Query 026645
Match_columns 235
No_of_seqs 221 out of 1680
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 10:45:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0177 Nth Predicted EndoIII- 100.0 1.7E-57 3.6E-62 377.1 19.6 183 23-214 27-209 (211)
2 KOG1921 Endonuclease III [Repl 100.0 4.6E-54 1E-58 356.6 17.0 223 2-229 54-278 (286)
3 PRK10702 endonuclease III; Pro 100.0 3.1E-52 6.7E-57 349.5 21.7 184 22-214 26-209 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 1E-50 2.2E-55 352.4 21.5 207 14-225 12-223 (275)
5 PRK10880 adenine DNA glycosyla 100.0 9.1E-51 2E-55 362.3 20.1 207 14-225 16-227 (350)
6 COG1194 MutY A/G-specific DNA 100.0 8.2E-47 1.8E-51 330.8 16.2 210 13-227 20-234 (342)
7 TIGR01083 nth endonuclease III 100.0 1.8E-45 4E-50 305.0 20.5 169 22-199 23-191 (191)
8 PRK13910 DNA glycosylase MutY; 100.0 5.7E-45 1.2E-49 317.5 18.9 175 34-218 1-176 (289)
9 PRK13913 3-methyladenine DNA g 100.0 4.6E-39 1E-43 269.9 20.1 172 14-194 18-216 (218)
10 COG2231 Uncharacterized protei 100.0 7.9E-36 1.7E-40 243.1 18.7 186 18-212 23-214 (215)
11 KOG2457 A/G-specific adenine D 100.0 2.3E-36 4.9E-41 265.0 12.5 195 13-212 102-309 (555)
12 smart00478 ENDO3c endonuclease 100.0 3.7E-33 8.1E-38 222.3 16.5 148 34-189 1-148 (149)
13 cd00056 ENDO3c endonuclease II 100.0 8.9E-33 1.9E-37 222.1 17.2 154 26-188 1-158 (158)
14 PRK01229 N-glycosylase/DNA lya 100.0 5.9E-30 1.3E-34 213.1 16.1 157 22-186 34-200 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 100.0 5.6E-27 1.2E-31 207.5 18.9 155 14-173 109-290 (310)
16 COG0122 AlkA 3-methyladenine D 99.9 2.2E-25 4.7E-30 194.7 17.1 162 15-186 95-273 (285)
17 PRK10308 3-methyl-adenine DNA 99.9 7.4E-25 1.6E-29 191.5 16.9 154 13-183 101-272 (283)
18 TIGR03252 uncharacterized HhH- 99.9 1.1E-24 2.5E-29 176.1 13.1 107 22-128 15-137 (177)
19 KOG2875 8-oxoguanine DNA glyco 99.9 2.9E-21 6.3E-26 163.8 13.5 145 22-170 114-283 (323)
20 KOG1918 3-methyladenine DNA gl 99.9 3.8E-21 8.3E-26 158.1 11.4 159 16-187 66-242 (254)
21 PF00730 HhH-GPD: HhH-GPD supe 99.8 7.6E-20 1.6E-24 137.8 12.5 105 30-173 1-107 (108)
22 COG1059 Thermostable 8-oxoguan 99.3 3.8E-11 8.2E-16 97.2 10.1 140 23-171 37-185 (210)
23 PF00633 HHH: Helix-hairpin-he 98.7 3.1E-09 6.6E-14 61.6 0.4 29 97-125 2-30 (30)
24 PF10576 EndIII_4Fe-2S: Iron-s 98.3 2.4E-07 5.3E-12 46.4 0.5 17 192-208 1-17 (17)
25 smart00525 FES FES domain. iro 97.6 1.5E-05 3.3E-10 44.4 0.6 21 191-211 1-21 (26)
26 PF09674 DUF2400: Protein of u 96.8 0.041 8.8E-07 47.0 12.9 161 25-189 16-230 (232)
27 PF03352 Adenine_glyco: Methyl 96.5 0.039 8.5E-07 45.3 10.5 100 25-125 26-163 (179)
28 smart00278 HhH1 Helix-hairpin- 96.0 0.0055 1.2E-07 34.0 2.0 20 107-126 2-21 (26)
29 TIGR02757 conserved hypothetic 95.6 0.0053 1.1E-07 52.2 1.4 55 132-189 173-227 (229)
30 PRK10353 3-methyl-adenine DNA 95.5 0.4 8.6E-06 39.6 12.0 70 25-94 31-103 (187)
31 PF14716 HHH_8: Helix-hairpin- 95.5 0.066 1.4E-06 36.7 6.3 57 68-125 10-66 (68)
32 PRK13901 ruvA Holliday junctio 95.5 0.074 1.6E-06 44.3 7.7 64 54-129 61-130 (196)
33 PF12826 HHH_2: Helix-hairpin- 95.2 0.034 7.3E-07 37.7 4.0 35 90-125 16-54 (64)
34 COG2818 Tag 3-methyladenine DN 95.1 0.45 9.7E-06 39.1 11.0 101 24-125 31-169 (188)
35 TIGR00624 tag DNA-3-methyladen 94.9 0.86 1.9E-05 37.4 12.1 71 25-95 30-103 (179)
36 PRK14601 ruvA Holliday junctio 94.4 0.22 4.8E-06 41.0 7.7 64 54-129 62-131 (183)
37 PRK14606 ruvA Holliday junctio 94.0 0.31 6.6E-06 40.3 7.7 63 54-128 62-130 (188)
38 PF14520 HHH_5: Helix-hairpin- 93.9 0.18 4E-06 33.4 5.2 41 47-90 18-58 (60)
39 PRK14602 ruvA Holliday junctio 93.5 0.39 8.5E-06 40.2 7.7 62 54-127 63-130 (203)
40 COG0632 RuvA Holliday junction 93.5 0.38 8.3E-06 40.2 7.4 64 54-129 62-131 (201)
41 PRK14604 ruvA Holliday junctio 93.4 0.41 9E-06 39.8 7.6 63 54-128 62-130 (195)
42 TIGR00084 ruvA Holliday juncti 93.3 0.28 6.1E-06 40.6 6.3 64 54-125 61-126 (191)
43 PRK14605 ruvA Holliday junctio 93.2 0.46 1E-05 39.5 7.5 59 54-124 62-126 (194)
44 PRK14603 ruvA Holliday junctio 93.1 0.51 1.1E-05 39.3 7.6 61 54-126 61-127 (197)
45 PRK14600 ruvA Holliday junctio 92.1 0.33 7.1E-06 40.1 5.3 61 54-127 62-128 (186)
46 TIGR00426 competence protein C 92.0 0.67 1.5E-05 31.5 5.9 58 60-125 9-66 (69)
47 PRK02515 psbU photosystem II c 91.9 0.42 9E-06 37.1 5.2 58 55-125 49-106 (132)
48 PRK14973 DNA topoisomerase I; 91.9 0.58 1.3E-05 47.8 7.7 99 46-148 814-918 (936)
49 PF02371 Transposase_20: Trans 91.8 0.13 2.9E-06 36.8 2.3 41 106-150 2-42 (87)
50 COG0353 RecR Recombinational D 91.2 0.15 3.3E-06 42.2 2.3 30 100-129 6-35 (198)
51 cd00141 NT_POLXc Nucleotidyltr 91.1 0.82 1.8E-05 40.7 7.1 49 73-123 50-102 (307)
52 smart00483 POLXc DNA polymeras 90.9 0.95 2.1E-05 40.8 7.3 50 73-124 53-107 (334)
53 PF14229 DUF4332: Domain of un 90.9 1.6 3.5E-05 33.4 7.7 84 47-147 8-93 (122)
54 PRK13844 recombination protein 90.8 0.17 3.7E-06 42.2 2.2 29 101-129 10-38 (200)
55 PRK00076 recR recombination pr 90.5 0.25 5.4E-06 41.1 3.0 29 101-129 6-34 (196)
56 PRK00116 ruvA Holliday junctio 90.4 0.93 2E-05 37.5 6.4 20 106-125 108-127 (192)
57 TIGR00615 recR recombination p 90.3 0.27 5.9E-06 40.8 3.0 29 101-129 6-34 (195)
58 TIGR00608 radc DNA repair prot 90.1 0.53 1.1E-05 39.9 4.7 57 64-123 14-77 (218)
59 PF14520 HHH_5: Helix-hairpin- 90.1 0.36 7.8E-06 32.0 3.0 26 104-129 3-28 (60)
60 TIGR00575 dnlj DNA ligase, NAD 89.8 2.2 4.8E-05 42.0 9.3 77 45-125 443-549 (652)
61 PRK00116 ruvA Holliday junctio 89.7 0.56 1.2E-05 38.8 4.5 20 105-124 72-91 (192)
62 PF12836 HHH_3: Helix-hairpin- 88.3 0.56 1.2E-05 31.7 2.9 22 104-125 12-33 (65)
63 PRK07956 ligA NAD-dependent DN 87.9 3.3 7.1E-05 40.9 9.1 76 46-125 457-562 (665)
64 TIGR01954 nusA_Cterm_rpt trans 87.7 2.7 5.9E-05 26.3 5.8 44 46-92 5-48 (50)
65 PRK08097 ligB NAD-dependent DN 87.5 4.3 9.4E-05 39.2 9.4 78 44-125 435-539 (562)
66 PRK14350 ligA NAD-dependent DN 87.3 3.7 8.1E-05 40.5 9.0 79 44-126 446-561 (669)
67 PRK08609 hypothetical protein; 87.2 1.6 3.4E-05 42.3 6.4 49 73-123 53-105 (570)
68 PRK00024 hypothetical protein; 86.5 1.1 2.4E-05 38.1 4.4 56 64-123 24-83 (224)
69 PF11731 Cdd1: Pathogenicity l 86.4 0.76 1.7E-05 33.6 2.9 27 103-129 9-35 (93)
70 smart00483 POLXc DNA polymeras 86.4 1.9 4.1E-05 38.8 6.1 48 76-125 20-67 (334)
71 COG1555 ComEA DNA uptake prote 85.9 0.73 1.6E-05 36.7 2.8 23 104-126 95-117 (149)
72 COG1555 ComEA DNA uptake prote 85.6 1.9 4.1E-05 34.3 5.1 55 61-124 91-145 (149)
73 PRK14351 ligA NAD-dependent DN 84.9 5.7 0.00012 39.4 9.0 77 45-125 473-579 (689)
74 TIGR01259 comE comEA protein. 84.8 0.96 2.1E-05 34.6 2.9 22 104-125 66-87 (120)
75 PF09171 DUF1886: Domain of un 84.7 0.59 1.3E-05 40.2 1.9 156 31-194 45-232 (246)
76 PRK07945 hypothetical protein; 84.6 1.9 4.1E-05 38.8 5.2 58 67-125 8-68 (335)
77 TIGR00084 ruvA Holliday juncti 84.4 0.91 2E-05 37.6 2.9 23 103-125 69-91 (191)
78 PRK14605 ruvA Holliday junctio 84.0 0.99 2.1E-05 37.5 2.9 23 103-125 70-92 (194)
79 PF11798 IMS_HHH: IMS family H 84.0 0.75 1.6E-05 26.7 1.6 15 108-122 13-27 (32)
80 COG1796 POL4 DNA polymerase IV 83.8 2.1 4.6E-05 38.2 5.0 56 69-125 15-72 (326)
81 PF10391 DNA_pol_lambd_f: Fing 83.7 1.2 2.6E-05 28.9 2.6 22 106-127 2-23 (52)
82 TIGR01259 comE comEA protein. 83.6 2.8 6E-05 32.0 5.1 61 56-125 57-117 (120)
83 PRK13901 ruvA Holliday junctio 83.4 0.98 2.1E-05 37.6 2.6 23 103-125 69-91 (196)
84 PRK14601 ruvA Holliday junctio 83.0 0.99 2.1E-05 37.2 2.5 23 103-125 70-92 (183)
85 PRK14603 ruvA Holliday junctio 82.8 0.99 2.1E-05 37.6 2.4 23 103-125 69-91 (197)
86 COG1415 Uncharacterized conser 82.4 3.3 7.2E-05 37.3 5.7 70 102-174 274-346 (373)
87 PRK00024 hypothetical protein; 82.2 4.7 0.0001 34.2 6.4 62 27-92 27-88 (224)
88 smart00279 HhH2 Helix-hairpin- 81.8 1.2 2.6E-05 26.6 1.9 16 109-124 19-34 (36)
89 PRK14606 ruvA Holliday junctio 81.6 1.1 2.4E-05 37.0 2.3 23 103-125 70-92 (188)
90 cd00141 NT_POLXc Nucleotidyltr 81.6 3.2 7E-05 36.9 5.4 42 82-125 23-64 (307)
91 COG2003 RadC DNA repair protei 79.7 3 6.5E-05 35.4 4.3 56 64-122 24-82 (224)
92 PRK02515 psbU photosystem II c 79.6 1.7 3.6E-05 33.8 2.5 29 96-124 48-79 (132)
93 TIGR00608 radc DNA repair prot 79.6 6.9 0.00015 33.1 6.5 61 27-91 17-81 (218)
94 PRK01172 ski2-like helicase; P 79.4 5.8 0.00013 39.0 6.9 47 48-97 626-672 (674)
95 PRK14973 DNA topoisomerase I; 79.0 8.1 0.00018 39.7 7.9 47 44-94 754-800 (936)
96 PF05559 DUF763: Protein of un 78.4 4.1 8.8E-05 36.4 4.8 46 100-148 263-311 (319)
97 COG2003 RadC DNA repair protei 76.9 8 0.00017 32.8 6.0 63 26-92 26-88 (224)
98 PF12836 HHH_3: Helix-hairpin- 76.6 2.8 6.1E-05 28.2 2.7 51 63-122 10-60 (65)
99 PRK14600 ruvA Holliday junctio 75.2 2.4 5.3E-05 34.9 2.5 23 103-125 70-92 (186)
100 TIGR00426 competence protein C 73.4 4.1 8.9E-05 27.6 2.9 22 104-125 14-36 (69)
101 KOG2841 Structure-specific end 72.8 3.7 8E-05 35.1 3.0 39 50-92 211-249 (254)
102 PRK14602 ruvA Holliday junctio 72.7 3.4 7.3E-05 34.6 2.8 23 103-125 71-93 (203)
103 cd00080 HhH2_motif Helix-hairp 72.0 2.9 6.4E-05 29.1 1.9 18 108-125 24-41 (75)
104 PRK14604 ruvA Holliday junctio 71.2 3.4 7.4E-05 34.3 2.5 23 103-125 70-92 (195)
105 PRK12766 50S ribosomal protein 70.8 13 0.00027 31.8 5.8 44 46-92 15-58 (232)
106 PF12826 HHH_2: Helix-hairpin- 70.7 11 0.00024 25.2 4.5 43 45-91 14-56 (64)
107 PF04904 NCD1: NAB conserved r 70.7 12 0.00027 26.3 4.7 53 41-94 19-71 (82)
108 PRK07758 hypothetical protein; 69.9 21 0.00046 26.2 6.0 46 44-95 44-89 (95)
109 PRK13482 DNA integrity scannin 69.9 5.4 0.00012 36.2 3.6 36 87-123 297-336 (352)
110 PRK13482 DNA integrity scannin 69.5 16 0.00034 33.3 6.4 47 45-95 298-344 (352)
111 PRK08609 hypothetical protein; 69.1 9.7 0.00021 36.9 5.4 55 69-125 13-67 (570)
112 PRK04301 radA DNA repair and r 69.0 14 0.0003 32.8 6.0 45 45-92 17-61 (317)
113 COG0272 Lig NAD-dependent DNA 68.5 5.2 0.00011 39.2 3.4 79 43-125 454-562 (667)
114 COG0632 RuvA Holliday junction 67.5 4.5 9.7E-05 33.8 2.4 46 103-149 70-116 (201)
115 PTZ00035 Rad51 protein; Provis 67.4 16 0.00035 32.8 6.2 48 45-95 34-81 (337)
116 TIGR02236 recomb_radA DNA repa 66.8 17 0.00036 32.0 6.1 44 45-91 10-53 (310)
117 TIGR02238 recomb_DMC1 meiotic 66.7 18 0.0004 32.2 6.3 48 45-95 12-59 (313)
118 PF10343 DUF2419: Protein of u 66.0 34 0.00073 30.3 7.7 97 54-150 62-202 (287)
119 PF00416 Ribosomal_S13: Riboso 65.2 7.6 0.00016 28.9 3.1 22 104-125 13-34 (107)
120 PLN03187 meiotic recombination 62.9 23 0.00051 32.0 6.3 48 45-95 42-89 (344)
121 KOG2534 DNA polymerase IV (fam 61.7 18 0.0004 32.4 5.2 42 82-125 34-75 (353)
122 PF11691 DUF3288: Protein of u 61.3 60 0.0013 23.5 7.0 63 26-95 11-74 (90)
123 PF14490 HHH_4: Helix-hairpin- 60.6 18 0.00039 26.1 4.3 53 66-125 8-65 (94)
124 PF11372 DUF3173: Domain of un 57.4 54 0.0012 21.9 5.7 29 64-96 4-32 (59)
125 PF03118 RNA_pol_A_CTD: Bacter 57.2 11 0.00023 25.6 2.4 20 104-123 42-61 (66)
126 PRK12766 50S ribosomal protein 57.2 24 0.00053 30.1 5.0 23 103-125 33-55 (232)
127 TIGR01448 recD_rel helicase, p 55.9 18 0.0004 36.0 4.8 84 57-148 68-155 (720)
128 COG4277 Predicted DNA-binding 53.9 9.9 0.00022 33.9 2.2 22 104-125 328-349 (404)
129 PF00570 HRDC: HRDC domain Blo 52.4 25 0.00054 23.2 3.7 21 101-121 39-59 (68)
130 PF01367 5_3_exonuc: 5'-3' exo 51.0 3 6.5E-05 31.0 -1.2 16 110-125 22-37 (101)
131 PRK07758 hypothetical protein; 49.5 15 0.00032 27.0 2.2 20 104-123 65-84 (95)
132 PRK14976 5'-3' exonuclease; Pr 47.9 12 0.00027 32.8 1.9 16 110-125 195-210 (281)
133 TIGR02239 recomb_RAD51 DNA rep 47.7 77 0.0017 28.2 7.0 46 45-93 12-57 (316)
134 PF13592 HTH_33: Winged helix- 47.7 33 0.00072 22.4 3.6 17 135-151 23-39 (60)
135 PRK09482 flap endonuclease-lik 46.0 14 0.00031 32.1 2.0 17 109-125 185-201 (256)
136 COG3547 Transposase and inacti 45.8 36 0.00078 29.4 4.6 37 85-123 169-205 (303)
137 PF14290 DUF4370: Domain of un 45.7 58 0.0013 27.3 5.4 73 37-113 80-155 (239)
138 PRK00254 ski2-like helicase; P 44.9 64 0.0014 32.1 6.6 21 105-125 677-697 (720)
139 PLN03186 DNA repair protein RA 44.6 92 0.002 28.2 7.1 45 46-93 40-84 (342)
140 COG1948 MUS81 ERCC4-type nucle 44.3 57 0.0012 28.3 5.4 23 103-125 211-233 (254)
141 cd00008 53EXOc 5'-3' exonuclea 44.2 15 0.00032 31.4 1.8 18 108-125 185-202 (240)
142 smart00475 53EXOc 5'-3' exonuc 44.0 16 0.00036 31.6 2.1 18 108-125 188-205 (259)
143 COG1796 POL4 DNA polymerase IV 42.9 60 0.0013 29.1 5.4 30 98-127 85-115 (326)
144 PLN02749 Uncharacterized prote 42.9 71 0.0015 25.5 5.2 72 38-113 15-89 (173)
145 PF13297 Telomere_Sde2_2: Telo 42.7 48 0.001 22.2 3.6 24 55-78 6-29 (60)
146 COG1623 Predicted nucleic-acid 41.6 37 0.00081 30.1 3.9 95 27-122 235-341 (349)
147 KOG2534 DNA polymerase IV (fam 41.2 1E+02 0.0022 27.8 6.5 60 66-128 55-119 (353)
148 PRK14667 uvrC excinuclease ABC 40.8 52 0.0011 32.0 5.1 22 103-125 543-564 (567)
149 CHL00137 rps13 ribosomal prote 40.2 17 0.00036 27.9 1.4 22 104-125 15-36 (122)
150 TIGR01448 recD_rel helicase, p 38.8 35 0.00076 34.1 3.7 43 77-125 124-166 (720)
151 COG0258 Exo 5'-3' exonuclease 38.7 48 0.001 29.3 4.3 14 111-124 203-216 (310)
152 COG0864 NikR Predicted transcr 38.3 47 0.001 26.0 3.6 36 58-98 12-47 (136)
153 PRK14666 uvrC excinuclease ABC 38.2 74 0.0016 31.7 5.7 23 103-125 666-688 (694)
154 COG0272 Lig NAD-dependent DNA 37.8 4E+02 0.0087 26.5 10.5 25 164-188 555-579 (667)
155 COG1491 Predicted RNA-binding 37.8 32 0.0007 28.4 2.7 25 101-125 125-149 (202)
156 PF09597 IGR: IGR protein moti 36.8 86 0.0019 20.7 4.2 36 54-93 18-54 (57)
157 PRK05179 rpsM 30S ribosomal pr 36.8 20 0.00043 27.5 1.3 21 105-125 16-36 (122)
158 COG0099 RpsM Ribosomal protein 36.1 26 0.00056 26.8 1.8 28 99-126 7-37 (121)
159 COG1948 MUS81 ERCC4-type nucle 36.0 52 0.0011 28.6 3.9 22 104-125 180-201 (254)
160 PTZ00134 40S ribosomal protein 34.4 23 0.00049 28.4 1.3 27 99-125 20-49 (154)
161 PRK00254 ski2-like helicase; P 34.2 75 0.0016 31.6 5.2 42 47-91 658-699 (720)
162 TIGR03629 arch_S13P archaeal r 34.2 22 0.00048 28.1 1.2 21 105-125 20-40 (144)
163 COG1468 CRISPR-associated prot 33.9 22 0.00048 29.4 1.3 15 195-209 173-187 (190)
164 TIGR03631 bact_S13 30S ribosom 33.8 21 0.00046 26.9 1.1 21 105-125 14-34 (113)
165 PRK07571 bidirectional hydroge 33.0 54 0.0012 26.6 3.4 74 67-144 22-95 (169)
166 PRK14667 uvrC excinuclease ABC 32.3 96 0.0021 30.2 5.4 31 54-88 533-563 (567)
167 PRK09202 nusA transcription el 31.9 2.5E+02 0.0054 26.7 8.0 71 47-120 369-440 (470)
168 PRK04053 rps13p 30S ribosomal 31.7 29 0.00064 27.6 1.6 27 99-125 15-44 (149)
169 PF04919 DUF655: Protein of un 31.7 30 0.00065 28.4 1.6 21 105-125 115-135 (181)
170 PF13543 KSR1-SAM: SAM like do 31.7 1.4E+02 0.0029 23.2 5.2 53 26-86 69-121 (129)
171 PRK00558 uvrC excinuclease ABC 31.4 63 0.0014 31.6 4.1 18 106-123 575-592 (598)
172 PRK14672 uvrC excinuclease ABC 31.4 76 0.0016 31.6 4.6 26 103-128 637-662 (691)
173 PRK14670 uvrC excinuclease ABC 29.5 98 0.0021 30.2 5.0 23 103-125 543-565 (574)
174 TIGR00375 conserved hypothetic 29.4 1.4E+02 0.0031 27.4 5.8 48 24-72 297-345 (374)
175 TIGR00372 cas4 CRISPR-associat 29.0 31 0.00067 27.4 1.3 14 196-209 164-177 (178)
176 PF01930 Cas_Cas4: Domain of u 28.8 33 0.00072 26.9 1.5 14 196-209 148-161 (162)
177 TIGR00596 rad1 DNA repair prot 28.4 49 0.0011 33.6 2.9 23 103-125 754-776 (814)
178 PRK14672 uvrC excinuclease ABC 28.2 1.2E+02 0.0027 30.2 5.4 36 54-92 627-662 (691)
179 PRK14670 uvrC excinuclease ABC 28.2 1.1E+02 0.0024 29.7 5.2 35 54-91 533-567 (574)
180 PF14579 HHH_6: Helix-hairpin- 28.1 42 0.0009 23.9 1.7 20 106-125 27-46 (90)
181 PF13751 DDE_Tnp_1_6: Transpos 28.1 30 0.00066 25.8 1.1 16 196-211 30-45 (125)
182 COG2019 AdkA Archaeal adenylat 27.9 67 0.0015 26.4 3.0 42 109-151 10-52 (189)
183 PRK04301 radA DNA repair and r 27.4 46 0.00099 29.4 2.2 25 104-128 37-61 (317)
184 PF14475 Mso1_Sec1_bdg: Sec1-b 27.2 40 0.00088 20.7 1.3 15 134-148 17-31 (41)
185 smart00341 HRDC Helicase and R 26.4 1.2E+02 0.0026 20.5 3.8 28 84-119 33-60 (81)
186 PHA00439 exonuclease 26.3 42 0.0009 29.7 1.7 17 108-125 190-206 (286)
187 smart00540 LEM in nuclear memb 26.0 99 0.0021 19.3 2.9 34 60-93 2-41 (44)
188 PRK01151 rps17E 30S ribosomal 25.8 49 0.0011 22.0 1.6 20 82-101 4-23 (58)
189 cd00128 XPG Xeroderma pigmento 25.1 47 0.001 29.4 1.9 17 109-125 226-242 (316)
190 PRK14669 uvrC excinuclease ABC 24.8 52 0.0011 32.3 2.3 21 105-125 551-571 (624)
191 COG1379 PHP family phosphoeste 24.7 2.8E+02 0.0061 25.2 6.5 49 23-72 303-352 (403)
192 PRK14671 uvrC excinuclease ABC 24.6 58 0.0013 32.0 2.5 21 105-125 568-588 (621)
193 TIGR00596 rad1 DNA repair prot 24.6 1.3E+02 0.0028 30.7 5.0 41 47-92 770-810 (814)
194 PRK03980 flap endonuclease-1; 24.5 49 0.0011 29.2 1.8 15 110-124 193-207 (292)
195 PF14635 HHH_7: Helix-hairpin- 24.5 74 0.0016 23.7 2.5 38 76-118 56-93 (104)
196 KOG3835 Transcriptional corepr 23.9 1.1E+02 0.0024 28.2 4.0 40 40-79 20-59 (495)
197 PF04891 NifQ: NifQ; InterPro 23.9 95 0.0021 25.2 3.3 73 114-208 83-165 (167)
198 PF01706 FliG_C: FliG C-termin 23.7 94 0.002 22.9 3.0 48 46-95 11-58 (110)
199 PF14199 DUF4317: Domain of un 23.2 1.5E+02 0.0032 27.3 4.7 71 23-94 236-310 (371)
200 PF02467 Whib: Transcription f 23.2 14 0.00029 25.1 -1.5 15 198-212 31-45 (66)
201 PF11842 DUF3362: Domain of un 23.1 1.6E+02 0.0034 23.5 4.3 43 162-204 44-86 (150)
202 COG1701 Uncharacterized protei 22.9 3.2E+02 0.007 23.3 6.2 47 40-94 197-243 (256)
203 PRK14669 uvrC excinuclease ABC 22.7 1.6E+02 0.0034 29.1 5.0 21 103-125 581-601 (624)
204 PF09384 UTP15_C: UTP15 C term 22.6 3.8E+02 0.0082 20.9 6.7 71 26-98 34-108 (148)
205 TIGR00194 uvrC excinuclease AB 22.3 63 0.0014 31.4 2.3 21 105-125 540-560 (574)
206 PRK14668 uvrC excinuclease ABC 22.1 1.2E+02 0.0025 29.6 4.0 39 87-125 535-576 (577)
207 TIGR03674 fen_arch flap struct 21.1 62 0.0013 29.2 1.8 16 109-124 239-254 (338)
208 PTZ00217 flap endonuclease-1; 21.1 62 0.0013 29.9 1.9 16 109-124 238-253 (393)
209 PRK02362 ski2-like helicase; P 21.0 1.7E+02 0.0037 29.2 5.1 60 83-147 633-692 (737)
210 smart00611 SEC63 Domain of unk 20.8 1.5E+02 0.0033 25.7 4.3 51 67-122 117-167 (312)
211 PF03755 YicC_N: YicC-like fam 20.8 1.8E+02 0.004 22.9 4.4 36 80-115 81-116 (159)
212 PRK14666 uvrC excinuclease ABC 20.4 1.3E+02 0.0029 29.9 4.1 23 105-128 636-658 (694)
213 TIGR00593 pola DNA polymerase 20.2 65 0.0014 33.1 2.0 15 110-124 189-203 (887)
214 PF08823 PG_binding_2: Putativ 20.1 83 0.0018 21.8 1.9 26 55-80 4-32 (74)
215 PF13523 Acetyltransf_8: Acety 20.0 1.2E+02 0.0027 22.9 3.2 40 111-150 92-138 (152)
No 1
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-57 Score=377.12 Aligned_cols=183 Identities=40% Similarity=0.728 Sum_probs=177.9
Q ss_pred CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCCh
Q 026645 23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIP 102 (235)
Q Consensus 23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~ 102 (235)
.|||++||++||||||+++++.+++.+|++ .++||++++++++++|+++|+..|||++||++|+++++.|+++|+|++|
T Consensus 27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~-~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP 105 (211)
T COG0177 27 KDPFELLVAVILSAQTTDEVVNKATPALFK-RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVP 105 (211)
T ss_pred CCcHHHHHHHHHhccCchHHHHHHHHHHHH-HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCC
Confidence 799999999999999999999999999999 5999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINP 182 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~ 182 (235)
+++++|++|||||+|||++||+++||.+ +|+|||||+||++|+||++ +.++++++..+++++|.+.|..+|.
T Consensus 106 ~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~-------~~~p~~ve~~L~~~iP~~~~~~~h~ 177 (211)
T COG0177 106 DTREELLSLPGVGRKTANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVP-------GKTPEEVEEALMKLIPKELWTDLHH 177 (211)
T ss_pred chHHHHHhCCCcchHHHHHHHHhhcCCC-cccccchHHHHHHHhCCCC-------CCCHHHHHHHHHHHCCHHHHHHHHH
Confidence 9999999999999999999999999996 9999999999999999986 5789999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026645 183 LLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE 214 (235)
Q Consensus 183 ~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~ 214 (235)
+|+.|||.+|++++|+|+.||+++.|+++.+.
T Consensus 178 ~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 178 WLILHGRYICKARKPRCEECPLADLCPSAGKT 209 (211)
T ss_pred HHHHhhhhhccCCCCCcCcccchhhCchhccc
Confidence 99999999999999999999999999987654
No 2
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=4.6e-54 Score=356.58 Aligned_cols=223 Identities=58% Similarity=0.992 Sum_probs=208.8
Q ss_pred CCCCCCccccCCCCCC-CCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChH
Q 026645 2 KTLEPVYSLGVDETDS-SLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYT 80 (235)
Q Consensus 2 ~~~~~~~~~g~~~~~~-~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~ 80 (235)
+..||||.|||+..+. ..++.+..|++||+.+||.||.+++...++.+|.+++..|+++|.++++..|.++|.++|||.
T Consensus 54 k~~APVD~mGc~~~~~~~~~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~ 133 (286)
T KOG1921|consen 54 KIVAPVDTMGCSRIPSLKADPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYT 133 (286)
T ss_pred cccCCccccccccCccccCChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchH
Confidence 3789999999999998 788889999999999999999999999999999998779999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCC
Q 026645 81 RKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSS 160 (235)
Q Consensus 81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~ 160 (235)
+||.||+.+|+.+.++|+||+|++.++|++|||||||.|..+|..+||....|.||+||+|+++||||++. +.++
T Consensus 134 rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~-----ktks 208 (286)
T KOG1921|consen 134 RKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT-----KTKS 208 (286)
T ss_pred HHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc-----ccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999973 4678
Q ss_pred HHHHHHHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcc-cccCcccccCCCCCCCCCccccchh
Q 026645 161 PEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTV-SEYCPSAFKESSTSSSKSKKSESSS 229 (235)
Q Consensus 161 ~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl-~~~C~~~~~~~~~~~~k~~~~~~~~ 229 (235)
+|+++.+|+.|+|.+.|.++|..|+.||+.||+|++|+|+.|-+ ++.|++.++..+....+.++++..+
T Consensus 209 pE~TR~aLq~wLPk~lW~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~~~~~~~~~~~~~~~~~k 278 (286)
T KOG1921|consen 209 PEQTRVALQQWLPKSLWVEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSFKEASSLTKELKKSIMVK 278 (286)
T ss_pred HHHHHHHHHHhCcHHHHhhhhceeecccceeeecCCCCccccccCcccCchhhhhccchhHHHHhhhhhc
Confidence 99999999999999999999999999999999999999999999 6999998877666656555554443
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=3.1e-52 Score=349.51 Aligned_cols=184 Identities=31% Similarity=0.497 Sum_probs=175.4
Q ss_pred CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026645 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI 101 (235)
Q Consensus 22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~ 101 (235)
.++||++||++||||||++.++.+++.+|+. .||||++|++++.++|+++|+++|||++||++|+++|+.+.++|+|++
T Consensus 26 ~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~-~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~ 104 (211)
T PRK10702 26 FSSPFELLIAVLLSAQATDVSVNKATAKLYP-VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEV 104 (211)
T ss_pred CCChHHHHHHHHHHhhcCHHHHHHHHHHHHH-HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 5799999999999999999999999999998 699999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026645 102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN 181 (235)
Q Consensus 102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~ 181 (235)
|+++++|++|||||+|||++||+|+|++ ++||||+||+||++|+|+.. ..++++++..++..+|.+.|.++|
T Consensus 105 p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~Rv~~r~g~~~-------~~~~~~~~~~l~~~lp~~~~~~~~ 176 (211)
T PRK10702 105 PEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIFRVCNRTQFAP-------GKNVEQVEEKLLKVVPAEFKVDCH 176 (211)
T ss_pred CchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHHHHHHHhCCCC-------CCCHHHHHHHHHHhCCchHHHHHH
Confidence 9999999999999999999999999998 68999999999999999864 357889999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCCCCCCcccccCcccccC
Q 026645 182 PLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE 214 (235)
Q Consensus 182 ~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~ 214 (235)
.+||+||+.+|++++|+|+.|||++.|+++.+.
T Consensus 177 ~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~~ 209 (211)
T PRK10702 177 HWLILHGRYTCIARKPRCGSCIIEDLCEYKEKV 209 (211)
T ss_pred HHHHHHhHHHcCCCCCCCCCCcChhhcCccccc
Confidence 999999999999999999999999999976543
No 4
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY 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=100.00 E-value=1e-50 Score=352.38 Aligned_cols=207 Identities=23% Similarity=0.407 Sum_probs=180.7
Q ss_pred CCCC-CCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026645 14 ETDS-SLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA 90 (235)
Q Consensus 14 ~~~~-~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a 90 (235)
++++ ++||+ .|||++||++||+|||++++|.+++.+|.+ .||||++|+++++++|.++|+++||| +||++|+++|
T Consensus 12 ~~~r~~lpWr~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~-~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A 89 (275)
T TIGR01084 12 KYGRKTLPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLE-RFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAA 89 (275)
T ss_pred HhCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHH-hCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHH
Confidence 5676 89997 589999999999999999999999999999 59999999999999999999999999 5799999999
Q ss_pred HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026645 91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170 (235)
Q Consensus 91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~ 170 (235)
+.|.++|+|.+|+++++|++|||||+|||++|++|+|+++ .++||+||+||+.|+++++...+ .....+.++..++.
T Consensus 90 ~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~-~~~vD~~v~RVl~Rl~~~~~~~~--~~~~~~~l~~~~~~ 166 (275)
T TIGR01084 90 QEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKP-YPILDGNVKRVLSRLFAVEGWPG--KKKVENRLWTLAES 166 (275)
T ss_pred HHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCC-CCcchHhHHHHHHHHccCcCCCC--HHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999985 56799999999999987653211 11122334455899
Q ss_pred hCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC--CCCCCCCCccc
Q 026645 171 WLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE--SSTSSSKSKKS 225 (235)
Q Consensus 171 ~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~--~~~~~~k~~~~ 225 (235)
++|.+.+..+|++||+||+.||++++|+|+.|||++.|.++... ..+|.+++|++
T Consensus 167 ~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~~~~~ 223 (275)
T TIGR01084 167 LLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAA 223 (275)
T ss_pred HCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCHhhcCCCCCCCC
Confidence 99999999999999999999999999999999999999987653 46666554443
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=9.1e-51 Score=362.28 Aligned_cols=207 Identities=21% Similarity=0.345 Sum_probs=179.3
Q ss_pred CCCC-CCCCC--CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026645 14 ETDS-SLPPK--ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA 90 (235)
Q Consensus 14 ~~~~-~~p~~--~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a 90 (235)
++++ ++||+ .|||++||++||+|||++++|.+++.+|++ .|||+++|+++++++|.++|+++|||+ ||++|+++|
T Consensus 16 ~~~r~~lpWr~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~-~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A 93 (350)
T PRK10880 16 KYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMA-RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAA 93 (350)
T ss_pred HcCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHH-HCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHH
Confidence 5675 78998 489999999999999999999999999999 599999999999999999999999996 899999999
Q ss_pred HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026645 91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170 (235)
Q Consensus 91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~ 170 (235)
+.++++|+|.+|+++++|++|||||+|||++||+|+|++ +.++||+||+||+.|++.+....+ .....+.+++.++.
T Consensus 94 ~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~-~~~iVD~nV~RV~~Rl~~i~~~~~--~~~~~~~l~~~~~~ 170 (350)
T PRK10880 94 QQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGK-HFPILDGNVKRVLARCYAVSGWPG--KKEVENRLWQLSEQ 170 (350)
T ss_pred HHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHCCC-CeecccHHHHHHHHHHhcccCCCC--hHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998 466689999999999876642111 11122234455678
Q ss_pred hCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccC--CCCCCCCCccc
Q 026645 171 WLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKE--SSTSSSKSKKS 225 (235)
Q Consensus 171 ~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~--~~~~~~k~~~~ 225 (235)
++|.+.++++|++||+||+.||++++|+|+.|||++.|.++... ...|.+++|++
T Consensus 171 l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~~~~P~k~~k~~ 227 (350)
T PRK10880 171 VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQT 227 (350)
T ss_pred hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCHhhCCCCCCCCC
Confidence 89999999999999999999999999999999999999987654 35665544443
No 6
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.2e-47 Score=330.84 Aligned_cols=210 Identities=24% Similarity=0.416 Sum_probs=183.7
Q ss_pred CCCCCCCCCCC--ChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026645 13 DETDSSLPPKE--RRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA 90 (235)
Q Consensus 13 ~~~~~~~p~~~--~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a 90 (235)
+++++++||++ +||.+|||+||+|||++++|.+++.++.+ .|||+++||.|+.+++..+|.++|||.| |++|+++|
T Consensus 20 ~~~~R~LPWR~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~-rfPti~~LA~A~~~evl~~W~gLGYysR-ArnL~~~A 97 (342)
T COG1194 20 DKNGRDLPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLE-RFPTIKALAAAPEDEVLKAWEGLGYYSR-ARNLHKAA 97 (342)
T ss_pred HHhCCcCCCCCCCCcceehhHHHHhhhccHhhhhhhHHHHHH-hCCCHHHHhcCCHHHHHHHHHhcChHHH-HHHHHHHH
Confidence 46788999996 68999999999999999999999999999 5999999999999999999999998765 99999999
Q ss_pred HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHH
Q 026645 91 KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQR 170 (235)
Q Consensus 91 ~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~ 170 (235)
+.++++|+|.+|++.+.|.+|||||+|||.+|++|+|+++ ...||+||.||+.|+..+..+. .+..+...++..++.
T Consensus 98 ~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~-~~~lDgNV~RVl~R~f~i~~~~--~~~~~~~~~~~~~~~ 174 (342)
T COG1194 98 QEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQP-EPVLDGNVKRVLSRLFAISGDI--GKPKTKKELWELAEQ 174 (342)
T ss_pred HHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCC-Cceeecchheeehhhhcccccc--cccchhHHHHHHHHH
Confidence 9999999999999999999999999999999999999985 4459999999999998776432 223456678888888
Q ss_pred hCCcc-cHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccccCC--CCCCCCCccccc
Q 026645 171 WLPKE-EWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAFKES--STSSSKSKKSES 227 (235)
Q Consensus 171 ~~p~~-~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~--~~~~~k~~~~~~ 227 (235)
+++++ ...+||++||++|+.||++.+|+|+.|||++.|..+.... .+|.++.|++.+
T Consensus 175 ll~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~~ 234 (342)
T COG1194 175 LLTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKLP 234 (342)
T ss_pred hcCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCcccCCCcCcccccc
Confidence 55544 4999999999999999999999999999999999776543 566555444444
No 7
>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=100.00 E-value=1.8e-45 Score=305.02 Aligned_cols=169 Identities=31% Similarity=0.613 Sum_probs=162.1
Q ss_pred CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC
Q 026645 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI 101 (235)
Q Consensus 22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~ 101 (235)
.+|||++||++||||||+++++.+++.+|++ .||||++|+++++++|+++|+++||+++||++|+++|+++.++|+|++
T Consensus 23 ~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~-~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~ 101 (191)
T TIGR01083 23 YNNPFELLVATILSAQATDKSVNKATKKLFE-VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEV 101 (191)
T ss_pred CCCHHHHHHHHHHHhhCcHHHHHHHHHHHHH-HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCC
Confidence 4799999999999999999999999999999 699999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026645 102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN 181 (235)
Q Consensus 102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~ 181 (235)
|+.++.|++|||||+|||++||+|+++++ .||||+|++|++.|+|+.. ..+++++++.++.++|.+.|.++|
T Consensus 102 ~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~Ri~~r~g~~~-------~~~~~~~~~~l~~~~p~~~~~~~h 173 (191)
T TIGR01083 102 PEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVFRVSNRLGLSK-------GKDPDKVEEELLKLIPREFWTKLH 173 (191)
T ss_pred chHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHHHHHHHcCCCC-------CCCHHHHHHHHHHHCCchhHHHHH
Confidence 99999999999999999999999999985 6999999999999999874 346899999999999999999999
Q ss_pred HHHHHHHhhhcCCCCCCC
Q 026645 182 PLLVGFGQTICTPLRPRC 199 (235)
Q Consensus 182 ~~l~~~G~~iC~~~~P~C 199 (235)
++|++||+.+|++++|+|
T Consensus 174 ~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 174 HWLILHGRYTCKARKPLC 191 (191)
T ss_pred HHHHHHhHHhcCCCCCCC
Confidence 999999999999999999
No 8
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=5.7e-45 Score=317.49 Aligned_cols=175 Identities=25% Similarity=0.490 Sum_probs=157.9
Q ss_pred HhccccHHHHHH-HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCC
Q 026645 34 LSSLTKDKVADG-ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALP 112 (235)
Q Consensus 34 Lsqqt~~~~~~~-~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~ 112 (235)
|+|||+++++.. ++.+|++ .|||+++|+++++++|.++|+++|||+ ||++|+++|+.+.++|+|.+|.++++|++||
T Consensus 1 mlQQT~v~~v~~~yy~rf~~-~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~P~~~~~L~~Lp 78 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLE-AFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHSQLPNDYQSLLKLP 78 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCCCCChhHHHHHhCC
Confidence 689999999975 9999999 599999999999999999999999995 7999999999999999999999999999999
Q ss_pred CCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHhhhc
Q 026645 113 GIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQTIC 192 (235)
Q Consensus 113 GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC 192 (235)
|||+|||++||+|+|++ ++++||+||+||+.|++++.. ..+.++++...+.++|...+..+|++||+||+.||
T Consensus 79 GIG~kTA~aIl~~af~~-~~~~VD~nV~RVl~Rl~g~~~------~~~~~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~iC 151 (289)
T PRK13910 79 GIGAYTANAILCFGFRE-KSACVDANIKRVLLRLFGLDP------NIHAKDLQIKANDFLNLNESFNHNQALIDLGALIC 151 (289)
T ss_pred CCCHHHHHHHHHHHCCC-CcCcccHHHHHHHHHHhcCCC------CccHHHHHHHHHHhCCccchHHHHHHHHHHhHHHc
Confidence 99999999999999998 478999999999999854432 23456677778889999999999999999999999
Q ss_pred CCCCCCCCCCcccccCcccccCCCCC
Q 026645 193 TPLRPRCGMCTVSEYCPSAFKESSTS 218 (235)
Q Consensus 193 ~~~~P~C~~Cpl~~~C~~~~~~~~~~ 218 (235)
++ +|+|+.|||++.|.++......+
T Consensus 152 ~~-~P~C~~CPl~~~C~~~~~~~~~~ 176 (289)
T PRK13910 152 SP-KPKCAICPLNPYCLGKNNPEKHT 176 (289)
T ss_pred CC-CCCCCCCcChhhhhhhhcCCccc
Confidence 99 79999999999999876544443
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=4.6e-39 Score=269.89 Aligned_cols=172 Identities=17% Similarity=0.235 Sum_probs=152.7
Q ss_pred CCCCCCCC-CCChHHHHHHHHHhccccHHHHHHHHHHHHHc------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHH
Q 026645 14 ETDSSLPP-KERRFAVLLSALLSSLTKDKVADGALQRLLQN------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNM 86 (235)
Q Consensus 14 ~~~~~~p~-~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l 86 (235)
+.+...|| +.+||++||++||+|||+++++.+++.+|.+. ++|||++|++++.++|+++|++.||+++||++|
T Consensus 18 ~~~~~~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~L 97 (218)
T PRK13913 18 KNAPAWWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRL 97 (218)
T ss_pred hcCCCCCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHH
Confidence 33444455 58999999999999999999999999999874 367999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCC----CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHH
Q 026645 87 KKIAKICLTKYDG----DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPE 162 (235)
Q Consensus 87 ~~~a~~i~~~~~g----~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~ 162 (235)
+++|+.+.++|++ ..++++++|+++||||+|||++||+|++++ ++|+||+|++||++|+|+.. .+++
T Consensus 98 k~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r-p~fvVDty~~Rv~~RlG~~~--------~~y~ 168 (218)
T PRK13913 98 IDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAK-EVMVVDKYSYLFLKKLGIEI--------EDYD 168 (218)
T ss_pred HHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCC-CccccchhHHHHHHHcCCCC--------CCHH
Confidence 9999999999876 256789999999999999999999999998 58999999999999999963 3689
Q ss_pred HHHHHHHHhC-----------Cc-----ccHHHHHHHHHHHHhhhcCC
Q 026645 163 QTREALQRWL-----------PK-----EEWVRINPLLVGFGQTICTP 194 (235)
Q Consensus 163 ~~~~~l~~~~-----------p~-----~~~~~~~~~l~~~G~~iC~~ 194 (235)
+++..++..+ |. ..|.+||..|++||+..|.-
T Consensus 169 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 169 ELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred HHHHHHHHhhhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999998876 21 24899999999999999964
No 10
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.9e-36 Score=243.05 Aligned_cols=186 Identities=25% Similarity=0.415 Sum_probs=166.7
Q ss_pred CCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhc
Q 026645 18 SLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKY 97 (235)
Q Consensus 18 ~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~ 97 (235)
+.|+..+.+|+++++||.|+|+|++|.+++++|...+..++++|...+.++|.++|++.|||++||.+|+.+...+...|
T Consensus 23 ~WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~ 102 (215)
T COG2231 23 GWWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFF 102 (215)
T ss_pred cCCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHh
Confidence 46667788999999999999999999999999999888899999999999999999999999999999988887777654
Q ss_pred CC---CChh-hHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026645 98 DG---DIPS-SLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP 173 (235)
Q Consensus 98 ~g---~~~~-~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p 173 (235)
.+ .-+. .+++|++++|||+.|||+||++++++ ++|+||.+..|++.|+|.+. ..+++++++.++..+|
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r-p~FVvD~Yt~R~l~rlg~i~-------~k~ydeik~~fe~~l~ 174 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYALDR-PVFVVDKYTRRLLSRLGGIE-------EKKYDEIKELFEENLP 174 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcC-cccchhHHHHHHHHHhcccc-------cccHHHHHHHHHhcch
Confidence 32 2222 59999999999999999999999988 69999999999999999986 3479999999999888
Q ss_pred ccc--HHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccc
Q 026645 174 KEE--WVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF 212 (235)
Q Consensus 174 ~~~--~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~ 212 (235)
.+. |.++|..++.||+.+|+. +|.|+.|||...|.++.
T Consensus 175 ~~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 175 ENLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred hHHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 764 899999999999999998 59999999999998653
No 11
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-36 Score=264.96 Aligned_cols=195 Identities=24% Similarity=0.394 Sum_probs=176.4
Q ss_pred CCCCCCCCCCCC-----------hHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCH-HHHHHhhccCCChH
Q 026645 13 DETDSSLPPKER-----------RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADE-ATIKDLIYPVAFYT 80 (235)
Q Consensus 13 ~~~~~~~p~~~~-----------~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~-e~l~~~l~~~G~~~ 80 (235)
+.+.+++||+.. .|+++|++||+|||+++.|.++|.++++ .+||..+++.|+. +++.++|.++|||+
T Consensus 102 D~~KRdLPWR~r~sEde~DwerRaYeVwVSEiMLQQTrV~TV~~YYt~WMq-kwPTl~dla~Asl~~eVn~lWaGlGyY~ 180 (555)
T KOG2457|consen 102 DVNKRDLPWRNRRSEDEKDWERRAYEVWVSEIMLQQTRVQTVMKYYTRWMQ-KWPTLYDLAQASLEKEVNELWAGLGYYR 180 (555)
T ss_pred hhhcccCccccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCchHHHHHHHHHHHHHHHHHhhhhHHH
Confidence 456778888743 5999999999999999999999999999 6999999999999 79999999999997
Q ss_pred HHHHHHHHHHHHHHHhcCCCChhhHHHHHc-CCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCC
Q 026645 81 RKACNMKKIAKICLTKYDGDIPSSLDELLA-LPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTS 159 (235)
Q Consensus 81 ~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~-l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~ 159 (235)
+ +++|.+.|+.+++.++|.+|.+-+.|++ +||||+|||.+|++++|+++..+ ||.||.|++.|.--+..+ ..+++
T Consensus 181 R-~rrL~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tGi-VDGNVirvlsRalAIhsD--cSkgk 256 (555)
T KOG2457|consen 181 R-ARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGI-VDGNVIRVLSRALAIHSD--CSKGK 256 (555)
T ss_pred H-HHHHHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhhcCcccc-cccchHHHhHHhHhhcCC--cchhh
Confidence 6 9999999999999999999999999998 99999999999999999997665 999999999998766643 33455
Q ss_pred CHHHHHHHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcccccCcccc
Q 026645 160 SPEQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTVSEYCPSAF 212 (235)
Q Consensus 160 ~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl~~~C~~~~ 212 (235)
--..++..+..++.+..+++||+++|++|+.+|+|.+|.|+.||+...|+.+.
T Consensus 257 ~~q~~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q 309 (555)
T KOG2457|consen 257 FFQSSWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQ 309 (555)
T ss_pred HHHHHHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHh
Confidence 55677888899999999999999999999999999999999999999999764
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=100.00 E-value=3.7e-33 Score=222.30 Aligned_cols=148 Identities=42% Similarity=0.721 Sum_probs=140.9
Q ss_pred HhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCC
Q 026645 34 LSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPG 113 (235)
Q Consensus 34 Lsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~G 113 (235)
|+|||+++++..++.+|.+ .||||++|+++++++|.++|+++||+++||++|+++++.+.+.+++++|+.++.|++|||
T Consensus 1 l~qq~~~~~a~~~~~~l~~-~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~G 79 (149)
T smart00478 1 LSQQTSDEAVNKATERLFE-KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPG 79 (149)
T ss_pred CCCcccHHHHHHHHHHHHH-HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCC
Confidence 6899999999999999999 599999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026645 114 IGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ 189 (235)
Q Consensus 114 IG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 189 (235)
||+|||++|++|++++ +.+|+|+|+.|++.|+|+.+. ..++++++..++.++|.+.|..+|++++++|+
T Consensus 80 IG~~tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~------~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~g~ 148 (149)
T smart00478 80 VGRKTANAVLSFALGK-PFIPVDTHVLRIAKRLGLVDK------KSTPEEVEKLLEKLLPKEDWRELNLLLIDFGR 148 (149)
T ss_pred CcHHHHHHHHHHHCCC-CCCccchHHHHHHHHhCCCCC------CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHcC
Confidence 9999999999999998 789999999999999998862 45789999999999999899999999999997
No 13
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=100.00 E-value=8.9e-33 Score=222.07 Aligned_cols=154 Identities=39% Similarity=0.645 Sum_probs=144.4
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC---
Q 026645 26 FAVLLSALLSSLTKDKVADGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI--- 101 (235)
Q Consensus 26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~--- 101 (235)
|++|+++||+|||+++++..++.+|.+. | |||++|+.+++++|++++.+.| +++||++|+++++.+.+.+++..
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~-~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~~~ 78 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFER-YGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVLDD 78 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHH-hCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccCCC
Confidence 7899999999999999999999999994 8 9999999999999999999999 78899999999999999988866
Q ss_pred hhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHH
Q 026645 102 PSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRIN 181 (235)
Q Consensus 102 ~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~ 181 (235)
++.++.|++|||||+|||+++++|+++ .++||+|+|+.|++.|+|+++. ..+++++++.++.+.|...+..+|
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~ 151 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG-PDAFPVDTHVRRVLKRLGLIPK------KKTPEELEELLEELLPKPYWGEAN 151 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCccchhHHHHHHHhCCCCC------CCCHHHHHHHHHHHCCHHHHHHHH
Confidence 889999999999999999999999999 6899999999999999998642 568899999999999977889999
Q ss_pred HHHHHHH
Q 026645 182 PLLVGFG 188 (235)
Q Consensus 182 ~~l~~~G 188 (235)
+.|++||
T Consensus 152 ~~l~~~g 158 (158)
T cd00056 152 QALMDLG 158 (158)
T ss_pred HHHHHcC
Confidence 9999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.97 E-value=5.9e-30 Score=213.12 Aligned_cols=157 Identities=17% Similarity=0.169 Sum_probs=131.5
Q ss_pred CCChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHH---HHHh
Q 026645 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKI---CLTK 96 (235)
Q Consensus 22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~---i~~~ 96 (235)
.++||+.||++||||||++.++.+++.+|. ++.+ .++.++|+++|++.| ||++||++|+++++. +.+.
T Consensus 34 ~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~ 106 (208)
T PRK01229 34 EEDLFSELSFCILTANSSAEGGIKAQKEIG------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEI 106 (208)
T ss_pred cCChHHHHHHHHhcCcCcHHHHHHHHHhcC------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999999999884 3455 899999999999995 999999999999987 6566
Q ss_pred c--CCCChhhHHHHH-cCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026645 97 Y--DGDIPSSLDELL-ALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP 173 (235)
Q Consensus 97 ~--~g~~~~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p 173 (235)
+ +++.|+++++|+ ++||||+|||++||.....+ ++|+||+|++|++.|+|+++.........+|.+++..+.++.+
T Consensus 107 ~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~-~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~ 185 (208)
T PRK01229 107 IKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE-DLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAE 185 (208)
T ss_pred HhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC-CeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHH
Confidence 5 889999999999 99999999999999654444 6899999999999999998753223345789999999988887
Q ss_pred ccc--HHHHHHHHHH
Q 026645 174 KEE--WVRINPLLVG 186 (235)
Q Consensus 174 ~~~--~~~~~~~l~~ 186 (235)
.-. .+.+.+.|+.
T Consensus 186 ~~~~~~~~Ldl~~w~ 200 (208)
T PRK01229 186 ELGISLGELDLYIWY 200 (208)
T ss_pred HcCCCHHHHHHHHHH
Confidence 544 3444455544
No 15
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=99.95 E-value=5.6e-27 Score=207.46 Aligned_cols=155 Identities=21% Similarity=0.267 Sum_probs=125.0
Q ss_pred CCCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCCh
Q 026645 14 ETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFY 79 (235)
Q Consensus 14 ~~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~ 79 (235)
-.|.++|.. ||||++|++|+|||+++.++.+++.+|.+. .||||++|+.++.++ .|+.+||.
T Consensus 109 ~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g 184 (310)
T TIGR00588 109 FQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG 184 (310)
T ss_pred CCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH
Confidence 345677765 999999999999999999999999999762 389999999876542 34455884
Q ss_pred HHHHHHHHHHHHHHHHhcCCC----------ChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCc
Q 026645 80 TRKACNMKKIAKICLTKYDGD----------IPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWV 149 (235)
Q Consensus 80 ~~Ka~~l~~~a~~i~~~~~g~----------~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~ 149 (235)
.||++|+++|+++.+.+++. .++.+++|++|||||+|||++|++|+++++++||+|+||+|++.|++..
T Consensus 185 -~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~ 263 (310)
T TIGR00588 185 -YRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPW 263 (310)
T ss_pred -HHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcc
Confidence 36999999999999977654 5678999999999999999999999999999999999999999998654
Q ss_pred CCCCCC---CCCCCHHHHHHHHHHhCC
Q 026645 150 TQPGTK---QKTSSPEQTREALQRWLP 173 (235)
Q Consensus 150 ~~~~~~---~~~~~~~~~~~~l~~~~p 173 (235)
...... ....+++++++...+.++
T Consensus 264 ~~~~~~~~~~~~~~~~~i~~~~~~~~g 290 (310)
T TIGR00588 264 HPKTSRAKGPSPFARKELGNFFRSLWG 290 (310)
T ss_pred cccccccccCChhHHHHHHHHHHHHhc
Confidence 321111 234567777777776555
No 16
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.94 E-value=2.2e-25 Score=194.73 Aligned_cols=162 Identities=24% Similarity=0.304 Sum_probs=135.0
Q ss_pred CCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc-C--------CCCHHHHhcCCHHHHHHhhccCCChHHHHHH
Q 026645 15 TDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-G--------LHTAEAIDKADEATIKDLIYPVAFYTRKACN 85 (235)
Q Consensus 15 ~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~--------~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~ 85 (235)
.|...|...+||+.||++|++||.|.+.+.+++++|.+. + ||||++|+.++++.+.++ |++.+|++|
T Consensus 95 ~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~~~----g~s~~Ka~y 170 (285)
T COG0122 95 PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRC----GLSGRKAEY 170 (285)
T ss_pred cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHHHh----CCcHHHHHH
Confidence 345567789999999999999999999999999999885 4 899999999999998876 999999999
Q ss_pred HHHHHHHHHHhc-------CCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceee-cchHHHHHHHHhcCcCCCCCCCC
Q 026645 86 MKKIAKICLTKY-------DGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGIC-VDTHVHRICNRLGWVTQPGTKQK 157 (235)
Q Consensus 86 l~~~a~~i~~~~-------~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~p-vDt~v~Rv~~Rlg~~~~~~~~~~ 157 (235)
|+++|+++.+.. +.+..++++.|++|+|||+|||++||+|+++++++|| .|.++++.+++++..+ +
T Consensus 171 i~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~------~ 244 (285)
T COG0122 171 IISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLP------T 244 (285)
T ss_pred HHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCC------C
Confidence 999999998731 1123357999999999999999999999999999999 5677777788887322 2
Q ss_pred CCCHHHHHHHHHHhCCcccHHHHHHHHHH
Q 026645 158 TSSPEQTREALQRWLPKEEWVRINPLLVG 186 (235)
Q Consensus 158 ~~~~~~~~~~l~~~~p~~~~~~~~~~l~~ 186 (235)
..+...++...+.|-|...+..++.|-..
T Consensus 245 ~~~~~~~~~~~e~w~p~rs~A~~yLw~~~ 273 (285)
T COG0122 245 RPTEKEVRELAERWGPYRSYAALYLWRYA 273 (285)
T ss_pred CchHHHHHHHHhcccCHHHHHHHHHHHhh
Confidence 33445577888999999888888876543
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.93 E-value=7.4e-25 Score=191.50 Aligned_cols=154 Identities=23% Similarity=0.321 Sum_probs=132.3
Q ss_pred CCCCCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc------------CCCCHHHHhcCCHHHHHHhhccCCChH
Q 026645 13 DETDSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN------------GLHTAEAIDKADEATIKDLIYPVAFYT 80 (235)
Q Consensus 13 ~~~~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~------------~~pt~~~la~a~~e~l~~~l~~~G~~~ 80 (235)
...|.++|...|+||.+|++|++||.+...+.....+|.+. .||||++|++++.++|.++ |++.
T Consensus 101 ~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl~~ 176 (283)
T PRK10308 101 ARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GMPL 176 (283)
T ss_pred hCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CCCH
Confidence 45677889899999999999999999999999999998763 3799999999999998765 9999
Q ss_pred HHHHHHHHHHHHHHHh-cC----CCChhhHHHHHcCCCCcHHHHHHHHHHhcCCccee-ecchHHHHHHHHhcCcCCCCC
Q 026645 81 RKACNMKKIAKICLTK-YD----GDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGI-CVDTHVHRICNRLGWVTQPGT 154 (235)
Q Consensus 81 ~Ka~~l~~~a~~i~~~-~~----g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~-pvDt~v~Rv~~Rlg~~~~~~~ 154 (235)
+|+++|+++|+++.+. .. .+..+.++.|++|||||+|||++|++|+++++++| +.|.+++|.+ +
T Consensus 177 ~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~------- 246 (283)
T PRK10308 177 KRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P------- 246 (283)
T ss_pred HHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c-------
Confidence 9999999999999871 11 12234689999999999999999999999999999 6899888743 1
Q ss_pred CCCCCCHHHHHHHHHHhCCcccHHHHHHH
Q 026645 155 KQKTSSPEQTREALQRWLPKEEWVRINPL 183 (235)
Q Consensus 155 ~~~~~~~~~~~~~l~~~~p~~~~~~~~~~ 183 (235)
..++++++...+.|-|.+.|..+|.|
T Consensus 247 ---~~~~~~~~~~a~~w~P~rsya~~~LW 272 (283)
T PRK10308 247 ---GMTPAQIRRYAERWKPWRSYALLHIW 272 (283)
T ss_pred ---cCCHHHHHHHHHhcCCHHHHHHHHHH
Confidence 23578899999999999999999876
No 18
>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=99.92 E-value=1.1e-24 Score=176.11 Aligned_cols=107 Identities=28% Similarity=0.350 Sum_probs=97.5
Q ss_pred CCChHHHHHHHHHhccccHHHHHHHHHHHHH-cCCCCHHHHhcCCHHHHHHhhccC----CChHHHHHHHHHHHHHHHHh
Q 026645 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQ-NGLHTAEAIDKADEATIKDLIYPV----AFYTRKACNMKKIAKICLTK 96 (235)
Q Consensus 22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~-~~~pt~~~la~a~~e~l~~~l~~~----G~~~~Ka~~l~~~a~~i~~~ 96 (235)
.++||++||++||||||++++|.+++.+|+. .+.+||++|++++.++|+++|++. |||++||++|+++++.|+++
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~ 94 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDT 94 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999975 344899999999999999999765 99999999999999999999
Q ss_pred cCCCC--------hhh---HHHHHcCCCCcHHHHHHHHHHhcC
Q 026645 97 YDGDI--------PSS---LDELLALPGIGPKMANMVMTLGWF 128 (235)
Q Consensus 97 ~~g~~--------~~~---~~~L~~l~GIG~~tA~~il~~~~~ 128 (235)
|+|++ |++ +++|++|||||+|||++||.+.-.
T Consensus 95 y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 95 YDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred hCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 99987 654 789999999999999999997543
No 19
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.86 E-value=2.9e-21 Score=163.84 Aligned_cols=145 Identities=21% Similarity=0.307 Sum_probs=115.3
Q ss_pred CCChHHHHHHHHHhccccHHHHHHHHHHHHHc--------------CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH
Q 026645 22 KERRFAVLLSALLSSLTKDKVADGALQRLLQN--------------GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK 87 (235)
Q Consensus 22 ~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~--------------~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~ 87 (235)
+++|+|.|++.|+|+|.+.+++..+.++|... +|||.++++. +++++-||.+||..| |+||.
T Consensus 114 rQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGYR-AkYI~ 189 (323)
T KOG2875|consen 114 RQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGYR-AKYIS 189 (323)
T ss_pred hcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcchh-HHHHH
Confidence 68999999999999999999999999988763 7999999985 455555666677554 99999
Q ss_pred HHHHHHHHhcCC----------CChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCC-C
Q 026645 88 KIAKICLTKYDG----------DIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTK-Q 156 (235)
Q Consensus 88 ~~a~~i~~~~~g----------~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~-~ 156 (235)
..|++|.++++| .++++++.|+.+||||+|+||||++++++...++|||+|+.|+++-....+..+.+ .
T Consensus 190 ~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y~l~~~~g~k~l 269 (323)
T KOG2875|consen 190 ATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDYILPGLSGAKEL 269 (323)
T ss_pred HHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcccCCCccccccC
Confidence 999999999887 24578999999999999999999999999999999999999999943111111211 2
Q ss_pred CCCCHHHHHHHHHH
Q 026645 157 KTSSPEQTREALQR 170 (235)
Q Consensus 157 ~~~~~~~~~~~l~~ 170 (235)
+...+.++...+..
T Consensus 270 ~~ki~~ev~~~f~~ 283 (323)
T KOG2875|consen 270 TPKINGEVSNFFRS 283 (323)
T ss_pred CcchhHHHHHHHHH
Confidence 33445556555543
No 20
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.86 E-value=3.8e-21 Score=158.06 Aligned_cols=159 Identities=18% Similarity=0.243 Sum_probs=128.9
Q ss_pred CCCCCCCCChHHHHHHHHHhccccHHHHHHHHHHHHHc-----CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026645 16 DSSLPPKERRFAVLLSALLSSLTKDKVADGALQRLLQN-----GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA 90 (235)
Q Consensus 16 ~~~~p~~~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-----~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a 90 (235)
+..+-..+.||+.|+++|+|||.+.+.+..++++|... .||+|+.+..++.++|.++ ||+.+|+.||+.+|
T Consensus 66 p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~lrkc----G~S~rK~~yLh~lA 141 (254)
T KOG1918|consen 66 PLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEELRKC----GFSKRKASYLHSLA 141 (254)
T ss_pred CCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHHHHHh----CcchhhHHHHHHHH
Confidence 34455578999999999999999999999999999874 5899999999999999888 99999999999999
Q ss_pred HHHHHhcCCCCh-----------hhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchH-HHHHHHHhcCcCCCCCCCCC
Q 026645 91 KICLTKYDGDIP-----------SSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTH-VHRICNRLGWVTQPGTKQKT 158 (235)
Q Consensus 91 ~~i~~~~~g~~~-----------~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~-v~Rv~~Rlg~~~~~~~~~~~ 158 (235)
++..+. -+| +..+.|..++|||+||+.++|.|+++++|++|+|.- +++-++.+....+ .
T Consensus 142 ~~~~ng---~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~------~ 212 (254)
T KOG1918|consen 142 EAYTNG---YIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP------L 212 (254)
T ss_pred HHHhcC---CCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC------C
Confidence 998873 244 356788999999999999999999999999998655 4555666655432 3
Q ss_pred CCHHHHHHHHHHhCCcccHH-HHHHHHHHH
Q 026645 159 SSPEQTREALQRWLPKEEWV-RINPLLVGF 187 (235)
Q Consensus 159 ~~~~~~~~~l~~~~p~~~~~-~~~~~l~~~ 187 (235)
..+.+++...+.|-|.+... .+.|-+++.
T Consensus 213 p~~~evekl~e~~kpyRtvaawYlWki~~~ 242 (254)
T KOG1918|consen 213 PLPKEVEKLCEKCKPYRTVAAWYLWKIIKL 242 (254)
T ss_pred CchHHHHHHhhhccchHHHHHHHHHhhhhh
Confidence 45778888888888876533 334444443
No 21
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.83 E-value=7.6e-20 Score=137.82 Aligned_cols=105 Identities=34% Similarity=0.480 Sum_probs=92.0
Q ss_pred HHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHH
Q 026645 30 LSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDEL 108 (235)
Q Consensus 30 v~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L 108 (235)
|++||+|||+++++.+++.+|.+. +||||++|+++++++|+++|+++||+++||++|+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~-------------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL-------------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH--------------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh--------------
Confidence 689999999999999999999996 57999999999999999999999999999999999999987
Q ss_pred HcCCCCcHHHHHHHHHHhcCCcc-eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCC
Q 026645 109 LALPGIGPKMANMVMTLGWFNVQ-GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLP 173 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~~~~~~~~-~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p 173 (235)
++++ ++|+|+|+.|++.|+++++. ..+++++++.++++.|
T Consensus 67 -------------------~~~d~~~~~D~~v~r~~~r~~~~~~------~~~~~~~~~~~~e~~~ 107 (108)
T PF00730_consen 67 -------------------GRPDPFPPVDTHVRRVLQRLGGIPE------KKTKEETEKKLEELWP 107 (108)
T ss_dssp -------------------C-SSSS-TTSHHHHHHHHHHTSSSS------STTHHHHHHHHHHHGT
T ss_pred -------------------hcccceecCcHHHHHHHHHHcCCCC------CCCHHHHHHHHHhhCc
Confidence 4444 78999999999999999863 3678899988866654
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.27 E-value=3.8e-11 Score=97.21 Aligned_cols=140 Identities=19% Similarity=0.212 Sum_probs=105.6
Q ss_pred CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCC--ChHHHHHHHHHHHHHHHHh----
Q 026645 23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVA--FYTRKACNMKKIAKICLTK---- 96 (235)
Q Consensus 23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G--~~~~Ka~~l~~~a~~i~~~---- 96 (235)
.+.|.-|..+||.+|++...+.++.+.|-+ +|.. ++.|||++.|+..| ||+.||+||.++-+.+-+-
T Consensus 37 e~lf~ELsFCILTANsSA~~~~~~q~~lG~-gfly------~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v 109 (210)
T COG1059 37 EDLFKELSFCILTANSSATMGLRAQNELGD-GFLY------LSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIV 109 (210)
T ss_pred HHHHHHHHHHhccccchHHHHHHHHHHhcc-cccc------CCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999999999886 6654 68899999999875 7899999999876654210
Q ss_pred cCCCChh-hHHHHH-cCCCCcHHHHHHHH-HHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHh
Q 026645 97 YDGDIPS-SLDELL-ALPGIGPKMANMVM-TLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRW 171 (235)
Q Consensus 97 ~~g~~~~-~~~~L~-~l~GIG~~tA~~il-~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~ 171 (235)
-..+.+. +++.|. .++|||-|-|..+| +.++. +...+|.|+.|.+.|.|.+...+.....+.|-++++.+..+
T Consensus 110 ~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~--D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~i 185 (210)
T COG1059 110 KADENEKVARELLVENIKGIGYKEASHFLRNVGFE--DLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSI 185 (210)
T ss_pred hcCcchHHHHHHHHHHcccccHHHHHHHHHhcChh--HHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHH
Confidence 0122233 788888 89999999999999 45553 45569999999999999987543333333444555555444
No 23
>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=98.71 E-value=3.1e-09 Score=61.59 Aligned_cols=29 Identities=55% Similarity=1.052 Sum_probs=25.2
Q ss_pred cCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 97 YDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 97 ~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
|+|.+|.++++|+++||||+|||+.|+.|
T Consensus 2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 2 LDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 45678899999999999999999999976
No 24
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=98.26 E-value=2.4e-07 Score=46.39 Aligned_cols=17 Identities=41% Similarity=1.376 Sum_probs=11.6
Q ss_pred cCCCCCCCCCCcccccC
Q 026645 192 CTPLRPRCGMCTVSEYC 208 (235)
Q Consensus 192 C~~~~P~C~~Cpl~~~C 208 (235)
|++++|+|+.|||+++|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999998
No 25
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=97.65 E-value=1.5e-05 Score=44.44 Aligned_cols=21 Identities=43% Similarity=1.187 Sum_probs=19.3
Q ss_pred hcCCCCCCCCCCcccccCccc
Q 026645 191 ICTPLRPRCGMCTVSEYCPSA 211 (235)
Q Consensus 191 iC~~~~P~C~~Cpl~~~C~~~ 211 (235)
+|++++|+|+.||+++.|.++
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~ 21 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAY 21 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhh
Confidence 699999999999999999864
No 26
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=96.80 E-value=0.041 Score=47.02 Aligned_cols=161 Identities=22% Similarity=0.239 Sum_probs=88.9
Q ss_pred hHHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHH-HHhcCCHHHHHHhhccCC--ChH-HHHHHHHHHHHHHHHhcCC-
Q 026645 25 RFAVLLSALLSSLTKDKVADGALQRLLQNGLHTAE-AIDKADEATIKDLIYPVA--FYT-RKACNMKKIAKICLTKYDG- 99 (235)
Q Consensus 25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~-~la~a~~e~l~~~l~~~G--~~~-~Ka~~l~~~a~~i~~~~~g- 99 (235)
-.-.+|+++|+-. +.++..+..+.|++.--++|. -|...+.+++.+.+.+.- |++ .-...+....+.+.++|++
T Consensus 16 Ei~afiaA~lAyG-~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL 94 (232)
T PF09674_consen 16 EIAAFIAALLAYG-NRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL 94 (232)
T ss_pred HHHHHHHHHHHcc-CHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH
Confidence 4667888888766 667777777777664234554 355666666766666432 221 1233344444444455432
Q ss_pred ------------CChh----hHHHHHcC------------------CCCcHHHHHHHHHHhcCCcc--------------
Q 026645 100 ------------DIPS----SLDELLAL------------------PGIGPKMANMVMTLGWFNVQ-------------- 131 (235)
Q Consensus 100 ------------~~~~----~~~~L~~l------------------~GIG~~tA~~il~~~~~~~~-------------- 131 (235)
++-+ ..+.+.++ +|-.-|--+++|-..-.+..
T Consensus 95 e~~f~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~p~~~SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~ 174 (232)
T PF09674_consen 95 EEAFAKGYNKSEDVLEAICAFIEEFFELPHSSRGYKHLFGLLPPPEKGSACKRLNMFLRWMVRKDSPVDFGLWSSIDPSD 174 (232)
T ss_pred HHHHHhhccCCCCHHHHHHHHHHHHHHhhcccccccccccccCCCCCCcHHHHHHHHHHhhccCCCCCCCcCCCCCCHHH
Confidence 1111 12223331 12222444556533222211
Q ss_pred -eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026645 132 -GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ 189 (235)
Q Consensus 132 -~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 189 (235)
.+|+||||.|++.+||++..... .-++..++-+.+.++.| +++..+..+|..+|.
T Consensus 175 LiiPLDtHv~~var~LGL~~rk~~--d~k~A~elT~~lr~~~p-~DPvKYDFAL~~~Gi 230 (232)
T PF09674_consen 175 LIIPLDTHVFRVARKLGLLKRKSA--DWKAARELTEALREFDP-DDPVKYDFALFRLGI 230 (232)
T ss_pred ccccchHhHHHHHHHcCCccCCCc--cHHHHHHHHHHHHhcCC-CCCcchhhhcccCCc
Confidence 47999999999999999864211 12244556666777776 566666777777664
No 27
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=96.53 E-value=0.039 Score=45.26 Aligned_cols=100 Identities=17% Similarity=0.204 Sum_probs=69.0
Q ss_pred hHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCC--hHHHHHHHHHHHHHHHH---hc
Q 026645 25 RFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAF--YTRKACNMKKIAKICLT---KY 97 (235)
Q Consensus 25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~--~~~Ka~~l~~~a~~i~~---~~ 97 (235)
-||.|+-+++..--++..+.+-...+.+. | .+|+.+|..+++++++++..-|. +++|.+.+++=|+++.+ +|
T Consensus 26 LFe~L~Le~fQaGLsW~~Il~Kr~~~r~a-F~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~ 104 (179)
T PF03352_consen 26 LFEMLTLEGFQAGLSWSTILKKREAFREA-FAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEF 104 (179)
T ss_dssp HHHHHHHHHHTTTS-HHHHHHTHHHHHHH-TGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHHHH-HHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 49999999999999999999988888874 5 57999999999999999998887 56777777777777653 33
Q ss_pred CC----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHH
Q 026645 98 DG----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTL 125 (235)
Q Consensus 98 ~g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~ 125 (235)
|+ ++|. .-+.|.+ ++-|||.|+.++|.-
T Consensus 105 gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vysflqA 163 (179)
T PF03352_consen 105 GSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYSFLQA 163 (179)
T ss_dssp S-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHHHHHH
T ss_pred CCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHHHHHH
Confidence 32 1111 2244553 677888888888765
No 28
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=96.00 E-value=0.0055 Score=33.97 Aligned_cols=20 Identities=50% Similarity=0.894 Sum_probs=17.6
Q ss_pred HHHcCCCCcHHHHHHHHHHh
Q 026645 107 ELLALPGIGPKMANMVMTLG 126 (235)
Q Consensus 107 ~L~~l~GIG~~tA~~il~~~ 126 (235)
.|.++||||+++|..++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998754
No 29
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=95.63 E-value=0.0053 Score=52.24 Aligned_cols=55 Identities=27% Similarity=0.379 Sum_probs=37.2
Q ss_pred eeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHHh
Q 026645 132 GICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPKEEWVRINPLLVGFGQ 189 (235)
Q Consensus 132 ~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 189 (235)
.+|+|||+.||+.+||++...... -++..++-+.+.++.| +++..+..+|..+|.
T Consensus 173 iiPLDtH~~rvar~LgL~~Rk~~d--~kaa~ElT~~Lr~~dp-~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLLKRKSYD--LKAAIEITEALRELNP-EDPIKYDFALFRLGQ 227 (229)
T ss_pred eeechHhHHHHHHHhCCcccCchh--HHHHHHHHHHHHhcCC-CCCcchhhhcccCCc
Confidence 579999999999999998642111 1233445555666666 566667777777774
No 30
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=95.52 E-value=0.4 Score=39.64 Aligned_cols=70 Identities=9% Similarity=-0.037 Sum_probs=57.5
Q ss_pred hHHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCCh--HHHHHHHHHHHHHHH
Q 026645 25 RFAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFY--TRKACNMKKIAKICL 94 (235)
Q Consensus 25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~--~~Ka~~l~~~a~~i~ 94 (235)
-||.|+=+.+..-.++..+.+-...+.+. .-.+|+.+|..+++++++++..-|.- ++|.+.+++=|+++.
T Consensus 31 LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l 103 (187)
T PRK10353 31 LFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYL 103 (187)
T ss_pred HHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHH
Confidence 49999999999999999999988888774 23689999999999999999988874 456666666555554
No 31
>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=95.51 E-value=0.066 Score=36.68 Aligned_cols=57 Identities=23% Similarity=0.233 Sum_probs=36.6
Q ss_pred HHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 68 TIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 68 ~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
++.+...-.|=..-|+..-.+++..|.. +...+.+..+.+.+|||||+.+|..|--|
T Consensus 10 ~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~~i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 10 ELADLYELQGGDPFRARAYRRAAAAIKA-LPYPITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS-HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCHhHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 3333333333234467888888888655 55555554224999999999999988644
No 32
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.50 E-value=0.074 Score=44.29 Aligned_cols=64 Identities=17% Similarity=0.158 Sum_probs=42.9
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++. +-++.++.--|-..+.|-.|. ++.++|.. .+.+.|.++||||+|||.-+..---
T Consensus 61 GF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 61 GFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR-------EDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 78887663 444455544455455566665 45555544 4678999999999999999986544
Q ss_pred CC
Q 026645 128 FN 129 (235)
Q Consensus 128 ~~ 129 (235)
++
T Consensus 129 dK 130 (196)
T PRK13901 129 GK 130 (196)
T ss_pred Hh
Confidence 33
No 33
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.20 E-value=0.034 Score=37.74 Aligned_cols=35 Identities=37% Similarity=0.738 Sum_probs=23.6
Q ss_pred HHHHHHhcCCCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 90 AKICLTKYDGDIP----SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 90 a~~i~~~~~g~~~----~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
|+.+.+.|+ +++ .+.++|.+++|||+.+|..|..|
T Consensus 16 ak~L~~~f~-sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 16 AKLLAKHFG-SLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHCCS-CHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHcC-CHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 444555554 443 46899999999999999999877
No 34
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.15 E-value=0.45 Score=39.14 Aligned_cols=101 Identities=14% Similarity=0.159 Sum_probs=73.5
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHcCC--CCHHHHhcCCHHHHHHhhccCCChH--HHHHHHHHHHHHHH---Hh
Q 026645 24 RRFAVLLSALLSSLTKDKVADGALQRLLQNGL--HTAEAIDKADEATIKDLIYPVAFYT--RKACNMKKIAKICL---TK 96 (235)
Q Consensus 24 ~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~--pt~~~la~a~~e~l~~~l~~~G~~~--~Ka~~l~~~a~~i~---~~ 96 (235)
.-||.|+-++...-.++..+.+-.+++.+. | .+|+.+|..++++++.++...|.-+ .|.+.++.=|+++. ++
T Consensus 31 ~LFE~l~Le~fQAGLSW~tVL~KRe~frea-F~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e 109 (188)
T COG2818 31 RLFELLCLEGFQAGLSWLTVLKKREAFREA-FHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKE 109 (188)
T ss_pred HHHHHHHHHHHhccchHHHHHHhHHHHHHH-HhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 359999999999999999999988888773 3 5899999999999999999988754 44555555555543 34
Q ss_pred cCC----------------------CChh-------hHHHHHc--CCCCcHHHHHHHHHH
Q 026645 97 YDG----------------------DIPS-------SLDELLA--LPGIGPKMANMVMTL 125 (235)
Q Consensus 97 ~~g----------------------~~~~-------~~~~L~~--l~GIG~~tA~~il~~ 125 (235)
||+ ++|. .-+.|.+ ++-|||.|+..+|.-
T Consensus 110 ~Gsf~~flWsf~~~~~~~~~~~~~~~~pa~t~~S~~mskaLKkrGf~fvGpTt~yafmqA 169 (188)
T COG2818 110 FGSFSEFLWSFVGGKPSRNQVNDGSEVPASTELSDAMSKALKKRGFKFVGPTTVYAFMQA 169 (188)
T ss_pred cCCHHHHHHHhcCCCcccccccchhhccccchhHHHHHHHHHHccCeecCcHHHHHHHHH
Confidence 432 1111 1244553 677888888877765
No 35
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.87 E-value=0.86 Score=37.39 Aligned_cols=71 Identities=8% Similarity=-0.041 Sum_probs=57.2
Q ss_pred hHHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCChH--HHHHHHHHHHHHHHH
Q 026645 25 RFAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFYT--RKACNMKKIAKICLT 95 (235)
Q Consensus 25 ~f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~~--~Ka~~l~~~a~~i~~ 95 (235)
-||.|+-+++..-.++..+.+-...+.+. .-.+|+.+|..+++++++++..-|.-+ .|.+.+++=|+++.+
T Consensus 30 LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 30 LFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 59999999999999999999988888764 236899999999999999999888754 445556655665543
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.42 E-value=0.22 Score=41.02 Aligned_cols=64 Identities=19% Similarity=0.145 Sum_probs=39.8
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++- +-++.++.--|-..+.|-.|. ++..+|.. .+.+.|.++||||+|||.-+..---
T Consensus 62 GF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 62 GFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSL-------GDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 78776662 344444443444444455443 23334333 4678999999999999999986544
Q ss_pred CC
Q 026645 128 FN 129 (235)
Q Consensus 128 ~~ 129 (235)
++
T Consensus 130 dK 131 (183)
T PRK14601 130 DA 131 (183)
T ss_pred HH
Confidence 43
No 37
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.97 E-value=0.31 Score=40.35 Aligned_cols=63 Identities=16% Similarity=0.169 Sum_probs=38.8
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++- +-++.++.--|-..+.|-.|. ++.++|.. .+.+.|.++||||+|||.-+..---
T Consensus 62 GF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 62 GFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS-------QDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred CCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 67776652 333444443344444455543 23444433 4678999999999999999985543
Q ss_pred C
Q 026645 128 F 128 (235)
Q Consensus 128 ~ 128 (235)
+
T Consensus 130 d 130 (188)
T PRK14606 130 D 130 (188)
T ss_pred H
Confidence 3
No 38
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=93.88 E-value=0.18 Score=33.45 Aligned_cols=41 Identities=20% Similarity=0.338 Sum_probs=22.0
Q ss_pred HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH
Q 026645 47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA 90 (235)
Q Consensus 47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a 90 (235)
..+|.+.+|.|+++|+.++.++|.++ . |+...+|+.|.+.+
T Consensus 18 a~~L~~~G~~t~~~l~~a~~~~L~~i-~--Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 18 AEKLYEAGIKTLEDLANADPEELAEI-P--GIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHHHHTTCSSHHHHHTSHHHHHHTS-T--TSSHHHHHHHHHHH
T ss_pred HHHHHhcCCCcHHHHHcCCHHHHhcC-C--CCCHHHHHHHHHHH
Confidence 34455545666666666666655443 2 44444555555443
No 39
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.52 E-value=0.39 Score=40.18 Aligned_cols=62 Identities=19% Similarity=0.188 Sum_probs=38.3
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++- +-++.++.--|...+.|-.|.. ++++|.+ .+.+.|.++||||+|||+-+..---
T Consensus 63 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~-------~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 63 GFATWDER-----QTFIVLISISKVGAKTALAILSQFRPDDLRRLVAE-------EDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CCCCHHHH-----HHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHh-------CCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 67776652 3344444434444445555543 2333332 4678999999999999999985433
No 40
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.47 E-value=0.38 Score=40.20 Aligned_cols=64 Identities=22% Similarity=0.222 Sum_probs=39.1
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHH------HHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMK------KIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~------~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++ .+-+..+++--|-..+-|-.|. +++++|.. ++.+.|.++||||+|||+-++.---
T Consensus 62 GF~~~~E-----R~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~-------~d~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 62 GFLTEEE-----RELFRLLISVNGIGPKLALAILSNLDPEELAQAIAN-------EDVKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred CCCCHHH-----HHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHh-------cChHhhhcCCCCCHHHHHHHHHHHh
Confidence 6887665 3445555554444433333332 22333332 4678999999999999999986543
Q ss_pred CC
Q 026645 128 FN 129 (235)
Q Consensus 128 ~~ 129 (235)
++
T Consensus 130 ~K 131 (201)
T COG0632 130 GK 131 (201)
T ss_pred hh
Confidence 33
No 41
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.42 E-value=0.41 Score=39.80 Aligned_cols=63 Identities=21% Similarity=0.161 Sum_probs=38.8
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++- +-+..++.--|...+.|-.|.. +..+|.+ .+.+.|.++||||+|||+-+..---
T Consensus 62 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~-------~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 62 GFSTPAQR-----QLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAG-------GDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 67776552 3344444434444455555543 2333332 4678999999999999999985543
Q ss_pred C
Q 026645 128 F 128 (235)
Q Consensus 128 ~ 128 (235)
+
T Consensus 130 ~ 130 (195)
T PRK14604 130 G 130 (195)
T ss_pred H
Confidence 3
No 42
>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=93.25 E-value=0.28 Score=40.65 Aligned_cols=64 Identities=20% Similarity=0.252 Sum_probs=39.6
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHH--HHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIA--KICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a--~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
||.|.++ .+-+..++.--|...++|..|.... ..+.+ --...+...|.++||||+|||.-|+.-
T Consensus 61 GF~~~~E-----r~lF~~L~~V~GIGpK~Al~iL~~~~~~el~~---aI~~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 61 GFNTLEE-----RELFKELIKVNGVGPKLALAILSNMSPEEFVY---AIETEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCCHHH-----HHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHH---HHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 7888766 3455556655566566676664321 11111 001135678999999999999999843
No 43
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.19 E-value=0.46 Score=39.47 Aligned_cols=59 Identities=24% Similarity=0.346 Sum_probs=37.3
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHH------HHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKI------AKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~------a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~ 124 (235)
||.|.++- +-+..++.--|.....|..|.+. ..+|. .++.+.|.++||||+|||.-+..
T Consensus 62 GF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~-------~~D~~~L~~vpGIGkKtAerIil 126 (194)
T PRK14605 62 GFATTEEL-----SLFETLIDVSGIGPKLGLAMLSAMNAEALASAII-------SGNAELLSTIPGIGKKTASRIVL 126 (194)
T ss_pred CCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHH-------hCCHHHHHhCCCCCHHHHHHHHH
Confidence 67776652 34444544444445556666553 22222 24678899999999999999663
No 44
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.07 E-value=0.51 Score=39.32 Aligned_cols=61 Identities=16% Similarity=0.199 Sum_probs=37.1
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHh
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLG 126 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~ 126 (235)
||.|.++- +-+..++.--|...+.|-.|.. +.++|.. .+.+.|.++||||+|||.-+..--
T Consensus 61 GF~~~~Er-----~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~-------~D~~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 61 GFPDEDSL-----ELFELLLGVSGVGPKLALALLSALPPALLARALLE-------GDARLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred CcCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHH
Confidence 67775552 3333444333444444554433 3344333 467899999999999999998543
No 45
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.12 E-value=0.33 Score=40.10 Aligned_cols=61 Identities=18% Similarity=0.227 Sum_probs=37.5
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH------HHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhc
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK------IAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~------~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~ 127 (235)
||.|.++- +-++.++.--|-..+.|-.|.. +.++|.+ .+.+.| ++||||+|||+-++.---
T Consensus 62 GF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~-------~D~~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 62 GFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN-------EDKAAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred CCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc-------CCHhhe-ECCCCcHHHHHHHHHHHH
Confidence 68776662 4444444444444445555543 3334333 356888 999999999999985433
No 46
>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=91.98 E-value=0.67 Score=31.53 Aligned_cols=58 Identities=21% Similarity=0.460 Sum_probs=38.2
Q ss_pred HHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 60 AIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 60 ~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.|-.++.++|..++.++|. .+|+.|.+--. .+ |.+ ...++|..++|||.++++-++.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R~----~~-g~~-~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYRE----EY-GPF-KTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHHH----Hc-CCc-CCHHHHHcCCCCCHHHHHHHHhh
Confidence 4445788888887676665 33433332211 12 223 37899999999999999988765
No 47
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=91.93 E-value=0.42 Score=37.09 Aligned_cols=58 Identities=14% Similarity=0.340 Sum_probs=39.8
Q ss_pred CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 55 LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 55 ~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+...=+|-.++.+++..+ . |++..+|+.|.. +|.+ ...++|.++||||+++.+.+--+
T Consensus 49 ~~~kIdiN~A~~~el~~l-p--GigP~~A~~IV~---------nGpf-~sveDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 49 FGEKIDLNNSSVRAFRQF-P--GMYPTLAGKIVK---------NAPY-DSVEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCcccCCccCHHHHHHC-C--CCCHHHHHHHHH---------CCCC-CCHHHHHcCCCCCHHHHHHHHHh
Confidence 344555667788887763 4 666777777762 2444 56888899999999887766544
No 48
>PRK14973 DNA topoisomerase I; Provisional
Probab=91.91 E-value=0.58 Score=47.77 Aligned_cols=99 Identities=15% Similarity=0.226 Sum_probs=63.3
Q ss_pred HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH-HHHHh-c----CCCChhhHHHHHcCCCCcHHHH
Q 026645 46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK-ICLTK-Y----DGDIPSSLDELLALPGIGPKMA 119 (235)
Q Consensus 46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~-~i~~~-~----~g~~~~~~~~L~~l~GIG~~tA 119 (235)
..+.+.+.||-++++++.+++++|... .|+....+..+...|. .+... . ...+...+.+|++++|||++|+
T Consensus 814 ~~~~~~~~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~ 890 (936)
T PRK14973 814 SLKKYQEAGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTL 890 (936)
T ss_pred HHHHHHHhcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHH
Confidence 445556669999999999999998776 5887655666655444 33221 0 0112234456999999999999
Q ss_pred HHHHHHhcCCcceeecchHHHHHHHHhcC
Q 026645 120 NMVMTLGWFNVQGICVDTHVHRICNRLGW 148 (235)
Q Consensus 120 ~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~ 148 (235)
+..-.-+.-..+.+..+ ...+++.+-|+
T Consensus 891 ~~l~~ag~~~~e~l~~~-d~~~la~~~~i 918 (936)
T PRK14973 891 EKLYLAGVYDGDLLVSA-DPKKLAKVTGI 918 (936)
T ss_pred HHHHHcCCCCHHHhccC-CHHHHhhhcCC
Confidence 77666555443333222 45566666655
No 49
>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=91.82 E-value=0.13 Score=36.83 Aligned_cols=41 Identities=20% Similarity=0.330 Sum_probs=29.2
Q ss_pred HHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcC
Q 026645 106 DELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVT 150 (235)
Q Consensus 106 ~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~ 150 (235)
+.|+++||||+-||..++... ++...|+-..+ +...+|+.+
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~---l~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQ---LASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhcccchh---hhhcccccc
Confidence 468899999999999998876 45456644444 555566654
No 50
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=91.16 E-value=0.15 Score=42.15 Aligned_cols=30 Identities=33% Similarity=0.424 Sum_probs=24.4
Q ss_pred CChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 100 DIPSSLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 100 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
.+....+.|.+|||||+|+|.=+..+-+.+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 345678899999999999999887776654
No 51
>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=91.11 E-value=0.82 Score=40.67 Aligned_cols=49 Identities=29% Similarity=0.489 Sum_probs=33.8
Q ss_pred hccCCChHHHHHHHHHHHHH----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHH
Q 026645 73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDIPSSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il 123 (235)
|.++| ..-|..|.++.+. ..++...+.|....+|+++|||||++|..+-
T Consensus 50 ipgiG--~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 50 LPGIG--KKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CCCcc--HHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 34444 4456677666543 2233334578888999999999999998776
No 52
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=90.87 E-value=0.95 Score=40.76 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=34.3
Q ss_pred hccCCChHHHHHHHHHHHHH-----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026645 73 IYPVAFYTRKACNMKKIAKI-----CLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 73 l~~~G~~~~Ka~~l~~~a~~-----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~ 124 (235)
|.++| ..=|..|.++.+. +.+.....+|....+|+++|||||++|..+-.
T Consensus 53 lpgIG--~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~ 107 (334)
T smart00483 53 LPGIG--DKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred CCCcc--HHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence 35455 3345666666443 23334456788899999999999999987755
No 53
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=90.86 E-value=1.6 Score=33.37 Aligned_cols=84 Identities=23% Similarity=0.428 Sum_probs=55.7
Q ss_pred HHHHHHcCCCCHHHHhcCCHHHHHH--hhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026645 47 LQRLLQNGLHTAEAIDKADEATIKD--LIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 47 ~~~l~~~~~pt~~~la~a~~e~l~~--~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~ 124 (235)
..+|.+.|..|+++|.+.+...... +....|...+ +|.+.. .+..|..+||||+..|..++.
T Consensus 8 ~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~---~l~~w~-------------~~AdL~ri~gi~~~~a~LL~~ 71 (122)
T PF14229_consen 8 AAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISER---NLLKWV-------------NQADLMRIPGIGPQYAELLEH 71 (122)
T ss_pred HHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHH---HHHHHH-------------hHHHhhhcCCCCHHHHHHHHH
Confidence 4556666889999999988877766 6666676533 333322 245677899999999998887
Q ss_pred HhcCCcceeecchHHHHHHHHhc
Q 026645 125 LGWFNVQGICVDTHVHRICNRLG 147 (235)
Q Consensus 125 ~~~~~~~~~pvDt~v~Rv~~Rlg 147 (235)
-+..-...+ ...+..++..+++
T Consensus 72 AGv~Tv~~L-A~~~p~~L~~~l~ 93 (122)
T PF14229_consen 72 AGVDTVEEL-AQRNPQNLHQKLG 93 (122)
T ss_pred hCcCcHHHH-HhCCHHHHHHHHH
Confidence 776543322 4455555555543
No 54
>PRK13844 recombination protein RecR; Provisional
Probab=90.78 E-value=0.17 Score=42.19 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=24.1
Q ss_pred ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 101 IPSSLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
+....+.|.+|||||+|+|.-+..+-+..
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 44667889999999999999888877754
No 55
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.50 E-value=0.25 Score=41.12 Aligned_cols=29 Identities=34% Similarity=0.433 Sum_probs=24.3
Q ss_pred ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 101 IPSSLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
+.+..+.|.+|||||+|+|.=+..+-+..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~ 34 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQR 34 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 44667889999999999999888887754
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=90.45 E-value=0.93 Score=37.52 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=12.7
Q ss_pred HHHHcCCCCcHHHHHHHHHH
Q 026645 106 DELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 106 ~~L~~l~GIG~~tA~~il~~ 125 (235)
+.|.++||||+++|+.|+..
T Consensus 108 ~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 108 KALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 45666777777777666533
No 57
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.30 E-value=0.27 Score=40.84 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=23.9
Q ss_pred ChhhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 101 IPSSLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 101 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
+.+..+.|.+|||||+|+|.-+..+-+..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~ 34 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKR 34 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 44667889999999999999888777654
No 58
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.12 E-value=0.53 Score=39.87 Aligned_cols=57 Identities=18% Similarity=0.264 Sum_probs=40.8
Q ss_pred CCHHHHHHhhccCCChHHHHH-HHHHHHHHHHHhcC--CCCh----hhHHHHHcCCCCcHHHHHHHH
Q 026645 64 ADEATIKDLIYPVAFYTRKAC-NMKKIAKICLTKYD--GDIP----SSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 64 a~~e~l~~~l~~~G~~~~Ka~-~l~~~a~~i~~~~~--g~~~----~~~~~L~~l~GIG~~tA~~il 123 (235)
.+..||.++|=..|.. -+ ...++|+.+.++|. |.+. ...++|++++|||+..|..++
T Consensus 14 Lsd~ELLailL~~g~~---~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 14 LSDYELLAIILRTGTP---KGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred CCHHHHHHHHHhCCCC---CCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 4566777765455553 34 67789999999883 4554 367899999999997776554
No 59
>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=90.05 E-value=0.36 Score=32.00 Aligned_cols=26 Identities=42% Similarity=0.749 Sum_probs=19.1
Q ss_pred hHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 104 SLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
....|.++||||+++|..+...++.-
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t 28 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKT 28 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSS
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCc
Confidence 35678888888888888777766553
No 60
>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=89.78 E-value=2.2 Score=41.96 Aligned_cols=77 Identities=22% Similarity=0.461 Sum_probs=50.9
Q ss_pred HHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHH-------------------------HHhcC
Q 026645 45 GALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC-------------------------LTKYD 98 (235)
Q Consensus 45 ~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i-------------------------~~~~~ 98 (235)
+.+..|++.++ -++++|..+..++|.++ . ||....+..|.+..+.- .+.|
T Consensus 443 k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L-~--GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f- 518 (652)
T TIGR00575 443 KVIEQLFEKKLVRSVADLYALKKEDLLEL-E--GFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHF- 518 (652)
T ss_pred HHHHHHHHcCCcCCHHHHHhcCHHHHhhc-c--CccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHh-
Confidence 34566666544 58999999998887765 3 66666677776655431 1222
Q ss_pred CCChh----hHHHHHcCCCCcHHHHHHHHHH
Q 026645 99 GDIPS----SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 99 g~~~~----~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+++.. +.++|.+++|||+++|..|..|
T Consensus 519 ~sl~~l~~As~eeL~~i~GIG~~~A~~I~~f 549 (652)
T TIGR00575 519 GTLDKLKAASLEELLSVEGVGPKVAESIVNF 549 (652)
T ss_pred CCHHHHHhCCHHHHhcCCCcCHHHHHHHHHH
Confidence 22322 3567888999999999988877
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=89.71 E-value=0.56 Score=38.82 Aligned_cols=20 Identities=30% Similarity=0.750 Sum_probs=17.5
Q ss_pred HHHHHcCCCCcHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~ 124 (235)
...|.++|||||++|..++.
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 56788999999999998875
No 62
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=88.26 E-value=0.56 Score=31.69 Aligned_cols=22 Identities=55% Similarity=0.875 Sum_probs=17.5
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++|.++||||++.|..|+.+
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHH
Confidence 5789999999999999999976
No 63
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=87.92 E-value=3.3 Score=40.88 Aligned_cols=76 Identities=21% Similarity=0.395 Sum_probs=50.0
Q ss_pred HHHHHHHcC-CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHhcCC
Q 026645 46 ALQRLLQNG-LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTKYDG 99 (235)
Q Consensus 46 ~~~~l~~~~-~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~~~g 99 (235)
.+..|.+.+ ..++++|..+..++|.++ . ||...++..|.+..+. +...| +
T Consensus 457 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f-~ 532 (665)
T PRK07956 457 IIEQLFEKGLIHDPADLFKLTAEDLLGL-E--GFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHF-G 532 (665)
T ss_pred HHHHHHHcCCCCCHHHHHhcCHHHHhcC-c--CcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHc-C
Confidence 445566543 468999998888877665 2 6666666666544332 22222 2
Q ss_pred CCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 100 DIP----SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 100 ~~~----~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
++. .+.++|.+++|||+++|..|..|
T Consensus 533 sl~~l~~As~eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 533 SLEALRAASEEELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred CHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 222 24578999999999999999877
No 64
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=87.68 E-value=2.7 Score=26.25 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=35.8
Q ss_pred HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
....|...||-|.++++.+++++|.++ -|+...++..|+..++.
T Consensus 5 ~~~~L~~~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 5 IAQLLVEEGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred HHHHHHHcCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 456677779999999999999999886 47777788888777663
No 65
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=87.46 E-value=4.3 Score=39.16 Aligned_cols=78 Identities=17% Similarity=0.180 Sum_probs=53.2
Q ss_pred HHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH----------------------hcCCC
Q 026645 44 DGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT----------------------KYDGD 100 (235)
Q Consensus 44 ~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~----------------------~~~g~ 100 (235)
.+.+..|++.++ -++.+|..+..++|.++ -||...++..|.+..+.-.+ .| ++
T Consensus 435 e~~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~-~~ 510 (562)
T PRK08097 435 EGTWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDD-RS 510 (562)
T ss_pred HHHHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhc-CC
Confidence 345666777665 68999999998877665 36766677776555433110 11 22
Q ss_pred Ch----hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 101 IP----SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 101 ~~----~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+. .+.++|.+++|||+.+|+.|..|
T Consensus 511 i~~l~~a~~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 511 WQQLLSRSEQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHHcCCHHHHhcCCCchHHHHHHHHHH
Confidence 22 24578999999999999999888
No 66
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=87.31 E-value=3.7 Score=40.49 Aligned_cols=79 Identities=18% Similarity=0.292 Sum_probs=50.4
Q ss_pred HHHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HH-Hh
Q 026645 44 DGALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CL-TK 96 (235)
Q Consensus 44 ~~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~-~~ 96 (235)
...+..|++.++ -++.+|..+..++|.++ =||...++..|.+..+. +. ..
T Consensus 446 ~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l---~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~ 522 (669)
T PRK14350 446 DKTIEFLFEKKFISSEIDLYTFNFDRLINL---KGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNN 522 (669)
T ss_pred HHHHHHHHHcCCcCCHHHHhhCCHHHHhhc---cCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHh
Confidence 345677777654 46888888887776655 26666666665443322 22 12
Q ss_pred cCCCCh----------hhHHHHHcCCCCcHHHHHHHHHHh
Q 026645 97 YDGDIP----------SSLDELLALPGIGPKMANMVMTLG 126 (235)
Q Consensus 97 ~~g~~~----------~~~~~L~~l~GIG~~tA~~il~~~ 126 (235)
| +.+. .+.++|++++|||+.+|..+..|-
T Consensus 523 f-~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 523 L-NSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred h-CCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHH
Confidence 2 1222 244679999999999999998883
No 67
>PRK08609 hypothetical protein; Provisional
Probab=87.19 E-value=1.6 Score=42.27 Aligned_cols=49 Identities=22% Similarity=0.383 Sum_probs=32.1
Q ss_pred hccCCChHHHHHHHHHHHHH----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHH
Q 026645 73 IYPVAFYTRKACNMKKIAKI----CLTKYDGDIPSSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 73 l~~~G~~~~Ka~~l~~~a~~----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il 123 (235)
|.++| ..=|..|.++.+. ..++...++|....+|+++|||||++|..+-
T Consensus 53 ipgIG--~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 53 LKGIG--KGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred CCCcC--HHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHH
Confidence 34444 3445666666543 1233334677788899999999999997654
No 68
>PRK00024 hypothetical protein; Reviewed
Probab=86.48 E-value=1.1 Score=38.08 Aligned_cols=56 Identities=21% Similarity=0.393 Sum_probs=40.1
Q ss_pred CCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCCh----hhHHHHHcCCCCcHHHHHHHH
Q 026645 64 ADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIP----SSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 64 a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~----~~~~~L~~l~GIG~~tA~~il 123 (235)
.+..||.+++=..|.. -+....+|+.+.++|++ +. ...++|.+++|||+..|..++
T Consensus 24 Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgs-L~~l~~as~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 24 LSDAELLAILLRTGTK---GKSVLDLARELLQRFGS-LRGLLDASLEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred CCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCC-HHHHHhCCHHHHhhccCccHHHHHHHH
Confidence 4566777765455553 34667889999988863 43 357899999999999886554
No 69
>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=86.42 E-value=0.76 Score=33.61 Aligned_cols=27 Identities=30% Similarity=0.452 Sum_probs=22.7
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHHhcCC
Q 026645 103 SSLDELLALPGIGPKMANMVMTLGWFN 129 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~~~~~ 129 (235)
+....|..|||||+.+|.-+...++..
T Consensus 9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 9 AGLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 356789999999999999888877754
No 70
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=86.40 E-value=1.9 Score=38.85 Aligned_cols=48 Identities=27% Similarity=0.393 Sum_probs=33.5
Q ss_pred CCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 76 VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 76 ~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.|=...|..+..++|..|.. +..++.+ .+.|.+|||||+.+|+.|--+
T Consensus 20 ~gen~~k~~ay~~Aa~~i~~-l~~~i~~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 20 FGENKRKCSYFRKAASVLKS-LPFPINS-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred hcccHHHHHHHHHHHHHHHh-CCCCCCC-HHHHhcCCCccHHHHHHHHHH
Confidence 34334467777777777543 4455543 468999999999999988743
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=85.88 E-value=0.73 Score=36.66 Aligned_cols=23 Identities=52% Similarity=0.830 Sum_probs=20.8
Q ss_pred hHHHHHcCCCCcHHHHHHHHHHh
Q 026645 104 SLDELLALPGIGPKMANMVMTLG 126 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~~ 126 (235)
+.++|..|||||++.|..|..+-
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHH
Confidence 57889999999999999999874
No 72
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=85.62 E-value=1.9 Score=34.28 Aligned_cols=55 Identities=24% Similarity=0.340 Sum_probs=38.2
Q ss_pred HhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHH
Q 026645 61 IDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 61 la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~ 124 (235)
|-.|+.++| +.|.++|- .||+.|.+-- +++ | .-...+.|...+|||+++.+-...
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~yR----e~~-G-~f~sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIIDYR----EEN-G-PFKSVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHHHH----HHc-C-CCCcHHHHHhccCCCHHHHHHHHh
Confidence 445788888 66677775 4676665532 333 3 336789999999999999876543
No 73
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=84.86 E-value=5.7 Score=39.35 Aligned_cols=77 Identities=18% Similarity=0.301 Sum_probs=48.8
Q ss_pred HHHHHHHHcCC-CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHhcC
Q 026645 45 GALQRLLQNGL-HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTKYD 98 (235)
Q Consensus 45 ~~~~~l~~~~~-pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~~~ 98 (235)
+.+..|.+.++ -++.+|..+..++|.++ . ||...++..|.+..+. +...|
T Consensus 473 k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l-~--g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F- 548 (689)
T PRK14351 473 ERVQQLVDAGLVESLADLYDLTVADLAEL-E--GWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREF- 548 (689)
T ss_pred HHHHHHHHcCCCCCHHHHHHcCHHHHhcC-c--CcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHh-
Confidence 34566666554 58999999988876554 2 5655556655443222 22233
Q ss_pred CCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 99 GDIP----SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 99 g~~~----~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+++. .+.++|.+++|||+++|..|..|
T Consensus 549 ~si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 549 GTFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 2232 24567888999999999888777
No 74
>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=84.77 E-value=0.96 Score=34.58 Aligned_cols=22 Identities=55% Similarity=0.907 Sum_probs=20.3
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++|.++||||++.|..|+.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 5789999999999999999877
No 75
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=84.66 E-value=0.59 Score=40.25 Aligned_cols=156 Identities=16% Similarity=0.175 Sum_probs=79.2
Q ss_pred HHHHhccccHHHHHHHHHHHHHcCCC--CHHHHhcCCHHHHHHhhccC----CChHHHHHHHHHHHHHHHH--------h
Q 026645 31 SALLSSLTKDKVADGALQRLLQNGLH--TAEAIDKADEATIKDLIYPV----AFYTRKACNMKKIAKICLT--------K 96 (235)
Q Consensus 31 ~~iLsqqt~~~~~~~~~~~l~~~~~p--t~~~la~a~~e~l~~~l~~~----G~~~~Ka~~l~~~a~~i~~--------~ 96 (235)
.++.|-|-+..- ...|..|.+. |. +++++ .+++.+.+... -+.+.|.++|.++...+.. .
T Consensus 45 NaLvSYqLs~kG-Ee~W~~Fs~y-fs~~~~~~~----~~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~l~l~~~~~~ 118 (246)
T PF09171_consen 45 NALVSYQLSGKG-EEYWWEFSEY-FSKRPIEDI----CEAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLENLSLQDNPLY 118 (246)
T ss_dssp HHHT-SS-TT-H-HHHHHHHHHH-HCTS--SSH----HHHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHTT-HHHHHHH
T ss_pred HHHHHHhcCCch-HHHHHHHHHH-HhcCCchhH----HHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 456677766543 4566666553 22 12222 46666777643 2456888898888655322 2
Q ss_pred cCCCChhhHHHHHcCCCCcH---HHHHHHH------HHhcCCc------ceeecchHHHHHHHHhcCcCCCCCCCCCCCH
Q 026645 97 YDGDIPSSLDELLALPGIGP---KMANMVM------TLGWFNV------QGICVDTHVHRICNRLGWVTQPGTKQKTSSP 161 (235)
Q Consensus 97 ~~g~~~~~~~~L~~l~GIG~---~tA~~il------~~~~~~~------~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~ 161 (235)
| .++...++.|...-|-.+ .++-++- ..++|.. -.+|||.|+.++..+.|+++...... ..+.
T Consensus 119 y-~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~~~~~~-~~~~ 196 (246)
T PF09171_consen 119 Y-EDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIECEREEM-MRTR 196 (246)
T ss_dssp H-CTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS-----TTS-----HHHHHHHHCTTS-SS-HHHH-HCTC
T ss_pred h-hhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCcccCCCCccHHHHHHHHHhccccccHHhh-hccH
Confidence 3 677777777777555443 2233333 3343441 14699999999999999976321100 0222
Q ss_pred HHHHHHHHHhCCcc--cHHHHHHHHH-HHHhhhcCC
Q 026645 162 EQTREALQRWLPKE--EWVRINPLLV-GFGQTICTP 194 (235)
Q Consensus 162 ~~~~~~l~~~~p~~--~~~~~~~~l~-~~G~~iC~~ 194 (235)
+.++..+....-.. .+-.++..|+ -+|+.....
T Consensus 197 ~~v~~~W~~Va~~sgIpplhLDs~lW~l~G~~~~~~ 232 (246)
T PF09171_consen 197 EEVQKAWREVAKESGIPPLHLDSLLWPLLGRARDVK 232 (246)
T ss_dssp CHHHHHHHHHHHHHT--HHHHHHHHHHHHCCHHCCT
T ss_pred HHHHHHHHHHHhhcCCCchhhhhHHHHhcccchhhh
Confidence 33444433221111 2456677888 889887654
No 76
>PRK07945 hypothetical protein; Provisional
Probab=84.58 E-value=1.9 Score=38.81 Aligned_cols=58 Identities=24% Similarity=0.328 Sum_probs=37.3
Q ss_pred HHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCC-ChhhHH--HHHcCCCCcHHHHHHHHHH
Q 026645 67 ATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGD-IPSSLD--ELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 67 e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~-~~~~~~--~L~~l~GIG~~tA~~il~~ 125 (235)
+++..+|.-.|=..-|++.-+++|+.|.. .+.+ +.+..+ .|.+|||||+-+|..|.-+
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA-LDAAERARRARAGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cChhHHHHHHhcCCcccCCCcCHHHHHHHHHH
Confidence 34444444445444477888888888644 3333 333222 5889999999999988754
No 77
>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=84.42 E-value=0.91 Score=37.60 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=19.4
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.+..|++++||||++|-.+|..
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHhc
Confidence 35688999999999999888653
No 78
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.00 E-value=0.99 Score=37.49 Aligned_cols=23 Identities=30% Similarity=0.663 Sum_probs=20.0
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.+++||||++|-.|+..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 35688999999999999999874
No 79
>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=83.96 E-value=0.75 Score=26.66 Aligned_cols=15 Identities=33% Similarity=0.445 Sum_probs=11.4
Q ss_pred HHcCCCCcHHHHHHH
Q 026645 108 LLALPGIGPKMANMV 122 (235)
Q Consensus 108 L~~l~GIG~~tA~~i 122 (235)
+.+++|||++|+.-+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 457899999999764
No 80
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=83.83 E-value=2.1 Score=38.18 Aligned_cols=56 Identities=23% Similarity=0.240 Sum_probs=39.0
Q ss_pred HHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHH--HHcCCCCcHHHHHHHHHH
Q 026645 69 IKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDE--LLALPGIGPKMANMVMTL 125 (235)
Q Consensus 69 l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~--L~~l~GIG~~tA~~il~~ 125 (235)
+...+.-.|=..-|+..-+.+|+.+. .-+-+++...+. ++.|||||+.+|+.|.-+
T Consensus 15 iA~~me~~Gen~fk~~aYr~Aa~sle-~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 15 IADYMELEGENPFKIRAYRKAAQSLE-NLTEDLEEIEERGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred HHHHHHhcCCCccchHHHHHHHHhhh-hcccchHHHHhhcccCCCCCccHHHHHHHHHH
Confidence 33333333433346777777788754 345678887777 999999999999999854
No 81
>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=83.72 E-value=1.2 Score=28.91 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=16.4
Q ss_pred HHHHcCCCCcHHHHHHHHHHhc
Q 026645 106 DELLALPGIGPKMANMVMTLGW 127 (235)
Q Consensus 106 ~~L~~l~GIG~~tA~~il~~~~ 127 (235)
+.++.+.|||+.||.-....++
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~ 23 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGI 23 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT-
T ss_pred cchhhcccccHHHHHHHHHhCC
Confidence 5788999999999998887665
No 82
>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=83.62 E-value=2.8 Score=32.00 Aligned_cols=61 Identities=23% Similarity=0.303 Sum_probs=40.5
Q ss_pred CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 56 HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 56 pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
..+-.|-.++.++|..+ .++| ..+|+.|.+--.. .|.+ ...++|..++|||+++++-+..+
T Consensus 57 ~~~iniNtA~~~eL~~l-pGIG--~~~A~~Ii~~R~~-----~g~f-~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 57 LAAVNINAASLEELQAL-PGIG--PAKAKAIIEYREE-----NGAF-KSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CCCEeCCcCCHHHHhcC-CCCC--HHHHHHHHHHHHh-----cCCc-CCHHHHHcCCCCCHHHHHHHHhc
Confidence 34555667888888764 4444 4566666543222 1333 56899999999999999887654
No 83
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.37 E-value=0.98 Score=37.63 Aligned_cols=23 Identities=35% Similarity=0.634 Sum_probs=19.7
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.||||++|=.||+.
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 35788999999999999999853
No 84
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.97 E-value=0.99 Score=37.19 Aligned_cols=23 Identities=30% Similarity=0.421 Sum_probs=19.7
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.|||||+|=.+|+.
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHcC
Confidence 35788999999999999988854
No 85
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.75 E-value=0.99 Score=37.60 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=19.8
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|+++.||||++|=.+|..
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs~ 91 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLSA 91 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 35678999999999999999873
No 86
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=82.42 E-value=3.3 Score=37.31 Aligned_cols=70 Identities=20% Similarity=0.278 Sum_probs=47.8
Q ss_pred hhhHHHHHcCCCCcHHHHHHHHHH---hcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCc
Q 026645 102 PSSLDELLALPGIGPKMANMVMTL---GWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK 174 (235)
Q Consensus 102 ~~~~~~L~~l~GIG~~tA~~il~~---~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~ 174 (235)
|.++++|+-.|||||.|+-++.+. .+|.+..+ -|-- +.+.-+|+-+.-..+....+|+++-+++++.+..
T Consensus 274 p~Df~elLl~~GiGpstvRALalVAEvIyg~~~s~-rDP~--~yafA~GGKDgvP~pV~~~~yde~I~~l~~~ve~ 346 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVAEVIYGEPPSF-RDPV--KYAFAVGGKDGVPFPVNRKTYDELIEFLEELVEK 346 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHHHHHhCCCCCc-CCch--hhhhhhcCCCCCCCCcchhhHHHHHHHHHHHHHh
Confidence 568899999999999999887765 45544333 1211 2666677655444555677888888888777654
No 87
>PRK00024 hypothetical protein; Reviewed
Probab=82.23 E-value=4.7 Score=34.23 Aligned_cols=62 Identities=24% Similarity=0.268 Sum_probs=48.0
Q ss_pred HHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 27 AVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 27 ~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
..|++.+|..-+....+....++|.+ .|.+...+..++.++|.++ .++| ..||..|..+.+.
T Consensus 27 ~ELLa~lL~~g~~~~~~~~LA~~LL~-~fgsL~~l~~as~~eL~~i-~GIG--~akA~~L~a~~El 88 (224)
T PRK00024 27 AELLAILLRTGTKGKSVLDLARELLQ-RFGSLRGLLDASLEELQSI-KGIG--PAKAAQLKAALEL 88 (224)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHH-HcCCHHHHHhCCHHHHhhc-cCcc--HHHHHHHHHHHHH
Confidence 34778888888888888889999998 4999999999999999875 5555 4567666544433
No 88
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=81.85 E-value=1.2 Score=26.56 Aligned_cols=16 Identities=38% Similarity=0.609 Sum_probs=12.9
Q ss_pred HcCCCCcHHHHHHHHH
Q 026645 109 LALPGIGPKMANMVMT 124 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~ 124 (235)
-.+||||+++|.-++.
T Consensus 19 ~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 19 PGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCcccHHHHHHHHH
Confidence 3689999999987663
No 89
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.62 E-value=1.1 Score=37.00 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=19.5
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.||||++|=.+|..
T Consensus 70 ~lF~~Li~V~GIGpK~AL~iLs~ 92 (188)
T PRK14606 70 ELFLSLTKVSRLGPKTALKIISN 92 (188)
T ss_pred HHHHHHhccCCccHHHHHHHHcC
Confidence 35688999999999999998853
No 90
>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=81.58 E-value=3.2 Score=36.88 Aligned_cols=42 Identities=31% Similarity=0.449 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 82 KACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 82 Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
|++.-..+|..|.. +.-++. ..+++.+|||||+.+|+.|--+
T Consensus 23 r~~aY~~Aa~~l~~-l~~~i~-~~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 23 RVRAYRKAARALES-LPEPIE-SLEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred hHHHHHHHHHHHHh-CCcccC-CHHHhcCCCCccHHHHHHHHHH
Confidence 67777777777644 444443 3567899999999999998755
No 91
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.66 E-value=3 Score=35.37 Aligned_cols=56 Identities=21% Similarity=0.316 Sum_probs=41.1
Q ss_pred CCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCC---ChhhHHHHHcCCCCcHHHHHHH
Q 026645 64 ADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGD---IPSSLDELLALPGIGPKMANMV 122 (235)
Q Consensus 64 a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~---~~~~~~~L~~l~GIG~~tA~~i 122 (235)
.+..||.+++=..|- |-.....+|+.+.++||+- .....++|++++|||+.-|--+
T Consensus 24 Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l 82 (224)
T COG2003 24 LSDAELLAILLRTGT---KGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQI 82 (224)
T ss_pred cchHHHHHHHHhcCC---CCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHH
Confidence 345677777655665 4567889999999998751 2346899999999998665444
No 92
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=79.64 E-value=1.7 Score=33.78 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=22.5
Q ss_pred hcCCCCh---hhHHHHHcCCCCcHHHHHHHHH
Q 026645 96 KYDGDIP---SSLDELLALPGIGPKMANMVMT 124 (235)
Q Consensus 96 ~~~g~~~---~~~~~L~~l~GIG~~tA~~il~ 124 (235)
+++..+. ...++|.++|||||..|..|..
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHH
Confidence 3444443 3678899999999999999984
No 93
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.62 E-value=6.9 Score=33.12 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=47.4
Q ss_pred HHHHHHHHhccccHH-HHHHHHHHHHHcCC---CCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026645 27 AVLLSALLSSLTKDK-VADGALQRLLQNGL---HTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91 (235)
Q Consensus 27 ~~lv~~iLsqqt~~~-~~~~~~~~l~~~~~---pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~ 91 (235)
..|++.+|..-+... .+....++|.+ .| .+...+..++.++|.++ +++| ..||..|..+.+
T Consensus 17 ~ELLailL~~g~~~~~~~~~lA~~ll~-~f~~~g~l~~l~~a~~~eL~~i-~GiG--~aka~~l~a~~E 81 (218)
T TIGR00608 17 YELLAIILRTGTPKGLDVLSLSKRLLD-VFGRQDSLGHLLSAPPEELSSV-PGIG--EAKAIQLKAAVE 81 (218)
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHH-HhcccCCHHHHHhCCHHHHHhC-cCCc--HHHHHHHHHHHH
Confidence 347788888888777 88888899998 48 89999999999999875 6555 457777755433
No 94
>PRK01172 ski2-like helicase; Provisional
Probab=79.39 E-value=5.8 Score=38.96 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=37.6
Q ss_pred HHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhc
Q 026645 48 QRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKY 97 (235)
Q Consensus 48 ~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~ 97 (235)
++|.+.|+-|+.+|+.++++++.+++ |+..+.++.|.+-|+.+++-|
T Consensus 626 ~~l~~~g~~~~~di~~~~~~~~~~i~---~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 626 RRLYDAGFKTVDDIARSSPERIKKIY---GFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred HHHHHcCCCCHHHHHhCCHHHHHHHh---ccCHHHHHHHHHHHHHHHHHh
Confidence 44444588899999999999998874 788888999999888887754
No 95
>PRK14973 DNA topoisomerase I; Provisional
Probab=79.05 E-value=8.1 Score=39.67 Aligned_cols=47 Identities=21% Similarity=0.316 Sum_probs=38.1
Q ss_pred HHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026645 44 DGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL 94 (235)
Q Consensus 44 ~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~ 94 (235)
.++++.|...|..+.++|+.+++..|.+. |++..+++.+.+-|+-++
T Consensus 754 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~sE~~~~~~~~~a~~~~ 800 (936)
T PRK14973 754 AKIMKALISSGINDIAALARADPADLKKA----GLSEAEAASLLAEAKSLC 800 (936)
T ss_pred HHHHHHHHhcCcchHHHHhhCCHHHHHHc----CCCHHHHHHHHHHHHHHH
Confidence 34556666668889999999999998877 999999999999886443
No 96
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=78.36 E-value=4.1 Score=36.36 Aligned_cols=46 Identities=22% Similarity=0.321 Sum_probs=30.7
Q ss_pred CChhhHHHHHcCCCCcHHHHHHHHHH---hcCCcceeecchHHHHHHHHhcC
Q 026645 100 DIPSSLDELLALPGIGPKMANMVMTL---GWFNVQGICVDTHVHRICNRLGW 148 (235)
Q Consensus 100 ~~~~~~~~L~~l~GIG~~tA~~il~~---~~~~~~~~pvDt~v~Rv~~Rlg~ 148 (235)
.-|+++++|+.++||||+|..++.+. .+|.+..+ -|- + |.+--+|+
T Consensus 263 ~~p~~feeLL~~~GvGp~TlRALaLvaelIyg~p~s~-~DP-a-kfsfA~GG 311 (319)
T PF05559_consen 263 RQPSDFEELLLIKGVGPSTLRALALVAELIYGVPPSF-RDP-A-KFSFAHGG 311 (319)
T ss_pred CCccCHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCc-cCh-h-HHHHhhcC
Confidence 34788999999999999998887765 34443333 111 1 55555555
No 97
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=76.88 E-value=8 Score=32.85 Aligned_cols=63 Identities=24% Similarity=0.243 Sum_probs=50.8
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
-+-|++.+|-.-|....|....+.|..+ |.+...|..++.+++..+ .++|. .|+-.|+.+.+.
T Consensus 26 d~ELLailLrtG~~~~~~~~la~~lL~~-fg~L~~l~~a~~~el~~v-~GiG~--aka~~l~a~~El 88 (224)
T COG2003 26 DAELLAILLRTGTKGESVLDLAKELLQE-FGSLAELLKASVEELSSV-KGIGL--AKAIQIKAAIEL 88 (224)
T ss_pred hHHHHHHHHhcCCCCCCHHHHHHHHHHH-cccHHHHHhCCHHHHhhC-CCccH--HHHHHHHHHHHH
Confidence 3557889999999999999999999994 999999999999999776 66664 466666555443
No 98
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=76.58 E-value=2.8 Score=28.20 Aligned_cols=51 Identities=25% Similarity=0.426 Sum_probs=29.7
Q ss_pred cCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHH
Q 026645 63 KADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMV 122 (235)
Q Consensus 63 ~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~i 122 (235)
.|+.++|..+ -|+....|+.|.+.=+. . |.+ ...++|..++|||+.+.+-+
T Consensus 10 ~as~~eL~~l---pgi~~~~A~~Iv~~R~~----~-G~f-~s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 10 TASAEELQAL---PGIGPKQAKAIVEYREK----N-GPF-KSLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TS-HHHHHTS---TT--HHHHHHHHHHHHH----H--S--SSGGGGGGSTT--HHHHHHH
T ss_pred cCCHHHHHHc---CCCCHHHHHHHHHHHHh----C-cCC-CCHHHHhhCCCCCHHHHHHH
Confidence 4667776654 26666667777654333 1 333 45788999999999998765
No 99
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.22 E-value=2.4 Score=34.95 Aligned_cols=23 Identities=22% Similarity=0.343 Sum_probs=19.9
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.||||++|=.+|+.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcc
Confidence 35688999999999999999873
No 100
>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=73.39 E-value=4.1 Score=27.56 Aligned_cols=22 Identities=27% Similarity=0.529 Sum_probs=19.2
Q ss_pred hHHHHHc-CCCCcHHHHHHHHHH
Q 026645 104 SLDELLA-LPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~-l~GIG~~tA~~il~~ 125 (235)
..+.|.. +||||+.+|..++.+
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHH
Confidence 4568888 999999999999977
No 101
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=72.80 E-value=3.7 Score=35.10 Aligned_cols=39 Identities=23% Similarity=0.275 Sum_probs=30.9
Q ss_pred HHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 50 LLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 50 l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
|.. .|+|.++|..|+.++|+.+ -|+..+||+.|.+...+
T Consensus 211 LL~-~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 211 LLQ-KFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHH-hcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhc
Confidence 444 5999999999999999887 36667899998887654
No 102
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.73 E-value=3.4 Score=34.57 Aligned_cols=23 Identities=17% Similarity=0.365 Sum_probs=19.9
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.||||++|=.+|..
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhh
Confidence 35678999999999999999874
No 103
>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=71.95 E-value=2.9 Score=29.05 Aligned_cols=18 Identities=39% Similarity=0.698 Sum_probs=14.7
Q ss_pred HHcCCCCcHHHHHHHHHH
Q 026645 108 LLALPGIGPKMANMVMTL 125 (235)
Q Consensus 108 L~~l~GIG~~tA~~il~~ 125 (235)
+..+||||++||.-++.-
T Consensus 24 i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 24 IPGVPGIGPKTALKLLKE 41 (75)
T ss_pred CCCCCcccHHHHHHHHHH
Confidence 447899999999888754
No 104
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.17 E-value=3.4 Score=34.35 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=19.9
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.++.|.++.||||++|=.+|..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 35688999999999999999874
No 105
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=70.75 E-value=13 Score=31.82 Aligned_cols=44 Identities=16% Similarity=0.209 Sum_probs=34.4
Q ss_pred HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
..+.|.++||.|.++|..++.++|.++ -|+...+|..|++.+..
T Consensus 15 rakkLl~~GF~Sve~Ik~AS~eEL~~V---~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 15 KAEALREAGFESVEDVRAADQSELAEV---DGIGNALAARIKADVGG 58 (232)
T ss_pred HHHHHHHcCCCCHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHhcc
Confidence 345667767999999999999999776 37777788888777654
No 106
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=70.75 E-value=11 Score=25.19 Aligned_cols=43 Identities=12% Similarity=0.096 Sum_probs=27.7
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~ 91 (235)
...+.|.+ .|.|.+.|..++.++|.++ . |.....|+.|.+.-+
T Consensus 14 ~~ak~L~~-~f~sl~~l~~a~~e~L~~i-~--gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 14 KTAKLLAK-HFGSLEALMNASVEELSAI-P--GIGPKIAQSIYEFFQ 56 (64)
T ss_dssp HHHHHHHH-CCSCHHHHCC--HHHHCTS-T--T--HHHHHHHHHHHH
T ss_pred HHHHHHHH-HcCCHHHHHHcCHHHHhcc-C--CcCHHHHHHHHHHHC
Confidence 34566777 5999999999999998654 4 444556777765543
No 107
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=70.70 E-value=12 Score=26.28 Aligned_cols=53 Identities=11% Similarity=0.161 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026645 41 KVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL 94 (235)
Q Consensus 41 ~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~ 94 (235)
++-..++..|.+.|--+.++|..+.++|+.+++.-+|+.. |--.++.+-+++.
T Consensus 19 AnLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~s-KPLHVrRlqKAL~ 71 (82)
T PF04904_consen 19 ANLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMAS-KPLHVRRLQKALQ 71 (82)
T ss_pred hhHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccC-ccHHHHHHHHHHH
Confidence 4456688888888888999999999999999999999863 3444444444443
No 108
>PRK07758 hypothetical protein; Provisional
Probab=69.89 E-value=21 Score=26.16 Aligned_cols=46 Identities=26% Similarity=0.322 Sum_probs=30.3
Q ss_pred HHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 44 DGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 44 ~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
.++++.|...++.|.++|+..++++|.++ +++| -+.|.++-+.+.+
T Consensus 44 vRA~N~Lk~AGI~TL~dLv~~te~ELl~i-knlG-----kKSL~EIkekL~E 89 (95)
T PRK07758 44 APARRALEHHGIHTVEELSKYSEKEILKL-HGMG-----PASLPKLRKALEE 89 (95)
T ss_pred HHHHHHHHHcCCCcHHHHHcCCHHHHHHc-cCCC-----HHHHHHHHHHHHH
Confidence 45667777778888999988888888775 4444 2345454444443
No 109
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=69.89 E-value=5.4 Score=36.20 Aligned_cols=36 Identities=17% Similarity=0.362 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcCCCCh----hhHHHHHcCCCCcHHHHHHHH
Q 026645 87 KKIAKICLTKYDGDIP----SSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 87 ~~~a~~i~~~~~g~~~----~~~~~L~~l~GIG~~tA~~il 123 (235)
+.+|+.++++|| .+. ...++|.+++|||++.|..|.
T Consensus 297 k~iAk~Ll~~FG-SL~~Il~As~eeL~~VeGIGe~rA~~I~ 336 (352)
T PRK13482 297 SAVIENLVEHFG-SLQGLLAASIEDLDEVEGIGEVRARAIR 336 (352)
T ss_pred HHHHHHHHHHcC-CHHHHHcCCHHHHhhCCCcCHHHHHHHH
Confidence 466888888885 444 457899999999999998743
No 110
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=69.47 E-value=16 Score=33.27 Aligned_cols=47 Identities=6% Similarity=0.118 Sum_probs=38.6
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
+..++|.+ .|.|...|..|+.++|.++ .++| ..||+.|++.++.+.+
T Consensus 298 ~iAk~Ll~-~FGSL~~Il~As~eeL~~V-eGIG--e~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 298 AVIENLVE-HFGSLQGLLAASIEDLDEV-EGIG--EVRARAIREGLSRLAE 344 (352)
T ss_pred HHHHHHHH-HcCCHHHHHcCCHHHHhhC-CCcC--HHHHHHHHHHHHHHHH
Confidence 45677888 4999999999999999887 4444 6789999999988766
No 111
>PRK08609 hypothetical protein; Provisional
Probab=69.09 E-value=9.7 Score=36.88 Aligned_cols=55 Identities=18% Similarity=0.222 Sum_probs=34.9
Q ss_pred HHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 69 IKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 69 l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+.+++.-.|=..-|++.-+++|+.|.. ...++. ....|.+|||||+.+|+.|--+
T Consensus 13 ~A~~le~~g~n~fr~~aYr~Aa~~i~~-l~~~i~-~~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 13 IATYMELKGENPFKISAFRKAAQALEL-DERSLS-EIDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHhcCCCcHHHHHHHHHHHHHHh-Cchhhh-hhhhhccCCCcCHHHHHHHHHH
Confidence 333333334222367777777887644 334443 3457899999999999988744
No 112
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=68.96 E-value=14 Score=32.79 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=36.8
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
...+.|.+.+|-|.++|+.+++++|.+.+ |+...++..|.+.++.
T Consensus 17 ~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~---g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 17 ATAEKLREAGYDTVEAIAVASPKELSEAA---GIGESTAAKIIEAARE 61 (317)
T ss_pred HHHHHHHHcCCCCHHHHHcCCHHHHHHhc---CCCHHHHHHHHHHHHH
Confidence 34677777799999999999999998874 7776778888887765
No 113
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=68.45 E-value=5.2 Score=39.19 Aligned_cols=79 Identities=20% Similarity=0.407 Sum_probs=49.3
Q ss_pred HHHHHHHHHHcC-CCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH-------------------------HHHh
Q 026645 43 ADGALQRLLQNG-LHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI-------------------------CLTK 96 (235)
Q Consensus 43 ~~~~~~~l~~~~-~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~-------------------------i~~~ 96 (235)
..+.+..|++.+ +-++.+|..+..+++..+ . |+...+++.|.+.-+. +...
T Consensus 454 G~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l-~--~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~ 530 (667)
T COG0272 454 GEKIIEQLFEKGLIKDIADLYTLTEEDLLSL-E--GFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARH 530 (667)
T ss_pred CHHHHHHHHHcCccCCHHHHHhCCHHHHhhc-c--chhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHHH
Confidence 345566777653 457888888888877665 2 3334455555443322 1111
Q ss_pred cCCCCh----hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 97 YDGDIP----SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 97 ~~g~~~----~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
| +.+. ...++|.+++|||..+|..|..|
T Consensus 531 f-~sl~~l~~a~~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 531 F-GTLEALLAASEEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred h-hhHHHHHhcCHHHHhhccchhHHHHHHHHHH
Confidence 1 1222 25688999999999999999877
No 114
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=67.53 E-value=4.5 Score=33.83 Aligned_cols=46 Identities=15% Similarity=0.261 Sum_probs=28.3
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH-hcCCcceeecchHHHHHHHHhcCc
Q 026645 103 SSLDELLALPGIGPKMANMVMTL-GWFNVQGICVDTHVHRICNRLGWV 149 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~-~~~~~~~~pvDt~v~Rv~~Rlg~~ 149 (235)
+.+..|+++.||||++|=++|+. ..... +-.+++.=...+.++-++
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l-~~aI~~~d~~~L~k~PGI 116 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEEL-AQAIANEDVKALSKIPGI 116 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHH-HHHHHhcChHhhhcCCCC
Confidence 35678999999999999998865 22221 112333333455555444
No 115
>PTZ00035 Rad51 protein; Provisional
Probab=67.37 E-value=16 Score=32.84 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=40.6
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
...++|.+.+|-|.++++.+++.+|.+. .|++..+|..|++.++.+..
T Consensus 34 ~~~~kL~~~g~~t~~~~~~~~~~~L~~~---~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 34 ADIKKLKEAGICTVESVAYATKKDLCNI---KGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHHh---hCCCHHHHHHHHHHHHHhcc
Confidence 4567788889999999999999999876 48888899999998888654
No 116
>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=66.76 E-value=17 Score=32.00 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=36.1
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~ 91 (235)
...++|.+.+|-|.++|+.++.++|.+.. |+...++..|.+.+.
T Consensus 10 ~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~---g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 10 ATAEKLREAGYDTFEAIAVASPKELSEIA---GISEGTAAKIIQAAR 53 (310)
T ss_pred HHHHHHHHcCCCCHHHHHcCCHHHHHhcc---CCCHHHHHHHHHHHH
Confidence 35677777789999999999999998874 777667888887776
No 117
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=66.73 E-value=18 Score=32.20 Aligned_cols=48 Identities=13% Similarity=0.218 Sum_probs=40.6
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
...++|.+.+|-|.++++.+++.+|.+. .|++..++..|++.+.....
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~~~~~L~~~---~gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMTTRRALCKI---KGLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHHh---cCCCHHHHHHHHHHHHhhhc
Confidence 4567788889999999999999999776 48888999999998887654
No 118
>PF10343 DUF2419: Protein of unknown function (DUF2419); InterPro: IPR019438 This entry contains proteins that have no known function.
Probab=66.03 E-value=34 Score=30.27 Aligned_cols=97 Identities=14% Similarity=0.339 Sum_probs=64.9
Q ss_pred CCC--CHHHHhcCCHHHHHHhhccC-----CChHHHHHHHHHHHHHHHHhcCCCChh-----------hHHHHH-cCCCC
Q 026645 54 GLH--TAEAIDKADEATIKDLIYPV-----AFYTRKACNMKKIAKICLTKYDGDIPS-----------SLDELL-ALPGI 114 (235)
Q Consensus 54 ~~p--t~~~la~a~~e~l~~~l~~~-----G~~~~Ka~~l~~~a~~i~~~~~g~~~~-----------~~~~L~-~l~GI 114 (235)
+.| +|+-+..++.++|..++++- -+-..|++.|+++.+.+.++|+|.+-+ ..+.|. .+||.
T Consensus 62 ~~pi~~~~~~~~~t~~~l~~if~s~~~~~iPll~eR~~~L~E~G~vL~~~f~gs~~~~i~~a~~sA~~Lv~~l~~~Fp~F 141 (287)
T PF10343_consen 62 GIPITDPKYYAKMTDEELRHIFRSDTEEEIPLLEERARLLREVGRVLLEKFDGSFANCIKSANGSAAKLVRLLVENFPSF 141 (287)
T ss_pred CCCCcCHHHHHhCCHHHHHHHhcCCCCCcCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccCHHHHHHHHHHhCCCc
Confidence 555 89999999999999999853 244577999999999999999987643 234444 37774
Q ss_pred cHH-----------------HHHHHHHHh---cCC---cce--eecchHHHHHHHHhcCcC
Q 026645 115 GPK-----------------MANMVMTLG---WFN---VQG--ICVDTHVHRICNRLGWVT 150 (235)
Q Consensus 115 G~~-----------------tA~~il~~~---~~~---~~~--~pvDt~v~Rv~~Rlg~~~ 150 (235)
-+. +||....|. ++. .+. +-.|--|=-++..+|.+.
T Consensus 142 rD~~~y~G~~V~~~KRAQIlvaDlw~~f~g~~~g~F~Did~lTmFADyrVPqvL~~lG~L~ 202 (287)
T PF10343_consen 142 RDEATYKGRQVYFYKRAQILVADLWACFKGQGLGEFPDIDQLTMFADYRVPQVLRHLGVLR 202 (287)
T ss_pred ccceEECCcEEEeeHHHHHHHHHHHHHhCCCCCCCcCCHhhcccccCCchHHHHHHCCcEE
Confidence 432 345555552 111 011 125766667777777764
No 119
>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=65.20 E-value=7.6 Score=28.95 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=19.3
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
..-.|.++.|||+.+|..|+..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~ 34 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKK 34 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHH
T ss_pred hHhHHhhhhccCHHHHHHHHHH
Confidence 5678999999999999988865
No 120
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=62.95 E-value=23 Score=32.04 Aligned_cols=48 Identities=15% Similarity=0.247 Sum_probs=40.2
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
...++|.+.+|-|.++|+.++..+|.+. .|++..++..|.+.++.++.
T Consensus 42 ~~~~kL~~~g~~tv~~~~~~~~~~L~~~---~g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 42 GDVKKLQDAGIYTCNGLMMHTKKNLTGI---KGLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHHh---cCCCHHHHHHHHHHHHHhhc
Confidence 4567788889999999999999998875 58888899999988877653
No 121
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=61.72 E-value=18 Score=32.36 Aligned_cols=42 Identities=31% Similarity=0.467 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 82 KACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 82 Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
|+..-..++..+ +.+.-.+ ...+++..|||||+++|..|--|
T Consensus 34 r~~~y~~Aasvl-k~~p~~I-~S~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 34 RARAYRRAASVL-KSLPFPI-TSGEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred HHHHHHHHHHHH-HhCCCCc-ccHHHhcCCCCCCHHHHHHHHHH
Confidence 344444545544 3332222 46789999999999999988755
No 122
>PF11691 DUF3288: Protein of unknown function (DUF3288); InterPro: IPR021705 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=61.31 E-value=60 Score=23.54 Aligned_cols=63 Identities=10% Similarity=0.076 Sum_probs=41.1
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHc-CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 26 FAVLLSALLSSLTKDKVADGALQRLLQN-GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~-~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
=..+|..+|..+.++.+-....+-++.+ +||...+| ..+|..+|+..|+.+ .-|-+-.+.|..
T Consensus 11 DR~~vd~Ll~~~p~d~~L~eLARL~iRY~gFPGA~di----q~DL~kiL~~W~lte---eeLf~kTR~I~~ 74 (90)
T PF11691_consen 11 DREIVDRLLAGEPTDYNLAELARLRIRYQGFPGARDI----QKDLDKILQKWGLTE---EELFEKTREIHA 74 (90)
T ss_pred hHHHHHHHHcCCCCchhHHHHHHHHHHhcCCCCHHHH----HHHHHHHHHHcCCCH---HHHHHHHHHHHH
Confidence 3567888888886555544444333332 89999998 478888898889863 344444555554
No 123
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=60.61 E-value=18 Score=26.07 Aligned_cols=53 Identities=23% Similarity=0.327 Sum_probs=31.6
Q ss_pred HHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHH----HHc-CCCCcHHHHHHHHHH
Q 026645 66 EATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDE----LLA-LPGIGPKMANMVMTL 125 (235)
Q Consensus 66 ~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~----L~~-l~GIG~~tA~~il~~ 125 (235)
..++...|...|++...+..| .+.|+.+.-+..++ |+. ++|||=++||.+..-
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl-------~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKL-------YKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHH-------HHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCHHHHHHH-------HHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH
Confidence 456666777889876554444 44455433333322 555 899999999998765
No 124
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=57.37 E-value=54 Score=21.86 Aligned_cols=29 Identities=21% Similarity=0.301 Sum_probs=22.1
Q ss_pred CCHHHHHHhhccCCChHHHHHHHHHHHHHHHHh
Q 026645 64 ADEATIKDLIYPVAFYTRKACNMKKIAKICLTK 96 (235)
Q Consensus 64 a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~ 96 (235)
.+-++|.++ ||+...|+.|..-|+.+.-+
T Consensus 4 v~k~dLi~l----Gf~~~tA~~IIrqAK~~lV~ 32 (59)
T PF11372_consen 4 VTKKDLIEL----GFSESTARDIIRQAKALLVQ 32 (59)
T ss_pred cCHHHHHHc----CCCHHHHHHHHHHHHHHHHH
Confidence 345667666 99998899998888886544
No 125
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=57.24 E-value=11 Score=25.63 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=16.6
Q ss_pred hHHHHHcCCCCcHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il 123 (235)
..+.|.+++|+|+++.+-|.
T Consensus 42 s~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 42 SEEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp -HHHHHTSTTSHHHHHHHHH
T ss_pred CHHHHHhCCCCCHhHHHHHH
Confidence 46889999999999988664
No 126
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=57.16 E-value=24 Score=30.12 Aligned_cols=23 Identities=26% Similarity=0.369 Sum_probs=20.5
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.+.++|.+++|||..+|..|..+
T Consensus 33 AS~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 33 ADQSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred CCHHHHHHccCCCHHHHHHHHHH
Confidence 35789999999999999999877
No 127
>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=55.92 E-value=18 Score=35.99 Aligned_cols=84 Identities=15% Similarity=0.190 Sum_probs=48.8
Q ss_pred CHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCC----hhhHHHHHcCCCCcHHHHHHHHHHhcCCcce
Q 026645 57 TAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDI----PSSLDELLALPGIGPKMANMVMTLGWFNVQG 132 (235)
Q Consensus 57 t~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~----~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~ 132 (235)
+.+.+.-.+.+.+...|...-|..- =...|+.|++.||.+. .+..+.|..+||||++.++.+..- |....
T Consensus 68 ~~~~~~p~~~~~i~~yL~s~~~~GI----G~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~-~~~~~- 141 (720)
T TIGR01448 68 RMELEAPTSKEGIVAYLSSRSIKGV----GKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQ-WSQQG- 141 (720)
T ss_pred EEEEeCCCCHHHHHHHHhcCCCCCc----CHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHH-HHHhH-
Confidence 3344445677888888764223210 1233555667776553 345678999999999999888753 43221
Q ss_pred eecchHHHHHHHHhcC
Q 026645 133 ICVDTHVHRICNRLGW 148 (235)
Q Consensus 133 ~pvDt~v~Rv~~Rlg~ 148 (235)
--..+.-.+..+|+
T Consensus 142 --~~~~~~~~L~~~gi 155 (720)
T TIGR01448 142 --DERRLLAGLQGLGI 155 (720)
T ss_pred --HHHHHHHHHHHcCC
Confidence 12333345555555
No 128
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=53.86 E-value=9.9 Score=33.92 Aligned_cols=22 Identities=41% Similarity=0.641 Sum_probs=19.1
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.+++|+.+||||.++|.-|++.
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred CHHHhcccCCCChHHHHHHHHH
Confidence 5799999999999999887754
No 129
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=52.44 E-value=25 Score=23.21 Aligned_cols=21 Identities=38% Similarity=0.901 Sum_probs=16.8
Q ss_pred ChhhHHHHHcCCCCcHHHHHH
Q 026645 101 IPSSLDELLALPGIGPKMANM 121 (235)
Q Consensus 101 ~~~~~~~L~~l~GIG~~tA~~ 121 (235)
.|.+.++|.+++|+|++-+.-
T Consensus 39 ~P~s~~~L~~i~g~~~~~~~~ 59 (68)
T PF00570_consen 39 LPTSIEELLQIPGMGKRKVRK 59 (68)
T ss_dssp --SSHHHHHTSTTCGHHHHHH
T ss_pred CCCCHHHHHHccCCCHHHHHH
Confidence 588999999999999987653
No 130
>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=50.99 E-value=3 Score=30.95 Aligned_cols=16 Identities=44% Similarity=0.829 Sum_probs=11.6
Q ss_pred cCCCCcHHHHHHHHHH
Q 026645 110 ALPGIGPKMANMVMTL 125 (235)
Q Consensus 110 ~l~GIG~~tA~~il~~ 125 (235)
.+||||+|||.-++.-
T Consensus 22 GV~GIG~KtA~~LL~~ 37 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQE 37 (101)
T ss_dssp --TTSTCHCCCCCHHH
T ss_pred CCCCCCHHHHHHHHHH
Confidence 5799999999776644
No 131
>PRK07758 hypothetical protein; Provisional
Probab=49.52 E-value=15 Score=26.99 Aligned_cols=20 Identities=35% Similarity=0.516 Sum_probs=17.6
Q ss_pred hHHHHHcCCCCcHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il 123 (235)
..++|++++|+|+++.+-|.
T Consensus 65 te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 65 SEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CHHHHHHccCCCHHHHHHHH
Confidence 57899999999999988765
No 132
>PRK14976 5'-3' exonuclease; Provisional
Probab=47.92 E-value=12 Score=32.81 Aligned_cols=16 Identities=38% Similarity=0.632 Sum_probs=12.9
Q ss_pred cCCCCcHHHHHHHHHH
Q 026645 110 ALPGIGPKMANMVMTL 125 (235)
Q Consensus 110 ~l~GIG~~tA~~il~~ 125 (235)
.+||||+|||.-++.-
T Consensus 195 GVpGIG~KtA~~LL~~ 210 (281)
T PRK14976 195 GVKGIGPKTAIKLLNK 210 (281)
T ss_pred CCCcccHHHHHHHHHH
Confidence 4799999999877743
No 133
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=47.71 E-value=77 Score=28.23 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=36.8
Q ss_pred HHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHH
Q 026645 45 GALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC 93 (235)
Q Consensus 45 ~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i 93 (235)
...++|.+.+|.|.++++.+++++|.++ .|++..++..+...+..+
T Consensus 12 ~~~~~l~~~g~~t~~~~~~~~~~~L~~i---~~ls~~~~~~~~~~~~~~ 57 (316)
T TIGR02239 12 ADIKKLQEAGLHTVESVAYAPKKQLLEI---KGISEAKADKILAEAAKL 57 (316)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHHH---hCCCHHHHHHHHHHHHHh
Confidence 3567788889999999999999999886 377777888777765544
No 134
>PF13592 HTH_33: Winged helix-turn helix
Probab=47.66 E-value=33 Score=22.45 Aligned_cols=17 Identities=35% Similarity=0.493 Sum_probs=14.2
Q ss_pred cchHHHHHHHHhcCcCC
Q 026645 135 VDTHVHRICNRLGWVTQ 151 (235)
Q Consensus 135 vDt~v~Rv~~Rlg~~~~ 151 (235)
-..++.|++.|+|+.-.
T Consensus 23 s~~~v~~lL~r~G~s~~ 39 (60)
T PF13592_consen 23 SPSGVYRLLKRLGFSYQ 39 (60)
T ss_pred cHHHHHHHHHHcCCccc
Confidence 57899999999998653
No 135
>PRK09482 flap endonuclease-like protein; Provisional
Probab=46.01 E-value=14 Score=32.05 Aligned_cols=17 Identities=35% Similarity=0.599 Sum_probs=13.4
Q ss_pred HcCCCCcHHHHHHHHHH
Q 026645 109 LALPGIGPKMANMVMTL 125 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~~ 125 (235)
-.+||||+|||.-++.-
T Consensus 185 pGVpGIG~KtA~~LL~~ 201 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQ 201 (256)
T ss_pred CCCCCcChHHHHHHHHH
Confidence 35789999999877654
No 136
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.82 E-value=36 Score=29.38 Aligned_cols=37 Identities=16% Similarity=0.302 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHH
Q 026645 85 NMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVM 123 (235)
Q Consensus 85 ~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il 123 (235)
.|.++...+........+... |+++||||+-+|..+.
T Consensus 169 ~i~~l~~~~~~~~~~~~~~~~--l~~~pgig~~~a~~i~ 205 (303)
T COG3547 169 EIAALDREIEARLGIGVVTDR--LASIPGIGELTAAAIA 205 (303)
T ss_pred HHHHHHHHHHHhhcccchHHH--HHhCCCccHHHHHHHH
Confidence 344444444444444444444 9999999999999888
No 137
>PF14290 DUF4370: Domain of unknown function (DUF4370)
Probab=45.67 E-value=58 Score=27.29 Aligned_cols=73 Identities=14% Similarity=0.112 Sum_probs=46.8
Q ss_pred cccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChH---HHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCC
Q 026645 37 LTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYT---RKACNMKKIAKICLTKYDGDIPSSLDELLALPG 113 (235)
Q Consensus 37 qt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~---~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~G 113 (235)
.+++..+..+++.|... +|.+|-+.-..+.+.++...+=-. .--+....+|++ +|+|+|.+-..+-+|-.+-|
T Consensus 80 ~i~Dp~i~~afKdLmAa---sW~elp~svv~~akkalSk~tdD~AGqeaL~nvfRAAeA-vEeFgG~L~tLrm~idDl~G 155 (239)
T PF14290_consen 80 AISDPEIEKAFKDLMAA---SWDELPDSVVNEAKKALSKNTDDKAGQEALKNVFRAAEA-VEEFGGILVTLRMEIDDLCG 155 (239)
T ss_pred CCCCHHHHHHHHHHHhc---chhhCCHHHHHHHHHHHhccCccchhHHHHHHHHHHHHH-HHHhhhhHHHHHHHHHHhcC
Confidence 45677888888888874 677776666777777776533211 112344555666 57799988776655555444
No 138
>PRK00254 ski2-like helicase; Provisional
Probab=44.87 E-value=64 Score=32.08 Aligned_cols=21 Identities=33% Similarity=0.545 Sum_probs=10.8
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
.++|.+++|||+++|..|..+
T Consensus 677 ~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 677 PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 344555555555555555443
No 139
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=44.58 E-value=92 Score=28.16 Aligned_cols=45 Identities=18% Similarity=0.277 Sum_probs=36.8
Q ss_pred HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHH
Q 026645 46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC 93 (235)
Q Consensus 46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i 93 (235)
..++|.+.+|.|.++++.+++.+|.++ .|++..++..+...+..+
T Consensus 40 ~i~kL~~~g~~T~~~~~~~~~~~L~~i---~~is~~~~~~~~~~~~~~ 84 (342)
T PLN03186 40 DIKKLKDAGIHTVESLAYAPKKDLLQI---KGISEAKVEKILEAASKL 84 (342)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHh---cCCCHHHHHHHHHHHHHh
Confidence 456777779999999999999999887 488888888887777554
No 140
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=44.26 E-value=57 Score=28.30 Aligned_cols=23 Identities=35% Similarity=0.556 Sum_probs=16.1
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
...++|+..+|||++.|..|--|
T Consensus 211 as~~eL~~v~gig~k~A~~I~~~ 233 (254)
T COG1948 211 ASEEELMKVKGIGEKKAREIYRF 233 (254)
T ss_pred cCHHHHHHhcCccHHHHHHHHHH
Confidence 34577777777777777777654
No 141
>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=44.20 E-value=15 Score=31.39 Aligned_cols=18 Identities=33% Similarity=0.599 Sum_probs=13.7
Q ss_pred HHcCCCCcHHHHHHHHHH
Q 026645 108 LLALPGIGPKMANMVMTL 125 (235)
Q Consensus 108 L~~l~GIG~~tA~~il~~ 125 (235)
+..+||||++||.-++.-
T Consensus 185 ipGv~GiG~ktA~~Ll~~ 202 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKE 202 (240)
T ss_pred CCCCCccCHHHHHHHHHH
Confidence 345799999999776643
No 142
>smart00475 53EXOc 5'-3' exonuclease.
Probab=43.99 E-value=16 Score=31.61 Aligned_cols=18 Identities=33% Similarity=0.599 Sum_probs=13.8
Q ss_pred HHcCCCCcHHHHHHHHHH
Q 026645 108 LLALPGIGPKMANMVMTL 125 (235)
Q Consensus 108 L~~l~GIG~~tA~~il~~ 125 (235)
+-.+||||+|||.-++.-
T Consensus 188 ipGV~GIG~KtA~~Ll~~ 205 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKE 205 (259)
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 345799999999877643
No 143
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=42.92 E-value=60 Score=29.15 Aligned_cols=30 Identities=37% Similarity=0.843 Sum_probs=23.5
Q ss_pred CCCChhhHHHHHcCCCCcH-HHHHHHHHHhc
Q 026645 98 DGDIPSSLDELLALPGIGP-KMANMVMTLGW 127 (235)
Q Consensus 98 ~g~~~~~~~~L~~l~GIG~-~tA~~il~~~~ 127 (235)
.+.+|.....|+.+||+|| +++..+.-+++
T Consensus 85 k~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi 115 (326)
T COG1796 85 KKEVPEGLEPLLKVPGLGPKKIVSLYKELGI 115 (326)
T ss_pred HHhCCcchHHHhhCCCCCcHHHHHHHHHHCc
Confidence 3467778899999999999 67777766654
No 144
>PLN02749 Uncharacterized protein At1g47420
Probab=42.91 E-value=71 Score=25.50 Aligned_cols=72 Identities=15% Similarity=0.111 Sum_probs=42.5
Q ss_pred ccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCCh---HHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCC
Q 026645 38 TKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFY---TRKACNMKKIAKICLTKYDGDIPSSLDELLALPG 113 (235)
Q Consensus 38 t~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~---~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~G 113 (235)
+++..+..+++.|... +|.+|-..-..+.++++....=- ..--+....+|++ +++|+|.+-..+-+|-.+-|
T Consensus 15 i~Dp~i~~afkdLma~---sW~elp~sv~~~~kkalsk~tddkagqeaL~nvfrAAeA-veeFgG~L~sLrmeidDl~G 89 (173)
T PLN02749 15 ISDPEILKAFKDLMAA---SWDELPDSVVNDAKKALSKNTDDKAGQEALKNVFRAAEA-VEEFGGTLVSLRMEIDDLIG 89 (173)
T ss_pred CCCHHHHHHHHHHHhc---chhhCChHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHH-HHHHhhHHHHHHHHHHHhcC
Confidence 4556677778888764 66666666666777776542111 0112344455666 56799977766655555444
No 145
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=42.72 E-value=48 Score=22.19 Aligned_cols=24 Identities=13% Similarity=0.314 Sum_probs=20.8
Q ss_pred CCCHHHHhcCCHHHHHHhhccCCC
Q 026645 55 LHTAEAIDKADEATIKDLIYPVAF 78 (235)
Q Consensus 55 ~pt~~~la~a~~e~l~~~l~~~G~ 78 (235)
|-|+++|...+.|.|.+.|..+|+
T Consensus 6 f~sa~eLe~lGldrLK~~L~a~GL 29 (60)
T PF13297_consen 6 FSSAEELEALGLDRLKSALMALGL 29 (60)
T ss_pred cCCHHHHHHhCHHHHHHHHHHcCC
Confidence 788999999999999998887776
No 146
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=41.62 E-value=37 Score=30.14 Aligned_cols=95 Identities=19% Similarity=0.235 Sum_probs=0.0
Q ss_pred HHHHHHHHhc-cccHHHHHHHHHHHHHcCCCCHHHHhcC-----CHHHHHHhhccCCCh--HHHHHHHHHHHHHHHHhcC
Q 026645 27 AVLLSALLSS-LTKDKVADGALQRLLQNGLHTAEAIDKA-----DEATIKDLIYPVAFY--TRKACNMKKIAKICLTKYD 98 (235)
Q Consensus 27 ~~lv~~iLsq-qt~~~~~~~~~~~l~~~~~pt~~~la~a-----~~e~l~~~l~~~G~~--~~Ka~~l~~~a~~i~~~~~ 98 (235)
+.+|.--... -+....+...+..|....+++++.|+.+ +.+-....+.+-||. +.=.+.=..+...++..|
T Consensus 235 ~l~i~DY~~~~e~d~~~~l~~l~~ls~~~lL~~~~i~kvlGY~~~~~~~d~~vspRGYR~l~kIpRlp~~iv~nlV~~F- 313 (349)
T COG1623 235 ELIIRDYHKEDEVDIEAVLEELQSLSDEELLDPENIAKVLGYPKTTEADDSLVSPRGYRLLNKIPRLPFAIVENLVRAF- 313 (349)
T ss_pred HHHHHHHhcCcccCHHHHHHHHHhccchhhCCHHHHHHHhCCCCcchhcccccCchhhHHHhcCcCccHHHHHHHHHHH-
Q ss_pred CCChh----hHHHHHcCCCCcHHHHHHH
Q 026645 99 GDIPS----SLDELLALPGIGPKMANMV 122 (235)
Q Consensus 99 g~~~~----~~~~L~~l~GIG~~tA~~i 122 (235)
|+++. +.+.|.++.|||..-|.+|
T Consensus 314 ~~l~~il~As~edL~~VeGIGe~rAr~i 341 (349)
T COG1623 314 GTLDGILEASAEDLDAVEGIGEARARAI 341 (349)
T ss_pred hhHHHHHHhcHhHHhhhcchhHHHHHHH
No 147
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=41.24 E-value=1e+02 Score=27.83 Aligned_cols=60 Identities=15% Similarity=0.170 Sum_probs=36.5
Q ss_pred HHHHHHhhccCCChHHHHHHHHHHHHH-----HHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcC
Q 026645 66 EATIKDLIYPVAFYTRKACNMKKIAKI-----CLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWF 128 (235)
Q Consensus 66 ~e~l~~~l~~~G~~~~Ka~~l~~~a~~-----i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~ 128 (235)
-++.+. |.++| ..-|+-|.+++.. +.+--+.+..+..+.+.++-|||.+||+-+-.-+|.
T Consensus 55 ~~ea~~-lP~iG--~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~Gfr 119 (353)
T KOG2534|consen 55 GEEAEK-LPGIG--PKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFR 119 (353)
T ss_pred HHHhcC-CCCCC--HHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhh
Confidence 344444 55555 3346666666544 100001123346788899999999999998877663
No 148
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=40.82 E-value=52 Score=31.96 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=17.7
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.+.++|.++ |||+++|..|..+
T Consensus 543 As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 543 ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred CCHHHHHHc-CCCHHHHHHHHHH
Confidence 567888888 9999888888765
No 149
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=40.19 E-value=17 Score=27.93 Aligned_cols=22 Identities=23% Similarity=0.173 Sum_probs=18.5
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
..-.|..+.|||+.+|..|+..
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~ 36 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEK 36 (122)
T ss_pred eeeeecccccccHHHHHHHHHH
Confidence 3456899999999999988865
No 150
>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=38.80 E-value=35 Score=34.06 Aligned_cols=43 Identities=21% Similarity=0.223 Sum_probs=23.5
Q ss_pred CChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 77 AFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 77 G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
|+...|++.|.+.-+ +. ....+...+|.. -||++..|.-+..+
T Consensus 124 gi~~~~~~~i~~~~~---~~--~~~~~~~~~L~~-~gi~~~~a~ki~~~ 166 (720)
T TIGR01448 124 GISKANLEKFVSQWS---QQ--GDERRLLAGLQG-LGIGIKLAQRIYKF 166 (720)
T ss_pred CCCHHHHHHHHHHHH---Hh--HHHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 555555555544332 21 113334444444 79999988877654
No 151
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=38.66 E-value=48 Score=29.31 Aligned_cols=14 Identities=43% Similarity=0.743 Sum_probs=11.6
Q ss_pred CCCCcHHHHHHHHH
Q 026645 111 LPGIGPKMANMVMT 124 (235)
Q Consensus 111 l~GIG~~tA~~il~ 124 (235)
++|||++||--++.
T Consensus 203 V~GIG~ktA~~Ll~ 216 (310)
T COG0258 203 VKGIGPKTALKLLQ 216 (310)
T ss_pred CCCcCHHHHHHHHH
Confidence 89999999976653
No 152
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=38.34 E-value=47 Score=26.00 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=28.5
Q ss_pred HHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcC
Q 026645 58 AEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYD 98 (235)
Q Consensus 58 ~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~ 98 (235)
|++|+ ++|.+++..-||..| ++.|+++.+..+++|.
T Consensus 12 p~~Ll----~elD~~i~~rg~~sR-SE~IrdAir~yl~e~~ 47 (136)
T COG0864 12 PEELL----EELDELIEERGYSSR-SELIRDALREYLEEYR 47 (136)
T ss_pred cHHHH----HHHHHHHHHcCCCcH-HHHHHHHHHHHHHHhh
Confidence 55553 677778887898776 9999999999988754
No 153
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=38.22 E-value=74 Score=31.69 Aligned_cols=23 Identities=35% Similarity=0.549 Sum_probs=19.0
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
...++|.+++|||++.|..|+.+
T Consensus 666 AS~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 666 AGEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred cCHHHHHhcCCcCHHHHHHHHHH
Confidence 45677899999999999988755
No 154
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=37.85 E-value=4e+02 Score=26.54 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=11.2
Q ss_pred HHHHHHHhCCcccHHHHHHHHHHHH
Q 026645 164 TREALQRWLPKEEWVRINPLLVGFG 188 (235)
Q Consensus 164 ~~~~l~~~~p~~~~~~~~~~l~~~G 188 (235)
+...+..|+....-..+-..|...|
T Consensus 555 vA~si~~ff~~~~~~~li~~L~~~g 579 (667)
T COG0272 555 VARSIIEFFANEENRELIDELLAAG 579 (667)
T ss_pred HHHHHHHHHcCHHHHHHHHHHHHcC
Confidence 3344445554433344444455444
No 155
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=37.76 E-value=32 Score=28.41 Aligned_cols=25 Identities=36% Similarity=0.490 Sum_probs=20.3
Q ss_pred ChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 101 IPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 101 ~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+..-.-.|.-|||||.|+...||--
T Consensus 125 It~RLH~LELLpGiGkK~m~~ILeE 149 (202)
T COG1491 125 ITLRLHQLELLPGIGKKTMWAILEE 149 (202)
T ss_pred chHHHHHHHhcccccHHHHHHHHHH
Confidence 3345677889999999999999865
No 156
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=36.84 E-value=86 Score=20.71 Aligned_cols=36 Identities=11% Similarity=0.133 Sum_probs=28.0
Q ss_pred CCCC-HHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHH
Q 026645 54 GLHT-AEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKIC 93 (235)
Q Consensus 54 ~~pt-~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i 93 (235)
.|++ |++|...+..+|.+. |..-+--+||....+.+
T Consensus 18 kf~~~w~~lf~~~s~~LK~~----GIp~r~RryiL~~~ek~ 54 (57)
T PF09597_consen 18 KFESDWEKLFTTSSKQLKEL----GIPVRQRRYILRWREKY 54 (57)
T ss_pred HHHHHHHHHHhcCHHHHHHC----CCCHHHHHHHHHHHHHH
Confidence 4778 999999999998887 88765567787766654
No 157
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=36.81 E-value=20 Score=27.49 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=17.9
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
.-.|..+.|||+.+|..|+..
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~ 36 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAA 36 (122)
T ss_pred EeeecccccccHHHHHHHHHH
Confidence 456899999999999988855
No 158
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=36.06 E-value=26 Score=26.84 Aligned_cols=28 Identities=29% Similarity=0.379 Sum_probs=21.2
Q ss_pred CCChhh---HHHHHcCCCCcHHHHHHHHHHh
Q 026645 99 GDIPSS---LDELLALPGIGPKMANMVMTLG 126 (235)
Q Consensus 99 g~~~~~---~~~L~~l~GIG~~tA~~il~~~ 126 (235)
-++|.. .=.|+.|.|||..+|..|+.-+
T Consensus 7 vdip~~K~v~iALt~IyGIG~~~a~~I~~~~ 37 (121)
T COG0099 7 VDIPGNKRVVIALTYIYGIGRRRAKEICKKA 37 (121)
T ss_pred cCCCCCceEeehhhhhccccHHHHHHHHHHc
Confidence 355543 3468999999999999998653
No 159
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=35.97 E-value=52 Score=28.56 Aligned_cols=22 Identities=41% Similarity=0.703 Sum_probs=17.6
Q ss_pred hHHHHHcCCCCcHHHHHHHHHH
Q 026645 104 SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~ 125 (235)
....|.++||||+..|.-++..
T Consensus 180 q~~il~s~pgig~~~a~~ll~~ 201 (254)
T COG1948 180 QLYILESIPGIGPKLAERLLKK 201 (254)
T ss_pred HHHHHHcCCCccHHHHHHHHHH
Confidence 3456779999999999888743
No 160
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=34.43 E-value=23 Score=28.38 Aligned_cols=27 Identities=26% Similarity=0.372 Sum_probs=20.8
Q ss_pred CCChh---hHHHHHcCCCCcHHHHHHHHHH
Q 026645 99 GDIPS---SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 99 g~~~~---~~~~L~~l~GIG~~tA~~il~~ 125 (235)
-++|. ..-.|..|.|||+.+|..|+.-
T Consensus 20 ~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~ 49 (154)
T PTZ00134 20 TNVDGKRKVPYALTAIKGIGRRFAYLVCKK 49 (154)
T ss_pred ccCCCCCEEEEeecccccccHHHHHHHHHH
Confidence 45554 3457899999999999988754
No 161
>PRK00254 ski2-like helicase; Provisional
Probab=34.20 E-value=75 Score=31.58 Aligned_cols=42 Identities=14% Similarity=0.143 Sum_probs=31.5
Q ss_pred HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026645 47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91 (235)
Q Consensus 47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~ 91 (235)
.++|.+.||.|+++|..++.++|.++ .|+....|+.|++...
T Consensus 658 ~~~l~~~g~~s~~~i~~a~~~el~~~---~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 658 ARALYNAGFRSIEDIVNAKPSELLKV---EGIGAKIVEGIFKHLG 699 (720)
T ss_pred HHHHHHccCCCHHHHHhCCHHHHhcC---CCCCHHHHHHHHHHhc
Confidence 34444547999999999999999776 2666677888877654
No 162
>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=34.15 E-value=22 Score=28.10 Aligned_cols=21 Identities=24% Similarity=0.359 Sum_probs=17.7
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
.-.|.++.|||+.+|..|+..
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~ 40 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARK 40 (144)
T ss_pred EEeecceeccCHHHHHHHHHH
Confidence 456899999999999988754
No 163
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=33.88 E-value=22 Score=29.36 Aligned_cols=15 Identities=27% Similarity=0.735 Sum_probs=13.7
Q ss_pred CCCCCCCCcccccCc
Q 026645 195 LRPRCGMCTVSEYCP 209 (235)
Q Consensus 195 ~~P~C~~Cpl~~~C~ 209 (235)
.+|+|..|+++..|.
T Consensus 173 ~~~~C~~C~y~~iC~ 187 (190)
T COG1468 173 KKKKCKKCAYREICF 187 (190)
T ss_pred CCCcCCCCCcceecc
Confidence 579999999999996
No 164
>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=33.81 E-value=21 Score=26.93 Aligned_cols=21 Identities=24% Similarity=0.213 Sum_probs=17.8
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
.-.|.++.|||+.+|..|+..
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~ 34 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEK 34 (113)
T ss_pred eeeeeeeecccHHHHHHHHHH
Confidence 456889999999999988755
No 165
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=32.98 E-value=54 Score=26.57 Aligned_cols=74 Identities=7% Similarity=-0.061 Sum_probs=49.5
Q ss_pred HHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHH
Q 026645 67 ATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICN 144 (235)
Q Consensus 67 e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~ 144 (235)
+++.+++...+. +...|..+.+.+.+.||---++..+.+...=||-+--+.-+..|-- ....-|+-.|+.||+.
T Consensus 22 ~~i~~ii~~~~~---~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVatFY~-~f~~~P~Gk~~I~VC~ 95 (169)
T PRK07571 22 KVLEATMKRNQY---RQDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYH-LFSLKPSGEHTCVVCT 95 (169)
T ss_pred HHHHHHHHHcCC---CHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHHHcc-ccCcCCCCCEEEEEcC
Confidence 345556554443 5678999999999988665567888888888998887777777721 1112255666655543
No 166
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=32.33 E-value=96 Score=30.17 Aligned_cols=31 Identities=26% Similarity=0.264 Sum_probs=21.7
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHH
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKK 88 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~ 88 (235)
.|.|.+.|..|+.|||.++ |.+...|+.|.+
T Consensus 533 ~Fgs~~~ik~As~eeL~~v----gi~~~~A~~I~~ 563 (567)
T PRK14667 533 NFKTLYDFLKADDEELKKL----GIPPSVKQEVKK 563 (567)
T ss_pred HhCCHHHHHhCCHHHHHHc----CCCHHHHHHHHH
Confidence 4778888888888888775 555555666544
No 167
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=31.89 E-value=2.5e+02 Score=26.67 Aligned_cols=71 Identities=20% Similarity=0.273 Sum_probs=49.7
Q ss_pred HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhh-HHHHHcCCCCcHHHHH
Q 026645 47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSS-LDELLALPGIGPKMAN 120 (235)
Q Consensus 47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~-~~~L~~l~GIG~~tA~ 120 (235)
...|...+|-+.++++.++.++|.++ -|+....+..|.+.++............. -+.|.+++|+....+.
T Consensus 369 ~~~l~~~g~~~~e~~~~~~~~el~~i---~~~~ee~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 440 (470)
T PRK09202 369 AQLLVEEGFSSLEELAYVPVEELLEI---EGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAF 440 (470)
T ss_pred HHHHHHcCcccHHHHhcCCHHHHhhc---cCCCHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhccccCHHHHH
Confidence 45555568999999999999999744 36777777788777776554322222222 3678889999887775
No 168
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=31.68 E-value=29 Score=27.57 Aligned_cols=27 Identities=22% Similarity=0.315 Sum_probs=20.9
Q ss_pred CCChh---hHHHHHcCCCCcHHHHHHHHHH
Q 026645 99 GDIPS---SLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 99 g~~~~---~~~~L~~l~GIG~~tA~~il~~ 125 (235)
-++|. ..-.|..+.|||+.+|..|+.-
T Consensus 15 ~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~ 44 (149)
T PRK04053 15 TDLDGTKPVEYALTGIKGIGRRTARAIARK 44 (149)
T ss_pred ccCCCCCEEeeeccccccccHHHHHHHHHH
Confidence 45654 3567899999999999988754
No 169
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=31.66 E-value=30 Score=28.42 Aligned_cols=21 Identities=38% Similarity=0.520 Sum_probs=15.4
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
.-.|-=|||||.|+...||--
T Consensus 115 lH~LeLLPGIGKK~m~~ILeE 135 (181)
T PF04919_consen 115 LHSLELLPGIGKKTMWKILEE 135 (181)
T ss_dssp SBGGGGSTT--HHHHHHHHHH
T ss_pred HHHHhhcccccHHHHHHHHHH
Confidence 456778999999999999853
No 170
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=31.65 E-value=1.4e+02 Score=23.23 Aligned_cols=53 Identities=13% Similarity=0.134 Sum_probs=34.6
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHH
Q 026645 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNM 86 (235)
Q Consensus 26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l 86 (235)
+..++..+=..+.+. +.+.. ...|.+++.+++++++.+++...|++.-=-.+|
T Consensus 69 l~~WL~vVgl~~~~i-------~~i~~-~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL 121 (129)
T PF13543_consen 69 LRQWLRVVGLRPESI-------QAILS-KVLTLEALLEMSDEELKEILNRCGAREEECRRL 121 (129)
T ss_pred HHHHhhhcCCCHHHH-------HHHHH-hhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHH
Confidence 556666553333332 22333 367999999999999999999999864333333
No 171
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=31.40 E-value=63 Score=31.57 Aligned_cols=18 Identities=39% Similarity=0.741 Sum_probs=8.5
Q ss_pred HHHHcCCCCcHHHHHHHH
Q 026645 106 DELLALPGIGPKMANMVM 123 (235)
Q Consensus 106 ~~L~~l~GIG~~tA~~il 123 (235)
++|.++||||+++|..+.
T Consensus 575 eeL~~v~Gig~~~A~~I~ 592 (598)
T PRK00558 575 EELAKVPGISKKLAEAIY 592 (598)
T ss_pred HHHhhcCCcCHHHHHHHH
Confidence 344444444444444443
No 172
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=31.38 E-value=76 Score=31.57 Aligned_cols=26 Identities=8% Similarity=0.019 Sum_probs=21.1
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHHhcC
Q 026645 103 SSLDELLALPGIGPKMANMVMTLGWF 128 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~~~~ 128 (235)
.+.++|.+++|||.++|..|+--+-.
T Consensus 637 As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 637 ATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 56788889999999999888876654
No 173
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=29.47 E-value=98 Score=30.16 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=20.0
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.+.++|.++||||.++|..|..+
T Consensus 543 As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 543 LNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHH
Confidence 46789999999999999998766
No 174
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=29.42 E-value=1.4e+02 Score=27.41 Aligned_cols=48 Identities=13% Similarity=0.115 Sum_probs=39.9
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCC-HHHHhcCCHHHHHHh
Q 026645 24 RRFAVLLSALLSSLTKDKVADGALQRLLQNGLHT-AEAIDKADEATIKDL 72 (235)
Q Consensus 24 ~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt-~~~la~a~~e~l~~~ 72 (235)
=|.+.++++.+.-....+.|...|.+|.++ |.| .+-|.+++.|+|.++
T Consensus 297 iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~-fG~E~~iL~~~~~eel~~~ 345 (374)
T TIGR00375 297 IPLAEVIGVGPKKGIFTKAVQSLWEKLKKA-FGTEIAVLHEAAEEDLARV 345 (374)
T ss_pred CCHHHHHhhhcCCCCccHHHHHHHHHHHHH-hccHHHHHhcCCHHHHHHH
Confidence 478889999988777889999999999995 755 677778999988765
No 175
>TIGR00372 cas4 CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Probab=29.03 E-value=31 Score=27.36 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=12.6
Q ss_pred CCCCCCCcccccCc
Q 026645 196 RPRCGMCTVSEYCP 209 (235)
Q Consensus 196 ~P~C~~Cpl~~~C~ 209 (235)
++.|..|+++..|.
T Consensus 164 ~~~C~~C~y~~~C~ 177 (178)
T TIGR00372 164 SRKCKFCPYREICL 177 (178)
T ss_pred CCcCCCCCCccccC
Confidence 57899999999996
No 176
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=28.83 E-value=33 Score=26.90 Aligned_cols=14 Identities=29% Similarity=0.895 Sum_probs=12.6
Q ss_pred CCCCCCCcccccCc
Q 026645 196 RPRCGMCTVSEYCP 209 (235)
Q Consensus 196 ~P~C~~Cpl~~~C~ 209 (235)
+++|..|.+++.|.
T Consensus 148 ~~~C~~C~y~~~C~ 161 (162)
T PF01930_consen 148 SKKCRRCSYREFCW 161 (162)
T ss_pred CCCCCCCCCcCcCC
Confidence 47899999999996
No 177
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=28.41 E-value=49 Score=33.60 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=19.5
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
+..+.|.+|||||++.|..+|.-
T Consensus 754 ~~q~~L~~lPgI~~~~a~~ll~~ 776 (814)
T TIGR00596 754 GPQDFLLKLPGVTKKNYRNLRKK 776 (814)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHH
Confidence 45677999999999999988865
No 178
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=28.24 E-value=1.2e+02 Score=30.16 Aligned_cols=36 Identities=11% Similarity=0.094 Sum_probs=23.5
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
.|.|.+.|..|+.+||.++ -|+....|..|..+|..
T Consensus 627 ~FgS~~~i~~As~eel~~v---~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 627 HFGSFRSLQSATPQDIATA---IHIPLTQAHTILHAATR 662 (691)
T ss_pred HhcCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHhhc
Confidence 3677777777777777665 25555666666666554
No 179
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=28.18 E-value=1.1e+02 Score=29.74 Aligned_cols=35 Identities=26% Similarity=0.248 Sum_probs=27.8
Q ss_pred CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHH
Q 026645 54 GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAK 91 (235)
Q Consensus 54 ~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~ 91 (235)
.|.|.+.|..|+.|||.++ -|++...|+.|.+...
T Consensus 533 ~Fgs~~~I~~As~eeL~~v---~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 533 SLGTYKDILLLNEDEIAEK---MKINIKMAKKIKKFAE 567 (574)
T ss_pred HhCCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHHH
Confidence 4999999999999999776 3777777777766543
No 180
>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=28.08 E-value=42 Score=23.89 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=15.5
Q ss_pred HHHHcCCCCcHHHHHHHHHH
Q 026645 106 DELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 106 ~~L~~l~GIG~~tA~~il~~ 125 (235)
--|..++|||..+|..|+.-
T Consensus 27 ~gl~~Ikglg~~~a~~I~~~ 46 (90)
T PF14579_consen 27 LGLSAIKGLGEEVAEKIVEE 46 (90)
T ss_dssp -BGGGSTTS-HHHHHHHHHH
T ss_pred ehHhhcCCCCHHHHHHHHHh
Confidence 34889999999999988854
No 181
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=28.05 E-value=30 Score=25.82 Aligned_cols=16 Identities=25% Similarity=0.791 Sum_probs=13.9
Q ss_pred CCCCCCCcccccCccc
Q 026645 196 RPRCGMCTVSEYCPSA 211 (235)
Q Consensus 196 ~P~C~~Cpl~~~C~~~ 211 (235)
...|..||+++.|...
T Consensus 30 ~~~C~~Cp~r~~C~~~ 45 (125)
T PF13751_consen 30 KEDCKNCPLREQCTKS 45 (125)
T ss_pred chhccCCCccccCCCc
Confidence 4789999999999865
No 182
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=27.87 E-value=67 Score=26.40 Aligned_cols=42 Identities=14% Similarity=0.214 Sum_probs=30.4
Q ss_pred HcCCCCcHHHHHHHHHHhc-CCcceeecchHHHHHHHHhcCcCC
Q 026645 109 LALPGIGPKMANMVMTLGW-FNVQGICVDTHVHRICNRLGWVTQ 151 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~~~~-~~~~~~pvDt~v~Rv~~Rlg~~~~ 151 (235)
..+||||..|.--++.-.+ .. ..+-..+-+..++.+.|++..
T Consensus 10 tGVpGvGKTTVl~~~~~~l~~~-~ivNyG~~Mle~A~k~glve~ 52 (189)
T COG2019 10 TGVPGVGKTTVLKIALKELVKH-KIVNYGDLMLEIAKKKGLVEH 52 (189)
T ss_pred EcCCCCChHHHHHHHHHHHhhc-eeeeHhHHHHHHHHHhCCccc
Confidence 4689999999766665444 22 234467788999999999864
No 183
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=27.35 E-value=46 Score=29.42 Aligned_cols=25 Identities=28% Similarity=0.284 Sum_probs=19.3
Q ss_pred hHHHHHcCCCCcHHHHHHHHHHhcC
Q 026645 104 SLDELLALPGIGPKMANMVMTLGWF 128 (235)
Q Consensus 104 ~~~~L~~l~GIG~~tA~~il~~~~~ 128 (235)
..++|.++.|+++..|..+...+-+
T Consensus 37 ~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 37 SPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred CHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 4678888889998888888776544
No 184
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=27.16 E-value=40 Score=20.75 Aligned_cols=15 Identities=40% Similarity=0.412 Sum_probs=12.7
Q ss_pred ecchHHHHHHHHhcC
Q 026645 134 CVDTHVHRICNRLGW 148 (235)
Q Consensus 134 pvDt~v~Rv~~Rlg~ 148 (235)
+-||||+|++..++-
T Consensus 17 eddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 17 EDDTHVHRVLRKYYT 31 (41)
T ss_pred cchhHHHHHHHHHHH
Confidence 579999999998864
No 185
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=26.36 E-value=1.2e+02 Score=20.47 Aligned_cols=28 Identities=36% Similarity=0.647 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHH
Q 026645 84 CNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMA 119 (235)
Q Consensus 84 ~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA 119 (235)
..|.++|+. .|.+.+.|.+++|+|.+..
T Consensus 33 ~~L~~ia~~--------~P~~~~~L~~i~g~~~~~~ 60 (81)
T smart00341 33 ETLIKMAAA--------LPTNVSELLAIDGVGEEKA 60 (81)
T ss_pred HHHHHHHHH--------CCCCHHHHhcCCCCCHHHH
Confidence 455555554 4778999999999997654
No 186
>PHA00439 exonuclease
Probab=26.29 E-value=42 Score=29.68 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=13.4
Q ss_pred HHcCCCCcHHHHHHHHHH
Q 026645 108 LLALPGIGPKMANMVMTL 125 (235)
Q Consensus 108 L~~l~GIG~~tA~~il~~ 125 (235)
+-.+|||| |||.-+|.-
T Consensus 190 IPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 190 YSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCCCCcC-HHHHHHHhC
Confidence 33579999 999988764
No 187
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=25.97 E-value=99 Score=19.28 Aligned_cols=34 Identities=18% Similarity=0.274 Sum_probs=24.9
Q ss_pred HHhcCCHHHHHHhhccCCCh------HHHHHHHHHHHHHH
Q 026645 60 AIDKADEATIKDLIYPVAFY------TRKACNMKKIAKIC 93 (235)
Q Consensus 60 ~la~a~~e~l~~~l~~~G~~------~~Ka~~l~~~a~~i 93 (235)
++..++.+||.+-+...|+. ..|.-|++.+.+.+
T Consensus 2 d~~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 2 DVDRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred chhHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 34567889999999988985 35567777776654
No 188
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=25.81 E-value=49 Score=21.96 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHhcCCCC
Q 026645 82 KACNMKKIAKICLTKYDGDI 101 (235)
Q Consensus 82 Ka~~l~~~a~~i~~~~~g~~ 101 (235)
|..+|+.+|+.|+|+|...+
T Consensus 4 r~k~IKr~a~~lieky~~~f 23 (58)
T PRK01151 4 RPKYIKRTAEELLEKYPDLF 23 (58)
T ss_pred chHHHHHHHHHHHHHhHHHh
Confidence 57899999999999875533
No 189
>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=25.11 E-value=47 Score=29.36 Aligned_cols=17 Identities=35% Similarity=0.606 Sum_probs=13.5
Q ss_pred HcCCCCcHHHHHHHHHH
Q 026645 109 LALPGIGPKMANMVMTL 125 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~~ 125 (235)
..+||||++||--++.-
T Consensus 226 ~gv~giG~k~A~~li~~ 242 (316)
T cd00128 226 EGIPGIGPVTALKLIKK 242 (316)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 36899999999777644
No 190
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=24.81 E-value=52 Score=32.33 Aligned_cols=21 Identities=33% Similarity=0.672 Sum_probs=17.3
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
...|.++||||++++..+|..
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~ 571 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKH 571 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 456889999999999887754
No 191
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.65 E-value=2.8e+02 Score=25.24 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=39.1
Q ss_pred CChHHHHHHHHHhccccHHHHHHHHHHHHHcCCCC-HHHHhcCCHHHHHHh
Q 026645 23 ERRFAVLLSALLSSLTKDKVADGALQRLLQNGLHT-AEAIDKADEATIKDL 72 (235)
Q Consensus 23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt-~~~la~a~~e~l~~~ 72 (235)
.-|.+.+++.-+.--++.+.|..+|++|.+. |.| .+.|-+++.|+|..+
T Consensus 303 liPLaeIi~~~~g~gi~tK~V~~~we~lv~~-FGtEi~vLi~a~~e~La~V 352 (403)
T COG1379 303 LIPLAEIISMALGKGITTKAVKRTWERLVRA-FGTEIDVLIDAPIEELARV 352 (403)
T ss_pred cccHHHHHHHHhccceechhHHHHHHHHHHH-hcchhhhHhcCCHHHHhhh
Confidence 3467777877788888889999999999994 765 677778888888666
No 192
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=24.63 E-value=58 Score=32.01 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=17.1
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
...|..+||||+++|..++..
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~ 588 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEH 588 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHH
Confidence 456889999999999877654
No 193
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=24.56 E-value=1.3e+02 Score=30.70 Aligned_cols=41 Identities=10% Similarity=0.228 Sum_probs=30.9
Q ss_pred HHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHH
Q 026645 47 LQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKI 92 (235)
Q Consensus 47 ~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~ 92 (235)
+.+|.. .|.|.++|++++.++|.++ +| ...+|+.|.++...
T Consensus 770 a~~ll~-~f~si~~l~~as~eeL~~~---iG-~~~~A~~i~~fl~~ 810 (814)
T TIGR00596 770 YRNLRK-KVKSIRELAKLSQNELNEL---IG-DEEAAKRLYDFLRT 810 (814)
T ss_pred HHHHHH-HcCCHHHHHhCCHHHHHHH---hC-CHHHHHHHHHHhcc
Confidence 345555 4999999999999999986 46 45668888876543
No 194
>PRK03980 flap endonuclease-1; Provisional
Probab=24.52 E-value=49 Score=29.23 Aligned_cols=15 Identities=40% Similarity=0.722 Sum_probs=12.5
Q ss_pred cCCCCcHHHHHHHHH
Q 026645 110 ALPGIGPKMANMVMT 124 (235)
Q Consensus 110 ~l~GIG~~tA~~il~ 124 (235)
.+||||++||--++.
T Consensus 193 GI~GIG~ktA~kLi~ 207 (292)
T PRK03980 193 GIKGIGPKTALKLIK 207 (292)
T ss_pred CCCCccHHHHHHHHH
Confidence 689999999977763
No 195
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=24.51 E-value=74 Score=23.69 Aligned_cols=38 Identities=26% Similarity=0.322 Sum_probs=23.0
Q ss_pred CCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHH
Q 026645 76 VAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKM 118 (235)
Q Consensus 76 ~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~t 118 (235)
.|+..|||..|.+..+. .+|.+ ..++.|...-.+|+++
T Consensus 56 ~GLGPRKA~~Ll~~l~~----~g~~l-~~R~~Lv~~~~~g~~V 93 (104)
T PF14635_consen 56 CGLGPRKAQALLKALKQ----NGGRL-ENRSQLVTKCLMGPKV 93 (104)
T ss_dssp TT--HHHHHHHHHHHHH----C-S-----TTHHHHTTSS-HHH
T ss_pred cCCChHHHHHHHHHHHH----cCCcc-ccHHHHHhcCCCCCeE
Confidence 57778999999887664 23444 5678888878888865
No 196
>KOG3835 consensus Transcriptional corepressor NAB1 [Transcription]
Probab=23.93 E-value=1.1e+02 Score=28.16 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCCh
Q 026645 40 DKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFY 79 (235)
Q Consensus 40 ~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~ 79 (235)
-++-..+|..|++.|-.+..+|.+++++|+.++..-+|+-
T Consensus 20 kANLlsYyd~FIqQGGDDvqQlceagEeEFLEIMaLVGMa 59 (495)
T KOG3835|consen 20 KANLLSYYDVFIQQGGDDVQQLCEAGEEEFLEIMALVGMA 59 (495)
T ss_pred HhhHHHHHHHHHHhcchHHHHHHHhhHHHHHHHHHHhccC
Confidence 4566778999998888899999999999999999999985
No 197
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=23.92 E-value=95 Score=25.17 Aligned_cols=73 Identities=21% Similarity=0.415 Sum_probs=47.5
Q ss_pred CcHHHHHHHHHHhcCCcceeecchHHHHHHHHhcCcCCCCCCCCCCCHHHHHHHHHHhCCc--------ccHHHH--HHH
Q 026645 114 IGPKMANMVMTLGWFNVQGICVDTHVHRICNRLGWVTQPGTKQKTSSPEQTREALQRWLPK--------EEWVRI--NPL 183 (235)
Q Consensus 114 IG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg~~~~~~~~~~~~~~~~~~~~l~~~~p~--------~~~~~~--~~~ 183 (235)
.+.|.|.+|..-+++. + |. -+-||+. +..++...+.+++|. -.|..| .+.
T Consensus 83 ~~~wlA~iiA~~~l~~-~------HL---WqDLGL~----------~R~eLs~Lm~r~Fp~Laa~N~~~MrWKKFfYrql 142 (167)
T PF04891_consen 83 EARWLAHIIARACLGP-D------HL---WQDLGLR----------SRAELSALMRRHFPPLAARNTRNMRWKKFFYRQL 142 (167)
T ss_pred HHHHHHHHHHHHHcCC-C------cc---HHhcCCC----------CHHHHHHHHHHHhHHHHHhccCCCcHHHHHHHHH
Confidence 5567888888777764 2 32 2334542 345667777777774 125443 344
Q ss_pred HHHHHhhhcCCCCCCCCCCcccccC
Q 026645 184 LVGFGQTICTPLRPRCGMCTVSEYC 208 (235)
Q Consensus 184 l~~~G~~iC~~~~P~C~~Cpl~~~C 208 (235)
--.-|-.+|++ |.|+.|.=...|
T Consensus 143 Ce~eG~~~C~a--PsC~~C~D~~~C 165 (167)
T PF04891_consen 143 CEREGLYLCRA--PSCEECSDYAVC 165 (167)
T ss_pred HHHcCCCcCCC--CCCCCcCCHhhc
Confidence 56778889986 999999877777
No 198
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=23.71 E-value=94 Score=22.92 Aligned_cols=48 Identities=13% Similarity=0.146 Sum_probs=28.9
Q ss_pred HHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHHH
Q 026645 46 ALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICLT 95 (235)
Q Consensus 46 ~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~ 95 (235)
....+.+ ...|.++|..++...+..+++.++...- +..|+.....+.+
T Consensus 11 la~~ir~-~~f~F~dl~~l~~~~l~~ll~~v~~~~l-a~ALkga~~e~~~ 58 (110)
T PF01706_consen 11 LAEKIRE-KMFTFDDLVRLDDRDLQKLLREVDPDDL-ALALKGASEELRE 58 (110)
T ss_dssp HHHHHHH-HCS-GGGGGGS-HHHHHHHHTTS-HHHH-HHHHCTS-HHHHH
T ss_pred HHHHHHH-HhhhHHHHHcCCHHHHHHHHHHCCHhHH-HHHHccCCHHHHH
Confidence 3445555 4789999999999999999998875432 4444444344333
No 199
>PF14199 DUF4317: Domain of unknown function (DUF4317)
Probab=23.17 E-value=1.5e+02 Score=27.32 Aligned_cols=71 Identities=13% Similarity=0.142 Sum_probs=52.6
Q ss_pred CChHHHHHHHHHhccccHHHHHHHHHHHHHc----CCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026645 23 ERRFAVLLSALLSSLTKDKVADGALQRLLQN----GLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL 94 (235)
Q Consensus 23 ~~~f~~lv~~iLsqqt~~~~~~~~~~~l~~~----~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~ 94 (235)
..-|+.+|...++-....+.+..++.+|-+. .--+++. ..++..+++.+|...|....+...+...-..+.
T Consensus 236 Ke~F~~iv~~~lged~~~e~v~~i~E~l~~~ie~~~e~~~Ep-~~L~~~~v~~iL~~sGv~~e~~e~~e~~y~~~~ 310 (371)
T PF14199_consen 236 KETFQEIVKEVLGEDCDYEVVQNIHEELNEMIEEHKEEEPEP-PTLDKKDVKRILEESGVEEEKLEKFEKAYEEVF 310 (371)
T ss_pred HHHHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhccCCCCC-cccCHHHHHHHHHHcCCchHHHHHHHHHHHHHh
Confidence 3569999999999999999888888888652 1013333 457889999999999998776666655544443
No 200
>PF02467 Whib: Transcription factor WhiB; InterPro: IPR003482 WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. The process of mycelium formation in Streptomyces, which occurs in response to nutrient limitation, is controlled by a number of whi genes, named for the white colour of aerial hyphae when mutations occur in these genes. The normal colour is grey. The exact role of WhiB is not clear, but a mutation in the gene results in white, tightly coiled aerial hyphae.
Probab=23.16 E-value=14 Score=25.13 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=11.9
Q ss_pred CCCCCcccccCcccc
Q 026645 198 RCGMCTVSEYCPSAF 212 (235)
Q Consensus 198 ~C~~Cpl~~~C~~~~ 212 (235)
.|..||++..|..+.
T Consensus 31 iC~~CPVr~~C~~~A 45 (66)
T PF02467_consen 31 ICARCPVRAECLEYA 45 (66)
T ss_pred HHcCChhHHHHHHHH
Confidence 367799999998764
No 201
>PF11842 DUF3362: Domain of unknown function (DUF3362); InterPro: IPR024560 This domain tends to occur to the C terminus of a radical SAM domain (PF04055 from PFAM) in members of the uncharacterised protein family UPF0313. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=23.15 E-value=1.6e+02 Score=23.49 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=33.8
Q ss_pred HHHHHHHHHhCCcccHHHHHHHHHHHHhhhcCCCCCCCCCCcc
Q 026645 162 EQTREALQRWLPKEEWVRINPLLVGFGQTICTPLRPRCGMCTV 204 (235)
Q Consensus 162 ~~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~Cpl 204 (235)
..++.+|..+-.++.|..+..+|...|+.-=.-..|+|-.=|-
T Consensus 44 r~lqkAll~Y~~PeN~~lvreAL~~~GR~DLIG~g~~cLip~~ 86 (150)
T PF11842_consen 44 RRLQKALLRYHDPENWPLVREALKKMGREDLIGNGPKCLIPPE 86 (150)
T ss_pred HHHHHHHHhhcChhhHHHHHHHHHHhhhhhcccCCCCccccCC
Confidence 4577778788777899999999999999977666677765443
No 202
>COG1701 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.91 E-value=3.2e+02 Score=23.29 Aligned_cols=47 Identities=9% Similarity=0.136 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhccCCChHHHHHHHHHHHHHHH
Q 026645 40 DKVADGALQRLLQNGLHTAEAIDKADEATIKDLIYPVAFYTRKACNMKKIAKICL 94 (235)
Q Consensus 40 ~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~~~G~~~~Ka~~l~~~a~~i~ 94 (235)
++++.+++.+|.+. ..++.+.+.|+++++++ +|.+. +.|.+....|.
T Consensus 197 VDnivRA~p~li~~----~~em~~~~reel~~iv~--~ydN~--~~l~eal~~I~ 243 (256)
T COG1701 197 VDNIVRAVPNLIEF----VKEMKNASREELEEIVE--NYDNK--EVLAEALKHIA 243 (256)
T ss_pred eHHHHHHHHHHHHH----HHHHhccCHHHHHHHHH--hhccH--HHHHHHHHHHH
Confidence 67788888888874 67888899999999987 45443 34444444443
No 203
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=22.67 E-value=1.6e+02 Score=29.11 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=13.6
Q ss_pred hhHHHHHcCCCCcHHHHHHHHHH
Q 026645 103 SSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 103 ~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
.+.++|.++ ||.++|..|..+
T Consensus 581 As~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 581 ATETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred CCHHHHHHH--hCHHHHHHHHHH
Confidence 345566666 777777777655
No 204
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=22.58 E-value=3.8e+02 Score=20.93 Aligned_cols=71 Identities=18% Similarity=0.221 Sum_probs=43.2
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHcCCCCHHHHhcCCHHHHHHhhc----cCCChHHHHHHHHHHHHHHHHhcC
Q 026645 26 FAVLLSALLSSLTKDKVADGALQRLLQNGLHTAEAIDKADEATIKDLIY----PVAFYTRKACNMKKIAKICLTKYD 98 (235)
Q Consensus 26 f~~lv~~iLsqqt~~~~~~~~~~~l~~~~~pt~~~la~a~~e~l~~~l~----~~G~~~~Ka~~l~~~a~~i~~~~~ 98 (235)
|...+...|....+.+.+..++..|..+ ----.+|+.-++++|..+|+ .++-++- ...+.+++..+.+-|+
T Consensus 34 y~~ALD~aL~~~~~p~~~vavl~EL~~R-~~L~~AL~~Rde~~L~piL~Fl~k~i~~pr~-~~~l~~v~~~ildiY~ 108 (148)
T PF09384_consen 34 YKKALDAALVKNKSPEVVVAVLEELIRR-GALRAALAGRDEESLEPILKFLIKNITDPRY-TRILVDVANIILDIYS 108 (148)
T ss_pred HHHHHHHHHhcCCChHHHHHHHHHHHHc-cHHHHHHHhCCHHHHHHHHHHHHHhCCCccc-HHHHHHHHHHHHHHHH
Confidence 5555556664555567777788888775 33456677777777777653 2332222 5566666666666554
No 205
>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=22.26 E-value=63 Score=31.42 Aligned_cols=21 Identities=29% Similarity=0.600 Sum_probs=17.0
Q ss_pred HHHHHcCCCCcHHHHHHHHHH
Q 026645 105 LDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~ 125 (235)
...|..+||||+++...+|..
T Consensus 540 ~S~Ld~I~GIG~kr~~~LL~~ 560 (574)
T TIGR00194 540 QSPLLKIPGVGEKRVQKLLKY 560 (574)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 356889999999999877643
No 206
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=22.08 E-value=1.2e+02 Score=29.63 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcCC---CChhhHHHHHcCCCCcHHHHHHHHHH
Q 026645 87 KKIAKICLTKYDG---DIPSSLDELLALPGIGPKMANMVMTL 125 (235)
Q Consensus 87 ~~~a~~i~~~~~g---~~~~~~~~L~~l~GIG~~tA~~il~~ 125 (235)
..-++.+.+.||. -.....++|.++||||.++|..+..+
T Consensus 535 ~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~~ 576 (577)
T PRK14668 535 PETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRER 576 (577)
T ss_pred HHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHh
No 207
>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=21.13 E-value=62 Score=29.17 Aligned_cols=16 Identities=38% Similarity=0.598 Sum_probs=13.2
Q ss_pred HcCCCCcHHHHHHHHH
Q 026645 109 LALPGIGPKMANMVMT 124 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~ 124 (235)
..+||||++||--++.
T Consensus 239 ~Gv~GIG~ktA~kli~ 254 (338)
T TIGR03674 239 EGVKGIGPKTALKLIK 254 (338)
T ss_pred CCCCCccHHHHHHHHH
Confidence 4789999999977763
No 208
>PTZ00217 flap endonuclease-1; Provisional
Probab=21.11 E-value=62 Score=29.87 Aligned_cols=16 Identities=38% Similarity=0.629 Sum_probs=13.2
Q ss_pred HcCCCCcHHHHHHHHH
Q 026645 109 LALPGIGPKMANMVMT 124 (235)
Q Consensus 109 ~~l~GIG~~tA~~il~ 124 (235)
-.+||||++||--++.
T Consensus 238 pgi~GIG~ktA~~Li~ 253 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIK 253 (393)
T ss_pred CCCCCccHHHHHHHHH
Confidence 3689999999987773
No 209
>PRK02362 ski2-like helicase; Provisional
Probab=20.97 E-value=1.7e+02 Score=29.18 Aligned_cols=60 Identities=18% Similarity=0.209 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHHHHHhcCCcceeecchHHHHHHHHhc
Q 026645 83 ACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMVMTLGWFNVQGICVDTHVHRICNRLG 147 (235)
Q Consensus 83 a~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~pvDt~v~Rv~~Rlg 147 (235)
+..+..+++.+.. .++...-.|++|||||++.|......++.....+. ...-.++..-+|
T Consensus 633 ~~~~~~l~~~l~~----gv~~~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~-~~~~~~l~~~~g 692 (737)
T PRK02362 633 ARAARELEKRVEY----GVREELLDLVGLRGVGRVRARRLYNAGIESRADLR-AADKSVVLAILG 692 (737)
T ss_pred HHHHHHHHHHHHh----CCCHHHHHHhCCCCCCHHHHHHHHHcCCCCHHHHH-hCCHHHHHHHHC
No 210
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=20.80 E-value=1.5e+02 Score=25.71 Aligned_cols=51 Identities=16% Similarity=0.307 Sum_probs=0.0
Q ss_pred HHHHHhhccCCChHHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCcHHHHHHH
Q 026645 67 ATIKDLIYPVAFYTRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIGPKMANMV 122 (235)
Q Consensus 67 e~l~~~l~~~G~~~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG~~tA~~i 122 (235)
..+.++....|+... +..+.++++.|.. |-.++... |.+|||||+..+..+
T Consensus 117 ~al~di~~~~~~~~~-~~~~l~L~q~i~q---~~w~~~~~-L~Qlp~i~~~~~~~l 167 (312)
T smart00611 117 QAMVDIALERGWLST-ALNALNLSQMIIQ---ALWPTDSP-LLQLPHLPEEILKRL 167 (312)
T ss_pred HHHHHHHHhcchHHH-HHHHHHHHHHHHH---hhCCCCCc-cccCCCCCHHHHHHH
No 211
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=20.77 E-value=1.8e+02 Score=22.93 Aligned_cols=36 Identities=31% Similarity=0.260 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCChhhHHHHHcCCCCc
Q 026645 80 TRKACNMKKIAKICLTKYDGDIPSSLDELLALPGIG 115 (235)
Q Consensus 80 ~~Ka~~l~~~a~~i~~~~~g~~~~~~~~L~~l~GIG 115 (235)
...++.+.+..+.+.+.++-..+-....|+++|||=
T Consensus 81 ~~l~~~y~~~l~~l~~~~~~~~~~~~~~ll~~p~v~ 116 (159)
T PF03755_consen 81 EELAKAYYEALKELAEELGLAGPISLDDLLRLPGVL 116 (159)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCCHHHHHcCCCcc
Confidence 345666777777777777655566789999999873
No 212
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=20.42 E-value=1.3e+02 Score=29.92 Aligned_cols=23 Identities=30% Similarity=0.460 Sum_probs=18.8
Q ss_pred HHHHHcCCCCcHHHHHHHHHHhcC
Q 026645 105 LDELLALPGIGPKMANMVMTLGWF 128 (235)
Q Consensus 105 ~~~L~~l~GIG~~tA~~il~~~~~ 128 (235)
...|..+||||++++..++.. ||
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~-FG 658 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWER-FG 658 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHH-hC
Confidence 467889999999999888764 44
No 213
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.24 E-value=65 Score=33.06 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=12.6
Q ss_pred cCCCCcHHHHHHHHH
Q 026645 110 ALPGIGPKMANMVMT 124 (235)
Q Consensus 110 ~l~GIG~~tA~~il~ 124 (235)
.+||||+|||.-++.
T Consensus 189 GVpGIG~KtA~kLL~ 203 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQ 203 (887)
T ss_pred CCCCcCHHHHHHHHH
Confidence 389999999987774
No 214
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=20.06 E-value=83 Score=21.82 Aligned_cols=26 Identities=12% Similarity=0.286 Sum_probs=18.7
Q ss_pred CCCHHHHhcCCHH---HHHHhhccCCChH
Q 026645 55 LHTAEAIDKADEA---TIKDLIYPVAFYT 80 (235)
Q Consensus 55 ~pt~~~la~a~~e---~l~~~l~~~G~~~ 80 (235)
.|.|+++...+.+ +|.+.|+.+|||.
T Consensus 4 ~~~p~~~~~l~~~~~~evq~~L~~lGyy~ 32 (74)
T PF08823_consen 4 KPRPEELLPLDGDVAREVQEALKRLGYYK 32 (74)
T ss_pred CCCchhhccCcHHHHHHHHHHHHHcCCcc
Confidence 4677777766654 6777788999964
No 215
>PF13523 Acetyltransf_8: Acetyltransferase (GNAT) domain; PDB: 2VQY_A 2BUE_A 1V0C_A 1YK3_D 2PR8_A 2QIR_A 2PRB_A 2QML_A 2PC1_A.
Probab=20.01 E-value=1.2e+02 Score=22.87 Aligned_cols=40 Identities=20% Similarity=0.392 Sum_probs=27.6
Q ss_pred CCCCcHHHHHHHHHHhcCC--cceeecch-----HHHHHHHHhcCcC
Q 026645 111 LPGIGPKMANMVMTLGWFN--VQGICVDT-----HVHRICNRLGWVT 150 (235)
Q Consensus 111 l~GIG~~tA~~il~~~~~~--~~~~pvDt-----~v~Rv~~Rlg~~~ 150 (235)
=+|+|......++.+++.+ .+.+.+|+ .+.++..++|+..
T Consensus 92 g~G~g~~~~~~~~~~~~~~~~~~~i~~~~~~~N~~~~~~~~k~GF~~ 138 (152)
T PF13523_consen 92 GQGLGKAMLRALIEFLFEDPGVDRIVLDPHEDNTRAIRLYEKAGFRK 138 (152)
T ss_dssp TSSHHHHHHHHHHHHHHTSTT--EEEEEEBTT-HHHHHHHHHTT-EE
T ss_pred CCCHHHHHHHHHHHHHHhCCCCCEEEEecCcCCHHHHHHHHHcCCEE
Confidence 4799999988888888765 34455555 5678888888753
Done!