Query 016711
Match_columns 384
No_of_seqs 315 out of 1870
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 09:18:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016711.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016711hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 1.5E-88 3.2E-93 671.4 40.6 350 1-351 1-351 (393)
2 TIGR03674 fen_arch flap struct 100.0 7.1E-78 1.5E-82 587.0 35.6 329 1-346 1-338 (338)
3 KOG2519 5'-3' exonuclease [Rep 100.0 8E-76 1.7E-80 569.5 26.4 347 1-352 1-348 (449)
4 PRK03980 flap endonuclease-1; 100.0 4.1E-71 9E-76 527.6 32.7 282 55-346 1-292 (292)
5 cd00128 XPG Xeroderma pigmento 100.0 1.2E-68 2.6E-73 520.4 33.4 315 1-328 1-315 (316)
6 KOG2518 5'-3' exonuclease [Rep 100.0 4.4E-52 9.4E-57 407.6 22.1 280 1-294 1-288 (556)
7 PRK14976 5'-3' exonuclease; Pr 100.0 1.4E-47 3E-52 364.6 24.5 264 28-319 3-281 (281)
8 TIGR00600 rad2 DNA excision re 100.0 8.1E-48 1.8E-52 411.3 22.8 218 128-350 763-1006(1034)
9 smart00475 53EXOc 5'-3' exonuc 100.0 4.8E-47 1E-51 356.9 21.3 209 29-268 2-220 (259)
10 COG0258 Exo 5'-3' exonuclease 100.0 5.7E-44 1.2E-48 346.2 26.0 291 21-346 4-309 (310)
11 cd00008 53EXOc 5'-3' exonuclea 100.0 3.5E-44 7.7E-49 335.1 20.8 207 29-269 2-218 (240)
12 TIGR00593 pola DNA polymerase 100.0 7.3E-44 1.6E-48 383.2 24.5 259 30-320 1-277 (887)
13 PRK05755 DNA polymerase I; Pro 100.0 2.9E-42 6.2E-47 375.0 24.1 261 28-320 2-278 (880)
14 PRK09482 flap endonuclease-lik 100.0 2.3E-41 4.9E-46 315.7 20.9 208 28-275 3-223 (256)
15 KOG2520 5'-3' exonuclease [Rep 100.0 1.3E-36 2.9E-41 315.7 15.3 213 131-348 460-701 (815)
16 PHA00439 exonuclease 100.0 2.8E-30 6.2E-35 242.7 17.5 196 27-263 5-219 (286)
17 PHA02567 rnh RnaseH; Provision 99.9 4.7E-26 1E-30 215.1 18.0 182 27-243 13-206 (304)
18 PF02739 5_3_exonuc_N: 5'-3' e 99.9 1.3E-26 2.9E-31 205.1 10.9 158 29-217 2-169 (169)
19 PF00867 XPG_I: XPG I-region; 99.9 9.7E-25 2.1E-29 175.0 6.7 88 147-234 1-94 (94)
20 PF00752 XPG_N: XPG N-terminal 99.9 1.9E-23 4.2E-28 169.7 9.4 100 1-107 1-100 (101)
21 smart00485 XPGN Xeroderma pigm 99.9 1.1E-22 2.5E-27 164.6 9.0 97 1-107 1-98 (99)
22 TIGR00600 rad2 DNA excision re 99.8 5.2E-20 1.1E-24 198.3 11.0 103 1-113 1-103 (1034)
23 smart00484 XPGI Xeroderma pigm 99.8 3.2E-19 7E-24 135.3 7.4 73 147-219 1-73 (73)
24 cd00080 HhH2_motif Helix-hairp 99.6 2.8E-15 6.1E-20 114.8 6.0 52 216-267 2-55 (75)
25 PF01367 5_3_exonuc: 5'-3' exo 99.5 3E-16 6.5E-21 126.4 -6.8 91 219-310 1-101 (101)
26 smart00279 HhH2 Helix-hairpin- 99.2 6.4E-12 1.4E-16 81.8 3.9 33 221-254 1-36 (36)
27 PF12813 XPG_I_2: XPG domain c 99.0 7.6E-10 1.6E-14 103.9 6.4 92 137-231 4-109 (246)
28 PF03159 XRN_N: XRN 5'-3' exon 98.6 2.9E-07 6.4E-12 85.7 10.5 179 1-187 1-222 (237)
29 PF04599 Pox_G5: Poxvirus G5 p 98.3 3.2E-05 7E-10 76.5 16.4 240 1-266 1-274 (425)
30 PHA03065 Hypothetical protein; 98.2 9.5E-05 2.1E-09 72.8 16.6 235 1-265 1-275 (438)
31 KOG2045 5'-3' exonuclease XRN1 97.6 0.00053 1.1E-08 73.0 11.6 243 1-251 1-307 (1493)
32 COG5049 XRN1 5'-3' exonuclease 97.4 0.0016 3.5E-08 67.8 11.8 243 1-251 1-336 (953)
33 COG5366 Protein involved in pr 97.0 0.00034 7.3E-09 69.5 2.0 100 141-242 133-233 (531)
34 PF05991 NYN_YacP: YacP-like N 96.2 0.0082 1.8E-07 53.1 5.5 38 149-186 66-109 (166)
35 TIGR00084 ruvA Holliday juncti 96.1 0.032 6.8E-07 50.5 8.8 113 210-331 53-172 (191)
36 PF12826 HHH_2: Helix-hairpin- 95.8 0.0065 1.4E-07 44.9 2.3 27 237-263 6-32 (64)
37 KOG2044 5'-3' exonuclease HKE1 95.6 0.091 2E-06 55.9 10.4 239 1-244 1-352 (931)
38 PRK14605 ruvA Holliday junctio 94.4 0.12 2.5E-06 46.9 6.7 113 210-331 54-173 (194)
39 PRK00116 ruvA Holliday junctio 94.3 0.16 3.5E-06 45.9 7.3 107 214-331 58-174 (192)
40 PRK14600 ruvA Holliday junctio 94.0 0.34 7.4E-06 43.6 8.8 110 210-331 54-170 (186)
41 PRK13901 ruvA Holliday junctio 93.5 0.3 6.5E-06 44.3 7.4 110 210-331 53-169 (196)
42 COG0632 RuvA Holliday junction 93.2 1.4 3.1E-05 40.1 11.4 118 207-333 51-183 (201)
43 PRK14606 ruvA Holliday junctio 93.0 0.35 7.6E-06 43.6 7.1 108 210-331 54-168 (188)
44 PRK14671 uvrC excinuclease ABC 93.0 0.53 1.2E-05 50.2 9.5 40 217-262 557-597 (621)
45 PRK14604 ruvA Holliday junctio 92.8 0.56 1.2E-05 42.6 8.2 108 213-331 57-174 (195)
46 PF11977 RNase_Zc3h12a: Zc3h12 92.8 0.41 8.9E-06 41.7 7.1 47 28-89 2-48 (155)
47 PRK14603 ruvA Holliday junctio 92.8 0.57 1.2E-05 42.6 8.2 111 212-331 55-177 (197)
48 PRK14601 ruvA Holliday junctio 92.4 0.45 9.8E-06 42.7 6.9 106 210-330 54-166 (183)
49 PRK14667 uvrC excinuclease ABC 91.4 0.15 3.2E-06 53.7 3.1 29 235-263 515-543 (567)
50 PF10391 DNA_pol_lambd_f: Fing 91.4 0.17 3.7E-06 35.7 2.4 25 238-262 6-31 (52)
51 PF00633 HHH: Helix-hairpin-he 91.4 0.15 3.4E-06 31.6 2.0 15 238-252 15-29 (30)
52 TIGR00194 uvrC excinuclease AB 91.4 0.15 3.2E-06 53.9 3.0 29 235-263 542-570 (574)
53 PF14520 HHH_5: Helix-hairpin- 91.2 0.19 4.1E-06 36.3 2.6 25 238-262 9-34 (60)
54 PRK14669 uvrC excinuclease ABC 91.2 0.15 3.4E-06 54.1 2.9 27 237-263 555-581 (624)
55 PRK14602 ruvA Holliday junctio 91.1 0.31 6.6E-06 44.5 4.5 112 211-331 56-180 (203)
56 PRK14670 uvrC excinuclease ABC 91.1 0.17 3.7E-06 53.3 3.1 29 235-263 515-543 (574)
57 PRK14672 uvrC excinuclease ABC 89.1 0.31 6.8E-06 51.9 3.1 29 235-263 609-637 (691)
58 COG2454 Uncharacterized conser 87.1 4 8.6E-05 36.9 8.3 26 21-46 59-84 (211)
59 PRK00558 uvrC excinuclease ABC 85.4 0.63 1.4E-05 49.5 2.9 27 237-263 546-572 (598)
60 PRK14668 uvrC excinuclease ABC 85.2 0.67 1.5E-05 49.0 3.0 28 236-263 527-554 (577)
61 PRK14666 uvrC excinuclease ABC 85.1 0.69 1.5E-05 49.5 3.0 27 237-263 640-666 (694)
62 smart00278 HhH1 Helix-hairpin- 85.0 0.77 1.7E-05 27.3 2.0 17 237-253 4-20 (26)
63 PRK12766 50S ribosomal protein 85.0 0.71 1.5E-05 42.7 2.6 28 236-263 5-33 (232)
64 PF02371 Transposase_20: Trans 84.5 0.86 1.9E-05 35.5 2.6 24 236-259 4-27 (87)
65 COG0322 UvrC Nuclease subunit 81.9 1.1 2.4E-05 47.2 3.0 29 235-263 531-559 (581)
66 PRK14601 ruvA Holliday junctio 81.4 1.8 4E-05 38.8 3.8 47 205-253 78-127 (183)
67 COG1948 MUS81 ERCC4-type nucle 81.1 1.4 3E-05 41.5 3.0 26 238-263 186-211 (254)
68 TIGR01448 recD_rel helicase, p 78.5 4 8.7E-05 44.5 6.0 39 219-265 75-113 (720)
69 PRK14603 ruvA Holliday junctio 78.4 2.6 5.5E-05 38.3 3.8 49 205-255 77-128 (197)
70 PRK13901 ruvA Holliday junctio 78.0 2.6 5.6E-05 38.3 3.6 46 206-253 78-126 (196)
71 PRK14606 ruvA Holliday junctio 77.1 3 6.5E-05 37.6 3.8 47 205-253 78-127 (188)
72 PRK14600 ruvA Holliday junctio 76.3 3.5 7.5E-05 37.1 4.0 48 205-254 78-127 (186)
73 PRK14602 ruvA Holliday junctio 76.1 3.1 6.8E-05 37.9 3.7 48 205-254 79-129 (203)
74 PRK02515 psbU photosystem II c 75.4 2.5 5.4E-05 35.6 2.6 24 239-262 66-91 (132)
75 PRK14604 ruvA Holliday junctio 75.3 3.6 7.8E-05 37.3 3.8 48 205-254 78-128 (195)
76 TIGR00575 dnlj DNA ligase, NAD 71.3 3.6 7.9E-05 44.2 3.4 25 238-262 502-526 (652)
77 TIGR00596 rad1 DNA repair prot 69.7 3.9 8.3E-05 45.1 3.2 25 238-262 761-785 (814)
78 PF11798 IMS_HHH: IMS family H 69.6 3.5 7.5E-05 25.9 1.7 13 238-250 15-27 (32)
79 PRK14351 ligA NAD-dependent DN 69.1 4.5 9.7E-05 43.8 3.4 25 238-262 532-556 (689)
80 TIGR01259 comE comEA protein. 68.6 5.3 0.00011 33.2 3.1 17 238-254 72-88 (120)
81 PRK13482 DNA integrity scannin 67.7 12 0.00026 37.0 5.8 54 210-263 243-316 (352)
82 PF01927 Mut7-C: Mut7-C RNAse 64.4 6.4 0.00014 33.9 2.9 89 137-233 7-99 (147)
83 COG0632 RuvA Holliday junction 64.3 11 0.00024 34.4 4.5 71 173-253 49-127 (201)
84 cd00141 NT_POLXc Nucleotidyltr 63.1 7.5 0.00016 37.8 3.5 26 238-264 89-116 (307)
85 smart00483 POLXc DNA polymeras 62.7 6.6 0.00014 38.7 3.0 25 238-263 93-119 (334)
86 COG1555 ComEA DNA uptake prote 62.4 8.4 0.00018 33.4 3.3 25 238-262 101-131 (149)
87 PRK13766 Hef nuclease; Provisi 61.7 7.1 0.00015 42.8 3.4 26 238-263 719-744 (773)
88 PRK07956 ligA NAD-dependent DN 61.5 5.9 0.00013 42.7 2.6 29 140-168 239-273 (665)
89 TIGR00305 probable toxin-antit 59.0 19 0.00042 29.1 4.7 29 157-185 85-113 (114)
90 TIGR00426 competence protein C 57.4 12 0.00027 27.5 3.0 15 239-253 22-36 (69)
91 PRK08609 hypothetical protein; 55.1 20 0.00044 38.0 5.3 28 238-265 92-121 (570)
92 PTZ00134 40S ribosomal protein 54.9 14 0.00031 32.1 3.4 34 222-255 9-51 (154)
93 COG0272 Lig NAD-dependent DNA 53.6 9.6 0.00021 40.7 2.5 26 238-263 515-540 (667)
94 PF14520 HHH_5: Helix-hairpin- 53.3 13 0.00027 26.6 2.4 17 238-254 42-58 (60)
95 TIGR00084 ruvA Holliday juncti 52.7 19 0.0004 32.6 3.9 46 206-253 78-126 (191)
96 PF12826 HHH_2: Helix-hairpin- 52.5 12 0.00025 27.4 2.1 21 238-258 39-59 (64)
97 TIGR00114 lumazine-synth 6,7-d 51.0 24 0.00051 30.2 4.1 44 134-177 14-64 (138)
98 PF11731 Cdd1: Pathogenicity l 50.0 31 0.00068 27.4 4.3 31 238-268 16-55 (93)
99 PF01850 PIN: PIN domain; Int 46.0 20 0.00044 28.5 2.9 49 132-186 70-118 (121)
100 TIGR00615 recR recombination p 45.0 14 0.0003 33.5 1.9 15 238-252 15-29 (195)
101 PRK04053 rps13p 30S ribosomal 44.9 30 0.00066 30.0 3.8 34 222-255 4-46 (149)
102 PRK00076 recR recombination pr 44.8 14 0.0003 33.5 1.8 15 238-252 15-29 (196)
103 COG0353 RecR Recombinational D 44.2 13 0.00028 33.6 1.5 15 237-251 15-29 (198)
104 PRK14605 ruvA Holliday junctio 43.8 17 0.00036 32.9 2.2 44 208-253 81-127 (194)
105 KOG2841 Structure-specific end 43.2 18 0.00039 33.7 2.3 28 236-263 197-224 (254)
106 PF04019 DUF359: Protein of un 42.2 28 0.0006 29.1 3.1 18 73-90 3-21 (121)
107 PF12482 DUF3701: Phage integr 41.9 32 0.00069 27.5 3.3 41 213-253 28-69 (96)
108 PRK12419 riboflavin synthase s 41.9 29 0.00064 30.3 3.3 45 133-177 23-74 (158)
109 PRK13844 recombination protein 41.1 17 0.00038 33.0 1.9 15 238-252 19-33 (200)
110 PF14490 HHH_4: Helix-hairpin- 40.7 62 0.0013 25.4 4.8 31 241-273 19-49 (94)
111 COG1412 Uncharacterized protei 39.6 80 0.0017 26.9 5.5 47 145-191 71-121 (136)
112 PF00885 DMRL_synthase: 6,7-di 36.7 45 0.00098 28.6 3.7 44 134-177 17-67 (144)
113 PLN02404 6,7-dimethyl-8-ribity 36.2 52 0.0011 28.2 3.9 44 134-177 21-71 (141)
114 PF00416 Ribosomal_S13: Riboso 36.0 34 0.00074 27.7 2.7 18 238-255 19-36 (107)
115 TIGR01083 nth endonuclease III 35.9 41 0.00088 30.1 3.4 15 238-252 110-124 (191)
116 PRK00061 ribH 6,7-dimethyl-8-r 35.8 49 0.0011 28.8 3.8 44 134-177 26-76 (154)
117 COG1569 Predicted nucleic acid 35.3 58 0.0013 27.8 4.0 46 159-216 91-136 (142)
118 PF05687 DUF822: Plant protein 35.2 1.8E+02 0.0039 25.0 6.9 69 89-188 5-73 (150)
119 TIGR03629 arch_S13P archaeal r 35.0 52 0.0011 28.3 3.8 17 239-255 26-42 (144)
120 PF05182 Fip1: Fip1 motif; In 34.5 64 0.0014 22.0 3.3 36 296-334 9-44 (45)
121 PRK01229 N-glycosylase/DNA lya 34.4 25 0.00055 32.2 1.8 15 238-252 123-137 (208)
122 COG0177 Nth Predicted EndoIII- 34.3 43 0.00092 30.8 3.3 17 239-255 114-131 (211)
123 PF14579 HHH_6: Helix-hairpin- 33.1 53 0.0011 25.5 3.3 27 238-264 31-62 (90)
124 PF04919 DUF655: Protein of un 32.7 45 0.00098 29.8 3.1 46 219-265 96-152 (181)
125 COG1656 Uncharacterized conser 32.5 62 0.0014 28.5 3.8 55 136-191 12-69 (165)
126 PF14716 HHH_8: Helix-hairpin- 31.5 34 0.00074 25.1 1.8 14 237-250 50-63 (68)
127 PF04900 Fcf1: Fcf1; InterPro 31.4 48 0.001 26.3 2.8 40 153-192 46-90 (101)
128 TIGR03252 uncharacterized HhH- 31.2 28 0.00062 31.0 1.6 16 238-253 119-134 (177)
129 COG0258 Exo 5'-3' exonuclease 31.0 27 0.00059 33.8 1.6 30 136-166 103-132 (310)
130 PF10454 DUF2458: Protein of u 30.3 1.3E+02 0.0027 26.1 5.4 37 122-158 90-126 (150)
131 cd00056 ENDO3c endonuclease II 30.0 34 0.00075 29.2 1.9 15 238-252 87-101 (158)
132 PRK10702 endonuclease III; Pro 29.7 33 0.00072 31.4 1.8 15 238-252 113-127 (211)
133 COG3688 Predicted RNA-binding 29.7 70 0.0015 28.1 3.6 56 28-90 3-59 (173)
134 TIGR00028 Mtu_PIN_fam Mycobact 29.4 54 0.0012 26.9 3.0 32 159-191 105-136 (142)
135 KOG3165 Predicted nucleic-acid 28.8 42 0.00091 29.4 2.1 28 159-186 137-164 (195)
136 PF14229 DUF4332: Domain of un 28.7 1.4E+02 0.0031 24.7 5.3 49 209-260 31-80 (122)
137 PRK10674 deoxyribodipyrimidine 28.2 1.1E+02 0.0023 31.7 5.4 13 242-254 203-215 (472)
138 PF09550 DUF2376: Conserved hy 27.9 1.9E+02 0.004 19.6 4.7 34 218-256 10-43 (43)
139 TIGR03631 bact_S13 30S ribosom 27.8 54 0.0012 27.0 2.6 17 239-255 20-36 (113)
140 PRK00124 hypothetical protein; 27.7 64 0.0014 28.0 3.1 91 159-263 56-146 (151)
141 PRK14350 ligA NAD-dependent DN 27.4 54 0.0012 35.5 3.2 25 238-262 506-531 (669)
142 TIGR02766 crypt_chrom_pln cryp 27.3 1.4E+02 0.003 30.7 6.1 32 297-331 307-338 (475)
143 TIGR03556 photolyase_8HDF deox 27.2 1.1E+02 0.0025 31.5 5.4 32 139-170 57-88 (471)
144 PF09288 UBA_3: Fungal ubiquit 27.0 81 0.0018 22.5 2.9 31 299-331 4-34 (55)
145 PRK13913 3-methyladenine DNA g 26.9 41 0.0009 31.0 1.9 15 238-252 125-139 (218)
146 PRK00116 ruvA Holliday junctio 26.8 47 0.001 29.9 2.2 18 238-255 112-129 (192)
147 TIGR02236 recomb_radA DNA repa 26.7 53 0.0011 31.6 2.8 25 238-262 3-28 (310)
148 smart00478 ENDO3c endonuclease 26.5 44 0.00095 28.3 1.9 15 238-252 76-90 (149)
149 PRK14487 cbb3-type cytochrome 26.2 91 0.002 28.7 3.9 15 158-172 194-208 (217)
150 PRK05179 rpsM 30S ribosomal pr 25.5 61 0.0013 27.0 2.5 17 239-255 22-38 (122)
151 cd06167 LabA_like LabA_like pr 25.4 1.1E+02 0.0023 25.7 4.1 46 142-187 57-116 (149)
152 COG2266 GTP:adenosylcobinamide 25.3 93 0.002 27.7 3.7 46 135-180 48-95 (177)
153 COG1491 Predicted RNA-binding 24.5 83 0.0018 28.2 3.2 45 220-265 111-166 (202)
154 CHL00137 rps13 ribosomal prote 23.9 69 0.0015 26.7 2.5 17 239-255 22-38 (122)
155 PRK00254 ski2-like helicase; P 22.9 66 0.0014 35.1 2.9 26 238-263 649-675 (720)
156 PF04895 DUF651: Archaeal prot 22.6 1.8E+02 0.004 23.8 4.7 54 278-345 57-110 (110)
157 PRK10308 3-methyl-adenine DNA 22.5 48 0.001 31.8 1.5 19 238-256 211-230 (283)
158 PRK09982 universal stress prot 22.5 2.5E+02 0.0054 23.3 5.8 28 150-177 81-108 (142)
159 PLN03060 inositol phosphatase- 22.4 2.7E+02 0.0059 25.5 6.2 102 211-328 76-179 (206)
160 PF01936 NYN: NYN domain; Int 22.1 1.2E+02 0.0027 24.9 3.9 46 142-187 52-112 (146)
161 PRK13910 DNA glycosylase MutY; 21.6 87 0.0019 30.2 3.1 14 239-252 77-90 (289)
162 PF00875 DNA_photolyase: DNA p 21.2 99 0.0021 26.6 3.2 39 136-174 52-90 (165)
163 cd04246 AAK_AK-DapG-like AAK_A 20.3 6.7E+02 0.014 22.9 10.8 30 64-93 16-45 (239)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.5e-88 Score=671.42 Aligned_cols=350 Identities=59% Similarity=1.008 Sum_probs=334.3
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhc-cCCCcccCcCCCchhHHHHHHHHHHHHHHcC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGR-TGTEMLTNEAGEVTSHLQGMFTRTIRLLEAG 79 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~-~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~g 79 (384)
|||+||+++|++.+|.++++.+++.|+|++|||||++||||++++++. ..+.+|+|+.|++|+|++||++++++|+++|
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~g 80 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAG 80 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCC
Confidence 999999999999999999999999999999999999999999999974 3455799999999999999999999999999
Q ss_pred CceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchH
Q 016711 80 MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSE 159 (384)
Q Consensus 80 i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~E 159 (384)
|+|+|||||.+|++|++++++|+++|+++++.+.++.+.|+.+++.++++|++.+|++|++.++++|+.||||||+||||
T Consensus 81 ikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~E 160 (393)
T PTZ00217 81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE 160 (393)
T ss_pred CCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC
Q 016711 160 AEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI 239 (384)
Q Consensus 160 ADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i 239 (384)
||||||+|++.|.+++|+|+|+|+|+||++.++++++..+..+.++++|+.+.+++.+|++++||+|+|+|+||||++||
T Consensus 161 Adaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi 240 (393)
T PTZ00217 161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI 240 (393)
T ss_pred HHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC
Confidence 99999999999999999999999999999999999876444455678999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCC
Q 016711 240 RGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN 319 (384)
Q Consensus 240 ~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~ 319 (384)
||||||||++||++|+++|+|+++++..++.+|++|++.+++.+|++|.|..+.++ +|.|++||.++|++||+++++|+
T Consensus 241 ~GIG~ktA~~Li~~~gsle~il~~~~~~k~~~p~~~~~~~~~~~f~~p~V~~~~~~-~l~w~~pD~~~l~~fl~~e~~f~ 319 (393)
T PTZ00217 241 KGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPENFDYKEARELFLNPEVTPAEEI-DLKWNEPDEEGLKKFLVKEKNFN 319 (393)
T ss_pred CCccHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCCChHHHHHHhcCCCcCCCCCC-CCCCCCCCHHHHHHHHHhccCCC
Confidence 99999999999999999999999999989999999999999999999999977666 79999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhccCCCCccccccCcCcC
Q 016711 320 SDRVTKAIEKIKAAKNKSSQGRLESFFKPVAN 351 (384)
Q Consensus 320 ~~~v~~~~~~l~~~~~~~~q~~l~~ff~~~~~ 351 (384)
++||++.|+||+++.+..+|+|||+||++.++
T Consensus 320 ~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~ 351 (393)
T PTZ00217 320 EERVEKYIERLKKAKTKKTQTRLDSFFTATKK 351 (393)
T ss_pred HHHHHHHHHHHHHHhccCccCCHHHhcCCCCC
Confidence 99999999999999888899999999998765
No 2
>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=7.1e-78 Score=587.01 Aligned_cols=329 Identities=44% Similarity=0.774 Sum_probs=306.4
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGM 80 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi 80 (384)
||| |||++|. .++.+++.|+|++|+||||+||||++++++...+.+++++.|++|+|++|+++++++|+++||
T Consensus 1 MGi-~l~~~~~------~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i 73 (338)
T TIGR03674 1 MGV-DLRDLLA------KEEIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGI 73 (338)
T ss_pred CCC-ChHHHhc------cCccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCC
Confidence 999 9999998 478899999999999999999999999997555678999999999999999999999999999
Q ss_pred ceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchHH
Q 016711 81 KPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEA 160 (384)
Q Consensus 81 ~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~EA 160 (384)
+|+|||||.+|++|.+++++|+++|+++++.+..+.+.|+.+++.++++|+..+|.+|++.++++|++|||||++|||||
T Consensus 74 ~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EA 153 (338)
T TIGR03674 74 KPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEG 153 (338)
T ss_pred eEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCc---------ceEEEeHHHHHHHhCCCHHHHHHHHHHh
Q 016711 161 EAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------PVMEFEVAKILEELNLTMDQFIDLCILS 231 (384)
Q Consensus 161 Da~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~---------~~~~~~~~~v~~~~gl~~~q~id~~~L~ 231 (384)
|||||+|++.|.+++|+|+|+|+|+||+++|++++...+.++. ..+.++.+.+++.+|++++||+|+|+|+
T Consensus 154 eaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~ 233 (338)
T TIGR03674 154 EAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILV 233 (338)
T ss_pred HHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhc
Confidence 9999999999999999999999999999999999876543221 3456999999999999999999999999
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHH
Q 016711 232 GCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINF 311 (384)
Q Consensus 232 G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f 311 (384)
||||++||||||||||++||++||++|+|+++++.. + + ++.+++++|.+|.|+.. . ++.|..||.++|.+|
T Consensus 234 G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~~---~-~--~~~~~~~~f~~~~v~~~--~-~~~~~~pd~e~l~~f 304 (338)
T TIGR03674 234 GTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGED---I-E--NYDEIREFFLNPPVTDD--Y-ELKWRKPDKEGIIEF 304 (338)
T ss_pred CCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcCC---C-C--CHHHHHHHhCCCCCCCC--C-CccCCCCCHHHHHHH
Confidence 999999999999999999999999999999997632 2 2 35799999999999853 4 789999999999999
Q ss_pred HHHhcCCCHHHHHHHHHHHHHhhccCCCCcccccc
Q 016711 312 LVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 346 (384)
Q Consensus 312 ~~~~~~f~~~~v~~~~~~l~~~~~~~~q~~l~~ff 346 (384)
++++++|+++||++.++||+++. +++|+|||+||
T Consensus 305 l~~e~~~~~~rv~~~~~~l~~~~-~~~q~~l~~ff 338 (338)
T TIGR03674 305 LCDEHDFSEDRVERALERLEAAY-KSKQKTLDRWF 338 (338)
T ss_pred HhhcCCCCHHHHHHHHHHHHHhh-cccccchhhcC
Confidence 99999999999999999999887 88999999998
No 3
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=8e-76 Score=569.54 Aligned_cols=347 Identities=60% Similarity=1.003 Sum_probs=332.5
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGM 80 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi 80 (384)
|||+||.+.+.+.+|+|+++.+++.|+|++||||||+||||++.+++.. ++..|++|+||.|+|+|+++|+++||
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~-----~~~~~~~~~HL~g~f~Rt~~l~~~gi 75 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSC-----RNEAGEPTSHLMGMFYRTIRLIENGI 75 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccc-----cccCCCchHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999999999999999998632 67789999999999999999999999
Q ss_pred ceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchHH
Q 016711 81 KPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEA 160 (384)
Q Consensus 81 ~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~EA 160 (384)
+|||||||.+|.+|.+++.+|..+|..+.+....+.+.|.....++|.+|.+.||.+++++|+.+|.+|||||+.||+||
T Consensus 76 ~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EA 155 (449)
T KOG2519|consen 76 KPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEA 155 (449)
T ss_pred cEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCC
Q 016711 161 EAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIR 240 (384)
Q Consensus 161 Da~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~ 240 (384)
+||||+|+++|.|++++|+|||.+.||++.+++++..+.+...++.+|+++.+++.++++.++|+|+|+|+|||||++|.
T Consensus 156 EAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~ 235 (449)
T KOG2519|consen 156 EAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPTIR 235 (449)
T ss_pred HHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCccccccc
Confidence 99999999999999999999999999999999999876677889999999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHHHhCCHHHHHH-HHhhccCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCC
Q 016711 241 GIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN 319 (384)
Q Consensus 241 giG~ktA~~li~~~~sle~il~-~~~~~~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~ 319 (384)
|||+++|++||++|+++++|++ +.+..++.+|++|++..++.+|..|+++.+...-++.|..||.+++.+|++.+.+|+
T Consensus 236 Gig~~~al~lir~~~~i~~ile~~~~~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~~~i~w~~pd~~~li~fl~~~~~f~ 315 (449)
T KOG2519|consen 236 GIGPKKALKLIRQHGDIENILEINSDLKEYPIPEDWSYKLARKLFLEPEFPNPESILDLKWKTPDTEGLIQFLVGEKQFN 315 (449)
T ss_pred ccChHHHHHHHHHhcCHHHHhhhccchhhcCCCCCccHHHHHHHhcCcccCCccceeecccCCCChHHHHHHHHhhhccC
Confidence 9999999999999999999999 766668899999999999999999999988773489999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhccCCCCccccccCcCcCC
Q 016711 320 SDRVTKAIEKIKAAKNKSSQGRLESFFKPVANT 352 (384)
Q Consensus 320 ~~~v~~~~~~l~~~~~~~~q~~l~~ff~~~~~~ 352 (384)
.+||++++.++.+.++..+|+|+|+||+..++.
T Consensus 316 ~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~ 348 (449)
T KOG2519|consen 316 EERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKG 348 (449)
T ss_pred HHHHhhhhHHHhhhhccccccchhhhhcccCCC
Confidence 999999999999999999999999999987765
No 4
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=4.1e-71 Score=527.64 Aligned_cols=282 Identities=45% Similarity=0.807 Sum_probs=264.7
Q ss_pred cCcCCCchhHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccC
Q 016711 55 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 134 (384)
Q Consensus 55 ~~~~G~~t~~l~g~~~~~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~v 134 (384)
+|+.|++|+|++|||+++++|+++||+|+|||||.+|++|++++++|+++|+++++.+..+.+.|+.+++.+++++++.+
T Consensus 1 ~~~~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~v 80 (292)
T PRK03980 1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRL 80 (292)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccC
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCc---------ce
Q 016711 135 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------PV 205 (384)
Q Consensus 135 t~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~---------~~ 205 (384)
|++|++.++++|++|||||++||||||||||+|++.|.+++|+|+|+|+|+||+++|++++...+.++. ..
T Consensus 81 t~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~ 160 (292)
T PRK03980 81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKP 160 (292)
T ss_pred CHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999876543321 24
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCC-chHHHHHHh
Q 016711 206 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDW-PYQEARRLF 284 (384)
Q Consensus 206 ~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~-~~~~~~~~~ 284 (384)
+.|+.+.+++.+|++++||+|+|+|+||||++||||||||||++||++|+|+|+|+++++ .++ ++.+++++|
T Consensus 161 e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~-------~~~~~~~~~r~~f 233 (292)
T PRK03980 161 ELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG-------FEIENYDEIREFF 233 (292)
T ss_pred eeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc-------CCCCCHHHHHHHh
Confidence 579999999999999999999999999999999999999999999999999999999653 233 369999999
Q ss_pred CCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhhccCCCCcccccc
Q 016711 285 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 346 (384)
Q Consensus 285 ~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~~~~~~~~q~~l~~ff 346 (384)
++|+|+. +. +++|+.||.++|++|||++++|+++||++.++||.+++++++|+|||+||
T Consensus 234 ~~p~v~~--~~-~~~~~~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~~~~~~~~q~~l~~ff 292 (292)
T PRK03980 234 LNPPVTD--DY-ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292 (292)
T ss_pred cCCCCCC--CC-CccCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccCcccchhhcC
Confidence 9999995 44 78999999999999999999999999999999999998888999999998
No 5
>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=1.2e-68 Score=520.43 Aligned_cols=315 Identities=51% Similarity=0.840 Sum_probs=292.0
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGM 80 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi 80 (384)
|||+|||+||++.++ +.+++.|+|++|+|||++||||++++++.. ....|.+++++.+|++++..|+++||
T Consensus 1 MGI~gL~~~l~~~~~----~~~i~~l~gk~laID~~~~l~r~~~a~~~~-----~~~~g~~~~~l~~~~~rl~~L~~~~i 71 (316)
T cd00128 1 MGIKGLWPLLKPVAR----PVHLEELRGKKVAIDASIWLYQFLKACRQE-----LGSGGETTSHLQGFFYRTCRLLELGI 71 (316)
T ss_pred CchhhHHHHHHhhCC----CCCHHHhCCcEEEecHHHHHHHHHHHhhhh-----ccCCCCCcHHHHHHHHHHHHHHHCCC
Confidence 999999999998754 458999999999999999999999998531 13678999999999999999999999
Q ss_pred ceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchHH
Q 016711 81 KPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEA 160 (384)
Q Consensus 81 ~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~EA 160 (384)
+|+|||||.+|++|.++..+|+++|.+.......+++.|+.+++.++.+++..+++.|++.++++|+.+||||++||+||
T Consensus 72 ~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EA 151 (316)
T cd00128 72 KPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEA 151 (316)
T ss_pred EEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCH
Confidence 99999999999999999999999999998899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCC
Q 016711 161 EAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIR 240 (384)
Q Consensus 161 Da~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~ 240 (384)
|||||+|++.|.+++|+|+|+|+|+||+++|+++++..+. ..++.|+.+.+++.+|++++||+|+|+|+||||++|||
T Consensus 152 daq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~--~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~ 229 (316)
T cd00128 152 EAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGA--KPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGIP 229 (316)
T ss_pred HHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCC--CceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCC
Confidence 9999999999999999999999999999999998875321 34688999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCH
Q 016711 241 GIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 320 (384)
Q Consensus 241 giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~ 320 (384)
|||||||++||++|++++++++++......+|++|++.+++++|.+|.|... .. .+.|..||.++|+.|++.+++|++
T Consensus 230 giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~-~~-~~~~~~p~~~~l~~~~~~~~~~~~ 307 (316)
T cd00128 230 GIGPVTALKLIKKYGDIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDD-FI-DLRWRDPDEEGIIEFLCKEHGFNE 307 (316)
T ss_pred CccHHHHHHHHHHcCChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCC-CC-ceeecCCCHHHHHHHccCCCCCCH
Confidence 9999999999999999999999998877788899999999999999998854 22 689999999999999999999999
Q ss_pred HHHHHHHH
Q 016711 321 DRVTKAIE 328 (384)
Q Consensus 321 ~~v~~~~~ 328 (384)
+||.+.+.
T Consensus 308 ~rv~~~~~ 315 (316)
T cd00128 308 DRVLKPLE 315 (316)
T ss_pred HHHHhhhc
Confidence 99998774
No 6
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-52 Score=407.61 Aligned_cols=280 Identities=29% Similarity=0.469 Sum_probs=248.9
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHH-HcC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLL-EAG 79 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll-~~g 79 (384)
|||+||.+++++. .++++++.|+|+++||||++||||+..+|.. .-..|.+|.....||..-++|| .+|
T Consensus 1 MGI~GLlp~~k~~----~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~------el~~~~pT~ryi~y~ik~v~lL~~~g 70 (556)
T KOG2518|consen 1 MGIQGLLPLLKPA----LKPIHISEYKGKTVAVDGYCWLHRGALACAE------KLAKGKPTDRYIQFFIKRVKLLLSYG 70 (556)
T ss_pred CCcchhHHHHHHH----hhhhhHHHhcCceEEEehhhHHhhhHHhHHH------HHhcCCChHHHHHHHHHHHHHHHhcC
Confidence 9999999999985 6889999999999999999999999999963 2346888887777777666766 589
Q ss_pred CceEEEEeCCCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchH
Q 016711 80 MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSE 159 (384)
Q Consensus 80 i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~E 159 (384)
|+|+.||||.+.+.|..+..+|+.+|++..+..++.+..|+..++..++++++.||++|...+.++|+..||+||+||||
T Consensus 71 ikPilVFDG~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyE 150 (556)
T KOG2518|consen 71 IKPILVFDGDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYE 150 (556)
T ss_pred CeEEEEecCCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhC----CCHHHHHHHHHHhCCCC
Q 016711 160 AEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELN----LTMDQFIDLCILSGCDY 235 (384)
Q Consensus 160 ADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~g----l~~~q~id~~~L~G~Dy 235 (384)
||||+|||.+.|.+++|||+|||+++||++.|+..+...+. ..+++...+-+..+ ++.++|..+|+|.||||
T Consensus 151 ADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~----~le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDY 226 (556)
T KOG2518|consen 151 ADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGN----GLEINRSKLPECKPLGDKFTEEKFRRMCILSGCDY 226 (556)
T ss_pred ccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCC----cccccHhhhhhccccccccCHHHHHHHHHhcCCcc
Confidence 99999999999999999999999999999999988876443 35567766655443 57899999999999999
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHH-HHhhccCCCCCCCc--hHHHHHHhCCCCCCChhh
Q 016711 236 CDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWP--YQEARRLFKEPEVVTDEE 294 (384)
Q Consensus 236 ~~~i~giG~ktA~~li~~~~sle~il~-~~~~~~~~~~~~~~--~~~~~~~~~~p~v~~~~~ 294 (384)
.++|||||.+||.++|++|.+.|.++. .+...+..+|++|. +.+|...|++.-|.++.+
T Consensus 227 l~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~tF~hQrVydP~~ 288 (556)
T KOG2518|consen 227 LSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLTFLHQRVYDPIE 288 (556)
T ss_pred cccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHhhhhhheeCchH
Confidence 999999999999999999999999975 34444668999887 467888999888876644
No 7
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=1.4e-47 Score=364.61 Aligned_cols=264 Identities=23% Similarity=0.289 Sum_probs=216.5
Q ss_pred CCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcC--CceEEEEeCCCCchhhHHHHHHHhhh
Q 016711 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKR 105 (384)
Q Consensus 28 g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R 105 (384)
.++++|||++++||+||+... ..+.+++++|.+|++++||+++++++++.. -.+++|||++.++||++.+++||++|
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~-~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR 81 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLK-QGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGR 81 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCc-cCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCC
Confidence 468999999999999999632 124588999999999999999999999742 34578999999999999999999999
Q ss_pred hcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHHc----CCeEEEEcCC
Q 016711 106 ADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASED 180 (384)
Q Consensus 106 ~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~~----g~~~~v~S~D 180 (384)
.++|+.+ ..|++.++++|+.+|||++.+|+ ||||+||+|++. |....|+|+|
T Consensus 82 ~~~p~~l-----------------------~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~D 138 (281)
T PRK14976 82 KKTPESL-----------------------ISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSD 138 (281)
T ss_pred CCCCHHH-----------------------HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence 9999988 68899999999999999999998 999999999874 5556699999
Q ss_pred CcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHH
Q 016711 181 MDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIE 258 (384)
Q Consensus 181 sD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~li~~~~sle 258 (384)
+|++|+++++|...... .. .....++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|
T Consensus 139 kDl~ql~~~~v~~~~~~--~~-~~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle 215 (281)
T PRK14976 139 KDLLQLVNENTDVLLKK--KG-TSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIE 215 (281)
T ss_pred CCcCccCCCCeEEEEec--CC-CCcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHH
Confidence 99999999876432221 11 124679999999999999999999999999 44444568999999999999999999
Q ss_pred HHHHHHhhccCCCCCCCchH-H----HHHHh-CCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCC
Q 016711 259 TILENINRERYQIPEDWPYQ-E----ARRLF-KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN 319 (384)
Q Consensus 259 ~il~~~~~~~~~~~~~~~~~-~----~~~~~-~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~ 319 (384)
+|++++++++.++.+.+... + +++|- ++.+|+.+.++.++.+.+||.+.|.+|| ++++|+
T Consensus 216 ~i~~~~~~~~~~~~~~L~~~~~~~~~s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~-~~~e~~ 281 (281)
T PRK14976 216 NIYENIDKIKKKIKNKLSEAKEKALLSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIF-EELELK 281 (281)
T ss_pred HHHHhHHHHhHHHHHHHHHhHHHHHHhhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHH-HHcCCC
Confidence 99999987754444443321 1 12222 3556776666767888899999999999 688884
No 8
>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=100.00 E-value=8.1e-48 Score=411.31 Aligned_cols=218 Identities=25% Similarity=0.434 Sum_probs=196.8
Q ss_pred hhhhccCCHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEE
Q 016711 128 SKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 207 (384)
Q Consensus 128 ~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~ 207 (384)
.+++..||.+|+..|+++|++||||||+||+|||||||+|++.|+|++|+|+|+|+|+||+++||++++.. ...+..
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~---~~~ve~ 839 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQ---NKFVEY 839 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCC---CCceEE
Confidence 56688999999999999999999999999999999999999999999999999999999999999998743 345788
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhC--CHHHHH---HHHhhc---------------
Q 016711 208 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG--SIETIL---ENINRE--------------- 267 (384)
Q Consensus 208 ~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~--sle~il---~~~~~~--------------- 267 (384)
|+.+.+++.+||+++||+++|+|+||||++|||||||+||++||++|+ ++++++ +|+...
T Consensus 840 ~~~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~~~~~~~~~~~~ 919 (1034)
T TIGR00600 840 YQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKV 919 (1034)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhccccccccchhhh
Confidence 999999999999999999999999999999999999999999999999 477666 454321
Q ss_pred -----cCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH-HhhccCCCCc
Q 016711 268 -----RYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK-AAKNKSSQGR 341 (384)
Q Consensus 268 -----~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~-~~~~~~~q~~ 341 (384)
++.+|++||+..++.+|++|.|+... ..|.|+.||.++|++||++++||+.+||++.|.++. +...+++|+|
T Consensus 920 ~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~--~~f~W~~PD~e~L~~Fl~~~~gws~eRv~~~l~plikk~~~~~~Q~~ 997 (1034)
T TIGR00600 920 KKKLRLLQLTPGFPNPAVADAYLRPVVDDSK--GSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLR 997 (1034)
T ss_pred hhcccccccCCCCCcHHHHHHhcCCCCCCCc--CCCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHccCCccC
Confidence 24689999999999999999999643 379999999999999999999999999999999974 4667889999
Q ss_pred cccccCcCc
Q 016711 342 LESFFKPVA 350 (384)
Q Consensus 342 l~~ff~~~~ 350 (384)
|++||+...
T Consensus 998 ld~FF~~~~ 1006 (1034)
T TIGR00600 998 IDSFFRLAQ 1006 (1034)
T ss_pred HHHhhCccc
Confidence 999998644
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=4.8e-47 Score=356.88 Aligned_cols=209 Identities=27% Similarity=0.410 Sum_probs=184.6
Q ss_pred CEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhhh
Q 016711 29 RKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKR 105 (384)
Q Consensus 29 ~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R 105 (384)
+.++|||++++||+||+.+ .+++++|.+|++++||+.++.++++. .+| ++|||+..++||++.+++||++|
T Consensus 2 ~lllIDg~~~i~R~~~a~~-----~l~~~~G~~t~a~~g~~~~l~~l~~~-~~p~~~~~~fD~~~~~~R~~l~p~YKa~R 75 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALP-----PLKNSKGEPTNAVYGFLRMLLKLIKE-EKPTYVAVVFDAKGKTFRHELYPEYKANR 75 (259)
T ss_pred cEEEEeCcHHHHHHHHCCC-----cccCCCCCcccHHHHHHHHHHHHHHH-cCCCeEEEEEeCCCCccccchhHHHHhCC
Confidence 4789999999999999873 48888999999999999999999974 466 78999999999999999999999
Q ss_pred hcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHHc----CCeEEEEcCC
Q 016711 106 ADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASED 180 (384)
Q Consensus 106 ~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~~----g~~~~v~S~D 180 (384)
.++|+++ ..|++.++++|+.+|||++.+|+ ||||+||+|++. |..++|+|+|
T Consensus 76 ~~~pe~L-----------------------~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~D 132 (259)
T smart00475 76 PKTPDEL-----------------------LEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGD 132 (259)
T ss_pred CCCCHHH-----------------------HHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence 9999998 67889999999999999999998 999999999984 6777899999
Q ss_pred CcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHH
Q 016711 181 MDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIE 258 (384)
Q Consensus 181 sD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~li~~~~sle 258 (384)
+|++|+++++|...... +.....+.++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|
T Consensus 133 kDl~ql~~~~v~~~~~~--~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle 210 (259)
T smart00475 133 KDLLQLVSDKVSVLDPT--KGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLE 210 (259)
T ss_pred CcHhhcCCCCEEEEecc--CCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHH
Confidence 99999999886543222 111224679999999999999999999999999 55566678999999999999999999
Q ss_pred HHHHHHhhcc
Q 016711 259 TILENINRER 268 (384)
Q Consensus 259 ~il~~~~~~~ 268 (384)
+|++++++++
T Consensus 211 ~i~~~~~~~~ 220 (259)
T smart00475 211 NILENLDKLK 220 (259)
T ss_pred HHHHHHHHHH
Confidence 9999998764
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.7e-44 Score=346.16 Aligned_cols=291 Identities=27% Similarity=0.452 Sum_probs=233.2
Q ss_pred ccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHH--cCCceEEEEeCCCCchhhHHH
Q 016711 21 QKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLE--AGMKPIYVFDGQPPDLKKQEL 98 (384)
Q Consensus 21 ~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~--~gi~Pv~VFDG~~~~~K~~~~ 98 (384)
..+..++|++++|||++|+||+|++++. .+.+..|.+++++++|+..+.++++ ..+.|++||||+++++|++++
T Consensus 4 ~~~~~~~~~l~~IDg~~~lyr~~~a~~~----~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~ 79 (310)
T COG0258 4 IQLMNKSGKLLLIDGSSLLYRALHALPQ----PLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELL 79 (310)
T ss_pred ccchhccCcEEEEechHHHHHHHHhcch----hcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHH
Confidence 4556678999999999999999999963 3777888888888888877777664 248999999999999999999
Q ss_pred HHHHhhhhc-chHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCC
Q 016711 99 AKRYSKRAD-ATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ 172 (384)
Q Consensus 99 ~~rk~~R~~-~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~ 172 (384)
++||++|++ +++++ ..|+..+.+++..+|++++..+| ||||.++++++ .|.
T Consensus 80 ~~yK~~R~~~~p~~l-----------------------~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~ 136 (310)
T COG0258 80 EEYKANREKEMPDEL-----------------------APQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGD 136 (310)
T ss_pred HHHHhCCCccCHHHH-----------------------HHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCC
Confidence 999999999 99988 67888889999999999999888 88888888876 688
Q ss_pred eEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHh-CCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHH
Q 016711 173 VYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEEL-NLTMDQFIDLCILSG--CDYCDSIRGIGGQTALK 249 (384)
Q Consensus 173 ~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~-gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~ 249 (384)
+++|+|+|+|++||+++++...... +..+...++...+.+.+ |++|+||+|+++|+| |||++||||||||||++
T Consensus 137 ~~~I~S~DkD~lql~~~~~~~~~~~---~~~~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~ 213 (310)
T COG0258 137 VVLIISGDKDLLQLVSPNVLVINGK---KGEPEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALK 213 (310)
T ss_pred eEEEEeCCcchhhhcCCCcEEEecc---CCCCcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHH
Confidence 9999999999999999996433222 11111258999999999 999999999999999 99999999999999999
Q ss_pred HHHHhCCHHHHHHHHhhccCCCCCCCchHHHHHHhCC-CCCCChhhhcccCCCCCCHHHHHHHHHHhcCCC---HHHHHH
Q 016711 250 LIRQHGSIETILENINRERYQIPEDWPYQEARRLFKE-PEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN---SDRVTK 325 (384)
Q Consensus 250 li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~~~~-p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~---~~~v~~ 325 (384)
||++||++|.++++++..+....+.+ ......+|++ +.|++..++ .+.|..++. ..+++.+++|+ ..++..
T Consensus 214 Ll~~~gs~e~i~~~~~~~~~~~~~~l-~~~~~~afl~~~l~t~~~d~-~l~~~~~~~---~~~~~~~~d~~~~~~~~~~~ 288 (310)
T COG0258 214 LLQEYGSLEGLYENLDIIKKKTREKL-LEDKEKAFLSKPLATIKTDV-PLEFDLEDI---LELLVPEHDFSKLLEERVEL 288 (310)
T ss_pred HHHHhCCHHHHHHhhhhhcchhhHHH-HHHHHHHhcCcccccccccc-cCCcCccch---hhhccCcccHHHHHHHHHHH
Confidence 99999999999999985544444432 3445566665 778776666 666777775 44554556666 566777
Q ss_pred HHHHHHHhhccCCCCcccccc
Q 016711 326 AIEKIKAAKNKSSQGRLESFF 346 (384)
Q Consensus 326 ~~~~l~~~~~~~~q~~l~~ff 346 (384)
.++++.+......|.+++.||
T Consensus 289 ~~~~l~~~~~~~~~~~~~~~~ 309 (310)
T COG0258 289 GFKRLLKAIGSVEQATLDEFF 309 (310)
T ss_pred hHHHHHHHHhhhccccccccc
Confidence 777776655444788887765
No 11
>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=3.5e-44 Score=335.07 Aligned_cols=207 Identities=27% Similarity=0.383 Sum_probs=182.6
Q ss_pred CEEEEehhHHHHHHHHhhhccCCCcccCc-CCCchhHHHHHHHHHHHHHHcC--CceEEEEeCCCCchhhHHHHHHHhhh
Q 016711 29 RKIAIDASMSIYQFLIVVGRTGTEMLTNE-AGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKR 105 (384)
Q Consensus 29 ~~i~IDas~~lyr~~~a~~~~~~~~l~~~-~G~~t~~l~g~~~~~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R 105 (384)
++++|||++++||++++.+ .+.+. .|.+|++++||+.++.++++.. ..+++||||..+++|++.+++||++|
T Consensus 2 ~~llIDg~~l~yr~~~a~~-----~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R 76 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALP-----PLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANR 76 (240)
T ss_pred cEEEEEChHHHHHHHHCCC-----CcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCC
Confidence 5799999999999999874 34455 7999999999999999999743 45688999999999999999999999
Q ss_pred hcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCCeEEEEcCC
Q 016711 106 ADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASED 180 (384)
Q Consensus 106 ~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~~~~v~S~D 180 (384)
.++|+.+ ..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..++|+|+|
T Consensus 77 ~~~p~~l-----------------------~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~D 133 (240)
T cd00008 77 KKMPEEL-----------------------REQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGD 133 (240)
T ss_pred CCCCHHH-----------------------HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence 9999998 68899999999999999999998 99999999986 47777899999
Q ss_pred CcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHH
Q 016711 181 MDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIE 258 (384)
Q Consensus 181 sD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~li~~~~sle 258 (384)
+|++|+++++|.. ....+ ...++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|
T Consensus 134 kD~~ql~~~~v~~--~~~~~----~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle 207 (240)
T cd00008 134 KDLLQLVSDNVKV--VSPMK----KKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLE 207 (240)
T ss_pred CChhhhCCCCEEE--EeCCC----ceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHH
Confidence 9999999887633 22221 3579999999999999999999999999 67777789999999999999999999
Q ss_pred HHHHHHhhccC
Q 016711 259 TILENINRERY 269 (384)
Q Consensus 259 ~il~~~~~~~~ 269 (384)
+|+++++..+.
T Consensus 208 ~i~~~~~~~~~ 218 (240)
T cd00008 208 GILENLDKIKG 218 (240)
T ss_pred HHHHhHHHHhH
Confidence 99999987543
No 12
>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=7.3e-44 Score=383.18 Aligned_cols=259 Identities=29% Similarity=0.437 Sum_probs=217.1
Q ss_pred EEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhhhh
Q 016711 30 KIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRA 106 (384)
Q Consensus 30 ~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~ 106 (384)
.++|||++++||+||+++ +.++++++|.+|++++||++++.++++. .+| ++|||++.++||++.+++||++|.
T Consensus 1 l~lIDg~~l~~Ra~~a~~---~~~l~~~~G~~t~av~Gf~~~l~~ll~~-~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~ 76 (887)
T TIGR00593 1 LLLIDGHSLAFRAYFALK---NKPLTNSKGEPTNAVYGFTKMLLKLLKE-EKPTYVAVAFDSGTPTFRHEAYAEYKANRA 76 (887)
T ss_pred CEEEeCcHHHHHHHHCCC---cccCcCCCCCEecHHHHHHHHHHHHHHh-cCCCEEEEEEcCCCCcchHHHHHHHHhCCC
Confidence 378999999999999984 1258899999999999999999999974 567 678999999999999999999999
Q ss_pred cchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHHc----CCeEEEEcCCC
Q 016711 107 DATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDM 181 (384)
Q Consensus 107 ~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~~----g~~~~v~S~Ds 181 (384)
++|+++ ..|++.++++|+++|||++.+|+ ||||+||+|++. |..++|+|+|+
T Consensus 77 ~~Pe~l-----------------------~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~Dk 133 (887)
T TIGR00593 77 PTPEEL-----------------------IEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDK 133 (887)
T ss_pred CChHHH-----------------------HHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCC
Confidence 999999 68999999999999999999999 999999999984 77778999999
Q ss_pred cccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCC---CCCCCcHHHHHHHHHHhCCHH
Q 016711 182 DSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQHGSIE 258 (384)
Q Consensus 182 D~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~---~i~giG~ktA~~li~~~~sle 258 (384)
|++|+++++|.. +..... .....++.+.+.+++|++|+||+|+++|+| |.|| ||||||||||.+||++|||+|
T Consensus 134 DllQLv~~~v~~--~~~~~~-~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~kLL~~ygsle 209 (887)
T TIGR00593 134 DLLQLVSDNVKV--LIPKGK-TSFTEITPEYVVEKYGVTPDQLVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLE 209 (887)
T ss_pred ChhhcCCCCEEE--EeccCC-CCceEEcHHHHHHHhCCCHHHHHHHHHHcC-CcccCCCCCCCcCHHHHHHHHHHcCCHH
Confidence 999999998632 222111 124579999999999999999999999999 6665 467899999999999999999
Q ss_pred HHHHHHhhccC-CCCCCCchH-HH----HHHh-CCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCH
Q 016711 259 TILENINRERY-QIPEDWPYQ-EA----RRLF-KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 320 (384)
Q Consensus 259 ~il~~~~~~~~-~~~~~~~~~-~~----~~~~-~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~ 320 (384)
+|++++++++. ++.+++... +. +.|- ++.+|+.+.+++++.+..||.+.|.+|| ++++|+.
T Consensus 210 ~i~~~~~~i~~~k~~~~L~~~~e~a~ls~~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~-~~lef~~ 277 (887)
T TIGR00593 210 NIYENLDQIKSAKMREKLIAHKEDAFLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL-QELEFKS 277 (887)
T ss_pred HHHHHHHHhccHHHHHHHHHhHHHHHHHHHhheeecCCCCCCCHHHhccCCCCHHHHHHHH-HHhCCcc
Confidence 99999998754 355544422 21 2222 3556776666667889999999999999 7999964
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=2.9e-42 Score=374.99 Aligned_cols=261 Identities=25% Similarity=0.383 Sum_probs=215.8
Q ss_pred CCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhh
Q 016711 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSK 104 (384)
Q Consensus 28 g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~ 104 (384)
.+.++|||++++||+||+.. +.+++.+|.+|++++||+.++.++++ ..+| ++|||++.++||++.+++||++
T Consensus 2 ~~~~liDg~~~~~r~~~a~~----~~~~~~~g~~~~a~~g~~~~l~~~~~-~~~p~~~~v~fD~~~~~~R~~~~~~YK~~ 76 (880)
T PRK05755 2 KTLLLIDGSSLLFRAFYALL----PTLRNSDGLPTGAVYGFLNMLLKLLK-EEKPTHVAVAFDAKGKTFRHELYPEYKAN 76 (880)
T ss_pred CeEEEEeCcHHHHHHHHCCC----CcccCCCCCcccHHHHHHHHHHHHHH-hcCCCEEEEEEECCCCccccccCHHHhCC
Confidence 35789999999999999872 46888999999999999999999996 3667 6789999999999999999999
Q ss_pred hhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCCeEEEEcC
Q 016711 105 RADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASE 179 (384)
Q Consensus 105 R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~~~~v~S~ 179 (384)
|.++|+++ ..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..++|+|+
T Consensus 77 R~~~p~~l-----------------------~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~ 133 (880)
T PRK05755 77 RPPMPEDL-----------------------REQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTG 133 (880)
T ss_pred CCCCcHHH-----------------------HHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcC
Confidence 99999998 68899999999999999999998 99999999986 4777789999
Q ss_pred CCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH
Q 016711 180 DMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSI 257 (384)
Q Consensus 180 DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~li~~~~sl 257 (384)
|+|++|+++++|.. +..... .....++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+
T Consensus 134 DkD~~ql~~~~v~~--~~~~~~-~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsl 210 (880)
T PRK05755 134 DKDLLQLVDDNVTL--LDTMGV-SKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSL 210 (880)
T ss_pred CCChhhhCCCCEEE--eeccCC-CCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCH
Confidence 99999999987622 222100 124679999999999999999999999999 4555567899999999999999999
Q ss_pred HHHHHHHhhccCCCCCCCchH-HH----HHHh-CCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCH
Q 016711 258 ETILENINRERYQIPEDWPYQ-EA----RRLF-KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 320 (384)
Q Consensus 258 e~il~~~~~~~~~~~~~~~~~-~~----~~~~-~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~ 320 (384)
|+|+++++.++.++.+++... +. +.+- +..+++.+.++.++.|..||.+.|.+|| ++++|+.
T Consensus 211 e~i~~~~~~~~~~~~~~l~~~~~~~~ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~ 278 (880)
T PRK05755 211 EGLYENLDEIKGKKKEKLRENKEQAFLSRKLATIKTDVPLEVDLEDLELQPPDREKLIALF-KELEFKS 278 (880)
T ss_pred HHHHHhHHHhchHHHHHHHHhHHHHHhhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHH-HHhCcHH
Confidence 999999998765555555432 11 1111 1334444444557889999999999999 8999964
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=2.3e-41 Score=315.66 Aligned_cols=208 Identities=21% Similarity=0.230 Sum_probs=176.5
Q ss_pred CCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCce---EEEEeCCCCc--hhhHHHHHHH
Q 016711 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPD--LKKQELAKRY 102 (384)
Q Consensus 28 g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~P---v~VFDG~~~~--~K~~~~~~rk 102 (384)
.+.++|||++++||+|++.. ++.|. |++++||++.+.++++. .+| +++||++.++ ||++.+++||
T Consensus 3 ~~llLiDg~~l~~R~~~a~~--------~~~g~-t~av~gf~~~l~~ll~~-~~p~~i~v~fD~~~~~~~fR~~l~p~YK 72 (256)
T PRK09482 3 NHLLIIDALNLIRRIHAVQP--------SPNDI-NACVETCQHALDKLIRH-SQPTHAVAVFDGDARSSGWRHQLLPDYK 72 (256)
T ss_pred CeEEEEeCcHHHHHHHhCCC--------CCCCc-chHHHHHHHHHHHHHHH-cCCCEEEEEEeCCCCCcccHHHHhHHHh
Confidence 45899999999999999852 14566 89999999999999963 445 4579998777 9999999999
Q ss_pred hhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHHc----CCeEEEE
Q 016711 103 SKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVA 177 (384)
Q Consensus 103 ~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~~----g~~~~v~ 177 (384)
++|.++|+++ ..|++.++++|.++|||++..|+ ||||+||+|+++ |.-..|+
T Consensus 73 a~R~~~Pe~l-----------------------~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~ 129 (256)
T PRK09482 73 AGRKPMPEAL-----------------------QQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIV 129 (256)
T ss_pred cCCCCCcHHH-----------------------HHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEE
Confidence 9999999999 78999999999999999999999 999999999873 5555689
Q ss_pred cCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC---CCCCcHHHHHHHHHHh
Q 016711 178 SEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQH 254 (384)
Q Consensus 178 S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~---i~giG~ktA~~li~~~ 254 (384)
|.|+|++|+..++|.. +.... .+.++.+.+.+++|++|+|++|+++|+| |.+|| |||||||||.+||++|
T Consensus 130 S~DKDl~Qlv~~~v~~--~~~~~----~~~~~~~~v~~~~Gv~P~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~~LL~~~ 202 (256)
T PRK09482 130 STDKGYCQLLSPTIQI--RDYFQ----KRWLDAPFIEQEFGVEPQQLPDYWGLAG-ISSSKIPGVAGIGPKSAAELLNQF 202 (256)
T ss_pred ECCCCccccCCCCeEE--Eeccc----cccCCHHHHHHHhCCCHHHHHHHHHHhC-CCccCCCCCCCcChHHHHHHHHHh
Confidence 9999999999888632 22211 2468999999999999999999999999 77776 5689999999999999
Q ss_pred CCHHHHHHHHhhccCCCCCCC
Q 016711 255 GSIETILENINRERYQIPEDW 275 (384)
Q Consensus 255 ~sle~il~~~~~~~~~~~~~~ 275 (384)
||+|+|++++++++.++.+.+
T Consensus 203 gsle~i~~~~~~~~~~~~~~L 223 (256)
T PRK09482 203 RSLENIYESLDALPEKWRKKL 223 (256)
T ss_pred CCHHHHHHhHHHhhHHHHHHH
Confidence 999999999987643333333
No 15
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-36 Score=315.67 Aligned_cols=213 Identities=28% Similarity=0.531 Sum_probs=186.3
Q ss_pred hccCCHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeH
Q 016711 131 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV 210 (384)
Q Consensus 131 ~~~vt~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~ 210 (384)
+-.+|..|+.+|+++|+.||||||+||+|||||||.|...+++++|||+|||+|+||+.+||+++|..++ .++.|.+
T Consensus 460 ~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~knk---~ve~y~~ 536 (815)
T KOG2520|consen 460 ADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKNK---YVEKYQL 536 (815)
T ss_pred CchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcCc---cceeeeh
Confidence 3468899999999999999999999999999999999999999999999999999999999999996543 4789999
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhC---CHHHHHHHHhh---------------------
Q 016711 211 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG---SIETILENINR--------------------- 266 (384)
Q Consensus 211 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~---sle~il~~~~~--------------------- 266 (384)
..+...||+++..+|-+|.|+|+|||.||+||||++|+++|.+|+ ++..+-+|+..
T Consensus 537 ~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~~~~~~~s~~~~~lrkkl~ 616 (815)
T KOG2520|consen 537 DDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGPADKEVGSTQQKMLRKKLK 616 (815)
T ss_pred HHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCccccccccHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999 55444445431
Q ss_pred -ccCCCCCCCchHHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHH----HHHHHHhhccCCCCc
Q 016711 267 -ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKA----IEKIKAAKNKSSQGR 341 (384)
Q Consensus 267 -~~~~~~~~~~~~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~----~~~l~~~~~~~~q~~ 341 (384)
.+..+|..||...+..+|++|.|++..+ .|.|+.||.+.|++||...+||+.++.+.. ++++.+...+..|.+
T Consensus 617 n~~~~l~~~fP~~~v~~AYLrP~VD~sk~--~f~WG~pdl~~lRef~~~~fgW~~~kT~~~l~p~~~~~~~~~~~~~~~~ 694 (815)
T KOG2520|consen 617 NPKIILPSDFPNPNVIEAYLRPEVDDSKE--KFRWGKPDLDILREFMKRLFGWPDEKTDEELIPVIKRLEKKKTQLKQDR 694 (815)
T ss_pred CcccccCcCCCchhHHHHhhCCccCCCcc--cccCCCCCHHHHHHHHHHHcCCCccccchhhhhhHHHHHHHhhhhcccc
Confidence 1246899999999999999999996655 699999999999999999999999987665 455665556667777
Q ss_pred cccccCc
Q 016711 342 LESFFKP 348 (384)
Q Consensus 342 l~~ff~~ 348 (384)
+..||-.
T Consensus 695 ~~~~f~~ 701 (815)
T KOG2520|consen 695 ISQFFED 701 (815)
T ss_pred HHHHHHh
Confidence 7777743
No 16
>PHA00439 exonuclease
Probab=99.97 E-value=2.8e-30 Score=242.72 Aligned_cols=196 Identities=15% Similarity=0.138 Sum_probs=153.7
Q ss_pred CCCEEEEehhHHHHHHHHhhhcc--CCCcccCcCCCchhHHHHHHHHHHHHHHc--CCce---EEEEeCCCCchhhHHHH
Q 016711 27 FGRKIAIDASMSIYQFLIVVGRT--GTEMLTNEAGEVTSHLQGMFTRTIRLLEA--GMKP---IYVFDGQPPDLKKQELA 99 (384)
Q Consensus 27 ~g~~i~IDas~~lyr~~~a~~~~--~~~~l~~~~G~~t~~l~g~~~~~~~ll~~--gi~P---v~VFDG~~~~~K~~~~~ 99 (384)
...+++|||++++||+||++... -+.++.+..|.+|++++||++.+.++++. ..+| +++|| ..++||++.++
T Consensus 5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~~tfR~elyp 83 (286)
T PHA00439 5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DSVNWRKEVVP 83 (286)
T ss_pred CCcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CCCChHhhhhh
Confidence 35689999999999999998311 12357899999999999999999999853 1445 35699 57899999999
Q ss_pred HHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCC-e
Q 016711 100 KRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ-V 173 (384)
Q Consensus 100 ~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~-~ 173 (384)
+||++|.++|+.. .+++.+++++..+|+|++..|| ||||.||+|++ .|. -
T Consensus 84 ~YKanR~~~p~~~------------------------~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~ 139 (286)
T PHA00439 84 TYKANRKAKRKPV------------------------GYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKK 139 (286)
T ss_pred HhcCCCCCCCCch------------------------hhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCe
Confidence 9999999887764 3567789999999999999999 99999999986 354 5
Q ss_pred EEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC---CCCcHHHHHHH
Q 016711 174 YAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKL 250 (384)
Q Consensus 174 ~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i---~giG~ktA~~l 250 (384)
.+|+|.|+|++|+....++ +.... ....++.+ .|+||+++.+|+| |.+||| |||| |||.+|
T Consensus 140 vvIvS~DKDl~QLv~~~~~---~~~~~---~~~~~~~~--------~p~~~~d~~AL~G-DsSDNIPGVpGIG-KTA~kL 203 (286)
T PHA00439 140 AVLVSCDKDFKTIPNCDFL---WCTTG---NILTQTPE--------TADRWHLFQTIKG-DSTDGYSGIPGWG-DTAEAF 203 (286)
T ss_pred EEEEeCCCCHhhcCcceEE---EccCC---ceEEcCcc--------cHHHHHhhhhccc-ccccCCCCCCCcC-HHHHHH
Confidence 5699999999999865433 11111 11113322 3899999999999 999976 5799 999999
Q ss_pred HHH---hCCHHHHHHH
Q 016711 251 IRQ---HGSIETILEN 263 (384)
Q Consensus 251 i~~---~~sle~il~~ 263 (384)
|++ |-.++.++++
T Consensus 204 L~~~~~~~~~~~~~~s 219 (286)
T PHA00439 204 LENPYIFEQVEKVLKS 219 (286)
T ss_pred HhCccccchhhHHhhc
Confidence 999 5555555554
No 17
>PHA02567 rnh RnaseH; Provisional
Probab=99.94 E-value=4.7e-26 Score=215.08 Aligned_cols=182 Identities=15% Similarity=0.108 Sum_probs=140.8
Q ss_pred CCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHH-HHHHHHHHHHc--CCc--eEEEEeCCC-CchhhHHHHH
Q 016711 27 FGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQG-MFTRTIRLLEA--GMK--PIYVFDGQP-PDLKKQELAK 100 (384)
Q Consensus 27 ~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g-~~~~~~~ll~~--gi~--Pv~VFDG~~-~~~K~~~~~~ 100 (384)
....++||||+++|+++++. +.+++|.+++.+++ ++..+.+++.. ..- .+++||++. ++||++.++.
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~-------l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~ 85 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMAN-------FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWY 85 (304)
T ss_pred CCCEEEEehHHHHHHHHHhh-------CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhH
Confidence 34589999999999999984 77888999999966 55555555531 222 256899975 7899999999
Q ss_pred HHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCCeEE
Q 016711 101 RYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYA 175 (384)
Q Consensus 101 rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~~~~ 175 (384)
||++|.++|+++...++ .+ ...+.+.+++++..+|++++..|+ ||||.+|+|++ .|....
T Consensus 86 YKAnR~~~Peel~~q~~--------~l-------~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~Vv 150 (304)
T PHA02567 86 YKKNRKKDREESPWDWE--------GL-------FEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVL 150 (304)
T ss_pred hhcCCCCCChHHHHHHH--------Hh-------hhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEE
Confidence 99999999998732110 00 012225678899999999999999 99999999987 455567
Q ss_pred EEcCCCcccccCC-CeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCc
Q 016711 176 VASEDMDSLTFGA-PRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIG 243 (384)
Q Consensus 176 v~S~DsD~l~fg~-~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG 243 (384)
|+|+|+|++|+.. ++|.. +.. ++.+.+.+++| .|+|++|+.+|+| |.+||||||-
T Consensus 151 IvS~DKDl~QLv~~~~v~~--~~~---------~~~~~V~~k~G-~P~q~iD~kaL~G-DsSDNIPGVp 206 (304)
T PHA02567 151 IVSSDGDFTQLHKYPGVKQ--WSP---------MQKKWVKPKYG-SPEKDLMTKIIKG-DKKDGVASIK 206 (304)
T ss_pred EEeCCCChhhccCCCCeEE--eec---------CCHHHHHHHhC-CHHHHHHHHHhCC-cccCCcCCCC
Confidence 9999999999984 65522 211 24577889999 5999999999999 9999999984
No 18
>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=99.94 E-value=1.3e-26 Score=205.07 Aligned_cols=158 Identities=26% Similarity=0.446 Sum_probs=130.4
Q ss_pred CEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhhh
Q 016711 29 RKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKR 105 (384)
Q Consensus 29 ~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R 105 (384)
+.++|||++++||+||+... ..+.++.|.+|++++||+..+.++++. .+| ++|||+..++||++.+++||++|
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~---~~l~~~~G~~t~ai~g~~~~l~~l~~~-~~p~~~vv~fD~~~~~fR~~l~p~YKanR 77 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPK---DPLRNSDGEPTNAIYGFLRMLLKLLKD-FKPDYVVVAFDSKGPTFRKELYPEYKANR 77 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTT---ST-BETTSEB-HHHHHHHHHHHHHHHH-TTEEEEEEEEEBSSCHHHHHCCTTTTHHH
T ss_pred eEEEEechHHHHHHHHhhcc---CCCcCCCCCChHHHHHHHHHHHHHHHH-cCCceEEEEecCCCcchHHHHHHHHHhCC
Confidence 57899999999999999853 478899999999999999999999874 444 56899998899999999999999
Q ss_pred hcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch-HHHHHHHHHHH----cCCeEEEEcCC
Q 016711 106 ADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASED 180 (384)
Q Consensus 106 ~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~-EADa~~A~L~~----~g~~~~v~S~D 180 (384)
.++|+++ ..|++.++++|+.+|++++..|| ||||.+|+|++ .|.-..|+|+|
T Consensus 78 ~~~p~~l-----------------------~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~D 134 (169)
T PF02739_consen 78 KPMPEEL-----------------------IPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGD 134 (169)
T ss_dssp HHHHHHH-----------------------HHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SS
T ss_pred CCCCHHH-----------------------HHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCC
Confidence 9999998 68899999999999999999999 99999999988 45666799999
Q ss_pred CcccccCCC--eeEEEeecCCCCCcceEEEeHHHHHHHh
Q 016711 181 MDSLTFGAP--RFLRHLMDPSSRKIPVMEFEVAKILEEL 217 (384)
Q Consensus 181 sD~l~fg~~--~v~~~l~~~~~~~~~~~~~~~~~v~~~~ 217 (384)
+|++|+..+ +|. +...+ ......++.+.+.|+|
T Consensus 135 kD~~QLv~~~~~V~--~~~~~--~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 135 KDLLQLVDENVNVY--LLDPG--KKKFKVYDPEEVEEKY 169 (169)
T ss_dssp GGGGGGTCS-TSEE--EEETT--TTCS-EB-HHHHHHHT
T ss_pred CCHHHhcCCCceEE--EeecC--CCCCEEEcHHHHhhcC
Confidence 999999999 543 33332 2235789999998875
No 19
>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=99.91 E-value=9.7e-25 Score=174.99 Aligned_cols=88 Identities=53% Similarity=0.847 Sum_probs=75.3
Q ss_pred HhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEee-cC-CC----CCcceEEEeHHHHHHHhCCC
Q 016711 147 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLM-DP-SS----RKIPVMEFEVAKILEELNLT 220 (384)
Q Consensus 147 ~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~-~~-~~----~~~~~~~~~~~~v~~~~gl~ 220 (384)
+++||||++||||||||||+|+++|.+++|+|+|||+|+||+++|+++++ .. +. ....+..++.+.+++.+|++
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~ 80 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT 80 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence 57899999999999999999999999999999999999999999999997 22 21 13568899999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 016711 221 MDQFIDLCILSGCD 234 (384)
Q Consensus 221 ~~q~id~~~L~G~D 234 (384)
++||+++|+|+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 99999999999998
No 20
>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=99.89 E-value=1.9e-23 Score=169.74 Aligned_cols=100 Identities=44% Similarity=0.745 Sum_probs=81.3
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGM 80 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi 80 (384)
|||+|||++|++.+ ++++.+++.|+|++|||||++|+||++++++. .+... ...++++.++++++..|+.+||
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~~----~~~~~-~~~~~~~~~~~~r~~~L~~~gI 73 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVSLSELRGKRVAIDASCWLHQFLFSCRE----ELGQG-VGTDSHLRGLFSRLCRLLEHGI 73 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEEGGGGTTCEEEEEHHHHHHHHHHHSBC----TTSCB--BS-HHHHHHHHHHHHHHHTTE
T ss_pred CCcccHHHHHHhhc--cCCccCHHHhCCCEEEEEcHHHHHHHHHHhHH----Hhccc-cchHHHHHHHHHHHHHHHHCCC
Confidence 99999999999985 56888999999999999999999999998753 12211 1226899999999999999999
Q ss_pred ceEEEEeCCCCchhhHHHHHHHhhhhc
Q 016711 81 KPIYVFDGQPPDLKKQELAKRYSKRAD 107 (384)
Q Consensus 81 ~Pv~VFDG~~~~~K~~~~~~rk~~R~~ 107 (384)
+|||||||.+|+.|.++..+|+.+|++
T Consensus 74 ~PifVFDG~~~~~K~~~~~~R~~~r~~ 100 (101)
T PF00752_consen 74 KPIFVFDGKPPPLKRETIQKRRKRREE 100 (101)
T ss_dssp EEEEEE--STTGGCHHHHHHHHHHHHH
T ss_pred EEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 999999999999999999999988865
No 21
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.88 E-value=1.1e-22 Score=164.63 Aligned_cols=97 Identities=49% Similarity=0.760 Sum_probs=84.5
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchh-HHHHHHHHHHHHHHcC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTS-HLQGMFTRTIRLLEAG 79 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~-~l~g~~~~~~~ll~~g 79 (384)
|||+|||++|++. .+..+++.|+|++|||||++||||++++++...+.. ..+. ++.++++++..|+++|
T Consensus 1 MGI~gL~~~l~~~----~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~~~~~~~------~~~~~~l~~~~~rl~~L~~~~ 70 (99)
T smart00485 1 MGIKGLWPLLKPV----VREVPLEALRGKTLAIDASIWLYQFLTACREKLGTP------LPNSKHLMGLFYRTCRLLEFG 70 (99)
T ss_pred CCHhHHHHHHHHh----cccCCHHHhCCceEeccHHHHHHHHHHHHhhhhcCC------CCchHHHHHHHHHHHHHHHCC
Confidence 9999999999986 477899999999999999999999999985322111 1223 8999999999999999
Q ss_pred CceEEEEeCCCCchhhHHHHHHHhhhhc
Q 016711 80 MKPIYVFDGQPPDLKKQELAKRYSKRAD 107 (384)
Q Consensus 80 i~Pv~VFDG~~~~~K~~~~~~rk~~R~~ 107 (384)
|+|||||||.+|+.|.++..+|+.+|++
T Consensus 71 I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 71 IKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred CeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 9999999999999999999999998875
No 22
>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=99.81 E-value=5.2e-20 Score=198.28 Aligned_cols=103 Identities=38% Similarity=0.548 Sum_probs=92.0
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGM 80 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi 80 (384)
|||+|||++|++. .++++++.|.|++||||||+||||++++++...+..++ .+||.|||+|+++|+.+||
T Consensus 1 MGI~GLw~ll~~~----~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~~g~~l~------n~hl~g~f~Ri~~Ll~~gI 70 (1034)
T TIGR00600 1 MGVQGLWKLLECS----GRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIK------NSHLLTLFHRLCKLLFFRI 70 (1034)
T ss_pred CChhHHHHHHHHh----cccccHHHhCCeEEEechHHHHHHHHHHHHhccCCccC------CHHHHHHHHHHHHHHHCCC
Confidence 9999999999986 47889999999999999999999999999754444443 3899999999999999999
Q ss_pred ceEEEEeCCCCchhhHHHHHHHhhhhcchHHHH
Q 016711 81 KPIYVFDGQPPDLKKQELAKRYSKRADATDDLA 113 (384)
Q Consensus 81 ~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~ 113 (384)
+|||||||.+|+.|.+++.+|+.+|+++.+...
T Consensus 71 ~PVfVFDG~~p~lK~~t~~~R~~rR~~a~~~a~ 103 (1034)
T TIGR00600 71 RPIFVFDGGAPLLKRQTLAKRRQRRDGASEDAR 103 (1034)
T ss_pred eEEEEECCCCchHhHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988766543
No 23
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.78 E-value=3.2e-19 Score=135.30 Aligned_cols=73 Identities=48% Similarity=0.752 Sum_probs=67.4
Q ss_pred HhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCC
Q 016711 147 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNL 219 (384)
Q Consensus 147 ~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl 219 (384)
+.+||||++||+|||||||+|++.|++++|+|+|+|+|+||++++++++...++...+++.++...+++.+|+
T Consensus 1 ~~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred CcCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 3589999999999999999999999999999999999999999999999877655567899999999999885
No 24
>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=99.58 E-value=2.8e-15 Score=114.81 Aligned_cols=52 Identities=50% Similarity=0.809 Sum_probs=49.5
Q ss_pred HhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhc
Q 016711 216 ELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRE 267 (384)
Q Consensus 216 ~~gl~~~q~id~~~L~G--~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~ 267 (384)
.+|++|+||+++|+|+| |||.+||||||+|||.+||++|+++++++++++..
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~ 55 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 57999999999999999 99999999999999999999999999999998764
No 25
>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=99.48 E-value=3e-16 Score=126.39 Aligned_cols=91 Identities=33% Similarity=0.448 Sum_probs=51.4
Q ss_pred CCHHHHHHHHHHhCCCCCCCC---CCCcHHHHHHHHHHhCCHHHHHHHHhhccC-CCCCCCch-----HHHHHHh-CCCC
Q 016711 219 LTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPY-----QEARRLF-KEPE 288 (384)
Q Consensus 219 l~~~q~id~~~L~G~Dy~~~i---~giG~ktA~~li~~~~sle~il~~~~~~~~-~~~~~~~~-----~~~~~~~-~~p~ 288 (384)
|+|+|++|+.+|+| |.+||| ||||+|||.+||++|||+|+|+++++.++. ++.+.+.. ..++.+. ++.+
T Consensus 1 V~P~q~~D~~aL~G-D~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~d 79 (101)
T PF01367_consen 1 VPPEQIADYKALVG-DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTD 79 (101)
T ss_dssp --GHHHHHHCCCC--CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S-
T ss_pred CCHHHHHHHHHHcC-CcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcC
Confidence 57999999999999 999986 579999999999999999999999987654 44432221 1233333 3667
Q ss_pred CCChhhhcccCCCCCCHHHHHH
Q 016711 289 VVTDEEQLQIKWSAPDEEGLIN 310 (384)
Q Consensus 289 v~~~~~~~~~~~~~pd~~~l~~ 310 (384)
|+.+.+++++.|..||.++|.+
T Consensus 80 v~l~~~l~~l~~~~~d~~~l~~ 101 (101)
T PF01367_consen 80 VPLPFSLEDLRLQPPDREKLIE 101 (101)
T ss_dssp ----------------HHHH--
T ss_pred CCCCCCcchhccCCCCHHHhcC
Confidence 7777888889999999998864
No 26
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.25 E-value=6.4e-12 Score=81.84 Aligned_cols=33 Identities=55% Similarity=0.945 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCCcHHHHHHHHHHh
Q 016711 221 MDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQH 254 (384)
Q Consensus 221 ~~q~id~~~L~G~Dy~~---~i~giG~ktA~~li~~~ 254 (384)
|+||+++|+|+| ||+| ||||||+|||++||++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 689999999999 9999 67899999999999987
No 27
>PF12813 XPG_I_2: XPG domain containing
Probab=98.97 E-value=7.6e-10 Score=103.87 Aligned_cols=92 Identities=27% Similarity=0.246 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHhc---CCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCC--CeeEEEeecC---C------CCC
Q 016711 137 QHNDDCKRLLKLM---GVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA--PRFLRHLMDP---S------SRK 202 (384)
Q Consensus 137 ~~~~~~~~lL~~~---Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~--~~v~~~l~~~---~------~~~ 202 (384)
-+.+.+.+.|+.+ |++++.+|+|||..||.+|++..+ .|+|+|||+++|.. ..-|..+..- . ...
T Consensus 4 f~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~ 82 (246)
T PF12813_consen 4 FLVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSY 82 (246)
T ss_pred chHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCe
Confidence 4567788999998 999999999999999999998777 59999999999987 3223333221 1 123
Q ss_pred cceEEEeHHHHHHHhCCCHHHHHHHHHHh
Q 016711 203 IPVMEFEVAKILEELNLTMDQFIDLCILS 231 (384)
Q Consensus 203 ~~~~~~~~~~v~~~~gl~~~q~id~~~L~ 231 (384)
.....|+.+.++..+|+. .++.+|...
T Consensus 83 i~~~~y~~~~i~~~l~l~--~Lp~lA~d~ 109 (246)
T PF12813_consen 83 ISAKVYSPDKICKRLGLP--LLPLLAYDY 109 (246)
T ss_pred eEEEEEcHHHHHHHcCCc--hhHHHHHHh
Confidence 456789999999999999 777776633
No 28
>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=98.60 E-value=2.9e-07 Score=85.71 Aligned_cols=179 Identities=20% Similarity=0.282 Sum_probs=80.1
Q ss_pred CCccchHHHHhhhcCCCccccccccc--CCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHc
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESY--FGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEA 78 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l--~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~ 78 (384)
|||+||+.||.+.-|.+++...-... .=--+.||.++++|.+.+.... ....... .-+..+|..+-.++..
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~----~~~~~~~---~~~~~i~~~id~l~~~ 73 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDS----SIPKTEE---EIFQRIFNYIDRLVRI 73 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS--------SHH---HHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCccc----CCCccHH---HHHHHHHHHHHHhhee
Confidence 99999999999988876655332211 1125899999999998765421 1100011 1223333333334432
Q ss_pred CCce---E-EEEeCCCCchhhHHHHHHHhhhhcchHHHHHHH--------HhCCH---H-HHHHHhhhhccCCHHHHHHH
Q 016711 79 GMKP---I-YVFDGQPPDLKKQELAKRYSKRADATDDLAEAV--------EAGNK---E-DIEKFSKRTVKVTKQHNDDC 142 (384)
Q Consensus 79 gi~P---v-~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~--------~~g~~---~-~~~~~~~~~~~vt~~~~~~~ 142 (384)
++| + +.+||.+|..|......|+-+............ ..|.. + ...+|..-.+..-.+-...+
T Consensus 74 -v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~ITPGT~FM~~l 152 (237)
T PF03159_consen 74 -VRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCITPGTEFMEKL 152 (237)
T ss_dssp -H-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGGSSTTSHHHHHH
T ss_pred -ecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccccceeccCCHHHHHH
Confidence 455 4 469999998777665555433322211111110 11110 0 01222222222211222222
Q ss_pred HHHHH--------h----cCCCccc----cchHHHHHHHHHHHc---------CCeEEEEcCCCcccccC
Q 016711 143 KRLLK--------L----MGVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMDSLTFG 187 (384)
Q Consensus 143 ~~lL~--------~----~Gip~i~----ap~EADa~~A~L~~~---------g~~~~v~S~DsD~l~fg 187 (384)
.+.|+ . -++.++. .|||+|--|..+.+. +...+|+|.|+|+++++
T Consensus 153 ~~~L~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 153 SDALRYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp HHHHHHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 22221 1 1344554 378999766655442 45778999999999886
No 29
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=98.29 E-value=3.2e-05 Score=76.49 Aligned_cols=240 Identities=19% Similarity=0.249 Sum_probs=125.3
Q ss_pred CCccchHHHHhhhcCCCcccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHH-HHHHHHHHHcC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGM-FTRTIRLLEAG 79 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~-~~~~~~ll~~g 79 (384)
|||++|-.+|.+. +.++..+ ...+++-|-||++++.+-..|.+.. ..-+... ..++-.+...+
T Consensus 1 MGIKNLK~lLl~~--gsL~~i~-~~~~~~~ifVD~msif~tiAysv~s-------------~~eL~~~~~~~i~~w~~~~ 64 (425)
T PF04599_consen 1 MGIKNLKALLLET--GSLKKID-NIEKNNEIFVDTMSIFMTIAYSVNS-------------LDELRNSFEEYIQQWIKNN 64 (425)
T ss_pred CchhHHHHHHHhc--CCceecc-CCCCCccEEEEcchhhhhhhhhhCC-------------HHHHHHHHHHHHHHHHhcC
Confidence 9999999999876 3344432 2234478999999988877776631 1223333 33333444444
Q ss_pred CceEEEEeCCCCchhhHHHHHHHhhhh-------cchHHHHHHHHhCC-----HHHHH--------HH-hhhhccCCHHH
Q 016711 80 MKPIYVFDGQPPDLKKQELAKRYSKRA-------DATDDLAEAVEAGN-----KEDIE--------KF-SKRTVKVTKQH 138 (384)
Q Consensus 80 i~Pv~VFDG~~~~~K~~~~~~rk~~R~-------~~~~~l~~a~~~g~-----~~~~~--------~~-~~~~~~vt~~~ 138 (384)
-+.++..|-+.-..|..+..+|+..-. +..+.+......-+ .++.+ +. +.-...-....
T Consensus 65 ~~VtlFvDRG~I~iK~~lReKRr~a~k~~~~RK~~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F~~fla~~~n~ 144 (425)
T PF04599_consen 65 GKVTLFVDRGSINIKEPLREKRRKALKNTIKRKREEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSFQLFLANSNNL 144 (425)
T ss_pred CeEEEEEecCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhcchhhH
Confidence 455555687765566666555532111 11111222211111 11111 11 00001111111
Q ss_pred HHHHHHHHHhc--CCCccccch-HHHHHHHHHHH-----cCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeH
Q 016711 139 NDDCKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV 210 (384)
Q Consensus 139 ~~~~~~lL~~~--Gip~i~ap~-EADa~~A~L~~-----~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~ 210 (384)
-..+.++|..+ +|.++.+.| .||=.+-+-|+ .|.-..++|.|-|.++|.+..-...+....+. .-.+-+
T Consensus 145 k~~l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~~~---~Y~~~P 221 (425)
T PF04599_consen 145 KTILESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTMNQ---LYKFIP 221 (425)
T ss_pred HHHHHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhHHh---HeeecC
Confidence 22345566655 899999999 99976655554 57777899999999999874321111110000 000100
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCC--cHHHH--HHHHHHhCCHHHHHHHHhh
Q 016711 211 AKILEELNLTMDQFIDLCILSGCDYCDSIRGI--GGQTA--LKLIRQHGSIETILENINR 266 (384)
Q Consensus 211 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~gi--G~ktA--~~li~~~~sle~il~~~~~ 266 (384)
. ..+.--=...++.=||||-+|+-|+ .+++- .+|...| ++++|++.+--
T Consensus 222 ~------~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~~ 274 (425)
T PF04599_consen 222 C------SKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLAI 274 (425)
T ss_pred C------chHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHhh
Confidence 0 0011111235666799999999985 44431 3333333 47888887653
No 30
>PHA03065 Hypothetical protein; Provisional
Probab=98.17 E-value=9.5e-05 Score=72.78 Aligned_cols=235 Identities=18% Similarity=0.245 Sum_probs=124.6
Q ss_pred CCccchHHHHhhhcCCCccccccccc-CCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHH-HHHHHHc
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKFESY-FGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTR-TIRLLEA 78 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l~~l-~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~-~~~ll~~ 78 (384)
|||++|-.+|-+. +.....+-... ...-|-||++++..-..|.+.. +..++..|.. +..+...
T Consensus 1 MGIKNLKtLLL~~--gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv~~-------------~~eL~~~~~~~iq~w~~~ 65 (438)
T PHA03065 1 MGIKNLKTLLLET--GSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSVNN-------------LDELRSTFEEYVQQWVKK 65 (438)
T ss_pred CchhhHHHHHHhc--CCcccccccccccCceEEEechhhhhhhhhhhCC-------------HHHHHHHHHHHHHHHHhc
Confidence 9999999999876 33444321111 2257999999988777776631 1223333333 3344343
Q ss_pred CCceEEEEeCCCCchhhHHHHHHHhhhhcc-------hHHHHHHHHhCC-----HHHHHHH-----hhhhcc---CCHHH
Q 016711 79 GMKPIYVFDGQPPDLKKQELAKRYSKRADA-------TDDLAEAVEAGN-----KEDIEKF-----SKRTVK---VTKQH 138 (384)
Q Consensus 79 gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~-------~~~l~~a~~~g~-----~~~~~~~-----~~~~~~---vt~~~ 138 (384)
.-+.++..|-+.-+.|..+.++||..-... .+.++.....-+ .++++.- .+-+.. -.+..
T Consensus 66 ~gkVtlFvDRG~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~n 145 (438)
T PHA03065 66 AGKVTLFVDRGSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNN 145 (438)
T ss_pred CCcEEEEEecCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhh
Confidence 334455567776667776666654322111 111211111111 2222111 000111 11222
Q ss_pred H-HHHHHHHHhc--CCCccccch-HHHHHHHHHHH-----cCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEe
Q 016711 139 N-DDCKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFE 209 (384)
Q Consensus 139 ~-~~~~~lL~~~--Gip~i~ap~-EADa~~A~L~~-----~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~ 209 (384)
+ ..+.+.|... +|.++.+.| .||=.+-.-++ .|.-..++|.|-|.++|.+..-...+
T Consensus 146 lk~~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki-------------- 211 (438)
T PHA03065 146 LKRLLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI-------------- 211 (438)
T ss_pred HHHHHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH--------------
Confidence 2 2334556677 899999999 99966554444 57777899999999999764311111
Q ss_pred HHHHHHHhCCCH-----HHHHHHHHHhCCCCCCCCCCC--cHHH--HHHHHHHhCCHHHHHHHHh
Q 016711 210 VAKILEELNLTM-----DQFIDLCILSGCDYCDSIRGI--GGQT--ALKLIRQHGSIETILENIN 265 (384)
Q Consensus 210 ~~~v~~~~gl~~-----~q~id~~~L~G~Dy~~~i~gi--G~kt--A~~li~~~~sle~il~~~~ 265 (384)
...+-+.+.+-| --=...++.=||||-+|+-|+ .+++ -++|...| +++|++..+-
T Consensus 212 I~t~~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~ 275 (438)
T PHA03065 212 IKTANQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLA 275 (438)
T ss_pred HHhHHHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHH
Confidence 011111222211 111234556699999999985 4443 24444444 3677777664
No 31
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=97.60 E-value=0.00053 Score=73.04 Aligned_cols=243 Identities=20% Similarity=0.299 Sum_probs=132.0
Q ss_pred CCccchHHHHhhhcCCC---cccccccccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHH
Q 016711 1 MGIKGLTKLLADNAPKS---MKEQKFESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLE 77 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~---~~~~~l~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~ 77 (384)
|||+-+..|+.+.-|.+ +.+..|-+|.+ +-.|-++.+|-+-|..- ...+-..-+ ..-...+|.-+-.|..
T Consensus 1 MGvPKFfR~iSERyP~lseliee~qIPEFDN--LYLDMNgIlHNCsH~nD----ddvt~rLtE-eEif~~IfnYIdhLf~ 73 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSELIEEHQIPEFDN--LYLDMNGILHNCSHPND----DDVTFRLTE-EEIFQEIFNYIDHLFY 73 (1493)
T ss_pred CCchHHHHHhhhhchHHHHHhhhccCCcccc--eeeecccccccCCCCCC----CccCcCCCH-HHHHHHHHHHHHHHHH
Confidence 99999999999887754 34445556666 57799988876554321 111111101 0112233333334444
Q ss_pred cCCce--EE--EEeCCCCchhhHHHHHHHhhh-hcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHh----
Q 016711 78 AGMKP--IY--VFDGQPPDLKKQELAKRYSKR-ADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKL---- 148 (384)
Q Consensus 78 ~gi~P--v~--VFDG~~~~~K~~~~~~rk~~R-~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~---- 148 (384)
-|+| +| ..||-.|-.|......|+-+- ..+..++.+|.++|+.-.-+.|-+-+++.-......+.+-|+.
T Consensus 74 -~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~rl~~~L~yfIkt 152 (1493)
T KOG2045|consen 74 -LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMVRLQEGLRYFIKT 152 (1493)
T ss_pred -hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHHHHHHHHHHHHHh
Confidence 3777 33 379999987775544444332 3455678888888874433555444444333333333333332
Q ss_pred --------cCCCcc----ccchHHHHHHHHHHHc---------CCeEEEEcCCCcccccCC----Ce--eEEEeecCCCC
Q 016711 149 --------MGVPVV----EAPSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR--FLRHLMDPSSR 201 (384)
Q Consensus 149 --------~Gip~i----~ap~EADa~~A~L~~~---------g~~~~v~S~DsD~l~fg~----~~--v~~~l~~~~~~ 201 (384)
-++.+| .+|||.|--|--+-+. +--..+..=|.|++.+|- ++ ++|.-..-+.+
T Consensus 153 KistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrr 232 (1493)
T KOG2045|consen 153 KISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRR 232 (1493)
T ss_pred ccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeecccc
Confidence 244454 5799999655544431 223346677999999983 22 22221111111
Q ss_pred ----Ccc---eEEEeHHHHHHH-------------hCCCH----HHHHHHHHHhCCCCCCCCCCCcH-HHHHHHH
Q 016711 202 ----KIP---VMEFEVAKILEE-------------LNLTM----DQFIDLCILSGCDYCDSIRGIGG-QTALKLI 251 (384)
Q Consensus 202 ----~~~---~~~~~~~~v~~~-------------~gl~~----~q~id~~~L~G~Dy~~~i~giG~-ktA~~li 251 (384)
... +-..+++-+.|. +.++. +.||.++.|+|+||.+++|++-+ ..|+-|+
T Consensus 233 n~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpll 307 (1493)
T KOG2045|consen 233 NKRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLL 307 (1493)
T ss_pred cccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHH
Confidence 111 111222222121 12233 56778899999999999999865 3466554
No 32
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=97.39 E-value=0.0016 Score=67.76 Aligned_cols=243 Identities=19% Similarity=0.300 Sum_probs=130.0
Q ss_pred CCccchHHHHhhhcCCCcccccc-cccCCCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQKF-ESYFGRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAG 79 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~~l-~~l~g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~g 79 (384)
|||+.|..||...-|.++..+.= ..-.+--+-.|-++.+|-+-|.--. .++++ +-+..-++..++.++ +..
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~~~P~~DNLYLDMNgIlH~CtHp~d~--~~pet--EeEm~~aVf~Yidhi---l~~- 72 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPNDG--SPPET--EEEMYKAVFEYIDHI---LLK- 72 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhccCCCCcceeEEecccccccCCCCCCC--CCCCC--HHHHHHHHHHHHHHH---HHh-
Confidence 99999999999887776655321 1234567889999988766543210 01221 112233444444443 332
Q ss_pred Cce---EE-EEeCCCCchhhHHHHHHHhhhh-cchHHHHHHHHhCC-----------HH---HH--HHHhhhhccCCHHH
Q 016711 80 MKP---IY-VFDGQPPDLKKQELAKRYSKRA-DATDDLAEAVEAGN-----------KE---DI--EKFSKRTVKVTKQH 138 (384)
Q Consensus 80 i~P---v~-VFDG~~~~~K~~~~~~rk~~R~-~~~~~l~~a~~~g~-----------~~---~~--~~~~~~~~~vt~~~ 138 (384)
|+| .| .-||-.|-.|......|+-+-. ++.....++..+|+ .. .. .+|-.-+++.-...
T Consensus 73 irPrKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~fDSNcITPGTpF 152 (953)
T COG5049 73 IRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFDSNCITPGTPF 152 (953)
T ss_pred cCcceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhccccccCCCCCChH
Confidence 566 23 5899999777655433332211 11112222222222 00 01 12222233322223
Q ss_pred HHHHHHHHHh------------cCCCcc----ccchHHHHHHHHHHHc---------CCeEEEEcCCCcccccCC----C
Q 016711 139 NDDCKRLLKL------------MGVPVV----EAPSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----P 189 (384)
Q Consensus 139 ~~~~~~lL~~------------~Gip~i----~ap~EADa~~A~L~~~---------g~~~~v~S~DsD~l~fg~----~ 189 (384)
.+.+.+.|+. -++.+| ..|||.|--|-.+-+. +-...|.+-|.|++.+|- +
T Consensus 153 MerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~P 232 (953)
T COG5049 153 MERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEP 232 (953)
T ss_pred HHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCC
Confidence 3344444432 133343 3589999888777663 346678999999999983 3
Q ss_pred e--eEE-Eeec-CCC----------------------CCcceEEEeHHHHHHHh-------CCCH--------HHHHHHH
Q 016711 190 R--FLR-HLMD-PSS----------------------RKIPVMEFEVAKILEEL-------NLTM--------DQFIDLC 228 (384)
Q Consensus 190 ~--v~~-~l~~-~~~----------------------~~~~~~~~~~~~v~~~~-------gl~~--------~q~id~~ 228 (384)
+ ++| ..+. ..+ .+.++.+++.+-+.+.+ +++. +.|+.+|
T Consensus 233 HF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~ 312 (953)
T COG5049 233 HFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLC 312 (953)
T ss_pred eeEEeechhccCcccccccccccccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeee
Confidence 3 333 1121 111 01245556666554432 2221 6778899
Q ss_pred HHhCCCCCCCCCCCcH-HHHHHHH
Q 016711 229 ILSGCDYCDSIRGIGG-QTALKLI 251 (384)
Q Consensus 229 ~L~G~Dy~~~i~giG~-ktA~~li 251 (384)
-++|+||.+++|++-. ..|+++|
T Consensus 313 FfvGNDFLPhLP~Ldir~gai~~l 336 (953)
T COG5049 313 FFVGNDFLPHLPCLDIREGAIETL 336 (953)
T ss_pred eeeccccCCCCCccccccchHHHH
Confidence 9999999999998754 2344443
No 33
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=96.99 E-value=0.00034 Score=69.48 Aligned_cols=100 Identities=30% Similarity=0.426 Sum_probs=80.1
Q ss_pred HHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccC-CCeeEEEeecCCCCCcceEEEeHHHHHHHhCC
Q 016711 141 DCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFG-APRFLRHLMDPSSRKIPVMEFEVAKILEELNL 219 (384)
Q Consensus 141 ~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg-~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl 219 (384)
.+-+.+..-|+.|+++|+-|..|||||+....|+++ -+-+|.+.+. .++++..+... ...-|+..+.....++..-.
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~-~gp~d~l~ld~vdr~il~m~fg-~d~Ppl~~~~vp~~lem~l~ 210 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYA-FGPSDILLLDGVDRIILDMSFG-SDKPPLDVFHVPRFLEMFLL 210 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhc-CCchHhHHHhhhhhheeecccC-CCCCCCcccccchHHHhccc
Confidence 556788889999999999999999999999888854 5668888885 45555555543 34456777888888888878
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCC
Q 016711 220 TMDQFIDLCILSGCDYCDSIRGI 242 (384)
Q Consensus 220 ~~~q~id~~~L~G~Dy~~~i~gi 242 (384)
+-.-|..+..|.|||.+..++.+
T Consensus 211 s~~lFya~~ll~~c~~~s~~~~C 233 (531)
T COG5366 211 SSRLFYALGLLLGCDFCSTIPRC 233 (531)
T ss_pred ccchhhhhccccccccccccccc
Confidence 88999999999999999988753
No 34
>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=96.25 E-value=0.0082 Score=53.07 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=28.2
Q ss_pred cCCCccccch--HHHHHHHHHHHc----CCeEEEEcCCCccccc
Q 016711 149 MGVPVVEAPS--EAEAQCAALCKS----GQVYAVASEDMDSLTF 186 (384)
Q Consensus 149 ~Gip~i~ap~--EADa~~A~L~~~----g~~~~v~S~DsD~l~f 186 (384)
-||.++.++. .||+.|-.++.. +.-..|+|+|...-..
T Consensus 66 ~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~ 109 (166)
T PF05991_consen 66 GGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRA 109 (166)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHH
Confidence 4788888773 899998888762 4455689999876544
No 35
>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=96.14 E-value=0.032 Score=50.51 Aligned_cols=113 Identities=19% Similarity=0.266 Sum_probs=68.0
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhcc---C-CCCCCCchHHHHHHh
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER---Y-QIPEDWPYQEARRLF 284 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~---~-~~~~~~~~~~~~~~~ 284 (384)
.++...-||+ +.++--.|..|++ |+|||||+|+.++..+ +++++.+.+.+.. . ++| .+-.+.|..+.
T Consensus 53 red~~~LyGF~~~~Er~lF~~L~~------V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ip-GiGkKtAerIi 124 (191)
T TIGR00084 53 REDAELLFGFNTLEERELFKELIK------VNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIP-GVGKKTAERLL 124 (191)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC------CCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHH
Confidence 3344556787 7788888888887 9999999999999875 5778887776321 1 122 22233333333
Q ss_pred C--CCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 285 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 285 ~--~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
. +..+.....+..-.-..+..+.+.+-| ..+||+...+++.+.++.
T Consensus 125 leLk~k~~~~~~~~~~~~~~~~~~e~~~aL-~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 125 LELKGKLKGNKNLEMFTPTEAARDELFEAL-VSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHhhhcccccccccccccchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1 111110000000000123456777777 589999999999998874
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.80 E-value=0.0065 Score=44.86 Aligned_cols=27 Identities=33% Similarity=0.571 Sum_probs=21.8
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 237 DSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 237 ~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
-||||||+++|..|+++|+|++++...
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 479999999999999999999988743
No 37
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=95.56 E-value=0.091 Score=55.91 Aligned_cols=239 Identities=19% Similarity=0.291 Sum_probs=122.4
Q ss_pred CCccchHHHHhhhcCCCcccc---cccccCCCE-----------------EEEehhHHHHHHHHhhhccCCCcccCcCCC
Q 016711 1 MGIKGLTKLLADNAPKSMKEQ---KFESYFGRK-----------------IAIDASMSIYQFLIVVGRTGTEMLTNEAGE 60 (384)
Q Consensus 1 MGI~gL~~~l~~~~~~~~~~~---~l~~l~g~~-----------------i~IDas~~lyr~~~a~~~~~~~~l~~~~G~ 60 (384)
|||+.+..||...-|..|.++ ...+..|.. +-.|-+.++|-+.|.- +.+.-.+ .-+
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPE---dkPaP~t-edE 76 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVDVDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPE---DKPAPET-EDE 76 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCcccCCCcccccccCCCCCCcccccceeeecCcccccCCCCC---CCCCCcc-HHH
Confidence 999999999988777654432 111223333 4455566665444321 1111111 112
Q ss_pred chhHHHHHHHHHHHHHHcCCceEE-EEeCCCCchhhHHHHHHH--hhhhcchHHHH------HHHHhCC----HHHHHHH
Q 016711 61 VTSHLQGMFTRTIRLLEAGMKPIY-VFDGQPPDLKKQELAKRY--SKRADATDDLA------EAVEAGN----KEDIEKF 127 (384)
Q Consensus 61 ~t~~l~g~~~~~~~ll~~gi~Pv~-VFDG~~~~~K~~~~~~rk--~~R~~~~~~l~------~a~~~g~----~~~~~~~ 127 (384)
..-++..++.|++.|.+- -+..| ..||-.|-.|......|+ +.|+.+....+ +....|. .+.-+.|
T Consensus 77 m~~avFeyiDrlf~mvRP-RkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~f 155 (931)
T KOG2044|consen 77 MFVAVFEYIDRLFSMVRP-RKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETF 155 (931)
T ss_pred HHHHHHHHHHHHHHhccc-hheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhcccc
Confidence 223455555555554431 12244 599999977765544332 22222222111 1111221 1111222
Q ss_pred hhhhccCCHHHHHHHHHHHHh------------cCCCccc----cchHHHHHHHHHHHc---------CCeEEEEcCCCc
Q 016711 128 SKRTVKVTKQHNDDCKRLLKL------------MGVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMD 182 (384)
Q Consensus 128 ~~~~~~vt~~~~~~~~~lL~~------------~Gip~i~----ap~EADa~~A~L~~~---------g~~~~v~S~DsD 182 (384)
-+-+++.-....+.+-..|+. -+|.||. +|||.|--|-.+.+. +-...+.+-|-|
T Consensus 156 DSNcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDAD 235 (931)
T KOG2044|consen 156 DSNCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDAD 235 (931)
T ss_pred ccCccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCcc
Confidence 222232222233334444432 2455554 489999877666552 236678999999
Q ss_pred ccccCCC------eeEEEeecCCC----------------------------------CCcceEEEeHHHHHHHh-----
Q 016711 183 SLTFGAP------RFLRHLMDPSS----------------------------------RKIPVMEFEVAKILEEL----- 217 (384)
Q Consensus 183 ~l~fg~~------~v~~~l~~~~~----------------------------------~~~~~~~~~~~~v~~~~----- 217 (384)
++.+|-- .|+|..+.++. .+.++..++..-+.|.|
T Consensus 236 LImLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~ 315 (931)
T KOG2044|consen 236 LIMLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELR 315 (931)
T ss_pred ceeeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhc
Confidence 9999831 34554443210 11345566665554433
Q ss_pred --C----CCH----HHHHHHHHHhCCCCCCCCCCCcH
Q 016711 218 --N----LTM----DQFIDLCILSGCDYCDSIRGIGG 244 (384)
Q Consensus 218 --g----l~~----~q~id~~~L~G~Dy~~~i~giG~ 244 (384)
+ ++- +.|+-+|-++|+||.+.+|-+-+
T Consensus 316 ~p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeI 352 (931)
T KOG2044|consen 316 MPNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEI 352 (931)
T ss_pred CCCCCccccHHhhhcceEEEEeeecCccCCCCCchhh
Confidence 2 122 55666899999999999996543
No 38
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.43 E-value=0.12 Score=46.93 Aligned_cols=113 Identities=18% Similarity=0.258 Sum_probs=64.3
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhcc----CCCCCCCchHHHHHHh
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER----YQIPEDWPYQEARRLF 284 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~----~~~~~~~~~~~~~~~~ 284 (384)
.++...-||+ +.++--.|..|++ |+|||||+|+.++..|+ .+.+++.+.... .++| ..-.+.|..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vp-GIGkKtAerIi 125 (194)
T PRK14605 54 REDALSLFGFATTEELSLFETLID------VSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIP-GIGKKTASRIV 125 (194)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC------CCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHH
Confidence 3444556787 7778888888876 99999999999999886 677766663211 0121 11223333322
Q ss_pred C--CCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 285 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 285 ~--~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
. +..+..........-.....+.+..+| ..+||+...+.+.+..+.
T Consensus 126 lELk~Ki~~~~~~~~~~~~~~~~~e~~~aL-~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 126 LELKDKIAKNWEAGVLSQVTEANSDILATL-TALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHHhhhhccccccccchHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 1 000000000000000011235667777 589999999998888764
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.29 E-value=0.16 Score=45.94 Aligned_cols=107 Identities=16% Similarity=0.260 Sum_probs=57.0
Q ss_pred HHHhCCC-HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhc---c-CCCCCCCchHHHHHHhC--C
Q 016711 214 LEELNLT-MDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRE---R-YQIPEDWPYQEARRLFK--E 286 (384)
Q Consensus 214 ~~~~gl~-~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~---~-~~~~~~~~~~~~~~~~~--~ 286 (384)
...+|+. .+.--.+..|.. |||||||+|.+++..|++ +.+.+.+... . ..+| .+....|..++. +
T Consensus 58 ~~l~gF~~~~ek~~f~~L~~------i~GIGpk~A~~il~~fg~-~~l~~~i~~~d~~~L~~v~-Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 58 ILLYGFLTKEERELFRLLIS------VSGVGPKLALAILSGLSP-EELVQAIANGDVKALTKVP-GIGKKTAERIVLELK 129 (192)
T ss_pred HHHcCcCCHHHHHHHHHHhc------CCCCCHHHHHHHHHhCCH-HHHHHHHHhCCHHHHHhCC-CCCHHHHHHHHHHHH
Confidence 3346663 332222445544 999999999999999997 3333222211 0 0111 122233333321 1
Q ss_pred CCCC---ChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 287 PEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 287 p~v~---~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
.... ..... . .-..+..+.+..+| ..+||+...+.+.+..+.
T Consensus 130 ~~~~~~~~~~~~-~-~~~~~~~~ev~~aL-~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 130 DKLAAAASAAAA-A-AAASSALEEAVSAL-VALGYKPKEASKAVAKIL 174 (192)
T ss_pred HHhhcccccccc-c-ccccchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1110 00000 0 11122367888999 599999998888888775
No 40
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.02 E-value=0.34 Score=43.60 Aligned_cols=110 Identities=15% Similarity=0.190 Sum_probs=64.0
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCc---hHHHHHHhC
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARRLFK 285 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~---~~~~~~~~~ 285 (384)
.++...-||+ +.++--.|-.|++ |.|||||+|+.++..+ +++++...+.+.....= ..| .+-|..+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Lis------V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLVK------VSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 4455566787 6777777777776 8899999999999875 57777777753211111 223 234444431
Q ss_pred --CCCCC-ChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 286 --EPEVV-TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 286 --~p~v~-~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
+-.+. ..... . . ..+..+.+..-| ..+||++..+++.+.++.
T Consensus 126 ELk~K~~~~~~~~-~-~-~~~~~~e~~~aL-~~LGy~~~ea~~al~~v~ 170 (186)
T PRK14600 126 ELQYKVSKLEINE-T-N-FIIINDDALAAL-ISLGYEKTKAFNAIQKIK 170 (186)
T ss_pred HHHHHhhcccccc-c-c-ccccHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 11111 00000 0 0 111234455555 489999999999998773
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.45 E-value=0.3 Score=44.25 Aligned_cols=110 Identities=21% Similarity=0.283 Sum_probs=61.5
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHh
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF 284 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~ 284 (384)
.++-..-||+ +.++--.|..|++ |.|||||+|+.++..+ +++++.+.+..... ++|- .-.+-|.++.
T Consensus 53 rED~~~LYGF~t~~Er~lF~~Lis------VsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRII 124 (196)
T PRK13901 53 REDELKLFGFLNSSEREVFEELIG------VDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKG-IGNKMAGKIF 124 (196)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHH
Confidence 3344556786 6777777777776 8899999999999875 46777776653211 1211 1123333333
Q ss_pred C--CCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 285 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 285 ~--~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
. +..+...... . . .....+...+-| ..+||++..+.+.+..+.
T Consensus 125 lELkdKl~~~~~~-~-~-~~~~~~ea~~AL-~~LGy~~~ea~~al~~v~ 169 (196)
T PRK13901 125 LKLRGKLVKNDEL-E-S-SLFKFKELEQSI-VNMGFDRKLVNSAIKEIM 169 (196)
T ss_pred HHHHHhhcccccc-c-c-CcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1 1111100000 0 0 112234445555 489999999998887654
No 42
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.24 E-value=1.4 Score=40.08 Aligned_cols=118 Identities=18% Similarity=0.220 Sum_probs=67.3
Q ss_pred EEeHHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCc---hHHHHH
Q 016711 207 EFEVAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARR 282 (384)
Q Consensus 207 ~~~~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~---~~~~~~ 282 (384)
.+-.++....||+ +.+.=..|..|.. |.|||||+|+.+|.. -+++++.+.+.......=..+| .+-|.+
T Consensus 51 ~~vREd~~~LyGF~~~~ER~lF~~Lis------VnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGIGkKtAer 123 (201)
T COG0632 51 LVVREDAHLLYGFLTEEERELFRLLIS------VNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGIGKKTAER 123 (201)
T ss_pred EeehhhHHHHcCCCCHHHHHHHHHHHc------cCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCCCHHHHHH
Confidence 3556667888898 5666667777766 889999999999985 4678888877643222112222 234444
Q ss_pred HhC--C---CCCCC--hhhhcccCCCC----CCHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q 016711 283 LFK--E---PEVVT--DEEQLQIKWSA----PDEEGLINFLVSENGFNSDRVTKAIEKIKAA 333 (384)
Q Consensus 283 ~~~--~---p~v~~--~~~~~~~~~~~----pd~~~l~~f~~~~~~f~~~~v~~~~~~l~~~ 333 (384)
+.. + +.... .... ...+.. |-.+.-.+-| ..+||++..+.+.+..+...
T Consensus 124 ivleLk~K~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~AL-~~LGy~~~e~~~av~~v~~~ 183 (201)
T COG0632 124 IVLELKGKLAAFLKGDGGSP-AEDLSLDESSPALEEAVEAL-VALGYKEKEIKKAVKKVLKE 183 (201)
T ss_pred HHHHHhhhhhhhcccccccc-cccccccccchhhhHHHHHH-HHcCCCHHHHHHHHHHHHhc
Confidence 432 1 11100 0000 111111 1122213334 47999999999988877643
No 43
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.04 E-value=0.35 Score=43.63 Aligned_cols=108 Identities=16% Similarity=0.194 Sum_probs=63.6
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHh
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF 284 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~ 284 (384)
.++...-||+ +.++--.|..|++ |.|||||+|+.++..+ +.+++.+.+..... ++|- .-.+-|..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAerIi 125 (188)
T PRK14606 54 SQDGITLYGFSNERKKELFLSLTK------VSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPG-ISKKTAERIV 125 (188)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhc------cCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHH
Confidence 3444556787 6777777777776 8999999999999875 57777777653211 1211 1123333333
Q ss_pred C--CCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 285 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 285 ~--~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
. +..+.. ... ......+.+..-| ..+||++..+++.+.++.
T Consensus 126 lELkdK~~~-~~~----~~~~~~~e~~~AL-~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 126 MELKDEFES-AGI----KDMRIYHESLEAL-VSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHhhcc-ccC----CCcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1 111110 000 0111334555555 489999999999988774
No 44
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=92.96 E-value=0.53 Score=50.18 Aligned_cols=40 Identities=30% Similarity=0.364 Sum_probs=29.8
Q ss_pred hCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHH
Q 016711 217 LNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE 262 (384)
Q Consensus 217 ~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~ 262 (384)
+|. .++.-.....| ++|||||+++|..|++.|||+++|..
T Consensus 557 yhr~~r~k~~~~s~L------~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 557 YHRKLRSKRTLQTEL------TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hChhhHHHHHhhhhh------hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 454 34443444555 45999999999999999999988865
No 45
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.83 E-value=0.56 Score=42.55 Aligned_cols=108 Identities=18% Similarity=0.227 Sum_probs=58.2
Q ss_pred HHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHhC--
Q 016711 213 ILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK-- 285 (384)
Q Consensus 213 v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~~-- 285 (384)
...-||+ +.++--.|..|++ |.|||||+|+.++..+ +.+++...+..... ++|- .-.+-|..+..
T Consensus 57 ~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpG-IGkKtAerIilEL 128 (195)
T PRK14604 57 ALTLYGFSTPAQRQLFELLIG------VSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPG-IGKKTAERIVLEL 128 (195)
T ss_pred CceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHHH
Confidence 3445676 6666666777766 8888888888888864 56777776653211 1111 11222222221
Q ss_pred CCCCC---ChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 286 EPEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 286 ~p~v~---~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
+..+. ...+... -.....+.+..-| ..+||++..+.+.+.++.
T Consensus 129 k~K~~~~~~~~~~~~--~~~~~~~e~~~aL-~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 129 KGKIDVRQLSGSTSP--AVSALDRELSEIL-ISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHhccccccccccc--cccccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 11110 0000000 0011134555566 489999999999998874
No 46
>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=92.78 E-value=0.41 Score=41.67 Aligned_cols=47 Identities=19% Similarity=0.207 Sum_probs=25.0
Q ss_pred CCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHHcCCceEEEEeCC
Q 016711 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQ 89 (384)
Q Consensus 28 g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~gi~Pv~VFDG~ 89 (384)
.+.|+|||++..|. +.. ... ..+.++..-+-.+.+.|.+++.||+..
T Consensus 2 ~r~VVIDG~NVA~~--~~~-----~~~--------f~~~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 2 LRPVVIDGSNVAYS--HGN-----QKF--------FSVRGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp B--EEEEHHHHHHH--HTT-----TTS--------EEHHHHHHHHHHHHHTT---EEEEEEG
T ss_pred CCEEEEeCHHHHhh--cCC-----CCC--------cCHHHHHHHHHHHHHcCCCeEEEEcch
Confidence 46899999999872 211 000 123344443335667899999999954
No 47
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.77 E-value=0.57 Score=42.58 Aligned_cols=111 Identities=16% Similarity=0.136 Sum_probs=56.2
Q ss_pred HHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHhC-
Q 016711 212 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 285 (384)
Q Consensus 212 ~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~~- 285 (384)
+...-||+ +.++-..|-.|++ |.|||||+|+.++..+ +.+++.+.+..... ++|- .-.+-|.++..
T Consensus 55 d~~~LyGF~~~~Er~lF~~L~~------V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpG-IGkKtAerIilE 126 (197)
T PRK14603 55 DALSLYGFPDEDSLELFELLLG------VSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASG-VGKKLAERIALE 126 (197)
T ss_pred CCceeeCcCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33445676 5566666666665 7788888888888764 46666666543210 1111 11122222220
Q ss_pred -CCCCC---Chhhh-cccCC-CCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 286 -EPEVV---TDEEQ-LQIKW-SAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 286 -~p~v~---~~~~~-~~~~~-~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
+..+. ..... ..... ..+..+.+.+-| ..+||+...+.+.+.++.
T Consensus 127 LkdK~~~~~~~~~~~~~~~~~~~~~~~ea~~AL-~~LGy~~~ea~~al~~i~ 177 (197)
T PRK14603 127 LKGKVPEHLLAGPAGGGGTKVSSTAAEDAVLAL-LALGFREAQVRSVVAELL 177 (197)
T ss_pred HHHHhhhhcccccccccccccCCccHHHHHHHH-HHcCCCHHHHHHHHHHHH
Confidence 00000 00000 00001 122334455556 589999999999998874
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.40 E-value=0.45 Score=42.69 Aligned_cols=106 Identities=14% Similarity=0.228 Sum_probs=60.2
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHh
Q 016711 210 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF 284 (384)
Q Consensus 210 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~ 284 (384)
.++...-||+ +.++--.|..|.+ |.|||||+|+.++..+ +.+++.+.+..... ++|- .-.+-|.++.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li~------VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIi 125 (183)
T PRK14601 54 KEDSNKLYGFLDKDEQKMFEMLLK------VNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPG-IGPKSAKRII 125 (183)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhc------cCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHH
Confidence 3344556776 6777777777776 8889999999988875 46777776653211 1221 1123333333
Q ss_pred C--CCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHH
Q 016711 285 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKI 330 (384)
Q Consensus 285 ~--~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l 330 (384)
. +..+.. ... .....+...+-| ..+||++..+++.+..+
T Consensus 126 lELkdK~~~---~~~---~~~~~~ea~~AL-~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 126 AELSDAKTK---LEN---VSDDKSEALAAL-LTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHhhc---cCC---CCccHHHHHHHH-HHcCCCHHHHHHHHHhc
Confidence 1 111110 000 011234444555 48999999999988776
No 49
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=91.44 E-value=0.15 Score=53.68 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=25.8
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 235 YCDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 235 y~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
--|+||||||++..+|++.|||+++|.++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 34689999999999999999999998764
No 50
>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=91.43 E-value=0.17 Score=35.70 Aligned_cols=25 Identities=28% Similarity=0.413 Sum_probs=17.9
Q ss_pred CCCCCcHHHHHHHHHH-hCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ-HGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-~~sle~il~ 262 (384)
+|.||||+||.++..+ +.|++++.+
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hcccccHHHHHHHHHhCCCCHHHHhh
Confidence 5899999999999985 779988843
No 51
>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=91.40 E-value=0.15 Score=31.60 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.7
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.|||||++||-.++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 489999999988764
No 52
>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=91.38 E-value=0.15 Score=53.86 Aligned_cols=29 Identities=28% Similarity=0.407 Sum_probs=25.6
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 235 YCDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 235 y~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
--++||||||++..+||+.|||+++|.++
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 34689999999999999999999998754
No 53
>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=91.20 E-value=0.19 Score=36.34 Aligned_cols=25 Identities=36% Similarity=0.476 Sum_probs=22.6
Q ss_pred CCCCCcHHHHHHHHHH-hCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ-HGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-~~sle~il~ 262 (384)
+|||||+++|..|... |.+++++..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~~~l~~ 34 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTLEDLAN 34 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred cCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence 5999999999999999 999988875
No 54
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=91.15 E-value=0.15 Score=54.09 Aligned_cols=27 Identities=30% Similarity=0.587 Sum_probs=24.8
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 237 DSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 237 ~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
++|||||++++.+|++.|||+++|..+
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 579999999999999999999999863
No 55
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.13 E-value=0.31 Score=44.55 Aligned_cols=112 Identities=14% Similarity=0.199 Sum_probs=61.5
Q ss_pred HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccC----CCCCCCchHHHHHHhC
Q 016711 211 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 285 (384)
Q Consensus 211 ~~v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~~~ 285 (384)
++...-||+ +.++--.|..|.+ |.|||||+|+.++..+ +.+++.+.+..... ++|- .-.+-|..+..
T Consensus 56 Ed~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~~ipG-IGkKtAerIil 127 (203)
T PRK14602 56 EDALELFGFATWDERQTFIVLIS------ISKVGAKTALAILSQF-RPDDLRRLVAEEDVAALTRVSG-IGKKTAQHIFL 127 (203)
T ss_pred cCcceeeCCCCHHHHHHHHHHhC------CCCcCHHHHHHHHhhC-CHHHHHHHHHhCCHHHHhcCCC-cCHHHHHHHHH
Confidence 344556787 7777777788876 8999999999999875 56777776653211 1211 11222322221
Q ss_pred --CCCC-----CChhhhcc-cCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 286 --EPEV-----VTDEEQLQ-IKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 286 --~p~v-----~~~~~~~~-~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
+..+ ........ ..-.....+...+-| ..+||++..+.+.+.++.
T Consensus 128 ELkdK~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL-~~LGy~~~ea~~av~~~~ 180 (203)
T PRK14602 128 ELKYKLKVEGLPAAAVLAGTGAVPGSVFRDALAGL-ANLGYGEEEARPVLKEVL 180 (203)
T ss_pred HHHHhhccccccccccccccccCCCchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1111 00000000 000111234444555 589999999999998774
No 56
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=91.06 E-value=0.17 Score=53.26 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=25.9
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 235 YCDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 235 y~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
--++||||||++..+|++.|||+++|.++
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 34689999999999999999999999764
No 57
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=89.08 E-value=0.31 Score=51.93 Aligned_cols=29 Identities=17% Similarity=0.352 Sum_probs=25.9
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 235 YCDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 235 y~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
-.++|||||++++..||+.|||+++|.++
T Consensus 609 ~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred ccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 34689999999999999999999998764
No 58
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=87.09 E-value=4 Score=36.94 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=20.7
Q ss_pred ccccccCCCEEEEehhHHHHHHHHhh
Q 016711 21 QKFESYFGRKIAIDASMSIYQFLIVV 46 (384)
Q Consensus 21 ~~l~~l~g~~i~IDas~~lyr~~~a~ 46 (384)
..++.++|+.+.|||++.|--.-..+
T Consensus 59 ~~~~~~rg~~l~iDGyNvLItleSl~ 84 (211)
T COG2454 59 MKINSLRGQDLVIDGYNVLITLESLL 84 (211)
T ss_pred ccCCCcccceEEEechhhhhhHHHHh
Confidence 56778999999999999887655544
No 59
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=85.35 E-value=0.63 Score=49.49 Aligned_cols=27 Identities=37% Similarity=0.634 Sum_probs=24.6
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 237 DSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 237 ~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
++|||||++++.+|++.|||+++|.++
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 469999999999999999999998864
No 60
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=85.23 E-value=0.67 Score=48.98 Aligned_cols=28 Identities=36% Similarity=0.671 Sum_probs=25.5
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 236 CDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 236 ~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
-+.|||||++++.+|++.|||+++|.++
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 3579999999999999999999999874
No 61
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=85.13 E-value=0.69 Score=49.52 Aligned_cols=27 Identities=30% Similarity=0.484 Sum_probs=24.9
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 237 DSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 237 ~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
+.|||||++++.+|++.|||+++|.+.
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 469999999999999999999999874
No 62
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=85.02 E-value=0.77 Score=27.26 Aligned_cols=17 Identities=35% Similarity=0.520 Sum_probs=14.4
Q ss_pred CCCCCCcHHHHHHHHHH
Q 016711 237 DSIRGIGGQTALKLIRQ 253 (384)
Q Consensus 237 ~~i~giG~ktA~~li~~ 253 (384)
..|||||+++|..++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 36899999999998863
No 63
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=84.99 E-value=0.71 Score=42.72 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=24.8
Q ss_pred CCCCCCCcHHHHHHHHHH-hCCHHHHHHH
Q 016711 236 CDSIRGIGGQTALKLIRQ-HGSIETILEN 263 (384)
Q Consensus 236 ~~~i~giG~ktA~~li~~-~~sle~il~~ 263 (384)
.+.|||||+++|.+|++. |+|+++|..+
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 357999999999999999 9999998754
No 64
>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=84.46 E-value=0.86 Score=35.54 Aligned_cols=24 Identities=42% Similarity=0.530 Sum_probs=20.2
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHH
Q 016711 236 CDSIRGIGGQTALKLIRQHGSIET 259 (384)
Q Consensus 236 ~~~i~giG~ktA~~li~~~~sle~ 259 (384)
...|||||+.+|..|+.+.++++.
T Consensus 4 l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 4 LTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred hcCCCCccHHHHHHHHHHHcCchh
Confidence 457999999999999999887643
No 65
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=81.93 E-value=1.1 Score=47.22 Aligned_cols=29 Identities=31% Similarity=0.493 Sum_probs=25.8
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 235 YCDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 235 y~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
--|+|||||+++...|++.|||+++|.++
T Consensus 531 ~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 531 SLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred ccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 34789999999999999999999988764
No 66
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.38 E-value=1.8 Score=38.80 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=35.3
Q ss_pred eEEEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHH
Q 016711 205 VMEFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 205 ~~~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~ 253 (384)
+.-+.+...+.-+ ++++++|.. |+..| |..- .+||||+|||-+++-+
T Consensus 78 VsGIGpK~Al~ILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 78 VNGIGANTAMAVCSSLDVNSFYK-ALSLG-DESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred cCCccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 3446777777777 579998874 55566 6643 6999999999999966
No 67
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=81.09 E-value=1.4 Score=41.49 Aligned_cols=26 Identities=42% Similarity=0.724 Sum_probs=23.9
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
++||||++.|..|++.|||+++++..
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 48999999999999999999998865
No 68
>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=78.48 E-value=4 Score=44.48 Aligned_cols=39 Identities=18% Similarity=0.468 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHh
Q 016711 219 LTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 265 (384)
Q Consensus 219 l~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~ 265 (384)
-+.+.++.+.. ++.|||||+++|.+|+..|| ++.++.+.
T Consensus 75 ~~~~~i~~yL~------s~~~~GIG~~~A~~iv~~fg--~~~~~~i~ 113 (720)
T TIGR01448 75 TSKEGIVAYLS------SRSIKGVGKKLAQRIVKTFG--EAAFDVLD 113 (720)
T ss_pred CCHHHHHHHHh------cCCCCCcCHHHHHHHHHHhC--HhHHHHHH
Confidence 35567776644 24699999999999999999 45555554
No 69
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.36 E-value=2.6 Score=38.34 Aligned_cols=49 Identities=22% Similarity=0.206 Sum_probs=36.7
Q ss_pred eEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHHhC
Q 016711 205 VMEFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQHG 255 (384)
Q Consensus 205 ~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~~~ 255 (384)
+.-+.+...+.-++ +++++|+. ++..| |..- .+||||+|||-+++-+..
T Consensus 77 V~GIGpK~AL~iLs~~~~~~l~~-aI~~~-D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 77 VSGVGPKLALALLSALPPALLAR-ALLEG-DARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred cCCcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHHH
Confidence 34467777788776 79998875 45556 6653 699999999999997643
No 70
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.01 E-value=2.6 Score=38.27 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=34.5
Q ss_pred EEEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHH
Q 016711 206 MEFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 206 ~~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~ 253 (384)
.-+.+...+.-+ .+++++|.. ++..| |..- .+||||+|||-++|-+
T Consensus 78 sGIGPK~ALaILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 78 DGIGPRAALRVLSGIKYNEFRD-AIDRE-DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CCcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 346677777777 478988875 45566 6653 6999999999999865
No 71
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.13 E-value=3 Score=37.60 Aligned_cols=47 Identities=21% Similarity=0.299 Sum_probs=35.7
Q ss_pred eEEEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHH
Q 016711 205 VMEFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 205 ~~~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~ 253 (384)
+.-+.+...+.-+ ++++++|+. |+..| |..- .+||||+|||-+|+-+
T Consensus 78 V~GIGpK~AL~iLs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 78 VSRLGPKTALKIISNEDAETLVT-MIASQ-DVEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred cCCccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 3446777778877 579998875 55566 6543 6999999999999866
No 72
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.30 E-value=3.5 Score=37.13 Aligned_cols=48 Identities=23% Similarity=0.368 Sum_probs=35.5
Q ss_pred eEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC-CCCCCcHHHHHHHHHHh
Q 016711 205 VMEFEVAKILEELN-LTMDQFIDLCILSGCDYCD-SIRGIGGQTALKLIRQH 254 (384)
Q Consensus 205 ~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~-~i~giG~ktA~~li~~~ 254 (384)
+.-+.+...+.-+. +++++|++ ++-.| |..- .+||||+|||-+++-+.
T Consensus 78 V~GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~vpGIGkKtAerIilEL 127 (186)
T PRK14600 78 VSGVNYKTAMSILSKLTPEQLFS-AIVNE-DKAALKVNGIGEKLINRIITEL 127 (186)
T ss_pred cCCcCHHHHHHHHccCCHHHHHH-HHHcC-CHhheECCCCcHHHHHHHHHHH
Confidence 34467777777775 79998875 45556 5532 79999999999999663
No 73
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.14 E-value=3.1 Score=37.95 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=35.4
Q ss_pred eEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCC--CCCCCCcHHHHHHHHHHh
Q 016711 205 VMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 254 (384)
Q Consensus 205 ~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~i~giG~ktA~~li~~~ 254 (384)
+.-+.+...+.-++ +++++|+. ++..| |.. -.+||||+|||-+++-+.
T Consensus 79 V~GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 79 ISKVGAKTALAILSQFRPDDLRR-LVAEE-DVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCCcCHHHHHHHHhhCCHHHHHH-HHHhC-CHHHHhcCCCcCHHHHHHHHHHH
Confidence 34467777777775 68888874 45556 654 369999999999999763
No 74
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=75.44 E-value=2.5 Score=35.63 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=20.0
Q ss_pred CCCCcHHHHHHHHHH--hCCHHHHHH
Q 016711 239 IRGIGGQTALKLIRQ--HGSIETILE 262 (384)
Q Consensus 239 i~giG~ktA~~li~~--~~sle~il~ 262 (384)
+|||||+.|-++++. |.++|++++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 699999999999973 678888765
No 75
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.35 E-value=3.6 Score=37.33 Aligned_cols=48 Identities=27% Similarity=0.309 Sum_probs=35.2
Q ss_pred eEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCC--CCCCCCcHHHHHHHHHHh
Q 016711 205 VMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 254 (384)
Q Consensus 205 ~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~i~giG~ktA~~li~~~ 254 (384)
+.-+.+..-+.-++ +++++|+. ++..| |.. ..+||||+|||-+++-+.
T Consensus 78 V~GIGpK~Al~iLs~~~~~el~~-aI~~~-D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 78 VSGVGPKAALNLLSSGTPDELQL-AIAGG-DVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred cCCcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 34466777777775 68988875 44455 654 369999999999999763
No 76
>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=71.30 E-value=3.6 Score=44.23 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=15.8
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~ 262 (384)
+|||||+++|..|++.|+|++++..
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~ 526 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKA 526 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 3566666666666666666666543
No 77
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=69.72 E-value=3.9 Score=45.11 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.3
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~ 262 (384)
++||||+++|..|+.+|+|++++..
T Consensus 761 ~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred HCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4799999999999999999999886
No 78
>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=69.58 E-value=3.5 Score=25.87 Aligned_cols=13 Identities=54% Similarity=0.695 Sum_probs=10.3
Q ss_pred CCCCCcHHHHHHH
Q 016711 238 SIRGIGGQTALKL 250 (384)
Q Consensus 238 ~i~giG~ktA~~l 250 (384)
.++|||++|+.+|
T Consensus 15 ~~~GIG~kt~~kL 27 (32)
T PF11798_consen 15 KFWGIGKKTAKKL 27 (32)
T ss_dssp GSTTS-HHHHHHH
T ss_pred hhCCccHHHHHHH
Confidence 5799999999885
No 79
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=69.13 E-value=4.5 Score=43.80 Aligned_cols=25 Identities=36% Similarity=0.622 Sum_probs=22.2
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~ 262 (384)
+|||||+++|..|++.|+|++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4899999999999999999988765
No 80
>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=68.62 E-value=5.3 Score=33.23 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=14.8
Q ss_pred CCCCCcHHHHHHHHHHh
Q 016711 238 SIRGIGGQTALKLIRQH 254 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~ 254 (384)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 47999999999999874
No 81
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=67.73 E-value=12 Score=37.02 Aligned_cols=54 Identities=30% Similarity=0.459 Sum_probs=39.3
Q ss_pred HHHHHHHh-CCCHHHHHHH---HHHhCCCC----CC------------CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 210 VAKILEEL-NLTMDQFIDL---CILSGCDY----CD------------SIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 210 ~~~v~~~~-gl~~~q~id~---~~L~G~Dy----~~------------~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
.+++++.+ .++.+++.|+ +-++|-.- .| +||+|++..|..|+.+|||+.+|+..
T Consensus 243 ~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 243 PEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred HHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 56677666 5777777655 45566211 12 26999999999999999999999864
No 82
>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=64.36 E-value=6.4 Score=33.89 Aligned_cols=89 Identities=16% Similarity=0.223 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCcccccCCCe--eEEEeecCCCCCcceEEEeHHHHH
Q 016711 137 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPR--FLRHLMDPSSRKIPVMEFEVAKIL 214 (384)
Q Consensus 137 ~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~--v~~~l~~~~~~~~~~~~~~~~~v~ 214 (384)
.|+..+-+.|+.+|+.++..+...|..+..+|....-. ++|-|.+++-..... ++. + .... ..-.+.+++
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~Ri-llTrd~~l~~~~~~~~~~~l-i-~~~~-----~~~QL~ev~ 78 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGRI-LLTRDRDLLKRRRVSGGVIL-I-RSDD-----PEEQLREVL 78 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCeE-EEECCHHHHHHhhccCCEEE-E-cCCC-----HHHHHHHHH
Confidence 34566788999999999999988899999998876553 789999988664322 221 1 1111 112355677
Q ss_pred HHhCCCH--HHHHHHHHHhCC
Q 016711 215 EELNLTM--DQFIDLCILSGC 233 (384)
Q Consensus 215 ~~~gl~~--~q~id~~~L~G~ 233 (384)
+.+|+.+ +.+..-|..|++
T Consensus 79 ~~~~l~~~~~~~~sRC~~CN~ 99 (147)
T PF01927_consen 79 ERFGLKLRLDPIFSRCPKCNG 99 (147)
T ss_pred HHcCCccccCCCCCccCCCCc
Confidence 7777655 333445666664
No 83
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=64.33 E-value=11 Score=34.37 Aligned_cols=71 Identities=27% Similarity=0.359 Sum_probs=46.6
Q ss_pred eEEEEcCCCcccccCCCe-----eEEEeecCCCCCcceEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCC--CCCCCCcH
Q 016711 173 VYAVASEDMDSLTFGAPR-----FLRHLMDPSSRKIPVMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGG 244 (384)
Q Consensus 173 ~~~v~S~DsD~l~fg~~~-----v~~~l~~~~~~~~~~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~i~giG~ 244 (384)
..-++.+|. ..+||-.. +++.+. .+.-+.+...+.-+. ++++.|+. |+-.+ |++ -.+||||.
T Consensus 49 t~~~vREd~-~~LyGF~~~~ER~lF~~Li-------sVnGIGpK~ALaiLs~~~~~~l~~-aI~~~-d~~~L~k~PGIGk 118 (201)
T COG0632 49 THLVVREDA-HLLYGFLTEEERELFRLLI-------SVNGIGPKLALAILSNLDPEELAQ-AIANE-DVKALSKIPGIGK 118 (201)
T ss_pred EEEeehhhH-HHHcCCCCHHHHHHHHHHH-------ccCCccHHHHHHHHcCCCHHHHHH-HHHhc-ChHhhhcCCCCCH
Confidence 556777888 77777432 111111 133466777777774 58888875 44455 665 36899999
Q ss_pred HHHHHHHHH
Q 016711 245 QTALKLIRQ 253 (384)
Q Consensus 245 ktA~~li~~ 253 (384)
|||-+|+-+
T Consensus 119 KtAerivle 127 (201)
T COG0632 119 KTAERIVLE 127 (201)
T ss_pred HHHHHHHHH
Confidence 999999866
No 84
>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=63.11 E-value=7.5 Score=37.78 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=21.3
Q ss_pred CCCCCcHHHHHHHHHH--hCCHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ--HGSIETILENI 264 (384)
Q Consensus 238 ~i~giG~ktA~~li~~--~~sle~il~~~ 264 (384)
+||||||+||.+|. + +.|++++..+.
T Consensus 89 ~i~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 89 RVPGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred cCCCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 48999999999999 5 45888887763
No 85
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=62.71 E-value=6.6 Score=38.69 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=20.8
Q ss_pred CCCCCcHHHHHHHHHHhC--CHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHG--SIETILEN 263 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~--sle~il~~ 263 (384)
+||||||+||..|.+ .| |++++.++
T Consensus 93 ~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 93 NVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred ccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 489999999999988 54 78888664
No 86
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=62.39 E-value=8.4 Score=33.35 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=19.1
Q ss_pred CCCCCcHHHHHHHHHH------hCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ------HGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~------~~sle~il~ 262 (384)
.+||||+++|-+++.. |.++|++.+
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 4789999999999863 567776654
No 87
>PRK13766 Hef nuclease; Provisional
Probab=61.74 E-value=7.1 Score=42.81 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=23.7
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
+|||||+++|.+|++.|||+++++..
T Consensus 719 ~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 719 SLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 58999999999999999999988753
No 88
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.50 E-value=5.9 Score=42.73 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=16.4
Q ss_pred HHHHHHHHhcCCCcccc------chHHHHHHHHHH
Q 016711 140 DDCKRLLKLMGVPVVEA------PSEAEAQCAALC 168 (384)
Q Consensus 140 ~~~~~lL~~~Gip~i~a------p~EADa~~A~L~ 168 (384)
.+..+.|+.+|+|+... ..|+.+.+.++.
T Consensus 239 ~e~l~~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~ 273 (665)
T PRK07956 239 SEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIE 273 (665)
T ss_pred HHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHH
Confidence 34556788888886522 124555555554
No 89
>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=59.04 E-value=19 Score=29.11 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=24.4
Q ss_pred chHHHHHHHHHHHcCCeEEEEcCCCcccc
Q 016711 157 PSEAEAQCAALCKSGQVYAVASEDMDSLT 185 (384)
Q Consensus 157 p~EADa~~A~L~~~g~~~~v~S~DsD~l~ 185 (384)
+-..|+-+..+|..+.+++++|+|+|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 45678888888888899999999999874
No 90
>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=57.43 E-value=12 Score=27.47 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.9
Q ss_pred CCCCcHHHHHHHHHH
Q 016711 239 IRGIGGQTALKLIRQ 253 (384)
Q Consensus 239 i~giG~ktA~~li~~ 253 (384)
+||||+++|.++|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 688999998888877
No 91
>PRK08609 hypothetical protein; Provisional
Probab=55.14 E-value=20 Score=37.99 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=20.6
Q ss_pred CCCCCcHHHHHHHHHHh--CCHHHHHHHHh
Q 016711 238 SIRGIGGQTALKLIRQH--GSIETILENIN 265 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~--~sle~il~~~~ 265 (384)
.|||||||||.+|-++. .|++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 48999999999888764 46777666543
No 92
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=54.85 E-value=14 Score=32.13 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCCCCCC---------CCCCcHHHHHHHHHHhC
Q 016711 222 DQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 222 ~q~id~~~L~G~Dy~~~---------i~giG~ktA~~li~~~~ 255 (384)
++|-.+.-++|+|-.++ |.|||+.+|..++++.|
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 57888888899887764 68999999999999866
No 93
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=53.65 E-value=9.6 Score=40.71 Aligned_cols=26 Identities=38% Similarity=0.643 Sum_probs=23.8
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
|||.||+++|..|.+.|+|++++++.
T Consensus 515 GIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 515 GIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred CCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 68999999999999999999998865
No 94
>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=53.27 E-value=13 Score=26.64 Aligned_cols=17 Identities=47% Similarity=0.642 Sum_probs=14.7
Q ss_pred CCCCCcHHHHHHHHHHh
Q 016711 238 SIRGIGGQTALKLIRQH 254 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~ 254 (384)
.|||||+++|-+|+.+.
T Consensus 42 ~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 42 EIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp TSTTSSHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 58999999999998753
No 95
>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=52.68 E-value=19 Score=32.56 Aligned_cols=46 Identities=20% Similarity=0.263 Sum_probs=31.5
Q ss_pred EEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHH
Q 016711 206 MEFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 206 ~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~ 253 (384)
.-+.+...+.-++ ++++++...+ ..+ |..- .|||||+|||-+++-+
T Consensus 78 ~GIGpK~Al~iL~~~~~~el~~aI-~~~-d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 78 NGVGPKLALAILSNMSPEEFVYAI-ETE-EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCCHHHHHHHHhcCCHHHHHHHH-HhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 3456666666676 4777777543 334 5442 6999999999999844
No 96
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=52.52 E-value=12 Score=27.39 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=14.7
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 016711 238 SIRGIGGQTALKLIRQHGSIE 258 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~sle 258 (384)
.|||||+++|..+..-|.+.+
T Consensus 39 ~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 39 AIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp TSTT--HHHHHHHHHHHH-HH
T ss_pred ccCCcCHHHHHHHHHHHCCHH
Confidence 689999999999887766544
No 97
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=51.04 E-value=24 Score=30.20 Aligned_cols=44 Identities=25% Similarity=0.290 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHHhcCCC-----ccccch--HHHHHHHHHHHcCCeEEEE
Q 016711 134 VTKQHNDDCKRLLKLMGVP-----VVEAPS--EAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 134 vt~~~~~~~~~lL~~~Gip-----~i~ap~--EADa~~A~L~~~g~~~~v~ 177 (384)
++..+.+.+.+.|+..|+. ++..|| |-=-.+..|++.+..|+|+
T Consensus 14 i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI 64 (138)
T TIGR00114 14 ITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVI 64 (138)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 4567888899999999875 778998 8777888888887766665
No 98
>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=49.96 E-value=31 Score=27.38 Aligned_cols=31 Identities=26% Similarity=0.174 Sum_probs=21.6
Q ss_pred CCCCCcHHHHHHHHHH-hC--------CHHHHHHHHhhcc
Q 016711 238 SIRGIGGQTALKLIRQ-HG--------SIETILENINRER 268 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-~~--------sle~il~~~~~~~ 268 (384)
.|||||+.+|..|..- +. +.+++++.+....
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~ 55 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALT 55 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHc
Confidence 5899999999999863 33 4455666665543
No 99
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=46.00 E-value=20 Score=28.46 Aligned_cols=49 Identities=22% Similarity=0.180 Sum_probs=37.5
Q ss_pred ccCCHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCccccc
Q 016711 132 VKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 186 (384)
Q Consensus 132 ~~vt~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~f 186 (384)
..++......+.++....+ .+-+|+.++.++....+..++|.|.|+..+
T Consensus 70 ~~~~~~~~~~~~~~~~~~~------~~~~Da~~~a~A~~~~~~~v~T~D~~f~~~ 118 (121)
T PF01850_consen 70 LPITSEVFERAAELMRKYG------LDFADALIAATAKENGAPLVVTFDKDFRKV 118 (121)
T ss_dssp EEBCHHHHHHHHHHHHHHH------SSHHHHHHHHHHHHHT-EEE-ESSHHHHHH
T ss_pred ccchhHHHHHHHHHHHhcc------CChhHHHHHHHHHHcCCEEEEECCcCHHhc
Confidence 4567777888888888777 557899999999988887777999997543
No 100
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.99 E-value=14 Score=33.48 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.6
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 15 KLPGIGPKSAQRLAF 29 (195)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988753
No 101
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=44.87 E-value=30 Score=29.95 Aligned_cols=34 Identities=32% Similarity=0.585 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCCCCC---------CCCCcHHHHHHHHHHhC
Q 016711 222 DQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 222 ~q~id~~~L~G~Dy~~~---------i~giG~ktA~~li~~~~ 255 (384)
++|-.+.-++|+|-.++ |.|||+.+|..++++.|
T Consensus 4 ~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 4 EEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 46667777889887765 57999999999999865
No 102
>PRK00076 recR recombination protein RecR; Reviewed
Probab=44.85 E-value=14 Score=33.52 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.7
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 15 KLPGIGPKSAQRLAF 29 (196)
T ss_pred HCCCCCHHHHHHHHH
Confidence 589999999988764
No 103
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=44.22 E-value=13 Score=33.64 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.2
Q ss_pred CCCCCCcHHHHHHHH
Q 016711 237 DSIRGIGGQTALKLI 251 (384)
Q Consensus 237 ~~i~giG~ktA~~li 251 (384)
..+||||||+|.++.
T Consensus 15 ~kLPGvG~KsA~R~A 29 (198)
T COG0353 15 KKLPGVGPKSAQRLA 29 (198)
T ss_pred hhCCCCChhHHHHHH
Confidence 358999999987764
No 104
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.79 E-value=17 Score=32.95 Aligned_cols=44 Identities=25% Similarity=0.360 Sum_probs=29.0
Q ss_pred EeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHH
Q 016711 208 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 208 ~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~--~i~giG~ktA~~li~~ 253 (384)
+.+...+.-+. +++++|+. ++..+ |..- .|||||+|||-+++-+
T Consensus 81 IGpK~Al~ILs~~~~~~l~~-aI~~~-D~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 81 IGPKLGLAMLSAMNAEALAS-AIISG-NAELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CCHHHHHHHHHhCCHHHHHH-HHHhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 44444444443 57777654 33345 6543 6999999999998865
No 105
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=43.22 E-value=18 Score=33.66 Aligned_cols=28 Identities=25% Similarity=0.433 Sum_probs=24.9
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 236 CDSIRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 236 ~~~i~giG~ktA~~li~~~~sle~il~~ 263 (384)
.-+||||+-..|..|+..|||++.|+.+
T Consensus 197 Lt~i~~VnKtda~~LL~~FgsLq~~~~A 224 (254)
T KOG2841|consen 197 LTTIPGVNKTDAQLLLQKFGSLQQISNA 224 (254)
T ss_pred HHhCCCCCcccHHHHHHhcccHHHHHhc
Confidence 3469999999999999999999998865
No 106
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=42.19 E-value=28 Score=29.09 Aligned_cols=18 Identities=44% Similarity=0.831 Sum_probs=14.5
Q ss_pred HHHHHcCCce-EEEEeCCC
Q 016711 73 IRLLEAGMKP-IYVFDGQP 90 (384)
Q Consensus 73 ~~ll~~gi~P-v~VFDG~~ 90 (384)
.+|+++|+.| +.|+||+.
T Consensus 3 ~~ll~~g~~P~laIvD~kT 21 (121)
T PF04019_consen 3 YNLLEAGIIPDLAIVDGKT 21 (121)
T ss_pred HHHHhCCCCCCEEEEeCcc
Confidence 3678899999 45899974
No 107
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=41.94 E-value=32 Score=27.50 Aligned_cols=41 Identities=17% Similarity=0.295 Sum_probs=33.6
Q ss_pred HHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHH
Q 016711 213 ILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ 253 (384)
Q Consensus 213 v~~~~gl-~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~ 253 (384)
-+..-|+ |-..+++.+...|.-.--.|||||+..|-.+..=
T Consensus 28 ~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~aw 69 (96)
T PF12482_consen 28 RLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAW 69 (96)
T ss_pred HHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHHH
Confidence 3555687 7899999999999777788999999999876543
No 108
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=41.93 E-value=29 Score=30.33 Aligned_cols=45 Identities=20% Similarity=0.347 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHHhcC-----CCccccch--HHHHHHHHHHHcCCeEEEE
Q 016711 133 KVTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 133 ~vt~~~~~~~~~lL~~~G-----ip~i~ap~--EADa~~A~L~~~g~~~~v~ 177 (384)
.|+..+++-+.+.|...| |.++..|| |-=-.+..|++.+..|+|+
T Consensus 23 ~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiI 74 (158)
T PRK12419 23 DIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIV 74 (158)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 355778888899999999 56888998 8878888888877666554
No 109
>PRK13844 recombination protein RecR; Provisional
Probab=41.14 E-value=17 Score=33.00 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=12.7
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||+|+|.+|.-
T Consensus 19 ~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 19 KLPTIGKKSSQRLAL 33 (200)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988764
No 110
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=40.66 E-value=62 Score=25.40 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=20.4
Q ss_pred CCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCC
Q 016711 241 GIGGQTALKLIRQHGSIETILENINRERYQIPE 273 (384)
Q Consensus 241 giG~ktA~~li~~~~sle~il~~~~~~~~~~~~ 273 (384)
||+++.|.+|.+.||+ +.++.+++.++.+-.
T Consensus 19 gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD--DAIEILKENPYRLIE 49 (94)
T ss_dssp T--HHHHHHHHHHH-T--THHHHHHH-STCCCB
T ss_pred CCCHHHHHHHHHHHhH--HHHHHHHHChHHHHH
Confidence 6888999999999996 566777777766544
No 111
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=39.62 E-value=80 Score=26.91 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=33.7
Q ss_pred HHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCccccc----CCCee
Q 016711 145 LLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF----GAPRF 191 (384)
Q Consensus 145 lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~f----g~~~v 191 (384)
+....+.+++.--..||+.+-..+.+..+++|+|+|..+-.- |.|.+
T Consensus 71 ~~~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi 121 (136)
T COG1412 71 LKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVI 121 (136)
T ss_pred HHHhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEE
Confidence 444668888888448888777777765577799999987543 55544
No 112
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=36.65 E-value=45 Score=28.63 Aligned_cols=44 Identities=30% Similarity=0.356 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHhcCC-----Cccccch--HHHHHHHHHHHcCCeEEEE
Q 016711 134 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 134 vt~~~~~~~~~lL~~~Gi-----p~i~ap~--EADa~~A~L~~~g~~~~v~ 177 (384)
++..+.+.+.+.|...|+ .++..|| |-=-.+..|.+.+..|+|+
T Consensus 17 i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi 67 (144)
T PF00885_consen 17 ITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVI 67 (144)
T ss_dssp HHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEE
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEE
Confidence 345677888889999987 6788898 8888899999988777776
No 113
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=36.22 E-value=52 Score=28.23 Aligned_cols=44 Identities=30% Similarity=0.308 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHhcCC-----Cccccch--HHHHHHHHHHHcCCeEEEE
Q 016711 134 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 134 vt~~~~~~~~~lL~~~Gi-----p~i~ap~--EADa~~A~L~~~g~~~~v~ 177 (384)
++..+.+-+.+.|...|+ .++..|| |-=-.+..|++.+..|+|+
T Consensus 21 I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavI 71 (141)
T PLN02404 21 ITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAIL 71 (141)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEE
Confidence 456778889999999996 5778898 8777888888877656554
No 114
>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=36.04 E-value=34 Score=27.71 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=15.2
Q ss_pred CCCCCcHHHHHHHHHHhC
Q 016711 238 SIRGIGGQTALKLIRQHG 255 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~ 255 (384)
.|.|||+.+|..+..+.|
T Consensus 19 ~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 19 KIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp TSTTBCHHHHHHHHHHTT
T ss_pred hhhccCHHHHHHHHHHcC
Confidence 378999999999888755
No 115
>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=35.95 E-value=41 Score=30.15 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.0
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||++||--++-
T Consensus 110 ~l~GIG~ktA~~ill 124 (191)
T TIGR01083 110 KLPGVGRKTANVVLN 124 (191)
T ss_pred hCCCCcHHHHHHHHH
Confidence 379999999977653
No 116
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=35.84 E-value=49 Score=28.80 Aligned_cols=44 Identities=32% Similarity=0.355 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHhcCC-----Cccccch--HHHHHHHHHHHcCCeEEEE
Q 016711 134 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 134 vt~~~~~~~~~lL~~~Gi-----p~i~ap~--EADa~~A~L~~~g~~~~v~ 177 (384)
++..+.+-+.+.|...|+ .++..|| |-=-.+..|++.+..|+|+
T Consensus 26 i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI 76 (154)
T PRK00061 26 ITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVI 76 (154)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEE
Confidence 446778889999999994 5677898 7777888888877666665
No 117
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=35.32 E-value=58 Score=27.84 Aligned_cols=46 Identities=20% Similarity=0.172 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHH
Q 016711 159 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 216 (384)
Q Consensus 159 EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~ 216 (384)
+=|.-.-.+|-.+.+++++|.|.|++.+-..+- .++..++.++++.
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~~n~------------~~~Iltp~eF~~~ 136 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRDENK------------RVEILTPQEFLEE 136 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheecccCC------------cEEEcCHHHHHHH
Confidence 456666667778899999999999987655331 2455666666554
No 118
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=35.22 E-value=1.8e+02 Score=25.03 Aligned_cols=69 Identities=19% Similarity=0.210 Sum_probs=41.1
Q ss_pred CCCchhhHHHHHHHhhhhcchHHHHHHHHhCCHHHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccchHHHHHHHHHH
Q 016711 89 QPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALC 168 (384)
Q Consensus 89 ~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~ 168 (384)
..|++|..+..+++++|.. .+...|-.-|+..|---+-.-..-.++++.||
T Consensus 5 r~pt~kErEnnk~RERrRR-----------------------------AIaakIfaGLR~~Gny~Lp~~aD~NeVLkALc 55 (150)
T PF05687_consen 5 RRPTWKERENNKRRERRRR-----------------------------AIAAKIFAGLRAHGNYKLPKHADNNEVLKALC 55 (150)
T ss_pred ccccHhhhHHHHHHHHHHH-----------------------------HHHHHHHHHHHHhcCCCCCCcCCHHHHHHHHH
Confidence 4677888777777666542 22333555677777655555556667888887
Q ss_pred HcCCeEEEEcCCCcccccCC
Q 016711 169 KSGQVYAVASEDMDSLTFGA 188 (384)
Q Consensus 169 ~~g~~~~v~S~DsD~l~fg~ 188 (384)
+..-. ||.+|-..+--++
T Consensus 56 ~eAGw--~Ve~DGTtyr~~~ 73 (150)
T PF05687_consen 56 REAGW--TVEPDGTTYRKGC 73 (150)
T ss_pred HhCCE--EEccCCCeeccCC
Confidence 75322 3466666555444
No 119
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=35.03 E-value=52 Score=28.31 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.4
Q ss_pred CCCCcHHHHHHHHHHhC
Q 016711 239 IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 239 i~giG~ktA~~li~~~~ 255 (384)
|.|||+.+|..++++.+
T Consensus 26 I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 26 IKGIGRRFARAIARKLG 42 (144)
T ss_pred eeccCHHHHHHHHHHcC
Confidence 67999999999988765
No 120
>PF05182 Fip1: Fip1 motif; InterPro: IPR007854 This short motif is about 40 amino acids in length and is found in the Fip1 protein that is a component of a Saccharomyces cerevisiae pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase []. This region of Fip1 is needed for the interaction with the Yth1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor [].
Probab=34.54 E-value=64 Score=22.02 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=28.2
Q ss_pred cccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhh
Q 016711 296 LQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAK 334 (384)
Q Consensus 296 ~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~~~~ 334 (384)
++-.|..|-.+ +.+|+ .+||++..-+.++.++.+.+
T Consensus 9 ~~KPWr~pGaD-isDyF--NYGf~E~tW~~Y~~kq~~~R 44 (45)
T PF05182_consen 9 EEKPWRKPGAD-ISDYF--NYGFNEETWREYCKKQRQLR 44 (45)
T ss_pred ccCCccCCCCC-hhhhc--CCCCCHHHHHHHHHHHHHhh
Confidence 35679888644 78898 79999999999988876543
No 121
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=34.38 E-value=25 Score=32.19 Aligned_cols=15 Identities=40% Similarity=0.724 Sum_probs=13.3
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
++||||+|||--++.
T Consensus 123 ~lpGIG~KTAd~vL~ 137 (208)
T PRK01229 123 NIKGIGYKEASHFLR 137 (208)
T ss_pred cCCCCcHHHHHHHHH
Confidence 689999999988775
No 122
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=34.28 E-value=43 Score=30.79 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=13.0
Q ss_pred CCCCcHHHHHHHHHH-hC
Q 016711 239 IRGIGGQTALKLIRQ-HG 255 (384)
Q Consensus 239 i~giG~ktA~~li~~-~~ 255 (384)
+||||+|||-=.+.. ||
T Consensus 114 LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 114 LPGVGRKTANVVLSFAFG 131 (211)
T ss_pred CCCcchHHHHHHHHhhcC
Confidence 589999999776654 44
No 123
>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=33.13 E-value=53 Score=25.52 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=21.0
Q ss_pred CCCCCcHHHHHHHHHH-----hCCHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ-----HGSIETILENI 264 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-----~~sle~il~~~ 264 (384)
.|+|||...|.+++.+ |.|++++++.+
T Consensus 31 ~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 31 AIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred hcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 3799999999999975 67888888776
No 124
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=32.67 E-value=45 Score=29.78 Aligned_cols=46 Identities=24% Similarity=0.369 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHhCCCCCCC------CCCCcHHHHHHHHHH-----hCCHHHHHHHHh
Q 016711 219 LTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENIN 265 (384)
Q Consensus 219 l~~~q~id~~~L~G~Dy~~~------i~giG~ktA~~li~~-----~~sle~il~~~~ 265 (384)
=+.+.|+++---+| --|.. +||||-|+..++|.+ |.|.++|-+.+.
T Consensus 96 ~~E~~FV~FfN~A~-PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~ 152 (181)
T PF04919_consen 96 ENEERFVDFFNEAQ-PITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVK 152 (181)
T ss_dssp TTHHHHHHHH------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST
T ss_pred hChHHHHHHhhcCC-CChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhc
Confidence 46789999988887 33332 599999999999975 788888777653
No 125
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.51 E-value=62 Score=28.45 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeEEEEcCCCccccc---CCCee
Q 016711 136 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF---GAPRF 191 (384)
Q Consensus 136 ~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l~f---g~~~v 191 (384)
..|+-.+-+.|+.+|.+.+..-.+.|+.+..++..... +++|-|.-++-. |...+
T Consensus 12 D~mLG~LARwLRllGydt~~~~~~~d~~i~~i~~~e~r-IllTRDr~L~~r~k~g~~~i 69 (165)
T COG1656 12 DAMLGKLARWLRLLGYDTVYSSNESDDEIILIAKKEGR-ILLTRDRELYKRAKLGIKAI 69 (165)
T ss_pred HHhHHHHHHHHHHcCCceeeeccCCcHHHHHHHhcCCe-EEEeccHHHHHHhhccCceE
Confidence 46778889999999999998878999999988887444 378999998887 44444
No 126
>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=31.51 E-value=34 Score=25.12 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=11.8
Q ss_pred CCCCCCcHHHHHHH
Q 016711 237 DSIRGIGGQTALKL 250 (384)
Q Consensus 237 ~~i~giG~ktA~~l 250 (384)
..|||||+++|.++
T Consensus 50 ~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 50 KKLPGIGKSIAKKI 63 (68)
T ss_dssp CTSTTTTHHHHHHH
T ss_pred hhCCCCCHHHHHHH
Confidence 56999999998875
No 127
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=31.37 E-value=48 Score=26.30 Aligned_cols=40 Identities=25% Similarity=0.318 Sum_probs=28.7
Q ss_pred ccccchHHHHHHHHHHHcCCeEEEEcCCCccc-----ccCCCeeE
Q 016711 153 VVEAPSEAEAQCAALCKSGQVYAVASEDMDSL-----TFGAPRFL 192 (384)
Q Consensus 153 ~i~ap~EADa~~A~L~~~g~~~~v~S~DsD~l-----~fg~~~v~ 192 (384)
.+..+..||+.+..++..+..++|+|+|.++- .-|.|.++
T Consensus 46 h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~ 90 (101)
T PF04900_consen 46 HKETPGSADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIY 90 (101)
T ss_pred CCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEE
Confidence 33335689999999997655478999999875 34666554
No 128
>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=31.20 E-value=28 Score=31.01 Aligned_cols=16 Identities=25% Similarity=0.412 Sum_probs=12.8
Q ss_pred CCCCCcHHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ 253 (384)
Q Consensus 238 ~i~giG~ktA~~li~~ 253 (384)
.+||||+|||-=.+..
T Consensus 119 ~LpGVG~KTAnvVL~~ 134 (177)
T TIGR03252 119 ALPGFGKQKAKIFLAL 134 (177)
T ss_pred cCCCCCHHHHHHHHHH
Confidence 4899999999766654
No 129
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=31.00 E-value=27 Score=33.84 Aligned_cols=30 Identities=33% Similarity=0.281 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhcCCCccccchHHHHHHHH
Q 016711 136 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAA 166 (384)
Q Consensus 136 ~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~ 166 (384)
..+......+|+.+|+| +.+|.|++||+|+
T Consensus 103 ~~~~~~~~~~l~~~G~e-add~i~t~A~~a~ 132 (310)
T COG0258 103 ELLVALGIPLLELMGIE-ADDPIETLAQKAY 132 (310)
T ss_pred HHHHHhCcHhhhcCCCC-cchhHHHHHHHHH
Confidence 44556678899999999 8999999999998
No 130
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=30.30 E-value=1.3e+02 Score=26.14 Aligned_cols=37 Identities=27% Similarity=0.469 Sum_probs=26.9
Q ss_pred HHHHHHhhhhccCCHHHHHHHHHHHHhcCCCccccch
Q 016711 122 EDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 158 (384)
Q Consensus 122 ~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gip~i~ap~ 158 (384)
.++.+|-.+...-...|.......|+.+|||++....
T Consensus 90 ~EL~~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 90 AELDKFDEKVYKASKQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeCCC
Confidence 3456666555555577888889999999999876543
No 131
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=30.01 E-value=34 Score=29.24 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.2
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.||||||+||--++.
T Consensus 87 ~l~GIG~~tA~~~l~ 101 (158)
T cd00056 87 ALPGVGRKTANVVLL 101 (158)
T ss_pred cCCCCCHHHHHHHHH
Confidence 489999999877654
No 132
>PRK10702 endonuclease III; Provisional
Probab=29.68 E-value=33 Score=31.43 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=12.1
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||+|||--++-
T Consensus 113 ~lpGVG~ktA~~ill 127 (211)
T PRK10702 113 ALPGVGRKTANVVLN 127 (211)
T ss_pred cCCcccHHHHHHHHH
Confidence 479999999977653
No 133
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=29.67 E-value=70 Score=28.08 Aligned_cols=56 Identities=20% Similarity=0.227 Sum_probs=28.8
Q ss_pred CCEEEEehhHHHHHHHHhhhccCCCcccCcCCCchhHHHHHHHHHHHHHH-cCCceEEEEeCCC
Q 016711 28 GRKIAIDASMSIYQFLIVVGRTGTEMLTNEAGEVTSHLQGMFTRTIRLLE-AGMKPIYVFDGQP 90 (384)
Q Consensus 28 g~~i~IDas~~lyr~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~-~gi~Pv~VFDG~~ 90 (384)
.+.++|||++++=++-.-- .+.+..| ...+=..++..+..--. .|++-++|||..-
T Consensus 3 ~~iLLVDGYNmIgaWp~Lk------~lkd~~~-LE~AR~~LIe~l~~Y~s~~g~~iivVFDA~~ 59 (173)
T COG3688 3 MRILLVDGYNMIGAWPELK------QLKDRNG-LEAARDKLIEALAEYQSFTGYKIIVVFDAHY 59 (173)
T ss_pred ceEEEeccchhccccHHHH------HHHhhcc-HHHHHHHHHHHHHHhhcccCceEEEEEEccc
Confidence 4689999999875432211 1221111 11222233333333222 3788999999863
No 134
>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=29.42 E-value=54 Score=26.94 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHcCCeEEEEcCCCcccccCCCee
Q 016711 159 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRF 191 (384)
Q Consensus 159 EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v 191 (384)
-+|+.++..+....+ .++|.|.|+-.|+.-.+
T Consensus 105 ~~D~~i~a~A~~~~~-~lvT~D~~f~~~~~~~i 136 (142)
T TIGR00028 105 VTDAHLAALAREHGA-ELVTFDRGFARFAGIRW 136 (142)
T ss_pred chHHHHHHHHHHcCC-EEEecCCCccccCCCee
Confidence 589999988886555 47799999766655443
No 135
>KOG3165 consensus Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=28.81 E-value=42 Score=29.45 Aligned_cols=28 Identities=21% Similarity=0.143 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHcCCeEEEEcCCCccccc
Q 016711 159 EAEAQCAALCKSGQVYAVASEDMDSLTF 186 (384)
Q Consensus 159 EADa~~A~L~~~g~~~~v~S~DsD~l~f 186 (384)
-|||-+..-+.+..|++|+|.|.|+-+=
T Consensus 137 YADDClv~RV~qHkCYIVAT~D~dLK~R 164 (195)
T KOG3165|consen 137 YADDCLVQRVTQHKCYIVATNDRDLKQR 164 (195)
T ss_pred chhhHHHHHHhhcceEEEEeccHHHHHH
Confidence 6999999999999999999999999764
No 136
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=28.65 E-value=1.4e+02 Score=24.68 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=35.2
Q ss_pred eHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHH-hCCHHHH
Q 016711 209 EVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ-HGSIETI 260 (384)
Q Consensus 209 ~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~-~~sle~i 260 (384)
....+....|++...+..+..++ |.. -|||||+..|.=|... +.|++++
T Consensus 31 ~r~~La~~~~i~~~~l~~w~~~A--dL~-ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 31 GRKALAKKLGISERNLLKWVNQA--DLM-RIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred HHHHHHHhcCCCHHHHHHHHhHH--Hhh-hcCCCCHHHHHHHHHhCcCcHHHH
Confidence 44557788899998888876664 666 8999999988766654 3454443
No 137
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=28.17 E-value=1.1e+02 Score=31.70 Aligned_cols=13 Identities=31% Similarity=0.623 Sum_probs=9.8
Q ss_pred CcHHHHHHHHHHh
Q 016711 242 IGGQTALKLIRQH 254 (384)
Q Consensus 242 iG~ktA~~li~~~ 254 (384)
.|...|++-|+.|
T Consensus 203 gGe~~A~~~L~~f 215 (472)
T PRK10674 203 VGEKAAIAQLRQF 215 (472)
T ss_pred CCHHHHHHHHHHH
Confidence 3788888877766
No 138
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=27.94 E-value=1.9e+02 Score=19.55 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC
Q 016711 218 NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGS 256 (384)
Q Consensus 218 gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~s 256 (384)
.+||.+| .+|.|-+- +-..++--.=-+|+++|++
T Consensus 10 ~lTP~El---~a~~g~~~--~~~pl~R~~L~~Lm~~~PD 43 (43)
T PF09550_consen 10 RLTPAEL---RAMLGADA--GAAPLDRAELDALMRRFPD 43 (43)
T ss_pred hcCHHHH---HHhcCccc--CCCCCCHHHHHHHHHHCcC
Confidence 4555555 67788443 3356666666777877764
No 139
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=27.80 E-value=54 Score=26.97 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.9
Q ss_pred CCCCcHHHHHHHHHHhC
Q 016711 239 IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 239 i~giG~ktA~~li~~~~ 255 (384)
|.|||+.+|..++.+.|
T Consensus 20 i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 20 IYGIGRTRARKILEKAG 36 (113)
T ss_pred eecccHHHHHHHHHHhC
Confidence 67999999999988766
No 140
>PRK00124 hypothetical protein; Validated
Probab=27.68 E-value=64 Score=28.04 Aligned_cols=91 Identities=13% Similarity=0.126 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHcCCeEEEEcCCCcccccCCCeeEEEeecCCCCCcceEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC
Q 016711 159 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 238 (384)
Q Consensus 159 EADa~~A~L~~~g~~~~v~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ 238 (384)
.||..++.+++.| |+|||.|-=+-...-.+-..-+...+ +.|+.+++-..|. .+..+-++- =.| -.+.|
T Consensus 56 ~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~Kga~vl~prG------~~yt~~nI~~~L~-~R~~~~~lR-~~G-~~t~G 124 (151)
T PRK00124 56 AADNEIVQLAEKG--DIVITQDYGLAALALEKGAIVLNPRG------YIYTNDNIDQLLA-MRDLMATLR-RSG-IRTGG 124 (151)
T ss_pred hHHHHHHHhCCCC--CEEEeCCHHHHHHHHHCCCEEECCCC------cCCCHHHHHHHHH-HHHHHHHHH-HcC-CCCCC
Confidence 8999999999988 56899997654443222111233221 4688887765552 122222221 124 34555
Q ss_pred CCCCcHHHHHHHHHHhCCHHHHHHH
Q 016711 239 IRGIGGQTALKLIRQHGSIETILEN 263 (384)
Q Consensus 239 i~giG~ktA~~li~~~~sle~il~~ 263 (384)
-+..+++.-..+.+. |+.+|..
T Consensus 125 p~~~~~~Dr~~F~~~---L~~~l~~ 146 (151)
T PRK00124 125 PKPFTQEDRSRFEAE---LDKLIRR 146 (151)
T ss_pred CCCCCHHHHHHHHHH---HHHHHHH
Confidence 566666665555543 5555554
No 141
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.39 E-value=54 Score=35.51 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=16.4
Q ss_pred CCCCCcHHHHHHHH-HHhCCHHHHHH
Q 016711 238 SIRGIGGQTALKLI-RQHGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li-~~~~sle~il~ 262 (384)
|||+||.++|..|. +.|++++++.+
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 36677777777666 66777666553
No 142
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=27.30 E-value=1.4e+02 Score=30.73 Aligned_cols=32 Identities=16% Similarity=0.343 Sum_probs=18.3
Q ss_pred ccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 297 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 297 ~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
.+.|. .|.+.+..|...+-||. -|+.+++.|+
T Consensus 307 ~~~w~-~~~~~f~aW~~G~TG~P--~VDA~MRqL~ 338 (475)
T TIGR02766 307 FFPWA-VDENYFKAWRQGRTGYP--LVDAGMRELW 338 (475)
T ss_pred cCCCC-CCHHHHHHHHcCCCCCc--chhHHHHHHH
Confidence 35564 46677777776666664 3444444443
No 143
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=27.19 E-value=1.1e+02 Score=31.46 Aligned_cols=32 Identities=6% Similarity=0.095 Sum_probs=17.4
Q ss_pred HHHHHHHHHhcCCCccccchHHHHHHHHHHHc
Q 016711 139 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS 170 (384)
Q Consensus 139 ~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~ 170 (384)
+.++.+-|+.+|++.++..|+....+..|++.
T Consensus 57 L~~L~~~L~~~G~~L~v~~G~p~~vl~~l~~~ 88 (471)
T TIGR03556 57 LQELQQRYQQAGSQLLILQGDPVQLIPQLAQQ 88 (471)
T ss_pred HHHHHHHHHHCCCCeEEEECCHHHHHHHHHHH
Confidence 34444555555666665555555555555543
No 144
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=26.99 E-value=81 Score=22.50 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=20.4
Q ss_pred CCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 016711 299 KWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 331 (384)
Q Consensus 299 ~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~ 331 (384)
.....|.+-+.+|. .+||..++|...++++.
T Consensus 4 ~~~Gi~~~lVd~F~--~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 4 ALYGIDKDLVDQFE--NMGFERDKVVEVLRRLG 34 (55)
T ss_dssp S----SHHHHHHHH--HHT--HHHHHHHHHHS-
T ss_pred HHcCCCHHHHHHHH--HcCCcHHHHHHHHHHhC
Confidence 34467888888885 79999999999998864
No 145
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=26.87 E-value=41 Score=31.03 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=12.5
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||++||--++-
T Consensus 125 ~l~GIG~kTAd~iLl 139 (218)
T PRK13913 125 DQKGIGKESADAILC 139 (218)
T ss_pred cCCCccHHHHHHHHH
Confidence 489999999977664
No 146
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=26.81 E-value=47 Score=29.91 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=15.8
Q ss_pred CCCCCcHHHHHHHHHHhC
Q 016711 238 SIRGIGGQTALKLIRQHG 255 (384)
Q Consensus 238 ~i~giG~ktA~~li~~~~ 255 (384)
.+||||+|+|.+++.++.
T Consensus 112 ~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 112 KVPGIGKKTAERIVLELK 129 (192)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 589999999999998754
No 147
>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=26.73 E-value=53 Score=31.62 Aligned_cols=25 Identities=32% Similarity=0.395 Sum_probs=21.0
Q ss_pred CCCCCcHHHHHHHHHH-hCCHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ-HGSIETILE 262 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-~~sle~il~ 262 (384)
.+||||+++|.+|.+. |.+++++..
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~~ 28 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIAV 28 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 4799999999999998 888776643
No 148
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=26.54 E-value=44 Score=28.30 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.7
Q ss_pred CCCCCcHHHHHHHHH
Q 016711 238 SIRGIGGQTALKLIR 252 (384)
Q Consensus 238 ~i~giG~ktA~~li~ 252 (384)
.+||||++||--++.
T Consensus 76 ~l~GIG~~tA~~~l~ 90 (149)
T smart00478 76 KLPGVGRKTANAVLS 90 (149)
T ss_pred cCCCCcHHHHHHHHH
Confidence 589999999865543
No 149
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=26.16 E-value=91 Score=28.71 Aligned_cols=15 Identities=33% Similarity=0.295 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHHcCC
Q 016711 158 SEAEAQCAALCKSGQ 172 (384)
Q Consensus 158 ~EADa~~A~L~~~g~ 172 (384)
.|.||.+|||...|.
T Consensus 194 te~~AliAYLq~LG~ 208 (217)
T PRK14487 194 TEMDALIAYLQSLGT 208 (217)
T ss_pred cHHHHHHHHHHHhcc
Confidence 488999999998775
No 150
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=25.55 E-value=61 Score=27.04 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=14.9
Q ss_pred CCCCcHHHHHHHHHHhC
Q 016711 239 IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 239 i~giG~ktA~~li~~~~ 255 (384)
|.|||+.+|..++.+.|
T Consensus 22 I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 22 IYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccHHHHHHHHHHhC
Confidence 68999999999988765
No 151
>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=25.42 E-value=1.1e+02 Score=25.67 Aligned_cols=46 Identities=15% Similarity=0.137 Sum_probs=30.8
Q ss_pred HHHHHHhcCCCccccch--------HHHHHHHHH----HHc--CCeEEEEcCCCcccccC
Q 016711 142 CKRLLKLMGVPVVEAPS--------EAEAQCAAL----CKS--GQVYAVASEDMDSLTFG 187 (384)
Q Consensus 142 ~~~lL~~~Gip~i~ap~--------EADa~~A~L----~~~--g~~~~v~S~DsD~l~fg 187 (384)
..+.|+..|+.++..|. .+|-.++.- +.. -.+.+++|+|+|+....
T Consensus 57 ~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i 116 (149)
T cd06167 57 FLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLV 116 (149)
T ss_pred HHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHH
Confidence 45677888998887772 366555432 222 24667899999998764
No 152
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=25.26 E-value=93 Score=27.74 Aligned_cols=46 Identities=35% Similarity=0.415 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHhcCCCccccchH--HHHHHHHHHHcCCeEEEEcCC
Q 016711 135 TKQHNDDCKRLLKLMGVPVVEAPSE--AEAQCAALCKSGQVYAVASED 180 (384)
Q Consensus 135 t~~~~~~~~~lL~~~Gip~i~ap~E--ADa~~A~L~~~g~~~~v~S~D 180 (384)
+....+.++.++..-||+++..||| -+|.-..+...|.-..|+|.|
T Consensus 48 isp~tp~t~~~~~~~gv~vi~tpG~GYv~Dl~~al~~l~~P~lvvsaD 95 (177)
T COG2266 48 ISPHTPKTKEYLESVGVKVIETPGEGYVEDLRFALESLGTPILVVSAD 95 (177)
T ss_pred eCCCCHhHHHHHHhcCceEEEcCCCChHHHHHHHHHhcCCceEEEecc
Confidence 3456678888999999999999975 334444455556544566655
No 153
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=24.52 E-value=83 Score=28.24 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHhCCCCCC------CCCCCcHHHHHHHHHH-----hCCHHHHHHHHh
Q 016711 220 TMDQFIDLCILSGCDYCD------SIRGIGGQTALKLIRQ-----HGSIETILENIN 265 (384)
Q Consensus 220 ~~~q~id~~~L~G~Dy~~------~i~giG~ktA~~li~~-----~~sle~il~~~~ 265 (384)
..+.|+++.-=++ --+- -+||||-|++-.+|.+ |.|.++|-+.+.
T Consensus 111 ~E~rFV~fFN~A~-PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~Rv~ 166 (202)
T COG1491 111 NEDRFVKFFNEAE-PITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKERVK 166 (202)
T ss_pred hhhHHHHHhcccC-cchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHHHhc
Confidence 4566666654333 1111 1599999999999975 778888877664
No 154
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=23.88 E-value=69 Score=26.73 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=14.7
Q ss_pred CCCCcHHHHHHHHHHhC
Q 016711 239 IRGIGGQTALKLIRQHG 255 (384)
Q Consensus 239 i~giG~ktA~~li~~~~ 255 (384)
|.|||+.+|..+....|
T Consensus 22 i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 22 IYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccHHHHHHHHHHcC
Confidence 68999999999888755
No 155
>PRK00254 ski2-like helicase; Provisional
Probab=22.92 E-value=66 Score=35.11 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=23.3
Q ss_pred CCCCCcHHHHHHHHHH-hCCHHHHHHH
Q 016711 238 SIRGIGGQTALKLIRQ-HGSIETILEN 263 (384)
Q Consensus 238 ~i~giG~ktA~~li~~-~~sle~il~~ 263 (384)
.|||||+++|.+|++. |+|+++|.+.
T Consensus 649 ~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 649 RLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred cCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 4799999999999999 9999988764
No 156
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=22.63 E-value=1.8e+02 Score=23.80 Aligned_cols=54 Identities=15% Similarity=0.211 Sum_probs=32.1
Q ss_pred HHHHHHhCCCCCCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhhccCCCCccccc
Q 016711 278 QEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESF 345 (384)
Q Consensus 278 ~~~~~~~~~p~v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~~l~~~~~~~~q~~l~~f 345 (384)
+-+++++.++... + -+.+...+++...+..+.......-.-|+.. .+|++||+|
T Consensus 57 E~vR~A~~~~p~~---------f--~~l~eAl~~~~~~l~~~~~~w~~~s~ll~~~---~~Q~tL~~F 110 (110)
T PF04895_consen 57 ENVRKAMKGKPEK---------F--ETLEEALEYVSSRLKLPIKEWLRKSKLLKRI---RRQKTLDDF 110 (110)
T ss_pred HHHHHHHhCCCcc---------c--CCHHHHHHHHHHHhCCCHHHHHHHhHHHHHH---hcccccccC
Confidence 4567777655322 1 1556667777777777765544333333322 279999998
No 157
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=22.52 E-value=48 Score=31.82 Aligned_cols=19 Identities=32% Similarity=0.400 Sum_probs=12.7
Q ss_pred CCCCCcHHHHHHH-HHHhCC
Q 016711 238 SIRGIGGQTALKL-IRQHGS 256 (384)
Q Consensus 238 ~i~giG~ktA~~l-i~~~~s 256 (384)
.||||||+||--+ +..++.
T Consensus 211 ~LpGIGpwTA~~vllr~lg~ 230 (283)
T PRK10308 211 TFPGIGRWTANYFALRGWQA 230 (283)
T ss_pred cCCCcCHHHHHHHHHHhCCC
Confidence 3799999998543 344443
No 158
>PRK09982 universal stress protein UspD; Provisional
Probab=22.47 E-value=2.5e+02 Score=23.25 Aligned_cols=28 Identities=7% Similarity=-0.022 Sum_probs=16.9
Q ss_pred CCCccccchHHHHHHHHHHHcCCeEEEE
Q 016711 150 GVPVVEAPSEAEAQCAALCKSGQVYAVA 177 (384)
Q Consensus 150 Gip~i~ap~EADa~~A~L~~~g~~~~v~ 177 (384)
++.+....|+.-..+...++...+|.|+
T Consensus 81 ~~~~~v~~G~p~~~I~~~A~~~~aDLIV 108 (142)
T PRK09982 81 KTKLRIERGEMPETLLEIMQKEQCDLLV 108 (142)
T ss_pred cceEEEEecCHHHHHHHHHHHcCCCEEE
Confidence 4555666676666666677665555443
No 159
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=22.42 E-value=2.7e+02 Score=25.49 Aligned_cols=102 Identities=19% Similarity=0.224 Sum_probs=55.4
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhhccCCCCCCCchHH--HHHHhCCCC
Q 016711 211 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQE--ARRLFKEPE 288 (384)
Q Consensus 211 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~i~giG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~--~~~~~~~p~ 288 (384)
+.+|...|.+|+|+..-+.=+. +. ..|.+...-..++..-+..++.+.++-. ...-.++|-|.+ |..+|.=-.
T Consensus 76 ~Alc~a~~~dp~~~r~dA~~l~-~~---a~~~s~~~l~~~l~~~~~~~~~l~~~~~-~~~~~~~f~YSRl~AIGL~~LLe 150 (206)
T PLN03060 76 KAYIEALGEDPDQYRKDAKKLE-EW---ASSQSASGIADFNSGDGEVEAVLKDIAE-RAAGKTKFHYSRFFAIGLFRLLE 150 (206)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-HH---HhcCCHHHHHHHHhcccccchHHHHHHH-HhhcCCCcchHHHHHHHHHHHHH
Confidence 3567777888888876654443 22 2345555556666655544444433211 011234565543 555553110
Q ss_pred CCChhhhcccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHH
Q 016711 289 VVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIE 328 (384)
Q Consensus 289 v~~~~~~~~~~~~~pd~~~l~~f~~~~~~f~~~~v~~~~~ 328 (384)
.. .-. |.+.+.+++ +.+|++.++|.+-|.
T Consensus 151 ~a--------~~~--d~~~l~~l~-~~L~ls~~kv~kDL~ 179 (206)
T PLN03060 151 CA--------KAS--DPAVLEKLS-KALNVSKRSVDRDLD 179 (206)
T ss_pred Hc--------CCC--CHHHHHHHH-HHcCCCHHHHHhhHH
Confidence 00 001 445777776 899999999987653
No 160
>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=22.12 E-value=1.2e+02 Score=24.87 Aligned_cols=46 Identities=20% Similarity=0.219 Sum_probs=22.0
Q ss_pred HHHHHHhcCCCccccch---------HHHHHHHH----HH--HcCCeEEEEcCCCcccccC
Q 016711 142 CKRLLKLMGVPVVEAPS---------EAEAQCAA----LC--KSGQVYAVASEDMDSLTFG 187 (384)
Q Consensus 142 ~~~lL~~~Gip~i~ap~---------EADa~~A~----L~--~~g~~~~v~S~DsD~l~fg 187 (384)
+.+.|+..|+++...|. .+|-.++. ++ ......+++|+|+|+....
T Consensus 52 ~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v 112 (146)
T PF01936_consen 52 FQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLV 112 (146)
T ss_dssp HHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHH
T ss_pred HHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHH
Confidence 44566778887765543 35544442 22 1235667999999987664
No 161
>PRK13910 DNA glycosylase MutY; Provisional
Probab=21.65 E-value=87 Score=30.24 Aligned_cols=14 Identities=36% Similarity=0.544 Sum_probs=12.0
Q ss_pred CCCCcHHHHHHHHH
Q 016711 239 IRGIGGQTALKLIR 252 (384)
Q Consensus 239 i~giG~ktA~~li~ 252 (384)
+||||++||--++.
T Consensus 77 LpGIG~kTA~aIl~ 90 (289)
T PRK13910 77 LPGIGAYTANAILC 90 (289)
T ss_pred CCCCCHHHHHHHHH
Confidence 79999999987765
No 162
>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=21.16 E-value=99 Score=26.58 Aligned_cols=39 Identities=18% Similarity=0.248 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHcCCeE
Q 016711 136 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVY 174 (384)
Q Consensus 136 ~~~~~~~~~lL~~~Gip~i~ap~EADa~~A~L~~~g~~~ 174 (384)
.+.+.++++-|+..|++.++-.|++...+..|++.-.+.
T Consensus 52 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~ 90 (165)
T PF00875_consen 52 LESLADLQESLRKLGIPLLVLRGDPEEVLPELAKEYGAT 90 (165)
T ss_dssp HHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHHHTES
T ss_pred HHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHhcCcC
Confidence 345677888889999999999998888888887743333
No 163
>cd04246 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulati
Probab=20.31 E-value=6.7e+02 Score=22.92 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHcCCceEEEEeCCCCch
Q 016711 64 HLQGMFTRTIRLLEAGMKPIYVFDGQPPDL 93 (384)
Q Consensus 64 ~l~g~~~~~~~ll~~gi~Pv~VFDG~~~~~ 93 (384)
.+..++..+..+.+.|.+|++|--|..+..
T Consensus 16 ~~~~~~~~i~~l~~~g~~~viV~sg~g~~~ 45 (239)
T cd04246 16 RIKRVAERIKKAVKKGYQVVVVVSAMGGTT 45 (239)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEECCCCchH
Confidence 345555555556667899999999754433
Done!