Query 020010
Match_columns 332
No_of_seqs 192 out of 1422
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 06:18:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020010.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020010hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09482 flap endonuclease-lik 100.0 2.2E-62 4.7E-67 460.1 24.1 230 79-331 2-241 (256)
2 smart00475 53EXOc 5'-3' exonuc 100.0 1.5E-60 3.2E-65 449.2 25.1 232 81-331 2-245 (259)
3 PRK14976 5'-3' exonuclease; Pr 100.0 2.1E-60 4.5E-65 452.9 25.0 233 79-331 2-250 (281)
4 cd00008 53EXOc 5'-3' exonuclea 100.0 7.3E-58 1.6E-62 426.3 23.7 227 80-329 1-240 (240)
5 TIGR00593 pola DNA polymerase 100.0 1.9E-55 4E-60 471.6 24.2 231 82-331 1-245 (887)
6 PRK05755 DNA polymerase I; Pro 100.0 2.1E-52 4.5E-57 449.9 24.4 233 79-331 1-246 (880)
7 COG0258 Exo 5'-3' exonuclease 100.0 1.1E-48 2.3E-53 376.5 21.5 233 78-331 9-257 (310)
8 PHA00439 exonuclease 100.0 3.7E-45 8.1E-50 347.0 17.6 190 79-299 5-220 (286)
9 PHA02567 rnh RnaseH; Provision 100.0 6.9E-40 1.5E-44 312.5 18.0 178 79-270 13-205 (304)
10 PTZ00217 flap endonuclease-1; 100.0 1.3E-36 2.9E-41 301.4 20.9 233 79-329 27-293 (393)
11 PF02739 5_3_exonuc_N: 5'-3' e 100.0 3.4E-37 7.3E-42 273.8 13.4 153 80-246 1-169 (169)
12 TIGR03674 fen_arch flap struct 100.0 1.6E-35 3.4E-40 288.8 19.9 210 78-301 19-268 (338)
13 cd00128 XPG Xeroderma pigmento 100.0 3E-33 6.4E-38 269.6 20.5 209 79-301 23-255 (316)
14 PRK03980 flap endonuclease-1; 100.0 1.4E-32 3.1E-37 263.2 20.5 191 96-300 6-220 (292)
15 PF01367 5_3_exonuc: 5'-3' exo 99.9 3.1E-26 6.7E-31 187.7 -9.2 78 248-331 1-78 (101)
16 KOG2519 5'-3' exonuclease [Rep 99.8 1.7E-20 3.6E-25 186.1 15.8 207 80-300 28-261 (449)
17 cd00080 HhH2_motif Helix-hairp 99.8 6.2E-20 1.3E-24 142.8 6.4 74 245-327 2-75 (75)
18 TIGR00600 rad2 DNA excision re 99.8 2.7E-18 5.9E-23 185.8 14.8 122 163-297 772-896 (1034)
19 KOG2518 5'-3' exonuclease [Rep 99.7 7.6E-17 1.7E-21 162.1 18.3 197 79-299 23-255 (556)
20 smart00279 HhH2 Helix-hairpin- 99.5 3.8E-15 8.2E-20 100.4 3.7 36 250-289 1-36 (36)
21 KOG2520 5'-3' exonuclease [Rep 99.3 1.1E-11 2.4E-16 131.5 9.7 116 162-290 465-581 (815)
22 PF00867 XPG_I: XPG I-region; 99.0 1E-09 2.3E-14 88.5 5.6 81 174-261 2-92 (94)
23 smart00484 XPGI Xeroderma pigm 98.2 4.6E-06 1E-10 64.8 7.4 70 174-248 2-73 (73)
24 PF05991 NYN_YacP: YacP-like N 97.5 0.00016 3.6E-09 64.2 5.4 44 176-219 67-111 (166)
25 PF12813 XPG_I_2: XPG domain c 97.0 0.0016 3.5E-08 61.5 6.9 85 166-258 7-107 (246)
26 PF00752 XPG_N: XPG N-terminal 96.4 0.0039 8.4E-08 50.3 4.0 57 80-138 26-93 (101)
27 PF12826 HHH_2: Helix-hairpin- 96.3 0.0044 9.6E-08 46.6 3.4 27 269-299 7-33 (64)
28 smart00485 XPGN Xeroderma pigm 95.9 0.016 3.5E-07 46.7 5.2 64 79-144 23-97 (99)
29 PRK14605 ruvA Holliday junctio 94.3 0.099 2.1E-06 47.8 6.0 43 244-299 59-102 (194)
30 PRK14602 ruvA Holliday junctio 94.1 0.11 2.3E-06 47.9 5.7 25 275-300 80-104 (203)
31 TIGR00084 ruvA Holliday juncti 94.0 0.11 2.4E-06 47.3 5.7 45 244-301 58-103 (191)
32 TIGR00600 rad2 DNA excision re 94.0 0.14 3.1E-06 57.2 7.5 66 79-146 23-98 (1034)
33 PRK14601 ruvA Holliday junctio 93.6 0.14 3.1E-06 46.5 5.5 25 275-300 79-103 (183)
34 PF11977 RNase_Zc3h12a: Zc3h12 93.4 0.19 4.1E-06 44.0 5.8 98 80-212 2-110 (155)
35 COG3688 Predicted RNA-binding 93.4 0.36 7.9E-06 43.1 7.5 34 179-212 75-109 (173)
36 PF14520 HHH_5: Helix-hairpin- 93.3 0.15 3.2E-06 37.5 4.2 24 275-298 11-35 (60)
37 PRK14604 ruvA Holliday junctio 92.5 0.23 4.9E-06 45.5 5.3 25 275-300 79-103 (195)
38 PRK00116 ruvA Holliday junctio 92.4 0.22 4.9E-06 45.2 5.0 23 275-297 79-104 (192)
39 PRK14670 uvrC excinuclease ABC 91.8 0.15 3.2E-06 54.0 3.5 26 275-300 520-545 (574)
40 PRK14666 uvrC excinuclease ABC 91.7 0.22 4.8E-06 53.6 4.7 46 275-320 643-692 (694)
41 PRK14669 uvrC excinuclease ABC 91.2 0.15 3.2E-06 54.4 2.8 26 275-300 558-583 (624)
42 TIGR00194 uvrC excinuclease AB 90.9 0.18 3.8E-06 53.4 3.1 25 275-299 547-571 (574)
43 PRK14667 uvrC excinuclease ABC 90.7 0.19 4E-06 53.1 3.1 26 275-300 520-545 (567)
44 PF10391 DNA_pol_lambd_f: Fing 89.7 0.34 7.4E-06 35.2 2.8 23 275-297 8-31 (52)
45 PF00633 HHH: Helix-hairpin-he 89.2 0.3 6.5E-06 31.5 2.0 13 275-287 17-29 (30)
46 PRK14603 ruvA Holliday junctio 88.6 0.88 1.9E-05 41.7 5.4 45 275-320 78-131 (197)
47 PRK02515 psbU photosystem II c 88.1 0.55 1.2E-05 40.6 3.4 41 275-319 67-109 (132)
48 PRK14671 uvrC excinuclease ABC 88.1 0.39 8.4E-06 51.3 3.1 27 268-298 572-598 (621)
49 PRK14668 uvrC excinuclease ABC 87.9 0.38 8.2E-06 50.9 2.8 32 265-300 525-556 (577)
50 PHA03065 Hypothetical protein; 87.8 7.8 0.00017 39.6 11.8 116 169-301 151-276 (438)
51 PRK13901 ruvA Holliday junctio 87.1 1.2 2.7E-05 40.9 5.4 44 244-300 58-102 (196)
52 PRK00558 uvrC excinuclease ABC 87.1 0.53 1.2E-05 50.0 3.4 26 275-300 549-574 (598)
53 PRK12766 50S ribosomal protein 87.1 0.55 1.2E-05 44.2 3.1 29 267-299 5-34 (232)
54 PRK14672 uvrC excinuclease ABC 87.0 0.49 1.1E-05 50.9 3.1 26 275-300 614-639 (691)
55 PRK14606 ruvA Holliday junctio 86.5 1.4 3E-05 40.2 5.3 45 244-301 59-104 (188)
56 PRK14600 ruvA Holliday junctio 86.2 1.5 3.2E-05 39.9 5.3 45 244-301 59-104 (186)
57 smart00278 HhH1 Helix-hairpin- 84.5 0.73 1.6E-05 28.4 1.8 13 275-287 7-19 (26)
58 PF03159 XRN_N: XRN 5'-3' exon 84.4 7.1 0.00015 36.9 9.2 43 182-225 182-233 (237)
59 PF09293 RNaseH_C: T4 RNase H, 83.7 0.52 1.1E-05 40.2 1.1 24 249-272 2-25 (122)
60 COG0632 RuvA Holliday junction 82.5 6.1 0.00013 36.5 7.7 50 239-301 54-104 (201)
61 COG1948 MUS81 ERCC4-type nucle 81.8 1.7 3.8E-05 41.4 4.0 26 275-300 188-213 (254)
62 TIGR00575 dnlj DNA ligase, NAD 80.1 1.4 3E-05 47.4 3.0 26 274-299 503-528 (652)
63 cd06167 LabA_like LabA_like pr 79.2 3 6.5E-05 35.2 4.3 50 170-219 59-117 (149)
64 cd00141 NT_POLXc Nucleotidyltr 78.9 3.5 7.7E-05 40.1 5.2 24 275-299 91-116 (307)
65 COG0322 UvrC Nuclease subunit 78.6 1.6 3.5E-05 46.3 2.9 26 275-300 536-561 (581)
66 PF01936 NYN: NYN domain; Int 77.7 2.8 6.2E-05 34.8 3.7 49 171-219 55-113 (146)
67 PRK08609 hypothetical protein; 76.6 5 0.00011 42.5 5.9 26 275-300 94-121 (570)
68 PRK14351 ligA NAD-dependent DN 76.5 2.5 5.5E-05 45.8 3.7 25 275-299 534-558 (689)
69 PF04599 Pox_G5: Poxvirus G5 p 74.7 6.7 0.00014 40.1 5.9 116 169-301 149-274 (425)
70 PRK13901 ruvA Holliday junctio 73.5 2.2 4.7E-05 39.3 2.0 34 249-288 93-126 (196)
71 smart00483 POLXc DNA polymeras 72.8 2.9 6.4E-05 41.2 2.8 25 275-300 95-121 (334)
72 PF02371 Transposase_20: Trans 72.3 2.7 5.9E-05 33.1 2.0 22 275-296 8-29 (87)
73 PRK13766 Hef nuclease; Provisi 72.2 3 6.5E-05 45.1 3.0 26 275-300 721-746 (773)
74 PRK07956 ligA NAD-dependent DN 71.5 3 6.4E-05 45.0 2.7 24 275-298 517-540 (665)
75 PRK14601 ruvA Holliday junctio 70.2 4.2 9E-05 37.0 3.0 35 248-288 93-127 (183)
76 PF11798 IMS_HHH: IMS family H 70.1 2.9 6.2E-05 27.2 1.4 15 275-290 17-31 (32)
77 PTZ00349 dehydrodolichyl dipho 69.2 31 0.00068 34.2 9.0 93 105-215 9-121 (322)
78 TIGR01448 recD_rel helicase, p 68.2 7.9 0.00017 42.1 5.1 38 250-299 77-116 (720)
79 PRK13482 DNA integrity scannin 68.0 8.2 0.00018 38.6 4.8 28 273-300 291-318 (352)
80 PRK14600 ruvA Holliday junctio 67.9 4.9 0.00011 36.6 3.0 34 248-288 93-126 (186)
81 TIGR00596 rad1 DNA repair prot 67.4 4.2 9.1E-05 44.9 2.9 26 275-300 763-788 (814)
82 cd01012 YcaC_related YcaC rela 66.6 10 0.00022 32.7 4.6 43 167-209 78-120 (157)
83 cd01015 CSHase N-carbamoylsarc 66.3 10 0.00022 33.4 4.7 43 167-209 104-146 (179)
84 PRK14829 undecaprenyl pyrophos 66.3 28 0.0006 33.0 7.8 83 116-216 15-114 (243)
85 cd00431 cysteine_hydrolases Cy 66.2 9.7 0.00021 32.4 4.4 43 167-209 100-142 (161)
86 PRK14602 ruvA Holliday junctio 66.0 2.7 5.9E-05 38.7 0.9 34 249-288 95-128 (203)
87 TIGR01259 comE comEA protein. 65.2 6.5 0.00014 33.1 3.0 23 275-297 74-102 (120)
88 TIGR00028 Mtu_PIN_fam Mycobact 65.1 8.3 0.00018 31.7 3.7 37 186-229 105-141 (142)
89 TIGR00426 competence protein C 64.4 8.9 0.00019 28.7 3.4 23 275-297 23-51 (69)
90 PRK14606 ruvA Holliday junctio 64.2 6.6 0.00014 35.8 3.1 35 248-288 93-127 (188)
91 PRK11440 putative hydrolase; P 64.1 13 0.00028 33.0 4.9 43 167-209 111-153 (188)
92 PRK14835 undecaprenyl pyrophos 62.9 65 0.0014 31.2 9.7 66 116-198 42-117 (275)
93 TIGR00288 conserved hypothetic 61.8 11 0.00023 33.8 3.8 49 170-219 73-123 (160)
94 COG0272 Lig NAD-dependent DNA 61.3 5.8 0.00012 42.7 2.4 44 269-317 515-563 (667)
95 PRK14827 undecaprenyl pyrophos 61.0 37 0.00081 33.2 7.7 82 116-215 68-166 (296)
96 COG1555 ComEA DNA uptake prote 60.2 8.7 0.00019 33.7 3.0 24 275-298 103-132 (149)
97 TIGR03614 RutB pyrimidine util 59.7 15 0.00033 33.8 4.7 43 167-209 141-183 (226)
98 cd01013 isochorismatase Isocho 59.5 13 0.00028 33.7 4.1 43 167-209 132-174 (203)
99 PRK14604 ruvA Holliday junctio 59.4 9.9 0.00021 34.8 3.3 34 249-288 94-127 (195)
100 PRK14841 undecaprenyl pyrophos 58.4 37 0.0008 32.1 7.0 83 115-215 3-102 (233)
101 KOG2841 Structure-specific end 57.8 12 0.00026 35.5 3.6 26 275-300 201-226 (254)
102 PRK14837 undecaprenyl pyrophos 57.5 40 0.00087 31.8 7.1 82 116-215 7-105 (230)
103 PRK14603 ruvA Holliday junctio 57.3 10 0.00022 34.8 3.1 35 248-288 92-126 (197)
104 TIGR00084 ruvA Holliday juncti 57.0 11 0.00024 34.3 3.2 21 261-286 104-124 (191)
105 cd01014 nicotinamidase_related 56.5 18 0.00039 31.1 4.3 44 166-209 88-131 (155)
106 KOG1602 Cis-prenyltransferase 56.1 47 0.001 32.0 7.3 83 116-216 37-139 (271)
107 PF14229 DUF4332: Domain of un 55.9 10 0.00023 31.9 2.7 26 275-300 1-27 (122)
108 PRK14833 undecaprenyl pyrophos 54.5 46 0.001 31.4 7.0 65 116-197 5-79 (233)
109 COG1412 Uncharacterized protei 52.8 11 0.00023 32.9 2.3 41 175-220 75-115 (136)
110 PRK14838 undecaprenyl pyrophos 52.6 53 0.0011 31.2 7.1 82 116-215 11-107 (242)
111 PRK14842 undecaprenyl pyrophos 52.5 49 0.0011 31.4 6.8 82 116-215 9-107 (241)
112 PLN02621 nicotinamidase 52.4 23 0.0005 31.8 4.6 43 167-209 117-159 (197)
113 cd00475 CIS_IPPS Cis (Z)-Isopr 52.0 46 0.001 31.1 6.5 82 116-215 1-99 (221)
114 PF14520 HHH_5: Helix-hairpin- 51.1 13 0.00029 27.0 2.2 21 264-288 37-57 (60)
115 PRK14831 undecaprenyl pyrophos 50.4 67 0.0014 30.6 7.4 82 116-215 21-119 (249)
116 PF00857 Isochorismatase: Isoc 50.0 17 0.00036 31.3 3.1 44 166-209 101-144 (174)
117 PRK14828 undecaprenyl pyrophos 50.0 73 0.0016 30.5 7.6 64 116-196 27-101 (256)
118 PRK14834 undecaprenyl pyrophos 49.9 72 0.0016 30.4 7.6 82 116-215 15-113 (249)
119 COG0632 RuvA Holliday junction 47.9 11 0.00025 34.7 1.8 20 265-288 108-127 (201)
120 COG0353 RecR Recombinational D 47.8 9.3 0.0002 35.2 1.2 11 275-285 18-28 (198)
121 COG1335 PncA Amidases related 46.4 37 0.0008 30.2 4.9 43 167-209 123-165 (205)
122 PF11731 Cdd1: Pathogenicity l 46.2 21 0.00046 29.1 2.9 22 275-296 18-40 (93)
123 PRK11609 nicotinamidase/pyrazi 45.2 32 0.0007 31.1 4.3 43 167-209 132-174 (212)
124 PRK14836 undecaprenyl pyrophos 45.2 22 0.00048 33.9 3.4 90 108-215 7-113 (253)
125 TIGR00264 alpha-NAC-related pr 44.6 1.1E+02 0.0024 26.0 7.0 56 164-239 10-65 (116)
126 PRK14605 ruvA Holliday junctio 44.6 15 0.00033 33.5 2.1 22 260-286 104-125 (194)
127 TIGR00305 probable toxin-antit 43.7 15 0.00033 29.8 1.8 28 185-216 86-113 (114)
128 TIGR00055 uppS undecaprenyl di 43.6 84 0.0018 29.6 6.9 81 117-215 1-98 (226)
129 TIGR02236 recomb_radA DNA repa 43.5 21 0.00044 34.3 2.9 26 275-300 5-31 (310)
130 PF01927 Mut7-C: Mut7-C RNAse 43.4 28 0.00061 30.1 3.5 88 164-261 8-98 (147)
131 TIGR00615 recR recombination p 43.3 13 0.00029 34.2 1.5 12 275-286 17-28 (195)
132 PRK14832 undecaprenyl pyrophos 43.2 33 0.00072 32.8 4.2 82 116-215 19-117 (253)
133 PRK00076 recR recombination pr 42.8 14 0.00029 34.1 1.4 12 275-286 17-28 (196)
134 PRK00254 ski2-like helicase; P 42.7 28 0.0006 37.7 4.1 27 274-300 650-677 (720)
135 cd01011 nicotinamidase Nicotin 42.5 41 0.00089 30.2 4.5 44 166-209 127-170 (196)
136 PRK14839 undecaprenyl pyrophos 41.9 35 0.00076 32.4 4.1 84 115-216 9-109 (239)
137 PRK14830 undecaprenyl pyrophos 40.9 1.2E+02 0.0026 28.9 7.6 82 116-215 23-121 (251)
138 COG2379 GckA Putative glycerat 40.2 2.3E+02 0.0049 29.2 9.6 121 164-300 259-392 (422)
139 PTZ00331 alpha/beta hydrolase; 39.8 46 0.001 30.4 4.5 44 166-209 135-178 (212)
140 PF12826 HHH_2: Helix-hairpin- 39.8 6.8 0.00015 29.2 -0.8 30 259-292 29-58 (64)
141 PF14229 DUF4332: Domain of un 39.5 1E+02 0.0022 25.9 6.2 73 239-326 32-105 (122)
142 PRK13844 recombination protein 38.9 18 0.00039 33.4 1.6 12 275-286 21-32 (200)
143 COG0177 Nth Predicted EndoIII- 37.1 45 0.00098 31.1 4.0 37 240-291 94-132 (211)
144 PF14579 HHH_6: Helix-hairpin- 35.0 78 0.0017 24.9 4.6 26 275-300 33-63 (90)
145 PRK14840 undecaprenyl pyrophos 34.6 47 0.001 31.8 3.7 82 115-215 18-121 (250)
146 COG1491 Predicted RNA-binding 33.5 72 0.0016 29.4 4.5 27 274-300 135-166 (202)
147 TIGR00575 dnlj DNA ligase, NAD 32.8 48 0.001 35.9 3.9 13 275-287 472-484 (652)
148 TIGR03252 uncharacterized HhH- 32.0 24 0.00051 32.1 1.2 17 275-291 121-137 (177)
149 PF04900 Fcf1: Fcf1; InterPro 31.9 23 0.0005 28.4 1.0 31 185-219 51-81 (101)
150 PF13052 DUF3913: Protein of u 31.8 24 0.00051 25.5 0.9 14 264-281 18-31 (57)
151 PRK14175 bifunctional 5,10-met 31.3 39 0.00085 32.8 2.7 79 199-288 179-273 (286)
152 PF04919 DUF655: Protein of un 31.3 50 0.0011 30.2 3.1 50 249-300 97-152 (181)
153 PRK01229 N-glycosylase/DNA lya 29.9 37 0.00079 31.5 2.1 17 275-291 125-141 (208)
154 PRK13910 DNA glycosylase MutY; 29.8 66 0.0014 31.3 4.0 17 275-291 78-95 (289)
155 PRK14351 ligA NAD-dependent DN 28.9 59 0.0013 35.5 3.8 36 267-306 498-538 (689)
156 PTZ00441 sporozoite surface pr 28.8 5.1E+02 0.011 27.9 10.5 55 64-126 34-92 (576)
157 KOG4700 Uncharacterized homolo 28.8 1.7E+02 0.0036 27.0 6.0 69 201-284 59-127 (207)
158 PF14716 HHH_8: Helix-hairpin- 28.3 47 0.001 24.8 2.1 15 267-285 49-63 (68)
159 PRK00116 ruvA Holliday junctio 28.2 38 0.00082 30.7 1.9 20 267-290 110-129 (192)
160 PRK10792 bifunctional 5,10-met 28.1 49 0.0011 32.2 2.7 85 194-288 175-274 (285)
161 PRK14350 ligA NAD-dependent DN 27.0 54 0.0012 35.7 3.1 23 275-297 508-531 (669)
162 PRK07956 ligA NAD-dependent DN 26.5 1.6E+02 0.0034 32.1 6.4 46 274-320 450-502 (665)
163 COG1569 Predicted nucleic acid 26.1 39 0.00085 29.6 1.5 35 201-245 102-136 (142)
164 cd00056 ENDO3c endonuclease II 26.0 43 0.00094 28.6 1.8 14 275-288 89-102 (158)
165 PF00875 DNA_photolyase: DNA p 25.6 1.3E+02 0.0027 25.9 4.7 50 161-214 51-100 (165)
166 TIGR02432 lysidine_TilS_N tRNA 25.2 2.2E+02 0.0047 24.8 6.2 61 166-229 89-149 (189)
167 PRK14178 bifunctional 5,10-met 25.1 59 0.0013 31.5 2.7 86 192-288 166-266 (279)
168 KOG1921 Endonuclease III [Repl 24.9 92 0.002 30.1 3.8 21 275-295 165-186 (286)
169 PRK14176 bifunctional 5,10-met 24.8 56 0.0012 31.9 2.4 83 194-288 180-278 (287)
170 COG4365 Uncharacterized protei 24.7 4.5E+02 0.0098 27.4 8.8 117 102-253 209-326 (537)
171 smart00670 PINc Large family o 24.5 59 0.0013 25.4 2.2 25 187-215 86-110 (111)
172 PRK10702 endonuclease III; Pro 24.4 45 0.00098 30.8 1.7 16 275-290 115-131 (211)
173 cd01080 NAD_bind_m-THF_DH_Cycl 24.0 68 0.0015 28.5 2.7 20 265-288 142-162 (168)
174 PF15632 ATPgrasp_Ter: ATP-gra 24.0 1E+02 0.0022 30.6 4.1 59 164-225 54-112 (329)
175 PRK04301 radA DNA repair and r 23.8 67 0.0015 31.0 2.8 24 275-298 12-36 (317)
176 PF14097 SpoVAE: Stage V sporu 23.5 1.2E+02 0.0026 27.6 4.1 42 82-126 3-62 (180)
177 smart00478 ENDO3c endonuclease 23.3 52 0.0011 27.8 1.8 16 275-290 78-94 (149)
178 PF00416 Ribosomal_S13: Riboso 23.1 72 0.0016 26.2 2.5 16 275-290 21-36 (107)
179 TIGR01083 nth endonuclease III 23.0 52 0.0011 29.6 1.8 13 275-287 112-124 (191)
180 COG1936 Predicted nucleotide k 23.0 56 0.0012 29.8 1.9 17 275-291 9-25 (180)
181 PRK13913 3-methyladenine DNA g 22.5 55 0.0012 30.6 1.9 17 275-291 127-144 (218)
182 PRK10880 adenine DNA glycosyla 21.9 1.1E+02 0.0025 30.5 4.1 17 275-291 115-132 (350)
183 KOG2841 Structure-specific end 21.7 95 0.0021 29.7 3.2 96 175-288 150-246 (254)
184 COG0099 RpsM Ribosomal protein 21.7 94 0.002 26.6 2.9 25 275-299 23-48 (121)
185 PLN02743 nicotinamidase 20.2 1.2E+02 0.0026 28.5 3.7 42 168-209 142-191 (239)
No 1
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=2.2e-62 Score=460.11 Aligned_cols=230 Identities=25% Similarity=0.380 Sum_probs=206.2
Q ss_pred CCcEEEEeCcchhhhhc--Cc--h--hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCch--hhhhhchhHHhcchhhhh
Q 020010 79 KKRVFFLDVNPLCYEGS--RP--S--LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTE--HRRQLLPSYKAHRRKFLR 148 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~--~p--~--~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~--fR~el~p~YKanR~~~p~ 148 (332)
+++++||||++++||+| .| . .+++.+|++++++.++. ++++++|||++ +++ ||+++||+||+||+++|
T Consensus 2 ~~~llLiDg~~l~~R~~~a~~~~~g~t~av~gf~~~l~~ll~~~~p~~i~v~fD~~-~~~~~fR~~l~p~YKa~R~~~P- 79 (256)
T PRK09482 2 MNHLLIIDALNLIRRIHAVQPSPNDINACVETCQHALDKLIRHSQPTHAVAVFDGD-ARSSGWRHQLLPDYKAGRKPMP- 79 (256)
T ss_pred CCeEEEEeCcHHHHHHHhCCCCCCCcchHHHHHHHHHHHHHHHcCCCEEEEEEeCC-CCCcccHHHHhHHHhcCCCCCc-
Confidence 56799999999999986 22 1 24566777777766643 66799999995 555 99999999999999885
Q ss_pred hhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecC
Q 020010 149 QLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPL 228 (332)
Q Consensus 149 p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~ 228 (332)
++|..|++.++++++++||+++..+||||||+|||+|+++...|..|+|+|+|||++||++++|++|++.
T Consensus 80 ----------e~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~ 149 (256)
T PRK09482 80 ----------EALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF 149 (256)
T ss_pred ----------HHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc
Confidence 6799999999999999999999999999999999999999989999999999999999999999999875
Q ss_pred CCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCchH
Q 020010 229 QDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDY 308 (332)
Q Consensus 229 ~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~~ 308 (332)
+ ...++.+.+.++||++|+|++||++|+||+||||||| ||||||||.+||++|||+|+|+++++. . +++
T Consensus 150 ~----~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGV----pGIG~KtA~~LL~~~gsle~i~~~~~~--~-~~~ 218 (256)
T PRK09482 150 Q----KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGV----AGIGPKSAAELLNQFRSLENIYESLDA--L-PEK 218 (256)
T ss_pred c----cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCC----CCcChHHHHHHHHHhCCHHHHHHhHHH--h-hHH
Confidence 3 2458999999999999999999999999999999999 999999999999999999999999984 3 246
Q ss_pred HHHHHHHhHHHHHhhcccceecc
Q 020010 309 AQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 309 ~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
++++|.++++++++||+|++|++
T Consensus 219 ~~~~L~~~~~~a~lsr~L~~l~~ 241 (256)
T PRK09482 219 WRKKLEEHKEMARLCRKLAQLQT 241 (256)
T ss_pred HHHHHHHhHHHHHHHHhhheEee
Confidence 89999999999999999999986
No 2
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.5e-60 Score=449.18 Aligned_cols=232 Identities=31% Similarity=0.562 Sum_probs=206.6
Q ss_pred cEEEEeCcchhhhhcC--ch--------hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchhhhh
Q 020010 81 RVFFLDVNPLCYEGSR--PS--------LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLR 148 (332)
Q Consensus 81 ~vllIDg~~l~yra~~--p~--------~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~ 148 (332)
+++||||++++||++. +. .+++.+|++++.+.++. ++++++|||++ +++||+++||+||+||+++|
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~-~~~~R~~l~p~YKa~R~~~p- 79 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAK-GKTFRHELYPEYKANRPKTP- 79 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCC-CCccccchhHHHHhCCCCCC-
Confidence 5899999999999751 11 24456677766666543 56689999985 68999999999999999885
Q ss_pred hhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecC
Q 020010 149 QLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPL 228 (332)
Q Consensus 149 p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~ 228 (332)
++|..|++.++++|+.+|||++..+||||||+||+||+++...|..++|+|+|||++||++++|.+|.+.
T Consensus 80 ----------e~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~ 149 (259)
T smart00475 80 ----------DELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPT 149 (259)
T ss_pred ----------HHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEecc
Confidence 6799999999999999999999999999999999999998888999999999999999999999998876
Q ss_pred CCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCchH
Q 020010 229 QDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDY 308 (332)
Q Consensus 229 ~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~~ 308 (332)
++...+..++.+.+.++||++|+||+|+++|+||+||||||| ||||||||.+||++|||+|+|+++++. . +++
T Consensus 150 ~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV----~GIG~KtA~~Ll~~ygsle~i~~~~~~--~-~~~ 222 (259)
T smart00475 150 KGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGV----PGIGEKTAAKLLKEFGSLENILENLDK--L-KKK 222 (259)
T ss_pred CCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCC----CCCCHHHHHHHHHHhCCHHHHHHHHHH--H-HHH
Confidence 543345789999999999999999999999999999999999 999999999999999999999999985 2 246
Q ss_pred HHHHHHHhHHHHHhhcccceecc
Q 020010 309 AQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 309 ~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
++++|++++|++++|++|++|++
T Consensus 223 ~~~~l~~~~~~~~ls~~L~~l~~ 245 (259)
T smart00475 223 LREKLLAHKEDAKLSRKLATIET 245 (259)
T ss_pred HHHHHHhcHHHHHHhhhhheeee
Confidence 89999999999999999999986
No 3
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=2.1e-60 Score=452.92 Aligned_cols=233 Identities=22% Similarity=0.412 Sum_probs=208.7
Q ss_pred CCcEEEEeCcchhhhhcC------ch--------hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhc
Q 020010 79 KKRVFFLDVNPLCYEGSR------PS--------LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAH 142 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~~------p~--------~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKan 142 (332)
+++++||||++++||++. +. .+++.+|++++++.++. ++++++|||++ +++||+++||+||+|
T Consensus 2 ~~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~-~~~~R~~l~p~YKan 80 (281)
T PRK14976 2 MKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAG-RKTFRHQLYDEYKQG 80 (281)
T ss_pred CCcEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECC-CCcccccccHHHhcC
Confidence 467999999999999751 11 24567788877777654 45689999985 689999999999999
Q ss_pred chhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCe
Q 020010 143 RRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDV 222 (332)
Q Consensus 143 R~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v 222 (332)
|+++| ++|..|++.++++++.+|||++..+|+||||+||++|+++...|..|+|+|+|||++||++++|
T Consensus 81 R~~~p-----------~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v 149 (281)
T PRK14976 81 RKKTP-----------ESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENT 149 (281)
T ss_pred CCCCC-----------HHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCe
Confidence 99885 6789999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhc
Q 020010 223 QLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVR 302 (332)
Q Consensus 223 ~v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~ 302 (332)
.++.+.++. ++..++.+.+.++||++|+||+|+++|+||+||||||| ||||||||.+||++|||+|+|+++++.
T Consensus 150 ~~~~~~~~~-~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGV----pGIG~KtA~~LL~~~gsle~i~~~~~~- 223 (281)
T PRK14976 150 DVLLKKKGT-SHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGV----KGIGPKTAIKLLNKYGNIENIYENIDK- 223 (281)
T ss_pred EEEEecCCC-CcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCC----CcccHHHHHHHHHHcCCHHHHHHhHHH-
Confidence 999876542 25679999999999999999999999999999999999 999999999999999999999999985
Q ss_pred ccCchHHHHHHHHhHHHHHhhcccceecc
Q 020010 303 TVGRDYAQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 303 ~~~~~~~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
. +++++++|.+++|++++|++|++|++
T Consensus 224 -~-~~~~~~~L~~~~~~~~~s~~L~~l~~ 250 (281)
T PRK14976 224 -I-KKKIKNKLSEAKEKALLSKKLATIKT 250 (281)
T ss_pred -H-hHHHHHHHHHhHHHHHHhhhhhEEee
Confidence 2 23689999999999999999999986
No 4
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=100.00 E-value=7.3e-58 Score=426.32 Aligned_cols=227 Identities=33% Similarity=0.576 Sum_probs=203.1
Q ss_pred CcEEEEeCcchhhhhc--Cc------h---hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchhh
Q 020010 80 KRVFFLDVNPLCYEGS--RP------S---LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKF 146 (332)
Q Consensus 80 ~~vllIDg~~l~yra~--~p------~---~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~~ 146 (332)
++++||||++++||++ .+ . .+++.+|++++++.++. ++++++|||++ +++||+++||+||+||+++
T Consensus 1 ~~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~-~~~~R~~l~p~YK~~R~~~ 79 (240)
T cd00008 1 KRLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAG-GKTFRHELYPEYKANRKKM 79 (240)
T ss_pred CcEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCC-CCcccccccHHHHcCCCCC
Confidence 4699999999999975 11 0 23566777777776654 46689999995 6899999999999999987
Q ss_pred hhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEe
Q 020010 147 LRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVM 226 (332)
Q Consensus 147 p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~ 226 (332)
| ++|..|++.++++|+.+|||++..+|+||||+||+||+++...|..++|+|+|||++||++++|.+++
T Consensus 80 p-----------~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~ 148 (240)
T cd00008 80 P-----------EELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVS 148 (240)
T ss_pred C-----------HHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEe
Confidence 5 67899999999999999999999999999999999999999899999999999999999999999988
Q ss_pred cCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCc
Q 020010 227 PLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGR 306 (332)
Q Consensus 227 ~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~ 306 (332)
+.+ ...++.+.+.+++|++|+||+|+++|+||+||||||| ||||||||.+||++|||+|+|+++++. . +
T Consensus 149 ~~~----~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv----~GiG~ktA~~Ll~~~gsle~i~~~~~~--~-~ 217 (240)
T cd00008 149 PMK----KKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGV----PGIGEKTAAKLLKEYGSLEGILENLDK--I-K 217 (240)
T ss_pred CCC----ceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCC----CccCHHHHHHHHHHhCCHHHHHHhHHH--H-h
Confidence 753 3578999999999999999999999999999999999 999999999999999999999999985 2 2
Q ss_pred hHHHHHHHHhHHHHHhhccccee
Q 020010 307 DYAQEALTKHADYLRRNYEVLAL 329 (332)
Q Consensus 307 ~~~~~~L~~~~~~~~~s~~L~~L 329 (332)
++++++|.+++|++++|++|++|
T Consensus 218 ~~~~~~l~~~~~~~~~s~~L~~l 240 (240)
T cd00008 218 GKLREKLEEGKEMAFLSKRLATI 240 (240)
T ss_pred HHHHHHHHHhHHHHHHHHHhhcC
Confidence 37899999999999999999986
No 5
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.9e-55 Score=471.63 Aligned_cols=231 Identities=27% Similarity=0.451 Sum_probs=207.3
Q ss_pred EEEEeCcchhhhhc--Cc---h-------hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchhhh
Q 020010 82 VFFLDVNPLCYEGS--RP---S-------LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFL 147 (332)
Q Consensus 82 vllIDg~~l~yra~--~p---~-------~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~~p 147 (332)
++||||++++||++ .| . .+++.||++++++.++. +++++||||++ +++||+++||+||+||+++|
T Consensus 1 l~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~-~~tfR~~~~~~YKa~R~~~P 79 (887)
T TIGR00593 1 LLLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSG-TPTFRHEAYAEYKANRAPTP 79 (887)
T ss_pred CEEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCC-CCcchHHHHHHHHhCCCCCh
Confidence 58999999999985 22 1 24567788887777654 56699999985 78999999999999999985
Q ss_pred hhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEec
Q 020010 148 RQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMP 227 (332)
Q Consensus 148 ~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~ 227 (332)
++|..|++.++++|+++|||++..+||||||+|||||+++...|+.|+|+|+|||++||++++|+++++
T Consensus 80 -----------e~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~ 148 (887)
T TIGR00593 80 -----------EELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIP 148 (887)
T ss_pred -----------HHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEec
Confidence 679999999999999999999999999999999999999998999999999999999999999999987
Q ss_pred CCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCch
Q 020010 228 LQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRD 307 (332)
Q Consensus 228 ~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~ 307 (332)
.++. ....++.+.|.++||++|+||+||++|+||+||||||| ||||||||.+||++|||+|+||++++. .+++
T Consensus 149 ~~~~-~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGV----pGIG~KtA~kLL~~ygsle~i~~~~~~--i~~~ 221 (887)
T TIGR00593 149 KGKT-SFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGV----KGIGEKTAAKLLQEFGSLENIYENLDQ--IKSA 221 (887)
T ss_pred cCCC-CceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCC----CCcCHHHHHHHHHHcCCHHHHHHHHHH--hccH
Confidence 5432 35679999999999999999999999999999999999 999999999999999999999999985 3223
Q ss_pred HHHHHHHHhHHHHHhhcccceecc
Q 020010 308 YAQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 308 ~~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
+++++|++++|++++||+|++|+|
T Consensus 222 k~~~~L~~~~e~a~ls~~L~ti~~ 245 (887)
T TIGR00593 222 KMREKLIAHKEDAFLSKELATIVT 245 (887)
T ss_pred HHHHHHHHhHHHHHHHHHhheeec
Confidence 689999999999999999999986
No 6
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=2.1e-52 Score=449.86 Aligned_cols=233 Identities=27% Similarity=0.483 Sum_probs=206.7
Q ss_pred CCcEEEEeCcchhhhhc--C-ch--------hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchh
Q 020010 79 KKRVFFLDVNPLCYEGS--R-PS--------LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRK 145 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~--~-p~--------~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~ 145 (332)
+++++||||++++||++ . +. .+++.+|++++.+.+.. ++++++|||++ +++||+++||+||+||++
T Consensus 1 ~~~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~-~~~~R~~~~~~YK~~R~~ 79 (880)
T PRK05755 1 MKTLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAK-GKTFRHELYPEYKANRPP 79 (880)
T ss_pred CCeEEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECC-CCccccccCHHHhCCCCC
Confidence 35699999999999975 2 11 24566777777666643 56699999985 789999999999999998
Q ss_pred hhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEE
Q 020010 146 FLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLV 225 (332)
Q Consensus 146 ~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~ 225 (332)
+| ++|..|++.++++|+.+||+++..|||||||+||+||+++...|..|+|+|+|||++||++++|+++
T Consensus 80 ~p-----------~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~ 148 (880)
T PRK05755 80 MP-----------EDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLL 148 (880)
T ss_pred Cc-----------HHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEe
Confidence 85 6789999999999999999999999999999999999998888999999999999999999999999
Q ss_pred ecCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccC
Q 020010 226 MPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVG 305 (332)
Q Consensus 226 ~~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~ 305 (332)
.++.+ .+...++.+.|.++||++|+||+|+++|+||+||||||| ||||||||.+||++|||+|+|+++++. .
T Consensus 149 ~~~~~-~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv----~GiG~ktA~~Ll~~~gsle~i~~~~~~--~- 220 (880)
T PRK05755 149 DTMGV-SKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGV----PGIGEKTAAKLLQEYGSLEGLYENLDE--I- 220 (880)
T ss_pred eccCC-CCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCC----CCccHHHHHHHHHHcCCHHHHHHhHHH--h-
Confidence 87532 235679999999999999999999999999999999999 999999999999999999999999984 2
Q ss_pred chHHHHHHHHhHHHHHhhcccceecc
Q 020010 306 RDYAQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 306 ~~~~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
+++++++|.+++|++++|++|++|++
T Consensus 221 ~~~~~~~l~~~~~~~~ls~~l~~l~~ 246 (880)
T PRK05755 221 KGKKKEKLRENKEQAFLSRKLATIKT 246 (880)
T ss_pred chHHHHHHHHhHHHHHhhhhhheeee
Confidence 23578899999999999999999986
No 7
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-48 Score=376.53 Aligned_cols=233 Identities=27% Similarity=0.465 Sum_probs=202.5
Q ss_pred CCCcEEEEeCcchhhhhc--C----------ch--hhHHHHHHHHHHHHhcCCCcEEEEEcCCCCchhhhhhchhHHhcc
Q 020010 78 SKKRVFFLDVNPLCYEGS--R----------PS--LQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHR 143 (332)
Q Consensus 78 ~~~~vllIDg~~l~yra~--~----------p~--~~~~~~~l~~ll~~i~~~~pvivvFD~~~~~~fR~el~p~YKanR 143 (332)
.++++++|||++++||++ . |+ ..++.+++.++++..+ +.+.++|||+ ++++||+++++.||++|
T Consensus 9 ~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~-~~~~~~vFD~-~~~tfR~~~~~~yK~~R 86 (310)
T COG0258 9 KSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLE-PTHPVVVFDG-KPPTFRHELLEEYKANR 86 (310)
T ss_pred ccCcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcC-CCcEEEEEcC-CCCcchHHHHHHHHhCC
Confidence 346899999999999985 1 11 2334444444444443 3557889999 58999999999999999
Q ss_pred hh-hhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCe
Q 020010 144 RK-FLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDV 222 (332)
Q Consensus 144 ~~-~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v 222 (332)
.+ +| ++|..|++.+++++.++|++++..+|+||||+|+++|+++.+.|+.++|+|+|||++||+++++
T Consensus 87 ~~~~p-----------~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~ 155 (310)
T COG0258 87 EKEMP-----------DELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNV 155 (310)
T ss_pred CccCH-----------HHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCc
Confidence 99 75 6799999999999999999999999999999999999999989999999999999999999999
Q ss_pred EEEecCCCCCccEEeeHHHHHHHh-CCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 223 QLVMPLQDLDRWSFYTLKHYIAQY-NCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 223 ~v~~~~~~~~~~~~~~~~~v~e~~-Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~ 301 (332)
.+++++++... ..++...+.++| |++|+|++|+++|+||+||||||| +|||||||.+||++|||+|.|+++++.
T Consensus 156 ~~~~~~~~~~~-~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV----~GIG~ktA~~Ll~~~gs~e~i~~~~~~ 230 (310)
T COG0258 156 LVINGKKGEPE-KFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGV----KGIGPKTALKLLQEYGSLEGLYENLDI 230 (310)
T ss_pred EEEeccCCCCc-ccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCC----CCcCHHHHHHHHHHhCCHHHHHHhhhh
Confidence 99988765221 147899999999 999999999999999999999999 999999999999999999999999983
Q ss_pred cccCchHHHHHHHHhHHHHHhhcccceecc
Q 020010 302 RTVGRDYAQEALTKHADYLRRNYEVLALRR 331 (332)
Q Consensus 302 ~~~~~~~~~~~L~~~~~~~~~s~~L~~L~~ 331 (332)
. +++.+++|.++++.+++|++|+++++
T Consensus 231 --~-~~~~~~~l~~~~~~afl~~~l~t~~~ 257 (310)
T COG0258 231 --I-KKKTREKLLEDKEKAFLSKPLATIKT 257 (310)
T ss_pred --h-cchhhHHHHHHHHHHhcCcccccccc
Confidence 2 34588899999999999999999864
No 8
>PHA00439 exonuclease
Probab=100.00 E-value=3.7e-45 Score=346.98 Aligned_cols=190 Identities=23% Similarity=0.338 Sum_probs=155.0
Q ss_pred CCcEEEEeCcchhhhhc--C-------c-h-------hhHHHHHHHHHHHHhc-----CCCcEEEEEcCCCCchhhhhhc
Q 020010 79 KKRVFFLDVNPLCYEGS--R-------P-S-------LQSFGRWLSLFFDQVS-----HADPVIAVFDGEGGTEHRRQLL 136 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~--~-------p-~-------~~~~~~~l~~ll~~i~-----~~~pvivvFD~~~~~~fR~el~ 136 (332)
+++++||||++++|||+ . + . .+++.+|++++++.++ .++++++|||+ +++|||++|
T Consensus 5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~--~~tfR~ely 82 (286)
T PHA00439 5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTD--SVNWRKEVV 82 (286)
T ss_pred CCcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECC--CCChHhhhh
Confidence 57899999999999985 2 1 1 1355667777666653 36679999994 689999999
Q ss_pred hhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCC-eEEEEcCCCCcC
Q 020010 137 PSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGY-RAVVASPDKDFK 215 (332)
Q Consensus 137 p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~-~v~IvS~DKDl~ 215 (332)
|+||+||+++|+| ..|++.++++++.+|++++..+||||||+|||||+++...|+ .|+|+|+||||+
T Consensus 83 p~YKanR~~~p~~------------~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~ 150 (286)
T PHA00439 83 PTYKANRKAKRKP------------VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFK 150 (286)
T ss_pred hHhcCCCCCCCCc------------hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHh
Confidence 9999999999744 357889999999999999999999999999999999888887 999999999999
Q ss_pred ccCCCCeEEEecCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh---cCCH
Q 020010 216 QLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK---HGSL 292 (332)
Q Consensus 216 QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~---ygsl 292 (332)
||++. +.++.+.+ ....++.+ .|+||.|+++|+||+||||||| |||| |||.+||++ |..+
T Consensus 151 QLv~~-~~~~~~~~---~~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGV----pGIG-KTA~kLL~~~~~~~~~ 213 (286)
T PHA00439 151 TIPNC-DFLWCTTG---NILTQTPE--------TADRWHLFQTIKGDSTDGYSGI----PGWG-DTAEAFLENPYIFEQV 213 (286)
T ss_pred hcCcc-eEEEccCC---ceEEcCcc--------cHHHHHhhhhcccccccCCCCC----CCcC-HHHHHHHhCccccchh
Confidence 99976 33443322 11113322 2999999999999999999999 9999 999999999 6667
Q ss_pred HHHHHHh
Q 020010 293 ENLLNAA 299 (332)
Q Consensus 293 e~il~~~ 299 (332)
|..+...
T Consensus 214 ~~~~~sg 220 (286)
T PHA00439 214 EKVLKSG 220 (286)
T ss_pred hHHhhcc
Confidence 7777664
No 9
>PHA02567 rnh RnaseH; Provisional
Probab=100.00 E-value=6.9e-40 Score=312.54 Aligned_cols=178 Identities=23% Similarity=0.301 Sum_probs=142.5
Q ss_pred CCcEEEEeCcchhhhhcC---------ch--h-hHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHhcchh
Q 020010 79 KKRVFFLDVNPLCYEGSR---------PS--L-QSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKAHRRK 145 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~~---------p~--~-~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKanR~~ 145 (332)
+..++|||||+++||++. ++ + +++.+.+..+.+.++. +.++++|||++++++||+++||+||+||++
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~ 92 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKK 92 (304)
T ss_pred CCCEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCC
Confidence 467999999999999852 11 1 2344444444554432 344899999864478999999999999999
Q ss_pred hhhhhhhhhhcchhhHHHhH-HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCC-CCeE
Q 020010 146 FLRQLTASQRFSRGRVGRSH-QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLIS-EDVQ 223 (332)
Q Consensus 146 ~p~p~~~~~~~~~~~L~~ql-~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~-~~v~ 223 (332)
+|+++..+. +.+..++ +.++++++.+||+++..+|+||||+|||||+++.+.|..|+|+|+||||+||+. ++|.
T Consensus 93 ~Peel~~q~----~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~ 168 (304)
T PHA02567 93 DREESPWDW----EGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVK 168 (304)
T ss_pred CChHHHHHH----HHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeE
Confidence 975422111 1234444 677888999999999999999999999999999988999999999999999995 8898
Q ss_pred EEecCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCc
Q 020010 224 LVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGI 270 (332)
Q Consensus 224 v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI 270 (332)
+|.+. +.+.|.++||. |+|++|+++|+||+|||||||
T Consensus 169 ~~~~~---------~~~~V~~k~G~-P~q~iD~kaL~GDsSDNIPGV 205 (304)
T PHA02567 169 QWSPM---------QKKWVKPKYGS-PEKDLMTKIIKGDKKDGVASI 205 (304)
T ss_pred EeecC---------CHHHHHHHhCC-HHHHHHHHHhCCcccCCcCCC
Confidence 88764 34778999995 999999999999999999999
No 10
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.3e-36 Score=301.40 Aligned_cols=233 Identities=22% Similarity=0.201 Sum_probs=180.8
Q ss_pred CCcEEEEeCcchhhhhc--C-------ch-------hhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHh
Q 020010 79 KKRVFFLDVNPLCYEGS--R-------PS-------LQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKA 141 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~--~-------p~-------~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKa 141 (332)
.+++++|||++|+||++ . +. ...+.+++.++++.++. .+| ++||||. .+.+|++.++.||+
T Consensus 27 ~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~gikP-v~VFDG~-~p~~K~~~~~~Rk~ 104 (393)
T PTZ00217 27 FGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAGIKP-VYVFDGK-PPELKSGELEKRRE 104 (393)
T ss_pred CCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCCCCE-EEEEcCC-CchhhHHHHHHHHH
Confidence 57899999999999963 1 10 13467888888887753 678 6899996 78899999999999
Q ss_pred cchhhhhhhhhhhhcc-hhhH-----------HHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 142 HRRKFLRQLTASQRFS-RGRV-----------GRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 142 nR~~~p~p~~~~~~~~-~~~L-----------~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
+|.++++......... .++. ..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..+.|+|
T Consensus 105 ~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~-EAdaq~A~L~~----~g~v~~ViS 179 (393)
T PTZ00217 105 RREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPC-EAEAQCAELVK----KGKVYAVAT 179 (393)
T ss_pred HHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCc-CHHHHHHHHHH----CCCeEEEeC
Confidence 9998864321000000 0111 35789999999999999999998 99999999985 588888999
Q ss_pred CCCCcCccCCCCeEEEecC---CCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHH
Q 020010 210 PDKDFKQLISEDVQLVMPL---QDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLL 286 (332)
Q Consensus 210 ~DKDl~QLv~~~v~v~~~~---~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL 286 (332)
+|+|++|++++.+ +++.. ......+.++.+.+.+.+|++|+||+|+++|+| |||+||| ||||+|||.+||
T Consensus 180 ~D~D~l~fg~~~v-i~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G--~Dy~pgi----~GIG~ktA~~Li 252 (393)
T PTZ00217 180 EDMDALTFGTPVL-LRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCG--CDYCDTI----KGIGPKTAYKLI 252 (393)
T ss_pred CCcCeeecCCcEE-EEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCC----CCccHHHHHHHH
Confidence 9999999998743 33322 112346789999999999999999999999999 9999999 999999999999
Q ss_pred HhcCCHHHHHHHhhhcc--cCchHHHHHHHHhHHHHHhhccccee
Q 020010 287 KKHGSLENLLNAAAVRT--VGRDYAQEALTKHADYLRRNYEVLAL 329 (332)
Q Consensus 287 ~~ygsle~il~~~~~~~--~~~~~~~~~L~~~~~~~~~s~~L~~L 329 (332)
++|||+|+|+++++... .+..+ .-.....++++..+.+.
T Consensus 253 ~~~gsle~il~~~~~~k~~~p~~~----~~~~~~~~f~~p~V~~~ 293 (393)
T PTZ00217 253 KKYKSIEEILEHLDKTKYPVPENF----DYKEARELFLNPEVTPA 293 (393)
T ss_pred HHcCCHHHHHHHHHhcCCCCCCCC----ChHHHHHHhcCCCcCCC
Confidence 99999999999988421 11111 13456677888777654
No 11
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=100.00 E-value=3.4e-37 Score=273.81 Aligned_cols=153 Identities=29% Similarity=0.549 Sum_probs=126.8
Q ss_pred CcEEEEeCcchhhhhc--Cc--h--------hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchh
Q 020010 80 KRVFFLDVNPLCYEGS--RP--S--------LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRK 145 (332)
Q Consensus 80 ~~vllIDg~~l~yra~--~p--~--------~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~ 145 (332)
++++||||++++||++ .+ . .+++.+|++++.+.+.. ++++++|||++ +++||+++||+||+||++
T Consensus 1 k~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~-~~~fR~~l~p~YKanR~~ 79 (169)
T PF02739_consen 1 KKLLLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSK-GPTFRKELYPEYKANRKP 79 (169)
T ss_dssp -EEEEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBS-SCHHHHHCCTTTTHHHHH
T ss_pred CeEEEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCC-CcchHHHHHHHHHhCCCC
Confidence 5799999999999986 22 1 24566777777666654 45589999996 569999999999999998
Q ss_pred hhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCC--CeE
Q 020010 146 FLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISE--DVQ 223 (332)
Q Consensus 146 ~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~--~v~ 223 (332)
+| ++|..|++.++++++.+|++++..+|+||||+||+||+++..+|.+|+|+|+||||+||+++ +|.
T Consensus 80 ~p-----------~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~ 148 (169)
T PF02739_consen 80 MP-----------EELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVY 148 (169)
T ss_dssp HH-----------HHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEE
T ss_pred CC-----------HHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEE
Confidence 86 56889999999999999999999999999999999999999999999999999999999999 566
Q ss_pred EEecCCCCCccEEeeHHHHHHHh
Q 020010 224 LVMPLQDLDRWSFYTLKHYIAQY 246 (332)
Q Consensus 224 v~~~~~~~~~~~~~~~~~v~e~~ 246 (332)
++++. ......++.++|.|+|
T Consensus 149 ~~~~~--~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 149 LLDPG--KKKFKVYDPEEVEEKY 169 (169)
T ss_dssp EEETT--TTCS-EB-HHHHHHHT
T ss_pred EeecC--CCCCEEEcHHHHhhcC
Confidence 66663 2356889999999986
No 12
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.6e-35 Score=288.80 Aligned_cols=210 Identities=20% Similarity=0.269 Sum_probs=166.5
Q ss_pred CCCcEEEEeCcchhhhhcC--------ch-------hhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHh
Q 020010 78 SKKRVFFLDVNPLCYEGSR--------PS-------LQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKA 141 (332)
Q Consensus 78 ~~~~vllIDg~~l~yra~~--------p~-------~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKa 141 (332)
-.+++++|||++|+||++. +. ..++.+++.++++.++. .+| ++||||. .+.+|++.++.|++
T Consensus 19 ~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P-v~VFDG~-~p~~K~~~~~~R~~ 96 (338)
T TIGR03674 19 LSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP-VYVFDGK-PPELKAETLEERRE 96 (338)
T ss_pred hCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE-EEEECCC-ChhhhHhhHHHHHH
Confidence 3578999999999999741 11 13567888888887765 677 8899996 68899999999999
Q ss_pred cchhhhhhhhhh---------hhcch---hhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 142 HRRKFLRQLTAS---------QRFSR---GRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 142 nR~~~p~p~~~~---------~~~~~---~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
+|.+.++..... .++.. .--.+|++.++++|+.+|||++.+|| |||++||+|++ .|....|+|
T Consensus 97 ~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~-EAeaq~a~L~~----~g~vd~v~S 171 (338)
T TIGR03674 97 IREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQAAYMAK----KGDVDYVGS 171 (338)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCc-cHHHHHHHHHH----CCCeeEEec
Confidence 998865331100 00000 00124689999999999999999999 99999999985 477778999
Q ss_pred CCCCcCccCCCCeEEEecC-CCCC-----------ccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCc
Q 020010 210 PDKDFKQLISEDVQLVMPL-QDLD-----------RWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGF 277 (332)
Q Consensus 210 ~DKDl~QLv~~~v~v~~~~-~~~~-----------~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GI 277 (332)
+|+|++|+++++| +.+.. .+.. ..+.++.+.+.+++|++|+||+|+++|+|| .|| ||| |||
T Consensus 172 ~D~D~l~fg~~~v-i~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~-dyn-~Gv----~GI 244 (338)
T TIGR03674 172 QDYDSLLFGAPRL-VRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGT-DYN-EGV----KGI 244 (338)
T ss_pred CCcCeeeecCCEE-EEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCC-CCC-CCC----CCc
Confidence 9999999999976 33211 1100 245689999999999999999999999999 677 999 999
Q ss_pred cHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 278 GRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 278 G~KTA~kLL~~ygsle~il~~~~~ 301 (332)
|+|||.+||++|||+|+|+++++.
T Consensus 245 G~ktA~kli~~~gsie~il~~~~~ 268 (338)
T TIGR03674 245 GPKTALKLIKEHGDLEKVLKARGE 268 (338)
T ss_pred cHHHHHHHHHHcCCHHHHHHhhcC
Confidence 999999999999999999999763
No 13
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=3e-33 Score=269.64 Aligned_cols=209 Identities=19% Similarity=0.230 Sum_probs=162.3
Q ss_pred CCcEEEEeCcchhhhhcC----------chhhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchh-------hhhhchhHH
Q 020010 79 KKRVFFLDVNPLCYEGSR----------PSLQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEH-------RRQLLPSYK 140 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~~----------p~~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~f-------R~el~p~YK 140 (332)
++++++|||++|+||++. .....+.+|++++.+.++. .+| ++||||. .+.+ |++..++||
T Consensus 23 ~gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~~i~p-vfVFDG~-~~~~K~~~~~~R~~~r~~~~ 100 (316)
T cd00128 23 RGKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLELGIKP-VFVFDGK-PPPLKAETLAKRRERREEAE 100 (316)
T ss_pred CCcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHCCCEE-EEEEcCC-CchhhHHHHHHHHHHHHHHH
Confidence 577999999999999741 1123456677776655543 444 7899995 4554 888889999
Q ss_pred hcchhhhhhhh--hhhhcc---hhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcC
Q 020010 141 AHRRKFLRQLT--ASQRFS---RGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 141 anR~~~p~p~~--~~~~~~---~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~ 215 (332)
++|..+++... ...++. ......|++.++++|+.+|||++.+| +||||+||+|++ .|....|+|+|+|++
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap-~EAdaq~a~l~~----~g~v~~i~S~DsD~l 175 (316)
T cd00128 101 EEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAP-YEAEAQCAYLAK----KGLVDAIITEDSDLL 175 (316)
T ss_pred HHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECC-cCHHHHHHHHHh----CCCeeEEEecCCCee
Confidence 99988753210 000000 01235678999999999999999998 599999999986 477778999999999
Q ss_pred ccCCCCeEEEecCCCC-CccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHH
Q 020010 216 QLISEDVQLVMPLQDL-DRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLEN 294 (332)
Q Consensus 216 QLv~~~v~v~~~~~~~-~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~ 294 (332)
|+.+++|.. +..... ...+.++.+.+.+.+|++|+||+|+++|+| |||+||| ||||+|||.+||++|||+++
T Consensus 176 ~fg~~~vi~-~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G--~Dy~~gv----~giG~k~A~~li~~~~~~~~ 248 (316)
T cd00128 176 LFGAPRVYR-NLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLG--CDYTEGI----PGIGPVTALKLIKKYGDIEK 248 (316)
T ss_pred eecCceEEE-ecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcC--CCCCCCC----CCccHHHHHHHHHHcCChHH
Confidence 999876432 211111 256789999999999999999999999999 9999999 99999999999999999999
Q ss_pred HHHHhhh
Q 020010 295 LLNAAAV 301 (332)
Q Consensus 295 il~~~~~ 301 (332)
+++++..
T Consensus 249 ~~~~l~~ 255 (316)
T cd00128 249 DIERLKK 255 (316)
T ss_pred HHHHHHH
Confidence 9998874
No 14
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.4e-32 Score=263.20 Aligned_cols=191 Identities=21% Similarity=0.290 Sum_probs=152.6
Q ss_pred CchhhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhh---------hhcchh---hHH
Q 020010 96 RPSLQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTAS---------QRFSRG---RVG 162 (332)
Q Consensus 96 ~p~~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~---------~~~~~~---~L~ 162 (332)
.+|. .+.+++.++++.++. .+| ++||||. ++.+|++.++.||++|.++++..... .++... -..
T Consensus 6 ~~Ts-~l~g~~~r~~~ll~~gi~P-vfVFDG~-~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~ 82 (292)
T PRK03980 6 RITS-HLSGIFYRTINLLENGIKP-VYVFDGK-PPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTD 82 (292)
T ss_pred cCcH-HHHHHHHHHHHHHHCCCEE-EEEECCC-CchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCH
Confidence 3443 467788888887765 677 8899996 78999999999999999886442110 000000 012
Q ss_pred HhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEE-EecCCCC----------
Q 020010 163 RSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQL-VMPLQDL---------- 231 (332)
Q Consensus 163 ~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v-~~~~~~~---------- 231 (332)
.|++.++++|+.+|||++.+|| |||..||+|++ .|..+.|+|+|+|++|++++++.. +......
T Consensus 83 ~~~~~~k~lL~~~GIp~i~AP~-EAEAq~A~L~~----~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~ 157 (292)
T PRK03980 83 EIVEDSKKLLDLMGIPYVQAPS-EGEAQAAYMAK----KGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVE 157 (292)
T ss_pred HHHHHHHHHHHHCCCCEEecCc-hHHHHHHHHHH----CCCeEEEecCCcCeeeecCCEEEEeecccccccCcccccccc
Confidence 3789999999999999999998 99999999985 588889999999999999987521 1111100
Q ss_pred CccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 232 DRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 232 ~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
...+.++.+.+.+++|++|+||+|+++|+| |||+||| ||||+|||.+||++|||+|+|+++.+
T Consensus 158 ~~~e~~~~~~vl~~lgl~~~q~id~~iL~G--~Dy~~GI----~GIG~ktA~kLi~~~~sle~i~~~~~ 220 (292)
T PRK03980 158 VKPELIELEEVLKELGITREQLIDIAILVG--TDYNPGI----KGIGPKTALKLIKKHGDLEKVLEERG 220 (292)
T ss_pred ccceeeeHHHHHHHhCCCHHHHHHHHHhcC--CCCCCCC----CCccHHHHHHHHHHCCCHHHHHHhcc
Confidence 134579999999999999999999999999 8999999 99999999999999999999999765
No 15
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=99.89 E-value=3.1e-26 Score=187.71 Aligned_cols=78 Identities=32% Similarity=0.534 Sum_probs=63.7
Q ss_pred CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCchHHHHHHHHhHHHHHhhcccc
Q 020010 248 CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVL 327 (332)
Q Consensus 248 v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~~~~~~L~~~~~~~~~s~~L~ 327 (332)
|+|+|++||++|+||+||||||| ||||+|||.+||++|||+|+||++++. .+.++++++|.+++|++++||+|+
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV----~GIG~KtA~~LL~~ygsle~i~~~~~~--~~~~k~~~~l~~~~e~a~ls~~L~ 74 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGV----PGIGPKTAAKLLQEYGSLENILANLDE--IKGKKIREKLRENKEQALLSRKLA 74 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB-------TTSTCHCCCCCHHHHTSCHCCCCC-SS--S-TSCCCHHHHTSCCCCCCHHHHH
T ss_pred CCHHHHHHHHHHcCCcccCCCCC----CCCCHHHHHHHHHHcCCHHHHHHhHHh--ccccHHHHHHHHHHHHHHHhHHHh
Confidence 57999999999999999999999 999999999999999999999999984 323357899999999999999999
Q ss_pred eecc
Q 020010 328 ALRR 331 (332)
Q Consensus 328 ~L~~ 331 (332)
+|+|
T Consensus 75 tl~~ 78 (101)
T PF01367_consen 75 TLKT 78 (101)
T ss_dssp -H-S
T ss_pred hhhc
Confidence 9986
No 16
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.85 E-value=1.7e-20 Score=186.12 Aligned_cols=207 Identities=22% Similarity=0.295 Sum_probs=150.1
Q ss_pred CcEEEEeCcchhhhhc-----------CchhhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHhcchhhh
Q 020010 80 KRVFFLDVNPLCYEGS-----------RPSLQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFL 147 (332)
Q Consensus 80 ~~vllIDg~~l~yra~-----------~p~~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKanR~~~p 147 (332)
++-+.||+|+++|+.. .++ +.+.+++.+.+..+.. .+| ++||||. +|.+..+.+.....-|....
T Consensus 28 ~kkVAID~s~~lyqfl~~v~~~~~~~~~~~-~HL~g~f~Rt~~l~~~gi~P-v~VfDG~-pP~lKs~e~~kR~~rr~~a~ 104 (449)
T KOG2519|consen 28 GKKVAIDASMWLYQFLIVVRSCRNEAGEPT-SHLMGMFYRTIRLIENGIKP-VYVFDGK-PPDLKSQELAKRSERRSEAD 104 (449)
T ss_pred CceEEEecceeHhhHhhhhccccccCCCch-HHHHHHHHHHHHHHHcCCcE-EEEECCC-CCCcchHHHHHHHHHhhhhh
Confidence 5569999999999953 122 3356677776666643 666 7799996 45554444443333332111
Q ss_pred ---hhhh---hhhhcch------hhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcC
Q 020010 148 ---RQLT---ASQRFSR------GRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 148 ---~p~~---~~~~~~~------~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~ 215 (332)
+|.. ....+.+ .-.+++...++.+|..||||++.+|+ ||+.+||.|++. |....++|.|.|.+
T Consensus 105 ~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~-EAEAqCA~Lnk~----g~V~~~at~DsD~l 179 (449)
T KOG2519|consen 105 KELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPG-EAEAQCAALNKA----GKVYAVATEDSDAL 179 (449)
T ss_pred hhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCc-hHHHHHHHHhhc----Cceeeeeccccchh
Confidence 0100 0001110 01123346899999999999999998 999999999874 77778999999999
Q ss_pred ccCCCCeEE-Ee-cCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHH
Q 020010 216 QLISEDVQL-VM-PLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLE 293 (332)
Q Consensus 216 QLv~~~v~v-~~-~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle 293 (332)
.+..+.+.. +. +.....++..|+.+.+.+.+++..++|+|+++|+| ||++++| .|||+++|++||++|+|++
T Consensus 180 ~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlG--CDYc~~I----~Gig~~~al~lir~~~~i~ 253 (449)
T KOG2519|consen 180 TFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLG--CDYCPTI----RGIGPKKALKLIRQHGDIE 253 (449)
T ss_pred hccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhc--Ccccccc----cccChHHHHHHHHHhcCHH
Confidence 998864311 11 11223578889999999999999999999999999 8999999 9999999999999999999
Q ss_pred HHHH-Hhh
Q 020010 294 NLLN-AAA 300 (332)
Q Consensus 294 ~il~-~~~ 300 (332)
+|++ +.+
T Consensus 254 ~ile~~~~ 261 (449)
T KOG2519|consen 254 NILEINSD 261 (449)
T ss_pred HHhhhccc
Confidence 9999 655
No 17
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.80 E-value=6.2e-20 Score=142.78 Aligned_cols=74 Identities=39% Similarity=0.606 Sum_probs=68.1
Q ss_pred HhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCchHHHHHHHHhHHHHHhhc
Q 020010 245 QYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNY 324 (332)
Q Consensus 245 ~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~~~~~~L~~~~~~~~~s~ 324 (332)
++|++|+||+|+++|+||+|||+||| ||||+|||.+||++|||+++++++++.. + .++++.++.+.+++|+
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv----~giG~k~A~~ll~~~~~~~~~~~~~~~~----~-~~~~~~~~~~~~~~~~ 72 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGV----PGIGPKTALKLLKEYGSLENLLENLDKI----K-LREKLLEHKELAKLSK 72 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCC----CcccHHHHHHHHHHhCCHHHHHHHHHHH----h-HHHhhhccHHHHHHHH
Confidence 57999999999999999999999999 9999999999999999999999998852 2 7888999999999998
Q ss_pred ccc
Q 020010 325 EVL 327 (332)
Q Consensus 325 ~L~ 327 (332)
.|.
T Consensus 73 ~l~ 75 (75)
T cd00080 73 LLA 75 (75)
T ss_pred hhC
Confidence 763
No 18
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.77 E-value=2.7e-18 Score=185.84 Aligned_cols=122 Identities=20% Similarity=0.221 Sum_probs=105.8
Q ss_pred HhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEec-CCCCCccEEeeHHH
Q 020010 163 RSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMP-LQDLDRWSFYTLKH 241 (332)
Q Consensus 163 ~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~-~~~~~~~~~~~~~~ 241 (332)
.++..++++|+.||||+|.+|+ |||++||+|++ .|....|+|.|.|++.+++.+| +.. .......+.|+...
T Consensus 772 ~m~~~~~~LL~~~GIP~i~AP~-EAEAqcA~L~~----~G~vd~V~TeDsD~llFGa~~v--~rn~~~~~~~ve~~~~~~ 844 (1034)
T TIGR00600 772 QMILESQELLRLFGIPYIVAPM-EAEAQCAILDL----LDQTSGTITDDSDIWLFGARHV--YKNFFNQNKFVEYYQYVD 844 (1034)
T ss_pred HHHHHHHHHHHHCCCCeeeCCc-cHHHHHHHHHh----CCCeEEEEccccceeccCCcee--eecccCCCCceEEeeHHH
Confidence 4578899999999999999995 99999999976 5889999999999998888754 322 22223457899999
Q ss_pred HHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcC--CHHHHHH
Q 020010 242 YIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHG--SLENLLN 297 (332)
Q Consensus 242 v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~yg--sle~il~ 297 (332)
+.+.+|++++||+++++|+| |||++|| +|||||||.+||++|| +++++++
T Consensus 845 i~~~lglt~~qli~laiL~G--~DY~~GI----~GIGpktAl~li~~~~~~~le~L~~ 896 (1034)
T TIGR00600 845 IHNQLGLDRNKLINLAYLLG--SDYTEGI----PTVGPVSAMEILNEFPGDGLEPLLK 896 (1034)
T ss_pred HHHHhCCCHHHHHHHHHeeC--CCCCCCC----CcccHHHHHHHHHHcCCCCHHHHHH
Confidence 99999999999999999999 8999999 9999999999999999 4777764
No 19
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.74 E-value=7.6e-17 Score=162.13 Aligned_cols=197 Identities=19% Similarity=0.197 Sum_probs=134.9
Q ss_pred CCcEEEEeCcchhhhhc----------CchhhHHHHHHHHHHHHhc--CCCcEEEEEcCCCC------chhhhhhchhHH
Q 020010 79 KKRVFFLDVNPLCYEGS----------RPSLQSFGRWLSLFFDQVS--HADPVIAVFDGEGG------TEHRRQLLPSYK 140 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~----------~p~~~~~~~~l~~ll~~i~--~~~pvivvFD~~~~------~~fR~el~p~YK 140 (332)
++.++.|||++|+|||. .||..-+..++..+ +.+. ...| ++||||..= ..-|++ .||
T Consensus 23 ~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v-~lL~~~gikP-ilVFDG~~LP~K~~te~~Rr~---~R~ 97 (556)
T KOG2518|consen 23 KGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRV-KLLLSYGIKP-ILVFDGDPLPSKKETERKRRE---RRK 97 (556)
T ss_pred cCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHH-HHHHhcCCeE-EEEecCCCcccccccchHHHH---HHH
Confidence 46799999999999983 35543333344333 3332 3567 669999521 113333 355
Q ss_pred hcchhhhhhhhhhhhcch-------hhHH-------HhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEE
Q 020010 141 AHRRKFLRQLTASQRFSR-------GRVG-------RSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAV 206 (332)
Q Consensus 141 anR~~~p~p~~~~~~~~~-------~~L~-------~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~ 206 (332)
+|+.... +.|.. +-+. +....+-++|+..||.+|.+| ||||.+++.|.+ .|..-.
T Consensus 98 ~n~~~a~------~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAP-yEADAQlayL~~----~~~i~~ 166 (556)
T KOG2518|consen 98 KNLDAAE------QLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAP-YEADAQLAYLER----EGIVDA 166 (556)
T ss_pred HhHHHHH------HHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecC-ccccchhHHHHh----cCcceE
Confidence 5554331 11111 1111 112334456677899999877 899999999985 577778
Q ss_pred EEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHHhC----CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHH
Q 020010 207 VASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYN----CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTA 282 (332)
Q Consensus 207 IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~~G----v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA 282 (332)
|+|+|.||+++++..|..-. .+.+....++...+.+.++ ++-++|..+++|.| ||+.+|| ||||-+||
T Consensus 167 IITEDSDLl~fGc~~vifK~--d~~G~~le~~~~~l~~~~~l~~~~~~ekfr~mciLSG--CDYl~sl----pGvGl~tA 238 (556)
T KOG2518|consen 167 IITEDSDLLVFGCKKVIFKM--DSFGNGLEINRSKLPECKPLGDKFTEEKFRRMCILSG--CDYLSSL----PGVGLATA 238 (556)
T ss_pred EEeccccccccCchhheeec--cCCCCcccccHhhhhhccccccccCHHHHHHHHHhcC--CcccccC----ccccHHHH
Confidence 99999999999998653322 2223445566666666554 45788999999999 8999999 99999999
Q ss_pred HHHHHhcCCHHHHHHHh
Q 020010 283 LKLLKKHGSLENLLNAA 299 (332)
Q Consensus 283 ~kLL~~ygsle~il~~~ 299 (332)
.++|.+|.+.|-++...
T Consensus 239 ~k~l~k~~~~d~vi~~~ 255 (556)
T KOG2518|consen 239 HKLLSKYNTPDRVIISH 255 (556)
T ss_pred HHHHHhcCcHHHHHHHH
Confidence 99999999999998533
No 20
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.54 E-value=3.8e-15 Score=100.39 Aligned_cols=36 Identities=44% Similarity=0.796 Sum_probs=35.0
Q ss_pred hhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhc
Q 020010 250 PHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKH 289 (332)
Q Consensus 250 P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~y 289 (332)
|+||+|+++|+||++|||||| ||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv----~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGV----KGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCC----CcccHHHHHHHHHhC
Confidence 689999999999999999999 999999999999987
No 21
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.28 E-value=1.1e-11 Score=131.53 Aligned_cols=116 Identities=18% Similarity=0.186 Sum_probs=100.4
Q ss_pred HHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCC-CCCccEEeeHH
Q 020010 162 GRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQ-DLDRWSFYTLK 240 (332)
Q Consensus 162 ~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~-~~~~~~~~~~~ 240 (332)
-..+..|+++|+.+|||+|.+|+ ||+.+||.|..- +..-.|+|.|.|.+.+++-+ ||..+- +.+..+.|...
T Consensus 465 ~~m~~e~QElL~~fGIPyI~APm-EAEAQCa~Le~~----~LvdGiITDDSDV~LFGg~~--VYrn~F~knk~ve~y~~~ 537 (815)
T KOG2520|consen 465 SDMFKELQELLRLFGIPYIIAPM-EAEAQCAFLEQL----NLVDGIITDDSDVFLFGGTR--VYRNFFNKNKYVEKYQLD 537 (815)
T ss_pred HHHHHHHHHHHHHcCCceecccc-cHHHHHHHHHHc----CCcceeecccccceeeccch--hhHHHhhcCccceeeehH
Confidence 34689999999999999999998 999999998763 55556999999999999864 565432 21234778899
Q ss_pred HHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcC
Q 020010 241 HYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHG 290 (332)
Q Consensus 241 ~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~yg 290 (332)
.+...||+....++-+..|.| ||+.-|| +||||.+|+.+|.+|+
T Consensus 538 di~kel~l~R~~lI~lA~LlG--sDYt~Gl----~giGpV~AlEil~Efp 581 (815)
T KOG2520|consen 538 DIEKELGLDRPNLISLAQLLG--SDYTEGL----KGIGPVSALEILAEFP 581 (815)
T ss_pred HHHHHHccCchhhHHHHHhcc--cccccCC----CcccchHHHHHHHHcC
Confidence 999999999999999999999 8999999 9999999999999999
No 22
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=98.96 E-value=1e-09 Score=88.51 Aligned_cols=81 Identities=17% Similarity=0.186 Sum_probs=62.2
Q ss_pred cCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCC--C--------CCccEEeeHHHHH
Q 020010 174 KCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQ--D--------LDRWSFYTLKHYI 243 (332)
Q Consensus 174 ~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~--~--------~~~~~~~~~~~v~ 243 (332)
.+|||++.+|+ |||.++|.|.+ .|....|+|+|.|++.+..+. ++.... . ......++.+.+.
T Consensus 2 ~~gv~~i~AP~-EAeAq~A~L~~----~g~vd~V~t~DsD~l~fG~~~--vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 74 (94)
T PF00867_consen 2 LMGVPYIVAPY-EAEAQCAYLER----NGLVDAVITEDSDLLLFGAPK--VIRKLSDKSSGKCSSKSEKEVEVIDLDDIL 74 (94)
T ss_dssp HHT-EEEE-SS--HHHHHHHHHH----TTSSSEEE-SSSHHHHTT-SE--EEESST-CSCCSTS-CCESEEEEEEHHHHH
T ss_pred CCCCeEEEcCc-hHHHHHHHHHH----hcceeEEEecCCCEEeeCCCE--EEEeccccccCCcccccccceEEEEHHHHH
Confidence 46999999995 99999999986 577778999999999997763 333222 1 1236789999999
Q ss_pred HHhCCChhHHHHhhhccc
Q 020010 244 AQYNCDPHSELSLRCIVG 261 (332)
Q Consensus 244 e~~Gv~P~q~~d~~aL~G 261 (332)
+.+|++.+||+++++|+|
T Consensus 75 ~~l~l~~~~fi~~~iL~G 92 (94)
T PF00867_consen 75 KELGLTREQFIDLCILCG 92 (94)
T ss_dssp HHHTTSHHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHheecC
Confidence 999999999999999999
No 23
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=98.23 E-value=4.6e-06 Score=64.76 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=54.4
Q ss_pred cCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCCC--CCccEEeeHHHHHHHhCC
Q 020010 174 KCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQD--LDRWSFYTLKHYIAQYNC 248 (332)
Q Consensus 174 ~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~--~~~~~~~~~~~v~e~~Gv 248 (332)
.+|||++.+|+ |||.+||.|.+ .|....|+|+|.|++.++.+++-......+ ...++.++.+.+.+++|+
T Consensus 2 ~~gi~~i~AP~-eAeAq~A~L~~----~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 2 LMGIPYIVAPY-EAEAQCAYLAK----SGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCC-cHHHHHHHHHh----CCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 47999999997 99999999986 577779999999999998886422211121 125788889999988774
No 24
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=97.49 E-value=0.00016 Score=64.22 Aligned_cols=44 Identities=27% Similarity=0.452 Sum_probs=37.1
Q ss_pred CCcEE-ecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCC
Q 020010 176 NVPVV-KIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLIS 219 (332)
Q Consensus 176 gi~~i-~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~ 219 (332)
||.++ ...|-.||++|--++......+..|+|||+|....+.+.
T Consensus 67 gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~ 111 (166)
T PF05991_consen 67 GIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAAR 111 (166)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHh
Confidence 67764 556789999999999987766789999999999988764
No 25
>PF12813 XPG_I_2: XPG domain containing
Probab=97.03 E-value=0.0016 Score=61.51 Aligned_cols=85 Identities=22% Similarity=0.182 Sum_probs=57.7
Q ss_pred HHHHHHHhcC---CCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCC-CC--eEEEecC-------CC-C
Q 020010 166 QFILDVLGKC---NVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLIS-ED--VQLVMPL-------QD-L 231 (332)
Q Consensus 166 ~~i~elL~~~---gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~-~~--v~v~~~~-------~~-~ 231 (332)
+.+.+.|+.+ |++++.++| |||.-||.+|++. | ..|+|+|.||+-+-- ++ +.-++.. .+ .
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~-EAD~~~A~~A~~~---~--~~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~ 80 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPG-EADRECAALARKW---G--CPVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSG 80 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCc-cchHHHHHHHHHc---C--CeEEccCCCEEEeccCCCceEEEeeeeEeecccccCCC
Confidence 4556667666 999999999 9999999999762 3 389999999987633 11 2111111 00 0
Q ss_pred --CccEEeeHHHHHHHhCCChhHHHHhhh
Q 020010 232 --DRWSFYTLKHYIAQYNCDPHSELSLRC 258 (332)
Q Consensus 232 --~~~~~~~~~~v~e~~Gv~P~q~~d~~a 258 (332)
-....|.++.+.+++|+. .++-+..
T Consensus 81 ~~i~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 81 SYISAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred CeeEEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 124569999999999986 4444433
No 26
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=96.42 E-value=0.0039 Score=50.33 Aligned_cols=57 Identities=16% Similarity=0.149 Sum_probs=31.1
Q ss_pred CcEEEEeCcchhhhhcC----------chhhHHHHHHHHHHHHhc-CCCcEEEEEcCCCCchhhhhhchh
Q 020010 80 KRVFFLDVNPLCYEGSR----------PSLQSFGRWLSLFFDQVS-HADPVIAVFDGEGGTEHRRQLLPS 138 (332)
Q Consensus 80 ~~vllIDg~~l~yra~~----------p~~~~~~~~l~~ll~~i~-~~~pvivvFD~~~~~~fR~el~p~ 138 (332)
++.+.|||+.|+|++.. .....+.++++.+..... ...| ++||||. .+....+....
T Consensus 26 g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~P-ifVFDG~-~~~~K~~~~~~ 93 (101)
T PF00752_consen 26 GKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKP-IFVFDGK-PPPLKRETIQK 93 (101)
T ss_dssp TCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEE-EEEE--S-TTGGCHHHHHH
T ss_pred CCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEE-EEEECCC-CchhhHHHHHH
Confidence 47899999999999631 111223445555544333 3566 7899995 44444333333
No 27
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.28 E-value=0.0044 Score=46.59 Aligned_cols=27 Identities=63% Similarity=0.895 Sum_probs=21.6
Q ss_pred CcccCCCCccHHHHHHHHHhcCCHHHHHHHh
Q 020010 269 GIQHVVPGFGRKTALKLLKKHGSLENLLNAA 299 (332)
Q Consensus 269 GI~~~~~GIG~KTA~kLL~~ygsle~il~~~ 299 (332)
|| ||||+++|..|++.|||++++.++-
T Consensus 7 GI----~~VG~~~ak~L~~~f~sl~~l~~a~ 33 (64)
T PF12826_consen 7 GI----PGVGEKTAKLLAKHFGSLEALMNAS 33 (64)
T ss_dssp TS----TT--HHHHHHHHHCCSCHHHHCC--
T ss_pred CC----CCccHHHHHHHHHHcCCHHHHHHcC
Confidence 67 9999999999999999999998653
No 28
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=95.88 E-value=0.016 Score=46.67 Aligned_cols=64 Identities=17% Similarity=0.260 Sum_probs=38.2
Q ss_pred CCcEEEEeCcchhhhhcC----------chhhHHHHHHHHHHHHhc-CCCcEEEEEcCCCCchhhhhhchhHHhcch
Q 020010 79 KKRVFFLDVNPLCYEGSR----------PSLQSFGRWLSLFFDQVS-HADPVIAVFDGEGGTEHRRQLLPSYKAHRR 144 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~~----------p~~~~~~~~l~~ll~~i~-~~~pvivvFD~~~~~~fR~el~p~YKanR~ 144 (332)
.++.+.||++.|+||+.. +....+.+++..+...+. ..+| ++||||. .+....+.....+..|.
T Consensus 23 ~g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~P-ifVFDG~-~~~~K~~t~~~R~~~r~ 97 (99)
T smart00485 23 RGKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKP-IFVFDGK-PPPLKSETLAKRRERRE 97 (99)
T ss_pred CCceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeE-EEEECCC-CchhhHHHHHHHHHHHh
Confidence 367999999999999731 111123445555544443 3566 7899996 44444444455444443
No 29
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.31 E-value=0.099 Score=47.79 Aligned_cols=43 Identities=19% Similarity=0.324 Sum_probs=30.1
Q ss_pred HHhCC-ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHh
Q 020010 244 AQYNC-DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAA 299 (332)
Q Consensus 244 e~~Gv-~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~ 299 (332)
..||+ +.+.--.|..|.+ | +|||||+|..+|..|+ .+++.+++
T Consensus 59 ~LyGF~~~~Er~lF~~Li~--------V----~GIGpK~Al~ILs~~~-~~~l~~aI 102 (194)
T PRK14605 59 SLFGFATTEELSLFETLID--------V----SGIGPKLGLAMLSAMN-AEALASAI 102 (194)
T ss_pred eeeCCCCHHHHHHHHHHhC--------C----CCCCHHHHHHHHHhCC-HHHHHHHH
Confidence 34665 3455555666654 5 8999999999999885 66766655
No 30
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.07 E-value=0.11 Score=47.92 Aligned_cols=25 Identities=32% Similarity=0.417 Sum_probs=18.5
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
.|||||+|..+|..+ +.+++.+++.
T Consensus 80 ~GIGpK~Al~iLs~~-~~~~l~~aI~ 104 (203)
T PRK14602 80 SKVGAKTALAILSQF-RPDDLRRLVA 104 (203)
T ss_pred CCcCHHHHHHHHhhC-CHHHHHHHHH
Confidence 788888888888775 5666666654
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=94.05 E-value=0.11 Score=47.33 Aligned_cols=45 Identities=20% Similarity=0.294 Sum_probs=31.0
Q ss_pred HHhCC-ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 244 AQYNC-DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 244 e~~Gv-~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~ 301 (332)
..||+ +.+.--.|..|++ | +|||||+|..+|..+ +++++.+++..
T Consensus 58 ~LyGF~~~~Er~lF~~L~~--------V----~GIGpK~Al~iL~~~-~~~el~~aI~~ 103 (191)
T TIGR00084 58 LLFGFNTLEERELFKELIK--------V----NGVGPKLALAILSNM-SPEEFVYAIET 103 (191)
T ss_pred eeeCCCCHHHHHHHHHHhC--------C----CCCCHHHHHHHHhcC-CHHHHHHHHHh
Confidence 34675 3444445556654 5 899999999998876 57777777663
No 32
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.00 E-value=0.14 Score=57.22 Aligned_cols=66 Identities=17% Similarity=0.199 Sum_probs=47.5
Q ss_pred CCcEEEEeCcchhhhhc--------Cc-hhhHHHHHHHHHHHHhc-CCCcEEEEEcCCCCchhhhhhchhHHhcchhh
Q 020010 79 KKRVFFLDVNPLCYEGS--------RP-SLQSFGRWLSLFFDQVS-HADPVIAVFDGEGGTEHRRQLLPSYKAHRRKF 146 (332)
Q Consensus 79 ~~~vllIDg~~l~yra~--------~p-~~~~~~~~l~~ll~~i~-~~~pvivvFD~~~~~~fR~el~p~YKanR~~~ 146 (332)
.++.+.||++.|+||+. .+ +...+.+|+.++.+.+. ...| |+||||. .+...++.....+..|...
T Consensus 23 ~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n~hl~g~f~Ri~~Ll~~gI~P-VfVFDG~-~p~lK~~t~~~R~~rR~~a 98 (1034)
T TIGR00600 23 EGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRP-IFVFDGG-APLLKRQTLAKRRQRRDGA 98 (1034)
T ss_pred CCeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHHHCCCeE-EEEECCC-CchHhHHHHHHHHHHHHHH
Confidence 47899999999999962 11 12335567777766654 3566 7899995 6777778788888888764
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.56 E-value=0.14 Score=46.45 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=16.1
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
.|||||+|..+|..+ +.+++.+++.
T Consensus 79 sGIGpK~Al~ILs~~-~~~el~~aI~ 103 (183)
T PRK14601 79 NGIGANTAMAVCSSL-DVNSFYKALS 103 (183)
T ss_pred CCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 667777777777664 5666665554
No 34
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=93.39 E-value=0.19 Score=43.97 Aligned_cols=98 Identities=17% Similarity=0.195 Sum_probs=46.4
Q ss_pred CcEEEEeCcchhhhhc---CchhhHHHHHHHHHHHHhcCCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhc
Q 020010 80 KRVFFLDVNPLCYEGS---RPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRF 156 (332)
Q Consensus 80 ~~vllIDg~~l~yra~---~p~~~~~~~~l~~ll~~i~~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~ 156 (332)
.|.++|||++++|..+ .++..++...+..+.+. ..+ .+++|+.. +|... ..+.... +
T Consensus 2 ~r~VVIDG~NVA~~~~~~~~f~~~~i~~~v~~~~~r--G~~-~v~v~~~~----~~~~~-----~~~~~~~-~------- 61 (155)
T PF11977_consen 2 LRPVVIDGSNVAYSHGNQKFFSVRGIQIAVEYFKSR--GHE-VVVVFPPN----YRYKK-----LAKKSDD-Q------- 61 (155)
T ss_dssp B--EEEEHHHHHHHHTTTTSEEHHHHHHHHHHHHHT--T----EEEEEEG----GGGS------TTS-EES-T-------
T ss_pred CCEEEEeCHHHHhhcCCCCCcCHHHHHHHHHHHHHc--CCC-eEEEEcch----hhhcc-----ccCCCCh-H-------
Confidence 5789999999988543 24555555444443322 223 56788852 44333 0111110 0
Q ss_pred chhhHHHhHHHHHHHHhcCCCcEEecCCch--------HHHHHHHHHHHHHhCCCeEEEEcCCC
Q 020010 157 SRGRVGRSHQFILDVLGKCNVPVVKIEGHE--------ADDVIATLVGQVLQKGYRAVVASPDK 212 (332)
Q Consensus 157 ~~~~L~~ql~~i~elL~~~gi~~i~~~g~E--------ADDvIAtLa~~~~~~g~~v~IvS~DK 212 (332)
+.+.++. ..|+-++...|.. +|=.|-++|.+ ...+|||+|+
T Consensus 62 ---------~~L~~l~-~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~-----~~a~IVSND~ 110 (155)
T PF11977_consen 62 ---------EELEKLI-RKGIIYFTPSGSNYGSRSRNYDDRYILYYAEE-----KDAVIVSNDR 110 (155)
T ss_dssp ---------CHHHHHH-HTTSEEEE-EEEETTEEEEB-HHHHHHHHHHH-----TT-EEE-S--
T ss_pred ---------HHHHHHH-HCCeEEEcCCCCCCCCcccccchHHHHHHHHH-----cCCEEEeCch
Confidence 1122322 2566556555655 66667777754 2457889995
No 35
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=93.36 E-value=0.36 Score=43.05 Aligned_cols=34 Identities=29% Similarity=0.451 Sum_probs=25.2
Q ss_pred EEecCCchHHHHHHHHHHHHHhCC-CeEEEEcCCC
Q 020010 179 VVKIEGHEADDVIATLVGQVLQKG-YRAVVASPDK 212 (332)
Q Consensus 179 ~i~~~g~EADDvIAtLa~~~~~~g-~~v~IvS~DK 212 (332)
++...|--||--|--+|....... ..|+|+|+|.
T Consensus 75 vyT~~~ETADs~IEr~~~el~~~~t~~V~VaTSD~ 109 (173)
T COG3688 75 VYTKEGETADSFIERYVAELRNAATHQVIVATSDR 109 (173)
T ss_pred EEecCCccHHHHHHHHHHHHhccccceEEEEeCch
Confidence 356777789999988887766333 4889999874
No 36
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=93.28 E-value=0.15 Score=37.53 Aligned_cols=24 Identities=50% Similarity=0.674 Sum_probs=22.5
Q ss_pred CCccHHHHHHHHHh-cCCHHHHHHH
Q 020010 275 PGFGRKTALKLLKK-HGSLENLLNA 298 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il~~ 298 (332)
||||+++|.+|... |+|+++++..
T Consensus 11 ~Gig~~~a~~L~~~G~~t~~~l~~a 35 (60)
T PF14520_consen 11 PGIGPKRAEKLYEAGIKTLEDLANA 35 (60)
T ss_dssp TTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred CCCCHHHHHHHHhcCCCcHHHHHcC
Confidence 99999999999999 9999999875
No 37
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.54 E-value=0.23 Score=45.52 Aligned_cols=25 Identities=40% Similarity=0.492 Sum_probs=19.3
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
.|||||+|..+|..+ +.+++.+++.
T Consensus 79 ~GIGpK~Al~iLs~~-~~~el~~aI~ 103 (195)
T PRK14604 79 SGVGPKAALNLLSSG-TPDELQLAIA 103 (195)
T ss_pred CCcCHHHHHHHHcCC-CHHHHHHHHH
Confidence 788888888888864 6777777665
No 38
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=92.37 E-value=0.22 Score=45.23 Aligned_cols=23 Identities=30% Similarity=0.494 Sum_probs=19.5
Q ss_pred CCccHHHHHHHHHhcCC---HHHHHH
Q 020010 275 PGFGRKTALKLLKKHGS---LENLLN 297 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygs---le~il~ 297 (332)
||||||||.++|..||+ .++|.+
T Consensus 79 ~GIGpk~A~~il~~fg~~~l~~~i~~ 104 (192)
T PRK00116 79 SGVGPKLALAILSGLSPEELVQAIAN 104 (192)
T ss_pred CCCCHHHHHHHHHhCCHHHHHHHHHh
Confidence 99999999999999998 555555
No 39
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=91.80 E-value=0.15 Score=53.96 Aligned_cols=26 Identities=35% Similarity=0.549 Sum_probs=24.1
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||||+..+||+.|||+++|.++..
T Consensus 520 ~GiG~kr~~~LL~~Fgs~~~I~~As~ 545 (574)
T PRK14670 520 KGIGEKKAKKILKSLGTYKDILLLNE 545 (574)
T ss_pred CCCCHHHHHHHHHHhCCHHHHHhCCH
Confidence 88999999999999999999998754
No 40
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=91.69 E-value=0.22 Score=53.58 Aligned_cols=46 Identities=33% Similarity=0.395 Sum_probs=32.6
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhhhcc--c-C-chHHHHHHHHhHHHH
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAAVRT--V-G-RDYAQEALTKHADYL 320 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~~~~--~-~-~~~~~~~L~~~~~~~ 320 (332)
||||+|++.+||+.|||+++|+++..+.. . | .++..+++.++...+
T Consensus 643 PGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 643 EGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLKTL 692 (694)
T ss_pred CCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHHh
Confidence 89999999999999999999998654221 1 1 134555666655443
No 41
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=91.20 E-value=0.15 Score=54.43 Aligned_cols=26 Identities=50% Similarity=0.742 Sum_probs=23.9
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||+|++.+||+.|||+++|.++-.
T Consensus 558 pGIG~kr~~~LL~~FgSi~~I~~As~ 583 (624)
T PRK14669 558 PGVGAKTVQRLLKHFGSLERVRAATE 583 (624)
T ss_pred CCCCHHHHHHHHHHcCCHHHHHhCCH
Confidence 88899999999999999999998654
No 42
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=90.93 E-value=0.18 Score=53.39 Aligned_cols=25 Identities=48% Similarity=0.725 Sum_probs=23.2
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAA 299 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~ 299 (332)
||||||+..+||+.|||+++|.++-
T Consensus 547 ~GIG~kr~~~LL~~Fgs~~~i~~As 571 (574)
T TIGR00194 547 PGVGEKRVQKLLKYFGSLKGIKKAS 571 (574)
T ss_pred CCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 8889999999999999999998764
No 43
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=90.75 E-value=0.19 Score=53.11 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=23.8
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||||+..+||+.|||+++|.++-.
T Consensus 520 ~GiG~kr~~~Ll~~Fgs~~~ik~As~ 545 (567)
T PRK14667 520 KGIGEVKKEIIYRNFKTLYDFLKADD 545 (567)
T ss_pred CCCCHHHHHHHHHHhCCHHHHHhCCH
Confidence 88899999999999999999988754
No 44
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=89.68 E-value=0.34 Score=35.20 Aligned_cols=23 Identities=43% Similarity=0.426 Sum_probs=17.0
Q ss_pred CCccHHHHHHHHHh-cCCHHHHHH
Q 020010 275 PGFGRKTALKLLKK-HGSLENLLN 297 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il~ 297 (332)
-||||+||.++..+ +.|+|++-.
T Consensus 8 ~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 8 WGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp TT--HHHHHHHHHTT--SHHHHHH
T ss_pred ccccHHHHHHHHHhCCCCHHHHhh
Confidence 89999999999986 779999944
No 45
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=89.20 E-value=0.3 Score=31.53 Aligned_cols=13 Identities=54% Similarity=0.833 Sum_probs=10.4
Q ss_pred CCccHHHHHHHHH
Q 020010 275 PGFGRKTALKLLK 287 (332)
Q Consensus 275 ~GIG~KTA~kLL~ 287 (332)
||||+|||..++.
T Consensus 17 pGIG~~tA~~I~~ 29 (30)
T PF00633_consen 17 PGIGPKTANAILS 29 (30)
T ss_dssp TT-SHHHHHHHHH
T ss_pred CCcCHHHHHHHHh
Confidence 9999999988763
No 46
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.57 E-value=0.88 Score=41.72 Aligned_cols=45 Identities=27% Similarity=0.260 Sum_probs=30.2
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhhhcc---------cCchHHHHHHHHhHHHH
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAAVRT---------VGRDYAQEALTKHADYL 320 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~~~~---------~~~~~~~~~L~~~~~~~ 320 (332)
.|||||+|..+|..+ +.+++.+++.... .|++.++..+.+-++.+
T Consensus 78 ~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 78 SGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred CCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 899999999999886 6888887765321 24444444444544443
No 47
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=88.12 E-value=0.55 Score=40.56 Aligned_cols=41 Identities=29% Similarity=0.383 Sum_probs=30.0
Q ss_pred CCccHHHHHHHHH--hcCCHHHHHHHhhhcccCchHHHHHHHHhHHH
Q 020010 275 PGFGRKTALKLLK--KHGSLENLLNAAAVRTVGRDYAQEALTKHADY 319 (332)
Q Consensus 275 ~GIG~KTA~kLL~--~ygsle~il~~~~~~~~~~~~~~~~L~~~~~~ 319 (332)
|||||++|.++++ .|.|+|++++- . ..+ ++.++.|+++++.
T Consensus 67 pGigP~~A~~IV~nGpf~sveDL~~V-~--GIg-ekqk~~l~k~~~~ 109 (132)
T PRK02515 67 PGMYPTLAGKIVKNAPYDSVEDVLNL-P--GLS-ERQKELLEANLDN 109 (132)
T ss_pred CCCCHHHHHHHHHCCCCCCHHHHHcC-C--CCC-HHHHHHHHHhhcc
Confidence 9999999999997 47799999873 2 233 3455667776654
No 48
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=88.06 E-value=0.39 Score=51.29 Aligned_cols=27 Identities=48% Similarity=0.693 Sum_probs=24.2
Q ss_pred CCcccCCCCccHHHHHHHHHhcCCHHHHHHH
Q 020010 268 PGIQHVVPGFGRKTALKLLKKHGSLENLLNA 298 (332)
Q Consensus 268 PGI~~~~~GIG~KTA~kLL~~ygsle~il~~ 298 (332)
.|| ||||+|+|..||+.|||+++|.++
T Consensus 572 ~~I----~GIG~k~a~~Ll~~Fgs~~~i~~A 598 (621)
T PRK14671 572 TDI----AGIGEKTAEKLLEHFGSVEKVAKA 598 (621)
T ss_pred hcC----CCcCHHHHHHHHHHcCCHHHHHhC
Confidence 467 999999999999999999999775
No 49
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=87.86 E-value=0.38 Score=50.93 Aligned_cols=32 Identities=31% Similarity=0.591 Sum_probs=27.4
Q ss_pred CCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 265 DGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 265 DNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
.-+..| ||||++++.+||+.|||+++|+++-.
T Consensus 525 ~~L~~I----pGIG~kr~~~LL~~FGS~~~I~~As~ 556 (577)
T PRK14668 525 TVLDDV----PGVGPETRKRLLRRFGSVEGVREASV 556 (577)
T ss_pred hHHhcC----CCCCHHHHHHHHHHcCCHHHHHhCCH
Confidence 344566 99999999999999999999998754
No 50
>PHA03065 Hypothetical protein; Provisional
Probab=87.84 E-value=7.8 Score=39.59 Aligned_cols=116 Identities=22% Similarity=0.324 Sum_probs=76.5
Q ss_pred HHHHhcC--CCcEEecCCchHHHHHHHHHHHHHh-CCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH
Q 020010 169 LDVLGKC--NVPVVKIEGHEADDVIATLVGQVLQ-KGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ 245 (332)
Q Consensus 169 ~elL~~~--gi~~i~~~g~EADDvIAtLa~~~~~-~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~ 245 (332)
.+.|..+ ++.++..+|.-|+=++..-|+..+. .|.=-.++|.|.|.+.+.+-. +.. + . ...+-+-
T Consensus 151 ~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D-----~~~---K-i---I~t~~~~ 218 (438)
T PHA03065 151 ESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCD-----RLP---K-I---IKTANQL 218 (438)
T ss_pred HHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecC-----cHH---H-H---HHhHHHH
Confidence 3445555 8999999999999999998887543 465557889999999887632 111 0 1 2333445
Q ss_pred hCCChhHHHHhh---hcccCCCCCCCCcccCCCC--ccHHHH--HHHHHhcCCHHHHHHHhhh
Q 020010 246 YNCDPHSELSLR---CIVGDDVDGVPGIQHVVPG--FGRKTA--LKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 246 ~Gv~P~q~~d~~---aL~GD~sDNIPGI~~~~~G--IG~KTA--~kLL~~ygsle~il~~~~~ 301 (332)
|.+-|.....|. +..=-.||.-||+ -| |.+|+- .+|..+| |+++++..+..
T Consensus 219 Y~~~P~~~t~YL~kL~~L~NGCDfFpGL----yG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~ 276 (438)
T PHA03065 219 YKFIPCAKTRYLSKLVALVNGCDFFPGL----YGISITPKSLNRIQLFDDF-TIDNVVRSLAI 276 (438)
T ss_pred heeCCChhHHHHHHHHHHHhcccccCcc----ceEEechhhccceechhhh-hHHHHHHHHHh
Confidence 666565544333 2222349999999 88 566654 3445555 68888888774
No 51
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.14 E-value=1.2 Score=40.89 Aligned_cols=44 Identities=16% Similarity=0.378 Sum_probs=30.6
Q ss_pred HHhCC-ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 244 AQYNC-DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 244 e~~Gv-~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
..||+ +.++--.|..|++ | .|||||+|..+|..+ +.+++.+++.
T Consensus 58 ~LYGF~t~~Er~lF~~Lis--------V----sGIGPK~ALaILs~~-~~~el~~aI~ 102 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIG--------V----DGIGPRAALRVLSGI-KYNEFRDAID 102 (196)
T ss_pred eeeCCCCHHHHHHHHHHhC--------c----CCcCHHHHHHHHcCC-CHHHHHHHHH
Confidence 34665 3444445556643 5 899999999999886 6777777765
No 52
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=87.13 E-value=0.53 Score=50.01 Aligned_cols=26 Identities=42% Similarity=0.659 Sum_probs=23.8
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||++++.+||+.|||+++|+++-.
T Consensus 549 pGIG~k~~k~Ll~~FgS~~~i~~As~ 574 (598)
T PRK00558 549 PGIGPKRRKALLKHFGSLKAIKEASV 574 (598)
T ss_pred CCcCHHHHHHHHHHcCCHHHHHhCCH
Confidence 99999999999999999999997643
No 53
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=87.05 E-value=0.55 Score=44.22 Aligned_cols=29 Identities=28% Similarity=0.352 Sum_probs=25.4
Q ss_pred CCCcccCCCCccHHHHHHHHHh-cCCHHHHHHHh
Q 020010 267 VPGIQHVVPGFGRKTALKLLKK-HGSLENLLNAA 299 (332)
Q Consensus 267 IPGI~~~~~GIG~KTA~kLL~~-ygsle~il~~~ 299 (332)
+-.| ||||+++|.+|++. |+|+++|..+-
T Consensus 5 L~~I----pGIG~krakkLl~~GF~Sve~Ik~AS 34 (232)
T PRK12766 5 LEDI----SGVGPSKAEALREAGFESVEDVRAAD 34 (232)
T ss_pred cccC----CCcCHHHHHHHHHcCCCCHHHHHhCC
Confidence 4556 99999999999999 99999997763
No 54
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=86.99 E-value=0.49 Score=50.91 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=23.8
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||+|++.+||+.|||+++|.++-.
T Consensus 614 pGiG~kr~~~LL~~FgS~~~i~~As~ 639 (691)
T PRK14672 614 PHVGKVRAHRLLAHFGSFRSLQSATP 639 (691)
T ss_pred CCCCHHHHHHHHHHhcCHHHHHhCCH
Confidence 88899999999999999999988754
No 55
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.51 E-value=1.4 Score=40.20 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=31.4
Q ss_pred HHhCCC-hhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 244 AQYNCD-PHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 244 e~~Gv~-P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~ 301 (332)
..||+. .++--.|..|.+ | .|||||+|..+|..+ +.+++.+++..
T Consensus 59 ~LyGF~~~~Er~lF~~Li~--------V----~GIGpK~AL~iLs~~-~~~el~~aI~~ 104 (188)
T PRK14606 59 TLYGFSNERKKELFLSLTK--------V----SRLGPKTALKIISNE-DAETLVTMIAS 104 (188)
T ss_pred eeeCCCCHHHHHHHHHHhc--------c----CCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 346763 444445555643 5 899999999999886 68888877653
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.20 E-value=1.5 Score=39.94 Aligned_cols=45 Identities=29% Similarity=0.417 Sum_probs=31.7
Q ss_pred HHhCC-ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 244 AQYNC-DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 244 e~~Gv-~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~ 301 (332)
..||+ +.+.--.|..|.+ | .|||||+|..+|..+ +.+++..++..
T Consensus 59 ~LyGF~~~~Er~lF~~Lis--------V----~GIGpK~Al~iLs~~-~~~~l~~aI~~ 104 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVK--------V----SGVNYKTAMSILSKL-TPEQLFSAIVN 104 (186)
T ss_pred eeeCCCCHHHHHHHHHHhC--------c----CCcCHHHHHHHHccC-CHHHHHHHHHc
Confidence 34665 3555555566654 5 899999999999886 67788777653
No 57
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=84.53 E-value=0.73 Score=28.37 Aligned_cols=13 Identities=62% Similarity=0.958 Sum_probs=12.2
Q ss_pred CCccHHHHHHHHH
Q 020010 275 PGFGRKTALKLLK 287 (332)
Q Consensus 275 ~GIG~KTA~kLL~ 287 (332)
||||+|+|.+++.
T Consensus 7 ~GiG~k~A~~il~ 19 (26)
T smart00278 7 PGIGPKTAEKILE 19 (26)
T ss_pred CCCCHHHHHHHHH
Confidence 9999999999986
No 58
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=84.38 E-value=7.1 Score=36.88 Aligned_cols=43 Identities=14% Similarity=0.271 Sum_probs=26.7
Q ss_pred cCCchHHHHHHHHHHHHHh-----CCCeEEEEcCCCCcCccC----CCCeEEE
Q 020010 182 IEGHEADDVIATLVGQVLQ-----KGYRAVVASPDKDFKQLI----SEDVQLV 225 (332)
Q Consensus 182 ~~g~EADDvIAtLa~~~~~-----~g~~v~IvS~DKDl~QLv----~~~v~v~ 225 (332)
.|| |++==|-...+.... .....+|+|.|.|+..|. .+++.++
T Consensus 182 vpG-EGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L~~~~~~~~il 233 (237)
T PF03159_consen 182 VPG-EGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSLATHEPNIYIL 233 (237)
T ss_dssp SSS--HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHHHTT-SSEEEE
T ss_pred CCC-ccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHHccCCCeEEEE
Confidence 478 999877776666443 346789999999998652 3455554
No 59
>PF09293 RNaseH_C: T4 RNase H, C terminal; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TFR_A 3H8S_A 2IHN_A 3H7I_A 3H8W_A 3H8J_A.
Probab=83.74 E-value=0.52 Score=40.21 Aligned_cols=24 Identities=38% Similarity=0.612 Sum_probs=19.8
Q ss_pred ChhHHHHhhhcccCCCCCCCCccc
Q 020010 249 DPHSELSLRCIVGDDVDGVPGIQH 272 (332)
Q Consensus 249 ~P~q~~d~~aL~GD~sDNIPGI~~ 272 (332)
+|+.-.-++++-||.+||||+|+.
T Consensus 2 s~~~d~~~KiiKGDkkDgVa~Ik~ 25 (122)
T PF09293_consen 2 SPEMDLMTKIIKGDKKDGVASIKV 25 (122)
T ss_dssp HHHHHHHHHHHHEBGGGTBE-TTS
T ss_pred ChhHHHHHHHHcCCccCCcCceee
Confidence 377788899999999999999943
No 60
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=82.54 E-value=6.1 Score=36.53 Aligned_cols=50 Identities=24% Similarity=0.268 Sum_probs=33.4
Q ss_pred HHHHHHHhCCC-hhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhh
Q 020010 239 LKHYIAQYNCD-PHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 239 ~~~v~e~~Gv~-P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~ 301 (332)
.++....||+. .+.=-.|.-|.. | .|||||+|..+|... +++++.++++.
T Consensus 54 REd~~~LyGF~~~~ER~lF~~Lis--------V----nGIGpK~ALaiLs~~-~~~~l~~aI~~ 104 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLLIS--------V----NGIGPKLALAILSNL-DPEELAQAIAN 104 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHHHc--------c----CCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 35556778874 333334444432 5 889999999999764 67788777663
No 61
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=81.82 E-value=1.7 Score=41.44 Aligned_cols=26 Identities=54% Similarity=0.841 Sum_probs=24.0
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||++.|..||+.|||++++..+-.
T Consensus 188 pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 188 PGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred CCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 89999999999999999999998744
No 62
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=80.08 E-value=1.4 Score=47.42 Aligned_cols=26 Identities=35% Similarity=0.475 Sum_probs=23.2
Q ss_pred CCCccHHHHHHHHHhcCCHHHHHHHh
Q 020010 274 VPGFGRKTALKLLKKHGSLENLLNAA 299 (332)
Q Consensus 274 ~~GIG~KTA~kLL~~ygsle~il~~~ 299 (332)
.||||+++|..|++.|||++++.++.
T Consensus 503 IpgVG~~~ak~L~~~f~sl~~l~~As 528 (652)
T TIGR00575 503 IRHVGEVTAKNLAKHFGTLDKLKAAS 528 (652)
T ss_pred CCCcCHHHHHHHHHHhCCHHHHHhCC
Confidence 39999999999999999999998754
No 63
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=79.18 E-value=3 Score=35.25 Aligned_cols=50 Identities=22% Similarity=0.177 Sum_probs=35.3
Q ss_pred HHHhcCCCcEEecCCc-------hHHHHHHHHHHHHHhC--CCeEEEEcCCCCcCccCC
Q 020010 170 DVLGKCNVPVVKIEGH-------EADDVIATLVGQVLQK--GYRAVVASPDKDFKQLIS 219 (332)
Q Consensus 170 elL~~~gi~~i~~~g~-------EADDvIAtLa~~~~~~--g~~v~IvS~DKDl~QLv~ 219 (332)
+.|+..|+.++..+.. .+|--|+.-+...... -+.++++|+|.|+..++.
T Consensus 59 ~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~ 117 (149)
T cd06167 59 DALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVE 117 (149)
T ss_pred HHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHH
Confidence 4466789888766642 3777777665544433 468899999999998865
No 64
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=78.86 E-value=3.5 Score=40.11 Aligned_cols=24 Identities=54% Similarity=0.696 Sum_probs=21.3
Q ss_pred CCccHHHHHHHHHhc--CCHHHHHHHh
Q 020010 275 PGFGRKTALKLLKKH--GSLENLLNAA 299 (332)
Q Consensus 275 ~GIG~KTA~kLL~~y--gsle~il~~~ 299 (332)
+|||||||.+|. +. .|+|++.+++
T Consensus 91 ~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 91 PGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred CCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 999999999999 54 4999999986
No 65
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=78.55 E-value=1.6 Score=46.31 Aligned_cols=26 Identities=42% Similarity=0.668 Sum_probs=23.8
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||+|+..+||+.|||+++|.++..
T Consensus 536 ~GiG~~r~~~LL~~Fgs~~~i~~As~ 561 (581)
T COG0322 536 PGIGPKRRKALLKHFGSLKGIKSASV 561 (581)
T ss_pred CCcCHHHHHHHHHHhhCHHHHHhcCH
Confidence 78899999999999999999988765
No 66
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=77.74 E-value=2.8 Score=34.82 Aligned_cols=49 Identities=20% Similarity=0.221 Sum_probs=24.8
Q ss_pred HHhcCCCcEEecCC--------chHHHHHHHHHHHHHh--CCCeEEEEcCCCCcCccCC
Q 020010 171 VLGKCNVPVVKIEG--------HEADDVIATLVGQVLQ--KGYRAVVASPDKDFKQLIS 219 (332)
Q Consensus 171 lL~~~gi~~i~~~g--------~EADDvIAtLa~~~~~--~g~~v~IvS~DKDl~QLv~ 219 (332)
.|+..|+++...+. -.+|-.|+.-+..... .-..++|+|+|.|+..++.
T Consensus 55 ~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 55 ALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVR 113 (146)
T ss_dssp HHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHH
T ss_pred HHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHH
Confidence 34455665543332 2466667665554442 2378999999999998875
No 67
>PRK08609 hypothetical protein; Provisional
Probab=76.63 E-value=5 Score=42.48 Aligned_cols=26 Identities=42% Similarity=0.616 Sum_probs=23.1
Q ss_pred CCccHHHHHHHHHhcC--CHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHG--SLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~yg--sle~il~~~~ 300 (332)
||||||||.+|-++.| |++++.+++.
T Consensus 94 ~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 94 PGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred CCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 9999999999998765 8999998875
No 68
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=76.54 E-value=2.5 Score=45.77 Aligned_cols=25 Identities=32% Similarity=0.615 Sum_probs=22.7
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAA 299 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~ 299 (332)
||||+++|.+|++.|+|++++.++-
T Consensus 534 pgIG~~~ak~L~~~F~si~~L~~As 558 (689)
T PRK14351 534 PEVGPTTARNLAREFGTFEAIMDAD 558 (689)
T ss_pred CCcCHHHHHHHHHHhCCHHHHHhCC
Confidence 9999999999999999999998654
No 69
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=74.71 E-value=6.7 Score=40.10 Aligned_cols=116 Identities=22% Similarity=0.317 Sum_probs=74.3
Q ss_pred HHHHhc--CCCcEEecCCchHHHHHHHHHHHHHh-CCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH
Q 020010 169 LDVLGK--CNVPVVKIEGHEADDVIATLVGQVLQ-KGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ 245 (332)
Q Consensus 169 ~elL~~--~gi~~i~~~g~EADDvIAtLa~~~~~-~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~ 245 (332)
.+.|.. .++.++..+|.-|+=+|..-|+..+. .|.=-.++|.|.|.+.|.+-.. .. +. ....-+.
T Consensus 149 ~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~-----~~---Ki----I~t~~~~ 216 (425)
T PF04599_consen 149 ESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDT-----PP---KI----IKTMNQL 216 (425)
T ss_pred HHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCc-----hH---HH----HHhHHhH
Confidence 444443 58899999999999999998887553 4554578899999999876321 11 00 2223334
Q ss_pred hCCChhHHHHhh---hcccCCCCCCCCcccCCCC--ccHHHHH--HHHHhcCCHHHHHHHhhh
Q 020010 246 YNCDPHSELSLR---CIVGDDVDGVPGIQHVVPG--FGRKTAL--KLLKKHGSLENLLNAAAV 301 (332)
Q Consensus 246 ~Gv~P~q~~d~~---aL~GD~sDNIPGI~~~~~G--IG~KTA~--kLL~~ygsle~il~~~~~ 301 (332)
|.+-|...--|+ +..=-.||+-||+ -| |.+++-. +|..+| |+++++..+..
T Consensus 217 Y~~~P~~~s~YL~kL~~L~NGCDfFpGL----yG~~it~~~l~~i~LF~dF-ti~Ni~~SL~~ 274 (425)
T PF04599_consen 217 YKFIPCSKSRYLSKLTALVNGCDFFPGL----YGISITKKSLNRIKLFEDF-TIDNILQSLAI 274 (425)
T ss_pred eeecCCchHHHHHHHHHHHhcccccCCc----ceeEechhhccceeccccc-cHHHHHHHHhh
Confidence 555554433332 2222339999999 88 5666543 344444 69999988764
No 70
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.54 E-value=2.2 Score=39.28 Aligned_cols=34 Identities=21% Similarity=0.193 Sum_probs=24.2
Q ss_pred ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 249 DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 249 ~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
+|+++... +..|| ..-+-.| ||||+|||.+++-+
T Consensus 93 ~~~el~~a-I~~~D-~~~L~~v----pGIGkKtAeRIIlE 126 (196)
T PRK13901 93 KYNEFRDA-IDRED-IELISKV----KGIGNKMAGKIFLK 126 (196)
T ss_pred CHHHHHHH-HHhCC-HHHHhhC----CCCCHHHHHHHHHH
Confidence 46665543 35565 5567778 99999999999844
No 71
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=72.80 E-value=2.9 Score=41.19 Aligned_cols=25 Identities=40% Similarity=0.533 Sum_probs=22.0
Q ss_pred CCccHHHHHHHHHhcC--CHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHG--SLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~yg--sle~il~~~~ 300 (332)
+|||||||.+|.+ .| |++++.++..
T Consensus 95 ~GiGpk~a~~l~~-lGi~tl~eL~~a~~ 121 (334)
T smart00483 95 FGVGPKTAAKWYR-KGIRTLEELKKNKE 121 (334)
T ss_pred CCcCHHHHHHHHH-hCCCCHHHHHhccc
Confidence 9999999999998 66 8999987765
No 72
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=72.28 E-value=2.7 Score=33.07 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=19.6
Q ss_pred CCccHHHHHHHHHhcCCHHHHH
Q 020010 275 PGFGRKTALKLLKKHGSLENLL 296 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il 296 (332)
||||+.||..||.+.|+++.+-
T Consensus 8 pGig~~~a~~llaeigd~~rF~ 29 (87)
T PF02371_consen 8 PGIGPITAATLLAEIGDISRFK 29 (87)
T ss_pred CCccHHHHHHHHHHHcCchhcc
Confidence 9999999999999999886653
No 73
>PRK13766 Hef nuclease; Provisional
Probab=72.19 E-value=3 Score=45.12 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=23.7
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||+++|.+|++.|||+++++++-.
T Consensus 721 pgig~~~a~~Ll~~fgs~~~i~~as~ 746 (773)
T PRK13766 721 PDVGPVLARNLLEHFGSVEAVMTASE 746 (773)
T ss_pred CCCCHHHHHHHHHHcCCHHHHHhCCH
Confidence 99999999999999999999987543
No 74
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=71.46 E-value=3 Score=45.04 Aligned_cols=24 Identities=42% Similarity=0.480 Sum_probs=21.8
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHH
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNA 298 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~ 298 (332)
||||+++|..|++.|+|++++.++
T Consensus 517 ~~IG~~~ak~L~~~f~sl~~l~~A 540 (665)
T PRK07956 517 RHVGEKAAKALARHFGSLEALRAA 540 (665)
T ss_pred cCcCHHHHHHHHHHcCCHHHHHhC
Confidence 899999999999999999998765
No 75
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.23 E-value=4.2 Score=36.99 Aligned_cols=35 Identities=26% Similarity=0.417 Sum_probs=24.2
Q ss_pred CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 248 CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 248 v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
++|+++.. .+..|| ..-+-.| ||||+|||.+++-+
T Consensus 93 ~~~~el~~-aI~~~D-~~~L~~v----pGIGkKtAeRIilE 127 (183)
T PRK14601 93 LDVNSFYK-ALSLGD-ESVLKKV----PGIGPKSAKRIIAE 127 (183)
T ss_pred CCHHHHHH-HHHhCC-HHHHhhC----CCCCHHHHHHHHHH
Confidence 35666554 344555 4566677 99999999999743
No 76
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=70.05 E-value=2.9 Score=27.22 Aligned_cols=15 Identities=60% Similarity=0.751 Sum_probs=10.5
Q ss_pred CCccHHHHHHHHHhcC
Q 020010 275 PGFGRKTALKLLKKHG 290 (332)
Q Consensus 275 ~GIG~KTA~kLL~~yg 290 (332)
+|||+||+.+ |+++|
T Consensus 17 ~GIG~kt~~k-L~~~G 31 (32)
T PF11798_consen 17 WGIGKKTAKK-LNKLG 31 (32)
T ss_dssp TTS-HHHHHH-HHCTT
T ss_pred CCccHHHHHH-HHHcc
Confidence 9999999888 44443
No 77
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=69.19 E-value=31 Score=34.17 Aligned_cols=93 Identities=8% Similarity=0.083 Sum_probs=54.5
Q ss_pred HHHHHHHHhcCCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec--
Q 020010 105 WLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI-- 182 (332)
Q Consensus 105 ~l~~ll~~i~~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~-- 182 (332)
++..+++.-.-+.||++++||. +---|+.-.+...+||... +.+++.+++|. .+||+++..
T Consensus 9 ~~~~~l~~g~iP~HVAiIMDGN-rRwAk~~gl~~~~GH~~G~------------~~l~~il~~c~----~lGIk~lTlYA 71 (322)
T PTZ00349 9 FITSLLRDFINIKHISIIMDGN-RRFAKEKGLHSAIGHFMGS------------KALIQIIEICI----KLKIKILSVFS 71 (322)
T ss_pred HHHHHhhcCCCCCcEEEEcCCC-HHHHHHCCCCHHHHHHHHH------------HHHHHHHHHHH----HcCCCEEEEEE
Confidence 3333444322367799999996 2222444567788888876 33444444444 469988765
Q ss_pred --------CCchHHHHHHHHHH----------HHHhCCCeEEEEcCCCCcC
Q 020010 183 --------EGHEADDVIATLVG----------QVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 183 --------~g~EADDvIAtLa~----------~~~~~g~~v~IvS~DKDl~ 215 (332)
+..|=+.++.-+.. ...+.|.++.+ .+|.|++
T Consensus 72 FStENwkRp~~EV~~Lm~L~~~~l~~~~~~~~~l~~~~irirv-iGd~~~L 121 (322)
T PTZ00349 72 FSLLNYNRSPEEIHFLFYLNLLILINEDFFFKFIKDNKIKIKI-IGNLSYI 121 (322)
T ss_pred eehhhhCCCHHHHHHHHHHHHHHHHHhhhhHHHHHHCCCEEEE-EeChhhC
Confidence 55688877654422 22334555544 5677664
No 78
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=68.19 E-value=7.9 Score=42.15 Aligned_cols=38 Identities=21% Similarity=0.365 Sum_probs=26.9
Q ss_pred hhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCC--HHHHHHHh
Q 020010 250 PHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGS--LENLLNAA 299 (332)
Q Consensus 250 P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygs--le~il~~~ 299 (332)
.+.++.|+. . +. + ||||||||.++++.||. ++-|.++.
T Consensus 77 ~~~i~~yL~-s----~~---~----~GIG~~~A~~iv~~fg~~~~~~i~~~~ 116 (720)
T TIGR01448 77 KEGIVAYLS-S----RS---I----KGVGKKLAQRIVKTFGEAAFDVLDDDP 116 (720)
T ss_pred HHHHHHHHh-c----CC---C----CCcCHHHHHHHHHHhCHhHHHHHHhCH
Confidence 456666655 2 22 5 88999999999999994 55555543
No 79
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=67.95 E-value=8.2 Score=38.62 Aligned_cols=28 Identities=29% Similarity=0.451 Sum_probs=25.0
Q ss_pred CCCCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 273 VVPGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 273 ~~~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
..|+++++.|..|+++|||+.+|+++-.
T Consensus 291 ~IPrl~k~iAk~Ll~~FGSL~~Il~As~ 318 (352)
T PRK13482 291 KIPRLPSAVIENLVEHFGSLQGLLAASI 318 (352)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHcCCH
Confidence 4599999999999999999999998644
No 80
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.93 E-value=4.9 Score=36.58 Aligned_cols=34 Identities=18% Similarity=0.359 Sum_probs=25.1
Q ss_pred CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 248 CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 248 v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
++|+++... +-.||. .-+ .| ||||+|||.+++-+
T Consensus 93 ~~~~~l~~a-I~~~D~-~~L-~v----pGIGkKtAerIilE 126 (186)
T PRK14600 93 LTPEQLFSA-IVNEDK-AAL-KV----NGIGEKLINRIITE 126 (186)
T ss_pred CCHHHHHHH-HHcCCH-hhe-EC----CCCcHHHHHHHHHH
Confidence 456766653 445774 567 88 99999999999844
No 81
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=67.36 E-value=4.2 Score=44.92 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=23.9
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
||||++.|..||++|||+++|..+-.
T Consensus 763 PgI~~~~a~~ll~~f~si~~l~~as~ 788 (814)
T TIGR00596 763 PGVTKKNYRNLRKKVKSIRELAKLSQ 788 (814)
T ss_pred CCCCHHHHHHHHHHcCCHHHHHhCCH
Confidence 99999999999999999999988543
No 82
>cd01012 YcaC_related YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.
Probab=66.55 E-value=10 Score=32.69 Aligned_cols=43 Identities=19% Similarity=0.248 Sum_probs=39.0
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..|+..+..-|..+|-++.+-++.+...|++|++++
T Consensus 78 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~~a~~~g~~v~v~~ 120 (157)
T cd01012 78 AFRKALKATGRKQVVLAGLETHVCVLQTALDLLEEGYEVFVVA 120 (157)
T ss_pred HHHHHHHhcCCCEEEEEEeeccHHHHHHHHHHHHCCCEEEEEe
Confidence 5667788899999999999999999999999999999999876
No 83
>cd01015 CSHase N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia. CSHase is involved in one of the two alternative pathways for creatinine degradation to glycine in microorganisms.This CSHase-containing pathway degrades creatinine via N-methylhydantoin N-carbamoylsarcosine and sarcosine to glycine. Enzymes of this pathway are used in the diagnosis for renal disfunction, for determining creatinine levels in urine and serum.
Probab=66.33 E-value=10 Score=33.36 Aligned_cols=43 Identities=19% Similarity=0.320 Sum_probs=38.9
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..||..+..-|.++|=++-+-++.+...|++|++++
T Consensus 104 ~L~~~L~~~gi~~vvi~G~~t~~CV~~Ta~~A~~~Gy~v~vv~ 146 (179)
T cd01015 104 SLAATLTARGVDTLIVAGCSTSGCIRATAVDAMQHGFRPIVVR 146 (179)
T ss_pred cHHHHHHHcCCCEEEEeeecccHhHHHHHHHHHHCCCeEEEee
Confidence 4667788899999999999999999999999999999999886
No 84
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=66.27 E-value=28 Score=33.05 Aligned_cols=83 Identities=14% Similarity=0.040 Sum_probs=49.5
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|+.-.+...+||... +.+.+.+++ +..+||+++.. +--
T Consensus 15 P~HvaiImDGN-rRwAk~~g~~~~~GH~~G~------------~~l~~iv~~----c~~~gI~~vTvYaFS~eN~kR~~~ 77 (243)
T PRK14829 15 PRHIAVVMDGN-GRWATQRGLKRTEGHKAGE------------PVLFDVVAG----AIEAGVPYLSLYTFSTENWKRSPD 77 (243)
T ss_pred CCeEEEecCCC-HHHHHHCCCChhHHHHHHH------------HHHHHHHHH----HHHcCCCEEEEeeecchhhCCCHH
Confidence 67899999995 2222444568888998876 224444444 44579998766 333
Q ss_pred hHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcCc
Q 020010 186 EADDVIATLVGQ-------VLQKGYRAVVASPDKDFKQ 216 (332)
Q Consensus 186 EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~Q 216 (332)
|=++++.-+... ..+.|.++. +.+|.|++.
T Consensus 78 Ev~~lm~L~~~~l~~~~~~~~~~~iri~-~iG~~~~Lp 114 (243)
T PRK14829 78 EVRFLMGFSRDVIHRRREQMDEWGVRVR-WSGRRPRLW 114 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCcEEE-EEechhhCC
Confidence 666665544322 233454444 346777663
No 85
>cd00431 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function.
Probab=66.19 E-value=9.7 Score=32.39 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=38.8
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..|+..+..-|.++|=++.+-+..+...|++|+|++
T Consensus 100 ~l~~~L~~~~i~~vil~G~~t~~CV~~T~~~a~~~G~~v~vi~ 142 (161)
T cd00431 100 DLDELLRERGIDTLVVCGIATDICVLATARDALDLGYRVIVVE 142 (161)
T ss_pred CHHHHHHHCCCCEEEEEecCcChhHHHHHHHHHHCCCEEEEeh
Confidence 4667788889999999999999999999999999999999886
No 86
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.95 E-value=2.7 Score=38.67 Aligned_cols=34 Identities=24% Similarity=0.373 Sum_probs=23.2
Q ss_pred ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 249 DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 249 ~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
+|+++.. .+..|| ..-+-.| ||||+|||.+++-+
T Consensus 95 ~~~~l~~-aI~~~D-~~~L~~i----pGIGkKtAerIilE 128 (203)
T PRK14602 95 RPDDLRR-LVAEED-VAALTRV----SGIGKKTAQHIFLE 128 (203)
T ss_pred CHHHHHH-HHHhCC-HHHHhcC----CCcCHHHHHHHHHH
Confidence 4554443 233444 5677788 99999999999743
No 87
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=65.18 E-value=6.5 Score=33.12 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=18.6
Q ss_pred CCccHHHHHHHHHh------cCCHHHHHH
Q 020010 275 PGFGRKTALKLLKK------HGSLENLLN 297 (332)
Q Consensus 275 ~GIG~KTA~kLL~~------ygsle~il~ 297 (332)
||||+++|.++|.. |.|+|++..
T Consensus 74 pGIG~~~A~~Ii~~R~~~g~f~s~eeL~~ 102 (120)
T TIGR01259 74 PGIGPAKAKAIIEYREENGAFKSVDDLTK 102 (120)
T ss_pred CCCCHHHHHHHHHHHHhcCCcCCHHHHHc
Confidence 99999999999987 456777743
No 88
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=65.11 E-value=8.3 Score=31.73 Aligned_cols=37 Identities=24% Similarity=0.419 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCC
Q 020010 186 EADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQ 229 (332)
Q Consensus 186 EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~ 229 (332)
-+|.+|+..|.. .| ..++|.|+|+.++. .+.+++|..
T Consensus 105 ~~D~~i~a~A~~---~~--~~lvT~D~~f~~~~--~~~i~~P~~ 141 (142)
T TIGR00028 105 VTDAHLAALARE---HG--AELVTFDRGFARFA--GIRWRDPLT 141 (142)
T ss_pred chHHHHHHHHHH---cC--CEEEecCCCccccC--CCeeeCCCC
Confidence 478888888764 34 46779999986553 467777753
No 89
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=64.44 E-value=8.9 Score=28.67 Aligned_cols=23 Identities=30% Similarity=0.456 Sum_probs=18.2
Q ss_pred CCccHHHHHHHHHh---cC---CHHHHHH
Q 020010 275 PGFGRKTALKLLKK---HG---SLENLLN 297 (332)
Q Consensus 275 ~GIG~KTA~kLL~~---yg---sle~il~ 297 (332)
||||+++|.++|.. +| +++++..
T Consensus 23 pgig~~~a~~Il~~R~~~g~~~s~~dL~~ 51 (69)
T TIGR00426 23 NGVGLKKAEAIVSYREEYGPFKTVEDLKQ 51 (69)
T ss_pred CCCCHHHHHHHHHHHHHcCCcCCHHHHHc
Confidence 89999999999987 66 5566543
No 90
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.22 E-value=6.6 Score=35.77 Aligned_cols=35 Identities=26% Similarity=0.485 Sum_probs=24.5
Q ss_pred CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 248 CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 248 v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
++|+++.. .+..|| ..-+-.+ ||||+|||.+++-+
T Consensus 93 ~~~~el~~-aI~~~D-~~~L~~v----pGIGkKtAerIilE 127 (188)
T PRK14606 93 EDAETLVT-MIASQD-VEGLSKL----PGISKKTAERIVME 127 (188)
T ss_pred CCHHHHHH-HHHhCC-HHHHhhC----CCCCHHHHHHHHHH
Confidence 35666554 345566 4566677 99999999999743
No 91
>PRK11440 putative hydrolase; Provisional
Probab=64.06 E-value=13 Score=33.00 Aligned_cols=43 Identities=12% Similarity=0.156 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..||..+..-|.++|=++-+-++.+...|++|+|++
T Consensus 111 ~L~~~L~~~gi~~lii~Gv~T~~CV~~Ta~~A~~~gy~v~vv~ 153 (188)
T PRK11440 111 DLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAE 153 (188)
T ss_pred CHHHHHHHCCCCEEEEeeechhHHHHHHHHHHHHCCCEEEEec
Confidence 3566788899999999999999999999999999999999886
No 92
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=62.90 E-value=65 Score=31.21 Aligned_cols=66 Identities=15% Similarity=0.211 Sum_probs=43.1
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec-----CCc-----
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI-----EGH----- 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~-----~g~----- 185 (332)
|.||++++||. +---|+.-.+...+||... +.+.+.++++. .+||.++.+ +++
T Consensus 42 P~HVAiImDGN-rRwAk~~g~~~~~GH~~G~------------~~l~~i~~~c~----~lGIk~lTvYaFS~EN~~R~~~ 104 (275)
T PRK14835 42 PRHLGLILDGN-RRFARALGLQREMGHEFGV------------QKAYEVLEWCL----ELGIPTVTIWVFSTDNFSRSPA 104 (275)
T ss_pred CCEEEEEecCc-hHHHHHCCCCHHHHHHHHH------------HHHHHHHHHHH----HcCCCEEEEEEEEccccCCCHH
Confidence 67899999995 2222555577788888876 33444455544 468886544 555
Q ss_pred hHHHHHHHHHHHH
Q 020010 186 EADDVIATLVGQV 198 (332)
Q Consensus 186 EADDvIAtLa~~~ 198 (332)
|-+.++.-+....
T Consensus 105 EV~~Lm~L~~~~l 117 (275)
T PRK14835 105 EVETLMNLFEREA 117 (275)
T ss_pred HHHHHHHHHHHHH
Confidence 8888877665543
No 93
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=61.75 E-value=11 Score=33.76 Aligned_cols=49 Identities=14% Similarity=0.209 Sum_probs=35.5
Q ss_pred HHHhcCCCcEEecCCchHHHHHHHHHHHHHh--CCCeEEEEcCCCCcCccCC
Q 020010 170 DVLGKCNVPVVKIEGHEADDVIATLVGQVLQ--KGYRAVVASPDKDFKQLIS 219 (332)
Q Consensus 170 elL~~~gi~~i~~~g~EADDvIAtLa~~~~~--~g~~v~IvS~DKDl~QLv~ 219 (332)
+.|...|+..+...| -.|=-|+.-|..... +=+.++++|+|.||..|+.
T Consensus 73 ~~l~~~Gf~pv~~kG-~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~ 123 (160)
T TIGR00288 73 EAVVNQGFEPIIVAG-DVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVIN 123 (160)
T ss_pred HHHHHCCceEEEecC-cccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHH
Confidence 456667888766777 566667766665542 3367899999999999974
No 94
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=61.28 E-value=5.8 Score=42.74 Aligned_cols=44 Identities=30% Similarity=0.471 Sum_probs=32.6
Q ss_pred CcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhc-----ccCchHHHHHHHHhH
Q 020010 269 GIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVR-----TVGRDYAQEALTKHA 317 (332)
Q Consensus 269 GI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~-----~~~~~~~~~~L~~~~ 317 (332)
|| +.||+++|..|.+.|+|+++++++..+. ..| ..+.+.+.+..
T Consensus 515 GI----r~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG-~~vA~si~~ff 563 (667)
T COG0272 515 GI----RHVGETTAKSLARHFGTLEALLAASEEELASIPGIG-EVVARSIIEFF 563 (667)
T ss_pred CC----chhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchh-HHHHHHHHHHH
Confidence 77 9999999999999999999999865431 122 34555666543
No 95
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=60.97 E-value=37 Score=33.23 Aligned_cols=82 Identities=13% Similarity=0.025 Sum_probs=49.2
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCc----------
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGH---------- 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~---------- 185 (332)
+.||++++||. +---|..-.+...+||... +.+.+.+++| ..+||+++..-.+
T Consensus 68 P~HVAiIMDGN-rRwAk~~gl~~~~GH~~G~------------~~l~~v~~~c----~~lGI~~lTvYaFStEN~kR~~~ 130 (296)
T PRK14827 68 PNHVAIVMDGN-GRWATQRGLARTEGHKMGE------------AVVIDIACGA----IELGIKWLSLYAFSTENWKRSPE 130 (296)
T ss_pred CCeEEEeccCc-hHHHHHCCCCHhHHHHHHH------------HHHHHHHHHH----HHcCCCEEEEeeecchhhcCCHH
Confidence 67899999996 3333445568888998876 2244444444 4479998876444
Q ss_pred hHHHHHHHHHH-------HHHhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVG-------QVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~-------~~~~~g~~v~IvS~DKDl~ 215 (332)
|=+.++.-+.. ...+.|.++.+ .+|.+.+
T Consensus 131 EV~~Lm~L~~~~l~~~~~~~~~~~irir~-iG~~~~L 166 (296)
T PRK14827 131 EVRFLMGFNRDVVRRRRDNLNKMGVRIRW-VGSRPRL 166 (296)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCcEEEE-EechhhC
Confidence 76666554432 23344555544 4566654
No 96
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=60.18 E-value=8.7 Score=33.70 Aligned_cols=24 Identities=29% Similarity=0.577 Sum_probs=19.3
Q ss_pred CCccHHHHHHHHH------hcCCHHHHHHH
Q 020010 275 PGFGRKTALKLLK------KHGSLENLLNA 298 (332)
Q Consensus 275 ~GIG~KTA~kLL~------~ygsle~il~~ 298 (332)
||||+|+|.+++. .|.|+|++..-
T Consensus 103 pgIG~~kA~aIi~yRe~~G~f~sv~dL~~v 132 (149)
T COG1555 103 PGIGPKKAQAIIDYREENGPFKSVDDLAKV 132 (149)
T ss_pred CCCCHHHHHHHHHHHHHcCCCCcHHHHHhc
Confidence 8999999999985 35688887654
No 97
>TIGR03614 RutB pyrimidine utilization protein B. RL Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.
Probab=59.70 E-value=15 Score=33.79 Aligned_cols=43 Identities=12% Similarity=0.127 Sum_probs=39.4
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..||..+..-|..+|=++-+-++.+...|++|+|++
T Consensus 141 ~L~~~Lr~~gI~~lvi~Gv~T~~CV~sTar~A~~~Gy~v~vv~ 183 (226)
T TIGR03614 141 PLDSMLRARGIRNLVFTGIATNVCVESTLRDGFHLEYFGVVLE 183 (226)
T ss_pred CHHHHHHHCCCCEEEEeccCccHhHHHHHHHHHHCCCEEEEec
Confidence 4677888999999999999999999999999999999999986
No 98
>cd01013 isochorismatase Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems. Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria.
Probab=59.51 E-value=13 Score=33.70 Aligned_cols=43 Identities=14% Similarity=0.084 Sum_probs=38.9
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..|+..+..-|.++|-++-+-|+.+...|++|+|++
T Consensus 132 ~L~~~Lr~~gi~~lii~Gv~T~~CV~~Ta~~A~~~Gy~v~vv~ 174 (203)
T cd01013 132 PLLERLKESGRDQLIITGVYAHIGCLSTAVDAFMRDIQPFVVA 174 (203)
T ss_pred CHHHHHHHcCCCEEEEEEeccChhHHHHHHHHHHCCCeEEEec
Confidence 4567788899999999999999999999999999999998876
No 99
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.35 E-value=9.9 Score=34.82 Aligned_cols=34 Identities=29% Similarity=0.482 Sum_probs=23.3
Q ss_pred ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 249 DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 249 ~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
+|+++... +-.|| ..-+-.| ||||+|||.+++-+
T Consensus 94 ~~~el~~a-I~~~D-~~~L~kv----pGIGkKtAerIilE 127 (195)
T PRK14604 94 TPDELQLA-IAGGD-VARLARV----PGIGKKTAERIVLE 127 (195)
T ss_pred CHHHHHHH-HHhCC-HHHHhhC----CCCCHHHHHHHHHH
Confidence 45555542 34455 4556677 99999999999754
No 100
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=58.39 E-value=37 Score=32.06 Aligned_cols=83 Identities=16% Similarity=0.208 Sum_probs=51.5
Q ss_pred CCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CC
Q 020010 115 HADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EG 184 (332)
Q Consensus 115 ~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g 184 (332)
-|.||++++||. +---|+.-.+.+.+|+... +.+.+.+++| ..+||+++.. |-
T Consensus 3 ~P~HVaiImDGN-rRwAk~~g~~~~~GH~~G~------------~~l~~i~~~~----~~lgIk~lTvYaFS~eN~~R~~ 65 (233)
T PRK14841 3 IPQHVAIIMDGN-GRWAKKRGLPRIKGHQRGA------------EVLHNTVKWS----LELGIKYLTAFSFSTENWKRPK 65 (233)
T ss_pred CCCEEEEEccCC-HHHHHHCCCchhhhHHHHH------------HHHHHHHHHH----HHcCCCEEEEEeeeHhhcCCCH
Confidence 367899999995 3333555578888888876 2344444444 4469987765 44
Q ss_pred chHHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 185 HEADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 185 ~EADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
-|=+.++.-+.... .+.|.++-+ .+|.+++
T Consensus 66 ~Ev~~Lm~L~~~~l~~~~~~~~~~~irvr~-iG~~~~L 102 (233)
T PRK14841 66 EEVEFLMDLFVQMIDREMELLRRERVRVRI-LGRKEGL 102 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCcEEEE-EeChhhC
Confidence 58888877665432 234555544 4466654
No 101
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=57.84 E-value=12 Score=35.54 Aligned_cols=26 Identities=42% Similarity=0.667 Sum_probs=23.6
Q ss_pred CCccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygsle~il~~~~ 300 (332)
|||+..-|..||.+||||+.|..+..
T Consensus 201 ~~VnKtda~~LL~~FgsLq~~~~AS~ 226 (254)
T KOG2841|consen 201 PGVNKTDAQLLLQKFGSLQQISNASE 226 (254)
T ss_pred CCCCcccHHHHHHhcccHHHHHhcCH
Confidence 88899999999999999999998754
No 102
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=57.50 E-value=40 Score=31.82 Aligned_cols=82 Identities=12% Similarity=0.174 Sum_probs=50.2
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|+.-.+.+.+||... +.+++.+++ +..+||+++.. |.-
T Consensus 7 P~HVAiImDGN-rRwAk~~gl~~~~GH~~G~------------~~~~~i~~~----c~~~GI~~lT~YaFS~EN~~Rp~~ 69 (230)
T PRK14837 7 PSHVGIIMDGN-RRWALKKGLSFFEGHKEGL------------KRAKEIVKH----SLKLGIKYLSLYVFSTENWNRTDS 69 (230)
T ss_pred CCeEEEEccCC-HHHHHHCCCchhhhHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEeehhhcCCCHH
Confidence 67899999995 2222444468888998876 234444444 44579987765 455
Q ss_pred hHHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
|=+.++.-+.... .+.|.++. +.+|.|++
T Consensus 70 EV~~Lm~L~~~~l~~~~~~~~~~~irvr-~iGd~~~L 105 (230)
T PRK14837 70 EIEHLMFLIADYLSSEFNFYKKNNIKII-VSGDIESL 105 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCcEEE-EEcChhhC
Confidence 7777766554322 23455554 45677765
No 103
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.34 E-value=10 Score=34.75 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=23.7
Q ss_pred CChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 248 CDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 248 v~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
++|+++... +-.|| ..-+-.| ||||+|||.+++-+
T Consensus 92 ~~~~~l~~a-I~~~D-~~~L~kv----pGIGkKtAerIilE 126 (197)
T PRK14603 92 LPPALLARA-LLEGD-ARLLTSA----SGVGKKLAERIALE 126 (197)
T ss_pred CCHHHHHHH-HHhCC-HHHHhhC----CCCCHHHHHHHHHH
Confidence 356666542 44555 3455667 99999999999844
No 104
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=57.01 E-value=11 Score=34.34 Aligned_cols=21 Identities=43% Similarity=0.675 Sum_probs=16.3
Q ss_pred cCCCCCCCCcccCCCCccHHHHHHHH
Q 020010 261 GDDVDGVPGIQHVVPGFGRKTALKLL 286 (332)
Q Consensus 261 GD~sDNIPGI~~~~~GIG~KTA~kLL 286 (332)
||. .-+-.| ||||+|||.+++
T Consensus 104 ~d~-~~L~~i----pGiGkKtAerIi 124 (191)
T TIGR00084 104 EEV-KALVKI----PGVGKKTAERLL 124 (191)
T ss_pred CCH-HHHHhC----CCCCHHHHHHHH
Confidence 552 345567 999999999997
No 105
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
Probab=56.45 E-value=18 Score=31.11 Aligned_cols=44 Identities=18% Similarity=0.249 Sum_probs=38.6
Q ss_pred HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 166 QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 166 ~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
+.+.++|+..|+..+..-|.++|=++..-+..+.+.|++|+|++
T Consensus 88 t~l~~~L~~~gi~~viv~G~~td~CV~~Ta~~a~~~g~~v~vi~ 131 (155)
T cd01014 88 TDLEEWLREAGIDHLVICGAMTEMCVDTTVRSAFDLGYDVTVVA 131 (155)
T ss_pred CCHHHHHHHCCCCEEEEEeeccchhHHHHHHHHHHCCCcEEEec
Confidence 34567788899999999999999999999999999999999864
No 106
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=56.14 E-value=47 Score=32.04 Aligned_cols=83 Identities=17% Similarity=0.259 Sum_probs=49.3
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.+|++++||. +..-|+.-++.-++|++.. ..|.+ +-+++..+||+.+.+ +..
T Consensus 37 P~HVaFIMDGN-RR~AKk~~L~~~~GH~aGf------------~~l~~----ile~C~~lGI~~vT~fAFSieNFkRs~e 99 (271)
T KOG1602|consen 37 PRHVAFIMDGN-RRYAKKRGLETSEGHEAGF------------EALKE----ILELCKELGIKEVTVFAFSIENFKRSPE 99 (271)
T ss_pred cceeEEEecCc-hHHHHhcCCCcccchHHHH------------HHHHH----HHHHHHHcCCcEEEEEEEehhhhCCCHH
Confidence 56699999996 3333455556677777765 22333 444555579998655 445
Q ss_pred hHHHHHHHHHHHH----------HhCCCeEEEEcCCCCcCc
Q 020010 186 EADDVIATLVGQV----------LQKGYRAVVASPDKDFKQ 216 (332)
Q Consensus 186 EADDvIAtLa~~~----------~~~g~~v~IvS~DKDl~Q 216 (332)
|-|-++.-.-.+. .+.|.++. +-+|.++++
T Consensus 100 EVd~LM~L~~~k~~~~~~~~~~~~~~gvrir-iiGdlslL~ 139 (271)
T KOG1602|consen 100 EVDGLMDLALEKIERLLEQGEKLDKYGVRIR-VIGDLSLLP 139 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhcCeEEE-EEcchhhCC
Confidence 7777765332221 12344444 457887776
No 107
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=55.93 E-value=10 Score=31.92 Aligned_cols=26 Identities=38% Similarity=0.505 Sum_probs=20.7
Q ss_pred CCccHHHHHHHHHh-cCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKK-HGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il~~~~ 300 (332)
||||++++.+|-+. ..|.+++++..+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~ 27 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGD 27 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCC
Confidence 79999999998433 348999998765
No 108
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=54.52 E-value=46 Score=31.38 Aligned_cols=65 Identities=11% Similarity=0.147 Sum_probs=43.4
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|..-.+...+||... +.+.+.+++|. .+||.++.. |.-
T Consensus 5 P~HVaiImDGN-rRwA~~~gl~~~~GH~~G~------------~~l~~~~~~c~----~~gI~~lTvyaFS~eN~~R~~~ 67 (233)
T PRK14833 5 LKHLAIIMDGN-GRWAKLRGKARAAGHKKGV------------KTLREITIWCA----NHKLECLTLYAFSTENWKRPKS 67 (233)
T ss_pred CCeEEEEccCC-HHHHHHCCCChhhhHHHHH------------HHHHHHHHHHH----HcCCCEEEEeecchhhcCcCHH
Confidence 67899999995 3333555678888999876 23444444444 468887765 445
Q ss_pred hHHHHHHHHHHH
Q 020010 186 EADDVIATLVGQ 197 (332)
Q Consensus 186 EADDvIAtLa~~ 197 (332)
|=++++.-+...
T Consensus 68 Ev~~Lm~L~~~~ 79 (233)
T PRK14833 68 EVDFLMKLLKKY 79 (233)
T ss_pred HHHHHHHHHHHH
Confidence 778887766554
No 109
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=52.76 E-value=11 Score=32.87 Aligned_cols=41 Identities=27% Similarity=0.428 Sum_probs=32.4
Q ss_pred CCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCC
Q 020010 175 CNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISE 220 (332)
Q Consensus 175 ~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~ 220 (332)
...+++.. +-.|||.|-..|.+ .| +++|+|+|+.+.+-+..
T Consensus 75 er~~~~~~-~~~aDe~i~~~a~~---~~-~~iVaTnD~eLk~rlr~ 115 (136)
T COG1412 75 ERLECIHK-GRYADECLLEAALK---HG-RYIVATNDKELKRRLRE 115 (136)
T ss_pred hccCcccc-CCChHHHHHHHHHH---cC-CEEEEeCCHHHHHHHHH
Confidence 35677776 56899999988875 33 79999999999997764
No 110
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional
Probab=52.63 E-value=53 Score=31.21 Aligned_cols=82 Identities=12% Similarity=0.131 Sum_probs=50.0
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|..-.+...+||... +.+.+.+++ +..+||.++.. |--
T Consensus 11 P~HVAiImDGN-rRwA~~~gl~~~~GH~~G~------------~~l~~i~~~----~~~~gI~~lT~YaFS~EN~kR~~~ 73 (242)
T PRK14838 11 PQHIAIIMDGN-GRWAKERGKERSFGHQAGA------------ETVHIITEE----AARLGVKFLTLYTFSTENWNRPSD 73 (242)
T ss_pred CCEEEEeccCC-HHHHHHCCCCHHHHHHHHH------------HHHHHHHHH----HHHcCCCEEEEEeechhhcCCCHH
Confidence 67899999996 3333455568888888876 223444444 44578987755 445
Q ss_pred hHHHHHHHHHHHHH-----hCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQVL-----QKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~~~-----~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+..... ..|.++.+ .+|.|++
T Consensus 74 Ev~~Lm~l~~~~l~~~~~~~~~irir~-iG~~~~L 107 (242)
T PRK14838 74 EVAALMSLLLDSIEEETFMKNNIRFRI-IGDIAKL 107 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCcEEEE-EeChhhC
Confidence 77777776655432 23444433 4566653
No 111
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=52.48 E-value=49 Score=31.43 Aligned_cols=82 Identities=16% Similarity=0.165 Sum_probs=49.7
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|+.-.+...+||... +.+.+.+++| ..+||+++.. +--
T Consensus 9 P~HVaiImDGN-rRwAk~~gl~~~~GH~~G~------------~~l~~i~~~c----~~lgI~~vTvYaFS~eN~~R~~~ 71 (241)
T PRK14842 9 PAHIAVIMDGN-GRWAESQGKKRSEGHREGA------------NAIDRLMDAS----LEYGLKNISLYAFSTENWKRPIT 71 (241)
T ss_pred CCeEEEEcCCC-HHHHHHCCCChhHhHHHHH------------HHHHHHHHHH----HHcCCCEEEEEEeehhhcCCCHH
Confidence 67799999996 3223444568888998876 2244444444 4469987765 335
Q ss_pred hHHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+.... .+.|.++. +.+|.+++
T Consensus 72 EV~~Lm~L~~~~l~~~~~~~~~~~irv~-~iG~~~~L 107 (241)
T PRK14842 72 EIRSIFGLLVEFIETRLDTIHARGIRIH-HSGSRKKL 107 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEE-EEeChhhC
Confidence 7777776555432 23344443 45666654
No 112
>PLN02621 nicotinamidase
Probab=52.45 E-value=23 Score=31.80 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=38.3
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..|+..+..-|.++|=++-+-++.+...|++|+|++
T Consensus 117 ~L~~~L~~~gi~~lvi~Gv~T~~CV~~Ta~~a~~~gy~v~v~~ 159 (197)
T PLN02621 117 RLEERLRKIGVKEVIVTGVMTNLCCETTAREAFVRGFRVFFST 159 (197)
T ss_pred cHHHHHHHCCCCEEEEEecccchhHHHHHHHHHHCCCEEEEec
Confidence 4566788899999999999999999999999999999998875
No 113
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=52.02 E-value=46 Score=31.10 Aligned_cols=82 Identities=13% Similarity=0.154 Sum_probs=48.9
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
+.||++++||. +---|..-.+...+||... +.+.+.+++ +..+||+++.. |.-
T Consensus 1 P~HvaiImDGN-rRwA~~~gl~~~~GH~~G~------------~~~~~i~~~----~~~~gI~~lTvyaFS~eN~~R~~~ 63 (221)
T cd00475 1 PKHVAFIMDGN-RRWAKQRGMDRIEGHKAGA------------EKLRDILRW----CLELGVKEVTLYAFSTENWKRPKE 63 (221)
T ss_pred CCeEEEecCCC-HHHHHHCCCChhHhHHHHH------------HHHHHHHHH----HHHcCCCEEEEEeechhhhCcCHH
Confidence 46789999995 2222444568888888876 223344444 44579988765 334
Q ss_pred hHHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+.... ...|.++.+ .+|.+++
T Consensus 64 EV~~Lm~l~~~~l~~~~~~~~~~~i~vr~-iGd~~~L 99 (221)
T cd00475 64 EVDFLMELFRDVLRRILKELEKLGVRIRI-IGDLSLL 99 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCcEEEE-EeChhhC
Confidence 7777776655432 233445544 4566643
No 114
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=51.08 E-value=13 Score=27.01 Aligned_cols=21 Identities=38% Similarity=0.675 Sum_probs=17.1
Q ss_pred CCCCCCcccCCCCccHHHHHHHHHh
Q 020010 264 VDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 264 sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
.|-+-.| +|||+++|.+|+..
T Consensus 37 ~~~L~~i----~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 37 PEELAEI----PGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHTS----TTSSHHHHHHHHHH
T ss_pred HHHHhcC----CCCCHHHHHHHHHH
Confidence 3556677 99999999999865
No 115
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=50.42 E-value=67 Score=30.62 Aligned_cols=82 Identities=17% Similarity=0.212 Sum_probs=48.5
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
+.||++++||. +---|+.-.+...+||... +.+.+-+.+ +..+||+++.. +.-
T Consensus 21 P~HVaiImDGN-rRwA~~~gl~~~~GH~~G~------------~~l~~i~~~----c~~~GI~~vT~yaFS~eN~kR~~~ 83 (249)
T PRK14831 21 PKHVAVIMDGN-GRWAKRRGLPRIMGHRRGV------------DALKDLLRC----CKDWGIGALTAYAFSTENWSRPLE 83 (249)
T ss_pred CCeEEEecCCc-HHHHHHCCCchhhhHHHHH------------HHHHHHHHH----HHHcCCCEEEEeecchhhhCcCHH
Confidence 67899999995 3333555567888988876 234444444 44579988765 334
Q ss_pred hHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQ-------VLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+... ..+.|.++.+ .+|.+++
T Consensus 84 Ev~~Lm~L~~~~l~~~~~~~~~~~iri~~-iG~~~~L 119 (249)
T PRK14831 84 EVNFLMTLFERVLRRELEELMEENVRIRF-VGDLDPL 119 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCcEEEE-EechhhC
Confidence 666665544332 2334444433 4566654
No 116
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
Probab=50.04 E-value=17 Score=31.26 Aligned_cols=44 Identities=20% Similarity=0.364 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 166 QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 166 ~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
..+.++|+..|+..+..-|+++|=++-+-++.+...|++|+|++
T Consensus 101 t~L~~~L~~~gi~~vil~G~~t~~CV~~Ta~~a~~~g~~v~v~~ 144 (174)
T PF00857_consen 101 TDLDEILRKRGIDTVILCGVATDVCVLATARDAFDRGYRVIVVE 144 (174)
T ss_dssp SSHHHHHHHTTESEEEEEEESTTTHHHHHHHHHHHTT-EEEEEE
T ss_pred ccccccccccccceEEEcccccCcEEehhHHHHHHCCCEEEEEC
Confidence 34567788899999999999999999999999999999998875
No 117
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=49.97 E-value=73 Score=30.49 Aligned_cols=64 Identities=17% Similarity=0.279 Sum_probs=39.2
Q ss_pred CCcEEEEEcCCCCchhhhhhchhH-HhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CC
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSY-KAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EG 184 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~Y-KanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g 184 (332)
|.||++++||. +---|+.-.+.. .+||... +.+.+.+++ +..+||+++.. +.
T Consensus 27 P~HvAiImDGN-rRwA~~~gl~~~~~GH~~G~------------~~l~~~~~~----~~~~gIk~lTvYaFS~eN~~R~~ 89 (256)
T PRK14828 27 PGHVGIIVDGN-RRWARKAGFTDVSQGHRAGA------------AKIGEFLGW----CDETDVNVVTLYLLSTDNLGRPS 89 (256)
T ss_pred CCEEEEEecCC-hHHHHHcCCCchHHHHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEEEhhhcCCCH
Confidence 67799999995 322344456777 7888766 224444444 44579987765 33
Q ss_pred chHHHHHHHHHH
Q 020010 185 HEADDVIATLVG 196 (332)
Q Consensus 185 ~EADDvIAtLa~ 196 (332)
-|=+.++.-+..
T Consensus 90 ~Ev~~Lm~L~~~ 101 (256)
T PRK14828 90 EELNPLLDIIED 101 (256)
T ss_pred HHHHHHHHHHHH
Confidence 466666654443
No 118
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=49.89 E-value=72 Score=30.44 Aligned_cols=82 Identities=20% Similarity=0.257 Sum_probs=47.7
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
+.||++++||. +---|..-.+...+||... +.+.+.+++ +..+||+++.. |--
T Consensus 15 P~HVAiImDGN-rRwAk~~g~~~~~GH~~G~------------~~l~~i~~~----c~~lgI~~lTvYaFS~eN~~R~~~ 77 (249)
T PRK14834 15 PRHVAIIMDGN-GRWAKARGLPRAAGHRAGV------------EALRRVVRA----AGELGIGYLTLFAFSSENWSRPAS 77 (249)
T ss_pred CCeEEEEecCc-hHHHHHCCCchhhhHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEEeccccCCCHH
Confidence 67799999995 3223444467888888876 234444444 44568987654 234
Q ss_pred hHHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
|-+.++.-+.... .+.|.++.+ .+|-+++
T Consensus 78 EV~~Lm~L~~~~l~~~~~~~~~~~iri~v-iGd~~~L 113 (249)
T PRK14834 78 EVSDLFGLLRLFIRRDLAELHRNGVRVRV-IGERAGL 113 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCcEEEE-EcChhhC
Confidence 6777665443322 234444443 4566554
No 119
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=47.90 E-value=11 Score=34.72 Aligned_cols=20 Identities=35% Similarity=0.705 Sum_probs=15.8
Q ss_pred CCCCCcccCCCCccHHHHHHHHHh
Q 020010 265 DGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 265 DNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
..+-.+ ||||+|||.+++-+
T Consensus 108 ~~L~k~----PGIGkKtAerivle 127 (201)
T COG0632 108 KALSKI----PGIGKKTAERIVLE 127 (201)
T ss_pred HhhhcC----CCCCHHHHHHHHHH
Confidence 345566 99999999999755
No 120
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.79 E-value=9.3 Score=35.25 Aligned_cols=11 Identities=55% Similarity=0.975 Sum_probs=10.3
Q ss_pred CCccHHHHHHH
Q 020010 275 PGFGRKTALKL 285 (332)
Q Consensus 275 ~GIG~KTA~kL 285 (332)
||||||+|.++
T Consensus 18 PGvG~KsA~R~ 28 (198)
T COG0353 18 PGVGPKSAQRL 28 (198)
T ss_pred CCCChhHHHHH
Confidence 99999999987
No 121
>COG1335 PncA Amidases related to nicotinamidase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=46.43 E-value=37 Score=30.19 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+..+|+..||..+..-|..+|-++-+-++.+...|+++++++
T Consensus 123 ~L~~~Lr~~~i~~l~v~G~~td~CV~~T~~~A~~~gy~v~v~~ 165 (205)
T COG1335 123 DLDDILRNLGIDTVVVCGIATDICVLATARDAFDLGYQVTLVE 165 (205)
T ss_pred CHHHHHHHCCCCEEEEeeeehhHHHHHHHHHHHHCCCeEEEeh
Confidence 3677888899999999999999999999999999999998876
No 122
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=46.23 E-value=21 Score=29.10 Aligned_cols=22 Identities=32% Similarity=0.288 Sum_probs=16.3
Q ss_pred CCccHHHHHHHHHh-cCCHHHHH
Q 020010 275 PGFGRKTALKLLKK-HGSLENLL 296 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il 296 (332)
||||+++|..|..- +.|++++.
T Consensus 18 P~IG~a~a~DL~~LGi~s~~~L~ 40 (93)
T PF11731_consen 18 PNIGKATAEDLRLLGIRSPADLK 40 (93)
T ss_pred CCccHHHHHHHHHcCCCCHHHHh
Confidence 99999999999753 44555543
No 123
>PRK11609 nicotinamidase/pyrazinamidase; Provisional
Probab=45.21 E-value=32 Score=31.07 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=38.9
Q ss_pred HHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 167 FILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 167 ~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
.+.++|+..||..+..-|...|=++-+-++.+...|++|+|++
T Consensus 132 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~dA~~~gy~v~v~~ 174 (212)
T PRK11609 132 ALDDWLREHGITELIVMGLATDYCVKFTVLDALALGYQVNVIT 174 (212)
T ss_pred cHHHHHHHcCCCEEEEEEeccCHHHHHHHHHHHHCCCEEEEEe
Confidence 5667888999999999999999999999999999999999876
No 124
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=45.18 E-value=22 Score=33.93 Aligned_cols=90 Identities=14% Similarity=0.229 Sum_probs=52.8
Q ss_pred HHHHHhcCCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec-----
Q 020010 108 LFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----- 182 (332)
Q Consensus 108 ~ll~~i~~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----- 182 (332)
++++.-.-|.||++++||. +---|+.-.+...+||... +.+.+.+. ++..+||+++..
T Consensus 7 ~~~~~~~~P~HVAiImDGN-rRwA~~~gl~~~~GH~~G~------------~~~~~iv~----~c~~~gI~~lTvYaFS~ 69 (253)
T PRK14836 7 MIPANENIPRHIAIIMDGN-GRWAKRRGKPRVEGHRAGV------------RAVRRTIE----FCLEKGIEMLTLFAFSS 69 (253)
T ss_pred cccccCCCCCeEEEecCCc-HHHHHHCCCchhhhHHHHH------------HHHHHHHH----HHHHcCCCEEehhHhhh
Confidence 3444433478899999995 2222444467788888876 22333444 444579987765
Q ss_pred -----CCchHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcC
Q 020010 183 -----EGHEADDVIATLVGQ-------VLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 183 -----~g~EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~ 215 (332)
+--|=+.++.-+... ..+.|.++. +.+|.|++
T Consensus 70 eN~~R~~~EV~~Lm~l~~~~l~~~~~~~~~~~irv~-viG~~~~L 113 (253)
T PRK14836 70 ENWLRPADEVSALMELFLKALDREVDKLHRNGIRVR-FIGDRSRL 113 (253)
T ss_pred hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEE-EEeccccC
Confidence 334667766655443 223455544 45677775
No 125
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=44.61 E-value=1.1e+02 Score=26.00 Aligned_cols=56 Identities=7% Similarity=0.157 Sum_probs=39.0
Q ss_pred hHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeH
Q 020010 164 SHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTL 239 (332)
Q Consensus 164 ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~ 239 (332)
++...+++++.||+.....+- ..|+|-+.|+++. +-.+.|+++... +...++..+.
T Consensus 10 ~~~~mkkmMk~MGi~~~eidV------------------~~ViIk~~~k~iv-f~~p~V~~m~~~-G~~tYqI~G~ 65 (116)
T TIGR00264 10 MLKQMQKMMKQMGMEMEDLDV------------------EEVIIVFDDEEWI-FENPKVQVMDIL-GVKTYQITGK 65 (116)
T ss_pred cHHHHHHHHHHcCCCcccccc------------------EEEEEEeCCceEE-EecCeeEEEecC-CcEEEEEecc
Confidence 566788889999987433221 3689999999998 888899888754 3233444443
No 126
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=44.57 E-value=15 Score=33.51 Aligned_cols=22 Identities=36% Similarity=0.744 Sum_probs=16.4
Q ss_pred ccCCCCCCCCcccCCCCccHHHHHHHH
Q 020010 260 VGDDVDGVPGIQHVVPGFGRKTALKLL 286 (332)
Q Consensus 260 ~GD~sDNIPGI~~~~~GIG~KTA~kLL 286 (332)
.|| ..-+-.| ||||+|||.+++
T Consensus 104 ~~D-~~~L~~v----pGIGkKtAerIi 125 (194)
T PRK14605 104 SGN-AELLSTI----PGIGKKTASRIV 125 (194)
T ss_pred hCC-HHHHHhC----CCCCHHHHHHHH
Confidence 465 3345667 999999999954
No 127
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=43.71 E-value=15 Score=29.83 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=20.7
Q ss_pred chHHHHHHHHHHHHHhCCCeEEEEcCCCCcCc
Q 020010 185 HEADDVIATLVGQVLQKGYRAVVASPDKDFKQ 216 (332)
Q Consensus 185 ~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~Q 216 (332)
-..|+.+..+|.. +..-+|+|+|||++-
T Consensus 86 D~~D~~~l~~A~~----~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 86 DKKDNKFLNTAYA----SKANALITGDTDLLV 113 (114)
T ss_pred CchhHHHHHHHHh----cCCCEEEECCHHHhh
Confidence 3668888877764 445589999999874
No 128
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=43.60 E-value=84 Score=29.56 Aligned_cols=81 Identities=15% Similarity=0.212 Sum_probs=48.6
Q ss_pred CcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCch
Q 020010 117 DPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGHE 186 (332)
Q Consensus 117 ~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~E 186 (332)
+||++++||. +---|+.-.+...+||... +.+++.+++ +..+||+++.. |--|
T Consensus 1 ~HVAiImDGN-rRwAk~~gl~~~~GH~~G~------------~~~~~v~~~----c~~~GI~~lT~yaFStEN~~Rp~~E 63 (226)
T TIGR00055 1 RHVAIIMDGN-GRWAKKKGKPRAYGHKAGV------------KSLRRILRW----CANLGVECLTLYAFSTENWKRPKEE 63 (226)
T ss_pred CcEEEEcCCC-HHHHHHCCCChhHhHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEeehhhcCcCHHH
Confidence 3688999996 2222444468888999876 234444444 44579987765 4457
Q ss_pred HHHHHHHHHHHH-------HhCCCeEEEEcCCCCcC
Q 020010 187 ADDVIATLVGQV-------LQKGYRAVVASPDKDFK 215 (332)
Q Consensus 187 ADDvIAtLa~~~-------~~~g~~v~IvS~DKDl~ 215 (332)
=+.++.-+.... .+.|.++-+ -+|.|++
T Consensus 64 V~~Lm~L~~~~l~~~~~~~~~~~irvr~-iGd~~~L 98 (226)
T TIGR00055 64 VDFLMELFEKKLDREVKELHRYNVRIRI-IGDLSLL 98 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEE-EeChhhC
Confidence 777776655433 234555544 4566653
No 129
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=43.54 E-value=21 Score=34.28 Aligned_cols=26 Identities=35% Similarity=0.455 Sum_probs=23.0
Q ss_pred CCccHHHHHHHHHh-cCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLKK-HGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il~~~~ 300 (332)
||||+++|.+|.+. |.|++++..+-.
T Consensus 5 ~gig~~~~~~L~~~Gi~ti~dl~~~~~ 31 (310)
T TIGR02236 5 PGVGPATAEKLREAGYDTFEAIAVASP 31 (310)
T ss_pred CCCCHHHHHHHHHcCCCCHHHHHcCCH
Confidence 99999999999998 999999976533
No 130
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=43.38 E-value=28 Score=30.10 Aligned_cols=88 Identities=11% Similarity=0.040 Sum_probs=53.2
Q ss_pred hHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCC-eEEEecCCCCCccEEeeHHHH
Q 020010 164 SHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISED-VQLVMPLQDLDRWSFYTLKHY 242 (332)
Q Consensus 164 ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~-v~v~~~~~~~~~~~~~~~~~v 242 (332)
++..+-.+|+.+|+.++...++ .|+-|..+|+. ..=+|+|.|+|+....... ..++....+ .. --..++
T Consensus 8 ~L~~Lar~LR~lG~Dt~~~~~~-~D~~il~~A~~-----e~RillTrd~~l~~~~~~~~~~~li~~~~--~~--~QL~ev 77 (147)
T PF01927_consen 8 MLGRLARWLRLLGYDTLYSRDI-DDDEILELARE-----EGRILLTRDRDLLKRRRVSGGVILIRSDD--PE--EQLREV 77 (147)
T ss_pred CHHHHHHHHHHCCCcEEEeCCC-ChHHHHHHhhh-----CCeEEEECCHHHHHHhhccCCEEEEcCCC--HH--HHHHHH
Confidence 3455677889999999988875 56666666653 3456889999999876543 112222111 00 113566
Q ss_pred HHHhCCCh--hHHHHhhhccc
Q 020010 243 IAQYNCDP--HSELSLRCIVG 261 (332)
Q Consensus 243 ~e~~Gv~P--~q~~d~~aL~G 261 (332)
.+.+|+.+ +.++.-|..++
T Consensus 78 ~~~~~l~~~~~~~~sRC~~CN 98 (147)
T PF01927_consen 78 LERFGLKLRLDPIFSRCPKCN 98 (147)
T ss_pred HHHcCCccccCCCCCccCCCC
Confidence 77888765 33344555554
No 131
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.25 E-value=13 Score=34.18 Aligned_cols=12 Identities=50% Similarity=0.886 Sum_probs=10.9
Q ss_pred CCccHHHHHHHH
Q 020010 275 PGFGRKTALKLL 286 (332)
Q Consensus 275 ~GIG~KTA~kLL 286 (332)
||||+|+|.++-
T Consensus 17 PGIG~KsA~RlA 28 (195)
T TIGR00615 17 PGIGPKSAQRLA 28 (195)
T ss_pred CCCCHHHHHHHH
Confidence 999999999884
No 132
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=43.17 E-value=33 Score=32.79 Aligned_cols=82 Identities=16% Similarity=0.169 Sum_probs=50.5
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
+.||++++||. +---|..-.+.+.+||... +.+.+.+++| ..+||+++.. |--
T Consensus 19 P~HVAiImDGN-rRwAk~~gl~~~~GH~~G~------------~~l~~i~~~c----~~~gI~~lTvyaFS~EN~~Rp~~ 81 (253)
T PRK14832 19 PQHIAVIMDGN-GRWATSQGLPRIAGHRQGA------------RTLKELLRCC----KDWGIKALTAYAFSTENWQRPIE 81 (253)
T ss_pred CCEEEEECCCC-HHHHHHCCCCHHHHHHHHH------------HHHHHHHHHH----HHcCCCEEEEEEeehhhcCCCHH
Confidence 67899999995 3333555578888999876 2344444444 4468987755 445
Q ss_pred hHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVGQ-------VLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+... ..+.|.++.+ .+|.|++
T Consensus 82 EV~~Lm~L~~~~l~~~~~~~~~~~irv~~-iGd~~~L 117 (253)
T PRK14832 82 EVDFLMLLFERLLRRELAQMHREGVRISF-IGDLSAL 117 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCEEEE-EeCchhC
Confidence 888887765433 2233444444 4566653
No 133
>PRK00076 recR recombination protein RecR; Reviewed
Probab=42.84 E-value=14 Score=34.14 Aligned_cols=12 Identities=50% Similarity=0.886 Sum_probs=11.0
Q ss_pred CCccHHHHHHHH
Q 020010 275 PGFGRKTALKLL 286 (332)
Q Consensus 275 ~GIG~KTA~kLL 286 (332)
||||+|+|.++-
T Consensus 17 PGIG~KsA~Rla 28 (196)
T PRK00076 17 PGIGPKSAQRLA 28 (196)
T ss_pred CCCCHHHHHHHH
Confidence 999999999875
No 134
>PRK00254 ski2-like helicase; Provisional
Probab=42.69 E-value=28 Score=37.69 Aligned_cols=27 Identities=37% Similarity=0.566 Sum_probs=24.1
Q ss_pred CCCccHHHHHHHHHh-cCCHHHHHHHhh
Q 020010 274 VPGFGRKTALKLLKK-HGSLENLLNAAA 300 (332)
Q Consensus 274 ~~GIG~KTA~kLL~~-ygsle~il~~~~ 300 (332)
.||||+++|.+|++. |+|+++|.++-+
T Consensus 650 ipgig~~~~~~l~~~g~~s~~~i~~a~~ 677 (720)
T PRK00254 650 LPMIGRKRARALYNAGFRSIEDIVNAKP 677 (720)
T ss_pred CCCCCHHHHHHHHHccCCCHHHHHhCCH
Confidence 399999999999999 999999988643
No 135
>cd01011 nicotinamidase Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA).
Probab=42.51 E-value=41 Score=30.18 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 166 QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 166 ~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
..+.++|+..||..+..-|...|=++.+-++.+...|++|+|++
T Consensus 127 t~L~~~L~~~~i~~lii~G~~t~~CV~~T~~~a~~~g~~v~v~~ 170 (196)
T cd01011 127 TGLAEYLRERGIDRVDVVGLATDYCVKATALDALKAGFEVRVLE 170 (196)
T ss_pred hhHHHHHHHCCCCEEEEEEecccHHHHHHHHHHHHCCCEEEEec
Confidence 45677888899999999999999999999999999999999886
No 136
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=41.92 E-value=35 Score=32.40 Aligned_cols=84 Identities=17% Similarity=0.213 Sum_probs=50.8
Q ss_pred CCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CC
Q 020010 115 HADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EG 184 (332)
Q Consensus 115 ~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g 184 (332)
.+.||++++||. +---|+.-.+...+||... +.+.+.+++ +..+||+++.. +-
T Consensus 9 ~P~HVAiImDGN-rRwAk~~gl~~~~GH~~G~------------~~l~~i~~~----c~~~GI~~lTvYaFS~EN~~R~~ 71 (239)
T PRK14839 9 SGLHVAIIMDGN-GRWATARGLPRLAGHRAGV------------EAIRRVVEA----APDLGIGTLTLYAFSSDNWRRPA 71 (239)
T ss_pred CCCEEEEEcCCC-HHHHHHCCCCHHHHHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEechhhcCCCH
Confidence 477899999995 3333555568888998876 223344444 44579987765 33
Q ss_pred chHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcCc
Q 020010 185 HEADDVIATLVGQ-------VLQKGYRAVVASPDKDFKQ 216 (332)
Q Consensus 185 ~EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~Q 216 (332)
-|=+.++.-+... ..+.|.++. +-+|.|++.
T Consensus 72 ~EV~~Lm~L~~~~l~~~~~~~~~~~irvr-~iGd~~~Lp 109 (239)
T PRK14839 72 AEVGGLMRLLRAYLRNETERLARNGVRLT-VIGRRDRLP 109 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCEEE-EEeChhhCC
Confidence 4777776644432 233455544 456777643
No 137
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=40.90 E-value=1.2e+02 Score=28.91 Aligned_cols=82 Identities=17% Similarity=0.307 Sum_probs=46.7
Q ss_pred CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec----------CCc
Q 020010 116 ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI----------EGH 185 (332)
Q Consensus 116 ~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~----------~g~ 185 (332)
|.||++++||. +---|+.-.+...+||... +.+.+.+++ +..+||+.+.+ +--
T Consensus 23 P~HVAiImDGN-rRwAk~~gl~~~~Gh~~G~------------~~l~~~l~~----c~~~GI~~vTvYaFS~eN~~R~~~ 85 (251)
T PRK14830 23 PKHIAIIMDGN-GRWAKKRMLPRIAGHKAGM------------DTVKKITKA----ASELGVKVLTLYAFSTENWKRPKD 85 (251)
T ss_pred CCeEEEEecCc-hHHHHHCCCchhhhHHHHH------------HHHHHHHHH----HHHcCCCEEEEEEEehhhcCCCHH
Confidence 67899999995 2222444467778888765 223344444 44578986654 334
Q ss_pred hHHHHHHHHHH-------HHHhCCCeEEEEcCCCCcC
Q 020010 186 EADDVIATLVG-------QVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 186 EADDvIAtLa~-------~~~~~g~~v~IvS~DKDl~ 215 (332)
|=++++.-+.. .....|.++.+ .+|-+++
T Consensus 86 Ev~~Lm~l~~~~l~~~~~~~~~~~iri~v-iG~~~~L 121 (251)
T PRK14830 86 EVKFLMNLPVEFLDKFVPELIENNVKVNV-IGDTDRL 121 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCEEEE-EcChhhC
Confidence 66666643332 22334555544 4566654
No 138
>COG2379 GckA Putative glycerate kinase [Carbohydrate transport and metabolism]
Probab=40.22 E-value=2.3e+02 Score=29.16 Aligned_cols=121 Identities=21% Similarity=0.188 Sum_probs=65.8
Q ss_pred hHHHHHHHHhcCCCcEEe----cCCchHHH---HHHHHHHHHHhCC----CeEEEEcCCCCcCccCCCC-eEEEecCCCC
Q 020010 164 SHQFILDVLGKCNVPVVK----IEGHEADD---VIATLVGQVLQKG----YRAVVASPDKDFKQLISED-VQLVMPLQDL 231 (332)
Q Consensus 164 ql~~i~elL~~~gi~~i~----~~g~EADD---vIAtLa~~~~~~g----~~v~IvS~DKDl~QLv~~~-v~v~~~~~~~ 231 (332)
.++.+...+...|+..+. .+| ||-| ++|.+++.....| ..++++|+ ++- |++--.-++
T Consensus 259 sleaaa~~~~~~G~~a~Il~d~ieG-EArevg~v~asiarev~~~g~Pf~~P~~llsG--------GETTVTvrG~gkG- 328 (422)
T COG2379 259 SLEAAASEARALGFKAVILGDTIEG-EAREVGRVHASIAREVARRGRPFKKPVVLLSG--------GETTVTVRGNGKG- 328 (422)
T ss_pred HHHHHHHHHHhcCCeeEEeeccccc-cHHHHHHHHHHHHHHHHHcCCCCCCCEEEEEC--------CceEEEecCCCCC-
Confidence 356667777888988542 345 5555 4888888877766 35677663 332 333322222
Q ss_pred CccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCC-ccHHHHHHHHHhcCCHHHHHHHhh
Q 020010 232 DRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPG-FGRKTALKLLKKHGSLENLLNAAA 300 (332)
Q Consensus 232 ~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~G-IG~KTA~kLL~~ygsle~il~~~~ 300 (332)
++...+-.+.-..--|. -++.+|.+| +|+|-|..+..-+ +-+-|+.++-..--++++.|++-+
T Consensus 329 GRN~E~~Ls~~~~~~~~-----~~~~~la~d-TDGiDG~~d~AGa~vd~~t~~rl~a~G~d~~~~L~~nd 392 (422)
T COG2379 329 GRNQEFLLSFAIAIEGL-----DGILALAAD-TDGIDGSEDAAGAIVDGDTIARLRAAGLDPRAALKNND 392 (422)
T ss_pred CccHHHHHHHHHHhcCC-----CceeEEecc-CCCCCCCCccccceeccchHHHHHHcccCHHHHHhcCc
Confidence 22222222222222232 257889988 6999998543323 334455555444345555555433
No 139
>PTZ00331 alpha/beta hydrolase; Provisional
Probab=39.81 E-value=46 Score=30.40 Aligned_cols=44 Identities=20% Similarity=0.175 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEc
Q 020010 166 QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVAS 209 (332)
Q Consensus 166 ~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS 209 (332)
..+.++|+..||..+..-|.++|=++.+-++.+...|++|+|++
T Consensus 135 t~L~~~L~~~gi~~lvi~G~~t~~CV~~Ta~~a~~~g~~v~vv~ 178 (212)
T PTZ00331 135 TGLAQILKAHGVRRVFICGLAFDFCVLFTALDAVKLGFKVVVLE 178 (212)
T ss_pred chHHHHHHHCCCCEEEEEEeccCHHHHHHHHHHHHCCCEEEEeC
Confidence 34567788899999999999999999999999999999999886
No 140
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=39.76 E-value=6.8 Score=29.21 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=17.3
Q ss_pred cccCCCCCCCCcccCCCCccHHHHHHHHHhcCCH
Q 020010 259 IVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSL 292 (332)
Q Consensus 259 L~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsl 292 (332)
|+--+.+-+--| +|||+++|..+.+=|.+.
T Consensus 29 l~~a~~e~L~~i----~gIG~~~A~si~~ff~~~ 58 (64)
T PF12826_consen 29 LMNASVEELSAI----PGIGPKIAQSIYEFFQDP 58 (64)
T ss_dssp HCC--HHHHCTS----TT--HHHHHHHHHHHH-H
T ss_pred HHHcCHHHHhcc----CCcCHHHHHHHHHHHCCH
Confidence 333344556677 999999999877655443
No 141
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.46 E-value=1e+02 Score=25.90 Aligned_cols=73 Identities=18% Similarity=0.169 Sum_probs=49.4
Q ss_pred HHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh-cCCHHHHHHHhhhcccCchHHHHHHHHhH
Q 020010 239 LKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK-HGSLENLLNAAAVRTVGRDYAQEALTKHA 317 (332)
Q Consensus 239 ~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~-ygsle~il~~~~~~~~~~~~~~~~L~~~~ 317 (332)
...+.++.|++...+..+.++ +|-. -| +|||+..|.=|.+- +.|++++-+.- ...+.+.+.+..
T Consensus 32 r~~La~~~~i~~~~l~~w~~~----AdL~-ri----~gi~~~~a~LL~~AGv~Tv~~LA~~~------p~~L~~~l~~~n 96 (122)
T PF14229_consen 32 RKALAKKLGISERNLLKWVNQ----ADLM-RI----PGIGPQYAELLEHAGVDTVEELAQRN------PQNLHQKLGRLN 96 (122)
T ss_pred HHHHHHhcCCCHHHHHHHHhH----HHhh-hc----CCCCHHHHHHHHHhCcCcHHHHHhCC------HHHHHHHHHHHH
Confidence 345667789999999888887 4555 77 99999998766654 55888875432 234555666655
Q ss_pred HHHHhhccc
Q 020010 318 DYLRRNYEV 326 (332)
Q Consensus 318 ~~~~~s~~L 326 (332)
....+.+.+
T Consensus 97 ~~~~~~r~~ 105 (122)
T PF14229_consen 97 RKLKLRRQL 105 (122)
T ss_pred HHhcCCcCC
Confidence 555555554
No 142
>PRK13844 recombination protein RecR; Provisional
Probab=38.91 E-value=18 Score=33.45 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=10.9
Q ss_pred CCccHHHHHHHH
Q 020010 275 PGFGRKTALKLL 286 (332)
Q Consensus 275 ~GIG~KTA~kLL 286 (332)
||||+|+|.++-
T Consensus 21 PGIG~KsA~Rla 32 (200)
T PRK13844 21 PTIGKKSSQRLA 32 (200)
T ss_pred CCCCHHHHHHHH
Confidence 999999999884
No 143
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=37.12 E-value=45 Score=31.09 Aligned_cols=37 Identities=30% Similarity=0.485 Sum_probs=24.0
Q ss_pred HHHHHHhCC-ChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh-cCC
Q 020010 240 KHYIAQYNC-DPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK-HGS 291 (332)
Q Consensus 240 ~~v~e~~Gv-~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~-ygs 291 (332)
..+.++||- -|...-++..| ||+|+|||-=.|.. ||-
T Consensus 94 ~~l~e~~~g~vP~~~~eL~~L---------------PGVGrKTAnvVL~~a~g~ 132 (211)
T COG0177 94 RILLEKFGGEVPDTREELLSL---------------PGVGRKTANVVLSFAFGI 132 (211)
T ss_pred HHHHHHcCCCCCchHHHHHhC---------------CCcchHHHHHHHHhhcCC
Confidence 334556653 24545555555 89999999888876 663
No 144
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=34.95 E-value=78 Score=24.88 Aligned_cols=26 Identities=27% Similarity=0.501 Sum_probs=20.8
Q ss_pred CCccHHHHHHHHH-----hcCCHHHHHHHhh
Q 020010 275 PGFGRKTALKLLK-----KHGSLENLLNAAA 300 (332)
Q Consensus 275 ~GIG~KTA~kLL~-----~ygsle~il~~~~ 300 (332)
+|+|+++|.++++ .|.|+++++..++
T Consensus 33 kglg~~~a~~I~~~R~~g~f~s~~df~~R~~ 63 (90)
T PF14579_consen 33 KGLGEEVAEKIVEERENGPFKSLEDFIQRLP 63 (90)
T ss_dssp TTS-HHHHHHHHHHHHCSS-SSHHHHHHHS-
T ss_pred CCCCHHHHHHHHHhHhcCCCCCHHHHHHHHh
Confidence 9999999999996 4679999999874
No 145
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=34.57 E-value=47 Score=31.75 Aligned_cols=82 Identities=13% Similarity=0.127 Sum_probs=49.0
Q ss_pred CCCcEEEEEcCCCCchhhhh-----hchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEec-------
Q 020010 115 HADPVIAVFDGEGGTEHRRQ-----LLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKI------- 182 (332)
Q Consensus 115 ~~~pvivvFD~~~~~~fR~e-----l~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~------- 182 (332)
-|.||++++||.+ -|=+. -.+.+.+||... +.+.+.+++|. .+||+++..
T Consensus 18 ~P~HVaiImDGNr--RwAk~~~~~~gl~~~~GH~~G~------------~~l~~v~~~c~----~~GIk~lTvYaFS~EN 79 (250)
T PRK14840 18 LPRHVAIIMDGNR--RWYRKHEQFCQKRAISGHYYGA------------KSLPQIVDTAL----HLGIEVLTLFAFSTEN 79 (250)
T ss_pred CCCeEEEEcCCCh--HHHhhCCCccCCCHHHHHHHHH------------HHHHHHHHHHH----HcCCCEEEEEEeehhh
Confidence 4778999999963 23222 257888999876 23444444444 468987765
Q ss_pred ---CCchHHHHHHHHHHH-------HHhCCCeEEEEcCCCCcC
Q 020010 183 ---EGHEADDVIATLVGQ-------VLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 183 ---~g~EADDvIAtLa~~-------~~~~g~~v~IvS~DKDl~ 215 (332)
+--|=++++.-+... ..+.|.++.+ .+|.|++
T Consensus 80 ~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~-iGd~~~L 121 (250)
T PRK14840 80 FSRSKEEVAELFSLFNSQLDSQLPYLHENEIRLRC-IGDLSKL 121 (250)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE-EeChhhC
Confidence 445777777655443 2234555444 4566654
No 146
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=33.51 E-value=72 Score=29.38 Aligned_cols=27 Identities=30% Similarity=0.608 Sum_probs=23.5
Q ss_pred CCCccHHHHHHHHHh-----cCCHHHHHHHhh
Q 020010 274 VPGFGRKTALKLLKK-----HGSLENLLNAAA 300 (332)
Q Consensus 274 ~~GIG~KTA~kLL~~-----ygsle~il~~~~ 300 (332)
.||||.|+...+|.+ |.|.++|-+.+.
T Consensus 135 LpGiGkK~m~~ILeERkkkpFeSFeDi~~Rv~ 166 (202)
T COG1491 135 LPGIGKKTMWAILEERKKKPFESFEDIKERVK 166 (202)
T ss_pred cccccHHHHHHHHHHHhcCCCcCHHHHHHHhc
Confidence 499999999999964 889999988876
No 147
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=32.83 E-value=48 Score=35.88 Aligned_cols=13 Identities=54% Similarity=0.902 Sum_probs=6.3
Q ss_pred CCccHHHHHHHHH
Q 020010 275 PGFGRKTALKLLK 287 (332)
Q Consensus 275 ~GIG~KTA~kLL~ 287 (332)
||+|+|+|.+|++
T Consensus 472 ~GfG~Ksa~nIl~ 484 (652)
T TIGR00575 472 EGFGEKSAQNLLN 484 (652)
T ss_pred cCccHHHHHHHHH
Confidence 4445555544443
No 148
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=32.01 E-value=24 Score=32.08 Aligned_cols=17 Identities=41% Similarity=0.757 Sum_probs=13.8
Q ss_pred CCccHHHHHHHHHhcCC
Q 020010 275 PGFGRKTALKLLKKHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygs 291 (332)
||||+|||-=.|..+|+
T Consensus 121 pGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 121 PGFGKQKAKIFLALLGK 137 (177)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 99999999887775553
No 149
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=31.90 E-value=23 Score=28.44 Aligned_cols=31 Identities=32% Similarity=0.589 Sum_probs=24.6
Q ss_pred chHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCC
Q 020010 185 HEADDVIATLVGQVLQKGYRAVVASPDKDFKQLIS 219 (332)
Q Consensus 185 ~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~ 219 (332)
.-|||.|-.++.+ .+ ..+|+|.|+++.+-+.
T Consensus 51 ~~addci~~~~~~---~~-~~~VaT~D~~Lr~~lr 81 (101)
T PF04900_consen 51 GSADDCILDLAGK---NN-KYIVATQDKELRRRLR 81 (101)
T ss_pred cCHHHHHHHHhcc---CC-eEEEEecCHHHHHHHh
Confidence 5799999998863 22 2899999999998665
No 150
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=31.83 E-value=24 Score=25.45 Aligned_cols=14 Identities=50% Similarity=0.814 Sum_probs=12.9
Q ss_pred CCCCCCcccCCCCccHHH
Q 020010 264 VDGVPGIQHVVPGFGRKT 281 (332)
Q Consensus 264 sDNIPGI~~~~~GIG~KT 281 (332)
.||+|.| |.||+|.
T Consensus 18 wdnvpti----prigekv 31 (57)
T PF13052_consen 18 WDNVPTI----PRIGEKV 31 (57)
T ss_pred hccCCCc----cccchhh
Confidence 6999999 9999986
No 151
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.34 E-value=39 Score=32.84 Aligned_cols=79 Identities=22% Similarity=0.280 Sum_probs=41.9
Q ss_pred HhCCCeEEEEcCC-CCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH-----hCCChhHHHHhhhcccCCCC-------
Q 020010 199 LQKGYRAVVASPD-KDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ-----YNCDPHSELSLRCIVGDDVD------- 265 (332)
Q Consensus 199 ~~~g~~v~IvS~D-KDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~-----~Gv~P~q~~d~~aL~GD~sD------- 265 (332)
..+|..|+++... +|+.+....---++.... ....++.+.+.+. .|+++. .+- -|+|| .|
T Consensus 179 ~~~gatVtv~~s~t~~l~~~~~~ADIVIsAvg---~p~~i~~~~vk~gavVIDvGi~~~--~~g-kl~GD-vd~~~~~~~ 251 (286)
T PRK14175 179 LQKNASVTILHSRSKDMASYLKDADVIVSAVG---KPGLVTKDVVKEGAVIIDVGNTPD--ENG-KLKGD-VDYDAVKEI 251 (286)
T ss_pred HHCCCeEEEEeCCchhHHHHHhhCCEEEECCC---CCcccCHHHcCCCcEEEEcCCCcC--CCC-CeecC-ccHHHHHhh
Confidence 3467888766654 344444433212222211 1223555444321 244441 111 37887 44
Q ss_pred --CCCCcccCCC-CccHHHHHHHHHh
Q 020010 266 --GVPGIQHVVP-GFGRKTALKLLKK 288 (332)
Q Consensus 266 --NIPGI~~~~~-GIG~KTA~kLL~~ 288 (332)
.|.+| | |+||.|.+-|++.
T Consensus 252 a~~iTPV----PGGVGp~T~a~L~~n 273 (286)
T PRK14175 252 AGAITPV----PGGVGPLTITMVLNN 273 (286)
T ss_pred ccCcCCC----CCCCHHHHHHHHHHH
Confidence 56777 7 5999999999876
No 152
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=31.29 E-value=50 Score=30.15 Aligned_cols=50 Identities=18% Similarity=0.239 Sum_probs=27.8
Q ss_pred ChhHHHHhhhcccCCCCCCC-CcccCCCCccHHHHHHHHH-----hcCCHHHHHHHhh
Q 020010 249 DPHSELSLRCIVGDDVDGVP-GIQHVVPGFGRKTALKLLK-----KHGSLENLLNAAA 300 (332)
Q Consensus 249 ~P~q~~d~~aL~GD~sDNIP-GI~~~~~GIG~KTA~kLL~-----~ygsle~il~~~~ 300 (332)
..+.|++|.=-+| .-++. ---...||||.|+..++|. .|.|.|+|-+.+.
T Consensus 97 ~E~~FV~FfN~A~--PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~ 152 (181)
T PF04919_consen 97 NEERFVDFFNEAQ--PITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVK 152 (181)
T ss_dssp THHHHHHHH-------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST
T ss_pred ChHHHHHHhhcCC--CChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhc
Confidence 4677888886666 11111 0012469999999999996 4889999988764
No 153
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=29.90 E-value=37 Score=31.54 Aligned_cols=17 Identities=35% Similarity=0.550 Sum_probs=13.9
Q ss_pred CCccHHHHHHHHHhcCC
Q 020010 275 PGFGRKTALKLLKKHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygs 291 (332)
||||+|||--+|...|-
T Consensus 125 pGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 125 KGIGYKEASHFLRNVGY 141 (208)
T ss_pred CCCcHHHHHHHHHHccC
Confidence 99999999999954443
No 154
>PRK13910 DNA glycosylase MutY; Provisional
Probab=29.78 E-value=66 Score=31.30 Aligned_cols=17 Identities=35% Similarity=0.444 Sum_probs=13.5
Q ss_pred CCccHHHHHHHHH-hcCC
Q 020010 275 PGFGRKTALKLLK-KHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~-~ygs 291 (332)
||||+|||--++. -||-
T Consensus 78 pGIG~kTA~aIl~~af~~ 95 (289)
T PRK13910 78 PGIGAYTANAILCFGFRE 95 (289)
T ss_pred CCCCHHHHHHHHHHHCCC
Confidence 9999999988765 4653
No 155
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=28.93 E-value=59 Score=35.46 Aligned_cols=36 Identities=28% Similarity=0.484 Sum_probs=22.5
Q ss_pred CCCcccCCCCccHHHHHHHHHhcC-----CHHHHHHHhhhcccCc
Q 020010 267 VPGIQHVVPGFGRKTALKLLKKHG-----SLENLLNAAAVRTVGR 306 (332)
Q Consensus 267 IPGI~~~~~GIG~KTA~kLL~~yg-----sle~il~~~~~~~~~~ 306 (332)
+..+ +|+|+|+|.+|++... +++.++.++.....|.
T Consensus 498 L~~l----~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~ 538 (689)
T PRK14351 498 LAEL----EGWGETSAENLLAELEASREPPLADFLVALGIPEVGP 538 (689)
T ss_pred HhcC----cCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCH
Confidence 5555 7777777777766542 5677777666544443
No 156
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=28.78 E-value=5.1e+02 Score=27.86 Aligned_cols=55 Identities=9% Similarity=0.137 Sum_probs=30.8
Q ss_pred ccccccCCCCcccCCCCcEEEEeCcchhhhhcCchhhHHHHHHHHHHHHhcC-C--CcE-EEEEcCC
Q 020010 64 GKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSH-A--DPV-IAVFDGE 126 (332)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~vllIDg~~l~yra~~p~~~~~~~~l~~ll~~i~~-~--~pv-ivvFD~~ 126 (332)
-..++|....+. +||||+|+-+-+... +.....|+..|+..+.. . ..+ ++.|++.
T Consensus 34 ~~e~vC~~~lDI------vFLLD~SgSMg~~Nf--le~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~ 92 (576)
T PTZ00441 34 YREEVCNEEVDL------YLLVDGSGSIGYHNW--ITHVIPMLMGLIQQLNLSDDAINLYMSLFSNN 92 (576)
T ss_pred cccccccCCceE------EEEEeCCCccCCccH--HHHHHHHHHHHHHHhccCCCceEEEEEEeCCC
Confidence 367778665555 999999988732211 12233455555555421 1 223 3578874
No 157
>KOG4700 consensus Uncharacterized homolog of ribosome-binding factor A [General function prediction only]
Probab=28.78 E-value=1.7e+02 Score=26.99 Aligned_cols=69 Identities=16% Similarity=0.168 Sum_probs=40.5
Q ss_pred CCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHH
Q 020010 201 KGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRK 280 (332)
Q Consensus 201 ~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~K 280 (332)
.+-++--|+-+.||-|+ ++|.--++.++ --..+++.++....-...+.-+.++| ++|-| +=||.|
T Consensus 59 l~vqiS~V~vt~dFS~~-----~vYWm~~~~ge--N~e~e~~L~rs~~~~rh~l~~~~~~g----~vP~I----kFV~DK 123 (207)
T KOG4700|consen 59 LQVQISRVRVTRDFSQV-----SVYWMCRGDGE--NSEIEDFLERSKHQIRHRLEESIGIG----TVPEI----KFVGDK 123 (207)
T ss_pred cceeEEEEEeccchhhh-----eeEEEecCCcc--HHHHHHHHHHHHHHHHHHHHHHhccc----cCCce----EEecch
Confidence 35667778889999886 33332222222 11235555543322233455567777 79999 889998
Q ss_pred HHHH
Q 020010 281 TALK 284 (332)
Q Consensus 281 TA~k 284 (332)
+-.-
T Consensus 124 ~~~~ 127 (207)
T KOG4700|consen 124 ALLM 127 (207)
T ss_pred HHHH
Confidence 7553
No 158
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=28.26 E-value=47 Score=24.81 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=12.6
Q ss_pred CCCcccCCCCccHHHHHHH
Q 020010 267 VPGIQHVVPGFGRKTALKL 285 (332)
Q Consensus 267 IPGI~~~~~GIG~KTA~kL 285 (332)
+.++ ||||+++|.++
T Consensus 49 ~~~l----~gIG~~ia~kI 63 (68)
T PF14716_consen 49 LKKL----PGIGKSIAKKI 63 (68)
T ss_dssp HCTS----TTTTHHHHHHH
T ss_pred HhhC----CCCCHHHHHHH
Confidence 4677 99999999886
No 159
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=28.25 E-value=38 Score=30.68 Aligned_cols=20 Identities=30% Similarity=0.619 Sum_probs=16.2
Q ss_pred CCCcccCCCCccHHHHHHHHHhcC
Q 020010 267 VPGIQHVVPGFGRKTALKLLKKHG 290 (332)
Q Consensus 267 IPGI~~~~~GIG~KTA~kLL~~yg 290 (332)
+-.| ||||+|+|.+++..+.
T Consensus 110 L~~v----~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 110 LTKV----PGIGKKTAERIVLELK 129 (192)
T ss_pred HHhC----CCCCHHHHHHHHHHHH
Confidence 4556 9999999999987643
No 160
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=28.12 E-value=49 Score=32.19 Aligned_cols=85 Identities=19% Similarity=0.230 Sum_probs=43.0
Q ss_pred HHHHHHhCCCeEEEEcCC-CCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH-----hCCChhHHHHhhhcccCCC---
Q 020010 194 LVGQVLQKGYRAVVASPD-KDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ-----YNCDPHSELSLRCIVGDDV--- 264 (332)
Q Consensus 194 La~~~~~~g~~v~IvS~D-KDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~-----~Gv~P~q~~d~~aL~GD~s--- 264 (332)
|+.-...+|..|+++... +|+......---++.... ....++.+.+.+. .|+++- .+ --++||-.
T Consensus 175 la~lL~~~~atVtv~hs~T~~l~~~~~~ADIvi~avG---~p~~v~~~~vk~gavVIDvGin~~--~~-gk~~GDvd~~~ 248 (285)
T PRK10792 175 MSLELLLAGCTVTVCHRFTKNLRHHVRNADLLVVAVG---KPGFIPGEWIKPGAIVIDVGINRL--ED-GKLVGDVEFET 248 (285)
T ss_pred HHHHHHHCCCeEEEEECCCCCHHHHHhhCCEEEEcCC---CcccccHHHcCCCcEEEEcccccc--cC-CCcCCCcCHHH
Confidence 333344567788776554 344433332212222221 1233444444331 233321 01 14778731
Q ss_pred -----CCCCCcccCCC-CccHHHHHHHHHh
Q 020010 265 -----DGVPGIQHVVP-GFGRKTALKLLKK 288 (332)
Q Consensus 265 -----DNIPGI~~~~~-GIG~KTA~kLL~~ 288 (332)
-.|.+| | |+||.|.+-|++.
T Consensus 249 ~~~~a~~itPv----PGGVGp~T~a~L~~N 274 (285)
T PRK10792 249 AAERASWITPV----PGGVGPMTVATLLEN 274 (285)
T ss_pred HHhhccCcCCC----CCCChHHHHHHHHHH
Confidence 257778 8 5999999999876
No 161
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.03 E-value=54 Score=35.67 Aligned_cols=23 Identities=22% Similarity=0.417 Sum_probs=20.8
Q ss_pred CCccHHHHHHHH-HhcCCHHHHHH
Q 020010 275 PGFGRKTALKLL-KKHGSLENLLN 297 (332)
Q Consensus 275 ~GIG~KTA~kLL-~~ygsle~il~ 297 (332)
|+||+++|..|. +.|++++++.+
T Consensus 508 ~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 508 KDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CchhHHHHHHHHHHhhCCHHHHHh
Confidence 999999999999 88999999875
No 162
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=26.45 E-value=1.6e+02 Score=32.10 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=29.1
Q ss_pred CCCccHHHHHHHHHhcC--CHHHHHHHhhh-cc--c-C-chHHHHHHHHhHHHH
Q 020010 274 VPGFGRKTALKLLKKHG--SLENLLNAAAV-RT--V-G-RDYAQEALTKHADYL 320 (332)
Q Consensus 274 ~~GIG~KTA~kLL~~yg--sle~il~~~~~-~~--~-~-~~~~~~~L~~~~~~~ 320 (332)
.+|+|||++.+|.++.+ +++++++ +.. .. + | +++..++|.+..+..
T Consensus 450 I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~ll~~Ie~s 502 (665)
T PRK07956 450 IDGLGEKIIEQLFEKGLIHDPADLFK-LTAEDLLGLEGFGEKSAQNLLDAIEKS 502 (665)
T ss_pred CCCcCHHHHHHHHHcCCCCCHHHHHh-cCHHHHhcCcCcchHHHHHHHHHHHHh
Confidence 38999999999998754 8999984 321 11 1 1 234445566665544
No 163
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=26.11 E-value=39 Score=29.63 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=23.7
Q ss_pred CCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH
Q 020010 201 KGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ 245 (332)
Q Consensus 201 ~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~ 245 (332)
.|..-+|+|+|+|++-+-+++- ..+..+++++.++
T Consensus 102 ~~kA~~lvTgD~dLL~lr~~n~----------~~~Iltp~eF~~~ 136 (142)
T COG1569 102 ESKADYLVTGDQDLLVLRDENK----------RVEILTPQEFLEE 136 (142)
T ss_pred hccCCEEEEcchhhheecccCC----------cEEEcCHHHHHHH
Confidence 3556689999999998877641 2345566666554
No 164
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=25.97 E-value=43 Score=28.58 Aligned_cols=14 Identities=57% Similarity=0.700 Sum_probs=11.9
Q ss_pred CCccHHHHHHHHHh
Q 020010 275 PGFGRKTALKLLKK 288 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ 288 (332)
||||+|||--++.-
T Consensus 89 ~GIG~~tA~~~l~~ 102 (158)
T cd00056 89 PGVGRKTANVVLLF 102 (158)
T ss_pred CCCCHHHHHHHHHH
Confidence 99999999887653
No 165
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=25.61 E-value=1.3e+02 Score=25.92 Aligned_cols=50 Identities=20% Similarity=0.308 Sum_probs=35.1
Q ss_pred HHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCc
Q 020010 161 VGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDF 214 (332)
Q Consensus 161 L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl 214 (332)
+.+.+..+++-|+.+|++.+...| ++.+++..++.+. +...++++.|-..
T Consensus 51 l~~sL~~L~~~L~~~g~~L~v~~g-~~~~~l~~l~~~~---~~~~V~~~~~~~~ 100 (165)
T PF00875_consen 51 LLESLADLQESLRKLGIPLLVLRG-DPEEVLPELAKEY---GATAVYFNEEYTP 100 (165)
T ss_dssp HHHHHHHHHHHHHHTTS-EEEEES-SHHHHHHHHHHHH---TESEEEEE---SH
T ss_pred HHHHHHHHHHHHHhcCcceEEEec-chHHHHHHHHHhc---CcCeeEeccccCH
Confidence 556788888889999999988888 7899999888753 4455555555443
No 166
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=25.25 E-value=2.2e+02 Score=24.80 Aligned_cols=61 Identities=25% Similarity=0.314 Sum_probs=35.6
Q ss_pred HHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCC
Q 020010 166 QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQ 229 (332)
Q Consensus 166 ~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~ 229 (332)
..+.++....|++++ +.|.-+||++.++..+.. +|....-+++-+...... ..+.++.|..
T Consensus 89 ~~l~~~a~~~g~~~i-~~Gh~~~D~~e~~l~~~~-~g~~~~~l~~~~~~~~~~-~~~~iirPL~ 149 (189)
T TIGR02432 89 DFFEEIAKKHGADYI-LTAHHADDQAETILLRLL-RGSGLRGLSGMKPIRILG-NGGQIIRPLL 149 (189)
T ss_pred HHHHHHHHHcCCCEE-EEcCccHHHHHHHHHHHH-cCCCcccccCCccccccC-CCCEEECCCC
Confidence 445566667899876 688899999988765544 343322233322222221 1467777764
No 167
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.07 E-value=59 Score=31.53 Aligned_cols=86 Identities=16% Similarity=0.220 Sum_probs=43.8
Q ss_pred HHHHHHHHhCCCeEEE-EcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH-----hCCChhHHHHhhhcccCCC-
Q 020010 192 ATLVGQVLQKGYRAVV-ASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ-----YNCDPHSELSLRCIVGDDV- 264 (332)
Q Consensus 192 AtLa~~~~~~g~~v~I-vS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~-----~Gv~P~q~~d~~aL~GD~s- 264 (332)
-.|+......|..|.+ .|..+|+.+....---+..... ....++.+.+.+. .|++. . + --|+||-.
T Consensus 166 rpla~lL~~~~atVtv~hs~t~~L~~~~~~ADIvI~Avg---k~~lv~~~~vk~GavVIDVgi~~--~-~-gkl~GDvdf 238 (279)
T PRK14178 166 RPMAALLLNADATVTICHSKTENLKAELRQADILVSAAG---KAGFITPDMVKPGATVIDVGINQ--V-N-GKLCGDVDF 238 (279)
T ss_pred HHHHHHHHhCCCeeEEEecChhHHHHHHhhCCEEEECCC---cccccCHHHcCCCcEEEEeeccc--c-C-CCCcCCccH
Confidence 3344444446776654 4555666665543222222221 1134555444221 12222 1 1 13788732
Q ss_pred -------CCCCCcccCCC-CccHHHHHHHHHh
Q 020010 265 -------DGVPGIQHVVP-GFGRKTALKLLKK 288 (332)
Q Consensus 265 -------DNIPGI~~~~~-GIG~KTA~kLL~~ 288 (332)
-.|.+| | |+||.|.+-|++.
T Consensus 239 ~~~~~~a~~iTPV----PGGVGp~T~a~L~~N 266 (279)
T PRK14178 239 DAVKEIAGAITPV----PGGVGPMTIATLMEN 266 (279)
T ss_pred HHHHhhccCcCCC----CCCCHHHHHHHHHHH
Confidence 256677 7 5999999999876
No 168
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=24.91 E-value=92 Score=30.06 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=15.4
Q ss_pred CCccHHHHHHHHHh-cCCHHHH
Q 020010 275 PGFGRKTALKLLKK-HGSLENL 295 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~i 295 (332)
||||||.|.-.++. +|.+.+|
T Consensus 165 PGVGPKMa~L~m~~AWn~i~GI 186 (286)
T KOG1921|consen 165 PGVGPKMAHLTMQVAWNKIVGI 186 (286)
T ss_pred CCCchHHHHHHHHHHhccceeE
Confidence 99999999877764 5654433
No 169
>PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.80 E-value=56 Score=31.87 Aligned_cols=83 Identities=18% Similarity=0.178 Sum_probs=42.7
Q ss_pred HHHHHHhCCCeEEEEcCC-CCcCccCCCCeEEEecCCCCCccEEeeHHHHHHH-----hCCChhHHHHhhhcccCCCC--
Q 020010 194 LVGQVLQKGYRAVVASPD-KDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQ-----YNCDPHSELSLRCIVGDDVD-- 265 (332)
Q Consensus 194 La~~~~~~g~~v~IvS~D-KDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~-----~Gv~P~q~~d~~aL~GD~sD-- 265 (332)
|+.-...+|..|.++... +|+......---+..... ....++.+.+.+. .|++.. +- -|+||- |
T Consensus 180 la~lL~~~~atVtv~hs~T~~l~~~~~~ADIvv~AvG---~p~~i~~~~vk~gavVIDvGin~~---~g-kl~GDv-d~~ 251 (287)
T PRK14176 180 MAAMLLNRNATVSVCHVFTDDLKKYTLDADILVVATG---VKHLIKADMVKEGAVIFDVGITKE---ED-KVYGDV-DFE 251 (287)
T ss_pred HHHHHHHCCCEEEEEeccCCCHHHHHhhCCEEEEccC---CccccCHHHcCCCcEEEEeccccc---CC-CccCCc-CHH
Confidence 333344567788777655 455544432211222111 1223444444321 243321 11 377873 3
Q ss_pred -------CCCCcccCCC-CccHHHHHHHHHh
Q 020010 266 -------GVPGIQHVVP-GFGRKTALKLLKK 288 (332)
Q Consensus 266 -------NIPGI~~~~~-GIG~KTA~kLL~~ 288 (332)
.|.+| | |+||.|.+-|++.
T Consensus 252 ~~~~~a~~iTPV----PGGVGp~T~a~L~~n 278 (287)
T PRK14176 252 NVIKKASLITPV----PGGVGPLTIAMLMKH 278 (287)
T ss_pred HHHhhceEcCCC----CCCChHHHHHHHHHH
Confidence 46677 7 5999999999875
No 170
>COG4365 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.70 E-value=4.5e+02 Score=27.41 Aligned_cols=117 Identities=15% Similarity=0.170 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHhcCCCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhhhhhhcchhhHHHhHHHHHHHHhcCCC-cEE
Q 020010 102 FGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNV-PVV 180 (332)
Q Consensus 102 ~~~~l~~ll~~i~~~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~~~~~~~~~~L~~ql~~i~elL~~~gi-~~i 180 (332)
+..|+..++..+-.+.- ++++|+ +.+.+|+-.-|-++.-=++. ..+...+..-.+-++..|+ +-|
T Consensus 209 ytD~Fa~Llh~lf~~eG-llvlds-~~p~lrkLeapmf~kiL~k~------------~~l~~af~dqq~rl~qaGy~~~I 274 (537)
T COG4365 209 YTDFFARLLHGLFAPEG-LLVLDS-GDPALRKLEAPMFAKILEKP------------LALSAAFEDQQERLSQAGYTPPI 274 (537)
T ss_pred HHHHHHHHHHHhhhhcc-eEEecC-CChHHHHHHHHHHHHHHhhh------------HhHHHHHHHHHHHHHhCCCCCcc
Confidence 34455555444333232 568998 46888887777766533322 2344455555566666666 333
Q ss_pred ecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHHhCCChhHH
Q 020010 181 KIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSE 253 (332)
Q Consensus 181 ~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~ 253 (332)
..+. -++-++-.|-|.++|++..-.-|...+. -.-|+.+++.+.....|+.|
T Consensus 275 ~~~~------------------tnanLF~eeEdsR~li~ydg~~f~ln~~---d~tytReELl~~le~hPerf 326 (537)
T COG4365 275 IRPA------------------TNANLFYEEEDSRRLIRYDGQSFSLNTH---DKTYTREELLAHLEAHPERF 326 (537)
T ss_pred ccCc------------------ccceeEEeecCceeeeeecCceeEeecc---cccccHHHHHHHHhhCHHhc
Confidence 2221 1222445567778887643211211110 12356666666555444443
No 171
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=24.53 E-value=59 Score=25.41 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHhCCCeEEEEcCCCCcC
Q 020010 187 ADDVIATLVGQVLQKGYRAVVASPDKDFK 215 (332)
Q Consensus 187 ADDvIAtLa~~~~~~g~~v~IvS~DKDl~ 215 (332)
.|+.+..+|... ..++|+|.|+++.
T Consensus 86 ~D~~il~~a~~~----~~~~lvT~D~~l~ 110 (111)
T smart00670 86 NDALILATAKEL----GNVVLVTNDRDLR 110 (111)
T ss_pred ChHHHHHHHHHC----CCCEEEeCCcccC
Confidence 477788777642 1688999999985
No 172
>PRK10702 endonuclease III; Provisional
Probab=24.36 E-value=45 Score=30.77 Aligned_cols=16 Identities=56% Similarity=0.854 Sum_probs=12.7
Q ss_pred CCccHHHHHHHH-HhcC
Q 020010 275 PGFGRKTALKLL-KKHG 290 (332)
Q Consensus 275 ~GIG~KTA~kLL-~~yg 290 (332)
||||+|||--+| --||
T Consensus 115 pGVG~ktA~~ill~a~~ 131 (211)
T PRK10702 115 PGVGRKTANVVLNTAFG 131 (211)
T ss_pred CcccHHHHHHHHHHHcC
Confidence 999999998876 3455
No 173
>cd01080 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well a
Probab=24.02 E-value=68 Score=28.49 Aligned_cols=20 Identities=30% Similarity=0.585 Sum_probs=16.4
Q ss_pred CCCCCcccCCC-CccHHHHHHHHHh
Q 020010 265 DGVPGIQHVVP-GFGRKTALKLLKK 288 (332)
Q Consensus 265 DNIPGI~~~~~-GIG~KTA~kLL~~ 288 (332)
-+++++ | |+||.|+..|+++
T Consensus 142 ~~~~~~----pggvgp~t~a~l~~n 162 (168)
T cd01080 142 SAITPV----PGGVGPMTVAMLMKN 162 (168)
T ss_pred cCcCCC----CCcChHHHHHHHHHH
Confidence 467777 7 5999999999876
No 174
>PF15632 ATPgrasp_Ter: ATP-grasp in the biosynthetic pathway with Ter operon
Probab=23.98 E-value=1e+02 Score=30.59 Aligned_cols=59 Identities=12% Similarity=0.209 Sum_probs=46.1
Q ss_pred hHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEE
Q 020010 164 SHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLV 225 (332)
Q Consensus 164 ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~ 225 (332)
-++++.++++..+|.++ .|+++...+.+.- ..+.+.|-++.+ +.|.+.+++.++....+
T Consensus 54 yv~~~l~~C~~~~Idv~-~P~~~~~~l~~~r-~~F~a~Gv~l~~-~~~~~~l~~~~dK~~~y 112 (329)
T PF15632_consen 54 YVDWCLDFCKEHGIDVF-VPGRNRELLAAHR-DEFEALGVKLLT-ASSAETLELADDKAAFY 112 (329)
T ss_pred HHHHHHHHHHHhCCeEE-EcCccHHHHHHHH-HHHHHhCCEEEe-cCCHHHHHHHhhHHHHH
Confidence 47888899999999987 7999999955543 456777877777 78999999988765444
No 175
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=23.76 E-value=67 Score=31.01 Aligned_cols=24 Identities=38% Similarity=0.470 Sum_probs=21.5
Q ss_pred CCccHHHHHHHHHh-cCCHHHHHHH
Q 020010 275 PGFGRKTALKLLKK-HGSLENLLNA 298 (332)
Q Consensus 275 ~GIG~KTA~kLL~~-ygsle~il~~ 298 (332)
||||+++|.+|.+. +.|+++++..
T Consensus 12 ~gIg~~~a~~L~~~Gi~t~~dl~~~ 36 (317)
T PRK04301 12 PGVGPATAEKLREAGYDTVEAIAVA 36 (317)
T ss_pred CCCCHHHHHHHHHcCCCCHHHHHcC
Confidence 99999999999987 8899999764
No 176
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=23.54 E-value=1.2e+02 Score=27.58 Aligned_cols=42 Identities=21% Similarity=0.412 Sum_probs=26.4
Q ss_pred EEEEeCcchhhhh-----------------cCchh-hHHHHHHHHHHHHhcCCCcEEEEEcCC
Q 020010 82 VFFLDVNPLCYEG-----------------SRPSL-QSFGRWLSLFFDQVSHADPVIAVFDGE 126 (332)
Q Consensus 82 vllIDg~~l~yra-----------------~~p~~-~~~~~~l~~ll~~i~~~~pvivvFD~~ 126 (332)
+++.||+..+.|+ +.||. ++- .++.. ++.- ..+|+++.||..
T Consensus 3 IlvTDGD~~A~ravE~aa~~iGgRCIS~S~GNPT~lsG~-elV~l-Ik~a-~~DPV~VMfDD~ 62 (180)
T PF14097_consen 3 ILVTDGDEYAKRAVEIAAKNIGGRCISQSAGNPTPLSGE-ELVEL-IKQA-PHDPVLVMFDDK 62 (180)
T ss_pred EEEECChHHHHHHHHHHHHHhCcEEEeccCCCCCcCCHH-HHHHH-HHhC-CCCCEEEEEeCC
Confidence 5788999999986 23442 322 23332 2222 468999999975
No 177
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=23.34 E-value=52 Score=27.83 Aligned_cols=16 Identities=56% Similarity=0.843 Sum_probs=11.7
Q ss_pred CCccHHHHHHHHH-hcC
Q 020010 275 PGFGRKTALKLLK-KHG 290 (332)
Q Consensus 275 ~GIG~KTA~kLL~-~yg 290 (332)
||||+|||--++- -++
T Consensus 78 ~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 78 PGVGRKTANAVLSFALG 94 (149)
T ss_pred CCCcHHHHHHHHHHHCC
Confidence 9999999966543 344
No 178
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 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 [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=23.08 E-value=72 Score=26.17 Aligned_cols=16 Identities=44% Similarity=0.683 Sum_probs=15.0
Q ss_pred CCccHHHHHHHHHhcC
Q 020010 275 PGFGRKTALKLLKKHG 290 (332)
Q Consensus 275 ~GIG~KTA~kLL~~yg 290 (332)
.|||+.+|.++..+.|
T Consensus 21 yGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 21 YGIGRRKAKQICKKLG 36 (107)
T ss_dssp TTBCHHHHHHHHHHTT
T ss_pred hccCHHHHHHHHHHcC
Confidence 9999999999999886
No 179
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=23.04 E-value=52 Score=29.55 Aligned_cols=13 Identities=62% Similarity=0.912 Sum_probs=11.3
Q ss_pred CCccHHHHHHHHH
Q 020010 275 PGFGRKTALKLLK 287 (332)
Q Consensus 275 ~GIG~KTA~kLL~ 287 (332)
||||+|||--+|-
T Consensus 112 ~GIG~ktA~~ill 124 (191)
T TIGR01083 112 PGVGRKTANVVLN 124 (191)
T ss_pred CCCcHHHHHHHHH
Confidence 9999999988764
No 180
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=22.97 E-value=56 Score=29.81 Aligned_cols=17 Identities=47% Similarity=0.837 Sum_probs=15.5
Q ss_pred CCccHHHHHHHHHhcCC
Q 020010 275 PGFGRKTALKLLKKHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~~ygs 291 (332)
||+|..|+.++|.++|-
T Consensus 9 PGvGKTT~~~~L~~lg~ 25 (180)
T COG1936 9 PGVGKTTVCKLLRELGY 25 (180)
T ss_pred CCCchHHHHHHHHHhCC
Confidence 99999999999998773
No 181
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=22.48 E-value=55 Score=30.56 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=13.3
Q ss_pred CCccHHHHHHHHH-hcCC
Q 020010 275 PGFGRKTALKLLK-KHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~-~ygs 291 (332)
||||++||--+|- -+|-
T Consensus 127 ~GIG~kTAd~iLlya~~r 144 (218)
T PRK13913 127 KGIGKESADAILCYVCAK 144 (218)
T ss_pred CCccHHHHHHHHHHHcCC
Confidence 9999999988764 4553
No 182
>PRK10880 adenine DNA glycosylase; Provisional
Probab=21.85 E-value=1.1e+02 Score=30.49 Aligned_cols=17 Identities=47% Similarity=0.737 Sum_probs=13.8
Q ss_pred CCccHHHHHHHHH-hcCC
Q 020010 275 PGFGRKTALKLLK-KHGS 291 (332)
Q Consensus 275 ~GIG~KTA~kLL~-~ygs 291 (332)
||||++||--++. -||-
T Consensus 115 pGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 115 PGVGRSTAGAILSLSLGK 132 (350)
T ss_pred CCccHHHHHHHHHHHCCC
Confidence 9999999998875 4654
No 183
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=21.73 E-value=95 Score=29.66 Aligned_cols=96 Identities=17% Similarity=0.198 Sum_probs=54.1
Q ss_pred CCCcEEecCCchH-HHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecCCCCCccEEeeHHHHHHHhCCChhHH
Q 020010 175 CNVPVVKIEGHEA-DDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSE 253 (332)
Q Consensus 175 ~gi~~i~~~g~EA-DDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~~~~~~~~~~~~~~v~e~~Gv~P~q~ 253 (332)
-++..+.+-..|+ --.|-++ +.+.++....+.--.|.|+++-+-.-++ ..++. ..-|...+..+||-
T Consensus 150 ~~~Tl~lA~s~EeaaryIE~~-k~~ek~p~dli~~~~~~d~ls~~~~~Lt---~i~~V---nKtda~~LL~~Fgs----- 217 (254)
T KOG2841|consen 150 NDVTLVLAWSMEEAARYIETY-KEYEKKPIDLIMERKDRDLLSSLLGFLT---TIPGV---NKTDAQLLLQKFGS----- 217 (254)
T ss_pred hceeeeeeccHHHHHHHHHHH-HHhhcCCchhhhhcccccHHHHHHHHHH---hCCCC---CcccHHHHHHhccc-----
Confidence 3445444444444 4444444 4444333333333667775552221111 12222 22355666777773
Q ss_pred HHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHh
Q 020010 254 LSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKK 288 (332)
Q Consensus 254 ~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ 288 (332)
++.+.+=+.+-+.-| +|+||..|.+|.+-
T Consensus 218 --Lq~~~~AS~~ele~~----~G~G~~kak~l~~~ 246 (254)
T KOG2841|consen 218 --LQQISNASEGELEQC----PGLGPAKAKRLHKF 246 (254)
T ss_pred --HHHHHhcCHhHHHhC----cCcCHHHHHHHHHH
Confidence 677777777888889 99999999988764
No 184
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.66 E-value=94 Score=26.61 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=18.7
Q ss_pred CCccHHHHHHHHHhcC-CHHHHHHHh
Q 020010 275 PGFGRKTALKLLKKHG-SLENLLNAA 299 (332)
Q Consensus 275 ~GIG~KTA~kLL~~yg-sle~il~~~ 299 (332)
.|||..+|.+++++-| +.+.-...+
T Consensus 23 yGIG~~~a~~I~~~~gi~~~~r~~eL 48 (121)
T COG0099 23 YGIGRRRAKEICKKAGIDPDKRVGEL 48 (121)
T ss_pred ccccHHHHHHHHHHcCCCHhHhhccC
Confidence 8999999999999887 444444333
No 185
>PLN02743 nicotinamidase
Probab=20.19 E-value=1.2e+02 Score=28.52 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=35.3
Q ss_pred HHHHHhcCCCcEEecCCchHHHHHH---HHHHHHHhCCC-----eEEEEc
Q 020010 168 ILDVLGKCNVPVVKIEGHEADDVIA---TLVGQVLQKGY-----RAVVAS 209 (332)
Q Consensus 168 i~elL~~~gi~~i~~~g~EADDvIA---tLa~~~~~~g~-----~v~IvS 209 (332)
+.++|+..||..+..-|...|=++- +-++.+...|+ +|+|++
T Consensus 142 L~~~Lr~~gI~~liv~Gv~T~~CV~~~~sTardA~~~Gy~~~~~~V~Vv~ 191 (239)
T PLN02743 142 FVDWVNNNKIKVILVVGICTDICVLDFVASALSARNHGILPPLEDVVVYS 191 (239)
T ss_pred HHHHHHHCCCCEEEEEEeCcchhccChHHHHHHHHHcCCCCCCceEEEeC
Confidence 4567888999999999999999984 66788888999 788875
Done!