integral me 20.4 52 0.0011 36.9 1.5 34 24-57 11-47 (403)
241 cd05781 DNA_polB_B3_exo DEDDy 20.3 40 0.00087 33.5 0.5 31 314-344 48-78 (188)
242 PF05582 Peptidase_U57: YabG p 20.2 98 0.0021 32.9 3.3 29 351-379 135-165 (287)
No 1
>KOG0968|consensus
Probab=100.00 E-value=5.4e-90 Score=776.05 Aligned_cols=444 Identities=41% Similarity=0.703 Sum_probs=405.1
Q ss_pred ccccCCCCCCccccccCCCCcccccccccCCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCC-CC---CceEE
Q psy5925 213 YAIDAMTPDTTGDYQMGLDNLNEVTSHVENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPP-EE---DRKVG 288 (696)
Q Consensus 213 ~~I~~~t~~~~~gfk~~~~~~~~~~~~~~~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~-~~---~~~~g 288 (696)
++|++|+.++.|+|+.++.+.++.++....+.||++|+|+|+.||+++-|||..|+|.+|+|+++.|.+ .| ....|
T Consensus 626 s~i~~p~~~s~~~~~~~v~~~q~~~~~~~~~~Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~g 705 (1488)
T KOG0968|consen 626 SQIRGPTAKSVYTFETSVAGAQKSKPVEQTQLLTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVG 705 (1488)
T ss_pred hhccCCccccccccchhhhcccccccccccceeeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcccceeeee
Confidence 348999999999999999999999999999999999999999999999999999999999999999865 22 23778
Q ss_pred EEEEcCCCCCcccccCccccccccchhhhhhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHH
Q psy5925 289 IILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQ 368 (696)
Q Consensus 289 ~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~ 368 (696)
+++++...... ... +. +. + | -.+.+|.++.+|++|++++.+++.+
T Consensus 706 v~Vv~~~~~ds-----~~~------------t~---~~--~-----~--------~~~~~V~~~~sE~elf~ev~~~i~q 750 (1488)
T KOG0968|consen 706 VIVVDKVCPDS-----HVQ------------TT---TL--G-----G--------IYGCRVVVMESELELFEEVAKLIVQ 750 (1488)
T ss_pred EEEEeccCccc-----ccc------------cc---cc--C-----C--------cCCceEEEehhHHHHHHHHHHHHHh
Confidence 99987542110 000 00 00 0 1 1367899999999999999999999
Q ss_pred hCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCC-----ccccceeeecccEEEehHHHHhhhcCC
Q psy5925 369 WDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRD-----EVKNTQLQMPGRIVINLWRLLRHEVNL 443 (696)
Q Consensus 369 ~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~-----~~~~~~~~i~GRl~lDl~~~~r~~~kl 443 (696)
+||||++||++++++||||++|++.+|+++...++|++.....+.+.. ....+.+.+.||+++++|+++|.+.+|
T Consensus 751 ~DPDIl~GyEi~~~SWGyl~eR~~~l~~di~~~lsRv~~~~~~n~~d~~~ewg~tt~S~i~i~GR~~lNiWRilR~eV~L 830 (1488)
T KOG0968|consen 751 YDPDILLGYEIHNLSWGYLIERAKLLGIDISRDLSRVKCYEKTNESDDEREWGYTTISGINIVGRHVLNIWRILRSEVAL 830 (1488)
T ss_pred cCcceeeeeeecccchHHHHHHHHHhcchHHHHHhcCCChhhhhhhhhhhhccceeeccccccchhhhhHHHHHhhhhhh
Confidence 999999999999999999999999999999988999986543332221 112567899999999999999999999
Q ss_pred CCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhc
Q psy5925 444 QSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLS 523 (696)
Q Consensus 444 ~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~ 523 (696)
++|+|++|+.++|+++.|.++++.+++||+++....+++++.|++.++.++++|+.++++|.++.||||++||+|.+|++
T Consensus 831 ~nYtlEsv~~nVL~kk~P~~~~~~Lt~~~~s~~~~~r~~~l~y~l~Ra~~NlelLsq~d~i~k~~E~ARv~GIdF~sV~t 910 (1488)
T KOG0968|consen 831 TNYTLESVVFNVLRKKIPMFDFAVLTRWWKSKRSAERNDVLNYLLSRARLNLELLSQLDWILKNSEMARVIGIDFHSVLT 910 (1488)
T ss_pred hhccHHHHHHHHHHhhcCCCcHHHHHHHHhcccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhHHHHHhhcceeeEEee
Confidence 99999999999999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred CcchhhhHHHhhcccccCCeeeeCCchhhhhccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccc
Q psy5925 524 RGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR 603 (696)
Q Consensus 524 rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~ 603 (696)
||||+||||+|+|.||++|||+|+|+.+|++.|+++++.++||||++.||++||+||||||||||||||||+|||||+|+
T Consensus 911 RGSQ~rVESmllRiAk~~Nyi~~SPs~kQv~~q~A~EcvPLVMEPeS~fY~~PViVLDFQSLYPSivIAYNyCySTcLG~ 990 (1488)
T KOG0968|consen 911 RGSQFRVESMLLRIAKPMNYIAPSPSHKQVAMQGAPECVPLVMEPESAFYFDPVIVLDFQSLYPSIVIAYNYCYSTCLGK 990 (1488)
T ss_pred ccchhhHHHHHHHHhcccccccCCccHHHHhhcCCccccceeecchhhhccCceEEEEchhhcchHHHhHHHHHHHhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCCcccccccChhHHhhcccceeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH
Q psy5925 604 VEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL 683 (696)
Q Consensus 604 ~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~ 683 (696)
+.+++..+++++|++.+..|++++.+..++|+++|||++|||+++|+|+||+||+|||++|.|||+.||+.+++..+.|+
T Consensus 991 v~~l~~~~e~~LG~s~~s~~~dil~~~~ndV~isPNgv~yVK~sVRkgvLpkmLeEIL~tRiMVKkaMK~~~~~~~L~Ri 1070 (1488)
T KOG0968|consen 991 VGNLNQMNEIKLGVSKYSLPPDILVLAKNDVTISPNGVMYVKPSVRKGVLPKMLEEILATRIMVKKAMKRTKDNKKLKRI 1070 (1488)
T ss_pred HHhhccccceeeeeeeccCCHHHHHHHhcceeeCCCceEEechhhhhhhHHHHHHHHHHHHHHHHHHHHHhcchHHHHHH
Confidence 99999988899999999999999998889999999999999999999999999999999999999999999999999999
Q ss_pred hhhccccc
Q psy5925 684 TMLNSMLL 691 (696)
Q Consensus 684 l~ansmy~ 691 (696)
|||+|+.+
T Consensus 1071 LnaRQLAL 1078 (1488)
T KOG0968|consen 1071 LNARQLAL 1078 (1488)
T ss_pred hhhHHHHH
Confidence 99988764
No 2
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=2.7e-75 Score=700.76 Aligned_cols=403 Identities=27% Similarity=0.364 Sum_probs=333.2
Q ss_pred CCccccccCCCCcccccc---c---ccCCCceEEEEEEEeecCCC-CCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEc
Q psy5925 221 DTTGDYQMGLDNLNEVTS---H---VENYYLTVLAVEIHAISRAL-LKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIG 293 (696)
Q Consensus 221 ~~~~gfk~~~~~~~~~~~---~---~~~~~LtilsleIe~~sr~~-~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~ 293 (696)
.+||.+++.+.... +.+ . ...|+|++|||||||.++.+ .||+|+.|||++|+.++............+++
T Consensus 235 ~s~c~~E~~~~~~~-l~~~~~~~~~~~~pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vf-- 311 (1054)
T PTZ00166 235 TSTCQIEVDCSYED-LIPLPPEGEYLTIAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIF-- 311 (1054)
T ss_pred CCcceEEEEEehhh-eeecccccccCCCCCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEE--
Confidence 46888777764322 221 1 23699999999999998876 49999999999999887654321101111111
Q ss_pred CCCCCcccccCccccccccchhhhhhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCE
Q psy5925 294 QESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDI 373 (696)
Q Consensus 294 ~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDI 373 (696)
++..+++ + .+..|..|++|++||.+|+++|+++||||
T Consensus 312 ------------------------------tl~~c~~-------i------~g~~V~~f~sE~eLL~~f~~~I~~~DPDI 348 (1054)
T PTZ00166 312 ------------------------------TLKECAS-------I------AGANVLSFETEKELLLAWAEFVIAVDPDF 348 (1054)
T ss_pred ------------------------------ecCcccc-------C------CCceEEEeCCHHHHHHHHHHHHHhcCCCE
Confidence 1222221 0 24678899999999999999999999999
Q ss_pred EEecccccccHHHHHHHHHHcCCCCcccccccccccc----cccC---CCccccceeeecccEEEehHHHHhhhcCCCCC
Q psy5925 374 LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEK----RNSS---RDEVKNTQLQMPGRIVINLWRLLRHEVNLQSY 446 (696)
Q Consensus 374 IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~----~~~~---~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sy 446 (696)
|+|||+++||||||++||+.+|++.+..|||++.... ..++ .|.+....+.+.||+++|+|++++++++|+||
T Consensus 349 I~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~~kl~sY 428 (1054)
T PTZ00166 349 LTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSY 428 (1054)
T ss_pred EEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEEEEHHHHHHHhcCcCcC
Confidence 9999999999999999999999998888999864321 1111 13334556899999999999999999999999
Q ss_pred CHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcc
Q psy5925 447 TFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGS 526 (696)
Q Consensus 447 sL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs 526 (696)
+|++||.++||++|+++++..|.+||+.++ ..+.++++||++|+.++++|++++++++.+.||||++|+|++++++||+
T Consensus 429 sL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~-~~~~~l~~Y~l~Da~L~~~L~~kl~~~~~~~e~arv~gip~~~v~~rG~ 507 (1054)
T PTZ00166 429 SLNYVSFEFLKEQKEDVHYSIISDLQNGSP-ETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQ 507 (1054)
T ss_pred CHHHHHHHHhCCCCCCCCHHHHHHHHhcCh-hhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccCCChHHhhcCCc
Confidence 999999999999999999999999997543 4688999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHhhcccccCCeeeeCCchhhhhccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCccccccc
Q psy5925 527 QFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEH 606 (696)
Q Consensus 527 ~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~ 606 (696)
|+|||++|+|+|+++||++|++...+. ....+|+||+|+||++|||++||+||||+||||||||||||||||+++..+.
T Consensus 508 q~kv~s~Llr~~~~~~~viP~~~~~~~-~~~~~yeGg~VleP~~G~y~~pV~vLDF~SLYPSIiia~NlcysTl~~~~~~ 586 (1054)
T PTZ00166 508 QIKVTSQLLRKCKKLNYVIPTVKYSGG-GSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDA 586 (1054)
T ss_pred chhHHHHHHHHHHhcCeeccCchhccc-cccCCCCCceeecCCCCCeeCceEEeecCCcccHHHHhcCCCcceeecchhh
Confidence 999999999999999999998765432 2346899999999999999999999999999999999999999999975320
Q ss_pred CCCCCCCCCcccccccChhHHhhcccceeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---
Q psy5925 607 LGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL--- 683 (696)
Q Consensus 607 ~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~--- 683 (696)
. .++ .+.+..+|+|.+|+++++++||||+||++||++|+++|+.||+.+ ++.++++
T Consensus 587 ~-------------~~~-------~~~~~~~p~g~~Fv~~~~r~Gilp~iL~~Ll~~R~~~K~~mk~~~-d~~~~~~ld~ 645 (1054)
T PTZ00166 587 N-------------NYP-------EDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK-DPLLKKVLNG 645 (1054)
T ss_pred c-------------cCC-------CcceeecCCCceeeecCCCCcccHHHHHHHHHHHHHHHHHHhhCC-CHHHHHHHHH
Confidence 0 001 346778999999999999999999999999999999999999887 5666555
Q ss_pred ------hhhcccccc
Q psy5925 684 ------TMLNSMLLI 692 (696)
Q Consensus 684 ------l~ansmy~~ 692 (696)
+.||||||.
T Consensus 646 rQ~AlKi~aNS~YG~ 660 (1054)
T PTZ00166 646 RQLALKISANSVYGY 660 (1054)
T ss_pred HHHhhhhhccccccc
Confidence 456999995
No 3
>KOG0969|consensus
Probab=100.00 E-value=5.2e-75 Score=636.43 Aligned_cols=380 Identities=28% Similarity=0.401 Sum_probs=331.1
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
.+|+++|||||||..|.+.||.|+.|||+.|.-.+. +. | |.++|-+.
T Consensus 271 ~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~-------------~~--------G------------e~~pf~rn 317 (1066)
T KOG0969|consen 271 IAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVT-------------LQ--------G------------ENEPFVRN 317 (1066)
T ss_pred cccccccceeEEeccCCCCCCccccChHHHHHHHHH-------------Hh--------c------------CCchHHHh
Confidence 689999999999999999999999999999851111 10 1 12334466
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccc
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQE 401 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~ 401 (696)
+.+++.|.|. .+..|..+.+|++||.+|.+++++.|||||+|||+.+||+|||++||+.||+..+..
T Consensus 318 vf~l~~capI-------------~G~~V~~~~~e~elL~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~ 384 (1066)
T KOG0969|consen 318 VFTLKTCAPI-------------VGSNVHSYETEKELLESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIENFPY 384 (1066)
T ss_pred hhcccCcCCC-------------CCceeEEeccHHHHHHHHHHHHHhcCCCeEecccccccccceecChHhhcCcccccc
Confidence 6677788762 357899999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccc----ccC---CCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhc
Q psy5925 402 LSRITEVEKR----NSS---RDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEH 474 (696)
Q Consensus 402 lgR~~~~~~~----~~~---~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~ 474 (696)
|||++....+ .++ .|.+....+.|.||+.+|+.+++.+++||.||+|++|+.|+|+++|+|+.+..|+++.+.
T Consensus 385 LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng 464 (1066)
T KOG0969|consen 385 LGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNG 464 (1066)
T ss_pred cceecccceeeeccccchhhcCcccceEEeecceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhhcC
Confidence 9999764322 122 356678889999999999999999999999999999999999999999999999999776
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhh
Q psy5925 475 RTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRA 554 (696)
Q Consensus 475 ~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~ 554 (696)
+. ..+.+++.||++|++|+++|+++|..|-.+.||||++|+|++.+++||+|+||-|+|+|.|+++++++|+-.. .+
T Consensus 465 ~~-~TRRRlA~YCLkDAYLPlRLlekLM~ivNy~EMARVTGVP~syLltRGqqIKVlSqLlRkakq~~~~~P~i~~--~~ 541 (1066)
T KOG0969|consen 465 NE-QTRRRLAVYCLKDAYLPLRLLEKLMVIVNYTEMARVTGVPISYLLTRGQQIKVLSQLLRKAKQKDFVIPNIKS--QG 541 (1066)
T ss_pred cH-HHHHHHHHHHhhhhcchHHHHHHHHHHHhHHhhhhhhCCcHHHHHhCCcchHHHHHHHHHHhhcCeeeeeecc--cC
Confidence 65 5789999999999999999999999999999999999999999999999999999999999999999975432 22
Q ss_pred ccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhc-ccc
Q psy5925 555 HMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKL-QQN 633 (696)
Q Consensus 555 ~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~-~d~ 633 (696)
...+.|+||.|+||.+|||+.||++|||+|||||||||||+||||++... ..+++ .++
T Consensus 542 s~~e~yEGatVIEp~kGfY~~PIATLDFaSLYPSIMmahNLCYtTLl~~~---------------------t~~~l~~~~ 600 (1066)
T KOG0969|consen 542 SDDEQYEGATVIEPRKGFYDKPIATLDFASLYPSIMMAHNLCYTTLLTKE---------------------TVEKLGDED 600 (1066)
T ss_pred CccccccccEEeecccccCCCCceeeehhhhhhHHHHHhhhhheeccccc---------------------hhhhcCccc
Confidence 23468999999999999999999999999999999999999999998521 12222 477
Q ss_pred eeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 634 LTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 634 i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
++.+|+|-.||++++|+|+||++|++||..|+.+|+.||+.+| ++.+.. +-|||.||.
T Consensus 601 ~~~TP~g~yFv~~~~rkGlLP~ILe~ll~aRKraK~dlk~ekD-p~kr~vldGRQLAlKisANSvYGF 667 (1066)
T KOG0969|consen 601 YTRTPTGDYFVKTEVRKGLLPEILEDLLTARKRAKADLKKEKD-PFKRAVLDGRQLALKISANSVYGF 667 (1066)
T ss_pred eeECCCCCeeeehhhhccccHHHHHHHHHHHHHHHHHHHhccC-HHHHhhhcchhhheeecccccccc
Confidence 8999999999999999999999999999999999999999886 455544 457999985
No 4
>KOG0970|consensus
Probab=100.00 E-value=1.7e-67 Score=594.92 Aligned_cols=431 Identities=22% Similarity=0.316 Sum_probs=351.7
Q ss_pred cccchhhHHHHH-HHhcCCc-cccccccccccCCCCCCccccccCCCCccccccc--cc--CCCceEEEEEEEeecCCCC
Q psy5925 187 IDFNPDLFKSFI-RKQLETP-KRRICDSYAIDAMTPDTTGDYQMGLDNLNEVTSH--VE--NYYLTVLAVEIHAISRALL 260 (696)
Q Consensus 187 ~~~~~~l~~~~l-~r~~~~p-~~~~~~~~~I~~~t~~~~~gfk~~~~~~~~~~~~--~~--~~~LtilsleIe~~sr~~~ 260 (696)
-+++++.||.|| .|++||| +..+-... .++.+.+||.+++.+.+|+.+... .. +|+|++|||.|+|. +
T Consensus 467 fgt~tn~lE~fll~rKimGPCWlkv~~~s--~~~~~~SwCk~Ev~v~sP~nI~~~~~~~a~~Ppl~llsL~i~T~----~ 540 (1429)
T KOG0970|consen 467 FGTNTNPLERFLLSRKIMGPCWLKVKGYS--DPPRNASWCKVEVTVKSPQNITVVCSKKAPPPPLTLLSLNIRTS----M 540 (1429)
T ss_pred hccCccHHHHHHHhccccCceEEEeecCC--CCCCCccceeeEEEecCCcceEEeecCCCCCCCeeEEEeeeeeh----h
Confidence 457999999999 9999999 77766554 355556799999999999988753 23 89999999999999 8
Q ss_pred CCCCCCCcEEEEEEEeecCCCCCCc-------eEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhccccCCCccc
Q psy5925 261 KPDPAYDEVKAIFYYLYTCPPEEDR-------KVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDIL 333 (696)
Q Consensus 261 ~Pdp~~D~I~~I~~~~~~~~~~~~~-------~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~ 333 (696)
+|.-++.+|++|+..+++...++.+ .+-.+|++|.+. .+|.+ +++++..
T Consensus 541 N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~-----~fP~g----------~~ela~~--------- 596 (1429)
T KOG0970|consen 541 NPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGT-----SFPLG----------LKELAKQ--------- 596 (1429)
T ss_pred ccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCC-----cCCch----------HHHHHHh---------
Confidence 8999999999999888876654421 333566666543 34665 2222111
Q ss_pred ccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccccccccccccc
Q psy5925 334 IGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNS 413 (696)
Q Consensus 334 ~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~ 413 (696)
....|..+++|+.||..|++.++..|||+|+|||+.+|++..|..|+..++++.|+.+||++.....++
T Consensus 597 -----------k~~~v~~~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kf 665 (1429)
T KOG0970|consen 597 -----------KLSKVVLHNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKF 665 (1429)
T ss_pred -----------ccCceEEecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhcccccc
Confidence 234588999999999999999999999999999999999999999999999999999999987644444
Q ss_pred CCCccccceeeecccEEEehHHHHhhh-cCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHH
Q psy5925 414 SRDEVKNTQLQMPGRIVINLWRLLRHE-VNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVT 492 (696)
Q Consensus 414 ~~~~~~~~~~~i~GRl~lDl~~~~r~~-~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~ 492 (696)
+.+.+......+.||++||+ ..+.++ .+..||+|.++++..|+....++...++.++|.+.. .+..++++++.|+.
T Consensus 666 g~~s~~~e~~~~aGRl~CD~-~~~a~~lik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~--~L~~ll~~~~~d~~ 742 (1429)
T KOG0970|consen 666 GRSSSFGEFFIIAGRLMCDL-NLAARELIKAQSYSLSELSQQILKEERKEINANEIPKMYEDSK--SLTYLLEHTITDAE 742 (1429)
T ss_pred CCcccccccccccceEEeeh-HHHHHhhhccccccHHHHHHHHHhhhcccCCHhHhhhhccChH--HHHHHHHHHhHHHH
Confidence 44333445556999999999 655554 589999999999999998777788899999998876 47888999999999
Q ss_pred HHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchh---h--------------hhc
Q psy5925 493 GIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIK---Q--------------RAH 555 (696)
Q Consensus 493 l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~---q--------------~~~ 555 (696)
+.++|+.++++++++.++++|+|..|.++|.+|++.|+|++|||+++++|||+|++... + .++
T Consensus 743 ~~l~i~~~l~~LpLs~qlTnIaGni~~RTL~G~RAeRnEylLLH~F~~~~fIvPDK~~ssk~~~d~d~~~eg~d~~~~~K 822 (1429)
T KOG0970|consen 743 LILQIMFRLNALPLSKQLTNIAGNIWARTLQGGRAERNEYLLLHEFYKNGFIVPDKQNSSKAQKDADETEEGADEPSKGK 822 (1429)
T ss_pred HHHHHHHHhccchHHHHHHHHHhHHHHHHhhccchhhhhHHHHHHHHHCCccCCCccchhhhhhhhhhhhcccccccccc
Confidence 99999999999999999999999999999999999999999999999999999986521 1 112
Q ss_pred cCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccc-cccCCCCCCCCCcccccccChhHHhhcccce
Q psy5925 556 MRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR-VEHLGVSDSFPFGCIDLNVSIRSLKKLQQNL 634 (696)
Q Consensus 556 ~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~-~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i 634 (696)
.+++|.||+||||+.|||+++|++|||||||||||++|||||||+-.. ++ .|.+
T Consensus 823 Kk~kYaGGLVlePkkGlYe~~VLllDFNSLYPSIIQEyNICFTTv~~~~~d-------------------------~Dql 877 (1429)
T KOG0970|consen 823 KKAKYAGGLVLEPKKGLYEKYVLLLDFNSLYPSIIQEYNICFTTVDRFSVD-------------------------SDQL 877 (1429)
T ss_pred ccccccCceeeccccchhhheeEEEEccccchHHHHHhhheeeeccccccC-------------------------cccC
Confidence 458999999999999999999999999999999999999999999652 11 1222
Q ss_pred eeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHH-----HHH---hhhcccccc
Q psy5925 635 TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESL-----RNL---TMLNSMLLI 692 (696)
Q Consensus 635 ~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l-----~~~---l~ansmy~~ 692 (696)
...| .+...+||||++|+.|++.|++||++||+..+.... ++. |+||||||-
T Consensus 878 p~lP------~s~~~~GiLPr~l~~LVerRk~VK~lMK~~~tp~~~~q~DIRQqALKLTANSMYGC 937 (1429)
T KOG0970|consen 878 PRLP------SSSSEQGILPRLLENLVERRKEVKKLMKQELTPEKRKQLDIRQQALKLTANSMYGC 937 (1429)
T ss_pred CCCC------CccccCCccHHHHHHHHHHHHHHHHHHhcCCCHHHHHhhhHHHHHHhhhhccchhh
Confidence 2223 133589999999999999999999999986332211 111 999999994
No 5
>PHA02528 43 DNA polymerase; Provisional
Probab=100.00 E-value=9.9e-64 Score=587.48 Aligned_cols=371 Identities=20% Similarity=0.230 Sum_probs=283.0
Q ss_pred CCCceEEEEEEEeecCCCCCCCCC--CCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPA--YDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFS 319 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~--~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~ 319 (696)
.|.|+++||||||.+++ .||+|+ .|||.+|++ ++.. ...++++.-.+. .++... +
T Consensus 103 ~p~lrv~s~DIE~~~~~-gfP~p~~~~d~IisIsl--~~~~-----~~~~~v~~~~~~------~~~~~~-~-------- 159 (881)
T PHA02528 103 RSKIRIANLDIEVTAED-GFPDPEEAKYEIDAITH--YDSI-----DDRFYVFDLGSV------EEWDAK-G-------- 159 (881)
T ss_pred CCCccEEEEEEEECCCC-CCCCcccCCCcEEEEEE--ecCC-----CCEEEEEEecCc------cccccc-C--------
Confidence 38999999999998765 499999 789999996 3221 113333321100 011100 0
Q ss_pred hhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHH-cCCCC
Q psy5925 320 TFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYV-LGLNL 398 (696)
Q Consensus 320 ~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~-lgi~~ 398 (696)
...+ .++ ..++.+..|++|++||.+|+++|+++|||||+|||+++||||||.+||+. +|...
T Consensus 160 -------~~~~-----~~~-----~~~v~~~~~~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~ 222 (881)
T PHA02528 160 -------DEVP-----QEI-----LDKVVYMPFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKT 222 (881)
T ss_pred -------Cccc-----ccc-----cCCeeEEEcCCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCccc
Confidence 0000 000 02467778999999999999999999999999999999999999999995 58765
Q ss_pred ccccccccccccccc-C-CCccccceeeecccEEEehHHHHhhh-c-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhc
Q psy5925 399 NQELSRITEVEKRNS-S-RDEVKNTQLQMPGRIVINLWRLLRHE-V-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEH 474 (696)
Q Consensus 399 ~~~lgR~~~~~~~~~-~-~~~~~~~~~~i~GRl~lDl~~~~r~~-~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~ 474 (696)
...+++.+....... + .+. ....+.++||+++|+|.++|+. + +++||+|++||+++||++|+++++++|.+||++
T Consensus 223 ~~~l~~~~~~~~~~~~~~~g~-~~~~~~i~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~ 301 (881)
T PHA02528 223 AKRLSPWGKVKERTIENMYGR-EEIAYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRET 301 (881)
T ss_pred ccccccccccccccccccccc-cceeEEEcceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhc
Confidence 333333221111000 0 111 1234789999999999999983 3 799999999999999999999999999999986
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhh
Q psy5925 475 RTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRA 554 (696)
Q Consensus 475 ~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~ 554 (696)
+ ..++++||++||.++++|+.++++++++.|+|+++|+++++|++ +...++++++++++++|+++|++..
T Consensus 302 d----~~~l~~Ynl~Da~Lv~~L~~kl~ll~~~~e~ArltGi~l~~v~s--q~~~~~~lll~~~~r~g~viP~~~~---- 371 (881)
T PHA02528 302 D----HQKYIEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVFS--PIKTWDAIIFNSLKEEKIVIPENKS---- 371 (881)
T ss_pred C----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHhcc--hHhHHHHHHHHHHHHcCcccCCccc----
Confidence 5 47899999999999999999999999999999999999999953 3333578999999999999976542
Q ss_pred ccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccce
Q psy5925 555 HMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNL 634 (696)
Q Consensus 555 ~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i 634 (696)
....+|.||+||||++|||+ +|+||||+||||||||+|||||+|+++..+... .+ + ...+......+++
T Consensus 372 ~~~~~y~Gg~V~eP~pGlY~-~VvVLDF~SLYPSIIiayNIcp~Tlv~~~~~~~-~~----~-----~~~~~~~~~~~~~ 440 (881)
T PHA02528 372 HKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAP-VH----E-----YINKTAPRPSDEY 440 (881)
T ss_pred cCCCCCCCcEEecCCCCccc-ceEEEeccccChHHHHHhCCChhhccccccccc-cc----c-----ccccccCCCCCce
Confidence 23467999999999999997 699999999999999999999999997543110 00 0 0001111113567
Q ss_pred eeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCC
Q psy5925 635 TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKF 676 (696)
Q Consensus 635 ~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~ 676 (696)
.++|||++|++. ++||||+||++|+++|+++|+.||+++.
T Consensus 441 ~~~p~G~~F~k~--~~GiLP~iL~~Ll~~R~~~Kk~Mk~~~~ 480 (881)
T PHA02528 441 SCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKKKMLAAER 480 (881)
T ss_pred eEcCCCCeEeCC--CCeehHHHHHHHHHHHHHHHHHHHhccc
Confidence 889999999986 8999999999999999999999988753
No 6
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=100.00 E-value=1.5e-60 Score=525.04 Aligned_cols=378 Identities=16% Similarity=0.175 Sum_probs=285.2
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCC--cEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYD--EVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFS 319 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D--~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~ 319 (696)
...++++.+||||.+. .||+|... ||.+|+. ++....+ ..+.+..-.. ...+|....
T Consensus 103 ~~~i~~~~~DIEv~~~--~fp~~~~a~~~i~~i~~--~d~~~~~---~~~~~~~~~~-----~~~~~~~~~--------- 161 (498)
T PHA02524 103 RDDVVIDVVDIEVTAP--EFPEPKYAKYEIDMISH--VRLHNGK---KTYYIFDLVK-----DVGHWDPKK--------- 161 (498)
T ss_pred hhhceEEEEEEEecCC--CCCChhhcCCceEEEEe--eecccCC---ccEEEEeccc-----cccCCCccc---------
Confidence 4679999999999764 69999864 9999984 2221111 1233332100 111232110
Q ss_pred hhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHH-cCCCC
Q psy5925 320 TFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYV-LGLNL 398 (696)
Q Consensus 320 ~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~-lgi~~ 398 (696)
.. +. .++ -.++.|..|++|++||.+|+++|+++|||||+|||+++||||||.+||+. +|+..
T Consensus 162 ~~---~~---------~~~-----~~~v~v~~f~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~ 224 (498)
T PHA02524 162 SV---LE---------KYI-----LDNVVYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKA 224 (498)
T ss_pred cc---cc---------ccc-----cCCeEEEEeCCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCcc
Confidence 00 00 001 14689999999999999999999999999999999999999999999974 89863
Q ss_pred ---cccccccccccccccCCCccccceeeecccEEEehHHHHhhh--cCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHh
Q psy5925 399 ---NQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHE--VNLQSYTFENIMYHVLHERIPLHSWKLLTCWWE 473 (696)
Q Consensus 399 ---~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~--~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~ 473 (696)
+..+||...... ....|. ...+.+.||+++|++.++++. .+++||+|++||.++||+.|.++.. .+.++|+
T Consensus 225 ~~~~~~~Gr~~~~~s-~~~~G~--~~~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~~-~I~~l~~ 300 (498)
T PHA02524 225 ANQLSPYGKITSKTI-TNLYGE--KIIYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYEG-PINKFRK 300 (498)
T ss_pred ccccccccccccccc-eeecCc--eeEEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHHHhcCCccccchh-hHHHHhc
Confidence 334666542111 111121 225799999999999999986 6999999999999999999988853 5888887
Q ss_pred cCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhh
Q psy5925 474 HRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQR 553 (696)
Q Consensus 474 ~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~ 553 (696)
++ +.++++||++||.++++|..++.+++++.++|+++|+|+++++ |+...++++|+++|+++|+++|+....
T Consensus 301 ~d----~~rla~YclkDa~L~~~L~~~~~ll~~~~~larvtglpl~~v~--~qikv~~~lllr~~~~~g~viP~~~~~-- 372 (498)
T PHA02524 301 AD----HQRYVDYCVRDTDIILLIDGRRCFIDLILSLSYYAKIRFDDVL--GTIKVWDSIIFNSLVESNVVIPAMKAS-- 372 (498)
T ss_pred Cc----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHhc--cHHHHHHHHHHHHHHHCCEecCCCCCC--
Confidence 64 5899999999999999999899999999999999999999995 455557789999999999999864321
Q ss_pred hccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccc
Q psy5925 554 AHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQN 633 (696)
Q Consensus 554 ~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~ 633 (696)
....|.||+|+||++|+|++ |+||||+||||||||+|||||+|+.+...... .+. ..+ .+++. ..++
T Consensus 373 --~~~~Y~GA~V~eP~~GlY~~-VivLDFaSLYPSII~a~NIsPeTl~~~~~~~~-~~~--~~~---~~~~~----~~~~ 439 (498)
T PHA02524 373 --PKQSFPGAYVKEPVPGGYRY-GLSFDLTSLYPSILRLLNISPEMIAGMFSPAR-LED--YIN---KVAPK----PSDQ 439 (498)
T ss_pred --CCCccCCeEEecCCCccccC-eEEEEccccCHHHHHHhCCCHHHhhccccccc-hhh--hcc---ccCCC----CCcc
Confidence 23579999999999999987 67899999999999999999999986432100 000 000 00110 1467
Q ss_pred eeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHH-HHHHh
Q psy5925 634 LTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSES-LRNLT 684 (696)
Q Consensus 634 i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~-l~~~l 684 (696)
+..+|||+.|+|. ++||||++|++|++.|+++|+.|+++.-+.. .++.|
T Consensus 440 ~~~~P~G~~F~K~--~~GilP~iLe~Ll~~RK~~Kk~M~~a~~~~~~~~~~~ 489 (498)
T PHA02524 440 FSCAPNGMMYKKG--VVGVLPNETEKVFLQRKSEKKMMLAAIRNQEAIKKIL 489 (498)
T ss_pred eEECCCCCEEecC--CCcccHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHH
Confidence 8899999999996 8999999999999999999999998764443 34444
No 7
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=2.9e-60 Score=578.93 Aligned_cols=424 Identities=20% Similarity=0.265 Sum_probs=334.9
Q ss_pred cchhhHHHHH-HHhcCCc-cccccccccccCCCCCCccccccCCCCccccc--ccccCCCceEEEEEEEeecCCCCCCCC
Q psy5925 189 FNPDLFKSFI-RKQLETP-KRRICDSYAIDAMTPDTTGDYQMGLDNLNEVT--SHVENYYLTVLAVEIHAISRALLKPDP 264 (696)
Q Consensus 189 ~~~~l~~~~l-~r~~~~p-~~~~~~~~~I~~~t~~~~~gfk~~~~~~~~~~--~~~~~~~LtilsleIe~~sr~~~~Pdp 264 (696)
++...++.|+ .|++++| +..+..... ......+||+++..+..++.+. ....+||+++|+|+|+ . ++|..
T Consensus 447 ~n~g~~erfll~rki~gp~WL~i~~p~~-~~~~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~-S----lyPsi 520 (1172)
T TIGR00592 447 SNTGNLERFLLLRKIKGPCWLAVKGPDE-LEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMK-S----LNPSI 520 (1172)
T ss_pred cCHHHHHHHHhcCCCCCCceEEeCCCcc-cCcCCccccceEEEEecCccccccccCCCCCeEEEEeeeE-E----ecCcc
Confidence 6888999999 7889999 665543221 1111246999998887666332 2334789999999999 2 78999
Q ss_pred CCCcEEEEEEEeecCCCCCC------ceEEEEE-EcCCCCCcccccCccccccccchhhhhhhhhhccccCCCccccccc
Q psy5925 265 AYDEVKAIFYYLYTCPPEED------RKVGIIL-IGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYE 337 (696)
Q Consensus 265 ~~D~I~~I~~~~~~~~~~~~------~~~g~il-v~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~~g~e 337 (696)
..++|+||+..++.+...+. ....++. .++.. ..+|++. .... .+.
T Consensus 521 ~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~-----~~~p~~~----------~~~~---~~~--------- 573 (1172)
T TIGR00592 521 IRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKD-----CSFPLDL----------KGEF---PGK--------- 573 (1172)
T ss_pred ccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCC-----CCCCchh----------hhhh---hcc---------
Confidence 99999999998876643211 0111211 22211 1223331 1000 000
Q ss_pred ccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCc
Q psy5925 338 IETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDE 417 (696)
Q Consensus 338 i~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~ 417 (696)
....+..+.+|++||.+|++.++++|||+++|||+.+|||+||.+||+.++++.|+++||++.... + +.
T Consensus 574 -------~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~--~--~~ 642 (1172)
T TIGR00592 574 -------KPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPK--F--GR 642 (1172)
T ss_pred -------CCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCC--c--cc
Confidence 234688999999999999999999999999999999999999999999999999999999875422 1 11
Q ss_pred cccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHH
Q psy5925 418 VKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRL 497 (696)
Q Consensus 418 ~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L 497 (696)
++ ...+.||+++|+|..+++.+++.+|+|++||.++||.++.++++.+|.++|.++. .+..++.||++|+.++++|
T Consensus 643 ~~--~~~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~--~~~~~~~y~~~Da~l~~~L 718 (1172)
T TIGR00592 643 RF--GERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESS--SLTYLLEHTWKDAMFILQI 718 (1172)
T ss_pred cc--cceECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcH--HHHHHHHHHHHHHHHHHHH
Confidence 22 2449999999999999999999999999999999999999999999999998654 5899999999999999999
Q ss_pred HHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhh---------------hccCCCCCC
Q psy5925 498 IEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQR---------------AHMRAPESL 562 (696)
Q Consensus 498 ~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~---------------~~~~~~~~G 562 (696)
+.++++++++.++|+++|++|.+++.+|+|.|+|++|+|+++++||++|++..... ...+++|+|
T Consensus 719 ~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~~~~~~~i~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~G 798 (1172)
T TIGR00592 719 MCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKLGDEDEEIDGYKKGKKAAYAG 798 (1172)
T ss_pred HHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHHHHhCCEEccCccccccccccccccccccccccccccCcCC
Confidence 99999999999999999999999999999999999999999999999998743211 012468999
Q ss_pred CeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeCCCCce
Q psy5925 563 PLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVA 642 (696)
Q Consensus 563 glVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~ 642 (696)
|+|+||++|||++||++|||+|||||||++|||||||+++..+. +++. .
T Consensus 799 g~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~t~~~~~~~-------------------------~~~~------~ 847 (1172)
T TIGR00592 799 GLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDE-------------------------DELP------E 847 (1172)
T ss_pred CeEecCCCCcccCCEEEEEcCCccHHHHHHhCcCccccCCCCcc-------------------------hhcc------c
Confidence 99999999999999999999999999999999999999863210 1111 1
Q ss_pred eecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 643 FVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 643 fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
+...+.++||||++|++|+++|+++|+.||+ ..++.++++ +.||||||.
T Consensus 848 ~~~~~~~~Gilp~il~~L~~~R~~~K~~mk~-~~~~~~~~~~d~~Q~AlKi~aNS~YG~ 905 (1172)
T TIGR00592 848 LPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGC 905 (1172)
T ss_pred CCcccccCcchHHHHHHHHHHHHHHHHHhhc-CCCHHHHHHHHHHHHHHHHhhhccccc
Confidence 2224568999999999999999999999998 445544433 667999995
No 8
>PHA03036 DNA polymerase; Provisional
Probab=100.00 E-value=3.9e-60 Score=551.50 Aligned_cols=409 Identities=14% Similarity=0.145 Sum_probs=303.9
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
.-+++.|||||||.. .+.||.|..|||++||+++.+... ....+++++.+.... .|..++.
T Consensus 157 ~~~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~~~~---~~~~~~l~n~~~~~~---------------~~~~~~~ 217 (1004)
T PHA03036 157 DIPRSYLFLDIECHF-DKKFPSVFINPVSHISCCYIDLSG---KEKRFTLINEDMLSE---------------DEIEEAV 217 (1004)
T ss_pred cCcceeEEEEEEecc-CCCCCCcccCcceEEEEEEEecCC---CeeEEEEeccccccc---------------cccccce
Confidence 458999999999996 668999999999999986664432 244588888764321 1112222
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCC--c
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNL--N 399 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~--~ 399 (696)
...+..+++ +.++ ....+..|.+|++|| .|++.+++.|||+|+|||+++||||||.+|++.|+... +
T Consensus 218 ~~~~~~~~~-------~~~~---~~~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~ 286 (1004)
T PHA03036 218 KRGYYEIES-------LLDM---DYSKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTGEKIIF 286 (1004)
T ss_pred eeeeecccc-------cccc---CCceeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHhccCceee
Confidence 222333332 1111 246788999999988 66999999999999999999999999999999985422 1
Q ss_pred cccccccccc----cccc----CCCc--cccceee-ecccEEEehHHHHhhhcCCCCCCHHHHHHHHc------------
Q psy5925 400 QELSRITEVE----KRNS----SRDE--VKNTQLQ-MPGRIVINLWRLLRHEVNLQSYTFENIMYHVL------------ 456 (696)
Q Consensus 400 ~~lgR~~~~~----~~~~----~~~~--~~~~~~~-i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L------------ 456 (696)
...++..... .+.. +.|. +....+. .+||+++|+|.++|+.++|+||+|++|++++|
T Consensus 287 ~~~~~~~~~~~~v~~r~~~s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~ 366 (1004)
T PHA03036 287 RSPDGKETVHLCIYERNLSSHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNN 366 (1004)
T ss_pred ccCCCcccccceeeccccccccccCccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCc
Confidence 2234432211 1111 1111 2233444 69999999999999999999999999999977
Q ss_pred -----C--------------------------C------------------------------------CcCCCChhhHH
Q psy5925 457 -----H--------------------------E------------------------------------RIPLHSWKLLT 469 (696)
Q Consensus 457 -----~--------------------------~------------------------------------~k~~~~~~~l~ 469 (696)
| + +|++++..+|.
T Consensus 367 ~~~~~g~~~~~~~~~~~~f~~vl~t~ny~~i~~~~~~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~KdDV~~~~i~ 446 (1004)
T PHA03036 367 EVTFIGDNTTDAKGKASIFSEVLSTGNYVTINDDDICKILDKDIIENSFTVKVICKNNYIPGDTYTLSFGKDDVDLSDMY 446 (1004)
T ss_pred eeEEccCcccccccchhhhhhhhcccceeeecccchhhhcccccccccceeeeecccccccccceeecccccCCCHHHHH
Confidence 4 4 78899999999
Q ss_pred HHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCc
Q psy5925 470 CWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPS 549 (696)
Q Consensus 470 ~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~ 549 (696)
+.|+.+ .+.+++.||++||.|+++|++++.++.+..++|+.+++|..+++..|+|.+++++|+|.|.++|+++|...
T Consensus 447 ~~~~~~---~r~rla~YClkDa~L~l~L~~~l~~~~~v~~~a~~~~lp~~~~i~~~~s~~i~~qllr~~~~~~~i~p~~~ 523 (1004)
T PHA03036 447 KNYNLE---IALEMARYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYRASTLIKGPLLKLLLEEKTILVRSE 523 (1004)
T ss_pred HHhChh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhheEeeeeccccccHHHHHHHHCCcccccCC
Confidence 999754 58999999999999999999999999999999999999999999999999999999999999999987322
Q ss_pred hhhhhccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCC-CCCCcccccccChhHHh
Q psy5925 550 IKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSD-SFPFGCIDLNVSIRSLK 628 (696)
Q Consensus 550 ~~q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~-~~~~G~~~~~~~~~~l~ 628 (696)
.....+|+||+|+||++|+|++||+||||+||||||||||||||||+++..+..+..+ ....+...-..++..
T Consensus 524 ----~~~~~~YeGa~VlEP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~~~~~~~i~~~~i~~~~p~~d-- 597 (1004)
T PHA03036 524 ----TKNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKYPYPR-- 597 (1004)
T ss_pred ----CCccCCcCceEEecCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccccccccccccccccccCCCcc--
Confidence 1123479999999999999998999999999999999999999999997533111000 000000000011000
Q ss_pred hcccceeeCCCCc-----eeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 629 KLQQNLTISPSGV-----AFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 629 ~~~d~i~~~p~g~-----~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
-..+.++|++. .|+.+.+++||||++|++|++.|+++|+.||+++++. .+++ +.||||||.
T Consensus 598 --y~~v~~~~~~~~~v~~~~vf~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~~~d~~-e~~~lD~rQlAlKI~aNS~YG~ 672 (1004)
T PHA03036 598 --YIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSSV-EKAIYDSMQYTYKIVANSVYGL 672 (1004)
T ss_pred --ceeeeccCCcccccccceeecCCCCcChHHHHHHHHHHHHHHHHHHhhCCChH-HHHHHHHHHHHHHHHHhccccc
Confidence 01223344322 3555567999999999999999999999999887543 2222 567999995
No 9
>PRK05762 DNA polymerase II; Reviewed
Probab=100.00 E-value=2.1e-59 Score=553.85 Aligned_cols=302 Identities=20% Similarity=0.285 Sum_probs=255.8
Q ss_pred EEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeeccc
Q psy5925 349 RHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGR 428 (696)
Q Consensus 349 V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GR 428 (696)
|..++||++||.+|+++|+++|||||+|||+++||||||.+||+.+|++.. +||.+....++..........+.++||
T Consensus 197 v~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~--~GR~~~~~~~~~~~~~~~~~~~~i~GR 274 (786)
T PRK05762 197 LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLR--LGRDGSELEWREHPFRSGYGFASVPGR 274 (786)
T ss_pred EEEcCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcc--cCcCCCccccccCCCCCCcceEEEeeE
Confidence 668999999999999999999999999999999999999999999999854 898765433321111122346789999
Q ss_pred EEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCCh----hhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcc
Q psy5925 429 IVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSW----KLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDF 503 (696)
Q Consensus 429 l~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~----~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~i 503 (696)
+++|+|.++|+.. ++++|+|++||+++||++|+..+. .+|.++|.++ +..+++||++||.++++|+.++++
T Consensus 275 v~lDl~~~~k~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~----~~~l~~Y~l~Da~lt~~L~~kl~l 350 (786)
T PRK05762 275 LVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED----KPALARYNLKDCELVTRIFEKTKL 350 (786)
T ss_pred EEEEHHHHHHHhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh----HHHHHHHHHHHHHHHHHHHHHhhH
Confidence 9999999999976 999999999999999999876554 7888999854 689999999999999999999999
Q ss_pred cchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhhccCCCCCCCeeeecccccccCceeeeecc
Q psy5925 504 IGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQ 583 (696)
Q Consensus 504 i~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~ 583 (696)
++++.++|+++|++++++. |++.++|++|+++|+++||++|++... ....|.||+|+||++|+|++ |++|||+
T Consensus 351 l~~~~ela~l~g~~~~~v~--~~~~~~e~lll~~~~~~g~v~P~~~~~----~~~~y~Gg~V~~p~~G~y~~-V~~lDF~ 423 (786)
T PRK05762 351 LPFLLERATVTGLPLDRVG--GSVAAFEHLYLPRAHRAGYVAPNLGER----PGEASPGGYVMDSKPGLYDS-VLVLDFK 423 (786)
T ss_pred HHHHHHHHHHhCcCHHHhC--ccHHhHHHHHHHHHHHCCEeCCCcccc----cccccCccEEecCCCCCcCc-eEEEEch
Confidence 9999999999999999985 778888999999999999999875422 24679999999999999976 9999999
Q ss_pred ccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeCCCCceeecCCCcccchHHHHHHHHHH
Q psy5925 584 SLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDT 663 (696)
Q Consensus 584 SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~ 663 (696)
|||||||++|||||+|++...++. ..+...+|+|++|++ ++||||++|++|+++
T Consensus 424 SLYPSIi~~~Ni~p~T~~~~~~~~-----------------------~~~~~~~~~~~~f~k---~~gilp~~l~~l~~~ 477 (786)
T PRK05762 424 SLYPSIIRTFNIDPDGLVEGLAQP-----------------------PEESVAGFLGARFSR---EKHFLPEIVERLWEG 477 (786)
T ss_pred hhhHHHHHHhCcCccceecCCCCC-----------------------CcccccCCCCccccc---cCcchHHHHHHHHHH
Confidence 999999999999999998532110 112245689999976 799999999999999
Q ss_pred HHHHHHHHhhCCCCHHHHHHhhhcccccc
Q psy5925 664 RLMVKQSMKEYKFSESLRNLTMLNSMLLI 692 (696)
Q Consensus 664 R~~vKk~mk~~~~~~~l~~~l~ansmy~~ 692 (696)
|+++|+.||+.. +.-.| +.+|||||.
T Consensus 478 R~~~K~~~~~~~--q~a~K-i~~Ns~YG~ 503 (786)
T PRK05762 478 RDEAKREMNKPL--SQAIK-IIMNAFYGV 503 (786)
T ss_pred HHHHHHHHHHHH--HHHHH-hhhhhcccc
Confidence 999999998721 11223 456999996
No 10
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=100.00 E-value=3.3e-55 Score=492.26 Aligned_cols=390 Identities=30% Similarity=0.434 Sum_probs=314.7
Q ss_pred CCceEEEEEEEeecCCCCCCCCC--CCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPA--YDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFST 320 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~--~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~ 320 (696)
++++++||||||.+.++.+|+|. .|+|++|++...+..... .....++.
T Consensus 1 ~~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~-~~~~~~~~---------------------------- 51 (471)
T smart00486 1 PPLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKG-PEERICFT---------------------------- 51 (471)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCC-CceeEEEE----------------------------
Confidence 57899999999999888899998 799999998887553211 01111111
Q ss_pred hhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcc
Q psy5925 321 FIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQ 400 (696)
Q Consensus 321 ~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~ 400 (696)
+..+.. + .+..+..+++|++||.+|++++++.|||+|+|||+.+|||+||.+|+..++++.+.
T Consensus 52 ----~~~~~~-------~------~~~~~~~~~~E~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~ 114 (471)
T smart00486 52 ----LGTCKE-------I------DGVEVYEFNNEKELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLS 114 (471)
T ss_pred ----ecCcCC-------C------CCCeEEecCCHHHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHH
Confidence 000100 0 23567888999999999999999999999999999999999999999999998876
Q ss_pred cccccccccccccC------CCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhc
Q psy5925 401 ELSRITEVEKRNSS------RDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEH 474 (696)
Q Consensus 401 ~lgR~~~~~~~~~~------~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~ 474 (696)
.+||.......... ..........+.||+++|+|..+++.+++.+|+|++||+++||++++++++.++.++|+.
T Consensus 115 ~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~ 194 (471)
T smart00486 115 FIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNL 194 (471)
T ss_pred HcCcCCCCCCcccccCccccccccccceeEeccEEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhc
Confidence 68887643111000 001234467899999999999999999999999999999999999999999999999998
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhh
Q psy5925 475 RTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRA 554 (696)
Q Consensus 475 ~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~ 554 (696)
+ ...+..+++||++|+.++++|+.++++++...++|+++|+++.+++.+|++.+||++++++++++|+++|++......
T Consensus 195 ~-~~~~~~~~~Y~~~D~~l~~~l~~~l~~~~~~~~~s~~~~~~~~~~~~~g~~~~v~~~l~~~~~~~~~~~P~~~~~~~~ 273 (471)
T smart00486 195 N-YKLRDELLEYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPQRRTLYYGSQIRVESLLLREAKKNNYILPSKSLIDFK 273 (471)
T ss_pred C-HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHHHhcCcHHHHHHHHHHHHhhCCEEeccchhcccc
Confidence 6 234789999999999999999999999999999999999999999999999999999999999999999987654322
Q ss_pred ------ccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHh
Q psy5925 555 ------HMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLK 628 (696)
Q Consensus 555 ------~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~ 628 (696)
+....|.||+|++|.+|+|++||+++||+|||||||++||+||+|+++........ .... .
T Consensus 274 ~~~~~~~~~~~y~gg~v~~p~~g~~~~~v~~lDf~SlYPsii~~~nl~~~t~~~~~~~~~~~--------~~~~-----~ 340 (471)
T smart00486 274 GSEPELKKKAKYPGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGRGENSGEL--------FLDV-----E 340 (471)
T ss_pred cccccccccccccccEEecCCCCcccCceEEeehhhccHHHHHHhCCCCccccccccccccc--------CCCh-----h
Confidence 23578999999999999999999999999999999999999999999754311100 0000 1
Q ss_pred hcccceeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCH-HHHHH---------hhhcccccc
Q psy5925 629 KLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSE-SLRNL---------TMLNSMLLI 692 (696)
Q Consensus 629 ~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~-~l~~~---------l~ansmy~~ 692 (696)
.........+++..|+++++++|+||++|++|++.|.++|+.|++.+++. ..+.+ +.+||+||.
T Consensus 341 ~~~~~~~~~~~~~~~~~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~~~~~~~~~~~d~~q~a~K~~~Ns~yG~ 414 (471)
T smart00486 341 DLLTIKYEKPEGYHFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGY 414 (471)
T ss_pred hcceeeecCCCcceeecCCCCCeehHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhcccccc
Confidence 11122445678899999988899999999999999999999999887543 23322 567999985
No 11
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-52 Score=495.68 Aligned_cols=359 Identities=30% Similarity=0.404 Sum_probs=296.5
Q ss_pred ccCCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhh
Q psy5925 240 VENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFS 319 (696)
Q Consensus 240 ~~~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~ 319 (696)
...|+|++|||||||.+++..+|++..|+|++|+++...... .+ ... .
T Consensus 149 ~~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~-------~~--~~~-----------~------------ 196 (792)
T COG0417 149 DVRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGG-------LI--EVF-----------I------------ 196 (792)
T ss_pred CcCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCC-------cc--ccc-----------c------------
Confidence 447999999999999999999999999999999988764421 00 000 0
Q ss_pred hhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCc
Q psy5925 320 TFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLN 399 (696)
Q Consensus 320 ~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~ 399 (696)
..+ ..+..|..+.+|.+||++|.+++..+|||||+|||+++||||||.+||+.+|++..
T Consensus 197 --------~~~-------------~~~~~v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~ 255 (792)
T COG0417 197 --------YTS-------------GEGFSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLR 255 (792)
T ss_pred --------ccC-------------CCCceeEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCcc
Confidence 000 02344889999999999999999999999999999999999999999999999988
Q ss_pred ccccccccccccccCCCccccceeeecccEEEehHHHHh-hhcCCCCCCHHHHHHHHcCCCc-CCCChhhHHHHHhcCCc
Q psy5925 400 QELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLR-HEVNLQSYTFENIMYHVLHERI-PLHSWKLLTCWWEHRTH 477 (696)
Q Consensus 400 ~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r-~~~kl~sysL~~Va~~~L~~~k-~~~~~~~l~~~~~~~~~ 477 (696)
+||.+........ ......||+++|+|..++ +..++.+|+|++|+..+|++.+ .+.....+.++|....
T Consensus 256 --~gr~~~~~~~~~~------~~~~~~Gr~~iDl~~~~~~~~~~~~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~- 326 (792)
T COG0417 256 --LGRDGSELRVRKS------GFSSQVGRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWA- 326 (792)
T ss_pred --ccccccccceeec------ccccccceEEEecHHHHhhhhcccccccHHHHHHHhcccccccccCccchhhccccCc-
Confidence 8888754332111 111112999999999999 6999999999999999999888 7888788777666543
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhhccC
Q psy5925 478 LYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMR 557 (696)
Q Consensus 478 ~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~ 557 (696)
....+.+.|++.|+.++.+++.+.+++++..|+|+++|++++++..+|++.++|++|+++|++.|+++|++..... .
T Consensus 327 ~~~~~~~~~~l~~~~l~~~~~~~~~~l~~~~e~s~vsg~~~~~~~~~~~~~~~~~~l~~~a~~~~~~iP~~~~~~~---~ 403 (792)
T COG0417 327 DSKLRLLLYNLSDADLVLRILLKNELLPLLIELSRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIPNKEERPE---R 403 (792)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCHHHHcccchhHHHHHHHHHHHhhcCEeccCccccch---h
Confidence 3468999999999999999999999999999999999999999999999999999999999999999987754322 1
Q ss_pred CCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeC
Q psy5925 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTIS 637 (696)
Q Consensus 558 ~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~ 637 (696)
..+.||+|++|++|+|++ |++|||+|||||||++|||||+|+....+. + ..+
T Consensus 404 ~~~~Gg~V~~P~~Gly~~-V~vLDF~SLYPSII~~~Ni~p~T~~~~~~~-------------------------~--~~~ 455 (792)
T COG0417 404 KKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCS-------------------------D--DYS 455 (792)
T ss_pred hhcCCCEEccCCccccCc-EEEEEccccChHHHHHhCCCcceecCCCcc-------------------------c--ccc
Confidence 578899999999999999 999999999999999999999999864221 1 123
Q ss_pred CCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 638 PSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 638 p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
|+|..++....++|++|++|++|++.|.++|+.||+.+++. .+++ +.|||+||-
T Consensus 456 ~~~~~~~~~~~~~G~lp~il~~L~~~R~~~K~~~k~~~~~~-e~~~~d~rQ~AlKvl~NS~YGy 518 (792)
T COG0417 456 PPGVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEKDPS-ERKLLDGRQLALKVLANSFYGY 518 (792)
T ss_pred CCCCcccccccCCCchHHHHHHHHHHHHHHHHHhcccCChH-HHHHHHHHHHHHHHHHhhcccc
Confidence 44545555555899999999999999999999999987764 1111 567999995
No 12
>PRK05761 DNA polymerase I; Reviewed
Probab=100.00 E-value=8.3e-50 Score=469.15 Aligned_cols=285 Identities=16% Similarity=0.185 Sum_probs=230.0
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
++|++||.+|+++|+++||||+ ||+++||||||.+||+.+|++.. .++|.. -.|+.++|
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~--yN~~~FDlPYL~~Ra~~lgi~~~-~~~~~~------------------~~~~~~iD 266 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKE-EIPIEP------------------GRAGIHID 266 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEE--EcCCcchHHHHHHHHHHhCCCch-hccccc------------------CCCceEEe
Confidence 5788999999999999999986 99999999999999999998754 122211 01344788
Q ss_pred hHHHHhh----------hcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHH--HH
Q psy5925 433 LWRLLRH----------EVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLI--EQ 500 (696)
Q Consensus 433 l~~~~r~----------~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~--~k 500 (696)
++..++. .+++++|+|++||+++||++|.+++ .++.+ ..+.++++||++||.++++|+ .+
T Consensus 267 l~~~~~~~~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~-~~i~~-------~~~~~l~~Y~l~Da~l~~~L~~f~~ 338 (787)
T PRK05761 267 LYKFFQNKAVRSYAFYGKYRHREARLDAVGRALLGISKVELE-TNISE-------LDLEELAEYNFRDAEITLKLTFFNN 338 (787)
T ss_pred chhheeecceeeeeccceeecccCChHHHHHHHhCCCccccc-ccccc-------cCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 8877653 2355699999999999999999887 45533 147899999999999999985 47
Q ss_pred hcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCch----hh-h----hccCCCCCCCeeeecccc
Q psy5925 501 LDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSI----KQ-R----AHMRAPESLPLILEPESR 571 (696)
Q Consensus 501 l~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~----~q-~----~~~~~~~~GglVleP~~G 571 (696)
..++++..+||+++|+|++++..+|++.+||++|+++|+++|+++|++.. .. . .....+|.||+|+||++|
T Consensus 339 ~~~l~~~~elarit~lpl~~v~r~~~g~~i~~~l~~~a~~~~~liP~~~~~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G 418 (787)
T PRK05761 339 ELVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPG 418 (787)
T ss_pred hhHHHHHHHHHHHHCcCHHHHhccCHHHHHHHHHHHHHHhCCEeCCCCccccccccccccccccccCCcCCcEEeccCCC
Confidence 77899999999999999999976667899999999999999999997654 11 0 012468999999999999
Q ss_pred cccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeCCCCceeecCCCccc
Q psy5925 572 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCG 651 (696)
Q Consensus 572 ly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~fvk~~~r~G 651 (696)
+|++ |++|||+|||||||++|||||+|+++..+.. . ......+.|+.|++. ++|
T Consensus 419 ~y~~-V~vlDF~SLYPSIi~~~Ni~p~T~~~~~~~~--~---------------------~~~~~~~~~~~~~~~--~~g 472 (787)
T PRK05761 419 IFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKC--H---------------------YDDEVPELGHSVCDD--RPG 472 (787)
T ss_pred ceee-EEEeeecccchHHHHHhCCChhhccCccccc--c---------------------ccCCCCCCCceeecC--CCC
Confidence 9987 9999999999999999999999998632110 0 011112467888885 899
Q ss_pred chHHHHHHHHHHHHHHHHHHhhCCC-CHHHHHH---------hhhcccccc
Q psy5925 652 ILPKMLQEILDTRLMVKQSMKEYKF-SESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 652 ILP~~L~~Ll~~R~~vKk~mk~~~~-~~~l~~~---------l~ansmy~~ 692 (696)
|+|.+|+.|++.|+++|+.|++.++ ++.++++ +.|||+||.
T Consensus 473 l~~~il~~l~~~R~~~k~~~~~~~~~~~~~~~~ld~~Q~AlKi~~NS~YGy 523 (787)
T PRK05761 473 LTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGV 523 (787)
T ss_pred chHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHhheeeeeccccc
Confidence 9999999999999999999998753 5665555 445999995
No 13
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=100.00 E-value=6.2e-44 Score=414.61 Aligned_cols=340 Identities=16% Similarity=0.098 Sum_probs=247.2
Q ss_pred cceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCc------------c-ccccccccccc
Q psy5925 345 YLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLN------------Q-ELSRITEVEKR 411 (696)
Q Consensus 345 ~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~------------~-~lgR~~~~~~~ 411 (696)
.++++..|.+|.+||.+|++.++++ -||+.-||. .||+..|.+|.+.+..... . .+++.+..-..
T Consensus 321 t~~~~~~c~~e~~~l~~fl~~~~~~-v~vlyv~n~-~fdv~vi~~rl~~y~~~~~~~~~~~~l~~~~~~~~s~~~~~~~~ 398 (1545)
T PHA03334 321 TRIEFVACADELEMLLAFLNRLRKS-VNVLYVYNA-EFDVQVIQSRLNYYAFKQRPHPLTKALMEAWEAFLSKDPQLVPA 398 (1545)
T ss_pred eeeEEEEeccHHHHHHHHHHHHHhh-ccEEEEecc-cccHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHhccCCccCCc
Confidence 3678999999999999999999984 589999998 5999999999987643211 0 12322211000
Q ss_pred --ccC------------------------------C------------------Cc----cccceeeecccEEEehHHHH
Q psy5925 412 --NSS------------------------------R------------------DE----VKNTQLQMPGRIVINLWRLL 437 (696)
Q Consensus 412 --~~~------------------------------~------------------~~----~~~~~~~i~GRl~lDl~~~~ 437 (696)
.++ . .. .-++.+.+.||+++|+|+++
T Consensus 399 ~~~f~~~~~~s~y~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~v~~f~~n~~~~~~~kv~~~GrviiDMy~Vc 478 (1545)
T PHA03334 399 QLLFGSDILNSNYLELLDVIESHKAQFKATCRKAAARKEEIGSYMKTRDTVQDFNDNDKKYLNSTSHGFGAHIIDLMRVC 478 (1545)
T ss_pred eeEehhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHhhcccccccccceeeeccEEEEehHHHH
Confidence 000 0 00 01457899999999999999
Q ss_pred hh---hcCCCCCCHHHHHHHHcCCCc-----------CCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcc
Q psy5925 438 RH---EVNLQSYTFENIMYHVLHERI-----------PLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDF 503 (696)
Q Consensus 438 r~---~~kl~sysL~~Va~~~L~~~k-----------~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~i 503 (696)
++ ++++.||+|++||+++||++| +|++|.+|.++|+.++ +.+.+++.||++|+.|+++|++++..
T Consensus 479 ~~K~~~~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~-e~RaRla~YCLkDA~LvlrLlkkl~~ 557 (1545)
T PHA03334 479 NTKSIKAKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGG-AALARYLIYNLVDSELLIRIAKNLDP 557 (1545)
T ss_pred hhcccccCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcCh-hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88 589999999999999999999 8999999999999875 68999999999999999999999999
Q ss_pred cchhhhHHHHhCCchhhhhcCc--------chhhhHHHhhcccc-cCCeeee------C---Cchh-hhhccCCCCCCCe
Q psy5925 504 IGRTSEMARLFGIQFYEVLSRG--------SQFRVESIMLRLSR-LNNFVAV------S---PSIK-QRAHMRAPESLPL 564 (696)
Q Consensus 504 i~~~~ela~l~gi~~~~vl~rG--------s~~rvEslLlr~~~-~~~~i~p------~---p~~~-q~~~~~~~~~Ggl 564 (696)
+....+++|.++.+....++|| ||+||-+.++++|+ +.|+++| + |... ...+++..|.||+
T Consensus 558 h~e~~eraRvT~~id~~~l~RG~v~fdG~vQQIKV~s~lL~kA~~~~~~~ia~~~i~~s~ilP~~~~~~~~~~~~YeGAt 637 (1545)
T PHA03334 558 VIEFLNRLRATYNIDYVAHGRGVMNFCGFVQSTKSVEVPLLKARLRIGIFVATGRIAESLCMPEKYARDCRQKIKLKGGY 637 (1545)
T ss_pred HHHHHHHHhcccCCceeecccceecccCccchhhHHHHHHHHHHHhcCcccccccccccccCCcccccccccccccCCeE
Confidence 9999999999987765555565 99999888888877 6677653 1 3221 1123567899999
Q ss_pred eeeccccc-----ccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhccccee-eCC
Q psy5925 565 ILEPESRL-----YTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLT-ISP 638 (696)
Q Consensus 565 VleP~~Gl-----y~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~-~~p 638 (696)
|+||++|| |.+||+||||+||||||||+|||||||++...+ .....+. .|....+++.+. .. .+.+. +.-
T Consensus 638 VLEP~~Gf~~~~~Y~~PVaVLDFASLYPSIIiahNLCYeTLV~~~c-~~~~~~~-~~~d~~k~p~gy-~~-~~~vy~V~~ 713 (1545)
T PHA03334 638 VFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAIVDPDC-TARVRGW-VVFDWKKIDRGF-GK-ATLMYTILR 713 (1545)
T ss_pred eecCCCCccccccCCCcEEEEEccccchHHHHHhCCCcccccCccc-hhhhccc-cccccccCCccc-Cc-cccceeecc
Confidence 99999999 678999999999999999999999999986421 1000000 000000111110 00 00000 000
Q ss_pred CCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 639 SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 639 ~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
.+..+++.....|++|++|++||+.|+++|+.||+.+++ .++++ +.||||||.
T Consensus 714 ~~~~~P~~~rf~SiLp~LL~eLL~~RK~~Kk~MKk~kDp-~er~iLD~rQlALKVtANSvYGy 775 (1545)
T PHA03334 714 TKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDP-KLKSYHNQLQNEMKICANSHYGV 775 (1545)
T ss_pred ccCcCCCcceecchHHHHHHHHHHHHHHHHHHHhhCCCH-HHHHHHHHHHHHHHHHHHhhcCc
Confidence 011122333456899999999999999999999988754 34444 456999995
No 14
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=100.00 E-value=1.7e-41 Score=347.31 Aligned_cols=221 Identities=37% Similarity=0.636 Sum_probs=183.3
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCC---ceEEEEEEcCCCCCcccccCccccccccchhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEED---RKVGIILIGQESELPEVRTKPIQMNFVSNEKELFS 319 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~---~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~ 319 (696)
++||+|||||||.|+++.||||+.|||++|+|+++++..... ...|++++....... .
T Consensus 2 ~~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------~------------ 62 (231)
T cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNA-------S------------ 62 (231)
T ss_pred CceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchh-------h------------
Confidence 689999999999999999999999999999999998765221 255677775532110 0
Q ss_pred hhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCc
Q psy5925 320 TFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLN 399 (696)
Q Consensus 320 ~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~ 399 (696)
.. ..... ..+..|..|++|++||.+|+++|+.+|||||+|||+++||||||++||+.+++..+
T Consensus 63 ~~--~~~~~---------------~~~~~v~~~~~E~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~ 125 (231)
T cd05778 63 NG--RIRSG---------------LSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDL 125 (231)
T ss_pred hh--ccccC---------------CCCCeEEEeCCHHHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcch
Confidence 00 00000 13578999999999999999999999999999999999999999999999999987
Q ss_pred -ccccccccccccccC-----CCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHh
Q psy5925 400 -QELSRITEVEKRNSS-----RDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWE 473 (696)
Q Consensus 400 -~~lgR~~~~~~~~~~-----~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~ 473 (696)
..+||++........ .+.+....+.+.||+++|+|+.+|++++++||||++||+++||++|+++++++|++||.
T Consensus 126 ~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~ 205 (231)
T cd05778 126 LDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYK 205 (231)
T ss_pred hhhccCCCCCCcccccccccccccccCCceEEeeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence 789998754332111 12223456899999999999999999999999999999999999999999999999998
Q ss_pred cCCcccHHHHHHHHHHHHHHHHHHHH
Q psy5925 474 HRTHLYKWMTVEHYLIRVTGIIRLIE 499 (696)
Q Consensus 474 ~~~~~~~~~~i~Y~l~D~~l~~~L~~ 499 (696)
++++..++++++||++|+.++++|++
T Consensus 206 ~~~~~~r~~v~~Y~l~d~~l~l~Ll~ 231 (231)
T cd05778 206 SGSASERWRVLEYYLKRVRLNLEILD 231 (231)
T ss_pred cCCHhHhHHHHHHHHHHHHHHHHhhC
Confidence 87767899999999999999999973
No 15
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=100.00 E-value=2.5e-39 Score=331.69 Aligned_cols=219 Identities=23% Similarity=0.285 Sum_probs=180.8
Q ss_pred cCCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhh
Q psy5925 241 ENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFST 320 (696)
Q Consensus 241 ~~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~ 320 (696)
+.|++++|||||||.++++.||||+.|+|++|++++..+.......++++++++
T Consensus 3 ~~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~-------------------------- 56 (230)
T cd05777 3 KIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKT-------------------------- 56 (230)
T ss_pred CCCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCC--------------------------
Confidence 479999999999999998899999999999999998755431111233433321
Q ss_pred hhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcc
Q psy5925 321 FIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQ 400 (696)
Q Consensus 321 ~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~ 400 (696)
+++ ..+..|..|++|++||.+|+++|+++|||||+|||+++||||||.+||+.+|++.+.
T Consensus 57 -------~~~-------------~~~~~v~~~~~E~eLL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~ 116 (230)
T cd05777 57 -------CAP-------------IVGAQVFSFETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFP 116 (230)
T ss_pred -------CCC-------------CCCCEEEEECCHHHHHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCcccc
Confidence 110 024578899999999999999999999999999999999999999999999999888
Q ss_pred ccccccccccc----ccC---CCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHh
Q psy5925 401 ELSRITEVEKR----NSS---RDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWE 473 (696)
Q Consensus 401 ~lgR~~~~~~~----~~~---~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~ 473 (696)
.+||.+..... ..+ .|.+....+.++||+++|+|+.++++++++||+|++||+++||++|+++++++|.+||+
T Consensus 117 ~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~ 196 (230)
T cd05777 117 FLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQN 196 (230)
T ss_pred ccccccCCceeEeCCcccccccccccceEEEEcCEEeeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHc
Confidence 89998653211 111 12233455789999999999999999999999999999999999999999999999997
Q ss_pred cCCcccHHHHHHHHHHHHHHHHHHHHHhcccch
Q psy5925 474 HRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGR 506 (696)
Q Consensus 474 ~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~ 506 (696)
+++ ..+.++++||++||.++++|+.+++++..
T Consensus 197 ~~~-~~~~~l~~Y~~~Da~l~l~L~~kl~~~~~ 228 (230)
T cd05777 197 GNP-ETRRRLAVYCLKDAYLPLRLLDKLMCLVN 228 (230)
T ss_pred cCH-hHhHHHHHhhHHHHHHHHHHHHHHhhHcc
Confidence 553 45789999999999999999999988764
No 16
>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=100.00 E-value=1e-35 Score=305.50 Aligned_cols=227 Identities=16% Similarity=0.188 Sum_probs=186.1
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCc------eEE-EEEEcCCCCCcccccCccccccccchh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDR------KVG-IILIGQESELPEVRTKPIQMNFVSNEK 315 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~------~~g-~ilv~~~~~~~~~~~~p~~~~~~~~~~ 315 (696)
|+|+++|+.+.|. .+++-+++||+|||+.++++.++|.+ ... ++++++.+.. ..|..
T Consensus 1 Ppl~v~sls~~T~----~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~----~~~~~-------- 64 (234)
T cd05776 1 PPLTVMSLSIKTV----LNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRS----PPPDL-------- 64 (234)
T ss_pred CCeEEEEEEeEEE----ecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCC----CCCch--------
Confidence 7999999999998 67888899999999999988875532 222 5556654321 11211
Q ss_pred hhhhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcC
Q psy5925 316 ELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLG 395 (696)
Q Consensus 316 e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lg 395 (696)
++.... ..+..|..|++|++||.+|+++|+++|||||+|||+++|||+||++||+.+|
T Consensus 65 --~~~~~~--------------------~~~~~v~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~ 122 (234)
T cd05776 65 --FEKNAK--------------------KKKTKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELK 122 (234)
T ss_pred --HHHHHH--------------------hcCCcEEEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhC
Confidence 111111 1345788999999999999999999999999999999999999999999999
Q ss_pred CCCcccccccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcC
Q psy5925 396 LNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHR 475 (696)
Q Consensus 396 i~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~ 475 (696)
++.|+++||.+.........+..+.....+.||+++|+|..+|+.++++||+|++||+++||+++.+++++++.++|.+.
T Consensus 123 i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~ 202 (234)
T cd05776 123 VPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDS 202 (234)
T ss_pred CCccccccccccccCccccccccccccccccCchhhccHHHHHHHhCCCCCChHHHHHHHhCcCcccCCHHHHHHHHhCH
Confidence 99999999987543322221223345678999999999999999999999999999999999999999999999999873
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHhcccchhhh
Q psy5925 476 THLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSE 509 (696)
Q Consensus 476 ~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~e 509 (696)
..+.++++||++||.++++|+.++++++++.+
T Consensus 203 --~~l~~l~~y~~~Da~l~~~L~~kl~il~Ltkq 234 (234)
T cd05776 203 --ESLLKLLEHTEKDAYLILQLMFKLNILPLTKQ 234 (234)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence 46899999999999999999999999999864
No 17
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=100.00 E-value=1.3e-35 Score=329.90 Aligned_cols=167 Identities=55% Similarity=0.859 Sum_probs=133.5
Q ss_pred cchhhhHHHhhcccccCCeeeeCCchhhhhccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCccccc
Q psy5925 525 GSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRV 604 (696)
Q Consensus 525 Gs~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~ 604 (696)
|||+|||++|+|+|+++||++|+++..+...++++++||+|+||++|||++||+||||+||||||||+|||||||+++..
T Consensus 1 g~q~rve~~llr~~~~~g~~~p~~~~~~~~~~~~~~~g~~V~eP~~G~y~~~V~vLDF~SLYPSIi~~~Nic~sT~~~~~ 80 (451)
T cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80 (451)
T ss_pred CCeEEeHHHHHHHHHHcCEEeecCchhccccccccccCcEeecCCcCcccCceEEEecccccHHHHHHhCcCcccccccc
Confidence 79999999999999999999999986665557788999999999999999999999999999999999999999999865
Q ss_pred ccCCCCC-CCCCcccccccCh--hHHhhcccceeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHH
Q psy5925 605 EHLGVSD-SFPFGCIDLNVSI--RSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLR 681 (696)
Q Consensus 605 ~~~~~~~-~~~~G~~~~~~~~--~~l~~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~ 681 (696)
++....+ ...++... .+++ .......+++.++|+|++|+++++++||||++|++|+++|+++|+.||+.++++.++
T Consensus 81 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~~~~~~ 159 (451)
T cd05534 81 EELNGGGKFGFLGVKL-YLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQ 159 (451)
T ss_pred cccccccccccccccc-cccccccccccCCCcEEECCCcceeecCCCCCCchHHHHHHHHHHHHHHHHHHhhCCCCHHHH
Confidence 4332111 00111000 0011 111112466889999999999999999999999999999999999999998877665
Q ss_pred HH---------hhhcccccc
Q psy5925 682 NL---------TMLNSMLLI 692 (696)
Q Consensus 682 ~~---------l~ansmy~~ 692 (696)
++ +.||||||.
T Consensus 160 ~~ld~~Q~AlKi~~NS~YGy 179 (451)
T cd05534 160 RILDARQLALKLLANVTYGY 179 (451)
T ss_pred HHHHHHHHHHHHHhhccccc
Confidence 55 446999995
No 18
>KOG1798|consensus
Probab=100.00 E-value=6.6e-33 Score=319.51 Aligned_cols=341 Identities=17% Similarity=0.197 Sum_probs=277.2
Q ss_pred Cc-cccccccccccCCCCCCccccccCCCCcccc--cccccCCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCC
Q psy5925 204 TP-KRRICDSYAIDAMTPDTTGDYQMGLDNLNEV--TSHVENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCP 280 (696)
Q Consensus 204 ~p-~~~~~~~~~I~~~t~~~~~gfk~~~~~~~~~--~~~~~~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~ 280 (696)
-| +.+++++..|.. ..||++.+........ ...-+.+.++||+|||||...+.+|||.+.|+|+||||.+.
T Consensus 205 VPyHvR~sID~~Irv---G~WY~V~~~~~~v~i~~r~~~i~radp~VlAFDIETtKlPLKFPDae~DqIMMISYMiD--- 278 (2173)
T KOG1798|consen 205 VPYHVRVSIDLDIRV---GQWYNVSYNSGPVEIERRTDLIERADPRVLAFDIETTKLPLKFPDAESDQIMMISYMID--- 278 (2173)
T ss_pred CceEEEEeecCCeee---eeeeeeeeeccceEEEecccccccCCceEEEEeeecccCCCCCCCcccceEEEEEEEec---
Confidence 45 888888877765 3599998754432322 23556899999999999999999999999999999999986
Q ss_pred CCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHH
Q psy5925 281 PEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFS 360 (696)
Q Consensus 281 ~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~ 360 (696)
.+|++++|++..+. ++|.|+...+ | |.+ .-+.|...++|.+||.
T Consensus 279 -----GqGfLItNREiVs~--------------DIedfEYTPK------p------E~e-----G~F~v~Ne~dEv~Ll~ 322 (2173)
T KOG1798|consen 279 -----GQGFLITNREIVSE--------------DIEDFEYTPK------P------EYE-----GPFCVFNEPDEVGLLQ 322 (2173)
T ss_pred -----CceEEEechhhhcc--------------chhhcccCCc------c------ccc-----cceEEecCCcHHHHHH
Confidence 45999998875432 2333443211 0 111 3467888899999999
Q ss_pred HHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHhhh
Q psy5925 361 IFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHE 440 (696)
Q Consensus 361 ~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~ 440 (696)
+|++.|++..|.||+.||++-|||||+..||+.+|+++...+|-.+... ..+.-+-.+|+|.++++|++
T Consensus 323 RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~-----------gEyks~~c~HmDcfrWVKRD 391 (2173)
T KOG1798|consen 323 RFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQ-----------GEYKSPFCIHMDCFRWVKRD 391 (2173)
T ss_pred HHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceeccc-----------ccccccceeehhhhhhhhhc
Confidence 9999999999999999999999999999999999999988888655421 23445557899999999987
Q ss_pred c--CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCch
Q psy5925 441 V--NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQF 518 (696)
Q Consensus 441 ~--kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~ 518 (696)
. ...|-.|+.|++.-||....++++++|.++..+.+ +.++.|.+.||..++.|+.|. +.|+.+.|+.|+.+..
T Consensus 392 SYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkP----Q~lasYSVSDAVATYyLYMkY-VhPFIFsLctIIPl~P 466 (2173)
T KOG1798|consen 392 SYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKP----QTLASYSVSDAVATYYLYMKY-VHPFIFSLCTIIPLNP 466 (2173)
T ss_pred ccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCc----hhhhhcchHHHHHHHHHHHHH-hhhHHhhhhhccccCh
Confidence 3 88899999999999999999999999999998887 899999999999999999997 8999999999999999
Q ss_pred hhhhcCcchhhhHHHhhcccccCCeeeeCCchhhh-----hc--cCCCCCCCeeeeccccccc-----------------
Q psy5925 519 YEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQR-----AH--MRAPESLPLILEPESRLYT----------------- 574 (696)
Q Consensus 519 ~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~-----~~--~~~~~~GglVleP~~Gly~----------------- 574 (696)
++||+.||++.+|.+|+-+|...|.++|++..... ++ ..+.|-||.|-.-++|+++
T Consensus 467 DevLRKGSGTLCE~LLmVeA~~~NIv~PNK~~e~~~~f~dGhlleSETYVGGHVE~LesGVFRSDip~~F~~dp~a~~eL 546 (2173)
T KOG1798|consen 467 DEVLRKGSGTLCEALLMVEAYHANIVFPNKHTEDPEKFYDGHLLESETYVGGHVECLESGVFRSDIPTEFRMDPSAYEEL 546 (2173)
T ss_pred HHHHhcCcchHHHHHHHHHHHhcCeecCCcCccchhhhccCeeeeeeeeechhhhhHhcccccccCcccccCCHHHHHHH
Confidence 99999999999999999999999999987653211 00 3456777777655555331
Q ss_pred ------------------------------------------------Cc-eeeeeccccchhhhhhccCCccCccc
Q psy5925 575 ------------------------------------------------DP-IIVLDFQSLYPSVIIAYNYCFSTCLG 602 (696)
Q Consensus 575 ------------------------------------------------~p-VvvLDF~SLYPSIIiayNiC~sT~~~ 602 (696)
.| |--||-+||||+||..--+=|..++.
T Consensus 547 i~~l~~~L~~~l~vE~k~~vd~v~nfeEv~~~I~~kL~~lrd~p~R~E~PlIYHLDVaaMYPNIilTNRLQP~siv~ 623 (2173)
T KOG1798|consen 547 IDELGETLDFALTVENKVRVDEVTNFEEVKDEILEKLEELRDVPIREEGPLIYHLDVAAMYPNIILTNRLQPDSIVD 623 (2173)
T ss_pred HHHHHHHHHHHHhhhcccchhhhcCHHHHHHHHHHHHHHhcCCCccccCCeEEEEehhhccCceeeecCCCCccccc
Confidence 13 45799999999999998888877764
No 19
>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=100.00 E-value=3.1e-32 Score=272.38 Aligned_cols=195 Identities=22% Similarity=0.301 Sum_probs=160.0
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
|++++++|||||.+.++ +|+|..|+|++|++..... ..++...+
T Consensus 1 p~l~i~~fDIEt~~~~g-~p~~~~d~Ii~Is~~~~~~-------~~~~~~~~---------------------------- 44 (195)
T cd05780 1 EDLKILSFDIEVLNHEG-EPNPEKDPIIMISFADEGG-------NKVITWKK---------------------------- 44 (195)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCcEEEEEEecCCC-------ceEEEecC----------------------------
Confidence 78999999999998774 8999999999999754211 11221100
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
.+ ...+..+++|++||.+|+++|+++|||+|+|||+++||||||.+||+.+|++. .+
T Consensus 45 -----~~----------------~~~v~~~~~E~~lL~~F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~--~~ 101 (195)
T cd05780 45 -----FD----------------LPFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--DL 101 (195)
T ss_pred -----CC----------------CCeEEEeCCHHHHHHHHHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCC--cc
Confidence 11 01456799999999999999999999999999999999999999999999984 37
Q ss_pred cccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHH
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWM 482 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~ 482 (696)
||......... .+. .....+.||+++|+|+.+++.++++||+|++||+++||.+|++++++++.+||.+++ .+.+
T Consensus 102 ~r~~~~~~~~~-~g~--~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~--~~~~ 176 (195)
T cd05780 102 GRDGSEIKIQR-GGF--NNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE--NLER 176 (195)
T ss_pred ccCCCceeEee-cce--eeeeccCCeEEEeHHHHHHhhCCCCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCC--chHH
Confidence 87653322111 111 234578999999999999999999999999999999999999999999999999875 5899
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q psy5925 483 TVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 483 ~i~Y~l~D~~l~~~L~~kl 501 (696)
+++||++||.++++|++++
T Consensus 177 l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 177 LFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred HHHHhHHHHHHHHHHHhhC
Confidence 9999999999999998764
No 20
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=99.97 E-value=6.6e-31 Score=263.36 Aligned_cols=201 Identities=17% Similarity=0.206 Sum_probs=155.7
Q ss_pred CceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIE 323 (696)
Q Consensus 244 ~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~ 323 (696)
++++|||||||.++++.||+|+.|+|++||+++... |..+........ .. +.|
T Consensus 1 ~lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~--------g~~~~~~~~~~~--~~------------~~~----- 53 (204)
T cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQ--------GYLIVNREIVSE--DI------------EDF----- 53 (204)
T ss_pred CceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecC--------CEEEeccccccc--cc------------ccc-----
Confidence 589999999999887889999999999999887643 222221110000 00 000
Q ss_pred ccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccc
Q psy5925 324 NVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403 (696)
Q Consensus 324 ~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lg 403 (696)
.+..++ +++ ..+.|..+++|++||.+|+++++++|||+|+|||+++||||||.+||+.+|+.....+|
T Consensus 54 ~~~~~~-------~~~-----~~~~v~~~~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g 121 (204)
T cd05779 54 EYTPKP-------EYE-----GPFKVFNEPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIG 121 (204)
T ss_pred cccCCC-------CCC-----CceEEecCCCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhC
Confidence 000010 011 23567789999999999999999999999999999999999999999999998664455
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhhhc--CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHH
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV--NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 481 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~--kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~ 481 (696)
|.... ...+.+.||+++|+|.++++.. ...+|+|++||+++||++|.++++.+|.++|+++. .
T Consensus 122 ~~~~~-----------~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~----~ 186 (204)
T cd05779 122 FRKDS-----------EGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP----Q 186 (204)
T ss_pred eEecC-----------CCeEEeccEEEEEhHHHHHHhhcCCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc----H
Confidence 42211 1145679999999999999865 45799999999999999999999999999998764 7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy5925 482 MTVEHYLIRVTGIIRLI 498 (696)
Q Consensus 482 ~~i~Y~l~D~~l~~~L~ 498 (696)
++++||++||.+++.|+
T Consensus 187 ~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 187 TLASYSVSDAVATYYLY 203 (204)
T ss_pred HHHhccHHHHHHHHHHh
Confidence 89999999999999885
No 21
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=99.97 E-value=1.7e-30 Score=258.06 Aligned_cols=184 Identities=22% Similarity=0.373 Sum_probs=150.8
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
|+|++|+|||||.++. .||+|.+|+|++|++...+.. +.+
T Consensus 1 p~l~~l~fDIEt~~~~-gfp~~~~d~Ii~Is~~~~~g~--------~~~------------------------------- 40 (188)
T cd05781 1 PDLKTLAFDIEVYSKY-GTPNPRRDPIIVISLATSNGD--------VEF------------------------------- 40 (188)
T ss_pred CCceEEEEEEEecCCC-CCCCCCCCCEEEEEEEeCCCC--------EEE-------------------------------
Confidence 7899999999999665 599999999999997553110 000
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
-...+.+|++||.+|+++|+++|||+|+|||+++||||||.+||+.+|++.. +
T Consensus 41 -------------------------~~~~~~~E~~lL~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~--~ 93 (188)
T cd05781 41 -------------------------ILAEGLDDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLD--V 93 (188)
T ss_pred -------------------------EEecCCCHHHHHHHHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcc--c
Confidence 0112479999999999999999999999999999999999999999999864 6
Q ss_pred cccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCC----CcCCCChhhHHHHHhcCCcc
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHE----RIPLHSWKLLTCWWEHRTHL 478 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~----~k~~~~~~~l~~~~~~~~~~ 478 (696)
||........ .....+.++||+++|+|.++++..++++|+|++||++ ||. .++++++.++.++|.++.
T Consensus 94 gr~~~~~~~~-----~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~~-Lg~~k~~~k~~~~~~~i~~~~~~~~-- 165 (188)
T cd05781 94 GRRGGSEPST-----GVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAEY-LGVMKKSERVLIEWYRIYEYWDDEK-- 165 (188)
T ss_pred ccCCCccccc-----CCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHHH-HCCCccccccCCCHHHHHHHHcCcc--
Confidence 7754321111 1133578999999999999999999999999999985 775 467899999999998753
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 479 YKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 479 ~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+.++++||++|+.+++.|++++
T Consensus 166 ~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 166 KRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhC
Confidence 47999999999999999998763
No 22
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.97 E-value=4.1e-33 Score=341.01 Aligned_cols=367 Identities=19% Similarity=0.161 Sum_probs=265.0
Q ss_pred cCCCceEEEEEEEeecCCC--C--CCCCCCCcEEEEEEE-eecCCCCCCceEEEEEEcCCCCCcccccCccccccccchh
Q psy5925 241 ENYYLTVLAVEIHAISRAL--L--KPDPAYDEVKAIFYY-LYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEK 315 (696)
Q Consensus 241 ~~~~LtilsleIe~~sr~~--~--~Pdp~~D~I~~I~~~-~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~ 315 (696)
..|+++++||||||.+..+ . +|+|..|+|++|+.. +. . +... + ..
T Consensus 194 ~~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~-~---------~~~~---~-----~~------------ 243 (1172)
T TIGR00592 194 GDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVI-A---------KQWD---Y-----ES------------ 243 (1172)
T ss_pred CCCcccccccccccccccccccCccccccccccccccccccc-c---------cccc---c-----CC------------
Confidence 3699999999999987643 3 366778999999732 00 0 0000 0 00
Q ss_pred hhhhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHH------
Q psy5925 316 ELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLE------ 389 (696)
Q Consensus 316 e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~------ 389 (696)
++..+.+.++..++|. .+..|..|.+|.+||.+|.+++++.|||||+|||+++||||||.+
T Consensus 244 ~~~~~~~~~~~~~~~~-------------~~~~v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~~~~~~~ 310 (1172)
T TIGR00592 244 EPEARVVTWKKPDKPT-------------TGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQF 310 (1172)
T ss_pred CccchhhhccCccccC-------------CCccceeccchHHHHhhHHHHHhhcCcchhcccccccCccceecCCceEEe
Confidence 0111223333445431 346788899999999999999999999999999999999999999
Q ss_pred -------HHHHcCCCCcccccccccccccc-cCCC-ccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCc
Q psy5925 390 -------RGYVLGLNLNQELSRITEVEKRN-SSRD-EVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERI 460 (696)
Q Consensus 390 -------Ra~~lgi~~~~~lgR~~~~~~~~-~~~~-~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k 460 (696)
|++.+|.-. .+||........ ...| .+....+.+.||+.+|++..+++.+++.+|+|+.|+++++|.+|
T Consensus 311 ~~da~~dr~~~~G~~~--lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~k 388 (1172)
T TIGR00592 311 YWDAYEDPAEKLGVVL--LFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKK 388 (1172)
T ss_pred eHHhhhHHhhCCCeEE--EecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcCc
Confidence 676665533 377731100000 0112 22344568899999999999999999999999999999999999
Q ss_pred CCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhccccc
Q psy5925 461 PLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRL 540 (696)
Q Consensus 461 ~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~ 540 (696)
.++.+..+.+.|..+.. .+.+.|+.+|+.+++.++.++..++.. .+++.|.++..++..+++..++.++.|.++.
T Consensus 389 ~dv~~k~I~~~~~~~~~---~~~v~y~~~~lkv~y~l~~~~~~l~~l--~~~~~g~~~~~vf~~n~g~~erfll~rki~g 463 (1172)
T TIGR00592 389 EKFRAKPIAKKYEFEAP---DIDAPYSSEYLEVTYELGKEFAPMEAL--PSDLKGQTFWHVFGSNTGNLERFLLLRKIKG 463 (1172)
T ss_pred CceeeEEehhhccCCCC---ccCCcCCcceEEEEEccCccchhhhhh--hhhccCCcchheeccCHHHHHHHHhcCCCCC
Confidence 99999999999987752 257899999999999987776444433 4567799999998877888888999999999
Q ss_pred CCeeeeC-Cchhhhh-ccCCCCCCCeeeec--ccccccC--ceeeeecc--ccchhhhhhccCCccCcccccccCCCCCC
Q psy5925 541 NNFVAVS-PSIKQRA-HMRAPESLPLILEP--ESRLYTD--PIIVLDFQ--SLYPSVIIAYNYCFSTCLGRVEHLGVSDS 612 (696)
Q Consensus 541 ~~~i~p~-p~~~q~~-~~~~~~~GglVleP--~~Gly~~--pVvvLDF~--SLYPSIIiayNiC~sT~~~~~~~~~~~~~ 612 (696)
.+++.+. |...... .....++|+.|.+| .+|+|.+ ||++|||+ |||||||+++|+|+||++.+..+++..
T Consensus 464 p~WL~i~~p~~~~~~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~-- 541 (1172)
T TIGR00592 464 PCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKP-- 541 (1172)
T ss_pred CceEEeCCCcccCcCCccccceEEEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeecccccCC--
Confidence 9988764 3321111 23467899999999 9999998 89999999 999999999999998887432111100
Q ss_pred CCCcccccccChhHHhhcccceeeCC-CCceeec-------CCCcccchHHHHHHHHHHHHHHHHHHhhCC
Q psy5925 613 FPFGCIDLNVSIRSLKKLQQNLTISP-SGVAFVD-------KSIRCGILPKMLQEILDTRLMVKQSMKEYK 675 (696)
Q Consensus 613 ~~~G~~~~~~~~~~l~~~~d~i~~~p-~g~~fvk-------~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~ 675 (696)
++ .+.....+ .++.|.. +..++|++|..|+.+++.|.++|+.|+...
T Consensus 542 ----------~~------~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~ 596 (1172)
T TIGR00592 542 ----------PP------EPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVK 596 (1172)
T ss_pred ----------CC------CCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHH
Confidence 00 00011111 1222211 124789999999999999999999999764
No 23
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=99.97 E-value=1.9e-29 Score=251.01 Aligned_cols=146 Identities=23% Similarity=0.340 Sum_probs=124.5
Q ss_pred eEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeec
Q psy5925 347 LERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMP 426 (696)
Q Consensus 347 ~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~ 426 (696)
..|..|++|++||.+|+++++++|||||+|||+++||||||.+||+.+|++. .+||.+....+... +.+....+.++
T Consensus 43 ~~v~~~~~E~~lL~~f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~--~~gR~~~~~~~~~~-g~~~~~~~~i~ 119 (193)
T cd05784 43 DNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSPLNWRQS-GKPGQGFLSLP 119 (193)
T ss_pred CEEEEECCHHHHHHHHHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCc--ccccCCCccccccC-CcCCcceEEEe
Confidence 4678899999999999999999999999999999999999999999999986 38887653322111 22234468999
Q ss_pred ccEEEehHHHHhh-hcCCCCCCHHHHHHHHcCCCcCCCC----hhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHH
Q psy5925 427 GRIVINLWRLLRH-EVNLQSYTFENIMYHVLHERIPLHS----WKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE 499 (696)
Q Consensus 427 GRl~lDl~~~~r~-~~kl~sysL~~Va~~~L~~~k~~~~----~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~ 499 (696)
||+++|+|..+|+ .++++||+|++||+++||++|.+++ +.+|.++|.++. .++++||++||.++++|++
T Consensus 120 GR~~~D~~~~~k~~~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~----~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 120 GRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK----LALARYNLQDCELVWRIFE 193 (193)
T ss_pred eEEEEEhHHHHHHccCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH----HHHHHHHHHHHHHHHHHhC
Confidence 9999999999987 5899999999999999999888764 468999998763 6899999999999999973
No 24
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=99.97 E-value=3.1e-29 Score=252.44 Aligned_cols=188 Identities=20% Similarity=0.208 Sum_probs=149.5
Q ss_pred cCCCceEEEEEEEeecCCCCC---CCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhh
Q psy5925 241 ENYYLTVLAVEIHAISRALLK---PDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKEL 317 (696)
Q Consensus 241 ~~~~LtilsleIe~~sr~~~~---Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~ 317 (696)
..|+|++|||||||.+.+..+ |++..|+|++|++..... ..
T Consensus 5 ~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~---------~~--------------------------- 48 (207)
T cd05785 5 TFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRG---------WE--------------------------- 48 (207)
T ss_pred CCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCC---------ce---------------------------
Confidence 368999999999999887654 566779999998642210 00
Q ss_pred hhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCC
Q psy5925 318 FSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLN 397 (696)
Q Consensus 318 ~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~ 397 (696)
.. ....+.+|++||.+|+++++++|||||+|||+++||||||.+||+.+|++
T Consensus 49 --~~--------------------------~~~~~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~ 100 (207)
T cd05785 49 --EV--------------------------LHAEDAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVP 100 (207)
T ss_pred --ee--------------------------eccCCCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCC
Confidence 00 00126899999999999999999999999999999999999999999998
Q ss_pred Ccccccccccccccc---cCCC--ccccceeeecccEEEehHHHHhh----hcCCCCCCHHHHHHHH--cCCCcCCCChh
Q psy5925 398 LNQELSRITEVEKRN---SSRD--EVKNTQLQMPGRIVINLWRLLRH----EVNLQSYTFENIMYHV--LHERIPLHSWK 466 (696)
Q Consensus 398 ~~~~lgR~~~~~~~~---~~~~--~~~~~~~~i~GRl~lDl~~~~r~----~~kl~sysL~~Va~~~--L~~~k~~~~~~ 466 (696)
.. +||......+. .+.+ .+....+.++||+++|+|.++++ ..+++||+|++||+++ +++++.++++.
T Consensus 101 ~~--~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~ 178 (207)
T cd05785 101 LA--IGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGR 178 (207)
T ss_pred cc--cccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHH
Confidence 64 67765422211 1111 11235688999999999999986 5689999999999997 67788999999
Q ss_pred hHHHHHhcCCcccHHHHHHHHHHHHHHHHHHH
Q psy5925 467 LLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLI 498 (696)
Q Consensus 467 ~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~ 498 (696)
+|.++|+++ ..++++||++||.++++|.
T Consensus 179 ~I~~l~~~~----~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 179 QIAEVWRSD----PARLLAYALDDVRETEGLA 206 (207)
T ss_pred HHHHHHhcC----HHHHHHHHHHHHHHHHHhh
Confidence 999999987 4899999999999999885
No 25
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.96 E-value=1.5e-28 Score=246.26 Aligned_cols=198 Identities=24% Similarity=0.324 Sum_probs=154.6
Q ss_pred EEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhccc
Q psy5925 247 VLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVR 326 (696)
Q Consensus 247 ilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~ 326 (696)
+++|||||.+.+ .+|+|..|+|++|+++...+.. .. +........ +.
T Consensus 1 v~~~DIEt~~~~-~~p~~~~d~Ii~I~~~~~~~g~----~~-~~~~~~~~~-------~~-------------------- 47 (199)
T cd05160 1 VLSFDIETTPPV-GGPEPDRDPIICITYADSFDGV----KV-VFLLKTSTV-------GD-------------------- 47 (199)
T ss_pred CccEEEeecCCC-CCcCCCCCCEEEEEEEEeeCCc----ee-eEEEeeccc-------CC--------------------
Confidence 589999999876 4789999999999987763321 11 111100000 00
Q ss_pred cCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccc
Q psy5925 327 QWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRIT 406 (696)
Q Consensus 327 ~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~ 406 (696)
..+ | -.+..|..+++|++||.+|+++++++|||||+|||+++||||||.+||+.+|++.+...+|..
T Consensus 48 -~~~----~--------i~~~~v~~~~~E~~lL~~f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~ 114 (199)
T cd05160 48 -DIE----F--------IDGIEVEYFADEKELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRS 114 (199)
T ss_pred -cCC----C--------CCCceEEEeCCHHHHHHHHHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCccccccccc
Confidence 000 0 025678899999999999999999999999999999999999999999999998863444443
Q ss_pred cccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHH
Q psy5925 407 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEH 486 (696)
Q Consensus 407 ~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y 486 (696)
..... .+......+.||+++|+|..+|+..++++|+|++||+++||.+|++++++.+.+|+..+ .+.++++|
T Consensus 115 ~~~~~-----~~~~~~~~~~gr~~~D~~~~~r~~~~l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~---~~~~~~~Y 186 (199)
T cd05160 115 GGEKS-----SGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEE---DPERLIEY 186 (199)
T ss_pred CCCcc-----CCcccceeeeccEeeehHHHHHHhcCcccCCHHHHHHHHhCCCCCcCCHHHHhhccCcc---hHHHHHHH
Confidence 22211 12345678999999999999999999999999999999999999999999998863333 48999999
Q ss_pred HHHHHHHHHHHH
Q psy5925 487 YLIRVTGIIRLI 498 (696)
Q Consensus 487 ~l~D~~l~~~L~ 498 (696)
|++||.++++|+
T Consensus 187 ~~~D~~~~~~l~ 198 (199)
T cd05160 187 NLKDAELTLQIL 198 (199)
T ss_pred HHHHHHHHHHhh
Confidence 999999999986
No 26
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=99.95 E-value=3.4e-27 Score=253.31 Aligned_cols=216 Identities=25% Similarity=0.444 Sum_probs=145.4
Q ss_pred chhhHHHHH-HHhcCCc-cccccccccccCCCCCCccccccCCCCccccc-cccc-CCCceEEEEEEEeecCCCCCCCCC
Q psy5925 190 NPDLFKSFI-RKQLETP-KRRICDSYAIDAMTPDTTGDYQMGLDNLNEVT-SHVE-NYYLTVLAVEIHAISRALLKPDPA 265 (696)
Q Consensus 190 ~~~l~~~~l-~r~~~~p-~~~~~~~~~I~~~t~~~~~gfk~~~~~~~~~~-~~~~-~~~LtilsleIe~~sr~~~~Pdp~ 265 (696)
.....++|| .+.|.++ +.++..... ......+++..++.+....... .... .|++++|||||||.++++.+|+|.
T Consensus 99 ~i~~~~rfl~~~~i~~~~wi~i~~~~~-~~~~~~s~~~~e~~~~~~~~~~~~~~~~~p~l~i~s~DIe~~~~~~~~P~~~ 177 (325)
T PF03104_consen 99 DIPPLERFLIDRNIRGPGWIKIKNPSK-PVKDRVSWCDIEFSVDYSNLKPLPDESIPPPLRILSFDIETYSNDGKFPDPE 177 (325)
T ss_dssp SS-HHHHHHHHTTHCTTEEEEEETTEC-HHHHHTCTCSCECECCHHHHECHTSSSSGGGSEEEEEEEEECSSSSSS-TTT
T ss_pred CCCHHHheeeecCcccceeeecccccc-ccccccccccccccccccccccccccccccccceeEEEEEEccccCCCCCCC
Confidence 455677788 7788888 665554310 0011245666666554222211 1122 299999999999999998899999
Q ss_pred CCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhccccCCCcccccccccccccCc
Q psy5925 266 YDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGY 345 (696)
Q Consensus 266 ~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~~ 345 (696)
.|+|.||++++++....+.....++.+.+ ++.. ..
T Consensus 178 ~d~I~~Is~~~~~~~~~~~~~~~~~~~~~---------------------------------~~~~------------~~ 212 (325)
T PF03104_consen 178 KDEIIMISYVVYRNGSSEPYRRKVFTLGS---------------------------------CDSI------------ED 212 (325)
T ss_dssp TSEEEEEEEEEEETTEEETTEEEEEECSC---------------------------------SCCT------------TC
T ss_pred CCeEEEEEEEEEeccccCCCceEEEEecC---------------------------------CCCC------------CC
Confidence 99999999999866311111112222111 1100 01
Q ss_pred ceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccc-------cccccccccCCCcc
Q psy5925 346 LLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR-------ITEVEKRNSSRDEV 418 (696)
Q Consensus 346 ~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR-------~~~~~~~~~~~~~~ 418 (696)
+..|..|++|++||.+|+++|+++|||||+|||+++||||||++||+.+|++.+...++ +..........+.+
T Consensus 213 ~~~v~~~~~E~~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 (325)
T PF03104_consen 213 NVEVIYFDSEKELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSR 292 (325)
T ss_dssp TTEEEEESSHHHHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCT
T ss_pred CcEEEEECCHHHHHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCc
Confidence 56888999999999999999999999999999999999999999999998886533332 22111111112334
Q ss_pred ccceeeecccEEEehHHHHhhhcCCCCCCHHHH
Q psy5925 419 KNTQLQMPGRIVINLWRLLRHEVNLQSYTFENI 451 (696)
Q Consensus 419 ~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~V 451 (696)
+.....++||+++|+|+++|+.+++++|+|++|
T Consensus 293 ~~~~~~~~Gr~~~D~~~~~~~~~~l~sY~L~~V 325 (325)
T PF03104_consen 293 KFSRIDIPGRLVLDLYRLARKDYKLDSYSLDNV 325 (325)
T ss_dssp TEEEEEETTSEEEEHHHHHHHHS--SS-SHHHH
T ss_pred ceeEEEECCChHhHHHHHHHhhCCCCCCCCCCC
Confidence 566789999999999999999999999999987
No 27
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=99.95 E-value=2e-26 Score=231.46 Aligned_cols=187 Identities=17% Similarity=0.185 Sum_probs=143.7
Q ss_pred CCCceEEEEEEEeecCC-CCCCCCCC--CcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhh
Q psy5925 242 NYYLTVLAVEIHAISRA-LLKPDPAY--DEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELF 318 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~-~~~Pdp~~--D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~ 318 (696)
.|+|++|||||||.+.. +.||+|+. |+|++|++. .++. ...+++++...... +.
T Consensus 2 ~P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~-~~~~-----~~~v~~~~~~~~~~------~~----------- 58 (204)
T cd05783 2 IPKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA-GSDG-----LKRVLVLKREGVEG------LE----------- 58 (204)
T ss_pred CCCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc-CCCC-----CcEEEEEecCCccc------cc-----------
Confidence 58999999999999865 68999998 799888864 1121 23466664421100 00
Q ss_pred hhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCC
Q psy5925 319 STFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNL 398 (696)
Q Consensus 319 ~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~ 398 (696)
. + ...+..|..|.+|++||.+|+++++++ |+|+|||+.+||||||.+||+.+|+..
T Consensus 59 ---------~--------~-----~~~~~~v~~~~~E~~lL~~F~~~i~~~--~~iig~N~~~FDlpyl~~R~~~~gi~~ 114 (204)
T cd05783 59 ---------G--------L-----LPEGAEVEFFDSEKELIREAFKIISEY--PIVLTFNGDNFDLPYLYNRALKLGIPK 114 (204)
T ss_pred ---------c--------c-----CCCCCeEEecCCHHHHHHHHHHHHhcC--CEEEEeCCCCcCHHHHHHHHHHhCCCh
Confidence 0 0 002456889999999999999999987 589999999999999999999999873
Q ss_pred c---ccccccccccccccCCCccccceeeecccEEEehHHHHhhh--------cCCCCCCHHHHHHHHcCCCcCCCChhh
Q psy5925 399 N---QELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHE--------VNLQSYTFENIMYHVLHERIPLHSWKL 467 (696)
Q Consensus 399 ~---~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~--------~kl~sysL~~Va~~~L~~~k~~~~~~~ 467 (696)
. ..++| ....+.||+++|+++.++.. .++.+|+|++||+++||++|.+++ .+
T Consensus 115 ~~~~~~~~~----------------~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va~~~lg~~K~~~~-~~ 177 (204)
T cd05783 115 EEIPIYLKR----------------DYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREYTLDAVAKALLGEGKVELE-KN 177 (204)
T ss_pred hhCceeecC----------------CceeccCcEEeECHHHhhccchhhhhhccccccCcHHHHHHHhcCCCcccCC-ch
Confidence 2 11222 23568999999999987652 167999999999999999999997 55
Q ss_pred HHHHHhcCCcccHHHHHHHHHHHHHHHHHHHH
Q psy5925 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE 499 (696)
Q Consensus 468 l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~ 499 (696)
+.++ .+.++++||++||.++++|++
T Consensus 178 i~~~-------~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 178 ISEL-------NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred hhhh-------cHHHHHHhhHHHHHHHHHHhc
Confidence 6655 268999999999999999864
No 28
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=99.95 E-value=1.6e-28 Score=276.77 Aligned_cols=157 Identities=36% Similarity=0.509 Sum_probs=115.9
Q ss_pred cchhhhHHHhhcccccCCeeeeCCchh-----hhhccCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccC
Q psy5925 525 GSQFRVESIMLRLSRLNNFVAVSPSIK-----QRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFST 599 (696)
Q Consensus 525 Gs~~rvEslLlr~~~~~~~i~p~p~~~-----q~~~~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT 599 (696)
|||+|||++|+++|+++|+++|++... ....+++.|.||+|++|++|+|++++.||||+|||||||++|||||||
T Consensus 1 gq~~~v~~~ll~~~~~~~~~~p~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G~~~~v~~~lDF~SLYPsii~~~Ni~~~T 80 (466)
T PF00136_consen 1 GQQIRVESLLLREAHRRNYIIPSKKERPEGFTSKSEQKEKYEGGYVLEPKPGLYENVVSVLDFASLYPSIIIAYNICPET 80 (466)
T ss_dssp -CHHHHHHHHHHHHHHTTBE-B-HHHHHHTHHHHHHHCTCEEEC-BE--HSSEEEEEEEEEEETTHHHHHHHHTTHSTTT
T ss_pred CchhhHHHHHHHHHHHCCEEeeCCcccccccccccccccccccceeeccccccccCceeeeecccccHHHHHhccCCcce
Confidence 899999999999999999999887654 223467899999999999999998666899999999999999999999
Q ss_pred cccccccCCCCCCCCCcccccccChhHHhhcccceeeCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHH
Q psy5925 600 CLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSES 679 (696)
Q Consensus 600 ~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~ 679 (696)
+++....... .+.+.........+...+++..|+++.+++||||++|+++++.|+++|+.|++.+++..
T Consensus 81 ~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gilp~~l~~~l~~R~~~K~~~~~~~~~~~ 149 (466)
T PF00136_consen 81 IVDDDECKDN-----------EVSPDIKYDYGPFIVGSPVGVRFVKKGVRPGILPEILEELLEKRKEIKKLMKKAKDPDE 149 (466)
T ss_dssp BTCTTHCSSE-----------EEHTTCCCCTCEEEECSCCSEEEESSTCSHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_pred Eecchhhhcc-----------cccccccccccceeecCCceeeecccCcccccChHHHHHHHHHHHHHhhhhhhhccchh
Confidence 9986410000 00000000001123345678899999999999999999999999999999999877654
Q ss_pred HHHH---------hhhcccccc
Q psy5925 680 LRNL---------TMLNSMLLI 692 (696)
Q Consensus 680 l~~~---------l~ansmy~~ 692 (696)
++.+ +.|||+||.
T Consensus 150 ~~~~~d~~Q~a~Ki~~NS~YG~ 171 (466)
T PF00136_consen 150 EYAILDARQLALKIIANSFYGY 171 (466)
T ss_dssp HHHHHHHHHHHHHHHHTTHHHH
T ss_pred hHHHHHHHHHhhcccceeeEee
Confidence 2222 456999994
No 29
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=99.94 E-value=4.6e-27 Score=258.08 Aligned_cols=114 Identities=32% Similarity=0.514 Sum_probs=95.8
Q ss_pred CCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeC
Q psy5925 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTIS 637 (696)
Q Consensus 558 ~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~ 637 (696)
++|.||+|+||++|||++||++|||+|||||||++|||||||+++..+.. + .+ .+++..+
T Consensus 1 ~~Y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~------~-------~~-------~~~~~~~ 60 (393)
T cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAK------K-------LP-------PEDYIKT 60 (393)
T ss_pred CCCCCeEeccCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCcccc------c-------CC-------CcceEEC
Confidence 36899999999999999999999999999999999999999998743210 0 01 2457788
Q ss_pred CCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 638 PSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 638 p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
|+|.+|++++.++||||++|++|+++|+++|++||+.+| +.++++ +.||||||.
T Consensus 61 p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d-~~~~~~ld~~Q~AlKi~~NS~YG~ 123 (393)
T cd05533 61 PNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETD-PFKKAVLDGRQLALKISANSVYGF 123 (393)
T ss_pred CCCceeecCCCCCCchHHHHHHHHHHHHHHHHHHhhCCC-HHHHHHHHHHHHhhheeeeecccc
Confidence 999999998889999999999999999999999998764 444443 456999995
No 30
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=99.91 E-value=5.4e-25 Score=240.14 Aligned_cols=107 Identities=30% Similarity=0.428 Sum_probs=89.5
Q ss_pred CCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeC
Q psy5925 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTIS 637 (696)
Q Consensus 558 ~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~ 637 (696)
.+|.||+|+||++|+|++ |++|||+|||||||++|||||||+++..++ +.....
T Consensus 2 ~~y~Gg~V~~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~-------------------------~~~~~~ 55 (371)
T cd05536 2 ESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCE-------------------------DCDVEP 55 (371)
T ss_pred CCCCceEEeCCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCcc-------------------------ccccCC
Confidence 579999999999999986 999999999999999999999999864221 111123
Q ss_pred CCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 638 PSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 638 p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
++|+.|++. ++||+|++|++|+++|.++|+.||+.++++.++++ +.||||||.
T Consensus 56 ~~~~~f~~~--~~Gilp~il~~ll~~R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~ 117 (371)
T cd05536 56 QVGHKFRKD--PPGFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGY 117 (371)
T ss_pred CCCcEEecC--CCCchHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHhccccc
Confidence 489999986 89999999999999999999999998877555444 456999995
No 31
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=99.90 E-value=1.4e-24 Score=239.03 Aligned_cols=108 Identities=32% Similarity=0.440 Sum_probs=86.4
Q ss_pred cCCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhccccee
Q psy5925 556 MRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLT 635 (696)
Q Consensus 556 ~~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~ 635 (696)
...+|.||+|+||++|+|++||++|||+|||||||++|||||||+++..+... ..
T Consensus 4 ~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~-------------------------~~ 58 (400)
T cd05532 4 KKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDE-------------------------DD 58 (400)
T ss_pred ccCCcCCceeecCCCCcccCceEEEeccccchHHHHHhcCChhhccccccccc-------------------------CC
Confidence 45789999999999999999999999999999999999999999997432110 00
Q ss_pred eCCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 636 ISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 636 ~~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
..+++.| ...++||||++|++|+++|.++|+.||+.+++ .++++ +.|||+||.
T Consensus 59 -~~~~~~~--~~~~~Gilp~~l~~l~~~R~~~K~~~k~~~d~-~~~~~~d~~Q~alKi~~NS~YG~ 120 (400)
T cd05532 59 -EEPPLPP--SDQEKGILPRIIRKLVERRRQVKKLMKSEKDP-DKKAQLDIRQLALKLTANSMYGC 120 (400)
T ss_pred -ccccccc--cccCCCchHHHHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHHHHHhhcccc
Confidence 0123334 44589999999999999999999999988743 44333 456999996
No 32
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=99.90 E-value=3.4e-24 Score=230.14 Aligned_cols=108 Identities=37% Similarity=0.542 Sum_probs=87.2
Q ss_pred CCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeC
Q psy5925 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTIS 637 (696)
Q Consensus 558 ~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~ 637 (696)
+.|.||+|+||++|+|+ ||++|||+|||||||++|||||||+++..+.... + .
T Consensus 1 ~~y~Gg~V~~P~~G~~~-~V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~~~----------------------~----~ 53 (323)
T cd00145 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAP----------------------E----D 53 (323)
T ss_pred CCCCCcEEecCcccccC-ceEEeecCCccHHHHHHhCCCcccccccccccCc----------------------c----c
Confidence 36899999999999996 6999999999999999999999999874221100 0 0
Q ss_pred CCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 638 PSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 638 p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
+.+..|+...+++||+|++|++|+++|+++|+.||++++++.++++ +.||||||.
T Consensus 54 ~~~~~~~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~ 117 (323)
T cd00145 54 YIGVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGY 117 (323)
T ss_pred ccCccccccCCCCCCCHHHHHHHHHHHHHHHHHHhhCcCCHHHHHHHHHHhhhhheeeecceee
Confidence 1134555556699999999999999999999999999886766555 456999995
No 33
>KOG0969|consensus
Probab=99.89 E-value=5.6e-24 Score=235.51 Aligned_cols=145 Identities=29% Similarity=0.504 Sum_probs=116.2
Q ss_pred ccccceeeeehhHHHHHHhhhCCCCCCCCCccCC-CCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCc
Q psy5925 57 DSMKGIVDVKCFEESSLERSMKPDDRPSPTRKNK-STRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCF 135 (696)
Q Consensus 57 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~ 135 (696)
.+..|| ++.++ |+|+|+|++.++++|+.+.. +.++.|+|++|+ +|.+|||+.||++||||||||||||||||||
T Consensus 510 LltRGq-qIKVl--SqLlRkakq~~~~~P~i~~~~s~~e~yEGatVI--Ep~kGfY~~PIATLDFaSLYPSIMmahNLCY 584 (1066)
T KOG0969|consen 510 LLTRGQ-QIKVL--SQLLRKAKQKDFVIPNIKSQGSDDEQYEGATVI--EPRKGFYDKPIATLDFASLYPSIMMAHNLCY 584 (1066)
T ss_pred HHhCCc-chHHH--HHHHHHHhhcCeeeeeecccCCccccccccEEe--ecccccCCCCceeeehhhhhhHHHHHhhhhh
Confidence 345677 89998 99999999999999999865 334799999999 9999999999999999999999999999999
Q ss_pred ccccc--ccCCCCCCCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH--HHh----c---CC
Q psy5925 136 STCLG--RVEHLGVSDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI--RKQ----L---ET 204 (696)
Q Consensus 136 ~t~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~----~---~~ 204 (696)
+||+. ..+.++.+||. ++|.| . +||+ +++++++++++++.+| ||. + .|
T Consensus 585 tTLl~~~t~~~l~~~~~~-----------~TP~g-~---yFv~------~~~rkGlLP~ILe~ll~aRKraK~dlk~ekD 643 (1066)
T KOG0969|consen 585 TTLLTKETVEKLGDEDYT-----------RTPTG-D---YFVK------TEVRKGLLPEILEDLLTARKRAKADLKKEKD 643 (1066)
T ss_pred eeccccchhhhcCcccee-----------ECCCC-C---eeee------hhhhccccHHHHHHHHHHHHHHHHHHHhccC
Confidence 99997 35666644443 23334 3 3888 9999999999999999 442 2 58
Q ss_pred c-ccccccccc--ccCCCCCCcccccc
Q psy5925 205 P-KRRICDSYA--IDAMTPDTTGDYQM 228 (696)
Q Consensus 205 p-~~~~~~~~~--I~~~t~~~~~gfk~ 228 (696)
| ++.+++--| ++- +-++.|||.=
T Consensus 644 p~kr~vldGRQLAlKi-sANSvYGFTG 669 (1066)
T KOG0969|consen 644 PFKRAVLDGRQLALKI-SANSVYGFTG 669 (1066)
T ss_pred HHHHhhhcchhhheee-cccccccccc
Confidence 8 666666555 222 4467899973
No 34
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.88 E-value=3.5e-23 Score=224.75 Aligned_cols=109 Identities=24% Similarity=0.380 Sum_probs=84.2
Q ss_pred CCCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceee
Q psy5925 557 RAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTI 636 (696)
Q Consensus 557 ~~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~ 636 (696)
..+|.||+||+|++|+|++ |++|||+|||||||++|||||||++...+.. ....+
T Consensus 10 ~~~y~Gg~V~~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~~~~~------------------------~~~~~ 64 (372)
T cd05530 10 GKKYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCEC------------------------KTNEV 64 (372)
T ss_pred CCCCCCCEeecCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccCcccc------------------------cceec
Confidence 3579999999999999998 9999999999999999999999998632100 01122
Q ss_pred CCCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCC-CHHHHHH---------hhhcccccc
Q psy5925 637 SPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKF-SESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 637 ~p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~-~~~l~~~---------l~ansmy~~ 692 (696)
...++.|++. ++||+|++|++|++.|+++|+.|++.+. ++.++++ +.|||+||.
T Consensus 65 p~~~~~~~~~--~~Gilp~il~~L~~~R~~~~k~~~k~~~~d~~~~~~ld~~Q~alKi~~NS~YG~ 128 (372)
T cd05530 65 PEVGHWVCKK--RPGITSQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGV 128 (372)
T ss_pred CCCCceEEec--CCCccHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHhccccc
Confidence 2255677775 8999999999999999998666654433 5555544 445999995
No 35
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.88 E-value=4.7e-23 Score=222.95 Aligned_cols=106 Identities=28% Similarity=0.389 Sum_probs=87.1
Q ss_pred CCCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeC
Q psy5925 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTIS 637 (696)
Q Consensus 558 ~~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~ 637 (696)
..|.||+|+||++|+|++ |++|||+|||||||++|||||+|+.+..+.. .. ..
T Consensus 3 ~~~~Gg~V~~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~~~~~-----------------------~~---~~ 55 (352)
T cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCEC-----------------------RD---HV 55 (352)
T ss_pred cCCCCcEEecCCCCccCc-eEEEEccccchHHHHHhCCChhhccccCccc-----------------------cc---CC
Confidence 478999999999999987 9999999999999999999999998632100 01 12
Q ss_pred CCCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH--hhhcccccc
Q psy5925 638 PSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL--TMLNSMLLI 692 (696)
Q Consensus 638 p~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~--l~ansmy~~ 692 (696)
+.++.|++. ++||+|++|++|+++|.++|+.||..++....|.. +.|||+||.
T Consensus 56 ~~~~~~~~~--~~gilp~~l~~l~~~R~~~K~~~k~~~~~d~~q~AlKi~~NS~YGy 110 (352)
T cd05531 56 YLGHRICLK--RRGFLPEVLEPLLERRLEYKRLKKEEDPYAGRQKALKWILVTSFGY 110 (352)
T ss_pred CCCceEecC--CCCchHHHHHHHHHHHHHHHHHhhcCCCchHHHhhheeeeeccccc
Confidence 567778775 89999999999999999999999987655444444 678999995
No 36
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=99.86 E-value=2.6e-22 Score=218.51 Aligned_cols=105 Identities=22% Similarity=0.345 Sum_probs=82.7
Q ss_pred CCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeCC
Q psy5925 559 PESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISP 638 (696)
Q Consensus 559 ~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p 638 (696)
...||+|+||++|+|++ |++|||+|||||||++|||||+|++...... . .+....+|
T Consensus 2 ~~~Gg~V~eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~~~~---~-------------------~~~~~~~~ 58 (371)
T cd05537 2 SSPGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAP---D-------------------PEDLIPGF 58 (371)
T ss_pred CCCCcEEeCCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCCCCC---C-------------------ccccccCC
Confidence 35799999999999986 9999999999999999999999987532110 0 12334567
Q ss_pred CCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHhhhcccccc
Q psy5925 639 SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNLTMLNSMLLI 692 (696)
Q Consensus 639 ~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~l~ansmy~~ 692 (696)
+|..|++. +||||++|++|+++|+++|+.|+... +.-.| +.||||||.
T Consensus 59 ~~~~f~~~---~Gilp~~l~~l~~~R~~~K~~~~~~~--q~AlK-i~~Ns~YG~ 106 (371)
T cd05537 59 LGARFSRE---KHILPDLIARLWAARDEAKREKNAPL--SQAIK-IIMNSFYGV 106 (371)
T ss_pred CCCeEecC---CCchHHHHHHHHHHHHHHHHhccHHH--HHhHh-hheecceee
Confidence 89999885 59999999999999999999886421 11222 457999995
No 37
>KOG0968|consensus
Probab=99.86 E-value=2.3e-23 Score=237.69 Aligned_cols=149 Identities=35% Similarity=0.534 Sum_probs=121.6
Q ss_pred cceeeeeh-------hHHHHHHhhhCCCCC--CCCCccCCCCcCCCCC-ccccCCCCCCCcccCceeeeeccccchhhhh
Q psy5925 60 KGIVDVKC-------FEESSLERSMKPDDR--PSPTRKNKSTRSSFDS-DMFPSSSSRDRLYTDPIIVLDFQSLYPSVII 129 (696)
Q Consensus 60 ~~~~~~~~-------~~~~~l~~~~~~~~~--~~p~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~ 129 (696)
-|+.+|+| .|||+|+|.|+++|| ++|..+++..+.+.+. .+|. +|+..||.+||+||||+|||||||+
T Consensus 901 ~GIdF~sV~tRGSQ~rVESmllRiAk~~Nyi~~SPs~kQv~~q~A~EcvPLVM--EPeS~fY~~PViVLDFQSLYPSivI 978 (1488)
T KOG0968|consen 901 IGIDFHSVLTRGSQFRVESMLLRIAKPMNYIAPSPSHKQVAMQGAPECVPLVM--EPESAFYFDPVIVLDFQSLYPSIVI 978 (1488)
T ss_pred hcceeeEEeeccchhhHHHHHHHHhcccccccCCccHHHHhhcCCccccceee--cchhhhccCceEEEEchhhcchHHH
Confidence 34445554 599999999999998 4666677666666654 3444 7788999999999999999999999
Q ss_pred hhccCccccccccCCCCCCCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHHHHhcCCc-ccc
Q psy5925 130 AYNYCFSTCLGRVEHLGVSDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFIRKQLETP-KRR 208 (696)
Q Consensus 130 ~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~r~~~~p-~~~ 208 (696)
||||||||+++.+++++..|-+.+|++ +..+|++ ++...++++++||||.++++++++++.|.||+++. .+|
T Consensus 979 AYNyCySTcLG~v~~l~~~~e~~LG~s----~~s~~~d---il~~~~ndV~isPNgv~yVK~sVRkgvLpkmLeEIL~tR 1051 (1488)
T KOG0968|consen 979 AYNYCYSTCLGKVGNLNQMNEIKLGVS----KYSLPPD---ILVLAKNDVTISPNGVMYVKPSVRKGVLPKMLEEILATR 1051 (1488)
T ss_pred hHHHHHHHhhhHHHhhccccceeeeee----eccCCHH---HHHHHhcceeeCCCceEEechhhhhhhHHHHHHHHHHHH
Confidence 999999999999999988776677774 3456767 44457889999999999999999999999998888 777
Q ss_pred ccccccccC
Q psy5925 209 ICDSYAIDA 217 (696)
Q Consensus 209 ~~~~~~I~~ 217 (696)
++.+.+.+.
T Consensus 1052 iMVKkaMK~ 1060 (1488)
T KOG0968|consen 1052 IMVKKAMKR 1060 (1488)
T ss_pred HHHHHHHHH
Confidence 777766433
No 38
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=99.84 E-value=9.6e-20 Score=183.81 Aligned_cols=134 Identities=13% Similarity=0.021 Sum_probs=112.0
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
.+.+|++||.+|+++|++++| +|+|||+.+||||||..||..+|++....+++-.. +. .....+.|| |
T Consensus 74 ~~~~E~elL~~F~~~i~~~~p-~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~---~~-------~y~~r~~~~-h 141 (208)
T cd05782 74 DGADEKELLEDFFQLIEKKNP-RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNK---DW-------NYRNRYSER-H 141 (208)
T ss_pred CCCCHHHHHHHHHHHHHHhCC-EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccc---hh-------hccCcCCCC-c
Confidence 357899999999999999988 89999999999999999999999975533443221 00 011234688 9
Q ss_pred EehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHH
Q psy5925 431 INLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE 499 (696)
Q Consensus 431 lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~ 499 (696)
+|++..++...++.+++|++||+.+...+|.++++.++.++|.+++ +.++++||.+||..++.|+.
T Consensus 142 ~DL~~~~~~~~~~~~~~L~~va~~lG~~~K~d~~G~~v~~~y~~g~---~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 142 LDLMDLLAFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGK---LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred ccHHHHHhccCccCCCCHHHHHHHhCCCCCcCCCHHHHHHHHHcCC---hHHHHHHHHHHHHHHHHHHh
Confidence 9999999887778999999999976667999999999999999875 89999999999999999875
No 39
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=99.79 E-value=4.6e-20 Score=223.48 Aligned_cols=143 Identities=23% Similarity=0.393 Sum_probs=108.0
Q ss_pred ccceeeeehhHHHHHHhhhCCCCCCCCCccCC--CCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCcc
Q psy5925 59 MKGIVDVKCFEESSLERSMKPDDRPSPTRKNK--STRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFS 136 (696)
Q Consensus 59 ~~~~~~~~~~~~~~l~~~~~~~~~~~p~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~ 136 (696)
..|| ++ .|||+|+|+|+++|+++|+++.. ....+|+||+|. +|++|+|.+||+||||+|||||||||||||||
T Consensus 504 ~rG~-q~--kv~s~Llr~~~~~~~viP~~~~~~~~~~~~yeGg~Vl--eP~~G~y~~pV~vLDF~SLYPSIiia~Nlcys 578 (1054)
T PTZ00166 504 TRGQ-QI--KVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEGATVL--EPKKGFYDEPIATLDFASLYPSIMIAHNLCYS 578 (1054)
T ss_pred cCCc-ch--hHHHHHHHHHHhcCeeccCchhccccccCCCCCceee--cCCCCCeeCceEEeecCCcccHHHHhcCCCcc
Confidence 4455 55 45699999999999999988742 345789999999 99999999999999999999999999999999
Q ss_pred ccccccC--CCCCCCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH--HHh-------cCCc
Q psy5925 137 TCLGRVE--HLGVSDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI--RKQ-------LETP 205 (696)
Q Consensus 137 t~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~-------~~~p 205 (696)
|+++..+ .++.+++. ..+++ +.|++ ++++.++++.+++.+| |++ ..||
T Consensus 579 Tl~~~~~~~~~~~~~~~------------~~p~g---~~Fv~------~~~r~Gilp~iL~~Ll~~R~~~K~~mk~~~d~ 637 (1054)
T PTZ00166 579 TLVPPNDANNYPEDTYV------------TTPTG---DKFVK------KEVRKGILPLIVEELIAARKKAKKEMKDEKDP 637 (1054)
T ss_pred eeecchhhccCCCccee------------ecCCC---ceeee------cCCCCcccHHHHHHHHHHHHHHHHHHhhCCCH
Confidence 9987532 23322111 11243 24898 9999999999999999 332 2477
Q ss_pred -ccccccccc--ccCCCCCCcccccc
Q psy5925 206 -KRRICDSYA--IDAMTPDTTGDYQM 228 (696)
Q Consensus 206 -~~~~~~~~~--I~~~t~~~~~gfk~ 228 (696)
+.++++..| ++- +.++.||+.-
T Consensus 638 ~~~~~ld~rQ~AlKi-~aNS~YG~~G 662 (1054)
T PTZ00166 638 LLKKVLNGRQLALKI-SANSVYGYTG 662 (1054)
T ss_pred HHHHHHHHHHHhhhh-hccccccccc
Confidence 555555555 444 5577888864
No 40
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=99.78 E-value=1.3e-19 Score=195.72 Aligned_cols=84 Identities=24% Similarity=0.319 Sum_probs=72.3
Q ss_pred CCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCcccccccCCCCCCCCCcccccccChhHHhhcccceeeCC
Q psy5925 559 PESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISP 638 (696)
Q Consensus 559 ~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~d~i~~~p 638 (696)
+|+||+|++|++|+|++ |++|||+|||||||++|||||+.
T Consensus 2 ~~~GG~v~~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~~--------------------------------------- 41 (347)
T cd05538 2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRICPAR--------------------------------------- 41 (347)
T ss_pred CcCCceEcccCCcCcCc-eEEEEcccchHHHHHHhCCCCCC---------------------------------------
Confidence 57899999999999986 99999999999999999999741
Q ss_pred CCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHH---------hhhcccccc
Q psy5925 639 SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNL---------TMLNSMLLI 692 (696)
Q Consensus 639 ~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~~l~~~---------l~ansmy~~ 692 (696)
.+.||+|++|++|++.|.++|+.||+.++. ..+.+ +.+|||||.
T Consensus 42 ---------~~~Gilp~il~~Ll~~R~~~K~~~k~~~~~-~~~~~~d~~Q~AlKi~~NS~YG~ 94 (347)
T cd05538 42 ---------DSLGIFLALLKYLVELRLAAKESARAAARP-AERDAFKAKQAAFKVLINSFYGY 94 (347)
T ss_pred ---------CCCcccHHHHHHHHHHHHHHHHHHhcCCCh-HHHHHHHHHHHHHhhhhhhchhh
Confidence 157999999999999999999999987753 33333 556999995
No 41
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=99.78 E-value=1.1e-19 Score=202.78 Aligned_cols=147 Identities=34% Similarity=0.501 Sum_probs=97.1
Q ss_pred hHHHHHHhhhCCCCCCCCCccCC--CC-cCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccCC
Q psy5925 68 FEESSLERSMKPDDRPSPTRKNK--ST-RSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEH 144 (696)
Q Consensus 68 ~~~~~l~~~~~~~~~~~p~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~~ 144 (696)
+|||+|+|+|+++|+++|+.... .. ...++|++|. +|++|+|.+||+||||+||||||||+||+||||+++..++
T Consensus 5 rve~~llr~~~~~g~~~p~~~~~~~~~~~~~~~g~~V~--eP~~G~y~~~V~vLDF~SLYPSIi~~~Nic~sT~~~~~~~ 82 (451)
T cd05534 5 RVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVM--EPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRVEE 82 (451)
T ss_pred EeHHHHHHHHHHcCEEeecCchhccccccccccCcEee--cCCcCcccCceEEEecccccHHHHHHhCcCcccccccccc
Confidence 35599999999999999987422 22 2457899999 9999999999999999999999999999999999875433
Q ss_pred CCCCC-eeeeeec------------ccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH--HHh-------c
Q psy5925 145 LGVSD-SFPFGCI------------ASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI--RKQ-------L 202 (696)
Q Consensus 145 ~~~~~-~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~-------~ 202 (696)
....+ ....... ..+.-...| ++ ..|++ ++++.++++++++.|+ |++ .
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p-~~---~~f~~------~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~ 152 (451)
T cd05534 83 LNGGGKFGFLGVKLYLPPPPLDLLLLKDDVTISP-NG---VMFVK------KSVRKGILPKMLEEILDTRIMVKKAMKKY 152 (451)
T ss_pred cccccccccccccccccccccccccCCCcEEECC-Cc---ceeec------CCCCCCchHHHHHHHHHHHHHHHHHHhhC
Confidence 22110 0000000 000000112 32 24777 8889999999999999 332 2
Q ss_pred CC-c-ccccccccc--ccCCCCCCccccc
Q psy5925 203 ET-P-KRRICDSYA--IDAMTPDTTGDYQ 227 (696)
Q Consensus 203 ~~-p-~~~~~~~~~--I~~~t~~~~~gfk 227 (696)
.+ | ....++..| ++- +.++.||+-
T Consensus 153 ~~~~~~~~~ld~~Q~AlKi-~~NS~YGy~ 180 (451)
T cd05534 153 KDDKKLQRILDARQLALKL-LANVTYGYT 180 (451)
T ss_pred CCCHHHHHHHHHHHHHHHH-Hhhcccccc
Confidence 22 4 333334333 333 456677764
No 42
>PHA03036 DNA polymerase; Provisional
Probab=99.77 E-value=2e-19 Score=211.57 Aligned_cols=146 Identities=16% Similarity=0.269 Sum_probs=102.1
Q ss_pred ehhHHHHHHhhhCCCCCCCCCccCCCCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccC--
Q psy5925 66 KCFEESSLERSMKPDDRPSPTRKNKSTRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVE-- 143 (696)
Q Consensus 66 ~~~~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~-- 143 (696)
+.+++++|+|.|.++++++|... .....+|+||+|. +|++|+|.+||+||||+||||||||||||||+|+++...
T Consensus 501 s~~i~~qllr~~~~~~~i~p~~~-~~~~~~YeGa~Vl--EP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~ 577 (1004)
T PHA03036 501 STLIKGPLLKLLLEEKTILVRSE-TKNKFPYEGGKVF--APKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVND 577 (1004)
T ss_pred ccccccHHHHHHHHCCcccccCC-CCccCCcCceEEe--cCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccc
Confidence 45678999999999999998543 2222379999999 999999999999999999999999999999999986421
Q ss_pred --------------CCCCCCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH--HHh------
Q psy5925 144 --------------HLGVSDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI--RKQ------ 201 (696)
Q Consensus 144 --------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~------ 201 (696)
.++..||..+....+ . .+.. -+.|+. .+++.++++++++.|+ |++
T Consensus 578 ~~~~~~i~~~~i~~~~p~~dy~~v~~~~~-----~-~~~v-~~~~vf------~~~rkGILP~iL~~Ll~~Rk~~Kk~mK 644 (1004)
T PHA03036 578 NRLEAEINKQELRRKYPYPRYIYVHCEPR-----S-PDLV-SEIAVF------DRRIEGIIPKLLKTFLEERARYKKLLK 644 (1004)
T ss_pred cccccccccccccccCCCccceeeeccCC-----c-cccc-ccceee------cCCCCcChHHHHHHHHHHHHHHHHHHh
Confidence 112233333222110 0 0110 012344 6789999999999999 331
Q ss_pred -cCCc-ccccccccc--ccCCCCCCcccccc
Q psy5925 202 -LETP-KRRICDSYA--IDAMTPDTTGDYQM 228 (696)
Q Consensus 202 -~~~p-~~~~~~~~~--I~~~t~~~~~gfk~ 228 (696)
..+| +..+.+..| ++- +.++.||+--
T Consensus 645 ~~~d~~e~~~lD~rQlAlKI-~aNS~YG~~G 674 (1004)
T PHA03036 645 EATSSVEKAIYDSMQYTYKI-VANSVYGLMG 674 (1004)
T ss_pred hCCChHHHHHHHHHHHHHHH-HHhccccccc
Confidence 3566 555666655 444 6677888853
No 43
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=99.71 E-value=4.4e-18 Score=200.11 Aligned_cols=162 Identities=12% Similarity=0.103 Sum_probs=104.5
Q ss_pred hhhhccccccc--eeeeehhHHHHHHhhhC-CCCCCC-----------CCccCC--CCcCCCCCccccCCCCCCCc----
Q psy5925 51 RMRIRRDSMKG--IVDVKCFEESSLERSMK-PDDRPS-----------PTRKNK--STRSSFDSDMFPSSSSRDRL---- 110 (696)
Q Consensus 51 r~~~r~~~~~~--~~~~~~~~~~~l~~~~~-~~~~~~-----------p~~~~~--~~~~~~~~~~~~~~~~~~~~---- 110 (696)
+..+++.+++| | |++++ ++++++|+ ++|+++ |....+ +...+|+||+|+ +|++|+
T Consensus 575 ~l~RG~v~fdG~vQ-QIKV~--s~lL~kA~~~~~~~ia~~~i~~s~ilP~~~~~~~~~~~~YeGAtVL--EP~~Gf~~~~ 649 (1545)
T PHA03334 575 AHGRGVMNFCGFVQ-STKSV--EVPLLKARLRIGIFVATGRIAESLCMPEKYARDCRQKIKLKGGYVF--APLTGLTFAG 649 (1545)
T ss_pred ecccceecccCccc-hhhHH--HHHHHHHHHhcCcccccccccccccCCcccccccccccccCCeEee--cCCCCccccc
Confidence 34556788899 9 99999 77777777 666654 543222 223579999999 999999
Q ss_pred -ccCceeeeeccccchhhhhhhccCcccccccc--CCCC---CCCeeeeeecccccccCCCCCCCcceeeec--cCCccc
Q psy5925 111 -YTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRV--EHLG---VSDSFPFGCIASRESNQSPPNKDSIHEAEI--THPDCS 182 (696)
Q Consensus 111 -~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~--~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 182 (696)
|++||+||||+||||||||+|||||+|++... +.+. +.|+.+... + .+... ....+. +..+.+
T Consensus 650 ~Y~~PVaVLDFASLYPSIIiahNLCYeTLV~~~c~~~~~~~~~~d~~k~p~--g-----y~~~~--~vy~V~~~~~~~P~ 720 (1545)
T PHA03334 650 PYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTARVRGWVVFDWKKIDR--G-----FGKAT--LMYTILRTKPEEPS 720 (1545)
T ss_pred cCCCcEEEEEccccchHHHHHhCCCcccccCccchhhhccccccccccCCc--c-----cCccc--cceeeccccCcCCC
Confidence 67899999999999999999999999998642 1111 111110000 0 00000 000011 111122
Q ss_pred CCcccccchhhHHHHH--HHh-------cCCc-ccccccccc--ccCCCCCCccccc
Q psy5925 183 KSSQIDFNPDLFKSFI--RKQ-------LETP-KRRICDSYA--IDAMTPDTTGDYQ 227 (696)
Q Consensus 183 ~~~~~~~~~~l~~~~l--~r~-------~~~p-~~~~~~~~~--I~~~t~~~~~gfk 227 (696)
.+...++.+++++.|| |++ ..|| +..+.+..| ++- +.++.||+.
T Consensus 721 ~~rf~SiLp~LL~eLL~~RK~~Kk~MKk~kDp~er~iLD~rQlALKV-tANSvYGyt 776 (1545)
T PHA03334 721 WRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYHNQLQNEMKI-CANSHYGVA 776 (1545)
T ss_pred cceecchHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHH-HHHhhcCcc
Confidence 3445678999999999 332 3577 666677766 555 668899984
No 44
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=99.69 E-value=1.8e-17 Score=184.01 Aligned_cols=118 Identities=18% Similarity=0.189 Sum_probs=82.6
Q ss_pred eeehhHHHHHHhhhCCCCCCCCCccCCCCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccC
Q psy5925 64 DVKCFEESSLERSMKPDDRPSPTRKNKSTRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVE 143 (696)
Q Consensus 64 ~~~~~~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~ 143 (696)
++++| +++|+|+|+++|+++|+.+... .++|+||+|. +|++|+|.+ |++|||+||||||||||||||+|+++...
T Consensus 347 qikv~-~~lllr~~~~~g~viP~~~~~~-~~~Y~GA~V~--eP~~GlY~~-VivLDFaSLYPSII~a~NIsPeTl~~~~~ 421 (498)
T PHA02524 347 TIKVW-DSIIFNSLVESNVVIPAMKASP-KQSFPGAYVK--EPVPGGYRY-GLSFDLTSLYPSILRLLNISPEMIAGMFS 421 (498)
T ss_pred HHHHH-HHHHHHHHHHCCEecCCCCCCC-CCccCCeEEe--cCCCccccC-eEEEEccccCHHHHHHhCCCHHHhhcccc
Confidence 45554 6899999999999999987544 3789999999 999999998 56899999999999999999999976422
Q ss_pred CCCCCCeeeeeec-ccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH
Q psy5925 144 HLGVSDSFPFGCI-ASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI 198 (696)
Q Consensus 144 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l 198 (696)
.-...++...... .+++-..+| +|. .|+| .+.++.+++++.+|
T Consensus 422 ~~~~~~~~~~~~~~~~~~~~~~P-~G~---~F~K--------~~~GilP~iLe~Ll 465 (498)
T PHA02524 422 PARLEDYINKVAPKPSDQFSCAP-NGM---MYKK--------GVVGVLPNETEKVF 465 (498)
T ss_pred ccchhhhccccCCCCCcceEECC-CCC---EEec--------CCCcccHHHHHHHH
Confidence 1000011100000 000001123 332 3666 34899999999999
No 45
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=99.59 E-value=7.1e-16 Score=169.78 Aligned_cols=110 Identities=25% Similarity=0.480 Sum_probs=78.8
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccC--CCCCCCeeeeeecccccccCCCCCCCcc
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVE--HLGVSDSFPFGCIASRESNQSPPNKDSI 171 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (696)
+.|+||+|. +|++|+|.+||++|||+|||||||++||+||+|++.... .++..++. ..| ++
T Consensus 1 ~~Y~Gg~V~--eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~~~~~~~~~-----------~~p-~~--- 63 (393)
T cd05533 1 EQYEGATVI--EPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLPPEDYI-----------KTP-NG--- 63 (393)
T ss_pred CCCCCeEec--cCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCcccccCCCcceE-----------ECC-CC---
Confidence 479999999 999999999999999999999999999999999987522 22222221 122 32
Q ss_pred eeeeccCCcccCCcccccchhhHHHHH--HHh-------cCCc-ccccccccc--ccCCCCCCccccc
Q psy5925 172 HEAEITHPDCSKSSQIDFNPDLFKSFI--RKQ-------LETP-KRRICDSYA--IDAMTPDTTGDYQ 227 (696)
Q Consensus 172 ~~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~-------~~~p-~~~~~~~~~--I~~~t~~~~~gfk 227 (696)
+.|++ ++.+.++.+.+++.|+ |++ ..|| .....+..| ++- ..++.||+-
T Consensus 64 ~~f~~------~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~ld~~Q~AlKi-~~NS~YG~~ 124 (393)
T cd05533 64 DYFVK------SSVRKGLLPEILEELLAARKRAKKDLKEETDPFKKAVLDGRQLALKI-SANSVYGFT 124 (393)
T ss_pred ceeec------CCCCCCchHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhhhe-eeeeccccc
Confidence 34777 8889999999999999 332 2356 333444444 333 556677774
No 46
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=99.58 E-value=1.6e-16 Score=179.43 Aligned_cols=113 Identities=26% Similarity=0.370 Sum_probs=83.3
Q ss_pred hhHHHHHHhhhCCCCCCCCCccCC--------CCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCcccc
Q psy5925 67 CFEESSLERSMKPDDRPSPTRKNK--------STRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTC 138 (696)
Q Consensus 67 ~~~~~~l~~~~~~~~~~~p~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~ 138 (696)
.++|++|++.|+++|+++|..... .....|+|++|. +|++|+|.+++++|||+|||||||++||+||+|+
T Consensus 4 ~~v~~~ll~~~~~~~~~~p~~~~~~~~~~~~~~~~~~y~Gg~V~--~P~~G~~~~v~~~lDF~SLYPsii~~~Ni~~~T~ 81 (466)
T PF00136_consen 4 IRVESLLLREAHRRNYIIPSKKERPEGFTSKSEQKEKYEGGYVL--EPKPGLYENVVSVLDFASLYPSIIIAYNICPETI 81 (466)
T ss_dssp HHHHHHHHHHHHHTTBE-B-HHHHHHTHHHHHHHCTCEEEC-BE----HSSEEEEEEEEEEETTHHHHHHHHTTHSTTTB
T ss_pred hhHHHHHHHHHHHCCEEeeCCcccccccccccccccccccceee--ccccccccCceeeeecccccHHHHHhccCCcceE
Confidence 456799999999999999987755 234789999999 9999999997779999999999999999999999
Q ss_pred cccc----CCCCC---CCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH
Q psy5925 139 LGRV----EHLGV---SDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI 198 (696)
Q Consensus 139 ~~~~----~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l 198 (696)
+... ..+.. .++..+.... + . -..|++ ++++.++++++++.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~---------~-~-~~~~~~------~~~~~gilp~~l~~~l 131 (466)
T PF00136_consen 82 VDDDECKDNEVSPDIKYDYGPFIVGS---------P-V-GVRFVK------KGVRPGILPEILEELL 131 (466)
T ss_dssp TCTTHCSSEEEHTTCCCCTCEEEECS---------C-C-SEEEES------STCSHHHHHHHHHHHH
T ss_pred ecchhhhcccccccccccccceeecC---------C-c-eeeecc------cCcccccChHHHHHHH
Confidence 9875 11211 1222222211 1 1 234666 8899999999999999
No 47
>PRK05761 DNA polymerase I; Reviewed
Probab=99.58 E-value=1.1e-15 Score=181.08 Aligned_cols=74 Identities=18% Similarity=0.294 Sum_probs=65.9
Q ss_pred eehhHHHHHHhhhCCCCCCCCCccC----CC--------CcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhc
Q psy5925 65 VKCFEESSLERSMKPDDRPSPTRKN----KS--------TRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYN 132 (696)
Q Consensus 65 ~~~~~~~~l~~~~~~~~~~~p~~~~----~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~ 132 (696)
...++|++|+++|+++|+++|++++ .. ...+|+||+|. +|++|+|.+ |++|||+|||||||++||
T Consensus 364 ~g~~i~~~l~~~a~~~~~liP~~~~~~~~~~~~~~~~~~~~~~y~Gg~V~--~P~~G~y~~-V~vlDF~SLYPSIi~~~N 440 (787)
T PRK05761 364 ISTWISNLEYWEHRKRGWLIPWKEDILRLDHEVYKKAIIKGKKYRGGLVF--QPPPGIFFN-VYVLDFASLYPSIIVKWN 440 (787)
T ss_pred HHHHHHHHHHHHHHhCCEeCCCCccccccccccccccccccCCcCCcEEe--ccCCCceee-EEEeeecccchHHHHHhC
Confidence 4567899999999999999999876 22 13579999999 999999998 999999999999999999
Q ss_pred cCccccccc
Q psy5925 133 YCFSTCLGR 141 (696)
Q Consensus 133 ~~~~t~~~~ 141 (696)
|||+|++..
T Consensus 441 i~p~T~~~~ 449 (787)
T PRK05761 441 LSPETVRIP 449 (787)
T ss_pred CChhhccCc
Confidence 999999864
No 48
>PHA02528 43 DNA polymerase; Provisional
Probab=99.58 E-value=2e-15 Score=179.44 Aligned_cols=74 Identities=22% Similarity=0.376 Sum_probs=65.2
Q ss_pred eehhHHHHHHhhhCCCCCCCCCccCCCCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccC
Q psy5925 65 VKCFEESSLERSMKPDDRPSPTRKNKSTRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVE 143 (696)
Q Consensus 65 ~~~~~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~ 143 (696)
.+++ +++|+++|+++|+++|++.... ..+|+||+|. +|++|+|. +|+||||+|||||||++||+||+|++....
T Consensus 348 ~~~~-~~lll~~~~r~g~viP~~~~~~-~~~y~Gg~V~--eP~pGlY~-~VvVLDF~SLYPSIIiayNIcp~Tlv~~~~ 421 (881)
T PHA02528 348 IKTW-DAIIFNSLKEEKIVIPENKSHK-KQKYAGAFVK--EPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFH 421 (881)
T ss_pred HhHH-HHHHHHHHHHcCcccCCccccC-CCCCCCcEEe--cCCCCccc-ceEEEeccccChHHHHHhCCChhhcccccc
Confidence 4554 7899999999999999987543 4789999999 99999997 699999999999999999999999997543
No 49
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=99.49 E-value=1.4e-14 Score=172.48 Aligned_cols=133 Identities=24% Similarity=0.441 Sum_probs=97.5
Q ss_pred eehhHHHHHHhhhCCCCCCCCCccCCCCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccCC
Q psy5925 65 VKCFEESSLERSMKPDDRPSPTRKNKSTRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEH 144 (696)
Q Consensus 65 ~~~~~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~~ 144 (696)
...++|++|+|+|++.|+++|++.+......|+|++|. +|++|+|.+ |++|||+|||||||++||+||+|+......
T Consensus 375 ~~~~~~~~l~~~a~~~~~~iP~~~~~~~~~~~~Gg~V~--~P~~Gly~~-V~vLDF~SLYPSII~~~Ni~p~T~~~~~~~ 451 (792)
T COG0417 375 SGARVEGLLLREAKRRGELIPNKEERPERKKYKGGLVL--EPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCS 451 (792)
T ss_pred hhHHHHHHHHHHHhhcCEeccCccccchhhhcCCCEEc--cCCccccCc-EEEEEccccChHHHHHhCCCcceecCCCcc
Confidence 35678999999999999999999876544689999999 999999999 999999999999999999999999875433
Q ss_pred CCCCCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH-HH-h----c---CCc-ccccccccc
Q psy5925 145 LGVSDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI-RK-Q----L---ETP-KRRICDSYA 214 (696)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l-~r-~----~---~~p-~~~~~~~~~ 214 (696)
.. ..+++.. +.. .+...++.+++++.|+ +| + . .++ +..+++..|
T Consensus 452 ~~----------------~~~~~~~----~~~------~~~~~G~lp~il~~L~~~R~~~K~~~k~~~~~~e~~~~d~rQ 505 (792)
T COG0417 452 DD----------------YSPPGVG----HGF------CKREKGFLPEILEELLDRRDEIKKKMKKEKDPSERKLLDGRQ 505 (792)
T ss_pred cc----------------ccCCCCc----ccc------cccCCCchHHHHHHHHHHHHHHHHHhcccCChHHHHHHHHHH
Confidence 00 0111211 222 6677899999999999 32 2 2 233 455666554
Q ss_pred --ccCCCCCCccccc
Q psy5925 215 --IDAMTPDTTGDYQ 227 (696)
Q Consensus 215 --I~~~t~~~~~gfk 227 (696)
++- .-++.||+-
T Consensus 506 ~AlKv-l~NS~YGy~ 519 (792)
T COG0417 506 LALKV-LANSFYGYL 519 (792)
T ss_pred HHHHH-HHhhccccc
Confidence 222 224567765
No 50
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=99.49 E-value=1.4e-12 Score=130.02 Aligned_cols=140 Identities=14% Similarity=0.108 Sum_probs=110.6
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
.+|++||..|.+.+.++.| .++|||+.+||+|||..||..+|++....+.+-. ++|. +.. .+..-+ |+|
T Consensus 35 ~~E~~lL~~F~~~~~~~~p-~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~--k~We-----nY~--~Ry~~~-H~D 103 (209)
T PF10108_consen 35 DDEKELLQDFFDLVEKYNP-QLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGN--KPWE-----NYR--NRYSER-HLD 103 (209)
T ss_pred CCHHHHHHHHHHHHHhCCC-eEEecCCccCCHHHHHHHHHHhCCCCchhhhcCC--CCcc-----ccc--cccCcc-ccc
Confidence 4699999999999999997 5799999999999999999999998754333322 2221 001 112224 899
Q ss_pred hHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccch
Q psy5925 433 LWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGR 506 (696)
Q Consensus 433 l~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~ 506 (696)
++..+...-.-.+.+|+.+|..+--.+|.+++..+..++|.+++ ..++..||..||..++.|+.++..+..
T Consensus 104 Lmd~l~~~g~~~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~---i~~I~~YCe~DVl~T~~lylR~~~~~G 174 (209)
T PF10108_consen 104 LMDLLSFYGAKARTSLDELAALLGIPGKDDIDGSQVAELYQEGD---IDEIREYCEKDVLNTYLLYLRFELLRG 174 (209)
T ss_pred HHHHHhccCccccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCC---HHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99987554456788999999876545799999999999998875 899999999999999999999865443
No 51
>KOG0970|consensus
Probab=99.49 E-value=1.8e-14 Score=166.01 Aligned_cols=72 Identities=26% Similarity=0.490 Sum_probs=63.7
Q ss_pred hhHHHHHHhhhCCCCCCCCCcc-------------CC-------CCcCCCCCccccCCCCCCCcccCceeeeeccccchh
Q psy5925 67 CFEESSLERSMKPDDRPSPTRK-------------NK-------STRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPS 126 (696)
Q Consensus 67 ~~~~~~l~~~~~~~~~~~p~~~-------------~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~ 126 (696)
-+.|.+||+++++.|+++|.+. ++ ++..+|.|++|+ +|++|||.+.|++|||+|||||
T Consensus 778 eRnEylLLH~F~~~~fIvPDK~~ssk~~~d~d~~~eg~d~~~~~KKk~kYaGGLVl--ePkkGlYe~~VLllDFNSLYPS 855 (1429)
T KOG0970|consen 778 ERNEYLLLHEFYKNGFIVPDKQNSSKAQKDADETEEGADEPSKGKKKAKYAGGLVL--EPKKGLYEKYVLLLDFNSLYPS 855 (1429)
T ss_pred hhhhHHHHHHHHHCCccCCCccchhhhhhhhhhhhccccccccccccccccCceee--ccccchhhheeEEEEccccchH
Confidence 4578999999999999999877 22 122579999999 9999999999999999999999
Q ss_pred hhhhhccCcccccc
Q psy5925 127 VIIAYNYCFSTCLG 140 (696)
Q Consensus 127 ~~~~~~~~~~t~~~ 140 (696)
|||.||+||||+-+
T Consensus 856 IIQEyNICFTTv~~ 869 (1429)
T KOG0970|consen 856 IIQEYNICFTTVDR 869 (1429)
T ss_pred HHHHhhheeeeccc
Confidence 99999999999954
No 52
>PRK05762 DNA polymerase II; Reviewed
Probab=99.47 E-value=3.5e-14 Score=169.34 Aligned_cols=69 Identities=23% Similarity=0.311 Sum_probs=63.0
Q ss_pred HHHHHHhhhCCCCCCCCCccCCCCcCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccc
Q psy5925 69 EESSLERSMKPDDRPSPTRKNKSTRSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR 141 (696)
Q Consensus 69 ~~~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~ 141 (696)
.|++|+++|+++|+++|++++.. ..+|+|++|. +|++|+|.+ |++|||+|||||||++||+||+|++..
T Consensus 375 ~e~lll~~~~~~g~v~P~~~~~~-~~~y~Gg~V~--~p~~G~y~~-V~~lDF~SLYPSIi~~~Ni~p~T~~~~ 443 (786)
T PRK05762 375 FEHLYLPRAHRAGYVAPNLGERP-GEASPGGYVM--DSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEG 443 (786)
T ss_pred HHHHHHHHHHHCCEeCCCccccc-ccccCccEEe--cCCCCCcCc-eEEEEchhhhHHHHHHhCcCccceecC
Confidence 39999999999999999987643 3789999999 999999986 999999999999999999999999853
No 53
>KOG1829|consensus
Probab=99.46 E-value=7.7e-15 Score=164.17 Aligned_cols=62 Identities=39% Similarity=0.940 Sum_probs=55.8
Q ss_pred CCCCCccceecCCCCCeeeecCCCCeeecCCCCceeeccccc-c-CCCccchhhhhccccccce
Q psy5925 1 LCLARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS-Q-LPCKRCIRMRIRRDSMKGI 62 (696)
Q Consensus 1 lc~~~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~-~-~~cp~c~r~~~r~~~~~~~ 62 (696)
||.++|||||+|+.+++||||+.++|.+|..|++|||+.||. + ..||||+|++.|+......
T Consensus 506 lC~~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~s~~CPrC~R~q~r~~~~~~~ 569 (580)
T KOG1829|consen 506 LCTGKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRKSPCCPRCERRQKRAEQGAQL 569 (580)
T ss_pred hhccCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhccCCCCCchHHHHHHhhccccc
Confidence 799999999999999999999999999999999999999997 3 3499999999998655443
No 54
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=99.44 E-value=3.9e-14 Score=156.51 Aligned_cols=105 Identities=23% Similarity=0.379 Sum_probs=74.1
Q ss_pred cCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccCCCCCCCeeeeeecccccccCCCCCCCcce
Q psy5925 93 RSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIASRESNQSPPNKDSIH 172 (696)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 172 (696)
...|+|++|. +|++|+|.+||++|||+|||||||++||+||+|+++....-.. .. ..
T Consensus 5 ~~~y~Gg~V~--eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~~------~~---------------~~ 61 (400)
T cd05532 5 KAKYAGGLVL--EPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDED------DE---------------EP 61 (400)
T ss_pred cCCcCCceee--cCCCCcccCceEEEeccccchHHHHHhcCChhhcccccccccC------Cc---------------cc
Confidence 3689999999 9999999999999999999999999999999999864321110 00 01
Q ss_pred eeeccCCcccCCcccccchhhHHHHH--HHh-------cCCc-ccccccccc--ccCCCCCCccccc
Q psy5925 173 EAEITHPDCSKSSQIDFNPDLFKSFI--RKQ-------LETP-KRRICDSYA--IDAMTPDTTGDYQ 227 (696)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~l~~~~l--~r~-------~~~p-~~~~~~~~~--I~~~t~~~~~gfk 227 (696)
.++. .+.+.++.+.+++.++ |++ ..|| +....+..| ++- ..++.||+-
T Consensus 62 ~~~~------~~~~~Gilp~~l~~l~~~R~~~K~~~k~~~d~~~~~~~d~~Q~alKi-~~NS~YG~~ 121 (400)
T cd05532 62 PLPP------SDQEKGILPRIIRKLVERRRQVKKLMKSEKDPDKKAQLDIRQLALKL-TANSMYGCL 121 (400)
T ss_pred cccc------cccCCCchHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH-HHhhccccc
Confidence 1333 6678999999999999 332 2355 444444443 322 345677774
No 55
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=99.43 E-value=7e-14 Score=150.49 Aligned_cols=77 Identities=27% Similarity=0.452 Sum_probs=60.6
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccCCCCCCCeeeeeecccccccCCCCCCCccee
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIASRESNQSPPNKDSIHE 173 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (696)
++|+|++|. +|.+|+|. ||++|||+|||||||++||+||+|++.........++. + . .
T Consensus 1 ~~y~Gg~V~--~P~~G~~~-~V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~~~~~~~---------------~-~---~ 58 (323)
T cd00145 1 EPYEGGYVF--DPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYI---------------G-V---G 58 (323)
T ss_pred CCCCCcEEe--cCcccccC-ceEEeecCCccHHHHHHhCCCcccccccccccCccccc---------------C-c---c
Confidence 369999999 99999996 69999999999999999999999998753322111110 1 1 1
Q ss_pred eeccCCcccCCcccccchhhHHHHH
Q psy5925 174 AEITHPDCSKSSQIDFNPDLFKSFI 198 (696)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~l~~~~l 198 (696)
++. ++.+.++++.+++.++
T Consensus 59 ~~~------~~~~~Gilp~iL~~Ll 77 (323)
T cd00145 59 FRS------PKDRKGLLPRILEELL 77 (323)
T ss_pred ccc------cCCCCCCCHHHHHHHH
Confidence 444 7788999999999999
No 56
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.37 E-value=2.2e-13 Score=148.42 Aligned_cols=45 Identities=27% Similarity=0.558 Sum_probs=42.8
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccc
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR 141 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~ 141 (696)
.+|+|++|. +|++|+|.+ |++|||+|||||||++||+||+|++..
T Consensus 11 ~~y~Gg~V~--~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~ 55 (372)
T cd05530 11 KKYRGAIVL--EPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCP 55 (372)
T ss_pred CCCCCCEee--cCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccC
Confidence 579999999 999999998 999999999999999999999999864
No 57
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=99.29 E-value=2.9e-12 Score=144.24 Aligned_cols=113 Identities=30% Similarity=0.474 Sum_probs=85.5
Q ss_pred hhHHHHHHhhhCCCCCCCCCccCCCC---------cCCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccc
Q psy5925 67 CFEESSLERSMKPDDRPSPTRKNKST---------RSSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFST 137 (696)
Q Consensus 67 ~~~~~~l~~~~~~~~~~~p~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t 137 (696)
..+|+++++.+++.|++.|....... ...|+||+|. +|.+|+|.+||++|||+|||||||++||+||+|
T Consensus 247 ~~v~~~l~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~y~gg~v~--~p~~g~~~~~v~~lDf~SlYPsii~~~nl~~~t 324 (471)
T smart00486 247 IRVESLLLREAKKNNYILPSKSLIDFKGSEPELKKKAKYPGGKVL--EPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYST 324 (471)
T ss_pred HHHHHHHHHHHhhCCEEeccchhcccccccccccccccccccEEe--cCCCCcccCceEEeehhhccHHHHHHhCCCCcc
Confidence 45789999999999999998765432 3579999999 999999999999999999999999999999999
Q ss_pred cccccCCCCC-----CCeeeeeecccccccCCCCCCCcceeeeccCCcccCCcccccchhhHHHHH
Q psy5925 138 CLGRVEHLGV-----SDSFPFGCIASRESNQSPPNKDSIHEAEITHPDCSKSSQIDFNPDLFKSFI 198 (696)
Q Consensus 138 ~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l 198 (696)
++......+. .++..+.. ..+. -..|++ ++++.++.+++++.++
T Consensus 325 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~----~~~~~~------~~~~~gil~~~l~~l~ 373 (471)
T smart00486 325 LVGRGENSGELFLDVEDLLTIKY-------EKPE----GYHFVK------KNIRKGILPKLLKKLL 373 (471)
T ss_pred cccccccccccCCChhhcceeee-------cCCC----cceeec------CCCCCeehHHHHHHHH
Confidence 9875432111 01111110 0111 234677 7777899999999999
No 58
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=99.27 E-value=3.5e-12 Score=139.67 Aligned_cols=76 Identities=28% Similarity=0.451 Sum_probs=58.3
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccccCCCCCCCeeeeeecccccccCCCCCCCccee
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIASRESNQSPPNKDSIHE 173 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (696)
++|+||+|. +|++|+|.+ |++|||+|||||||++||+||+|++..... |.. .. +.+ -+.
T Consensus 2 ~~y~Gg~V~--~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~----~~~-~~----------~~~---~~~ 60 (371)
T cd05536 2 ESYEGGIVL--EPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCE----DCD-VE----------PQV---GHK 60 (371)
T ss_pred CCCCceEEe--CCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCcc----ccc-cC----------CCC---CcE
Confidence 579999999 999999987 999999999999999999999999864221 100 00 112 233
Q ss_pred eeccCCcccCCcccccchhhHHHHH
Q psy5925 174 AEITHPDCSKSSQIDFNPDLFKSFI 198 (696)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~l~~~~l 198 (696)
|.+ .+.++++++++.|+
T Consensus 61 f~~--------~~~Gilp~il~~ll 77 (371)
T cd05536 61 FRK--------DPPGFIPSVLEDLL 77 (371)
T ss_pred Eec--------CCCCchHHHHHHHH
Confidence 544 25789999999999
No 59
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=99.27 E-value=3.6e-12 Score=139.28 Aligned_cols=45 Identities=31% Similarity=0.465 Sum_probs=41.3
Q ss_pred CCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCcccccccc
Q psy5925 95 SFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRV 142 (696)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~~ 142 (696)
+++|++|. +|++|+|.+ |++|||+|||||||++||+||+|++...
T Consensus 2 ~~~Gg~V~--eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~ 46 (371)
T cd05537 2 SSPGGYVM--DSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGL 46 (371)
T ss_pred CCCCcEEe--CCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCC
Confidence 46799999 999999986 9999999999999999999999997643
No 60
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.23 E-value=7.7e-12 Score=135.87 Aligned_cols=45 Identities=29% Similarity=0.471 Sum_probs=42.3
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCccccccc
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR 141 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~~~~ 141 (696)
.+|+|++|. +|++|+|.+ |++|||+|||||||++||+||+|++..
T Consensus 3 ~~~~Gg~V~--~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~ 47 (352)
T cd05531 3 LADRGGLVF--QPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCR 47 (352)
T ss_pred cCCCCcEEe--cCCCCccCc-eEEEEccccchHHHHHhCCChhhcccc
Confidence 579999999 999999987 999999999999999999999999764
No 61
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.78 E-value=1.6e-08 Score=98.08 Aligned_cols=117 Identities=21% Similarity=0.161 Sum_probs=76.5
Q ss_pred CHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEeh
Q psy5925 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINL 433 (696)
Q Consensus 354 sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl 433 (696)
+|.+.+.++++.+.+. +.+++||+.+||+|+|..|++.++++. ..-++|+
T Consensus 42 ~ee~~~~~~~~~l~~~--~~iv~yng~~FD~p~L~~~~~~~~~~~----------------------------~~~~iDl 91 (164)
T PF13482_consen 42 DEEEIILEFFELLDEA--DNIVTYNGKNFDIPFLKRRAKRYGLPP----------------------------PFNHIDL 91 (164)
T ss_dssp HHHHHHHH--HHHHTT----EEESSTTTTHHHHHHHHH-HHHH------------------------------GGGEEEH
T ss_pred HHHHHHHHHHHHHhcC--CeEEEEeCcccCHHHHHHHHHHcCCCc----------------------------ccchhhH
Confidence 3445555555666654 789999999999999999997776542 1247899
Q ss_pred HHHHhhhcCCCCCCHHHHHHHHcCCCc-CCCChhhHHHHHhc----CCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 434 WRLLRHEVNLQSYTFENIMYHVLHERI-PLHSWKLLTCWWEH----RTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 434 ~~~~r~~~kl~sysL~~Va~~~L~~~k-~~~~~~~l~~~~~~----~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+..+++... ++|+|++|++.+...+. ++++..++..+|.. ++...+..++.||..|+..+.+|.++|
T Consensus 92 ~~~~~~~~~-~~~~Lk~ve~~lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 92 LKIIKKHFL-ESYSLKNVEKFLGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHHHT-TTS-CCTT--SHHH-----------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhccC-CCCCHHHHhhhcccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999987555 99999999999655555 67888888887765 334568999999999999999999886
No 62
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=98.78 E-value=2.6e-09 Score=115.90 Aligned_cols=39 Identities=28% Similarity=0.486 Sum_probs=36.7
Q ss_pred CCCCccccCCCCCCCcccCceeeeeccccchhhhhhhccCcc
Q psy5925 95 SFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFS 136 (696)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~ 136 (696)
.|+|++|. +|.+|+|.+ |++|||+|||||||++||+|++
T Consensus 2 ~~~GG~v~--~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~ 40 (347)
T cd05538 2 KFEGGYAY--VFITGVLGP-IVHADVASLYPSIMLAYRICPA 40 (347)
T ss_pred CcCCceEc--ccCCcCcCc-eEEEEcccchHHHHHHhCCCCC
Confidence 58999999 899999986 9999999999999999999974
No 63
>PHA02563 DNA polymerase; Provisional
Probab=98.65 E-value=2e-07 Score=107.31 Aligned_cols=220 Identities=13% Similarity=0.080 Sum_probs=122.4
Q ss_pred HHHHHHHHH--Hh--CCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE--Ee
Q psy5925 359 FSIFIENVR--QW--DPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV--IN 432 (696)
Q Consensus 359 L~~f~~~I~--~~--DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~--lD 432 (696)
+..|++.+. .+ +.=++.-|| -.||--||+.=..+++......+ |.+... .....+...||+. .+
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN-~~FD~~Fil~~L~~~~~~~~~e~-~~~~~~--------~~~~~i~~~g~~~~i~~ 119 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHN-LKFDGSFILKWLLRNGFNWILEL-RVRSSK--------NFDTTIFINGRWYTITD 119 (630)
T ss_pred HHHHHHHHhhccccccceEEEEec-CCccHHHHHHHHHhhcccccccc-cccCcc--------cccceEeeCCEEEEEEE
Confidence 446677766 22 233778899 89999999998877775432111 111110 0112334455542 11
Q ss_pred hHHHHhhhcCCCCCCHHHHHHHHc-CCCcCCCChh--hHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhh
Q psy5925 433 LWRLLRHEVNLQSYTFENIMYHVL-HERIPLHSWK--LLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSE 509 (696)
Q Consensus 433 l~~~~r~~~kl~sysL~~Va~~~L-~~~k~~~~~~--~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~e 509 (696)
.+-.++..+.+-.-+|+.+|..+- ...+.++++. .-..++-..-...+...++|+.+|+..+..++...
T Consensus 120 ~~~~f~DS~~llp~~L~~l~~~F~~~~~k~~~d~~~~~~~~y~~~~~~~~~~e~~~Yl~~D~~il~~~~~i~-------- 191 (630)
T PHA02563 120 SFMKFRDSLKLLPFSLEKLKKDFGLTILKKDIDLNKERPVGYEFTTFEKLDPEELEYIHNDCVIIAGMLDIH-------- 191 (630)
T ss_pred EEEEEEehHhhhhHHHHHHHHHhCcccccCCcCccccccccceecccccccHHHHHHHHHHHHHHHHHHHHH--------
Confidence 112334455666778888888873 3333333321 11001100001134788999999998877776442
Q ss_pred HHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchhhhhccCCCCCCCeee---ecccccccCceeeeeccccc
Q psy5925 510 MARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLIL---EPESRLYTDPIIVLDFQSLY 586 (696)
Q Consensus 510 la~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~q~~~~~~~~~GglVl---eP~~Gly~~pVvvLDF~SLY 586 (696)
.+.++- ..-..+.+.++.-.++...+....-.|-++.....--+..|.||.|+ ++..|++++ +.++|++|||
T Consensus 192 ~~~~f~----~~TisS~a~~ifk~~~~~~~~~~~~~p~l~~~~~~fIr~sY~GGr~~~~~~~~~~~~~~-~~~yDvnSlY 266 (630)
T PHA02563 192 FSEGFT----RFTTGSDAMTVYKELYQKIKIKYTHFPILDLGFDDFIRKFYRGGRTWYNPKYIGKLIEE-GYVYDVNSLY 266 (630)
T ss_pred HHhccc----cCCcchHHHHHHHHHHhhcccccccCCCCCchHHHHHHHheeCceeecccccccccccc-cccccccccc
Confidence 122211 11111223444444443211111112333332222245689999998 999999976 7799999999
Q ss_pred hhhhhhccCCccCcc
Q psy5925 587 PSVIIAYNYCFSTCL 601 (696)
Q Consensus 587 PSIIiayNiC~sT~~ 601 (696)
||+|..+++++.+..
T Consensus 267 PsaM~~~~~P~g~p~ 281 (630)
T PHA02563 267 PYVMYNAKLPYGEPF 281 (630)
T ss_pred HHHHhhccCCCCCce
Confidence 999999999998744
No 64
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.29 E-value=1.7e-05 Score=79.84 Aligned_cols=118 Identities=14% Similarity=0.075 Sum_probs=89.6
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
+.|..+|+.|...+ |..+++.||+-.||||||. |+.+..++... -+-|+|
T Consensus 141 ~~E~avle~fl~~~---~~~~lvsfNGkaFD~Pfik-R~v~~~~el~l--------------------------~~~H~D 190 (278)
T COG3359 141 EEEVAVLENFLHDP---DFNMLVSFNGKAFDIPFIK-RMVRDRLELSL--------------------------EFGHFD 190 (278)
T ss_pred chhhHHHHHHhcCC---CcceEEEecCcccCcHHHH-HHHhcccccCc--------------------------cccchh
Confidence 46888999997755 5569999999999999999 88777666431 035899
Q ss_pred hHHHHhhhc--CCCCCCHHHHHHHHcCCCcCC----CChhhHHHHH-hcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 433 LWRLLRHEV--NLQSYTFENIMYHVLHERIPL----HSWKLLTCWW-EHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 433 l~~~~r~~~--kl~sysL~~Va~~~L~~~k~~----~~~~~l~~~~-~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
++...|+-. .|.+-+|.+|-+ +||.+..+ +..-++.+.| +.+++..+..++.||..|+.....|+..+
T Consensus 191 L~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvlnL~~i~~h~ 265 (278)
T COG3359 191 LYHPSRRLWKHLLPRCGLKTVER-ILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVLNLPTIIKHV 265 (278)
T ss_pred hhhhhhhhhhccCCCCChhhHHH-HhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHHHHHhHHHHHHHH
Confidence 999998854 689999999988 89865443 3334555544 44555567889999999998888887765
No 65
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.69 E-value=0.0014 Score=67.55 Aligned_cols=102 Identities=15% Similarity=0.114 Sum_probs=73.9
Q ss_pred EEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeeccc
Q psy5925 349 RHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGR 428 (696)
Q Consensus 349 V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GR 428 (696)
|.-.....+.+..|.+++. +.++++|||+..||+++|.+-++++|++... .
T Consensus 60 v~~~p~f~ev~~~~~~fi~--~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~---------------------------~ 110 (232)
T PRK06309 60 VADAPKFPEAYQKFIEFCG--TDNILVAHNNDAFDFPLLRKECRRHGLEPPT---------------------------L 110 (232)
T ss_pred HhCCCCHHHHHHHHHHHHc--CCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC---------------------------C
Confidence 3345678889999998885 3469999998889999999888888765320 1
Q ss_pred EEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 429 IVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 429 l~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
-.+|+.++.++.. .+.+++|+++++++ |... . + .+-++.||..+.+|+.++
T Consensus 111 ~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~--~-----------~--------aH~Al~Da~~t~~vl~~l 162 (232)
T PRK06309 111 RTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEE--N-----------Q--------AHRALDDVITLHRVFSAL 162 (232)
T ss_pred cEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCC--C-----------C--------CCCcHHHHHHHHHHHHHH
Confidence 2578988887754 56789999998876 3221 1 0 112467888888888875
No 66
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.67 E-value=0.0019 Score=67.36 Aligned_cols=165 Identities=12% Similarity=0.094 Sum_probs=103.8
Q ss_pred CceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIE 323 (696)
Q Consensus 244 ~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~ 323 (696)
..+.+.+|+||.. -+|..|+|+.|++..-+..... .....+++|.. |+. ..+.
T Consensus 6 ~~~~v~~D~ETTG-----l~~~~d~IIEIa~v~v~~~~~~--~~~~~li~P~~--------~I~------------~~a~ 58 (250)
T PRK06310 6 DTEFVCLDCETTG-----LDVKKDRIIEFAAIRFTFDEVI--DSVEFLINPER--------VVS------------AESQ 58 (250)
T ss_pred CCcEEEEEEeCCC-----CCCCCCeEEEEEEEEEECCeEE--EEEEEEECcCC--------CCC------------Hhhh
Confidence 4678999999983 3678899999987655432110 11234555532 111 0011
Q ss_pred ccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccc
Q psy5925 324 NVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403 (696)
Q Consensus 324 ~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lg 403 (696)
.++... +-.|.-..+..+++..|.+++.. .++++|||+ .||+++|.+-+..+|++...
T Consensus 59 ~ihgIt----------------~e~v~~~p~~~ev~~~~~~fl~~--~~~lvghn~-~FD~~~L~~~~~r~g~~~~~--- 116 (250)
T PRK06310 59 RIHHIS----------------DAMLRDKPKIAEVFPQIKGFFKE--GDYIVGHSV-GFDLQVLSQESERIGETFLS--- 116 (250)
T ss_pred hccCcC----------------HHHHhCCCCHHHHHHHHHHHhCC--CCEEEEECH-HHHHHHHHHHHHHcCCCccc---
Confidence 122221 11223446778899999888743 479999997 59999999888887765430
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHH
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMT 483 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~ 483 (696)
...-.+|+.++++......+|+|+++++.+ |.....
T Consensus 117 ----------------------~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~--------------------- 152 (250)
T PRK06310 117 ----------------------KHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDG--------------------- 152 (250)
T ss_pred ----------------------cCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCC---------------------
Confidence 002367888888765456789999999876 332110
Q ss_pred HHHHHHHHHHHHHHHHHh
Q psy5925 484 VEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 484 i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.|+..+.+++.++
T Consensus 153 aH~Al~Da~at~~vl~~l 170 (250)
T PRK06310 153 NHRAMKDVEINIKVFKHL 170 (250)
T ss_pred CcChHHHHHHHHHHHHHH
Confidence 122467888888888775
No 67
>PHA02735 putative DNA polymerase type B; Provisional
Probab=97.67 E-value=0.00026 Score=76.17 Aligned_cols=145 Identities=10% Similarity=-0.033 Sum_probs=89.1
Q ss_pred EEehHHHHhhhcCCCCCCHHHHHHHHcCCCcC--CCChhhH--HHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccc
Q psy5925 430 VINLWRLLRHEVNLQSYTFENIMYHVLHERIP--LHSWKLL--TCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIG 505 (696)
Q Consensus 430 ~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~--~~~~~~l--~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~ 505 (696)
|-|..+++- -+|++.+...||+.|- -++.... .++-. + ....+++|+-.|+.++..|...+
T Consensus 160 hyd~aqffy-------tsldna~~ewlge~ka~dgid~~~f~~k~yi~-~---n~~dilkyak~da~l~~dl~~e~---- 224 (716)
T PHA02735 160 HYDAAQFFY-------TSLDNAAEEWLGENKAKDGIDAGKFDAKEYIK-D---NFDDILKYAKIDAELTQDLAIEA---- 224 (716)
T ss_pred cccHHHHHH-------HHHHhHHHHHhccccccccccccccchHHHHh-h---hHHHHHHHHhhhHHHHHHHHHHH----
Confidence 456555541 3689999999998763 2221111 12222 2 26789999999999999997654
Q ss_pred hhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeeeeCCchh--hh-hccCCCCCCCeeeecccccccCceeeeec
Q psy5925 506 RTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIK--QR-AHMRAPESLPLILEPESRLYTDPIIVLDF 582 (696)
Q Consensus 506 ~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~p~p~~~--q~-~~~~~~~~GglVleP~~Gly~~pVvvLDF 582 (696)
...|.-..+|+.+-++.| +..+++|=.....+ |+.. -. .-.++.|.||.+---++|=+-. |+.-|.
T Consensus 225 --~n~~e~ldipmgrp~stg--yla~~yl~~~~~ek------p~lg~~~ma~~~wEsYyGGrfeV~KrgnvGE-v~~pDI 293 (716)
T PHA02735 225 --TNEAEELDIPMGRPFSTG--YLAAEYLDANLEEK------PGLGNEAMAKLAWESYAGGRFEVFKRGNVGE-VAAPDI 293 (716)
T ss_pred --hhhHhhcCCccCCCcccc--hhhHHHHhcccccC------CCCChHHHHHHHHHhhcCCceEEeccCccce-eeeccc
Confidence 223334456665555433 34444443222211 2211 00 1135689999887778887755 999999
Q ss_pred cccchhhhhhccCCccCcc
Q psy5925 583 QSLYPSVIIAYNYCFSTCL 601 (696)
Q Consensus 583 ~SLYPSIIiayNiC~sT~~ 601 (696)
||+||+||..-= -+.|+.
T Consensus 294 NSaYPaim~dlP-DpKTl~ 311 (716)
T PHA02735 294 NSAYPAILADLP-DPKTLN 311 (716)
T ss_pred cccchHHHHhCC-CCcccc
Confidence 999999999933 456643
No 68
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.51 E-value=0.0029 Score=66.28 Aligned_cols=163 Identities=9% Similarity=0.053 Sum_probs=103.2
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
......+.+|+||.. .+|..|+|+.|++....+.... ..--.++++... | ..
T Consensus 65 ~~~~~~vv~DiETTG-----~~~~~~~IIEIGAv~v~~g~i~--~~f~~~v~p~~i-------p--------------~~ 116 (257)
T PRK08517 65 IKDQVFCFVDIETNG-----SKPKKHQIIEIGAVKVKNGEII--DRFESFVKAKEV-------P--------------EY 116 (257)
T ss_pred CCCCCEEEEEEeCCC-----CCCCCCeEEEEEEEEEECCEEE--EEEEEEECCCCC-------C--------------hh
Confidence 446678889999982 5677889999998776443110 011233443211 1 01
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccc
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQE 401 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~ 401 (696)
+..++..+ - -.+....+..+.+.+|.+++.. ++++|||. .||+.+|.+-++++|+..+.
T Consensus 117 ~~~itGIt--------~--------e~l~~ap~~~evl~~f~~fl~~---~v~VaHNa-~FD~~fL~~~l~r~g~~~~~- 175 (257)
T PRK08517 117 ITELTGIT--------Y--------EDLENAPSLKEVLEEFRLFLGD---SVFVAHNV-NFDYNFISRSLEEIGLGPLL- 175 (257)
T ss_pred hhhhcCcC--------H--------HHHcCCCCHHHHHHHHHHHHCC---CeEEEECH-HHHHHHHHHHHHHcCCCCCC-
Confidence 11122221 1 1233456788999999998753 68999999 89999998888777765330
Q ss_pred ccccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHH
Q psy5925 402 LSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 481 (696)
Q Consensus 402 lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~ 481 (696)
.-.+|+.+..+..+...+|+|+++++. +|.....
T Consensus 176 --------------------------~~~ldtl~la~~~~~~~~~~L~~L~~~-lgi~~~~------------------- 209 (257)
T PRK08517 176 --------------------------NRKLCTIDLAKRTIESPRYGLSFLKEL-LGIEIEV------------------- 209 (257)
T ss_pred --------------------------CCcEehHHHHHHHccCCCCCHHHHHHH-cCcCCCC-------------------
Confidence 013677787777777889999999885 4433211
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy5925 482 MTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 482 ~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 210 --~HrAl~DA~ata~ll~~l 227 (257)
T PRK08517 210 --HHRAYADALAAYEIFKIC 227 (257)
T ss_pred --CCChHHHHHHHHHHHHHH
Confidence 012467888888887765
No 69
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=97.49 E-value=0.0034 Score=61.93 Aligned_cols=93 Identities=10% Similarity=0.068 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHhC-CCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHH
Q psy5925 357 ELFSIFIENVRQWD-PDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWR 435 (696)
Q Consensus 357 eLL~~f~~~I~~~D-PDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~ 435 (696)
++...+.+++...+ +.+++|||+..||+++|.+-++++|+... .....+|.++
T Consensus 83 ~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~--------------------------~~~~~iDtl~ 136 (177)
T cd06136 83 DTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLP--------------------------DDILCVDSLP 136 (177)
T ss_pred HHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCC--------------------------CCCEEEEeHH
Confidence 34444555555444 56999999999999999998888876421 0024568888
Q ss_pred HHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHH
Q psy5925 436 LLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQ 500 (696)
Q Consensus 436 ~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~k 500 (696)
..|+..+ +|++++++++|.....- +-++.||..+.+++.+
T Consensus 137 l~r~~~~----~L~~l~~~~~~~~~~~~---------------------H~A~~Da~at~~v~~~ 176 (177)
T cd06136 137 AFRELDQ----SLGSLYKRLFGQEPKNS---------------------HTAEGDVLALLKCALH 176 (177)
T ss_pred HHhhhHh----hHHHHHHHHhCCCcccc---------------------cchHHHHHHHHHHHhh
Confidence 7776543 89999988765543211 2246778887777654
No 70
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.45 E-value=0.0018 Score=70.28 Aligned_cols=198 Identities=11% Similarity=0.056 Sum_probs=112.1
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeec-CCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYT-CPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFST 320 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~-~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~ 320 (696)
+.....+++||||.. -+|..|+|+.|.+.... +... ...-..++++.... .|.
T Consensus 43 ~~~~~fVvlDiETTG-----Ldp~~drIIeIgAV~i~~~g~i--ve~f~tLVnP~~~~-----~p~-------------- 96 (377)
T PRK05601 43 IEAAPFVAVSIQTSG-----IHPSTSRLITIDAVTLTADGEE--VEHFHAVLNPGEDP-----GPF-------------- 96 (377)
T ss_pred CCCCCEEEEEEECCC-----CCCCCCeEEEEEEEEEEcCCEE--EEEEEEEECcCCCC-----CCc--------------
Confidence 556789999999982 37889999999877543 3321 12235677764311 011
Q ss_pred hhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCc-
Q psy5925 321 FIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLN- 399 (696)
Q Consensus 321 ~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~- 399 (696)
.++...+ -.+..-.+-.+++..|.+++.. .++++||. .|||+||..-++.......
T Consensus 97 ---~LHGIT~----------------e~La~AP~f~eVl~el~~fL~g---~vLVaHNA-~FD~~FL~~e~~r~~~~a~~ 153 (377)
T PRK05601 97 ---HLHGLSA----------------EEFAQGKRFSQILKPLDRLIDG---RTLILHNA-PRTWGFIVSEAKRAMNAAAR 153 (377)
T ss_pred ---cccCCCH----------------HHHhcCCCHHHHHHHHHHHhCC---CEEEEECc-HHHHHHHHHHHHHhhhhhhh
Confidence 1222211 1222345667889999998874 38999998 5999999887766543221
Q ss_pred ccccccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcc
Q psy5925 400 QELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHL 478 (696)
Q Consensus 400 ~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~ 478 (696)
....|.+...................+ -.++|++.+.|+.+ .+.+|+|++||.++ |...+.- -...
T Consensus 154 ~n~~~~r~~~~~~~~~rr~~~g~~p~p-~~~iDTL~LARrl~p~l~~~rL~~La~~l-Gi~~p~~-~A~~---------- 220 (377)
T PRK05601 154 ANRNRNRGNRRGGRGRRRQRVGHIPKP-VVIVDTLATARRQGVALDDIRIRGVAHTL-GLDAPAA-EASV---------- 220 (377)
T ss_pred cccccccccccccccccccccCCCCCC-CCEEEhHHHHHHHcCCCCCCCHHHHHHHh-CCCCCch-hhhh----------
Confidence 000111000000000000011112222 25799999999876 68999999999984 5443321 0111
Q ss_pred cHHHHHH--HHHHHHHHHHHHHHHh
Q psy5925 479 YKWMTVE--HYLIRVTGIIRLIEQL 501 (696)
Q Consensus 479 ~~~~~i~--Y~l~D~~l~~~L~~kl 501 (696)
.+...-+ .+..|+.++.+|+.++
T Consensus 221 ~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 221 ERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred hhhcCChhhhhhHHHHHHHHHHHHh
Confidence 1112211 2346999999999875
No 71
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.44 E-value=0.004 Score=67.06 Aligned_cols=161 Identities=12% Similarity=0.157 Sum_probs=102.2
Q ss_pred CceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIE 323 (696)
Q Consensus 244 ~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~ 323 (696)
+...+.+|+||. | -+|..|+|+.|++...++...- ..--.+++|.. |+. ..+.
T Consensus 7 ~~~~Vv~DlETT--G---l~p~~~eIIEIgaV~v~~g~i~--~~f~~lVkP~~--------~I~------------~~a~ 59 (313)
T PRK06807 7 PLDYVVIDFETT--G---FNPYNDKIIQVAAVKYRNHELV--DQFVSYVNPER--------PIP------------DRIT 59 (313)
T ss_pred CCCEEEEEEECC--C---CCCCCCeEEEEEEEEEECCEEE--EEEEEEECcCC--------CCC------------Hhhh
Confidence 457788999996 2 2466889999998766442100 01123455532 110 1111
Q ss_pred ccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccc
Q psy5925 324 NVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403 (696)
Q Consensus 324 ~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lg 403 (696)
.++..++ -.+.......+.+..|.+++. -++++|||+ .||+++|.+-+..+|++...
T Consensus 60 ~ihGIT~----------------e~l~~~~~~~evl~~f~~fl~---~~~lVaHNa-~FD~~fL~~~~~~~gl~~~~--- 116 (313)
T PRK06807 60 SLTGITN----------------YRVSDAPTIEEVLPLFLAFLH---TNVIVAHNA-SFDMRFLKSNVNMLGLPEPK--- 116 (313)
T ss_pred ccCCCCH----------------HHHhCCCCHHHHHHHHHHHHc---CCeEEEEcH-HHHHHHHHHHHHHcCCCCCC---
Confidence 1222211 112234678899999999875 468999999 89999999999888875320
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHH
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWM 482 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~ 482 (696)
...+|+....+..+ .+++++|++++.++ |.....
T Consensus 117 ------------------------~~~iDtl~la~~~~~~~~~~kL~~L~~~l-gi~~~~-------------------- 151 (313)
T PRK06807 117 ------------------------NKVIDTVFLAKKYMKHAPNHKLETLKRML-GIRLSS-------------------- 151 (313)
T ss_pred ------------------------CCEeeHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC--------------------
Confidence 02679888887766 47899999999775 432111
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q psy5925 483 TVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 483 ~i~Y~l~D~~l~~~L~~kl 501 (696)
+-++.||..+.+|+.++
T Consensus 152 --H~Al~DA~~ta~l~~~l 168 (313)
T PRK06807 152 --HNAFDDCITCAAVYQKC 168 (313)
T ss_pred --cChHHHHHHHHHHHHHH
Confidence 12467888888887776
No 72
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=97.40 E-value=0.00011 Score=83.36 Aligned_cols=196 Identities=18% Similarity=0.179 Sum_probs=87.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccc-cCCeeeeCCchhhhhccCC
Q psy5925 480 KWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSR-LNNFVAVSPSIKQRAHMRA 558 (696)
Q Consensus 480 ~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~-~~~~i~p~p~~~q~~~~~~ 558 (696)
....++||.+||....+++.+.+ ....+...+ .+....++- + ..-..+++.-. ..+.-++.++.......+.
T Consensus 132 ~~e~l~Yc~~DV~iL~~~~~~f~--~~~~~~~~i--~~~~~~~ti-~--sls~~ifk~~~~~~~~~i~~~~~~~~~~ir~ 204 (459)
T PF03175_consen 132 KKEILEYCKQDVRILYKVLEKFR--KIFEEEFNI--IDIFNSFTI-S--SLSMKIFKKNFDEKNKKIPNPSNKMYEFIRK 204 (459)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHH--TT--SSSHH--HHHHHHHHH-H--HHHHH-HHHHS----HHHHHHHHTT-----E
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhCC--CcccccccH-H--HHHHHHHHHhccccccCccccchhhHHHHHh
Confidence 47889999999999999998863 222222222 111111110 0 00011111111 1111122222211112355
Q ss_pred CCCCCeeeecccccccCceeeeeccccchhhhhhccCCccCccccccc-----CC-------------------------
Q psy5925 559 PESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEH-----LG------------------------- 608 (696)
Q Consensus 559 ~~~GglVleP~~Gly~~pVvvLDF~SLYPSIIiayNiC~sT~~~~~~~-----~~------------------------- 608 (696)
.+.||.+.--..|... .+.++|++|||||+|.. +.-|...-..+.. ..
T Consensus 205 s~~GGr~~~~~~~~~~-~i~~yDvnSLYP~~m~~-~~~P~G~p~~~~~~~~~~~~~~~~~~~~~v~~p~~~~~~~~lp~~ 282 (459)
T PF03175_consen 205 SYYGGRCEVFKPGIKN-KIYYYDVNSLYPSAMKR-NPMPYGHPKVIKDKIPKILEDPFGFFKCKVFPPKNLPYIPVLPIR 282 (459)
T ss_dssp EE-GGGB-TEEEESE----EEEEETTHHHHHHHH-S-EEEEEEEEEESS----TTS-EEEEEEEEEEEE-TT----BBES
T ss_pred hcCCceeeeeeccccc-ceeeeeccCCcHHHHhc-CCCCCCCeeccccccccchhhcccceeEEEeCCccCCcceeeeec
Confidence 7789988666677776 69999999999999982 2222111000000 00
Q ss_pred CCCC---CCCccccc---ccChhHHhh-cccc--eeeCC-CCceeecCCCcccchHHHHHHHHHHHHHHHHHHhhCCCCH
Q psy5925 609 VSDS---FPFGCIDL---NVSIRSLKK-LQQN--LTISP-SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSE 678 (696)
Q Consensus 609 ~~~~---~~~G~~~~---~~~~~~l~~-~~d~--i~~~p-~g~~fvk~~~r~GILP~~L~~Ll~~R~~vKk~mk~~~~~~ 678 (696)
.... +..|...- -...+.++. +... ..+.. .|..|-+ +.|+++.-++.+.+.|...|+.-...+
T Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~eL~~a~~~g~~~~~~~~~g~~~~~---~~~~F~~~i~~~~~~k~~~k~~~~~~~--- 356 (459)
T PF03175_consen 283 PNGKLLFFPLCPFCGKKGVWTSEELKKAIKYGYHYKIEVIEGYYFDE---KGGLFKEYIDKLYELKKNAKKKADKEK--- 356 (459)
T ss_dssp SSSSSSTTSBBSB-TTSEEEEHHHHHHHHHHEEEEEEEEEEEEEEEE---ES-TTHHHHHHHHHHHHH--HHHHH-----
T ss_pred CCCcceeccCCCeecceeEEEhHHHHHHHHhccceEEEEEEEEEecc---ccCchHHHHHHHHHhhhhhccCCchhH---
Confidence 0000 00110000 011111211 1111 11212 3455433 579999999999999998887655443
Q ss_pred HHHHHhhhccccc
Q psy5925 679 SLRNLTMLNSMLL 691 (696)
Q Consensus 679 ~l~~~l~ansmy~ 691 (696)
.+.|++. ||+||
T Consensus 357 ~i~KL~l-NSlyG 368 (459)
T PF03175_consen 357 SIAKLLL-NSLYG 368 (459)
T ss_dssp -HHHHHH-HHHHH
T ss_pred HHHHHHH-hhhhh
Confidence 5788865 99998
No 73
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.38 E-value=0.0078 Score=57.97 Aligned_cols=100 Identities=17% Similarity=0.188 Sum_probs=72.5
Q ss_pred eCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEE
Q psy5925 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVI 431 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~l 431 (696)
-..+.+.+..|.+++.. .++++||.-.||+.+|..-+.++|+.... ..+ .+
T Consensus 64 ~~~~~~~~~~~~~~l~~---~~~v~~n~~~fD~~~L~~~~~~~~~~~~~-------------------------~~~-~i 114 (169)
T smart00479 64 APTFEEVLEELLEFLKG---KILVAGNALNFDLRFLKLEHPRLGIKDPP-------------------------KNP-VI 114 (169)
T ss_pred CCCHHHHHHHHHHHhcC---CEEEEeCCHHHhHHHHHHHHHHhCCCCCc-------------------------CCC-ee
Confidence 46788899999988854 47889999899999999888877764220 011 67
Q ss_pred ehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 432 NLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 432 Dl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
|+..+.+......+++|+++++.+....... .+.++.||..+++|+.++
T Consensus 115 D~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~---------------------~H~A~~Da~~t~~l~~~~ 163 (169)
T smart00479 115 DTLKLARALNPGRKYSLKKLAERLGLEVIGR---------------------AHRALDDARATAKLFKKL 163 (169)
T ss_pred EHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC---------------------CcCcHHHHHHHHHHHHHH
Confidence 8888877766445999999998875432211 123577888888888776
No 74
>PRK07883 hypothetical protein; Validated
Probab=97.34 E-value=0.0042 Score=72.08 Aligned_cols=141 Identities=16% Similarity=0.142 Sum_probs=91.6
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
...+.+.||+||.. -+|..|+|+.|++..-++...- ..--.++++... +. ..+
T Consensus 13 ~~~~~Vv~D~ETTG-----l~p~~~~IIEIgaV~v~~g~iv--~~f~~lV~P~~~--------i~------------~~~ 65 (557)
T PRK07883 13 RDVTFVVVDLETTG-----GSPAGDAITEIGAVKVRGGEVL--GEFATLVNPGRP--------IP------------PFI 65 (557)
T ss_pred cCCCEEEEEEecCC-----CCCCCCeEEEEEEEEEECCEEE--EEEEEEECCCCC--------CC------------hhH
Confidence 34688999999982 2567799999998766443110 111245555321 10 011
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
..++..+ +-.+.....+.+.+..|.+++. .++++|||+ .||+++|..-++.+|++..
T Consensus 66 ~~itGIt----------------~e~l~~ap~~~evl~~f~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~g~~~~--- 122 (557)
T PRK07883 66 TVLTGIT----------------TAMVAGAPPIEEVLPAFLEFAR---GAVLVAHNA-PFDIGFLRAAAARCGYPWP--- 122 (557)
T ss_pred HhhcCCC----------------HHHHhCCCCHHHHHHHHHHHhc---CCEEEEeCc-HHHHHHHHHHHHHcCCCCC---
Confidence 1122221 1122345678899999999886 479999999 7999999999998887532
Q ss_pred cccccccccccCCCccccceeeecccEEEehHHHHhhhc---CCCCCCHHHHHHHHcCC
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV---NLQSYTFENIMYHVLHE 458 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~---kl~sysL~~Va~~~L~~ 458 (696)
....+|+..+.+..+ ...+|+|++++.. +|.
T Consensus 123 ------------------------~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~-~gi 156 (557)
T PRK07883 123 ------------------------GPPVLCTVRLARRVLPRDEAPNVRLSTLARL-FGA 156 (557)
T ss_pred ------------------------CCCcEecHHHHHHhcccCCCCCCCHHHHHHH-CCc
Confidence 012578888887755 5789999999985 444
No 75
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=97.32 E-value=0.0048 Score=66.40 Aligned_cols=136 Identities=9% Similarity=0.051 Sum_probs=87.2
Q ss_pred ceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhc
Q psy5925 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIEN 324 (696)
Q Consensus 245 LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~ 324 (696)
++.+.+|+||. ++..|+|+.|++....+.... ...-.+++|.... ..|.. ..
T Consensus 1 ~~~vviD~ETT-------g~~~d~IieIgav~v~~g~i~--~~f~~lv~P~~~~----~~~~~---------------~~ 52 (309)
T PRK06195 1 MNFVAIDFETA-------NEKRNSPCSIGIVVVKDGEIV--EKVHYLIKPKEMR----FMPIN---------------IG 52 (309)
T ss_pred CcEEEEEEeCC-------CCCCCceEEEEEEEEECCEEE--EEEEEEECCCCCC----CChhh---------------ee
Confidence 35678999986 246799999998766443211 1123566664210 01111 11
Q ss_pred cccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccc
Q psy5925 325 VRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR 404 (696)
Q Consensus 325 ~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR 404 (696)
++...+ -.|.-.....+.+..|.+++. -++++|||. .||+++|..-++.+++...
T Consensus 53 IhGIT~----------------e~v~~ap~f~ev~~~~~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~~~~~~----- 107 (309)
T PRK06195 53 IHGIRP----------------HMVEDELEFDKIWEKIKHYFN---NNLVIAHNA-SFDISVLRKTLELYNIPMP----- 107 (309)
T ss_pred ccCcCH----------------HHHhCCCCHHHHHHHHHHHhC---CCEEEEECc-HHHHHHHHHHHHHhCCCCC-----
Confidence 222221 122234567788888888885 479999999 6999999877777765422
Q ss_pred cccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 405 ITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
....+|++.++|..+ .+.+|+|++++.++
T Consensus 108 ----------------------~~~~idT~~lar~l~~~~~~~~L~~L~~~~ 137 (309)
T PRK06195 108 ----------------------SFEYICTMKLAKNFYSNIDNARLNTVNNFL 137 (309)
T ss_pred ----------------------CCCEEEHHHHHHHHcCCCCcCCHHHHHHHc
Confidence 012579999888876 56899999999986
No 76
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.31 E-value=0.0072 Score=65.16 Aligned_cols=161 Identities=12% Similarity=0.083 Sum_probs=101.0
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecC-CCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTC-PPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~-~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
.+...+.+|+||.. .+|..|+|+.|++...+. .... ..-..++++... |..
T Consensus 13 ~~~~fvvlD~ETTG-----l~p~~d~IIeIgav~v~~~g~i~--~~~~~lv~P~~~-------~~~-------------- 64 (313)
T PRK06063 13 YPRGWAVVDVETSG-----FRPGQARIISLAVLGLDADGNVE--QSVVTLLNPGVD-------PGP-------------- 64 (313)
T ss_pred CCCCEEEEEEECCC-----CCCCCCEEEEEEEEEEECCceee--eEEEEEECcCCC-------CCC--------------
Confidence 35678889999982 357789999999876542 2111 122355665321 111
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccc
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQE 401 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~ 401 (696)
..++...+ -.+.-...-.+.+..|.+++. -++++|||. .||+++|..-++.+|+...
T Consensus 65 -~~IhGIt~----------------e~l~~ap~f~ev~~~l~~~l~---~~~lVaHNa-~FD~~fL~~~~~r~g~~~~-- 121 (313)
T PRK06063 65 -THVHGLTA----------------EMLEGQPQFADIAGEVAELLR---GRTLVAHNV-AFDYSFLAAEAERAGAELP-- 121 (313)
T ss_pred -eecCCCCH----------------HHHhCCCCHHHHHHHHHHHcC---CCEEEEeCH-HHHHHHHHHHHHHcCCCCC--
Confidence 01122211 112233556788888888874 479999998 7999999888877765421
Q ss_pred ccccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccH
Q psy5925 402 LSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYK 480 (696)
Q Consensus 402 lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~ 480 (696)
....+|++...|... .+.+|+|+++++++ |......
T Consensus 122 -------------------------~~~~ldTl~lar~~~~~~~~~kL~~l~~~~-gi~~~~~----------------- 158 (313)
T PRK06063 122 -------------------------VDQVMCTVELARRLGLGLPNLRLETLAAHW-GVPQQRP----------------- 158 (313)
T ss_pred -------------------------CCCEEehHHHHHHhccCCCCCCHHHHHHHc-CCCCCCC-----------------
Confidence 012578888887754 67899999999875 4321110
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q psy5925 481 WMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 481 ~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+-++.||..+.+|+.++
T Consensus 159 ----H~Al~DA~ata~l~~~l 175 (313)
T PRK06063 159 ----HDALDDARVLAGILRPS 175 (313)
T ss_pred ----CCcHHHHHHHHHHHHHH
Confidence 12467888888887665
No 77
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=97.31 E-value=0.0011 Score=75.05 Aligned_cols=123 Identities=12% Similarity=0.138 Sum_probs=93.2
Q ss_pred CCHHHHHHHHHHHHHHhCCC-EEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEE
Q psy5925 353 SNEKELFSIFIENVRQWDPD-ILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVI 431 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPD-IIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~l 431 (696)
.+|++.+..|++++..+ |+ -|+.|| +|-.++|.+.|..++.... .+..+ . +-.+
T Consensus 326 ~~E~~~~~~f~~~l~~~-~~~~i~hY~--~~e~~~l~rla~~~~~~~~-~~~~l--------------------~-~~~v 380 (457)
T TIGR03491 326 NTEELAWQQFLQLLQSY-PDAPIYHYG--ETEKDSLRRLAKRYGTPEA-EIEEL--------------------L-KRFV 380 (457)
T ss_pred hHHHHHHHHHHHHHHHC-CCCeEEeeC--HHHHHHHHHHHHHcCCCHH-HHHHH--------------------H-HHhe
Confidence 68999999999999887 77 689999 4668999999988887621 11111 0 1478
Q ss_pred ehHHHHhhhc--CCCCCCHHHHHHHHcCCCc-CCCChhhHHHHHh----cCCcccHHHHHHHHHHHHHHHHHHHHH
Q psy5925 432 NLWRLLRHEV--NLQSYTFENIMYHVLHERI-PLHSWKLLTCWWE----HRTHLYKWMTVEHYLIRVTGIIRLIEQ 500 (696)
Q Consensus 432 Dl~~~~r~~~--kl~sysL~~Va~~~L~~~k-~~~~~~~l~~~~~----~~~~~~~~~~i~Y~l~D~~l~~~L~~k 500 (696)
|++..+++.+ ...||+|++|+..+--+.. +..+..+...||. +++...+..++.||..|+..+..|.+.
T Consensus 381 DL~~~vr~~~~~p~~sysLK~v~~~lg~~~~~~~~~G~~ai~~y~~~~~~~~~~~l~~l~~YN~dD~~At~~l~~w 456 (457)
T TIGR03491 381 DIHTIVRRSWILPIESYSLKSIARWLGFEWRQKEASGAKSLLWYRQWKKTGDRRLLERILRYNEDDCRATWIVADW 456 (457)
T ss_pred ehHHHHHhhEECCCCCCCHHHHHHHhCcccCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 9999999865 7899999999997643333 4578877777774 344445788999999999999988754
No 78
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=97.28 E-value=0.0064 Score=58.01 Aligned_cols=73 Identities=12% Similarity=0.085 Sum_probs=57.4
Q ss_pred eCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEE
Q psy5925 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVI 431 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~l 431 (696)
.....+.+.+|.+++.. ++++|||. .||+.+|..-++.+|++... ...+
T Consensus 61 ~~~~~~v~~~l~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~g~~~~~---------------------------~~~i 109 (156)
T cd06130 61 APTFPEVWPEIKPFLGG---SLVVAHNA-SFDRSVLRAALEAYGLPPPP---------------------------YQYL 109 (156)
T ss_pred CCCHHHHHHHHHHHhCC---CEEEEeCh-HHhHHHHHHHHHHcCCCCCC---------------------------CCEE
Confidence 34567889999998865 79999998 79999999888887765320 1267
Q ss_pred ehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 432 NLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 432 Dl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
|++...+..+ .+.+++|+++++.+
T Consensus 110 dt~~~~~~~~~~~~~~~L~~l~~~~ 134 (156)
T cd06130 110 CTVRLARRVWPLLPNHKLNTVAEHL 134 (156)
T ss_pred EHHHHHHHHhccCCCCCHHHHHHHc
Confidence 8888888766 46899999999975
No 79
>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=97.23 E-value=0.013 Score=56.91 Aligned_cols=103 Identities=17% Similarity=0.139 Sum_probs=70.3
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
......+.+..|.+++.. .+++|||+ .||+.+|..-++.+|+... .. .-...
T Consensus 64 ~~~~~~~v~~~l~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~~~~~~-----~~-------------------~~~~~ 115 (167)
T cd06131 64 DKPKFAEIADEFLDFIRG---AELVIHNA-SFDVGFLNAELSLLGLGKK-----II-------------------DFCRV 115 (167)
T ss_pred cCCCHHHHHHHHHHHHCC---CeEEEeCh-HHhHHHHHHHHHHhCCCcc-----cc-------------------cCCCc
Confidence 345678899999988754 56899999 6999999888777764321 00 00246
Q ss_pred EehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 431 INLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 431 lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+|+.+..++.+.-.+++|+++++++ |-..... -.+.++.|+..+.+|+.+|
T Consensus 116 idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~-------------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 116 IDTLALARKKFPGKPNSLDALCKRF-GIDNSHR-------------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred eEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC-------------------CCCChHHHHHHHHHHHHHh
Confidence 8998888887655788999999986 3221000 0123467888888888765
No 80
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=97.23 E-value=0.0089 Score=61.96 Aligned_cols=165 Identities=10% Similarity=0.021 Sum_probs=98.8
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
...+.+.+|+||.. -+|..|+|+.|++..-++........-..++++.. |+. ..+
T Consensus 45 ~~~~~vviD~ETTG-----l~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~--------~i~------------~~~ 99 (239)
T PRK09146 45 SEVPFVALDFETTG-----LDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRR--------PLE------------EES 99 (239)
T ss_pred ccCCEEEEEeECCC-----CCCCCCcEEEEEEEEEECCeEeecceEEEEECCCC--------CCC------------hhh
Confidence 46788999999982 34678999999987665432110011234555532 111 111
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
..++...+ -.+..-.+..+.+.+|.+++. .++++|||. .||+++|..-++.++....
T Consensus 100 ~~IhGIt~----------------e~l~~ap~~~evl~~l~~~~~---~~~lVaHna-~FD~~fL~~~l~~~~~~~~--- 156 (239)
T PRK09146 100 VVIHGITH----------------SELQDAPDLERILDELLEALA---GKVVVVHYR-RIERDFLDQALRNRIGEGI--- 156 (239)
T ss_pred hhhcCCCH----------------HHHhCCCCHHHHHHHHHHHhC---CCEEEEECH-HHHHHHHHHHHHHhcCCCC---
Confidence 11222221 112234567788999988864 479999997 6999999888765422110
Q ss_pred cccccccccccCCCccccceeeecccEEEehHHHHhhhc--------------CCCCCCHHHHHHHHcCCCcCCCChhhH
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV--------------NLQSYTFENIMYHVLHERIPLHSWKLL 468 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~--------------kl~sysL~~Va~~~L~~~k~~~~~~~l 468 (696)
. .-.+|+..+.++.+ ++.+|+|++++.++ |-. ...
T Consensus 157 -----------------------~-~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~-gl~--~~~---- 205 (239)
T PRK09146 157 -----------------------E-FPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRY-GLP--AYS---- 205 (239)
T ss_pred -----------------------C-CceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHc-CCC--CCC----
Confidence 0 12578888776532 24788999998874 322 110
Q ss_pred HHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 469 TCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 469 ~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 206 ---------------~H~Al~DA~ata~l~~~~ 223 (239)
T PRK09146 206 ---------------PHHALTDAIATAELLQAQ 223 (239)
T ss_pred ---------------CCCcHHHHHHHHHHHHHH
Confidence 012467888888888765
No 81
>PRK07740 hypothetical protein; Provisional
Probab=97.21 E-value=0.0065 Score=63.18 Aligned_cols=163 Identities=15% Similarity=0.093 Sum_probs=98.7
Q ss_pred CCceEEEEEEEeecCCCCCCCCCC-CcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAY-DEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~-D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
..++++.+|+||.. .+|.. |+|+.|++...++.... ...-..++++.. |+. ..
T Consensus 57 ~~~~~vv~D~ETTG-----l~p~~~deIIeIgaV~~~~~~i~-~~~f~~lv~P~~--------~i~------------~~ 110 (244)
T PRK07740 57 TDLPFVVFDLETTG-----FSPQQGDEILSIGAVKTKGGEVE-TDTFYSLVKPKR--------PIP------------EH 110 (244)
T ss_pred cCCCEEEEEEeCCC-----CCCCCCCeEEEEEEEEEECCEEE-EEEEEEEeCcCC--------CCC------------hh
Confidence 45778999999872 34555 89999998877553210 011123455532 111 11
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHc-CCCCcc
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVL-GLNLNQ 400 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~l-gi~~~~ 400 (696)
+..++...+ -.+.......+.+..|.+++. -++++|||+ .||+.+|.+-+... +.+.
T Consensus 111 ~~~ltGIt~----------------e~l~~ap~~~evl~~f~~fi~---~~~lVahna-~fD~~fL~~~~~~~~~~~~-- 168 (244)
T PRK07740 111 ILELTGITA----------------EDVAFAPPLAEVLHRFYAFIG---AGVLVAHHA-GHDKAFLRHALWRTYRQPF-- 168 (244)
T ss_pred heeccCCCH----------------HHHhCCCCHHHHHHHHHHHhC---CCEEEEeCH-HHHHHHHHHHHHHhcCCCc--
Confidence 111222211 123345678899999999875 469999997 79999987644332 1110
Q ss_pred cccccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCccc
Q psy5925 401 ELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLY 479 (696)
Q Consensus 401 ~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~ 479 (696)
..-.+|+...++... ...+++|++++.+ +|.....
T Consensus 169 --------------------------~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~----------------- 204 (244)
T PRK07740 169 --------------------------THRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPR----------------- 204 (244)
T ss_pred --------------------------CCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCC-----------------
Confidence 024688888877655 3568999999976 4432211
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q psy5925 480 KWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 480 ~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+.++.||..+++|+.++
T Consensus 205 ----~H~Al~Da~ata~l~~~l 222 (244)
T PRK07740 205 ----RHHALGDALMTAKLWAIL 222 (244)
T ss_pred ----CCCcHHHHHHHHHHHHHH
Confidence 123578888998888876
No 82
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.19 E-value=0.017 Score=59.53 Aligned_cols=169 Identities=11% Similarity=-0.018 Sum_probs=101.0
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecC-CCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTC-PPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFST 320 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~-~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~ 320 (696)
+...+++.||+||.. -+|..|+|+.|++...+. .... ...-.++++.. |+. .
T Consensus 3 ~~~~~~vv~D~ETTG-----l~p~~d~Iieig~v~v~~~g~~~--~~~~~lv~P~~--------~i~------------~ 55 (232)
T PRK07942 3 WHPGPLAAFDLETTG-----VDPETARIVTAALVVVDADGEVV--ESREWLADPGV--------EIP------------E 55 (232)
T ss_pred cccCcEEEEEeccCC-----CCCCCCeeEEEEEEEEeCCCccc--cceEEEECCCC--------CCC------------H
Confidence 345678899999982 367889999998876542 2111 11123555531 111 1
Q ss_pred hhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHh--CCCEEEecccccccHHHHHHHHHHcCCCC
Q psy5925 321 FIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQW--DPDILIGYEIETLSWGYLLERGYVLGLNL 398 (696)
Q Consensus 321 ~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~--DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~ 398 (696)
.+..++...+ .+++ ..-..+.+.+..|...+..+ +-.+++|||. .||+.+|..=++++|+..
T Consensus 56 ~a~~IhGIt~-----e~l~----------~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~~ 119 (232)
T PRK07942 56 EASAVHGITT-----EYAR----------AHGRPAAEVLAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLPS 119 (232)
T ss_pred HHHHHhCCCH-----HHHH----------hhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCCC
Confidence 1112222221 0010 01124567899999988763 4579999999 799999987777776542
Q ss_pred cccccccccccccccCCCccccceeeecccEEEehHHHHhhhc--CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCC
Q psy5925 399 NQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV--NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRT 476 (696)
Q Consensus 399 ~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~--kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~ 476 (696)
. ....++|.+.+.+... ...+++|+++++++ |.....
T Consensus 120 ~--------------------------~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~-gi~~~~-------------- 158 (232)
T PRK07942 120 L--------------------------VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHY-GVRLDN-------------- 158 (232)
T ss_pred c--------------------------cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHc-CCCCCC--------------
Confidence 2 0113568777665432 34679999999885 432111
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 477 HLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 477 ~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 159 -------aH~Al~Da~ata~l~~~l 176 (232)
T PRK07942 159 -------AHEATADALAAARVAWAL 176 (232)
T ss_pred -------CCChHHHHHHHHHHHHHH
Confidence 112467888888888876
No 83
>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=97.09 E-value=0.021 Score=58.65 Aligned_cols=102 Identities=17% Similarity=0.156 Sum_probs=70.9
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
....+.+..|.+++.. ..++|||. .||+++|..-+..+|... .+... . --++|
T Consensus 67 p~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g~~~----~~~~~-----------------~--~~~iD 119 (225)
T TIGR01406 67 PKFKEIADEFLDFIGG---SELVIHNA-AFDVGFLNYELERLGPTI----KKIGE-----------------F--CRVID 119 (225)
T ss_pred CCHHHHHHHHHHHhCC---CEEEEEec-HHHHHHHHHHHHHhCCCC----ccccc-----------------C--CCEEE
Confidence 5677899999998864 57899999 699999998887776311 10000 0 12689
Q ss_pred hHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 433 LWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 433 l~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
++...|+.+.-.+|+|+++++++ |..... +-.+-++.||.++.+++.++
T Consensus 120 Tl~lar~~~p~~~~~L~~L~~~~-gi~~~~-------------------r~~H~Al~DA~~~a~v~~~l 168 (225)
T TIGR01406 120 TLAMARERFPGQRNSLDALCKRF-KVDNSH-------------------RTLHGALLDAHLLAEVYLAL 168 (225)
T ss_pred HHHHHHHHcCCCCCCHHHHHHhc-CCCCCC-------------------CCCcCHHHHHHHHHHHHHHH
Confidence 99999888766789999999986 321110 00122578899998888765
No 84
>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=97.06 E-value=0.0082 Score=74.98 Aligned_cols=141 Identities=18% Similarity=0.168 Sum_probs=94.1
Q ss_pred CceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIE 323 (696)
Q Consensus 244 ~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~ 323 (696)
..+.+.||+||.. .+|..|+|+.|+++...+...- ..--.+++|.. |+. ..+.
T Consensus 189 ~~~~VVfDiETTG-----L~~~~d~IIEIGAVkv~~g~ii--d~f~~~V~P~~--------~I~------------~~~~ 241 (1213)
T TIGR01405 189 DATYVVFDIETTG-----LSPQYDEIIEFGAVKVKNGRII--DKFQFFIKPHE--------PLS------------AFVT 241 (1213)
T ss_pred CCcEEEEEeEecC-----CCCCCCeEEEEEEEEEECCeEE--EEEEEEECCCC--------CCC------------HHHH
Confidence 3489999999982 3567899999998877553210 11123455532 111 1111
Q ss_pred ccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccc
Q psy5925 324 NVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403 (696)
Q Consensus 324 ~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lg 403 (696)
.++..++ -.+.-..++.+.|.+|.+++. ..+++||| -.||+++|.+.++++|++.+.
T Consensus 242 ~ltGIT~----------------e~L~~ap~~~evl~~f~~fl~---~~iLVaHN-a~FD~~fL~~~~~r~g~~~~~--- 298 (1213)
T TIGR01405 242 ELTGITQ----------------DMLENAPEIEEVLEKFKEFFK---DSILVAHN-ASFDIGFLNTNFEKVGLEPLE--- 298 (1213)
T ss_pred HHhCCCH----------------HHHhCCCCHHHHHHHHHHHhC---CCeEEEEC-hHHHHHHHHHHHHHcCCCccC---
Confidence 1222211 112345688999999999986 37999999 589999999999888775320
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCC
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHER 459 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~ 459 (696)
.-.+|+..+.|..+ .+.+|+|+++++++ |..
T Consensus 299 ------------------------~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~ 330 (1213)
T TIGR01405 299 ------------------------NPVIDTLELARALNPEYKSHRLGNICKKL-GVD 330 (1213)
T ss_pred ------------------------CCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCC
Confidence 13679988888765 57899999999985 543
No 85
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=97.05 E-value=0.018 Score=57.95 Aligned_cols=162 Identities=14% Similarity=0.097 Sum_probs=95.0
Q ss_pred ceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhc
Q psy5925 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIEN 324 (696)
Q Consensus 245 LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~ 324 (696)
-..+++|+||.. .+|..|+|+.|++...++........--.++++... +. ..+..
T Consensus 29 ~~~vviD~ETTG-----l~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~--------i~------------~~~~~ 83 (202)
T PRK09145 29 DEWVALDCETTG-----LDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQS--------LS------------AESIK 83 (202)
T ss_pred CCEEEEEeECCC-----CCCCCCceEEEEEEEEECCEEeecCceEEEECCCCC--------CC------------HhHhh
Confidence 467889999982 357789999999877654311000011234555321 00 11111
Q ss_pred cccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHH-cCCCCccccc
Q psy5925 325 VRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYV-LGLNLNQELS 403 (696)
Q Consensus 325 ~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~-lgi~~~~~lg 403 (696)
++...+ -.+....++.+.+.+|.+++.. .+++|||. .||+.+|..-++. ++.+..
T Consensus 84 ihGIt~----------------~~l~~~~~~~~vl~~~~~~i~~---~~lv~hn~-~fD~~fL~~~~~~~~~~~~~---- 139 (202)
T PRK09145 84 IHRLRH----------------QDLEDGLSEEEALRQLLAFIGN---RPLVGYYL-EFDVAMLNRYVRPLLGIPLP---- 139 (202)
T ss_pred hcCcCH----------------HHHhcCCCHHHHHHHHHHHHcC---CeEEEeCH-HHHHHHHHHHHHHhcCCCCC----
Confidence 222211 1123456788999999999863 68999997 6999999887764 343321
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhh----hc--CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCc
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRH----EV--NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTH 477 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~----~~--kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~ 477 (696)
.-.+|+...+.. .+ ...+++|+++++++ |.....
T Consensus 140 ------------------------~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~--------------- 179 (202)
T PRK09145 140 ------------------------NPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL-DLPVLG--------------- 179 (202)
T ss_pred ------------------------CCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-CCCCCC---------------
Confidence 013566554422 11 24579999999875 322110
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 478 LYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 478 ~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 180 ------~H~Al~DA~ata~l~~~l 197 (202)
T PRK09145 180 ------RHDALNDAIMAALIFLRL 197 (202)
T ss_pred ------CCCcHHHHHHHHHHHHHH
Confidence 012467888888888776
No 86
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.95 E-value=0.012 Score=61.06 Aligned_cols=170 Identities=9% Similarity=0.012 Sum_probs=103.9
Q ss_pred CCceEEEEEEEeecCCCCCCCCC-CCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPA-YDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTF 321 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~-~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~ 321 (696)
++++.+.||+||.. -+|. .|+|+.|++.--.+..... ..--.+++|.. |+. ..
T Consensus 2 ~~~r~vvlDtETTG-----ldp~~~drIIEIGaV~v~~~~~~~-~~f~~~i~P~~--------~i~------------~~ 55 (240)
T PRK05711 2 AIMRQIVLDTETTG-----LNQREGHRIIEIGAVELINRRLTG-RNFHVYIKPDR--------LVD------------PE 55 (240)
T ss_pred CCCeEEEEEeeCCC-----cCCCCCCeEEEEEEEEEECCEEec-cEEEEEECcCC--------cCC------------HH
Confidence 46789999999982 2454 7999999876543321110 11124555532 110 11
Q ss_pred hhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccc
Q psy5925 322 IENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQE 401 (696)
Q Consensus 322 ~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~ 401 (696)
+..++...++ .+.--....+++..|.+++.. ..++|||. .||+++|..-++.+|....
T Consensus 56 a~~VHGIT~e----------------~l~~~p~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g~~~~-- 113 (240)
T PRK05711 56 ALAVHGITDE----------------FLADKPTFAEVADEFLDFIRG---AELIIHNA-PFDIGFMDYEFALLGRDIP-- 113 (240)
T ss_pred HhhhcCCCHH----------------HHcCCCCHHHHHHHHHHHhCC---CEEEEEcc-HHhHHHHHHHHHHhCCCCC--
Confidence 1123322211 122335678899999998864 46899999 7999999887777763211
Q ss_pred ccccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHH
Q psy5925 402 LSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 481 (696)
Q Consensus 402 lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~ 481 (696)
+.. .. .-++|++...|+.+.-.+++|+++++++ |.....
T Consensus 114 --~~~-----------------~~--~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~~------------------- 152 (240)
T PRK05711 114 --KTN-----------------TF--CKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNSH------------------- 152 (240)
T ss_pred --ccc-----------------cc--CceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCCC-------------------
Confidence 110 00 1278999999888766789999999975 321100
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy5925 482 MTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 482 ~~i~Y~l~D~~l~~~L~~kl 501 (696)
+-.+-++.|+.++.+++.++
T Consensus 153 r~~H~AL~DA~~~A~v~~~l 172 (240)
T PRK05711 153 RTLHGALLDAEILAEVYLAM 172 (240)
T ss_pred CCCCCHHHHHHHHHHHHHHH
Confidence 01223578899999888776
No 87
>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=96.93 E-value=0.017 Score=58.90 Aligned_cols=100 Identities=15% Similarity=0.019 Sum_probs=65.5
Q ss_pred eCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEE
Q psy5925 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVI 431 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~l 431 (696)
.....+.+..|.+++. .++++|||. .|||++|..-+.+++.... . ..-.+
T Consensus 71 ~p~~~ev~~~~~~~~~---~~~lVaHNa-~FD~~fL~~~~~r~~~~~~--------~------------------~~~~~ 120 (217)
T TIGR00573 71 KPDFKEIAEDFADYIR---GAELVIHNA-SFDVGFLNYEFSKLYKVEP--------K------------------TNDVI 120 (217)
T ss_pred CCCHHHHHHHHHHHhC---CCEEEEecc-HHHHHHHHHHHHHhcCCCC--------C------------------cccee
Confidence 3577789999999875 379999998 7999999887766532211 0 01245
Q ss_pred ehHHHHhh---hcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 432 NLWRLLRH---EVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 432 Dl~~~~r~---~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
|+...++. .++-.+++|+++++++ |-.... +-..-++.||..+.+|+.++
T Consensus 121 dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~-------------------~~~H~Al~DA~~ta~l~~~l 173 (217)
T TIGR00573 121 DTTDTLQYARPEFPGKRNTLDALCKRY-EITNSH-------------------RALHGALADAFILAKLYLVM 173 (217)
T ss_pred cHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC-------------------cccCCHHHHHHHHHHHHHHH
Confidence 65554443 3444678999998875 422110 01123578999999998886
No 88
>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=96.86 E-value=0.023 Score=53.49 Aligned_cols=75 Identities=17% Similarity=0.158 Sum_probs=54.7
Q ss_pred eCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEE
Q psy5925 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVI 431 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~l 431 (696)
-....+.+..|.+++.. ++++|||+ .||+.+|.+.+..++...+ ....+
T Consensus 63 ~~~~~~~~~~~~~~l~~---~~~v~~n~-~fD~~~l~~~~~~~~~~~~---------------------------~~~~i 111 (159)
T cd06127 63 APPFEEVLPEFLEFLGG---RVLVAHNA-SFDLRFLNRELRRLGGPPL---------------------------PNPWI 111 (159)
T ss_pred CCCHHHHHHHHHHHHCC---CEEEEeCc-HhhHHHHHHHHHHhCCCCC---------------------------CCCee
Confidence 34566888888888875 89999999 8999999999988872211 12478
Q ss_pred ehHHHHhhhc-CCCCCCHHHHHHHHcC
Q psy5925 432 NLWRLLRHEV-NLQSYTFENIMYHVLH 457 (696)
Q Consensus 432 Dl~~~~r~~~-kl~sysL~~Va~~~L~ 457 (696)
|+...++..+ ...+++|..+....++
T Consensus 112 Dt~~~~~~~~~~~~~~~l~~~~~~~~~ 138 (159)
T cd06127 112 DTLRLARRLLPGLRSHRLGLLLAERYG 138 (159)
T ss_pred EHHHHHHHHcCCCCcCchHHHHHHHcC
Confidence 9999887765 4567788877333333
No 89
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.81 E-value=0.024 Score=69.30 Aligned_cols=135 Identities=11% Similarity=0.101 Sum_probs=87.6
Q ss_pred EEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhccc
Q psy5925 247 VLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVR 326 (696)
Q Consensus 247 ilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~~~ 326 (696)
.+.+|+||.. .+|..|+|+.|+++.-++.... ..--.+++|.. |+. ..+..++
T Consensus 2 ~vvvD~ETTG-----~~~~~~~IIeig~v~v~~~~i~--~~f~~~v~P~~--------~i~------------~~~~~lt 54 (850)
T TIGR01407 2 YAVVDLETTG-----TQLSFDKIIQIGIVVVEDGEIV--DTFHTDVNPNE--------PIP------------PFIQELT 54 (850)
T ss_pred EEEEEEECCC-----CCCCCCeEEEEEEEEEECCEEE--EEEEEEeCCCC--------CCC------------hhhhhhc
Confidence 5789999983 4577899999998776443211 11234555532 111 1111122
Q ss_pred cCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccc
Q psy5925 327 QWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRIT 406 (696)
Q Consensus 327 ~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~ 406 (696)
|..- -.+.......+.+..|.+++. ..+++|||+ .||+++|.+-++.+|++.+.
T Consensus 55 --------GIt~--------e~l~~ap~~~ev~~~l~~~l~---~~~~VahN~-~fD~~fL~~~~~~~g~~~~~------ 108 (850)
T TIGR01407 55 --------GISD--------NMLQQAPYFSQVAQEIYDLLE---DGIFVAHNV-HFDLNFLAKALKDCGYEPLP------ 108 (850)
T ss_pred --------CcCH--------HHHhCCCCHHHHHHHHHHHhC---CCEEEEeCc-HHHHHHHHHHHHHcCCCCCC------
Confidence 2111 112235678889999988875 479999998 69999999888877765320
Q ss_pred cccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 407 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 407 ~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
...+|+..+.+..+ ...+|+|+++++++
T Consensus 109 ---------------------~~~iDt~~l~~~~~p~~~~~~L~~l~~~~ 137 (850)
T TIGR01407 109 ---------------------KPRIDTVELAQIFFPTEESYQLSELSEAL 137 (850)
T ss_pred ---------------------CCeEeHHHHHHHhcCCCCCCCHHHHHHHC
Confidence 12578888877665 57899999999984
No 90
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=96.79 E-value=0.011 Score=58.54 Aligned_cols=44 Identities=14% Similarity=0.070 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCC
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLN 397 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~ 397 (696)
.++.+++..|..++.+ ..++++|||.-.||+++|..=+.+++..
T Consensus 67 ~~~~~~l~~~~~~~~~-~~~~lVahn~~~FD~~fL~~~~~r~~~~ 110 (183)
T cd06138 67 LSEYEFIAKIHRLFNT-PGTCIVGYNNIRFDDEFLRFAFYRNLYD 110 (183)
T ss_pred CCHHHHHHHHHHHHcc-CCCcEEeeCchhhHHHHHHHHHHHCCCc
Confidence 5678899999999874 3468999997789999997766666654
No 91
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.79 E-value=0.028 Score=69.34 Aligned_cols=136 Identities=13% Similarity=0.115 Sum_probs=87.8
Q ss_pred eEEEEEEEeecCCCCCCCCC-CCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhc
Q psy5925 246 TVLAVEIHAISRALLKPDPA-YDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIEN 324 (696)
Q Consensus 246 tilsleIe~~sr~~~~Pdp~-~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~ 324 (696)
+.+.+|+||.. .+|. .|+|+.|+++.-.+...- .+--.+++|.. |+. ..+..
T Consensus 4 ~~vvvD~ETTG-----~~p~~~d~IIeigav~v~~~~i~--~~f~~~v~P~~--------~i~------------~~~~~ 56 (928)
T PRK08074 4 RFVVVDLETTG-----NSPKKGDKIIQIAAVVVEDGEIL--ERFSSFVNPER--------PIP------------PFITE 56 (928)
T ss_pred CEEEEEEeCCC-----CCCCCCCcEEEEEEEEEECCEEE--EEEEEEECcCC--------CCC------------HHHhh
Confidence 46789999882 2343 389999998776543211 11134566532 111 11112
Q ss_pred cccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccc
Q psy5925 325 VRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR 404 (696)
Q Consensus 325 ~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR 404 (696)
++..++ -.+.......+.+..|.+++. ..+++|||+ .|||++|.+-+...|++..
T Consensus 57 ltGIt~----------------~~l~~ap~f~ev~~~l~~~l~---~~~~VaHN~-~FD~~fL~~~~~~~g~~~~----- 111 (928)
T PRK08074 57 LTGISE----------------EMVKQAPLFEDVAPEIVELLE---GAYFVAHNV-HFDLNFLNEELERAGYTEI----- 111 (928)
T ss_pred cCCCCH----------------HHHhcCCCHHHHHHHHHHHhC---CCeEEEECh-HHHHHHHHHHHHHcCCCCC-----
Confidence 222221 123345677889999998875 469999998 5999999887777776432
Q ss_pred cccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 405 ITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
.+ -.+|+..+.+..+ .+.+|+|+++++++
T Consensus 112 ---------------------~~-~~iDt~~la~~~~p~~~~~~L~~l~~~l 141 (928)
T PRK08074 112 ---------------------HC-PKLDTVELARILLPTAESYKLRDLSEEL 141 (928)
T ss_pred ---------------------CC-CeeeHHHHHHHhcCCCCCCCHHHHHHhC
Confidence 01 2689988887766 57999999999985
No 92
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=96.78 E-value=0.043 Score=55.51 Aligned_cols=172 Identities=8% Similarity=-0.046 Sum_probs=100.7
Q ss_pred CceEEEEEEEeecCC-CCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRA-LLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 244 ~LtilsleIe~~sr~-~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
.++.+.+|+||..-. ...|....|+|+.|+++.-++....+.. -.+|+|.... ++ ...+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f--~~lV~P~~~~------~i------------~~~~ 62 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTF--SSYVKPKTFP------SL------------TERC 62 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhh--cceECCCccC------cc------------Chhh
Confidence 467899999987432 2345444689999998765443211111 2234443110 01 0111
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
..++... +-.+.--.+..+.+.+|.+++... +.++++| + +||+.+|.+-++.+|++.. +
T Consensus 63 ~~ltGIt----------------~~~l~~ap~~~evl~~f~~~~~~~-~~~iv~~-~-~fD~~fL~~~~~~~~~~~~--~ 121 (207)
T PRK07748 63 KSFLGIT----------------QEDVDKGISFEELVEKLAEYDKRC-KPTIVTW-G-NMDMKVLKHNCEKAGVPFP--F 121 (207)
T ss_pred hhhcCcC----------------HHHHccCCCHHHHHHHHHHHhCcC-CeEEEEE-C-HHHHHHHHHHHHHcCCCCc--c
Confidence 1222222 112234567788999999988643 2466666 4 7999999998888876532 0
Q ss_pred cccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHH
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 481 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~ 481 (696)
. +..+|+....++.+ ...+++|++++..+ |-.. . +.
T Consensus 122 -----------------------~-~~~~dl~~~~~~~~~~~~~~~L~~~~~~~-gi~~--~-----------~~----- 158 (207)
T PRK07748 122 -----------------------K-GQCRDLSLEYKKFFGERNQTGLWKAIEEY-GKEG--T-----------GK----- 158 (207)
T ss_pred -----------------------c-ccceeHHHHHHHHhCcCCCCCHHHHHHHc-CCCC--C-----------CC-----
Confidence 0 23577777766655 34568999988864 2211 0 00
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy5925 482 MTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 482 ~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 159 --~H~Al~DA~~ta~l~~~l 176 (207)
T PRK07748 159 --HHCALDDAMTTYNIFKLV 176 (207)
T ss_pred --CcChHHHHHHHHHHHHHH
Confidence 012578999999998876
No 93
>PRK05168 ribonuclease T; Provisional
Probab=96.76 E-value=0.11 Score=52.88 Aligned_cols=174 Identities=11% Similarity=0.012 Sum_probs=98.5
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeec-C--CCCCCceEEEEEEcCC-CCCcccccCccccccccchhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYT-C--PPEEDRKVGIILIGQE-SELPEVRTKPIQMNFVSNEKEL 317 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~-~--~~~~~~~~g~ilv~~~-~~~~~~~~~p~~~~~~~~~~e~ 317 (696)
...++.+++|+||.. .+|+.|+|+.|++..-. + ........--.++++. +. ++.
T Consensus 14 ~~~~~~vv~D~ETTG-----l~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~-------~i~---------- 71 (211)
T PRK05168 14 FRGFLPVVIDVETAG-----FNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGA-------NLE---------- 71 (211)
T ss_pred hcCCceEEEEeeCCC-----CCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCC-------CCC----------
Confidence 346788999999982 45678999999977543 1 1110001123455552 11 110
Q ss_pred hhhhhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHh------CCCEEEecccccccHHHHHHHH
Q psy5925 318 FSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQW------DPDILIGYEIETLSWGYLLERG 391 (696)
Q Consensus 318 ~~~~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~------DPDIIvGyNi~~fDl~YL~~Ra 391 (696)
..+..++...++ ..+..-..+.+.+..|++.+.++ +=.+++|||. .||+.+|..-+
T Consensus 72 --~~~~~ihGIt~e---------------~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~ 133 (211)
T PRK05168 72 --PEALAFNGIDPD---------------NPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAA 133 (211)
T ss_pred --HHHHhhcCCCch---------------hhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHH
Confidence 111122222210 00112235666777777776642 1259999999 79999999888
Q ss_pred HHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHH
Q psy5925 392 YVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471 (696)
Q Consensus 392 ~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~ 471 (696)
+++|+... +. ..--++|+..+.|..+ ..++|++++.++ |......
T Consensus 134 ~r~~~~~~------~~------------------~~~~~iDt~~lar~~~--~~~~L~~l~~~~-gl~~~~~-------- 178 (211)
T PRK05168 134 ERAGLKRN------PF------------------HPFSTFDTATLSGLAL--GQTVLAKACQAA-GIEFDNK-------- 178 (211)
T ss_pred HHhCCCCC------CC------------------CCCcEeeHHHHHHHHc--CCCCHHHHHHHC-CCCCCCC--------
Confidence 88876311 00 0001789999888765 346899988874 3221000
Q ss_pred HhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 472 ~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
. .+-++.||..+.+|+.++
T Consensus 179 ---~--------~H~Al~DA~ata~l~~~l 197 (211)
T PRK05168 179 ---E--------AHSALYDTEKTAELFCEI 197 (211)
T ss_pred ---C--------CCChHHHHHHHHHHHHHH
Confidence 0 112467888888887765
No 94
>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=96.73 E-value=0.081 Score=52.78 Aligned_cols=101 Identities=13% Similarity=0.097 Sum_probs=65.1
Q ss_pred CHHHHHHHHHHHHHHh------CCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecc
Q psy5925 354 NEKELFSIFIENVRQW------DPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPG 427 (696)
Q Consensus 354 sE~eLL~~f~~~I~~~------DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~G 427 (696)
.+++-+..|.+.+.++ +=.+++|||. .||+.+|..=++.+|+... + ...
T Consensus 79 ~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~------~------------------~~~ 133 (189)
T cd06134 79 DEKEALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRN------P------------------FHP 133 (189)
T ss_pred chHHHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCC------C------------------CCC
Confidence 4455666666666543 1258999999 6999999988888876310 0 000
Q ss_pred cEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 428 RIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 428 Rl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.-.+|+.++.+..+ .+++|++++..+ |-..... + .+-++.||..+.+|+.++
T Consensus 134 ~~~lDt~~la~~~~--~~~~L~~l~~~~-gi~~~~~-----------~--------~H~Al~DA~ata~lf~~l 185 (189)
T cd06134 134 FSTFDTATLAGLAY--GQTVLAKACQAA-GIEFDNK-----------E--------AHSALYDTQKTAELFCKI 185 (189)
T ss_pred CcEEEHHHHHHHHh--CCCcHHHHHHHC-CCCCCCC-----------C--------CcChHHHHHHHHHHHHHH
Confidence 12689999888765 467899998864 4321100 0 122467888888888776
No 95
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.53 E-value=0.041 Score=66.81 Aligned_cols=138 Identities=9% Similarity=0.106 Sum_probs=85.9
Q ss_pred CceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhh
Q psy5925 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIE 323 (696)
Q Consensus 244 ~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~ 323 (696)
.-+.+.+|+||.. . +| .|+|+.|++..-.+.... ..--.+++|.. |+. ..+.
T Consensus 6 ~~~~vvvD~ETTG---l--~~-~d~IIeIgaV~v~~g~i~--~~f~~lv~P~~--------~i~------------~~~~ 57 (820)
T PRK07246 6 LRKYAVVDLEATG---A--GP-NASIIQVGIVIIEGGEII--DSYTTDVNPHE--------PLD------------EHIK 57 (820)
T ss_pred CCCEEEEEEecCC---c--CC-CCeEEEEEEEEEECCEEE--EEEEEEeCcCC--------CCC------------HhHh
Confidence 3567889999983 2 23 489999998766443211 11134555532 111 1111
Q ss_pred ccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCccccc
Q psy5925 324 NVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403 (696)
Q Consensus 324 ~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lg 403 (696)
.++..+ +-.+.......+.+..|.+++. -.+++|||+ .||+++|.+-+...|.+..
T Consensus 58 ~ltGIt----------------~e~l~~ap~~~ev~~~~~~~l~---~~~lVaHN~-~FD~~fL~~~~~~~g~~~~---- 113 (820)
T PRK07246 58 HLTGIT----------------DQQLAQAPDFSQVARHIYDLIE---DCIFVAHNV-KFDANLLAEALFLEGYELR---- 113 (820)
T ss_pred hcCCCC----------------HHHHhcCCCHHHHHHHHHHHhC---CCEEEEECc-HHHHHHHHHHHHHcCCCCC----
Confidence 222221 1123345678889999998875 379999999 6999999665544443311
Q ss_pred ccccccccccCCCccccceeeecccEEEehHHHHhhhc-CCCCCCHHHHHHHHcCC
Q psy5925 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHE 458 (696)
Q Consensus 404 R~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~-kl~sysL~~Va~~~L~~ 458 (696)
...+|++...+..+ .+.+|+|++++.++ |.
T Consensus 114 ------------------------~~~iDT~~la~~~~p~~~~~~L~~L~~~l-gl 144 (820)
T PRK07246 114 ------------------------TPRVDTVELAQVFFPTLEKYSLSHLSREL-NI 144 (820)
T ss_pred ------------------------CCceeHHHHHHHHhCCCCCCCHHHHHHHc-CC
Confidence 01378888887766 57899999999874 53
No 96
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=96.34 E-value=0.02 Score=50.67 Aligned_cols=35 Identities=26% Similarity=0.335 Sum_probs=31.2
Q ss_pred HHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCC
Q psy5925 362 FIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLN 397 (696)
Q Consensus 362 f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~ 397 (696)
|..++++..|.+++|||. .||++||.+++++++++
T Consensus 35 f~~~l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 35 LKDILRDKPLAILVGHNG-SFDLPFLNNRCAELGLK 69 (96)
T ss_pred HHHHHhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCC
Confidence 777888877899999999 89999999999988765
No 97
>PRK06722 exonuclease; Provisional
Probab=96.25 E-value=0.16 Score=53.77 Aligned_cols=170 Identities=7% Similarity=-0.034 Sum_probs=95.7
Q ss_pred ceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhc
Q psy5925 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIEN 324 (696)
Q Consensus 245 LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~ 324 (696)
-+.+.+|+||. +.....+..|+|+.|+++.-++........--.+++|.. ++. .++..
T Consensus 5 ~~~vViD~ETT--~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--------~I~------------~~i~~ 62 (281)
T PRK06722 5 THFIVFDIERN--FRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--------RLT------------RHTTK 62 (281)
T ss_pred CEEEEEEeeCC--CCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--------cCC------------HhHhh
Confidence 45678999995 321112455899999977655431110001124555532 111 12222
Q ss_pred cccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccc
Q psy5925 325 VRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR 404 (696)
Q Consensus 325 ~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR 404 (696)
++..+ +-.|.-.+.-.+.+..|.+++.. +.++++|. .||+.+|..=++.+|++... +
T Consensus 63 LTGIT----------------~emV~~AP~f~eVl~ef~~fig~---~~lvahna-~FD~~FL~~~l~~~gi~~p~-~-- 119 (281)
T PRK06722 63 LTGIT----------------KKDLIGVEKFPQIIEKFIQFIGE---DSIFVTWG-KEDYRFLSHDCTLHSVECPC-M-- 119 (281)
T ss_pred hcCCC----------------HHHHcCCCCHHHHHHHHHHHHCC---CcEEEEEe-HHHHHHHHHHHHHcCCCCCc-c--
Confidence 22222 12233455677899999999863 34555554 79999999988877765320 0
Q ss_pred cccccccccCCCccccceeeecccEEEehHHHHhhhc---CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHH
Q psy5925 405 ITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV---NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 481 (696)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~---kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~ 481 (696)
.-.-.+|+.+.++..+ .-.+++|+++++++ |-... +.
T Consensus 120 ---------------------~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~~-------------g~----- 159 (281)
T PRK06722 120 ---------------------EKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIWE-------------GK----- 159 (281)
T ss_pred ---------------------cccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCCC-------------CC-----
Confidence 0011467777665433 12457899998875 22110 00
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy5925 482 MTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 482 ~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+.+|+.++
T Consensus 160 --~HrAL~DA~~TA~L~l~l 177 (281)
T PRK06722 160 --QHRALADAENTANILLKA 177 (281)
T ss_pred --CcCcHHHHHHHHHHHHHH
Confidence 122478999999998886
No 98
>PRK11779 sbcB exonuclease I; Provisional
Probab=96.20 E-value=0.17 Score=57.50 Aligned_cols=179 Identities=12% Similarity=0.016 Sum_probs=96.3
Q ss_pred CCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhh
Q psy5925 243 YYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFI 322 (696)
Q Consensus 243 ~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~ 322 (696)
...+.+.+|+||.. -+|..|+|+.|++..-+..-......-.+++++... ..|.. .+
T Consensus 4 ~~~~fvv~D~ETTG-----LdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~-----~lp~p-------------~a 60 (476)
T PRK11779 4 MQPTFLWHDYETFG-----ANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADD-----YLPSP-------------EA 60 (476)
T ss_pred CCCcEEEEEEECCC-----CCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcC-----cCCCH-------------HH
Confidence 45778999999982 357899999998765433210000112344444310 00100 00
Q ss_pred hccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccc
Q psy5925 323 ENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402 (696)
Q Consensus 323 ~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~l 402 (696)
..++...+ .+++ ..-.+|.+.+..+.+++.. ...+++|||...||+.+|..-+....++..
T Consensus 61 ~~IhGIT~-----e~l~----------~~g~~e~e~~~~i~~~l~~-~~~~lVGhNni~FD~eflr~~~~r~~~d~y--- 121 (476)
T PRK11779 61 VLITGITP-----QEAL----------EKGLPEAEFAARIHAEFSQ-PGTCILGYNNIRFDDEVTRYIFYRNFYDPY--- 121 (476)
T ss_pred HHHhCCCH-----HHHH----------hcCCCHHHHHHHHHHHHhc-CCCEEEEeCchhhcHHHHHHHHHhccchHH---
Confidence 11222221 1111 0112678889999888863 236899999889999999777653333211
Q ss_pred cccccccccccCCCccccceeeeccc-EEEehHHHHhhhc-----------CCCCCCHHHHHHHHcCCCcCCCChhhHHH
Q psy5925 403 SRITEVEKRNSSRDEVKNTQLQMPGR-IVINLWRLLRHEV-----------NLQSYTFENIMYHVLHERIPLHSWKLLTC 470 (696)
Q Consensus 403 gR~~~~~~~~~~~~~~~~~~~~i~GR-l~lDl~~~~r~~~-----------kl~sysL~~Va~~~L~~~k~~~~~~~l~~ 470 (696)
.+ .+.. -.+| -.+|+.+.++... ...||+|+++++++ |.. ...
T Consensus 122 ~~-----~~~~-----------~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~-gI~--~~~------ 176 (476)
T PRK11779 122 AR-----EWQN-----------GNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKAN-GIE--HEN------ 176 (476)
T ss_pred HH-----HhcC-----------CCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHc-CCC--CCC------
Confidence 00 0000 0011 1344444433310 25889999999985 221 110
Q ss_pred HHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 471 WWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 471 ~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+-++.||..+++|+.++
T Consensus 177 -------------AHdALsDa~aT~~la~~l 194 (476)
T PRK11779 177 -------------AHDAMSDVYATIAMAKLI 194 (476)
T ss_pred -------------CCCcHHHHHHHHHHHHHH
Confidence 122578899999888876
No 99
>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=96.19 E-value=0.35 Score=48.68 Aligned_cols=102 Identities=14% Similarity=0.087 Sum_probs=65.2
Q ss_pred CCHHHHHHHHHHHHHHh------CCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeec
Q psy5925 353 SNEKELFSIFIENVRQW------DPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMP 426 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~------DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~ 426 (696)
..+.+.+..|+..+.++ +-.+++|||. .||+.+|.+=++++|.... .+ .
T Consensus 81 ~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~-~~-----------------------~ 135 (200)
T TIGR01298 81 VSEYEALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRN-PF-----------------------H 135 (200)
T ss_pred cchHHHHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCC-CC-----------------------C
Confidence 45566677777766432 3358999998 5999999877777765311 00 0
Q ss_pred ccEEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 427 GRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 427 GRl~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
-.-.+|+..+.|..+ .+++|+++++.+ |-..... -.+-++.||..+.+|+.++
T Consensus 136 ~~~~lDTl~lar~~~--~~~~L~~l~~~~-gi~~~~~-------------------~~H~Al~Da~ata~lf~~l 188 (200)
T TIGR01298 136 PFSTFDTATLAGLAY--GQTVLAKACQAA-GXDFDST-------------------QAHSALYDTEKTAELFCEI 188 (200)
T ss_pred CCcEEEHHHHHHHHc--CcccHHHHHHHc-CCCcccc-------------------chhhhHHhHHHHHHHHHHH
Confidence 012789999888655 567899998864 3321100 1223567888888888776
No 100
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=96.17 E-value=0.0024 Score=49.87 Aligned_cols=39 Identities=26% Similarity=0.733 Sum_probs=30.0
Q ss_pred CccceecCCCCCeeeec-CCCCeeecCCCCceeeccccc-cCCCcc
Q psy5925 5 RGFICELCNSEEVIFPW-QLSSVHRCNQCGACFHTKCHS-QLPCKR 48 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~-~~~~~~~c~~c~~~~h~~c~~-~~~cp~ 48 (696)
.|-+|..|+.. | +.++.+.|+.|+|.||+.||. .+.|-.
T Consensus 4 ~~~~C~~Cg~~-----~~~~dDiVvCp~CgapyHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 4 EGCKCPVCGKK-----FKDGDDIVVCPECGAPYHRDCWEKAGGCIN 44 (54)
T ss_pred cCccChhhCCc-----ccCCCCEEECCCCCCcccHHHHhhCCceEe
Confidence 35678888863 4 136889999999999999996 356654
No 101
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=96.11 E-value=0.2 Score=50.39 Aligned_cols=94 Identities=19% Similarity=0.246 Sum_probs=60.3
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
--.+-.+.+..|.+++.. .+++|||...||+.+|.+ .|.+.. ....
T Consensus 67 ~ap~~~evl~~f~~f~~~---~~lVaHNa~~fD~~fL~~----~g~~~~---------------------------~~~~ 112 (195)
T PRK07247 67 DAPKVEEVLAAFKEFVGE---LPLIGYNAQKSDLPILAE----NGLDLS---------------------------DQYQ 112 (195)
T ss_pred CCCCHHHHHHHHHHHHCC---CeEEEEeCcHhHHHHHHH----cCCCcC---------------------------CCce
Confidence 445677899999998854 479999998899998732 233211 0123
Q ss_pred EehHHHH--hhh--c-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 431 INLWRLL--RHE--V-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 431 lDl~~~~--r~~--~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+|+++.. ++. + .+.+|+|+++|+++ |-.... +-++.||..+..|+.++
T Consensus 113 idt~~~~~~~~~~~~~~~~~~~L~~La~~~-gi~~~~----------------------HrAl~DA~~ta~v~~~l 165 (195)
T PRK07247 113 VDLYDEAFERRSSDLNGIANLKLQTVADFL-GIKGRG----------------------HNSLEDARMTARVYESF 165 (195)
T ss_pred eehHHHHHHhhccccCCCCCCCHHHHHHhc-CCCCCC----------------------cCCHHHHHHHHHHHHHH
Confidence 4555433 221 1 46789999999975 332100 11367888888888776
No 102
>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=96.10 E-value=0.051 Score=52.15 Aligned_cols=34 Identities=18% Similarity=0.163 Sum_probs=27.7
Q ss_pred EEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHH
Q psy5925 350 HFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYL 387 (696)
Q Consensus 350 ~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL 387 (696)
.-..+..+.+.+|.+++. ..+++|||. .||+.+|
T Consensus 59 ~~a~~~~~~~~~l~~~l~---~~vlVgHn~-~fD~~~L 92 (152)
T cd06144 59 KDAPDFEEVQKKVAELLK---GRILVGHAL-KNDLKVL 92 (152)
T ss_pred cCCCCHHHHHHHHHHHhC---CCEEEEcCc-HHHHHHh
Confidence 345577889999998885 379999999 6999887
No 103
>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=95.92 E-value=0.12 Score=49.81 Aligned_cols=104 Identities=19% Similarity=0.249 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHhCCC-EEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHH
Q psy5925 358 LFSIFIENVRQWDPD-ILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRL 436 (696)
Q Consensus 358 LL~~f~~~I~~~DPD-IIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~ 436 (696)
++..+.+++. ||+ +.+|||+ .||+..|.+. +|+.. . -++|+ .+
T Consensus 65 ~~~~l~~ll~--~~~i~kv~~n~-~~D~~~L~~~---~~i~~---------------------------~--~~~D~-~l 108 (176)
T PF01612_consen 65 ILDALKELLE--DPNIIKVGHNA-KFDLKWLYRS---FGIDL---------------------------K--NVFDT-ML 108 (176)
T ss_dssp HHHHHHHHHT--TTTSEEEESSH-HHHHHHHHHH---HTS-----------------------------S--SEEEH-HH
T ss_pred hHHHHHHHHh--CCCccEEEEEE-echHHHHHHH---hcccc---------------------------C--Cccch-hh
Confidence 3444545554 666 5899999 5899988776 33321 1 14677 55
Q ss_pred HhhhcCCCC-CCHHHHHHHHcCCCcCCCChhhHHHHHh-cCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 437 LRHEVNLQS-YTFENIMYHVLHERIPLHSWKLLTCWWE-HRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 437 ~r~~~kl~s-ysL~~Va~~~L~~~k~~~~~~~l~~~~~-~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+..-..... ++|++++..++| ....+.+....-|. ..+ .....+.|+..|+..+.+|..++
T Consensus 109 ~~~~l~~~~~~~L~~L~~~~l~--~~~~~~~~~~~~~~~~~~--l~~~~~~YAa~D~~~~~~l~~~l 171 (176)
T PF01612_consen 109 AAYLLDPTRSYSLKDLAEEYLG--NIDLDKKEQMSDWRKARP--LSEEQIEYAAQDAVVTFRLYEKL 171 (176)
T ss_dssp HHHHTTTSTTSSHHHHHHHHHS--EEE-GHCCTTSSTTTSSS---HHHHHHHHHHHHHTHHHHHHHH
T ss_pred hhhcccccccccHHHHHHHHhh--hccCcHHHhhccCCcCCC--ChHHHHHHHHHHHHHHHHHHHHH
Confidence 544443333 999999999999 22222222222222 222 35778899999999999999887
No 104
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=95.90 E-value=0.4 Score=46.49 Aligned_cols=104 Identities=12% Similarity=0.017 Sum_probs=71.0
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
......+.+.+|.+++....+.++++|. .||+..|.+.+...+.... + ....-.
T Consensus 71 ~~~~~~~vl~~~~~~l~~~~~~~~v~~~--~~d~~~l~~~~~~~~~~~~------~------------------~~~~~~ 124 (176)
T cd06133 71 NAPSFPEVLKEFLEWLGKNGKYAFVTWG--DWDLKDLLQNQCKYKIINL------P------------------PFFRQW 124 (176)
T ss_pred cCCCHHHHHHHHHHHHHhCCCeEEEeec--HhhHHHHHHHHHHhcCCCC------c------------------ccccce
Confidence 4578889999999999875445777775 6999999888776654310 0 001236
Q ss_pred EehHHHHhhhcC-CCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 431 INLWRLLRHEVN-LQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 431 lDl~~~~r~~~k-l~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+|+...++..+. ..+++|++++.++ |...+.- .+-++.||..+.+|+.++
T Consensus 125 ~D~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~~--------------------~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 125 IDLKKEFAKFYGLKKRTGLSKALEYL-GLEFEGR--------------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred EEHHHHHHHHhCCCCCCCHHHHHHHC-CCCCCCC--------------------CcCcHHHHHHHHHHHHHh
Confidence 899888887663 3699999999875 4322100 112467888888888775
No 105
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=95.16 E-value=0.16 Score=49.17 Aligned_cols=73 Identities=11% Similarity=0.097 Sum_probs=47.8
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
...+-.+.+.+|.+++.. .+++|||. .||+.+|-.. .. . -.+
T Consensus 60 ~a~~~~~v~~~l~~~l~~---~vlV~Hn~-~~D~~~l~~~-------~~-------~--------------------~~~ 101 (157)
T cd06149 60 NATPFAVAQKEILKILKG---KVVVGHAI-HNDFKALKYF-------HP-------K--------------------HMT 101 (157)
T ss_pred cCCCHHHHHHHHHHHcCC---CEEEEeCc-HHHHHHhccc-------CC-------C--------------------cCE
Confidence 345677899999998853 69999997 6898877421 00 0 012
Q ss_pred EehHH--HHhhh--c-CCCCCCHHHHHHHHcCCCcC
Q psy5925 431 INLWR--LLRHE--V-NLQSYTFENIMYHVLHERIP 461 (696)
Q Consensus 431 lDl~~--~~r~~--~-kl~sysL~~Va~~~L~~~k~ 461 (696)
+|+.. .+++. + ...+|+|+++++.+++.+.+
T Consensus 102 ~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~ 137 (157)
T cd06149 102 RDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQ 137 (157)
T ss_pred EECcccccchhhcCCcccCChhHHHHHHHHcChhhc
Confidence 34432 23332 2 45789999999999876553
No 106
>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=93.90 E-value=0.25 Score=47.82 Aligned_cols=66 Identities=17% Similarity=0.197 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHH
Q psy5925 356 KELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWR 435 (696)
Q Consensus 356 ~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~ 435 (696)
.+.+..|.+++.. -.+++|||. .||+.+|.. . ..-++|+..
T Consensus 71 ~~~~~~~~~~i~~--~~vlVgHn~-~fD~~fL~~---------------~---------------------~~~~iDT~~ 111 (161)
T cd06137 71 EAARAALWKFIDP--DTILVGHSL-QNDLDALRM---------------I---------------------HTRVVDTAI 111 (161)
T ss_pred HHHHHHHHHhcCC--CcEEEeccH-HHHHHHHhC---------------c---------------------CCCeeEehh
Confidence 4677777777752 159999999 599998731 0 012678888
Q ss_pred HHhhhcC-C---CCCCHHHHHHHHcCCCc
Q psy5925 436 LLRHEVN-L---QSYTFENIMYHVLHERI 460 (696)
Q Consensus 436 ~~r~~~k-l---~sysL~~Va~~~L~~~k 460 (696)
+++.... + .+|+|++++++++|...
T Consensus 112 l~~~~~~~~~~~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 112 LTREAVKGPLAKRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred hhhhccCCCcCCCCccHHHHHHHHCCchh
Confidence 8877553 3 68999999999988543
No 107
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=93.80 E-value=0.19 Score=61.18 Aligned_cols=76 Identities=18% Similarity=0.215 Sum_probs=63.0
Q ss_pred EEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeeccc
Q psy5925 349 RHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGR 428 (696)
Q Consensus 349 V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GR 428 (696)
+..-....+.|.+|.+++.. +|++.|| -+||++||..+.+++++..+. .
T Consensus 482 l~~a~~i~~vL~kf~~~~~d---~IlVAHN-asFD~gFl~~~~~k~~~~~~~---------------------------~ 530 (1444)
T COG2176 482 LENAPEIEEVLEKFREFIGD---SILVAHN-ASFDMGFLNTNYEKYGLEPLT---------------------------N 530 (1444)
T ss_pred HcCCccHHHHHHHHHHHhcC---cEEEecc-CccchhHHHHHHHHhCCcccc---------------------------C
Confidence 34556677888888888764 6999999 689999999999999876541 2
Q ss_pred EEEehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 429 IVINLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 429 l~lDl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
-++|+..+.|.-+ .+.||+|.++|+.+
T Consensus 531 pvIDTL~lar~L~P~~ksh~Lg~l~kk~ 558 (1444)
T COG2176 531 PVIDTLELARALNPEFKSHRLGTLCKKL 558 (1444)
T ss_pred chhhHHHHHHHhChhhhhcchHHHHHHh
Confidence 4889999999887 79999999999986
No 108
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=93.43 E-value=1.7 Score=46.57 Aligned_cols=32 Identities=16% Similarity=0.228 Sum_probs=24.4
Q ss_pred CCCceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeec
Q psy5925 242 NYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYT 278 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~ 278 (696)
.+..+++.+|+||.. -||..|+|+.|++..-+
T Consensus 34 ~~~~~~vvlD~ETTG-----Ld~~~d~IIEIg~V~v~ 65 (294)
T PRK09182 34 EFVRLGVILDTETTG-----LDPRKDEIIEIGMVAFE 65 (294)
T ss_pred CCCCeEEEEEeeCCC-----CCCCCCeEEEEEEEEEE
Confidence 355678999999982 35678999999876654
No 109
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.34 E-value=0.89 Score=58.25 Aligned_cols=74 Identities=20% Similarity=0.228 Sum_probs=57.1
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEE
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIV 430 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~ 430 (696)
...+..+.+..|.+++. -.++++||. .||+++|.+.++.+|++.+. ...
T Consensus 482 ~aps~~EaL~~f~~fig---g~vLVAHNa-~FD~~fL~~~l~rlgl~~l~---------------------------~~~ 530 (1437)
T PRK00448 482 DAPSIEEVLPKFKEFCG---DSILVAHNA-SFDVGFINTNYEKLGLEKIK---------------------------NPV 530 (1437)
T ss_pred CCCCHHHHHHHHHHHhC---CCEEEEeCc-cccHHHHHHHHHHcCCcccc---------------------------ccc
Confidence 34577888888888765 369999999 79999999999888875430 124
Q ss_pred EehHHHHhhhc-CCCCCCHHHHHHHH
Q psy5925 431 INLWRLLRHEV-NLQSYTFENIMYHV 455 (696)
Q Consensus 431 lDl~~~~r~~~-kl~sysL~~Va~~~ 455 (696)
+|+..+.+... ...+++|+++|+++
T Consensus 531 IDTLelar~l~p~~k~~kL~~LAk~l 556 (1437)
T PRK00448 531 IDTLELSRFLYPELKSHRLNTLAKKF 556 (1437)
T ss_pred eeHHHHHHHHcCccccccHHHHHHHc
Confidence 67777776655 57899999999975
No 110
>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=93.11 E-value=0.94 Score=43.35 Aligned_cols=68 Identities=15% Similarity=0.113 Sum_probs=50.7
Q ss_pred CCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 353 ~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
.++.+.+.+|.+++.. -.+|+|||. .||+.+|.. . . .-++|
T Consensus 60 ~~~~~v~~~~~~fl~~--~~vlVgHn~-~fD~~fL~~---------~------~---------------------~~~iD 100 (150)
T cd06145 60 TTLEDVQKKLLSLISP--DTILVGHSL-ENDLKALKL---------I------H---------------------PRVID 100 (150)
T ss_pred CCHHHHHHHHHHHhCC--CCEEEEcCh-HHHHHHhhc---------c------C---------------------CCEEE
Confidence 3788999999999851 159999999 599998731 0 0 01578
Q ss_pred hHHHHhhhc-CCCCCCHHHHHHHHcCCC
Q psy5925 433 LWRLLRHEV-NLQSYTFENIMYHVLHER 459 (696)
Q Consensus 433 l~~~~r~~~-kl~sysL~~Va~~~L~~~ 459 (696)
+..++++.. ...+|+|+++|+.+++..
T Consensus 101 T~~l~r~~~~~~~~~~L~~L~~~~~~~~ 128 (150)
T cd06145 101 TAILFPHPRGPPYKPSLKNLAKKYLGRD 128 (150)
T ss_pred cHHhccccCCCCCChhHHHHHHHHCCcc
Confidence 888877644 456899999999998754
No 111
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=92.05 E-value=1.6 Score=45.06 Aligned_cols=166 Identities=13% Similarity=0.152 Sum_probs=101.7
Q ss_pred ceEEEEEEEeecCCCCCCCCCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhhhhhc
Q psy5925 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIEN 324 (696)
Q Consensus 245 LtilsleIe~~sr~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~~~~~ 324 (696)
.+...+|+||..- +|..|.|+.|......+..+.. ..--.+++|. ... |. ....
T Consensus 13 ~~~vv~D~ETtg~-----~~~~~~iieIgav~~~~~~i~~-~~~~~~v~P~-~~i-----~~--------------~~~~ 66 (243)
T COG0847 13 TRFVVIDLETTGL-----NPKKDRIIEIGAVTLEDGRIVE-RSFHTLVNPE-RPI-----PP--------------EIFK 66 (243)
T ss_pred CcEEEEecccCCC-----CCCCCceEEEEeEEEECCeeec-ceeEEEECCC-CCC-----Ch--------------hhhh
Confidence 6788899999832 4488999999877765543111 0012455552 110 10 0111
Q ss_pred cccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCcccccc
Q psy5925 325 VRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR 404 (696)
Q Consensus 325 ~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR 404 (696)
++... +.++. .-+.=.+.+..|.+++... .++++|| ..||+++|..++..++.+..
T Consensus 67 i~git-----~e~l~-----------~~p~~~~v~~~~~~~i~~~--~~~Vahn-a~fD~~fl~~~~~~~~~~~~----- 122 (243)
T COG0847 67 IHGIT-----DEMLA-----------DAPKFAEVLPEFLDFIGGL--RLLVAHN-AAFDVGFLRVESERLGIEIP----- 122 (243)
T ss_pred hcCCC-----HHHHh-----------cCCCHHHHHHHHHHHHCCC--CeEEEEc-hhhcHHHHHHHHHHcCCCcc-----
Confidence 11111 10110 1133367777777777653 8999999 58999999999988876532
Q ss_pred cccccccccCCCccccceeeecccEEEehHHHHhhhcC-CCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHH
Q psy5925 405 ITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVN-LQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMT 483 (696)
Q Consensus 405 ~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~k-l~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~ 483 (696)
+-.++|.....|..+. ...++|+.++. .+|....... .
T Consensus 123 ----------------------~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~~~~---------------~--- 161 (243)
T COG0847 123 ----------------------GDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRNPFH---------------P--- 161 (243)
T ss_pred ----------------------cCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcCCcC---------------C---
Confidence 3457888888888774 59999999999 4454321000 0
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q psy5925 484 VEHYLIRVTGIIRLIEQLD 502 (696)
Q Consensus 484 i~Y~l~D~~l~~~L~~kl~ 502 (696)
.-.+.|+..+.+++.++.
T Consensus 162 -H~Al~Da~~~a~~~~~~~ 179 (243)
T COG0847 162 -HRALFDALALAELFLLLQ 179 (243)
T ss_pred -cchHHHHHHHHHHHHHHH
Confidence 114678888888777764
No 112
>PRK05359 oligoribonuclease; Provisional
Probab=91.62 E-value=1.2 Score=44.02 Aligned_cols=44 Identities=23% Similarity=0.193 Sum_probs=34.4
Q ss_pred eCCHHHHHHHHHHHHHHhC---CCEEEecccccccHHHHHHHHHHcCC
Q psy5925 352 VSNEKELFSIFIENVRQWD---PDILIGYEIETLSWGYLLERGYVLGL 396 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~D---PDIIvGyNi~~fDl~YL~~Ra~~lgi 396 (696)
-.++.+.+..|++++..+- -.+++|||+ .||+.||.+-+..++.
T Consensus 76 ~~~~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~ 122 (181)
T PRK05359 76 TVSEAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEA 122 (181)
T ss_pred CCCHHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcc
Confidence 3578899999999997642 246899887 7999999988876654
No 113
>PHA02563 DNA polymerase; Provisional
Probab=90.06 E-value=0.14 Score=59.97 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=34.6
Q ss_pred CCCCCccccC-CCCCCCcccCceeeeeccccchhhhhhhccCcccc
Q psy5925 94 SSFDSDMFPS-SSSRDRLYTDPIIVLDFQSLYPSVIIAYNYCFSTC 138 (696)
Q Consensus 94 ~~~~~~~~~~-~~~~~~~~~~~~~~~d~~s~y~~~~~~~~~~~~t~ 138 (696)
.+|-|+.+-. -++..|++.+ +.++|++|||||+|...++++.+-
T Consensus 236 ~sY~GGr~~~~~~~~~~~~~~-~~~yDvnSlYPsaM~~~~~P~g~p 280 (630)
T PHA02563 236 KFYRGGRTWYNPKYIGKLIEE-GYVYDVNSLYPYVMYNAKLPYGEP 280 (630)
T ss_pred HheeCceeecccccccccccc-ccccccccccHHHHhhccCCCCCc
Confidence 5788988721 0456778865 779999999999999999998764
No 114
>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=88.81 E-value=2 Score=42.97 Aligned_cols=100 Identities=14% Similarity=0.227 Sum_probs=65.2
Q ss_pred CCCEE-EecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHhhhc-------
Q psy5925 370 DPDIL-IGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV------- 441 (696)
Q Consensus 370 DPDII-vGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~------- 441 (696)
||+|+ +||++. +|...|.+. +|+... .. ..+ +-++|+...++...
T Consensus 80 d~~i~KVg~~~~-~D~~~L~~~---~~~~~~-----~~----------------~~~--~~v~Dl~~~a~~l~~~~~~~~ 132 (193)
T cd06146 80 DPDVLKLGFGFK-QDLKALSAS---YPALKC-----MF----------------ERV--QNVLDLQNLAKELQKSDMGRL 132 (193)
T ss_pred CCCeeEEEechH-HHHHHHHHh---cCcccc-----cc----------------ccC--CceEEHHHHHHHHhhcccccc
Confidence 68876 999995 598887543 232110 00 001 23678876655322
Q ss_pred ----CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 442 ----NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 442 ----kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
....++|.+++..+||.....- .+.+.|-. .+ -...-+.|+..||...+.|+++|
T Consensus 133 ~~~~~~~~~sL~~l~~~~lg~~l~K~--~q~SdW~~-rp--Ls~~Qi~YAA~Da~~l~~l~~~L 191 (193)
T cd06146 133 KGNLPSKTKGLADLVQEVLGKPLDKS--EQCSNWER-RP--LREEQILYAALDAYCLLEVFDKL 191 (193)
T ss_pred ccccCcccCCHHHHHHHHhCCCcCcc--cccCCCCC-CC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 1467999999999999765432 34555532 22 23567899999999999999987
No 115
>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=87.69 E-value=3.9 Score=39.51 Aligned_cols=117 Identities=15% Similarity=0.126 Sum_probs=71.1
Q ss_pred eEEEEeCCHHHHHHHHHHHHHHhCCCE-EEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeee
Q psy5925 347 LERHFVSNEKELFSIFIENVRQWDPDI-LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQM 425 (696)
Q Consensus 347 ~~V~~~~sE~eLL~~f~~~I~~~DPDI-IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i 425 (696)
+-+.-......+...|.+++. +|+| .+||++ .+|+..|.+ .+|+. +
T Consensus 50 ~~l~~~~~~~~~~~~l~~ll~--~~~i~kv~~~~-k~D~~~L~~---~~g~~---------------------------~ 96 (170)
T cd06141 50 CLLFQLAHMDKLPPSLKQLLE--DPSILKVGVGI-KGDARKLAR---DFGIE---------------------------V 96 (170)
T ss_pred EEEEEhhhhhcccHHHHHHhc--CCCeeEEEeee-HHHHHHHHh---HcCCC---------------------------C
Confidence 334333343445555666665 5666 489988 567766532 23332 1
Q ss_pred cccEEEehHHHHhhhcCC-CCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 426 PGRIVINLWRLLRHEVNL-QSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 426 ~GRl~lDl~~~~r~~~kl-~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.| ++|+......--.. .+.+|.+++..+||.....-.....+.|... + -...-++|+..||...+.|.+++
T Consensus 97 ~~--~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~r-p--Lt~~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 97 RG--VVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEAR-P--LSKEQILYAATDAYASLELYRKL 168 (170)
T ss_pred CC--eeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCC-C--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 12 37887765443322 3479999999999876543222334455332 2 23566799999999999999887
No 116
>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=87.42 E-value=2.2 Score=41.77 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=35.0
Q ss_pred EeCCHHHHHHHHHHHHHHh---CCCEEEecccccccHHHHHHHHHHcC
Q psy5925 351 FVSNEKELFSIFIENVRQW---DPDILIGYEIETLSWGYLLERGYVLG 395 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~---DPDIIvGyNi~~fDl~YL~~Ra~~lg 395 (696)
.-.++.+.+..|.+++... +-.+++|||. .||+.+|.+=+.++|
T Consensus 71 ~~~~~~~vl~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~ 117 (173)
T cd06135 71 STVTLAQAEAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELE 117 (173)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHh
Confidence 4467889999999999864 4458888886 799999988776665
No 117
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=86.70 E-value=0.63 Score=35.75 Aligned_cols=39 Identities=21% Similarity=0.683 Sum_probs=31.1
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeecccccc-----------CCCccchh
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ-----------LPCKRCIR 51 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~-----------~~cp~c~r 51 (696)
+|.+|+. +.+......|..|+..||..|..- -.||.|.+
T Consensus 1 ~C~vC~~-----~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQ-----SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTS-----SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCC-----cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5888988 566688999999999999999841 14888864
No 118
>PRK05755 DNA polymerase I; Provisional
Probab=84.90 E-value=16 Score=45.32 Aligned_cols=106 Identities=15% Similarity=0.112 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHhCCCE-EEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHH
Q psy5925 357 ELFSIFIENVRQWDPDI-LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWR 435 (696)
Q Consensus 357 eLL~~f~~~I~~~DPDI-IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~ 435 (696)
+.+..|.+++. |+++ +++||. .||+.+|.. +|+.. +| .++|+.-
T Consensus 357 ~~l~~l~~~L~--d~~v~kV~HNa-kfDl~~L~~----~gi~~---------------------------~~-~~~DT~i 401 (880)
T PRK05755 357 EVLAALKPLLE--DPAIKKVGQNL-KYDLHVLAR----YGIEL---------------------------RG-IAFDTML 401 (880)
T ss_pred HHHHHHHHHHh--CCCCcEEEecc-HhHHHHHHh----CCCCc---------------------------CC-CcccHHH
Confidence 45666777766 4564 799999 799998863 34331 11 2456655
Q ss_pred HHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCc---ccHHHHHHHHHHHHHHHHHHHHHhc
Q psy5925 436 LLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTH---LYKWMTVEHYLIRVTGIIRLIEQLD 502 (696)
Q Consensus 436 ~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~---~~~~~~i~Y~l~D~~l~~~L~~kl~ 502 (696)
..+--..-.+++|++++++++|.....+ +++ |..+.. ........|+..|+..+.+|..++.
T Consensus 402 Aa~Ll~~~~~~~L~~L~~~ylg~~~~~~--~~~---~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~ 466 (880)
T PRK05755 402 ASYLLDPGRRHGLDSLAERYLGHKTISF--EEV---AGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLK 466 (880)
T ss_pred HHHHcCCCCCCCHHHHHHHHhCCCccch--HHh---cCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4433222114999999999998763221 211 111100 0124567899999999998888763
No 119
>PTZ00315 2'-phosphotransferase; Provisional
Probab=84.75 E-value=21 Score=41.67 Aligned_cols=113 Identities=6% Similarity=-0.104 Sum_probs=65.5
Q ss_pred CCCceEEEEEEEeecCCCCCCC-CCCCcEEEEEEEeecCCCCCCceEEEEEEcCCCCCcccccCccccccccchhhhhhh
Q psy5925 242 NYYLTVLAVEIHAISRALLKPD-PAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFST 320 (696)
Q Consensus 242 ~~~LtilsleIe~~sr~~~~Pd-p~~D~I~~I~~~~~~~~~~~~~~~g~ilv~~~~~~~~~~~~p~~~~~~~~~~e~~~~ 320 (696)
.+.-..+.||+||... .|. ...|+|+-|.++..+.........--.+|+|.... + +..
T Consensus 53 q~~d~~IV~DlETTgl---~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p------~------------Ls~ 111 (582)
T PTZ00315 53 QPFDAYVVLDFEATCE---ADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNP------V------------LSR 111 (582)
T ss_pred CCCCeEEEEEEecCCC---CCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCC------C------------CCh
Confidence 3457888999999632 232 34689999998887422111001113566664210 1 112
Q ss_pred hhhccccCCCcccccccccccccCcceEEEEeCCHHHHHHHHHHHHHHhCC-------CEEEecccccccHH-HHHHHHH
Q psy5925 321 FIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDP-------DILIGYEIETLSWG-YLLERGY 392 (696)
Q Consensus 321 ~~~~~~~~~p~~~~g~ei~~~~~~~~~~V~~~~sE~eLL~~f~~~I~~~DP-------DIIvGyNi~~fDl~-YL~~Ra~ 392 (696)
++..++... .-.|....+-.+.+..|.+++..... .+++++|+ .||+. +|..-++
T Consensus 112 fct~LTGIT----------------qe~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~ 174 (582)
T PTZ00315 112 FCTELTGIT----------------QSMVSRADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMR 174 (582)
T ss_pred hHhhhcCcC----------------HHHHhcCCCHHHHHHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHH
Confidence 222222221 12334556777899999999987641 47889998 68985 6665555
No 120
>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=83.61 E-value=11 Score=36.78 Aligned_cols=108 Identities=13% Similarity=0.102 Sum_probs=67.1
Q ss_pred CHHHHHHHHHHHHHHhCCC-EEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEe
Q psy5925 354 NEKELFSIFIENVRQWDPD-ILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVIN 432 (696)
Q Consensus 354 sE~eLL~~f~~~I~~~DPD-IIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lD 432 (696)
+..+.+..|.+++.. .+ .++|||. .||+.+|.+ +|+.. .| .++|
T Consensus 51 ~~~~~~~~l~~~l~~--~~~~~v~hn~-k~d~~~l~~----~gi~~---------------------------~~-~~~D 95 (193)
T cd06139 51 PREEVLAALKPLLED--PSIKKVGQNL-KFDLHVLAN----HGIEL---------------------------RG-PAFD 95 (193)
T ss_pred CHHHHHHHHHHHHhC--CCCcEEeecc-HHHHHHHHH----CCCCC---------------------------CC-Cccc
Confidence 455677777777764 34 6899999 699998742 33331 12 2467
Q ss_pred hHHHHhhhcC-CCCCCHHHHHHHHcCCCcCCCChhhHHH----H--HhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 433 LWRLLRHEVN-LQSYTFENIMYHVLHERIPLHSWKLLTC----W--WEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 433 l~~~~r~~~k-l~sysL~~Va~~~L~~~k~~~~~~~l~~----~--~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+....+--.. ..+++|+++++.+++..+.. .+++.. + |... .......|+..|+..+.+|+.++
T Consensus 96 t~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~--~~~~~~k~~~~~~~~~~---~~~~~~~ya~~d~~~~~~l~~~l 166 (193)
T cd06139 96 TMLASYLLNPGRRRHGLDDLAERYLGHKTIS--FEDLVGKGKKQITFDQV---PLEKAAEYAAEDADITLRLYELL 166 (193)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHhCCCCcc--HHHHcCCCcCcCCcccc---CHHHHHHHHHHHHHHHHHHHHHH
Confidence 7665543222 23689999999999865322 111110 0 1111 13556789999999999998877
No 121
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=82.10 E-value=1.2 Score=33.17 Aligned_cols=34 Identities=24% Similarity=0.550 Sum_probs=27.0
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCceeecccc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCH 41 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~ 41 (696)
|+|..|.+..+++-+.. ...-|..||.|.+..-.
T Consensus 1 m~Cp~Cg~~~~~~D~~~-g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPER-GELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSEEEEETTT-TEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCceEEcCCC-CeEECCCCCCEeecccc
Confidence 68999999999999885 67799999999876543
No 123
>KOG2114|consensus
Probab=81.21 E-value=0.46 Score=56.06 Aligned_cols=33 Identities=27% Similarity=0.796 Sum_probs=26.1
Q ss_pred eecCCCCeeecCC----------CCceeeccccc--cCCCccchh
Q psy5925 19 FPWQLSSVHRCNQ----------CGACFHTKCHS--QLPCKRCIR 51 (696)
Q Consensus 19 ~p~~~~~~~~c~~----------c~~~~h~~c~~--~~~cp~c~r 51 (696)
+|||..+|..|.. |+..||+.|+. ...||||.-
T Consensus 836 ~i~q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~ 880 (933)
T KOG2114|consen 836 QIFQVSKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLP 880 (933)
T ss_pred ceeeeeeecccCCccccceeeeecccHHHHHhhccCcccCCccch
Confidence 4666666666654 88999999997 568999987
No 124
>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=80.87 E-value=7.5 Score=37.43 Aligned_cols=66 Identities=9% Similarity=0.031 Sum_probs=44.9
Q ss_pred EehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 431 INLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 431 lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
+|+....+---...+++|..++.++||...+. ..+.++| ...+ -...-+.|+..||...+.|+.+|
T Consensus 94 ~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K--~~~~s~W-~~rp--Lt~~qi~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 94 FDTTIAANLKGLPERWSLASLVEHFLGKTLDK--SISCADW-SYRP--LTEDQKLYAAADVYALLIIYTKL 159 (161)
T ss_pred hHHHHHHHHhCCCCCchHHHHHHHHhCCCCCc--cceeccC-CCCC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 57765443221224679999999999976532 2344454 3333 23667899999999999999887
No 125
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=73.58 E-value=1.5 Score=32.72 Aligned_cols=36 Identities=31% Similarity=0.781 Sum_probs=23.8
Q ss_pred ceecCCCCCeeeecC-CCCeeecCCCCceeeccccc-----cCCCccc
Q psy5925 8 ICELCNSEEVIFPWQ-LSSVHRCNQCGACFHTKCHS-----QLPCKRC 49 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~-~~~~~~c~~c~~~~h~~c~~-----~~~cp~c 49 (696)
.|-+|.+. |+ .+...... |+.+||.+|.. +..||-|
T Consensus 2 ~C~IC~~~-----~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~C 43 (44)
T PF13639_consen 2 ECPICLEE-----FEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVC 43 (44)
T ss_dssp CETTTTCB-----HHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTT
T ss_pred CCcCCChh-----hcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCcc
Confidence 36667653 11 24555666 99999999984 4679987
No 126
>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=72.76 E-value=37 Score=31.27 Aligned_cols=107 Identities=17% Similarity=0.119 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHhCCCE-EEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehH
Q psy5925 356 KELFSIFIENVRQWDPDI-LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLW 434 (696)
Q Consensus 356 ~eLL~~f~~~I~~~DPDI-IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~ 434 (696)
..++..|.+++. ++++ .+|||+ .||+..|.+ .++. ..| .++|+.
T Consensus 40 ~~~~~~l~~~l~--~~~~~~v~~~~-k~d~~~L~~----~~~~---------------------------~~~-~~~D~~ 84 (155)
T cd00007 40 EEDLEALKELLE--DEDITKVGHDA-KFDLVVLAR----DGIE---------------------------LPG-NIFDTM 84 (155)
T ss_pred HHHHHHHHHHHc--CCCCcEEeccH-HHHHHHHHH----CCCC---------------------------CCC-CcccHH
Confidence 345555666665 4564 789998 578777642 2211 111 356876
Q ss_pred HHHhhhcCCC-CCCHHHHHHHHcCCCcCCCChhhHHHHH---hcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 435 RLLRHEVNLQ-SYTFENIMYHVLHERIPLHSWKLLTCWW---EHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 435 ~~~r~~~kl~-sysL~~Va~~~L~~~k~~~~~~~l~~~~---~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
-...---... +++|+++++.+|+..... ..++..|- ... ........|...|+..+.+|..++
T Consensus 85 ~~ayll~~~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~y~~~da~~~~~l~~~l 151 (155)
T cd00007 85 LAAYLLNPGEGSHSLDDLAKEYLGIELDK--DEQIYGKGAKTFAR--PLSEELLEYAAEDADALLRLYEKL 151 (155)
T ss_pred HHHHHhCCCCCcCCHHHHHHHHcCCCCcc--HHHHhcCCCCcccc--CCHHHHHHHHHHhHHHHHHHHHHH
Confidence 5544332323 579999999999876322 12232220 011 124567789999999999888776
No 127
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=70.88 E-value=2.9 Score=31.14 Aligned_cols=31 Identities=32% Similarity=0.737 Sum_probs=19.9
Q ss_pred eecCCCCceeeccccc----cCCCccchhhhhccc
Q psy5925 27 HRCNQCGACFHTKCHS----QLPCKRCIRMRIRRD 57 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~----~~~cp~c~r~~~r~~ 57 (696)
.+|.+||..|....-. ...||+|.....+|+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGSTEVRRV 40 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEEe
Confidence 5788888777654432 346888887555543
No 128
>PF08408 DNA_pol_B_3: DNA polymerase family B viral insert; InterPro: IPR013617 This viral domain is found between the exonuclease domain of the DNA polymerase family B (IPR006133 from INTERPRO) and the IPR006134 from INTERPRO domain, connecting the two. ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=70.70 E-value=4.5 Score=38.25 Aligned_cols=63 Identities=6% Similarity=-0.152 Sum_probs=45.1
Q ss_pred cCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhCCchhhh
Q psy5925 456 LHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEV 521 (696)
Q Consensus 456 L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~ela~l~gi~~~~v 521 (696)
|--+|++++-.+|..=|+-+ ....+.+||++|+.|+..|.+..++...+.+-|.-+=+|-..+
T Consensus 84 lsfgKDDVdL~dmY~nYnl~---~a~em~~YCiHDacLCkyLw~Yy~i~~KidA~astYlLPQsmv 146 (149)
T PF08408_consen 84 LSFGKDDVDLSDMYKNYNLD---IALEMARYCIHDACLCKYLWDYYGIETKIDAAASTYLLPQSMV 146 (149)
T ss_pred EEecCCCCCHHHHHHhccHH---HHHHHHHHHHhHHHHHHHHHHHcCcceeeeccceeeecchhhe
Confidence 33466777666655444433 3578899999999999999999988888877776555554443
No 129
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=69.70 E-value=3 Score=31.05 Aligned_cols=28 Identities=32% Similarity=0.730 Sum_probs=25.1
Q ss_pred cceecCCCC-CeeeecCCCCeeecCCCCc
Q psy5925 7 FICELCNSE-EVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 7 ~~ce~c~~~-~~i~p~~~~~~~~c~~c~~ 34 (696)
|.|+-|+.. +++.|+.......|++|++
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 789999965 8999999778999999998
No 130
>KOG0954|consensus
Probab=65.82 E-value=2.3 Score=49.71 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=33.6
Q ss_pred CCCCccceecCCCCCeeeecCCCCeeecCCCCceeeccccc-----cC--CCccchhh
Q psy5925 2 CLARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS-----QL--PCKRCIRM 52 (696)
Q Consensus 2 c~~~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~-----~~--~cp~c~r~ 52 (696)
|..-..+|.+|.+++-=-. ..-+-|..|++|.|+.|+. .+ -|.+|+-.
T Consensus 267 e~dedviCDvCrspD~e~~---neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 267 EYDEDVICDVCRSPDSEEA---NEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALG 321 (893)
T ss_pred eccccceeceecCCCcccc---ceeEEeccchhHHHHhhhceeecCCCCeeehhcccc
Confidence 4445679999998742211 2345699999999999994 12 38888755
No 131
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=65.02 E-value=55 Score=33.45 Aligned_cols=78 Identities=10% Similarity=0.005 Sum_probs=49.9
Q ss_pred CCCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHhhhcCCCCCCHH
Q psy5925 370 DPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 449 (696)
Q Consensus 370 DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r~~~kl~sysL~ 449 (696)
.-++++|||. .||+.+|-. + +.-.+|+++..|+.+.-..|+|+
T Consensus 73 ~~~~lVaHNa-~FD~~~L~~------------~------------------------~~~~idTl~lar~l~p~~~~~l~ 115 (219)
T PRK07983 73 GSEWYVAHNA-SFDRRVLPE------------M------------------------PGEWICTMKLARRLWPGIKYSNM 115 (219)
T ss_pred CCCEEEEeCc-HhhHHHHhC------------c------------------------CCCcEeHHHHHHHHccCCCCCHH
Confidence 4579999999 599988720 0 01258999999887743459999
Q ss_pred HHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 450 NIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 450 ~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
++++++ |-.... + +. .-.+-++.||..+..|+.++
T Consensus 116 ~L~~~~-~l~~~~-~-~~--------------~~aHrAl~Da~ata~ll~~l 150 (219)
T PRK07983 116 ALYKSR-KLNVQT-P-PG--------------LHHHRALYDCYITAALLIDI 150 (219)
T ss_pred HHHHHc-CCCCCC-C-CC--------------CCCCcHHHHHHHHHHHHHHH
Confidence 998764 321100 0 00 00123577899998888776
No 132
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=63.56 E-value=2.8 Score=34.87 Aligned_cols=32 Identities=28% Similarity=0.516 Sum_probs=11.7
Q ss_pred ceecCCCCCeeeecCCCCeeecC--CCCceeecccc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCN--QCGACFHTKCH 41 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~--~c~~~~h~~c~ 41 (696)
.|-+|.+... .-+......|. .|+..||..|.
T Consensus 4 ~C~IC~~~~~--~~~~~p~~~C~n~~C~~~fH~~CL 37 (70)
T PF11793_consen 4 ECGICYSYRL--DDGEIPDVVCPNPSCGKKFHLLCL 37 (70)
T ss_dssp S-SSS--SS---TT-----B--S-TT----B-SGGG
T ss_pred CCCcCCcEec--CCCCcCceEcCCcccCCHHHHHHH
Confidence 5888887633 23333457897 99999999996
No 133
>PRK10829 ribonuclease D; Provisional
Probab=63.54 E-value=31 Score=38.32 Aligned_cols=101 Identities=17% Similarity=0.108 Sum_probs=65.4
Q ss_pred HHHHHHHHHhCCCEE-EecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHh
Q psy5925 360 SIFIENVRQWDPDIL-IGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLR 438 (696)
Q Consensus 360 ~~f~~~I~~~DPDII-vGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r 438 (696)
..|.+++. ||+|+ ++|+. .+|+.+|... +|+.. .-++|+....+
T Consensus 64 ~~L~~ll~--~~~ivKV~H~~-~~Dl~~l~~~---~g~~p-----------------------------~~~fDTqiaa~ 108 (373)
T PRK10829 64 SPFKALLR--DPQVTKFLHAG-SEDLEVFLNA---FGELP-----------------------------QPLIDTQILAA 108 (373)
T ss_pred HHHHHHHc--CCCeEEEEeCh-HhHHHHHHHH---cCCCc-----------------------------CCeeeHHHHHH
Confidence 34444443 78887 78887 5899988442 23211 13678855443
Q ss_pred hhcCCC-CCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 439 HEVNLQ-SYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 439 ~~~kl~-sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+... +.+|.++++++||...+.- ++.++|-. .+ --..-+.|+..||.....|..++
T Consensus 109 -~lg~~~~~gl~~Lv~~~lgv~ldK~--~~~sDW~~-RP--Ls~~ql~YAa~Dv~~L~~l~~~L 166 (373)
T PRK10829 109 -FCGRPLSCGFASMVEEYTGVTLDKS--ESRTDWLA-RP--LSERQCEYAAADVFYLLPIAAKL 166 (373)
T ss_pred -HcCCCccccHHHHHHHHhCCccCcc--cccCCCCC-CC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 33333 6899999999999765432 23345433 22 23567899999999999988876
No 134
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=62.95 E-value=9.8 Score=29.31 Aligned_cols=40 Identities=30% Similarity=0.725 Sum_probs=26.8
Q ss_pred CccceecCCCCCeeeecCCCCeeecCCCCceeecccccc--CCCc
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ--LPCK 47 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~--~~cp 47 (696)
++-.|..|+. .|+.+- ....+|..|+-..|++|... ..|+
T Consensus 10 ~~~~C~~C~~--~i~g~~-~~g~~C~~C~~~~H~~C~~~~~~~C~ 51 (53)
T PF00130_consen 10 KPTYCDVCGK--FIWGLG-KQGYRCSWCGLVCHKKCLSKVPPSCG 51 (53)
T ss_dssp STEB-TTSSS--BECSSS-SCEEEETTTT-EEETTGGCTSSSBSS
T ss_pred CCCCCcccCc--ccCCCC-CCeEEECCCCChHhhhhhhhcCCCCC
Confidence 3445777764 455544 57899999999999999974 3454
No 135
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=62.68 E-value=7.7 Score=29.37 Aligned_cols=31 Identities=26% Similarity=0.665 Sum_probs=24.9
Q ss_pred CCCccceecCCCCCeeeecCCCCeeecCCCCc
Q psy5925 3 LARGFICELCNSEEVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 3 ~~~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~ 34 (696)
-..||+|-.|++. -.|........+|..|+.
T Consensus 15 W~~g~~CP~Cg~~-~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 15 WPDGFVCPHCGST-KHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCCe-eeEEeCCCCeEECCCCCC
Confidence 3578999999998 667777668889999874
No 136
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=60.79 E-value=3.7 Score=30.69 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=26.0
Q ss_pred CccceecCCCCCeeeecCCCCeeecCCCCceeecccccc
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ 43 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~ 43 (696)
++-.|..|+..=. +.+ ...+|..|+.+.|+.|...
T Consensus 10 ~~~~C~~C~~~i~-~~~---~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIW-GSF---QGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccC-cCC---CCcCCCCCCchHHHHHHhh
Confidence 4567999987522 222 3689999999999999863
No 137
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=60.51 E-value=5 Score=30.28 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=26.8
Q ss_pred CccceecCCCCCeeeecCCCCeeecCCCCceeecccccc
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ 43 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~ 43 (696)
++-.|..|+..=.. . .....+|..|+-+.|+.|...
T Consensus 10 ~~~~C~~C~~~i~~--~-~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 10 KPTFCDVCRKSIWG--L-FKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCCChhhcchhhhc--c-ccceeEcCCCCCchhhhhhcc
Confidence 45678888875221 1 357789999999999999864
No 138
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=60.14 E-value=5.7 Score=30.67 Aligned_cols=31 Identities=29% Similarity=0.592 Sum_probs=18.6
Q ss_pred eecCCCCceeeccccc----cCCCccchhhhhccc
Q psy5925 27 HRCNQCGACFHTKCHS----QLPCKRCIRMRIRRD 57 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~----~~~cp~c~r~~~r~~ 57 (696)
.+|.+|+..|-..-.. ...||.|.....++.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 4788888766544221 235888887555443
No 139
>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=59.94 E-value=6 Score=36.87 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=28.5
Q ss_pred eCCHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHH
Q psy5925 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYV 393 (696)
Q Consensus 352 ~~sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~ 393 (696)
.....+.+..|.+++... .+++||| ..||++.+..=...
T Consensus 66 ~~~~~~~~~~~~~~~~~~--~~~v~~n-~~fd~~~l~~~~~~ 104 (164)
T PF00929_consen 66 APSFEEALDEFEEFLKKN--DILVGHN-ASFDIGFLRREDKR 104 (164)
T ss_dssp HCEHHHHHHHHHHHHHHH--TEEEETT-CCHEEESSHHHHHH
T ss_pred CCcHHHHHHhhhhhhhcc--ccccccc-ccchhhHHHHhhhh
Confidence 345666888888888855 6999999 78998776544443
No 140
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=58.91 E-value=2.1 Score=33.31 Aligned_cols=31 Identities=19% Similarity=0.456 Sum_probs=23.1
Q ss_pred CeeecCCCCceeeccccc---cCCCccchhhhhc
Q psy5925 25 SVHRCNQCGACFHTKCHS---QLPCKRCIRMRIR 55 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~---~~~cp~c~r~~~r 55 (696)
.+.||..|+++.-+.=.+ ...||||.-+..-
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 468999999987655443 5679999877653
No 141
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=58.19 E-value=6.6 Score=30.30 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=24.0
Q ss_pred cceecCCC-CCeeeecCCCCeeecCCCCc
Q psy5925 7 FICELCNS-EEVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 7 ~~ce~c~~-~~~i~p~~~~~~~~c~~c~~ 34 (696)
|.|+-|+. -+++.++..+....|+.|++
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 78999998 58889988667778999998
No 142
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.33 E-value=4.3 Score=35.94 Aligned_cols=31 Identities=23% Similarity=0.579 Sum_probs=22.6
Q ss_pred eecCCCCceeeccccc-cCCCccchhhhhccc
Q psy5925 27 HRCNQCGACFHTKCHS-QLPCKRCIRMRIRRD 57 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~-~~~cp~c~r~~~r~~ 57 (696)
+||..||++|-..=-. -..||+|....-+.+
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv 34 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCNKFLYV 34 (112)
T ss_pred ceecccccccccccHHHHccCccccchheEec
Confidence 6999999999875111 246999988765543
No 143
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.68 E-value=8.5 Score=29.06 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=15.3
Q ss_pred eeecCCCCceeeccccc-cCCCccchh
Q psy5925 26 VHRCNQCGACFHTKCHS-QLPCKRCIR 51 (696)
Q Consensus 26 ~~~c~~c~~~~h~~c~~-~~~cp~c~r 51 (696)
..+|+.||+.+...=.. ...||.|..
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 45777777776544221 345777753
No 144
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=54.20 E-value=5.4 Score=28.71 Aligned_cols=18 Identities=22% Similarity=0.739 Sum_probs=12.8
Q ss_pred CeeecCCCCceeeccccc
Q psy5925 25 SVHRCNQCGACFHTKCHS 42 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~ 42 (696)
...+|..|+-.+|+.|+.
T Consensus 3 ~ll~C~~C~v~VH~~CYG 20 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYG 20 (36)
T ss_dssp EEEE-SSS--EEEHHHHT
T ss_pred ceEEeCCCCCcCChhhCC
Confidence 346899999999999994
No 145
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=54.15 E-value=8.2 Score=27.99 Aligned_cols=25 Identities=28% Similarity=0.682 Sum_probs=16.3
Q ss_pred eecCCCCceeecccc----ccCCCccchh
Q psy5925 27 HRCNQCGACFHTKCH----SQLPCKRCIR 51 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~----~~~~cp~c~r 51 (696)
.+|.+|+..|-..-- ....||.|..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 578888887643321 2346888887
No 146
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=54.09 E-value=5 Score=30.10 Aligned_cols=24 Identities=29% Similarity=0.902 Sum_probs=13.6
Q ss_pred eeecC--CCCceeeccccc------cC-CCccc
Q psy5925 26 VHRCN--QCGACFHTKCHS------QL-PCKRC 49 (696)
Q Consensus 26 ~~~c~--~c~~~~h~~c~~------~~-~cp~c 49 (696)
-.+|+ +|+.-+|..|++ +. .||+|
T Consensus 11 G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 11 GQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp SEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred eccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 36899 699999999984 22 49988
No 147
>KOG0955|consensus
Probab=53.32 E-value=7.2 Score=48.31 Aligned_cols=46 Identities=24% Similarity=0.654 Sum_probs=35.1
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeecccccc-------CCCccchhhhhcc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ-------LPCKRCIRMRIRR 56 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~-------~~cp~c~r~~~r~ 56 (696)
+|-+|...+. +.......|..|+-++|..|+.- --|-+|..-+.|.
T Consensus 221 ~C~iC~~~~~---~n~n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 221 VCCICLDGEC---QNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSPQRP 273 (1051)
T ss_pred cceeeccccc---CCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCcCcc
Confidence 6889887653 22345678999999999999961 1399998887775
No 148
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=52.09 E-value=5.9 Score=28.45 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=24.8
Q ss_pred eecCCCCCeeeecCCCCeeecCCCCceeeccccc------cCCCccchh
Q psy5925 9 CELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIR 51 (696)
Q Consensus 9 ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r 51 (696)
|.+|...- .....-..|+-.||..|+. ...||-|..
T Consensus 2 C~iC~~~~-------~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF-------REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhh-------hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 66676542 2444556699999999984 346998854
No 149
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=51.99 E-value=9.7 Score=31.22 Aligned_cols=28 Identities=36% Similarity=0.805 Sum_probs=24.5
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
-|--|.+.+++|.-. .+..+|..|+++.
T Consensus 21 kCpdC~N~q~vFsha-st~V~C~~CG~~l 48 (67)
T COG2051 21 KCPDCGNEQVVFSHA-STVVTCLICGTTL 48 (67)
T ss_pred ECCCCCCEEEEeccC-ceEEEecccccEE
Confidence 488899999999988 5889999999875
No 150
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=51.65 E-value=15 Score=26.03 Aligned_cols=28 Identities=21% Similarity=0.585 Sum_probs=22.2
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
-.|+-|+++-+++ ..++-..|..|+++|
T Consensus 4 ~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 3688899888776 445778899999987
No 151
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=51.13 E-value=11 Score=25.90 Aligned_cols=30 Identities=27% Similarity=0.827 Sum_probs=22.1
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCceeecccc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCH 41 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~ 41 (696)
|.|++|... +-+|. ..+|..|.-..|..|.
T Consensus 1 ~~C~~C~~~--~~~~~---~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRK--IDGFY---FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCC--cCCCE---eEEeCCCCCeEcCccC
Confidence 578999654 33343 5799999999999883
No 152
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=50.52 E-value=5.3 Score=41.17 Aligned_cols=33 Identities=58% Similarity=1.040 Sum_probs=30.2
Q ss_pred cchhhhhhhhhhccccCCCcccccccccccccC
Q psy5925 312 SNEKELFSTFIENVRQWDPDILIGYEIETFSWG 344 (696)
Q Consensus 312 ~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~ 344 (696)
.+|++++.++..-++..|||+++|+++..|+++
T Consensus 79 ~~E~~LL~~f~~~i~~~DPDii~GyNi~~fd~~ 111 (231)
T cd05778 79 ESELELFEELIDLVRRFDPDILSGYEIQRSSWG 111 (231)
T ss_pred CCHHHHHHHHHHHHHHhCCCEEEEeccccCcHH
Confidence 468999999999999999999999999999875
No 153
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=49.56 E-value=7.8 Score=38.10 Aligned_cols=27 Identities=26% Similarity=0.490 Sum_probs=22.5
Q ss_pred eecCCCCceeeccccccCCCccchhhhhcc
Q psy5925 27 HRCNQCGACFHTKCHSQLPCKRCIRMRIRR 56 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~ 56 (696)
.||.+|+.+|+ ...+.||.|.-...|+
T Consensus 140 ~rC~GC~~~f~---~~~~~Cp~CG~~~~~~ 166 (177)
T COG1439 140 LRCHGCKRIFP---EPKDFCPICGSPLKRK 166 (177)
T ss_pred EEEecCceecC---CCCCcCCCCCCceEEe
Confidence 59999999999 6678899998775554
No 154
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=49.08 E-value=9.6 Score=36.21 Aligned_cols=25 Identities=20% Similarity=0.671 Sum_probs=19.6
Q ss_pred eeecCCCCceeeccccccCCCccchhhh
Q psy5925 26 VHRCNQCGACFHTKCHSQLPCKRCIRMR 53 (696)
Q Consensus 26 ~~~c~~c~~~~h~~c~~~~~cp~c~r~~ 53 (696)
-.+|.+||++||-. ...||+|-+..
T Consensus 29 g~kC~~CG~v~~PP---r~~Cp~C~~~~ 53 (140)
T COG1545 29 GTKCKKCGRVYFPP---RAYCPKCGSET 53 (140)
T ss_pred EEEcCCCCeEEcCC---cccCCCCCCCC
Confidence 46999999999743 45799998763
No 155
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.89 E-value=9.6 Score=46.55 Aligned_cols=42 Identities=26% Similarity=0.567 Sum_probs=25.1
Q ss_pred ccceecCCCCCeeeecCCCCeeecCCCCce-----eeccccc---cCCCccchhhhhc
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQCGAC-----FHTKCHS---QLPCKRCIRMRIR 55 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~-----~h~~c~~---~~~cp~c~r~~~r 55 (696)
...|.-|+... ...+|+.||+. |=..|-. ...||+|.+-...
T Consensus 626 ~RfCpsCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 626 RRKCPSCGKET--------FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred CccCCCCCCcC--------CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 34677777652 22477777764 2333432 2469999887654
No 156
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=47.31 E-value=1.3e+02 Score=28.20 Aligned_cols=101 Identities=16% Similarity=0.199 Sum_probs=59.9
Q ss_pred HHHHHHHHHhCCCE-EEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHHHHh
Q psy5925 360 SIFIENVRQWDPDI-LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLR 438 (696)
Q Consensus 360 ~~f~~~I~~~DPDI-IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~~~r 438 (696)
..+.+++. ++++ .+|||. .+|+..|. .+|+.. .| . +|+.-...
T Consensus 65 ~~l~~~l~--~~~~~kv~~d~-k~~~~~L~----~~gi~~---------------------------~~-~-~D~~laay 108 (172)
T smart00474 65 EILKDLLE--DETITKVGHNA-KFDLHVLA----RFGIEL---------------------------EN-I-FDTMLAAY 108 (172)
T ss_pred HHHHHHhc--CCCceEEEech-HHHHHHHH----HCCCcc---------------------------cc-h-hHHHHHHH
Confidence 33444444 4555 789998 67777663 245432 22 2 66655443
Q ss_pred hhc-CCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 439 HEV-NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 439 ~~~-kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
--. ...+++|++++..+|+...+..-.. ..|.. .. .....+.|+..|+..+.+|..++
T Consensus 109 ll~p~~~~~~l~~l~~~~l~~~~~~~~~~--~~~~~-~~--l~~~~~~ya~~~a~~~~~L~~~l 167 (172)
T smart00474 109 LLLGGPSKHGLATLLKEYLGVELDKEEQK--SDWGA-RP--LSEEQLQYAAEDADALLRLYEKL 167 (172)
T ss_pred HHcCCCCcCCHHHHHHHHhCCCCCcccCc--ccccc-CC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 211 2233799999999998763221111 24422 21 24667889999999999888776
No 157
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=47.29 E-value=5.6 Score=45.24 Aligned_cols=33 Identities=24% Similarity=0.324 Sum_probs=20.7
Q ss_pred CCCCCccccCCCCCCCcccCceeeeeccccchhhhh
Q psy5925 94 SSFDSDMFPSSSSRDRLYTDPIIVLDFQSLYPSVII 129 (696)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~s~y~~~~~ 129 (696)
++|-|+..-.. ..|... ++.++|+.||||++|.
T Consensus 204 ~s~~GGr~~~~--~~~~~~-~i~~yDvnSLYP~~m~ 236 (459)
T PF03175_consen 204 KSYYGGRCEVF--KPGIKN-KIYYYDVNSLYPSAMK 236 (459)
T ss_dssp EEE-GGGB-TE--EEESE----EEEEETTHHHHHHH
T ss_pred hhcCCceeeee--eccccc-ceeeeeccCCcHHHHh
Confidence 56777666311 345555 7999999999999976
No 158
>KOG4323|consensus
Probab=45.13 E-value=7.6 Score=43.74 Aligned_cols=51 Identities=20% Similarity=0.490 Sum_probs=35.9
Q ss_pred eecCCCCCeeeecCCCCeeecCCCCceeecccccc-------------CCCccchhhhhccccccce
Q psy5925 9 CELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ-------------LPCKRCIRMRIRRDSMKGI 62 (696)
Q Consensus 9 ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~-------------~~cp~c~r~~~r~~~~~~~ 62 (696)
|-.|+.+..- +|. ...+|.+|+..||..|-+- -.|-+|.|...+...+.++
T Consensus 171 c~vC~~g~~~-~~N--rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~t~~ 234 (464)
T KOG4323|consen 171 CSVCYCGGPG-AGN--RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRLTLR 234 (464)
T ss_pred eeeeecCCcC-ccc--eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccccccc
Confidence 7788765321 343 5689999999999999741 1399999988765544444
No 159
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=44.93 E-value=15 Score=29.62 Aligned_cols=28 Identities=39% Similarity=0.856 Sum_probs=24.0
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
.|.-|.+.++||.-- .+...|..|++..
T Consensus 13 kCp~C~n~q~vFsha-~t~V~C~~Cg~~L 40 (59)
T PRK00415 13 KCPDCGNEQVVFSHA-STVVRCLVCGKTL 40 (59)
T ss_pred ECCCCCCeEEEEecC-CcEEECcccCCCc
Confidence 588899999999988 5889999999764
No 160
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=44.05 E-value=18 Score=26.06 Aligned_cols=25 Identities=24% Similarity=0.707 Sum_probs=18.3
Q ss_pred eecCCCCceeeccccc---cCCCccchh
Q psy5925 27 HRCNQCGACFHTKCHS---QLPCKRCIR 51 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~---~~~cp~c~r 51 (696)
..|+.||++||-.=.. ...|..|.-
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 3699999999976432 356888864
No 161
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=43.09 E-value=18 Score=32.92 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=23.6
Q ss_pred CeeecCCCCce--eeccccccCCCccchhhhhccc
Q psy5925 25 SVHRCNQCGAC--FHTKCHSQLPCKRCIRMRIRRD 57 (696)
Q Consensus 25 ~~~~c~~c~~~--~h~~c~~~~~cp~c~r~~~r~~ 57 (696)
...+|+.|+.. +-.+|... .||+|......++
T Consensus 41 ~~~~C~~Cg~~~~~~~SCk~R-~CP~C~~~~~~~W 74 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSCKNR-HCPSCQAKATEQW 74 (111)
T ss_pred ceeecCCCCceEEecCcccCc-CCCCCCChHHHHH
Confidence 45689999987 34668754 8999988776544
No 162
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=42.59 E-value=12 Score=32.56 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=18.3
Q ss_pred eecCCCCceeeccccc-cCCCccch
Q psy5925 27 HRCNQCGACFHTKCHS-QLPCKRCI 50 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~-~~~cp~c~ 50 (696)
-+|..||-.|...=.. ...||+|.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred hhhcccCccccccccCCcccCCcch
Confidence 4799999999874443 45799996
No 163
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=42.04 E-value=12 Score=31.75 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=19.7
Q ss_pred CCccceecCCCCCeeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhcc
Q psy5925 4 ARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRR 56 (696)
Q Consensus 4 ~~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~ 56 (696)
..|-||++|...--+=.=- +--.-|.+|+.-.-+.|+. .+.||+|.-+-.|.
T Consensus 7 ~~~qiCqiCGD~VGl~~~G-e~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENG-EVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp -SS-B-SSS--B--B-SSS-SB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----
T ss_pred cCCcccccccCccccCCCC-CEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccc
Confidence 4678999998742222111 2335799999888999984 36799998655543
No 164
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=41.36 E-value=20 Score=25.82 Aligned_cols=29 Identities=31% Similarity=0.644 Sum_probs=22.5
Q ss_pred Cccc--eecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 5 RGFI--CELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 5 ~g~~--ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
+|+. |+.|.+. .|--+ +...-|.+|+.+.
T Consensus 5 ~~~~~~C~~C~~~--~~~~~-dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 5 RGPNEPCPVCGSR--WFYSD-DGFYYCDRCGHQS 35 (36)
T ss_pred ccCCCcCCCCCCe--EeEcc-CCEEEhhhCceEc
Confidence 5666 9999988 66666 6888999998763
No 165
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=40.92 E-value=15 Score=26.26 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=13.2
Q ss_pred CeeecCCCCceeeccccccCCCccch
Q psy5925 25 SVHRCNQCGACFHTKCHSQLPCKRCI 50 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~~~~cp~c~ 50 (696)
..++|..|+.++|-. ...||.|.
T Consensus 10 ~~~rC~~Cg~~~~pP---r~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPP---RPVCPHCG 32 (37)
T ss_dssp EEEE-TTT--EEES-----SEETTTT
T ss_pred EEEEcCCCCCEecCC---CcCCCCcC
Confidence 357899999998732 35688884
No 166
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=40.44 E-value=17 Score=28.90 Aligned_cols=28 Identities=25% Similarity=0.694 Sum_probs=20.2
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
.|.-|.+.++||.-- .++..|..|+++.
T Consensus 9 kCp~C~~~q~vFSha-~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHA-QTVVKCVVCGTVL 36 (55)
T ss_dssp E-TTT-SEEEEETT--SS-EE-SSSTSEE
T ss_pred ECCCCCCeeEEEecC-CeEEEcccCCCEe
Confidence 488899999999988 4889999999886
No 167
>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=40.23 E-value=12 Score=38.68 Aligned_cols=32 Identities=34% Similarity=0.781 Sum_probs=29.0
Q ss_pred cchhhhhhhhhhccccCCCccccccccccccc
Q psy5925 312 SNEKELFSTFIENVRQWDPDILIGYEIETFSW 343 (696)
Q Consensus 312 ~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~ 343 (696)
.+|++++..++..++..|||+++|+++..|++
T Consensus 80 ~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl 111 (234)
T cd05776 80 ENERALLNFFLAKLQKIDPDVLVGHDLEGFDL 111 (234)
T ss_pred CCHHHHHHHHHHHHhhcCCCEEEeeccCCCCH
Confidence 46899999999999999999999999998875
No 168
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.87 E-value=18 Score=25.98 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=5.1
Q ss_pred ecCCCCceee
Q psy5925 28 RCNQCGACFH 37 (696)
Q Consensus 28 ~c~~c~~~~h 37 (696)
.|+.|++.|.
T Consensus 4 ~Cp~C~~~y~ 13 (36)
T PF13717_consen 4 TCPNCQAKYE 13 (36)
T ss_pred ECCCCCCEEe
Confidence 4555555554
No 169
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=38.82 E-value=7.5e+02 Score=29.55 Aligned_cols=86 Identities=16% Similarity=0.101 Sum_probs=55.5
Q ss_pred EEEeCCHHHHHHHHHHHHHH-hC----CCEEEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCcccccee
Q psy5925 349 RHFVSNEKELFSIFIENVRQ-WD----PDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQL 423 (696)
Q Consensus 349 V~~~~sE~eLL~~f~~~I~~-~D----PDIIvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~ 423 (696)
...+++=+.|+..|++.|++ .. -=+++||=..-||+|.|.++.-.. ..|. +... ..+
T Consensus 248 F~nf~s~~~li~~FL~Wl~e~~~~n~~ti~LvGy~ss~FD~pLLra~wp~~--sGW~---~~~n-------------~~i 309 (651)
T PF03337_consen 248 FINFDSNKALISDFLKWLRECIMKNIRTIILVGYFSSFFDFPLLRAYWPKN--SGWN---FIGN-------------NTI 309 (651)
T ss_pred EEeCCCchHHHHHHHHHHHHHHhccCceEEEeehhhhhhccHHHHhhcccC--CCce---EecC-------------ceE
Confidence 34677777899999999998 43 338999999999999887665322 1221 1100 011
Q ss_pred eec-c--cEEEehHHHHhhhcCCCCCCHHHHHHHHcCC
Q psy5925 424 QMP-G--RIVINLWRLLRHEVNLQSYTFENIMYHVLHE 458 (696)
Q Consensus 424 ~i~-G--Rl~lDl~~~~r~~~kl~sysL~~Va~~~L~~ 458 (696)
... | -+++|+.++. .+.++.+-+++--|.
T Consensus 310 vs~~G~kvil~D~a~Fs------~~~~~~eYc~~W~~~ 341 (651)
T PF03337_consen 310 VSKDGLKVILVDAANFS------PGMSLSEYCEHWTGK 341 (651)
T ss_pred EeCCCcEEEEEehhhhc------cCCCHHHHHHhhccC
Confidence 111 1 2688988875 455777778877654
No 170
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=38.48 E-value=13 Score=38.40 Aligned_cols=54 Identities=22% Similarity=0.445 Sum_probs=34.8
Q ss_pred CCCccceecCCCCCeeeecCCCCeeecCCCCceeecc-c---cc--cCCCccchhhhhcc
Q psy5925 3 LARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTK-C---HS--QLPCKRCIRMRIRR 56 (696)
Q Consensus 3 ~~~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~-c---~~--~~~cp~c~r~~~r~ 56 (696)
..+-|.|+-|+..=--==.|...+.||.+|+.-|--- | |. .-.||+|.+-=..-
T Consensus 109 ~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 3578999999765111123457899999999887422 2 22 24699997765443
No 171
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=38.05 E-value=17 Score=33.01 Aligned_cols=32 Identities=22% Similarity=0.455 Sum_probs=21.3
Q ss_pred CeeecCCCCceeeccccccCCCccchhhhhcc
Q psy5925 25 SVHRCNQCGACFHTKCHSQLPCKRCIRMRIRR 56 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~ 56 (696)
+-+.|..||+-|---=.....||+|.-...-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 45789999998843222345699998665543
No 172
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.98 E-value=17 Score=33.44 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=24.4
Q ss_pred CeeecCCCCceeeccccccCCCccchhhhhccccccce
Q psy5925 25 SVHRCNQCGACFHTKCHSQLPCKRCIRMRIRRDSMKGI 62 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~~~~~~~ 62 (696)
-..+|..|+..|-..-+....||+|.-.. ..+..|+
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~--~~i~~G~ 105 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKN--VIITQGN 105 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCc--eEEecCC
Confidence 56789999988766554444599998653 3344555
No 173
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=37.68 E-value=22 Score=25.03 Aligned_cols=25 Identities=36% Similarity=0.907 Sum_probs=13.8
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~ 34 (696)
|+|--|+....|-+ .+..||..||.
T Consensus 1 Y~C~~Cg~~~~~~~---~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELKP---GDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BST---SSTSSBSSSS-
T ss_pred CCCCcCCCeeEcCC---CCcEECCcCCC
Confidence 46777776544332 34567777763
No 174
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=36.06 E-value=15 Score=34.36 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=20.4
Q ss_pred eecCCCCceeecccc-ccCCCccchhhhh
Q psy5925 27 HRCNQCGACFHTKCH-SQLPCKRCIRMRI 54 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~-~~~~cp~c~r~~~ 54 (696)
++|..||.+|-..=- --..||.|.-..=
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~kF 30 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGNKF 30 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCcce
Confidence 689999999975432 2356999986543
No 175
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=35.98 E-value=13 Score=35.17 Aligned_cols=28 Identities=25% Similarity=0.631 Sum_probs=22.8
Q ss_pred eeecCCCCceeeccccccCCCccchhhhhc
Q psy5925 26 VHRCNQCGACFHTKCHSQLPCKRCIRMRIR 55 (696)
Q Consensus 26 ~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r 55 (696)
...|..||++|... ....||.|.+...+
T Consensus 3 l~nC~~CgklF~~~--~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 3 LANCPKCGRLFVKT--GRDVCPSCYEEEER 30 (137)
T ss_pred Cccccccchhhhhc--CCccCHHHhHHHHH
Confidence 45899999999985 44679999987665
No 176
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=35.97 E-value=21 Score=44.28 Aligned_cols=49 Identities=20% Similarity=0.539 Sum_probs=35.7
Q ss_pred CCccceecCCCC----CeeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhccc
Q psy5925 4 ARGFICELCNSE----EVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRRD 57 (696)
Q Consensus 4 ~~g~~ce~c~~~----~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~~ 57 (696)
..|-||++|.++ .-=.|| +-|.+|+==.=+.|++ ++.||.|.-+=+|.+
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~F-----VAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr~k 73 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPF-----VACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKRHK 73 (1079)
T ss_pred cCCceeeecccccCcCCCCCEE-----EEeccCCCccccchhhhhhhcCCccCCccCCchhhhc
Confidence 356799999985 111244 5788888778888984 467999998877655
No 177
>PLN00209 ribosomal protein S27; Provisional
Probab=35.35 E-value=29 Score=30.04 Aligned_cols=29 Identities=21% Similarity=0.553 Sum_probs=25.4
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceee
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFH 37 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h 37 (696)
.|.-|.+.++||.-- .+++.|..|+++.=
T Consensus 38 kCp~C~n~q~VFShA-~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 38 KCQGCFNITTVFSHS-QTVVVCGSCQTVLC 66 (86)
T ss_pred ECCCCCCeeEEEecC-ceEEEccccCCEee
Confidence 588899999999988 48999999999863
No 178
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=35.17 E-value=14 Score=32.02 Aligned_cols=44 Identities=23% Similarity=0.543 Sum_probs=27.1
Q ss_pred cceecCCC------CCeeeecCCCCeeecCCCCceeeccccc--------cCCCccchh
Q psy5925 7 FICELCNS------EEVIFPWQLSSVHRCNQCGACFHTKCHS--------QLPCKRCIR 51 (696)
Q Consensus 7 ~~ce~c~~------~~~i~p~~~~~~~~c~~c~~~~h~~c~~--------~~~cp~c~r 51 (696)
=+|-+|+. ++--||=+. --.--.+|+..||..|.. ++.||=|.+
T Consensus 22 d~CgICr~~fdg~Cp~Ck~Pgd~-Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~ 79 (85)
T PF12861_consen 22 DVCGICRMPFDGCCPDCKFPGDD-CPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQ 79 (85)
T ss_pred CceeeEecccccCCCCccCCCCC-CceeeccCccHHHHHHHHHHHccccCCCCCCCcCC
Confidence 35666664 345566442 111224799999999952 357998854
No 179
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=34.75 E-value=16 Score=25.06 Aligned_cols=22 Identities=27% Similarity=0.668 Sum_probs=15.8
Q ss_pred ecCCCCceeeccccc------cCCCccc
Q psy5925 28 RCNQCGACFHTKCHS------QLPCKRC 49 (696)
Q Consensus 28 ~c~~c~~~~h~~c~~------~~~cp~c 49 (696)
.-..|+-.||..|.. ...||.|
T Consensus 12 ~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 12 VVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred EEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 334699999999984 3458866
No 180
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=34.40 E-value=32 Score=29.72 Aligned_cols=29 Identities=21% Similarity=0.540 Sum_probs=25.3
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceee
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFH 37 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h 37 (696)
.|.-|.+.++||.-- .+++.|..|+++.=
T Consensus 37 kCp~C~n~q~VFShA-~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 37 KCPGCSQITTVFSHA-QTVVLCGGCSSQLC 65 (85)
T ss_pred ECCCCCCeeEEEecC-ceEEEccccCCEee
Confidence 488899999999988 48999999999863
No 181
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=34.06 E-value=20 Score=32.18 Aligned_cols=31 Identities=23% Similarity=0.805 Sum_probs=25.6
Q ss_pred ccceecCCCCCeeeecCCCCeeecCC--CCceeecccccc
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQ--CGACFHTKCHSQ 43 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~--c~~~~h~~c~~~ 43 (696)
...|.+|+.. ...+.+|.. |...||-.|...
T Consensus 55 ~~~C~iC~~~-------~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKS-------GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CCcCcCCCCC-------CceeEEcCCCCCCcCCCHHHHHH
Confidence 5689999987 356789988 999999999753
No 182
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=33.97 E-value=53 Score=36.76 Aligned_cols=83 Identities=22% Similarity=0.243 Sum_probs=52.8
Q ss_pred ccchhhhHHHHhCCchhhhhcCcchhhhHHHhhcccccCCeee---eC--Cchhhhhcc-----CCCCCCCeeeeccccc
Q psy5925 503 FIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVA---VS--PSIKQRAHM-----RAPESLPLILEPESRL 572 (696)
Q Consensus 503 ii~~~~ela~l~gi~~~~vl~rGs~~rvEslLlr~~~~~~~i~---p~--p~~~q~~~~-----~~~~~GglVleP~~Gl 572 (696)
.+...+++||.+.+|+..+-.--..+-++-+.-|..+++|.|+ |+ |.-+..... ...+....+.--.+|+
T Consensus 121 wl~~~i~laRY~~IPlgNl~~D~~~f~~Di~yAR~L~~~~~VLW~S~~~~PDlGG~e~Dd~~~~~~~~~~~~~~in~pG~ 200 (396)
T PF08490_consen 121 WLSERIELARYAHIPLGNLPSDNPLFLIDIFYARRLRKNNHVLWWSPSPRPDLGGKEEDDNRLLWDMDELESPEINNPGA 200 (396)
T ss_pred HHHHHHHHHHHcCCCcccCCcchHHHHHHHHHHHHHHHCCeEEeCCCCCCCCCCcchhhhhcccccccccCceEEECCCc
Confidence 4566689999999999988555556778888899999999986 22 221111000 0111111222235799
Q ss_pred ccCceeeeecccc
Q psy5925 573 YTDPIIVLDFQSL 585 (696)
Q Consensus 573 y~~pVvvLDF~SL 585 (696)
|++-.+-||+..|
T Consensus 201 Y~~vcvEl~i~~L 213 (396)
T PF08490_consen 201 YRSVCVELDISNL 213 (396)
T ss_pred cceEEEEEEecce
Confidence 9987778888765
No 183
>PLN02400 cellulose synthase
Probab=33.74 E-value=25 Score=43.77 Aligned_cols=49 Identities=24% Similarity=0.544 Sum_probs=35.9
Q ss_pred CCccceecCCCC----CeeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhccc
Q psy5925 4 ARGFICELCNSE----EVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRRD 57 (696)
Q Consensus 4 ~~g~~ce~c~~~----~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~~ 57 (696)
..|-||++|.++ .-=.|| +-|.+|+-=.=+.|++ ++.||.|.-+=+|.+
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~F-----VAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR~K 92 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVF-----VACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRHK 92 (1085)
T ss_pred cCCceeeecccccCcCCCCCEE-----EEEccCCCccccchhheecccCCccCcccCCcccccc
Confidence 357799999985 111244 5788888888888984 367999998877654
No 184
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.55 E-value=1.9e+02 Score=36.05 Aligned_cols=108 Identities=18% Similarity=0.094 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHhCCCE-EEecccccccHHHHHHHHHHcCCCCcccccccccccccccCCCccccceeeecccEEEehHH
Q psy5925 357 ELFSIFIENVRQWDPDI-LIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWR 435 (696)
Q Consensus 357 eLL~~f~~~I~~~DPDI-IvGyNi~~fDl~YL~~Ra~~lgi~~~~~lgR~~~~~~~~~~~~~~~~~~~~i~GRl~lDl~~ 435 (696)
..+..|..++. |+++ ++|||. .||+.+|. .+|+... | .+.|++-
T Consensus 365 ~~~~~l~~~l~--~~~~~~v~~n~-K~d~~~l~----~~gi~~~---------------------------~-~~~Dt~l 409 (887)
T TIGR00593 365 LTDDKFARWLL--NEQIKKIGHDA-KFLMHLLK----REGIELG---------------------------G-VIFDTML 409 (887)
T ss_pred HHHHHHHHHHh--CCCCcEEEeeH-HHHHHHHH----hCCCCCC---------------------------C-cchhHHH
Confidence 34455555555 4554 689998 67887763 3555421 2 2345544
Q ss_pred HHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 436 LLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 436 ~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
...=--.-.+.+|++++..+|+.....+ .++..+-..-.......+..|+..|+..+.+|..++
T Consensus 410 a~yll~~~~~~~l~~la~~yl~~~~~~~--~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l 473 (887)
T TIGR00593 410 AAYLLDPAQVSTLDTLARRYLVEELILD--EKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEEL 473 (887)
T ss_pred HHHHcCCCCCCCHHHHHHHHcCcccccH--HHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3211111123599999999998654221 111110000000124567789999999998887755
No 185
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.54 E-value=23 Score=32.91 Aligned_cols=31 Identities=10% Similarity=-0.028 Sum_probs=21.6
Q ss_pred CeeecCCCCceeeccccccCCCccchhhhhc
Q psy5925 25 SVHRCNQCGACFHTKCHSQLPCKRCIRMRIR 55 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r 55 (696)
+-+.|+.|++-|---=.....||+|.-....
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 5578999999885433345679999866433
No 186
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=33.27 E-value=5 Score=30.92 Aligned_cols=42 Identities=31% Similarity=0.804 Sum_probs=32.2
Q ss_pred ccceecCCCCCeeeecCCCCeeecCCCCceeeccccccC--CCccchhh
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQL--PCKRCIRM 52 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~~--~cp~c~r~ 52 (696)
-|.|.+|++. |.+..-.||.-||.---.+||+.. .|--|.-+
T Consensus 7 ry~CDLCn~~-----~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~Gi 50 (57)
T PF14445_consen 7 RYSCDLCNSS-----HPISELRQCVLCGRWACNSCWQDEYYTCKSCNGI 50 (57)
T ss_pred hHhHHhhccc-----CcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhch
Confidence 4889999985 334577899999998889999743 47777654
No 187
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.12 E-value=28 Score=31.82 Aligned_cols=36 Identities=19% Similarity=0.377 Sum_probs=23.9
Q ss_pred CCeeecCCCCceeeccccccCCCccchhhhhccccccce
Q psy5925 24 SSVHRCNQCGACFHTKCHSQLPCKRCIRMRIRRDSMKGI 62 (696)
Q Consensus 24 ~~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~~~~~~~ 62 (696)
.-..+|..|+..|...=+ ...||+|.-. ...+..|+
T Consensus 68 p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~--~~~i~~G~ 103 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH-DAQCPHCHGE--RLRVDTGD 103 (113)
T ss_pred CcEEEcccCCCEEecCCc-CccCcCCCCC--CcEEccCC
Confidence 356799999988866422 2359999854 33455555
No 188
>KOG0320|consensus
Probab=32.91 E-value=12 Score=36.78 Aligned_cols=49 Identities=18% Similarity=0.543 Sum_probs=31.6
Q ss_pred cceecCCCC-CeeeecCCCCeeecCCCCceeeccccc-----cCCCccchhhhhccccccceeeeehh
Q psy5925 7 FICELCNSE-EVIFPWQLSSVHRCNQCGACFHTKCHS-----QLPCKRCIRMRIRRDSMKGIVDVKCF 68 (696)
Q Consensus 7 ~~ce~c~~~-~~i~p~~~~~~~~c~~c~~~~h~~c~~-----~~~cp~c~r~~~r~~~~~~~~~~~~~ 68 (696)
|-|-+|=.. .-+-||- .+||.+|-++|.. ...||-|-. .+...| +|++|
T Consensus 132 ~~CPiCl~~~sek~~vs-------TkCGHvFC~~Cik~alk~~~~CP~C~k-----kIt~k~-~~rI~ 186 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVS-------TKCGHVFCSQCIKDALKNTNKCPTCRK-----KITHKQ-FHRIY 186 (187)
T ss_pred cCCCceecchhhccccc-------cccchhHHHHHHHHHHHhCCCCCCccc-----ccchhh-heecc
Confidence 667777543 3344443 3699999999985 357999964 223333 77766
No 189
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=32.53 E-value=17 Score=37.21 Aligned_cols=32 Identities=38% Similarity=0.661 Sum_probs=28.9
Q ss_pred chhhhhhhhhhccccCCCcccccccccccccC
Q psy5925 313 NEKELFSTFIENVRQWDPDILIGYEIETFSWG 344 (696)
Q Consensus 313 ~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~ 344 (696)
+|++++..++..+...+||+++|+++..|+++
T Consensus 70 ~E~eLL~~f~~~i~~~DPDii~GyN~~~FDl~ 101 (230)
T cd05777 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLP 101 (230)
T ss_pred CHHHHHHHHHHHHHhcCCCEEEEecCCCCCHH
Confidence 58899999998899999999999999998864
No 190
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=32.46 E-value=13 Score=39.74 Aligned_cols=33 Identities=39% Similarity=0.888 Sum_probs=28.3
Q ss_pred cchhhhhhhhhhccccCCCcccccccccccccC
Q psy5925 312 SNEKELFSTFIENVRQWDPDILIGYEIETFSWG 344 (696)
Q Consensus 312 ~~~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~ 344 (696)
.+|++++.+++..+...+||+++|+++..|+++
T Consensus 220 ~~E~~lL~~f~~~i~~~dPDii~GyN~~~fD~~ 252 (325)
T PF03104_consen 220 DSEKELLEAFLDIIQEYDPDIITGYNIDGFDLP 252 (325)
T ss_dssp SSHHHHHHHHHHHHHHHS-SEEEESSTTTTHHH
T ss_pred CCHHHHHHHHHHHHHhcCCcEEEEecccCCCHH
Confidence 358899999999999999999999999998763
No 191
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=32.13 E-value=27 Score=40.36 Aligned_cols=47 Identities=19% Similarity=0.472 Sum_probs=25.4
Q ss_pred ccceecCCCCCeeeecC-------CCCeeecCCCCceeeccccccCCCccchhhhh
Q psy5925 6 GFICELCNSEEVIFPWQ-------LSSVHRCNQCGACFHTKCHSQLPCKRCIRMRI 54 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~-------~~~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~ 54 (696)
|..|+.|+..-.+==++ ...+..|..|+..++. |...-||+|.|...
T Consensus 53 ~~pc~~c~gkG~V~v~~~c~~c~G~gkv~~c~~cG~~~~~--~~~~lc~~c~~~~~ 106 (715)
T COG1107 53 EIPCPKCRGKGTVTVYDTCPECGGTGKVLTCDICGDIIVP--WEEGLCPECRRKPK 106 (715)
T ss_pred CCCCCeeccceeEEEEeecccCCCceeEEeeccccceecC--cccccChhHhhCCc
Confidence 45677776653322222 1234455556666654 22336999987654
No 192
>PLN02189 cellulose synthase
Probab=32.10 E-value=25 Score=43.55 Aligned_cols=48 Identities=27% Similarity=0.551 Sum_probs=34.8
Q ss_pred CccceecCCCC----CeeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhccc
Q psy5925 5 RGFICELCNSE----EVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRRD 57 (696)
Q Consensus 5 ~g~~ce~c~~~----~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~~ 57 (696)
.|-||.+|.+. +-=.|| +-|.+|+=-.=+.|++ ++.||+|..+=+|.+
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~f-----vaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~k 90 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLF-----VACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLK 90 (1040)
T ss_pred cCccccccccccCcCCCCCEE-----EeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence 46799999985 223344 5788887777788884 367999998777654
No 193
>KOG4299|consensus
Probab=32.02 E-value=17 Score=42.11 Aligned_cols=43 Identities=23% Similarity=0.676 Sum_probs=33.3
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeecccccc-----------CCCccchhhhhc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQ-----------LPCKRCIRMRIR 55 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~-----------~~cp~c~r~~~r 55 (696)
+|+.|++.... .....|..|..-||..|... -.||-|.-.-.-
T Consensus 255 fCsaCn~~~~F-----~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~i 308 (613)
T KOG4299|consen 255 FCSACNGSGLF-----NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVI 308 (613)
T ss_pred HHHHhCCcccc-----ccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeec
Confidence 79999998754 35679999999999999851 248888765443
No 194
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=31.15 E-value=29 Score=26.17 Aligned_cols=25 Identities=24% Similarity=0.584 Sum_probs=10.4
Q ss_pred eecCCCCceeeccccccCCCccchh
Q psy5925 27 HRCNQCGACFHTKCHSQLPCKRCIR 51 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~~~~cp~c~r 51 (696)
..|..||+-|--.=.....||.|.-
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 3455555544333011223555543
No 195
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=30.70 E-value=63 Score=36.40 Aligned_cols=71 Identities=11% Similarity=0.094 Sum_probs=52.6
Q ss_pred EEehHHHHhhhc--CCCCCCHHHHHHHHcCCCcC--CCChhhHH----HHHhcCCcccHHHHHHHHHHHHHHHHHHHHHh
Q psy5925 430 VINLWRLLRHEV--NLQSYTFENIMYHVLHERIP--LHSWKLLT----CWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQL 501 (696)
Q Consensus 430 ~lDl~~~~r~~~--kl~sysL~~Va~~~L~~~k~--~~~~~~l~----~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~~kl 501 (696)
.+|++.++++.+ .-.||+|+.++. +||..-. +.+..+.. +|...++..-+..++.||-.|+..+..+.+-+
T Consensus 388 ~vDi~~lvr~~v~~p~es~sLK~la~-~lG~~wrD~~~ag~~~~~~Y~~~~~agdeavl~~Il~YN~dDcRaT~~vrdwl 466 (474)
T COG2251 388 LVDIYALVRSSVVVPVESYSLKALAP-YLGFQWRDVEAAGDESLEMYERWLTAGDEAVLKQILRYNEDDCRATRAVRDWL 466 (474)
T ss_pred HhHHHHHHHhccccCccchhHHHhhh-hhCCCccccccchHHHHHHHHHHHhhchHHHHHHHHhcCccchHHHHHHHHHH
Confidence 789999999976 579999999999 7776333 33333333 45555554456788899999999998887654
No 196
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=30.37 E-value=27 Score=40.91 Aligned_cols=26 Identities=23% Similarity=0.452 Sum_probs=23.2
Q ss_pred eeeeeccccchhhhhhccCCccCccc
Q psy5925 577 IIVLDFQSLYPSVIIAYNYCFSTCLG 602 (696)
Q Consensus 577 VvvLDF~SLYPSIIiayNiC~sT~~~ 602 (696)
|--||-+||||+||.+.-+=|+.++.
T Consensus 92 IYHlDV~aMYpnIiltnRLQP~a~v~ 117 (621)
T cd05535 92 IYHLDVAAMYPNIILTNRLQPDAIVD 117 (621)
T ss_pred eeEeehhhccchhhhhccCCCcccCC
Confidence 45799999999999999999988874
No 197
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.10 E-value=32 Score=31.42 Aligned_cols=47 Identities=11% Similarity=0.138 Sum_probs=27.8
Q ss_pred CCCCeeeecCCCCeeecCCCCceeeccccccCCCccchhhhhccccccce
Q psy5925 13 NSEEVIFPWQLSSVHRCNQCGACFHTKCHSQLPCKRCIRMRIRRDSMKGI 62 (696)
Q Consensus 13 ~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~~~~~~~ 62 (696)
.+.++..=.. .-..+|..|+..|-..=+....||+|.-.. ..+..|.
T Consensus 58 egA~L~i~~~-p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~--~~i~~G~ 104 (114)
T PRK03681 58 EGCKLHLEEQ-EAECWCETCQQYVTLLTQRVRRCPQCHGDM--LRIVADD 104 (114)
T ss_pred CCCEEEEEee-CcEEEcccCCCeeecCCccCCcCcCcCCCC--cEEccCC
Confidence 3444444444 356799999988755422224699998543 3344554
No 198
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=29.60 E-value=29 Score=33.90 Aligned_cols=35 Identities=29% Similarity=0.847 Sum_probs=25.5
Q ss_pred CeeecCCCCceeecccccc-----------------CCCccchhhhhccccc
Q psy5925 25 SVHRCNQCGACFHTKCHSQ-----------------LPCKRCIRMRIRRDSM 59 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~~-----------------~~cp~c~r~~~r~~~~ 59 (696)
--.-|.+|...||+.|... -.|-+|+.+..-+...
T Consensus 16 ~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~ 67 (175)
T PF15446_consen 16 PLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPR 67 (175)
T ss_pred CeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCC
Confidence 3356999999999999731 1388888887665544
No 199
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=29.51 E-value=36 Score=32.60 Aligned_cols=32 Identities=22% Similarity=0.534 Sum_probs=20.7
Q ss_pred CeeecCCCCceeeccccc-cCCCccchhhhhcc
Q psy5925 25 SVHRCNQCGACFHTKCHS-QLPCKRCIRMRIRR 56 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~-~~~cp~c~r~~~r~ 56 (696)
.+..|.+||...|-.=-. =.+||+|....-+|
T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred ceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 567888888765543111 24799998765544
No 200
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=29.27 E-value=21 Score=24.32 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=11.5
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCceeecccc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCH 41 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~ 41 (696)
|.|..|+.+-.- ....+|..|.=..|.+|.
T Consensus 1 ~~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 1 FRCDACGKPIDG-----GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp ---TTTS----S-------EEE-TTT-----HHHH
T ss_pred CcCCcCCCcCCC-----CceEECccCCCccChhcC
Confidence 567778765321 256789999999999883
No 201
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.20 E-value=21 Score=35.39 Aligned_cols=30 Identities=27% Similarity=0.518 Sum_probs=23.6
Q ss_pred eecCCCCceeeccccccCCCccchhhhhccc
Q psy5925 27 HRCNQCGACFHTKCHSQLPCKRCIRMRIRRD 57 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~~ 57 (696)
.+|..|++..-+ =+....||+|.+...|+-
T Consensus 150 A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRKi 179 (188)
T COG1096 150 ARCSRCRAPLVK-KGNMLKCPNCGNTEKRKI 179 (188)
T ss_pred EEccCCCcceEE-cCcEEECCCCCCEEeeee
Confidence 479999998777 334567999999998874
No 202
>PHA02929 N1R/p28-like protein; Provisional
Probab=28.71 E-value=34 Score=35.54 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=28.1
Q ss_pred CccceecCCCCCeeeecCCCCeeecCCCCceeeccccc-----cCCCccchh
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS-----QLPCKRCIR 51 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~-----~~~cp~c~r 51 (696)
++..|-+|...-.-=+-.......=..|+.+||..|.. ...||-|.+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~ 224 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT 224 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCC
Confidence 46789999874100000000112335799999999973 467999943
No 203
>PLN02436 cellulose synthase A
Probab=28.18 E-value=33 Score=42.67 Aligned_cols=48 Identities=25% Similarity=0.550 Sum_probs=34.4
Q ss_pred CccceecCCCCC----eeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhccc
Q psy5925 5 RGFICELCNSEE----VIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRRD 57 (696)
Q Consensus 5 ~g~~ce~c~~~~----~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~~ 57 (696)
.|-||++|.++- -=.|| +-|.+|+=-.=+.|++ ++.||+|..+-+|.+
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~F-----VACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~k 92 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPF-----VACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIK 92 (1094)
T ss_pred CCccccccccccCcCCCCCEE-----EeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence 467999999851 11233 5788888778888884 367999998777654
No 204
>KOG0193|consensus
Probab=27.89 E-value=27 Score=40.73 Aligned_cols=36 Identities=31% Similarity=0.850 Sum_probs=25.9
Q ss_pred cceecCC--CCCeeeecCCCCeeecCCCCceeecccccc--CCCc
Q psy5925 7 FICELCN--SEEVIFPWQLSSVHRCNQCGACFHTKCHSQ--LPCK 47 (696)
Q Consensus 7 ~~ce~c~--~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~--~~cp 47 (696)
|.|-+|. ...++|-| .+|..|+--||++|-.. ..|+
T Consensus 187 ~~~~fC~~~~~~~l~~g-----frC~~C~~KfHq~Cs~~vp~~C~ 226 (678)
T KOG0193|consen 187 FPLAFCDSCCNKFLFTG-----FRCQTCGYKFHQSCSPRVPTSCV 226 (678)
T ss_pred cchhhhhhhcchhhhcc-----cccCCCCCccccccCCCCCCCCC
Confidence 4567777 33445444 48999999999999864 4587
No 205
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.63 E-value=52 Score=26.52 Aligned_cols=41 Identities=27% Similarity=0.669 Sum_probs=28.8
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeeccccc---c---CCCccch
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS---Q---LPCKRCI 50 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~---~---~~cp~c~ 50 (696)
+|.-|+ ..|-|.+......|+.||+.-=..|.. . -.||+|-
T Consensus 9 ~CtSCg--~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 9 KCTSCG--IEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cccCCC--CcccCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCC
Confidence 455554 457888877889999999984444653 2 2599985
No 206
>KOG3005|consensus
Probab=27.47 E-value=19 Score=37.58 Aligned_cols=44 Identities=27% Similarity=0.599 Sum_probs=29.6
Q ss_pred ceecCCCCCeeeecCC-CCeeec--CCCCceeeccccc--------------cCCCccchhhhhc
Q psy5925 8 ICELCNSEEVIFPWQL-SSVHRC--NQCGACFHTKCHS--------------QLPCKRCIRMRIR 55 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~-~~~~~c--~~c~~~~h~~c~~--------------~~~cp~c~r~~~r 55 (696)
.||+|...=. +. .....| ..|....|-.|.. .+.||+|.+.-.=
T Consensus 184 ~celc~~ei~----e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~w 244 (276)
T KOG3005|consen 184 ECELCEKEIL----ETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLSW 244 (276)
T ss_pred hhHHHHHHhc----cccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceeeH
Confidence 7999976421 22 233456 3599999999984 2569999985443
No 207
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=27.08 E-value=32 Score=40.22 Aligned_cols=27 Identities=22% Similarity=0.440 Sum_probs=24.4
Q ss_pred eeeeeccccchhhhhhhccCccccccc
Q psy5925 115 IIVLDFQSLYPSVIIAYNYCFSTCLGR 141 (696)
Q Consensus 115 ~~~~d~~s~y~~~~~~~~~~~~t~~~~ 141 (696)
|.=||-+||||.||.++.|=|+.++..
T Consensus 92 IYHlDV~aMYpnIiltnRLQP~a~v~e 118 (621)
T cd05535 92 IYHLDVAAMYPNIILTNRLQPDAIVDE 118 (621)
T ss_pred eeEeehhhccchhhhhccCCCcccCCH
Confidence 667999999999999999999999864
No 208
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=26.23 E-value=43 Score=30.10 Aligned_cols=37 Identities=24% Similarity=0.567 Sum_probs=27.4
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeeccccc--cCCCc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS--QLPCK 47 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~--~~~cp 47 (696)
.||+|...... |..+..-|..|+..|+..=.. ++-|.
T Consensus 37 aCeiC~~~GY~---q~g~~lvC~~C~~~~~~~~ig~~~GGCN 75 (102)
T PF10080_consen 37 ACEICGPKGYY---QEGDQLVCKNCGVRFNLPTIGGKSGGCN 75 (102)
T ss_pred eccccCCCceE---EECCEEEEecCCCEEehhhcccccCCCC
Confidence 49999555543 678999999999999977654 34453
No 209
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=26.18 E-value=25 Score=29.41 Aligned_cols=20 Identities=40% Similarity=0.954 Sum_probs=15.4
Q ss_pred CCCCceeeccccc-----cCCCccc
Q psy5925 30 NQCGACFHTKCHS-----QLPCKRC 49 (696)
Q Consensus 30 ~~c~~~~h~~c~~-----~~~cp~c 49 (696)
..|+-.||..|.. ...||=|
T Consensus 48 ~~C~H~FH~~Ci~~Wl~~~~~CP~C 72 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLKQNNTCPLC 72 (73)
T ss_dssp ETTSEEEEHHHHHHHHTTSSB-TTS
T ss_pred cccCCCEEHHHHHHHHhcCCcCCCC
Confidence 4699999999974 3579987
No 210
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.95 E-value=45 Score=29.81 Aligned_cols=59 Identities=10% Similarity=0.180 Sum_probs=34.4
Q ss_pred CCeeecCCCCceeeccccc-----cCCCccchhhhhccccccceeeeehhHHHHHHhhhCCCCCCCCC
Q psy5925 24 SSVHRCNQCGACFHTKCHS-----QLPCKRCIRMRIRRDSMKGIVDVKCFEESSLERSMKPDDRPSPT 86 (696)
Q Consensus 24 ~~~~~c~~c~~~~h~~c~~-----~~~cp~c~r~~~r~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~ 86 (696)
.+.+.|+.|++ ..-.|-. ...||.|.--..++ +-...+-+-+|.+|+ .++.+--.-.|.
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~-V~~l~epIDVY~~wi--D~~~eg~i~~~~ 82 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFE-VPSVYDEVDVYNKFI--DLYLEGKIEIKE 82 (99)
T ss_pred CcEeECCCCCC-eEeeeecCCCcceEECCCCCCccCEE-CCccccchhhHHHHH--HHHHhcCCCccc
Confidence 46778888884 2332321 24699998887775 445555778885554 444333333343
No 211
>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=25.75 E-value=2.6e+02 Score=27.69 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=31.2
Q ss_pred EEEehHHHHhhhcCCCCCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCcccHHHHHHHHHHHHHHHHHHH
Q psy5925 429 IVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLI 498 (696)
Q Consensus 429 l~lDl~~~~r~~~kl~sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~~~~~~~i~Y~l~D~~l~~~L~ 498 (696)
.++|+..++..-. ...++|..+|+.+||+....- .. -++.||..+++|+
T Consensus 125 ~viDTa~l~~~~~-~r~~sLk~La~~~L~~~IQ~~---------~H-----------dSvEDArAam~Ly 173 (174)
T cd06143 125 QVIDTVELFHLPG-QRKLSLRFLAWYLLGEKIQSE---------TH-----------DSIEDARTALKLY 173 (174)
T ss_pred ceEEcHHhccCCC-CCChhHHHHHHHHcCCcccCC---------Cc-----------CcHHHHHHHHHHh
Confidence 4566655543221 236899999999999876431 11 1367888887775
No 212
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.73 E-value=54 Score=28.50 Aligned_cols=36 Identities=22% Similarity=0.579 Sum_probs=26.5
Q ss_pred CccceecCCCCCeeeecCCCCeeecCCCCceeeccccc
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS 42 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~ 42 (696)
.-+.|.+|....+.= .-...-+|..|++.|-..+|.
T Consensus 34 ~~~~Cp~C~~~~VkR--~a~GIW~C~kCg~~fAGgay~ 69 (89)
T COG1997 34 AKHVCPFCGRTTVKR--IATGIWKCRKCGAKFAGGAYT 69 (89)
T ss_pred cCCcCCCCCCcceee--eccCeEEcCCCCCeecccccc
Confidence 357899999874432 123567899999999988885
No 213
>KOG1706|consensus
Probab=25.50 E-value=77 Score=34.00 Aligned_cols=43 Identities=14% Similarity=0.282 Sum_probs=27.1
Q ss_pred HHHHhhhCCCCCCCCCccCCC--Cc-----CCCCCcccc--CCCCCCCcccC
Q psy5925 71 SSLERSMKPDDRPSPTRKNKS--TR-----SSFDSDMFP--SSSSRDRLYTD 113 (696)
Q Consensus 71 ~~l~~~~~~~~~~~p~~~~~~--~~-----~~~~~~~~~--~~~~~~~~~~~ 113 (696)
+=|+..|++.|.++|.-+-.. .. -+|++++.- .-.|+++.|.-
T Consensus 159 ~Dl~eYakq~giPvpvT~k~pwsmDeNl~HiSyEagiLEdP~nqpp~~m~~~ 210 (412)
T KOG1706|consen 159 KDLLEYAKQHGIPVPVTPKNPWSMDENLMHISYEAGILEDPKNQPPKDMYKL 210 (412)
T ss_pred hHHHHHHHhcCCCccccCCCCccccccceeeeeccccccCcCCCCCcccccc
Confidence 678999999999998765321 11 267766553 33455666643
No 214
>KOG0825|consensus
Probab=25.15 E-value=37 Score=40.42 Aligned_cols=43 Identities=19% Similarity=0.651 Sum_probs=31.3
Q ss_pred ccceecCCCCCeeeecCCCCeeecCCCCce-eecccccc---------CCCccchhhh
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQCGAC-FHTKCHSQ---------LPCKRCIRMR 53 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~-~h~~c~~~---------~~cp~c~r~~ 53 (696)
.--|++|...+. .+--..|..|..+ ||..|..- --|+.|.-++
T Consensus 215 ~~~C~IC~~~Dp-----EdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 215 EVKCDICTVHDP-----EDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE 267 (1134)
T ss_pred cccceeeccCCh-----HHhheeecccccceeeccccCcccccccccceecCcchhhh
Confidence 345999988652 1334689999999 99999852 2399997554
No 215
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=24.45 E-value=30 Score=31.55 Aligned_cols=39 Identities=23% Similarity=0.503 Sum_probs=22.0
Q ss_pred CCCeeeecCCCCeeecCCCCceeeccccccCCCccchhhhh
Q psy5925 14 SEEVIFPWQLSSVHRCNQCGACFHTKCHSQLPCKRCIRMRI 54 (696)
Q Consensus 14 ~~~~i~p~~~~~~~~c~~c~~~~h~~c~~~~~cp~c~r~~~ 54 (696)
+.++..=.. .-..+|..|+..|--.=.. ..||+|.....
T Consensus 59 ~a~L~Ie~~-p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~~~ 97 (113)
T PF01155_consen 59 GAELEIEEV-PARARCRDCGHEFEPDEFD-FSCPRCGSPDV 97 (113)
T ss_dssp T-EEEEEEE---EEEETTTS-EEECHHCC-HH-SSSSSS-E
T ss_pred CCEEEEEec-CCcEECCCCCCEEecCCCC-CCCcCCcCCCc
Confidence 334444344 3567999999998655443 46999987643
No 216
>PRK12495 hypothetical protein; Provisional
Probab=24.26 E-value=44 Score=34.00 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=16.1
Q ss_pred ccceecCCCCCeeeecCCCCeeecCCCCceee
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQCGACFH 37 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h 37 (696)
.|.|+.|+.+ ||- ...+.+|..|...+-
T Consensus 42 a~hC~~CG~P--Ipa--~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 42 NAHCDECGDP--IFR--HDGQEFCPTCQQPVT 69 (226)
T ss_pred hhhcccccCc--ccC--CCCeeECCCCCCccc
Confidence 4677777654 442 235556666665544
No 217
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=24.14 E-value=38 Score=42.00 Aligned_cols=48 Identities=23% Similarity=0.497 Sum_probs=34.7
Q ss_pred CccceecCCCCC----eeeecCCCCeeecCCCCceeeccccc------cCCCccchhhhhccc
Q psy5925 5 RGFICELCNSEE----VIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIRMRIRRD 57 (696)
Q Consensus 5 ~g~~ce~c~~~~----~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r~~~r~~ 57 (696)
-|-||++|.++- -=.|| +-|.+|+--.-+.|++ ++.||+|..+-+|.+
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~F-----VAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~~~~ 71 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPF-----VACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYKRHK 71 (1044)
T ss_pred CcchhhccccccCcCCCCCEE-----EEeccCCCccccchhhhhhhcCCccCCccCCchhhhc
Confidence 467999999851 11244 5788888778888884 367999998777644
No 218
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.77 E-value=36 Score=24.91 Aligned_cols=22 Identities=27% Similarity=0.942 Sum_probs=17.1
Q ss_pred eecCCCCCeeeecCCCCeeecCCCCcee
Q psy5925 9 CELCNSEEVIFPWQLSSVHRCNQCGACF 36 (696)
Q Consensus 9 ce~c~~~~~i~p~~~~~~~~c~~c~~~~ 36 (696)
|.+|+..+.+.||. |..|+..|
T Consensus 1 C~~C~~~~~l~~f~------C~~C~~~F 22 (39)
T smart00154 1 CHFCRKKVGLTGFK------CRHCGNLF 22 (39)
T ss_pred CcccCCcccccCeE------CCccCCcc
Confidence 67888887777764 88888876
No 219
>KOG4793|consensus
Probab=23.64 E-value=90 Score=32.92 Aligned_cols=44 Identities=18% Similarity=0.295 Sum_probs=35.0
Q ss_pred CHHHHHHHHHHHHHHhCCCEEEecccccccHHHHHHHHHHcCCCCc
Q psy5925 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLN 399 (696)
Q Consensus 354 sE~eLL~~f~~~I~~~DPDIIvGyNi~~fDl~YL~~Ra~~lgi~~~ 399 (696)
+=..||.+|+..+. .|=-++.||++.||+|.|.+-...+|+...
T Consensus 105 dla~LL~afls~lp--~p~CLVaHng~~~dfpil~qela~lg~~lp 148 (318)
T KOG4793|consen 105 DLAKLLTAFLSRLP--TPGCLVAHNGNEYDFPILAQELAGLGYSLP 148 (318)
T ss_pred HHHHHHHHHHhcCC--CCceEEeecCCccccHHHHHHHHhcCccch
Confidence 44567777766443 577899999999999999999888988765
No 220
>KOG4628|consensus
Probab=23.25 E-value=45 Score=36.45 Aligned_cols=40 Identities=25% Similarity=0.611 Sum_probs=28.3
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCceeeccccc------cCCCccchh
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS------QLPCKRCIR 51 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~------~~~cp~c~r 51 (696)
+.|-+|-.+ |+..+-.|=-=|+..||..|.. ...||=|.|
T Consensus 230 ~~CaIClEd-----Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLED-----YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKR 275 (348)
T ss_pred ceEEEeecc-----cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCC
Confidence 567777654 3334445556699999999964 245999998
No 221
>KOG0827|consensus
Probab=23.07 E-value=18 Score=39.53 Aligned_cols=45 Identities=27% Similarity=0.587 Sum_probs=32.6
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeeccccc-------c-CCCccch-hhhhcc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS-------Q-LPCKRCI-RMRIRR 56 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~-------~-~~cp~c~-r~~~r~ 56 (696)
+|.+| .-.||-.. +..--..||-+||-.|.. + ..||-|. ..+.|.
T Consensus 6 ~C~Ic---~d~~p~~~-~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~ 59 (465)
T KOG0827|consen 6 ECHIC---IDGRPNDH-ELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERH 59 (465)
T ss_pred eeeEe---ccCCcccc-ccccccchhhHHHHHHHHHHHccCCccCCCCceeeccccee
Confidence 68899 44778773 555666799999999953 2 4799998 444454
No 222
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=23.06 E-value=28 Score=37.24 Aligned_cols=67 Identities=15% Similarity=0.156 Sum_probs=44.4
Q ss_pred ecCCCCCeeeecCCCCeeecCCCCceee--ccccccCCCccch-hhh-------------hccccccceeeeehhHHHHH
Q psy5925 10 ELCNSEEVIFPWQLSSVHRCNQCGACFH--TKCHSQLPCKRCI-RMR-------------IRRDSMKGIVDVKCFEESSL 73 (696)
Q Consensus 10 e~c~~~~~i~p~~~~~~~~c~~c~~~~h--~~c~~~~~cp~c~-r~~-------------~r~~~~~~~~~~~~~~~~~l 73 (696)
.+|.+..|.-||++..++. ..|-+..= ...-.+..||.|. .-. +=-++++..++|+.|.-|+|
T Consensus 86 PI~~s~~I~LPfdL~~~va-~~CLsLSpmG~~~~~G~~C~~C~~~g~~~~~~~d~~Al~LAf~~Qv~~Vvq~R~Fy~Sll 164 (316)
T PHA03328 86 PLIKTTPVSLPFDLNQTVA-DNCLSLSGMGYYLGIGGCCPTCSVSGEPRLGRTDRAALILAYVQQLNNIYEYRVFLASLR 164 (316)
T ss_pred CccccceeeeeeccccccC-CcceeccCcccccccCccCCCCCCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999976555 66666532 2222356799999 211 12234566779999988877
Q ss_pred Hhhh
Q psy5925 74 ERSM 77 (696)
Q Consensus 74 ~~~~ 77 (696)
-...
T Consensus 165 ~~s~ 168 (316)
T PHA03328 165 VLAG 168 (316)
T ss_pred Hhcc
Confidence 6554
No 223
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=22.93 E-value=22 Score=27.69 Aligned_cols=31 Identities=23% Similarity=0.533 Sum_probs=19.0
Q ss_pred eeecCCCCceeecc-cc--ccCCCccchhhhhcc
Q psy5925 26 VHRCNQCGACFHTK-CH--SQLPCKRCIRMRIRR 56 (696)
Q Consensus 26 ~~~c~~c~~~~h~~-c~--~~~~cp~c~r~~~r~ 56 (696)
..||..|+...-+. =+ -...||||..+..=+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 36888888775442 22 245688888776533
No 224
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.78 E-value=44 Score=23.16 Aligned_cols=23 Identities=35% Similarity=0.798 Sum_probs=9.6
Q ss_pred eecCCCCCeeeecCCCCeeecCCCCc
Q psy5925 9 CELCNSEEVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 9 ce~c~~~~~i~p~~~~~~~~c~~c~~ 34 (696)
|+.|++...+ ......-|+.|+.
T Consensus 5 Cp~C~se~~y---~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTY---EDGELLVCPECGH 27 (30)
T ss_dssp -TTT-----E---E-SSSEEETTTTE
T ss_pred CCCCCCccee---ccCCEEeCCcccc
Confidence 6777765444 2245666666654
No 225
>KOG3507|consensus
Probab=22.78 E-value=45 Score=26.76 Aligned_cols=25 Identities=36% Similarity=0.895 Sum_probs=18.2
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGA 34 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~ 34 (696)
|||--|.....|=+ .++.||.+||-
T Consensus 21 YiCgdC~~en~lk~---~D~irCReCG~ 45 (62)
T KOG3507|consen 21 YICGDCGQENTLKR---GDVIRCRECGY 45 (62)
T ss_pred EEeccccccccccC---CCcEehhhcch
Confidence 68888888776644 45678888873
No 226
>KOG4718|consensus
Probab=22.71 E-value=31 Score=34.86 Aligned_cols=37 Identities=27% Similarity=0.697 Sum_probs=27.5
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeeccccc-----cCCCccchh
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS-----QLPCKRCIR 51 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~-----~~~cp~c~r 51 (696)
.|.+|+.--+ -..||+.|+--||..|.+ ...||-|.-
T Consensus 183 ~Cn~Ch~LvI-------qg~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 183 NCNLCHCLVI-------QGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHhHhHHHhh-------eeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 5777766432 346999999999999974 357999953
No 227
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.41 E-value=66 Score=25.49 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=17.1
Q ss_pred ceecCCCCCeeeecCCC------CeeecCCCCc
Q psy5925 8 ICELCNSEEVIFPWQLS------SVHRCNQCGA 34 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~------~~~~c~~c~~ 34 (696)
-|.||....+..=.... -...|..|++
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 39999555544433322 4567999988
No 228
>PRK12496 hypothetical protein; Provisional
Probab=22.40 E-value=48 Score=32.33 Aligned_cols=30 Identities=17% Similarity=0.351 Sum_probs=21.4
Q ss_pred eecCCCCceeeccccccCCCccchhhhhccc
Q psy5925 27 HRCNQCGACFHTKCHSQLPCKRCIRMRIRRD 57 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~~~~cp~c~r~~~r~~ 57 (696)
.+|.+|+..|...= ....||.|.-.-.|+.
T Consensus 128 ~~C~gC~~~~~~~~-~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 128 KVCKGCKKKYPEDY-PDDVCEICGSPVKRKM 157 (164)
T ss_pred EECCCCCccccCCC-CCCcCCCCCChhhhcc
Confidence 58999999996532 1257999987655543
No 229
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.38 E-value=34 Score=33.19 Aligned_cols=29 Identities=31% Similarity=0.529 Sum_probs=17.3
Q ss_pred CCccceecCCCCCeeeecCC--CCeeecCCCCce
Q psy5925 4 ARGFICELCNSEEVIFPWQL--SSVHRCNQCGAC 35 (696)
Q Consensus 4 ~~g~~ce~c~~~~~i~p~~~--~~~~~c~~c~~~ 35 (696)
..+|+|..|. .-|.|+. +.-..|+.||+.
T Consensus 107 ~~~Y~Cp~c~---~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMC---VRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCC---cEeeHHHHHHcCCcCCCCCCE
Confidence 4578888877 4566553 223556666654
No 230
>PRK11032 hypothetical protein; Provisional
Probab=22.16 E-value=61 Score=31.55 Aligned_cols=34 Identities=15% Similarity=0.320 Sum_probs=20.5
Q ss_pred CeeecCCCCceeeccccc-cCCCccchhhhhcccc
Q psy5925 25 SVHRCNQCGACFHTKCHS-QLPCKRCIRMRIRRDS 58 (696)
Q Consensus 25 ~~~~c~~c~~~~h~~c~~-~~~cp~c~r~~~r~~~ 58 (696)
.+..|.+|+.-.|-.=-. =.+||+|-...-+|+.
T Consensus 123 G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~~ 157 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRP 157 (160)
T ss_pred ceEEecCCCCEEEecCCCcCCCCCCCCCCeeeeCC
Confidence 456788888554432111 1479999877666543
No 231
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=22.16 E-value=25 Score=30.00 Aligned_cols=20 Identities=25% Similarity=0.492 Sum_probs=14.9
Q ss_pred CCCceeeccccc-----cCCCccch
Q psy5925 31 QCGACFHTKCHS-----QLPCKRCI 50 (696)
Q Consensus 31 ~c~~~~h~~c~~-----~~~cp~c~ 50 (696)
.|.-.||..|.. ++.||=|.
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld~ 77 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLDR 77 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCCC
Confidence 377789999974 46799653
No 232
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=22.11 E-value=77 Score=35.14 Aligned_cols=59 Identities=12% Similarity=0.069 Sum_probs=39.7
Q ss_pred CCCeeecCCCCceeeccccc---cCCCccchhhhhccccccceeeeehhHHHHHHhhhCCCCC
Q psy5925 23 LSSVHRCNQCGACFHTKCHS---QLPCKRCIRMRIRRDSMKGIVDVKCFEESSLERSMKPDDR 82 (696)
Q Consensus 23 ~~~~~~c~~c~~~~h~~c~~---~~~cp~c~r~~~r~~~~~~~~~~~~~~~~~l~~~~~~~~~ 82 (696)
.....+|++|+..+---=.+ +..||||...-.|.....-+ .--.+--++|+=..-..++
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~~~~~~sl~-r~~a~A~s~LiLm~fa~~f 76 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLTRGGDWSLQ-RPAAYALAALILMPFALGF 76 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCCccccCCCCCcc-chHHHHHHHHHHHHHHcCC
Confidence 35678999999998655332 45799998876665555444 4445666777766666665
No 233
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.83 E-value=48 Score=41.91 Aligned_cols=42 Identities=26% Similarity=0.671 Sum_probs=24.9
Q ss_pred cceecCCCCCeeeecCCCCeeecCCCCcee-----eccccc--------cCCCccchhhhhcc
Q psy5925 7 FICELCNSEEVIFPWQLSSVHRCNQCGACF-----HTKCHS--------QLPCKRCIRMRIRR 56 (696)
Q Consensus 7 ~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~-----h~~c~~--------~~~cp~c~r~~~r~ 56 (696)
+.|.-|+... |. .+|+.||+-. +..|-. ...||+|.+-....
T Consensus 668 rkCPkCG~~t--~~------~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~ 722 (1337)
T PRK14714 668 RRCPSCGTET--YE------NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPY 722 (1337)
T ss_pred EECCCCCCcc--cc------ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccccc
Confidence 5677777642 21 1677777553 344533 12799999766553
No 234
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=21.81 E-value=65 Score=28.26 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=18.0
Q ss_pred ccceecCCCCCeeeecCCCCeeecCCCCceeeccccc
Q psy5925 6 GFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS 42 (696)
Q Consensus 6 g~~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c~~ 42 (696)
+=.|.+|+.. +........ -|+.+||..|..
T Consensus 78 ~~~C~vC~k~-----l~~~~f~~~-p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKP-----LGNSVFVVF-PCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCc-----CCCceEEEe-CCCeEEeccccc
Confidence 3468888873 121112222 356999999974
No 235
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.77 E-value=66 Score=22.50 Aligned_cols=26 Identities=19% Similarity=0.466 Sum_probs=16.7
Q ss_pred eecCCCCceeeccccccCCCccchhhh
Q psy5925 27 HRCNQCGACFHTKCHSQLPCKRCIRMR 53 (696)
Q Consensus 27 ~~c~~c~~~~h~~c~~~~~cp~c~r~~ 53 (696)
.+|..||-+|...- ....||.|...+
T Consensus 2 ~~C~~CGy~y~~~~-~~~~CP~Cg~~~ 27 (33)
T cd00350 2 YVCPVCGYIYDGEE-APWVCPVCGAPK 27 (33)
T ss_pred EECCCCCCEECCCc-CCCcCcCCCCcH
Confidence 46788887776543 234688886544
No 236
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=21.45 E-value=58 Score=27.85 Aligned_cols=35 Identities=26% Similarity=0.796 Sum_probs=25.9
Q ss_pred CccceecCCCCCeeeecCCCCeeecCC--CCceeeccccccCCC
Q psy5925 5 RGFICELCNSEEVIFPWQLSSVHRCNQ--CGACFHTKCHSQLPC 46 (696)
Q Consensus 5 ~g~~ce~c~~~~~i~p~~~~~~~~c~~--c~~~~h~~c~~~~~c 46 (696)
+.-.|.+|+.. ...+.+|.. |...||-.|.....|
T Consensus 35 ~~~~C~~C~~~-------~Ga~i~C~~~~C~~~fH~~CA~~~~~ 71 (90)
T PF13771_consen 35 RKLKCSICKKK-------GGACIGCSHPGCSRSFHVPCARKAGC 71 (90)
T ss_pred hCCCCcCCCCC-------CCeEEEEeCCCCCcEEChHHHccCCe
Confidence 45578899866 246778865 999999999865443
No 237
>KOG3657|consensus
Probab=21.28 E-value=1.5e+02 Score=35.90 Aligned_cols=60 Identities=7% Similarity=-0.199 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHcCCCcCCCChhhHHHHHhcCCc----ccHHHHHHHHHHHHHHHHHHHHHhcccchhhh
Q psy5925 445 SYTFENIMYHVLHERIPLHSWKLLTCWWEHRTH----LYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSE 509 (696)
Q Consensus 445 sysL~~Va~~~L~~~k~~~~~~~l~~~~~~~~~----~~~~~~i~Y~l~D~~l~~~L~~kl~ii~~~~e 509 (696)
-.||.+|++++.|....+= +.-+.|.+++. ++...++.||.+|+..+.+++.++ .|...|
T Consensus 322 ~NSL~dVhk~~c~~~~LdK---t~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~l--fP~Fle 385 (1075)
T KOG3657|consen 322 LNSLVDVHKFHCGIDALDK---TPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRL--FPLFLE 385 (1075)
T ss_pred hHHHHHHHHhhCCCCcccc---chHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHH--hHHHHH
Confidence 3578999999887653222 22233433331 246889999999999999999987 554443
No 238
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=20.77 E-value=27 Score=30.30 Aligned_cols=30 Identities=20% Similarity=0.672 Sum_probs=23.8
Q ss_pred ceecCCCCCeeeecCCCCeeecCCCCceeeccc
Q psy5925 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKC 40 (696)
Q Consensus 8 ~ce~c~~~~~i~p~~~~~~~~c~~c~~~~h~~c 40 (696)
+|.+|++...-|=|. +..|.+|.+.|++.=
T Consensus 1 ~C~VCg~~~~g~hyg---v~sC~aC~~FFRR~v 30 (87)
T cd07162 1 ICRVCGDRATGYHFN---AMTCEGCKGFFRRAM 30 (87)
T ss_pred CCcccCCcCcceEEC---cceehhhHHHHHhhh
Confidence 589999887777666 468999999997754
No 239
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.60 E-value=57 Score=23.48 Aligned_cols=29 Identities=28% Similarity=0.673 Sum_probs=18.3
Q ss_pred ceecCCCCCee----eecCCCCeeecCCCCceee
Q psy5925 8 ICELCNSEEVI----FPWQLSSVHRCNQCGACFH 37 (696)
Q Consensus 8 ~ce~c~~~~~i----~p~~~~~~~~c~~c~~~~h 37 (696)
.|.-|+..--| .|- .....+|+.|+.+|+
T Consensus 4 ~CP~C~~~f~v~~~~l~~-~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPA-GGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHccc-CCcEEECCCCCcEee
Confidence 46677663111 222 245789999999986
No 240
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=20.40 E-value=52 Score=36.93 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=0.0
Q ss_pred CCeeecCCCCceeecc---ccccCCCccchhhhhccc
Q psy5925 24 SSVHRCNQCGACFHTK---CHSQLPCKRCIRMRIRRD 57 (696)
Q Consensus 24 ~~~~~c~~c~~~~h~~---c~~~~~cp~c~r~~~r~~ 57 (696)
.....|++|+.+++.. --+...||||...-.|+.
T Consensus 11 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~ 47 (403)
T TIGR00155 11 AKHILCSQCDMLVALPRIESGQKAACPRCGTTLTVGW 47 (403)
T ss_pred CCeeeCCCCCCcccccCCCCCCeeECCCCCCCCcCCC
No 241
>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=20.32 E-value=40 Score=33.49 Aligned_cols=31 Identities=32% Similarity=1.009 Sum_probs=27.2
Q ss_pred hhhhhhhhhhccccCCCcccccccccccccC
Q psy5925 314 EKELFSTFIENVRQWDPDILIGYEIETFSWG 344 (696)
Q Consensus 314 ~~e~~~~~~~~~~~~~p~~~~g~ei~~~~~~ 344 (696)
|+++++++...++..+|++++|+++..|++.
T Consensus 48 E~~lL~~F~~~i~~~dPd~i~gyN~~~FDlp 78 (188)
T cd05781 48 DRKIIREFVKYVKEYDPDIIVGYNSNAFDWP 78 (188)
T ss_pred HHHHHHHHHHHHHHcCCCEEEecCCCcCcHH
Confidence 6788888888889999999999999998863
No 242
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=20.22 E-value=98 Score=32.89 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=25.7
Q ss_pred EeCCHHHHHHHHHHHHHHhCCCE--EEeccc
Q psy5925 351 FVSNEKELFSIFIENVRQWDPDI--LIGYEI 379 (696)
Q Consensus 351 ~~~sE~eLL~~f~~~I~~~DPDI--IvGyNi 379 (696)
.+-.|+++=....+++.++.||| |+||++
T Consensus 135 ~~~~E~eqp~~i~~Ll~~~~PDIlViTGHD~ 165 (287)
T PF05582_consen 135 IHVPEKEQPEKIYRLLEEYRPDILVITGHDG 165 (287)
T ss_pred EEechHHhhHHHHHHHHHcCCCEEEEeCchh
Confidence 55689999999999999999995 679986
Done!