Query 023471
Match_columns 281
No_of_seqs 274 out of 2010
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 04:17:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023471.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023471hhsearch_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 1E-52 2.3E-57 357.9 21.6 206 28-280 3-208 (211)
2 PRK10702 endonuclease III; Pro 100.0 1.8E-49 3.8E-54 342.5 22.4 205 29-280 4-208 (211)
3 TIGR01084 mutY A/G-specific ad 100.0 2.8E-44 6E-49 321.3 20.5 184 77-279 21-208 (275)
4 PRK10880 adenine DNA glycosyla 100.0 6.6E-44 1.4E-48 327.6 21.9 205 32-280 4-213 (350)
5 TIGR01083 nth endonuclease III 100.0 2E-43 4.3E-48 301.7 21.8 187 30-256 2-188 (191)
6 COG2231 Uncharacterized protei 100.0 1.6E-43 3.4E-48 295.3 19.8 207 28-279 5-214 (215)
7 KOG1921 Endonuclease III [Repl 100.0 8.4E-44 1.8E-48 302.6 17.4 212 49-279 46-261 (286)
8 PRK13913 3-methyladenine DNA g 100.0 1.1E-42 2.3E-47 300.0 20.2 188 30-255 3-217 (218)
9 PRK13910 DNA glycosylase MutY; 100.0 1.5E-38 3.2E-43 285.3 17.4 169 91-280 1-171 (289)
10 COG1194 MutY A/G-specific DNA 100.0 1.7E-36 3.7E-41 273.2 14.9 206 30-279 7-217 (342)
11 cd00056 ENDO3c endonuclease II 100.0 1E-32 2.2E-37 228.6 17.9 157 83-246 1-158 (158)
12 smart00478 ENDO3c endonuclease 100.0 1.3E-32 2.9E-37 225.8 17.3 149 91-248 1-149 (149)
13 PRK01229 N-glycosylase/DNA lya 100.0 1.2E-29 2.7E-34 217.1 15.5 142 78-232 33-186 (208)
14 KOG2457 A/G-specific adenine D 100.0 1.2E-29 2.6E-34 228.3 13.5 216 29-279 88-309 (555)
15 TIGR00588 ogg 8-oxoguanine DNA 99.9 1.6E-26 3.4E-31 210.8 17.5 148 80-231 117-290 (310)
16 COG0122 AlkA 3-methyladenine D 99.9 3E-25 6.4E-30 199.6 22.1 165 77-247 100-276 (285)
17 TIGR03252 uncharacterized HhH- 99.9 4E-25 8.6E-30 183.5 14.9 119 74-193 10-137 (177)
18 PRK10308 3-methyl-adenine DNA 99.9 3.6E-24 7.8E-29 192.8 17.9 186 31-241 71-272 (283)
19 KOG1918 3-methyladenine DNA gl 99.9 8.6E-22 1.9E-26 165.8 13.3 158 78-241 71-237 (254)
20 KOG2875 8-oxoguanine DNA glyco 99.9 2.3E-21 5E-26 168.6 13.6 128 78-209 113-257 (323)
21 PF00730 HhH-GPD: HhH-GPD supe 99.8 4.7E-19 1E-23 137.5 12.4 103 87-231 1-107 (108)
22 COG1059 Thermostable 8-oxoguan 99.4 3.9E-12 8.4E-17 105.4 9.6 127 78-216 35-166 (210)
23 PF00633 HHH: Helix-hairpin-he 98.1 1.5E-06 3.3E-11 51.4 1.6 25 166-190 6-30 (30)
24 TIGR00624 tag DNA-3-methyladen 97.2 0.016 3.5E-07 48.8 13.5 110 79-189 27-164 (179)
25 PRK10353 3-methyl-adenine DNA 97.1 0.012 2.7E-07 49.8 12.1 110 79-189 28-167 (187)
26 PF03352 Adenine_glyco: Methyl 96.9 0.018 3.9E-07 48.5 11.8 113 79-193 23-165 (179)
27 PF10576 EndIII_4Fe-2S: Iron-s 96.4 0.0011 2.3E-08 33.8 0.6 17 252-275 1-17 (17)
28 COG2818 Tag 3-methyladenine DN 96.4 0.09 1.9E-06 44.3 12.2 77 80-156 30-113 (188)
29 smart00525 FES FES domain. iro 95.5 0.0081 1.8E-07 34.0 1.4 22 251-279 1-22 (26)
30 smart00278 HhH1 Helix-hairpin- 95.3 0.013 2.9E-07 33.2 1.9 20 172-191 2-21 (26)
31 PF14716 HHH_8: Helix-hairpin- 95.1 0.14 2.9E-06 36.1 7.1 58 123-190 9-66 (68)
32 PF12826 HHH_2: Helix-hairpin- 95.1 0.045 9.7E-07 38.1 4.5 40 145-190 15-54 (64)
33 PF09674 DUF2400: Protein of u 93.9 2.4 5.3E-05 37.3 13.6 161 83-247 17-230 (232)
34 smart00483 POLXc DNA polymeras 93.5 0.28 6.1E-06 45.5 7.5 56 132-194 54-110 (334)
35 TIGR02757 conserved hypothetic 93.5 1.6 3.5E-05 38.3 11.7 157 88-247 22-227 (229)
36 PF14520 HHH_5: Helix-hairpin- 93.2 0.52 1.1E-05 32.1 6.6 49 130-190 9-57 (60)
37 PRK13901 ruvA Holliday junctio 92.7 0.41 9E-06 41.0 6.8 51 127-193 73-129 (196)
38 cd00141 NT_POLXc Nucleotidyltr 92.7 0.41 8.9E-06 43.9 7.2 55 132-194 51-106 (307)
39 PRK00116 ruvA Holliday junctio 91.7 0.27 5.8E-06 42.0 4.4 18 172-189 109-126 (192)
40 PRK02515 psbU photosystem II c 91.6 0.36 7.9E-06 38.4 4.7 62 105-189 44-105 (132)
41 TIGR00426 competence protein C 90.9 0.33 7.2E-06 34.0 3.6 58 116-190 9-66 (69)
42 PRK00076 recR recombination pr 90.9 0.31 6.7E-06 41.7 4.0 30 165-194 5-34 (196)
43 PRK13844 recombination protein 90.7 0.33 7.2E-06 41.6 4.0 30 165-194 9-38 (200)
44 TIGR00615 recR recombination p 90.7 0.34 7.3E-06 41.4 4.0 29 166-194 6-34 (195)
45 COG0353 RecR Recombinational D 90.4 0.35 7.5E-06 41.1 3.8 30 165-194 6-35 (198)
46 COG0632 RuvA Holliday junction 89.8 0.34 7.3E-06 41.7 3.3 39 156-194 93-131 (201)
47 TIGR00084 ruvA Holliday juncti 89.8 0.44 9.5E-06 40.7 4.0 55 126-190 72-126 (191)
48 PRK14601 ruvA Holliday junctio 89.6 0.34 7.4E-06 41.1 3.2 56 169-229 106-166 (183)
49 COG1555 ComEA DNA uptake prote 89.2 0.54 1.2E-05 38.5 3.9 54 117-188 91-144 (149)
50 TIGR00575 dnlj DNA ligase, NAD 89.1 3.1 6.8E-05 42.2 10.1 80 103-191 444-550 (652)
51 PRK08609 hypothetical protein; 88.6 1 2.2E-05 44.9 6.2 50 132-187 54-104 (570)
52 PRK00024 hypothetical protein; 88.1 0.96 2.1E-05 39.6 5.1 62 118-188 22-83 (224)
53 PRK14606 ruvA Holliday junctio 88.1 0.5 1.1E-05 40.2 3.2 57 169-230 106-168 (188)
54 PF14520 HHH_5: Helix-hairpin- 88.0 1.3 2.7E-05 30.2 4.6 42 103-147 17-59 (60)
55 PRK14603 ruvA Holliday junctio 87.9 0.51 1.1E-05 40.5 3.2 22 169-190 105-126 (197)
56 PRK14605 ruvA Holliday junctio 87.4 2.1 4.5E-05 36.6 6.6 21 169-189 106-126 (194)
57 PRK14605 ruvA Holliday junctio 87.3 0.75 1.6E-05 39.3 3.8 27 167-194 69-95 (194)
58 PRK14604 ruvA Holliday junctio 87.2 0.6 1.3E-05 40.0 3.2 25 169-193 106-130 (195)
59 PRK14602 ruvA Holliday junctio 87.0 0.56 1.2E-05 40.4 2.9 22 169-190 107-128 (203)
60 PF02371 Transposase_20: Trans 86.3 0.62 1.3E-05 34.3 2.5 41 171-214 2-42 (87)
61 PRK07945 hypothetical protein; 86.2 2 4.3E-05 39.9 6.3 61 123-192 8-70 (335)
62 PF09171 DUF1886: Domain of un 85.6 1.7 3.8E-05 38.4 5.3 160 86-254 43-232 (246)
63 TIGR00608 radc DNA repair prot 85.4 2.5 5.5E-05 36.8 6.2 62 119-189 13-78 (218)
64 PRK07956 ligA NAD-dependent DN 85.3 6.1 0.00013 40.2 9.7 79 103-190 457-562 (665)
65 PRK00024 hypothetical protein; 85.3 2.7 5.8E-05 36.8 6.3 61 85-148 28-88 (224)
66 PRK00116 ruvA Holliday junctio 85.2 1.5 3.2E-05 37.4 4.6 77 168-247 70-161 (192)
67 PF12836 HHH_3: Helix-hairpin- 84.7 1 2.2E-05 31.2 2.8 52 118-187 9-60 (65)
68 PRK14600 ruvA Holliday junctio 84.6 2.4 5.3E-05 36.0 5.6 55 170-230 107-170 (186)
69 COG2003 RadC DNA repair protei 84.3 14 0.0003 32.3 10.1 61 118-187 22-82 (224)
70 COG1796 POL4 DNA polymerase IV 84.2 2.6 5.7E-05 38.6 5.9 59 123-191 13-73 (326)
71 KOG2841 Structure-specific end 83.4 2.2 4.7E-05 37.4 4.8 42 105-149 209-250 (254)
72 PRK13482 DNA integrity scannin 82.6 3.8 8.2E-05 38.2 6.4 47 102-151 298-344 (352)
73 PF11731 Cdd1: Pathogenicity l 82.5 1.7 3.7E-05 32.6 3.4 28 167-194 8-35 (93)
74 TIGR00608 radc DNA repair prot 82.3 4 8.6E-05 35.6 6.1 61 85-148 18-82 (218)
75 PRK14350 ligA NAD-dependent DN 81.9 11 0.00023 38.5 9.8 23 169-191 539-561 (669)
76 smart00483 POLXc DNA polymeras 81.5 3.6 7.8E-05 38.2 5.9 56 124-190 12-67 (334)
77 PF12826 HHH_2: Helix-hairpin- 81.4 2.4 5.2E-05 29.3 3.6 43 102-147 14-56 (64)
78 PRK14351 ligA NAD-dependent DN 80.8 13 0.00028 38.1 9.9 79 103-190 474-579 (689)
79 TIGR00084 ruvA Holliday juncti 80.6 1.5 3.3E-05 37.4 2.9 23 167-189 68-90 (191)
80 PF12836 HHH_3: Helix-hairpin- 80.5 1.8 3.9E-05 30.0 2.8 23 169-191 12-34 (65)
81 TIGR01448 recD_rel helicase, p 80.4 3 6.5E-05 42.8 5.4 28 166-194 77-106 (720)
82 PF10391 DNA_pol_lambd_f: Fing 80.4 1.8 3.8E-05 28.9 2.5 23 171-193 2-24 (52)
83 TIGR01259 comE comEA protein. 80.1 4.4 9.5E-05 31.8 5.1 60 113-190 58-117 (120)
84 COG2003 RadC DNA repair protei 80.0 12 0.00027 32.6 8.2 62 84-148 27-88 (224)
85 PRK14973 DNA topoisomerase I; 79.3 6.7 0.00015 41.5 7.6 99 106-212 817-918 (936)
86 PF11798 IMS_HHH: IMS family H 78.9 1.7 3.6E-05 25.8 1.9 15 173-187 13-27 (32)
87 PRK08097 ligB NAD-dependent DN 78.4 12 0.00026 37.3 8.7 79 103-190 437-539 (562)
88 PF14490 HHH_4: Helix-hairpin- 78.0 4.9 0.00011 30.0 4.6 57 121-189 7-64 (94)
89 smart00279 HhH2 Helix-hairpin- 77.8 1.7 3.7E-05 26.5 1.7 17 173-189 18-34 (36)
90 PRK14603 ruvA Holliday junctio 77.6 2.2 4.7E-05 36.6 2.9 23 167-189 68-90 (197)
91 PRK14602 ruvA Holliday junctio 77.6 2.1 4.7E-05 36.8 2.9 23 167-189 70-92 (203)
92 TIGR01259 comE comEA protein. 76.5 2.6 5.6E-05 33.1 2.9 23 169-191 66-88 (120)
93 KOG2534 DNA polymerase IV (fam 76.4 26 0.00056 32.3 9.5 57 133-194 63-120 (353)
94 COG1555 ComEA DNA uptake prote 76.1 2.4 5.2E-05 34.7 2.7 33 169-201 95-128 (149)
95 PRK07758 hypothetical protein; 75.1 7.8 0.00017 29.1 4.9 31 154-188 54-84 (95)
96 PF05559 DUF763: Protein of un 74.9 7.2 0.00016 35.8 5.6 25 167-191 265-289 (319)
97 PF03118 RNA_pol_A_CTD: Bacter 72.5 11 0.00024 26.3 4.9 48 129-188 14-61 (66)
98 cd00141 NT_POLXc Nucleotidyltr 71.3 9.3 0.0002 35.0 5.6 57 124-191 9-65 (307)
99 PRK13901 ruvA Holliday junctio 71.2 3.9 8.4E-05 35.1 2.8 23 167-189 68-90 (196)
100 cd00080 HhH2_motif Helix-hairp 70.8 2.4 5.1E-05 30.4 1.3 20 171-190 22-41 (75)
101 PRK14600 ruvA Holliday junctio 70.5 3.9 8.5E-05 34.7 2.7 23 167-189 69-91 (186)
102 PRK14601 ruvA Holliday junctio 70.5 4 8.7E-05 34.6 2.8 23 167-189 69-91 (183)
103 PF10440 WIYLD: Ubiquitin-bind 70.0 12 0.00026 26.1 4.6 39 27-94 24-62 (65)
104 PRK14606 ruvA Holliday junctio 69.3 4.4 9.6E-05 34.5 2.8 24 166-189 68-91 (188)
105 PRK02515 psbU photosystem II c 69.2 4.3 9.4E-05 32.3 2.5 20 170-189 60-79 (132)
106 PRK08609 hypothetical protein; 68.0 13 0.00027 37.2 6.2 58 123-191 11-68 (570)
107 PRK14604 ruvA Holliday junctio 67.3 4.9 0.00011 34.4 2.7 23 167-189 69-91 (195)
108 TIGR00426 competence protein C 64.9 7.5 0.00016 27.0 2.8 21 170-190 15-36 (69)
109 PRK13482 DNA integrity scannin 64.7 13 0.00028 34.8 5.0 39 143-187 297-335 (352)
110 PRK14666 uvrC excinuclease ABC 64.0 17 0.00036 37.1 6.1 42 105-149 651-692 (694)
111 COG0272 Lig NAD-dependent DNA 64.0 15 0.00033 37.1 5.7 29 158-190 534-562 (667)
112 PF04904 NCD1: NAB conserved r 63.1 32 0.0007 24.8 5.7 52 99-151 20-72 (82)
113 PRK13280 N-glycosylase/DNA lya 62.3 88 0.0019 28.2 9.7 125 82-215 47-197 (269)
114 PF10343 DUF2419: Protein of u 61.8 77 0.0017 28.9 9.4 123 79-214 44-202 (287)
115 PRK14973 DNA topoisomerase I; 61.8 47 0.001 35.4 9.1 73 112-192 766-856 (936)
116 PRK14667 uvrC excinuclease ABC 60.8 14 0.0003 37.0 4.8 35 107-145 530-564 (567)
117 PRK12766 50S ribosomal protein 60.6 23 0.0005 31.1 5.6 44 103-149 15-59 (232)
118 PRK00254 ski2-like helicase; P 59.6 29 0.00062 35.6 7.1 17 173-189 680-696 (720)
119 COG0632 RuvA Holliday junction 59.3 8.5 0.00018 33.1 2.7 23 167-189 69-91 (201)
120 PF00416 Ribosomal_S13: Riboso 59.0 11 0.00024 28.8 3.1 22 168-189 12-33 (107)
121 PRK12766 50S ribosomal protein 57.9 28 0.00061 30.6 5.7 48 132-191 9-56 (232)
122 COG1379 PHP family phosphoeste 57.7 19 0.00041 33.3 4.7 50 80-129 303-353 (403)
123 COG4277 Predicted DNA-binding 56.7 8.2 0.00018 35.3 2.2 21 169-189 328-348 (404)
124 COG1948 MUS81 ERCC4-type nucle 53.9 56 0.0012 29.2 7.0 87 137-227 145-235 (254)
125 PF14229 DUF4332: Domain of un 53.6 78 0.0017 24.7 7.2 24 170-193 52-75 (122)
126 TIGR00375 conserved hypothetic 52.7 22 0.00048 33.6 4.5 50 79-128 295-345 (374)
127 PRK14666 uvrC excinuclease ABC 51.5 80 0.0017 32.4 8.4 46 132-190 643-688 (694)
128 PF00536 SAM_1: SAM domain (St 51.4 43 0.00094 22.4 4.8 49 121-181 4-52 (64)
129 PF14056 DUF4250: Domain of un 50.1 29 0.00063 23.4 3.6 34 105-138 14-50 (55)
130 COG0177 Nth Predicted EndoIII- 49.8 1.7E+02 0.0038 25.3 11.1 130 27-194 43-184 (211)
131 PF13174 TPR_6: Tetratricopept 49.1 35 0.00077 18.9 3.6 27 87-113 6-32 (33)
132 PF01367 5_3_exonuc: 5'-3' exo 48.0 4 8.6E-05 31.1 -1.0 19 173-191 20-38 (101)
133 TIGR00596 rad1 DNA repair prot 47.0 35 0.00077 35.6 5.4 40 104-147 770-809 (814)
134 PF13592 HTH_33: Winged helix- 47.0 31 0.00067 23.3 3.5 34 181-214 4-38 (60)
135 PRK14670 uvrC excinuclease ABC 46.9 36 0.00077 34.1 5.2 37 107-146 530-566 (574)
136 COG1948 MUS81 ERCC4-type nucle 46.6 49 0.0011 29.5 5.5 47 103-152 194-240 (254)
137 KOG0495 HAT repeat protein [RN 45.5 1.2E+02 0.0026 31.1 8.4 157 82-247 686-866 (913)
138 TIGR01954 nusA_Cterm_rpt trans 45.3 77 0.0017 19.9 5.7 41 104-147 6-47 (50)
139 COG1623 Predicted nucleic-acid 44.6 38 0.00082 30.9 4.4 44 102-148 304-347 (349)
140 TIGR01448 recD_rel helicase, p 43.5 83 0.0018 32.4 7.4 19 175-194 185-203 (720)
141 PRK14669 uvrC excinuclease ABC 43.4 45 0.00099 33.7 5.4 35 107-146 568-602 (624)
142 PF09597 IGR: IGR protein moti 43.2 72 0.0016 21.6 4.7 42 105-150 13-55 (57)
143 PRK14976 5'-3' exonuclease; Pr 41.7 16 0.00035 33.0 1.7 22 172-194 192-213 (281)
144 PRK14672 uvrC excinuclease ABC 41.0 47 0.001 33.9 5.0 39 107-148 624-662 (691)
145 smart00540 LEM in nuclear memb 40.3 59 0.0013 20.8 3.7 35 116-150 2-42 (44)
146 PRK09482 flap endonuclease-lik 39.8 18 0.0004 32.3 1.8 18 172-189 183-200 (256)
147 cd00008 53EXOc 5'-3' exonuclea 38.2 20 0.00044 31.5 1.8 19 171-189 183-201 (240)
148 PF00730 HhH-GPD: HhH-GPD supe 37.8 1.2E+02 0.0026 22.5 5.9 54 137-191 9-62 (108)
149 smart00475 53EXOc 5'-3' exonuc 37.7 21 0.00046 31.9 1.8 19 171-189 186-204 (259)
150 TIGR03764 ICE_PFGI_1_parB inte 37.1 1.4E+02 0.0031 26.7 6.9 91 119-227 136-237 (258)
151 KOG4217 Nuclear receptors of t 37.1 2.9E+02 0.0063 27.1 9.3 112 101-227 421-539 (605)
152 COG1491 Predicted RNA-binding 36.7 1.2E+02 0.0026 25.8 5.9 31 165-195 124-154 (202)
153 CHL00137 rps13 ribosomal prote 36.7 23 0.00051 27.9 1.7 23 168-190 14-36 (122)
154 PF13543 KSR1-SAM: SAM like do 36.3 1.3E+02 0.0028 24.0 5.9 58 81-145 67-124 (129)
155 TIGR02236 recomb_radA DNA repa 36.1 91 0.002 28.2 5.8 45 102-149 10-55 (310)
156 PRK05179 rpsM 30S ribosomal pr 34.6 27 0.00058 27.6 1.7 22 169-190 15-36 (122)
157 PF13297 Telomere_Sde2_2: Telo 34.5 1E+02 0.0022 21.2 4.3 34 109-142 4-42 (60)
158 COG2019 AdkA Archaeal adenylat 33.4 77 0.0017 26.8 4.3 42 173-214 9-51 (189)
159 PF14579 HHH_6: Helix-hairpin- 33.4 41 0.00089 24.6 2.5 37 169-205 25-61 (90)
160 KOG2534 DNA polymerase IV (fam 32.7 99 0.0021 28.6 5.2 43 137-190 33-75 (353)
161 KOG0028 Ca2+-binding protein ( 32.6 2.9E+02 0.0064 23.0 8.6 100 119-229 49-151 (172)
162 PF12482 DUF3701: Phage integr 32.4 1.6E+02 0.0034 22.2 5.5 21 171-191 50-70 (96)
163 cd00128 XPG Xeroderma pigmento 31.8 1E+02 0.0022 28.1 5.4 20 173-193 225-244 (316)
164 TIGR03631 bact_S13 30S ribosom 30.9 31 0.00066 26.8 1.5 23 168-190 12-34 (113)
165 PTZ00134 40S ribosomal protein 30.8 29 0.00062 28.6 1.4 22 168-189 27-48 (154)
166 COG1415 Uncharacterized conser 30.6 38 0.00083 31.5 2.3 62 167-231 274-345 (373)
167 COG1796 POL4 DNA polymerase IV 30.5 1.3E+02 0.0029 27.7 5.8 19 173-191 130-148 (326)
168 PF09288 UBA_3: Fungal ubiquit 30.3 1.5E+02 0.0033 20.0 4.5 50 175-230 4-54 (55)
169 PRK00558 uvrC excinuclease ABC 30.2 1E+02 0.0022 31.1 5.5 24 169-193 541-564 (598)
170 TIGR03629 arch_S13P archaeal r 29.4 34 0.00074 27.8 1.6 21 169-189 19-39 (144)
171 PRK01172 ski2-like helicase; P 29.3 1.6E+02 0.0034 30.0 6.8 39 112-153 634-672 (674)
172 COG0099 RpsM Ribosomal protein 29.3 43 0.00093 26.3 2.1 22 169-190 15-36 (121)
173 PF10588 NADH-G_4Fe-4S_3: NADH 29.3 14 0.0003 23.2 -0.6 32 237-279 4-35 (41)
174 COG0735 Fur Fe2+/Zn2+ uptake r 29.0 2.9E+02 0.0062 22.2 7.0 56 122-189 5-63 (145)
175 PRK14668 uvrC excinuclease ABC 29.0 1.1E+02 0.0024 30.7 5.4 36 106-144 540-575 (577)
176 PRK04053 rps13p 30S ribosomal 28.9 32 0.00069 28.1 1.4 22 168-189 22-43 (149)
177 PRK00558 uvrC excinuclease ABC 28.4 1.2E+02 0.0027 30.5 5.7 38 105-145 557-594 (598)
178 PRK14669 uvrC excinuclease ABC 28.4 62 0.0013 32.8 3.6 49 144-193 524-573 (624)
179 COG0322 UvrC Nuclease subunit 28.2 1.1E+02 0.0023 30.9 5.1 36 105-144 544-579 (581)
180 PRK07571 bidirectional hydroge 27.6 57 0.0012 27.2 2.7 72 124-207 23-94 (169)
181 PTZ00035 Rad51 protein; Provis 27.6 1.8E+02 0.0038 27.0 6.2 47 102-151 34-81 (337)
182 PF07499 RuvA_C: RuvA, C-termi 27.4 1.5E+02 0.0033 18.8 4.2 22 123-144 4-25 (47)
183 PRK04301 radA DNA repair and r 26.9 1.7E+02 0.0037 26.6 6.0 44 103-149 18-62 (317)
184 KOG0400 40S ribosomal protein 26.9 83 0.0018 25.2 3.3 53 163-215 27-83 (151)
185 PF13495 Phage_int_SAM_4: Phag 26.8 2.2E+02 0.0048 19.7 5.6 64 123-189 3-69 (85)
186 PRK00159 putative septation in 26.4 54 0.0012 24.3 2.1 11 1-11 1-11 (87)
187 KOG2841 Structure-specific end 26.2 1.1E+02 0.0023 27.1 4.2 17 170-186 226-242 (254)
188 PRK14456 ribosomal RNA large s 25.7 1.8E+02 0.0039 27.4 6.0 56 116-176 19-74 (368)
189 PRK13766 Hef nuclease; Provisi 25.6 1.5E+02 0.0033 30.5 6.0 42 103-147 727-768 (773)
190 TIGR02238 recomb_DMC1 meiotic 25.6 2E+02 0.0042 26.4 6.1 46 103-151 13-59 (313)
191 PRK14454 ribosomal RNA large s 25.4 1.9E+02 0.004 27.0 6.0 54 117-175 4-57 (342)
192 cd04752 Commd4 COMM_Domain con 25.2 3.9E+02 0.0084 22.1 7.4 63 120-189 22-84 (174)
193 PLN03187 meiotic recombination 25.1 2.1E+02 0.0045 26.7 6.2 47 102-151 42-89 (344)
194 TIGR00194 uvrC excinuclease AB 24.8 75 0.0016 31.9 3.4 25 168-193 538-562 (574)
195 PF07647 SAM_2: SAM domain (St 24.7 2.2E+02 0.0047 18.9 5.3 39 121-169 5-44 (66)
196 PF13751 DDE_Tnp_1_6: Transpos 24.4 35 0.00076 26.3 0.8 15 265-279 32-46 (125)
197 PRK14670 uvrC excinuclease ABC 23.8 44 0.00095 33.5 1.6 25 169-194 512-536 (574)
198 TIGR00048 radical SAM enzyme, 23.6 1.8E+02 0.004 27.2 5.6 56 116-176 8-63 (355)
199 PRK11194 ribosomal RNA large s 23.5 2E+02 0.0044 27.1 5.9 54 117-175 8-61 (372)
200 COG3547 Transposase and inacti 23.4 2.1E+02 0.0047 25.3 5.9 16 173-188 190-205 (303)
201 TIGR00596 rad1 DNA repair prot 23.4 71 0.0015 33.5 3.0 28 165-193 751-778 (814)
202 PF02037 SAP: SAP domain; Int 23.3 91 0.002 18.6 2.4 30 119-148 3-34 (35)
203 COG3743 Uncharacterized conser 22.5 42 0.0009 26.8 0.9 15 171-185 67-81 (133)
204 PRK14469 ribosomal RNA large s 22.4 2.1E+02 0.0045 26.5 5.7 55 117-176 4-58 (343)
205 PRK14463 ribosomal RNA large s 22.4 1.9E+02 0.0042 26.9 5.5 56 116-176 6-61 (349)
206 PF14635 HHH_7: Helix-hairpin- 22.4 84 0.0018 24.1 2.5 44 126-183 49-93 (104)
207 PF02467 Whib: Transcription f 22.2 26 0.00057 24.4 -0.3 13 266-278 32-44 (66)
208 PRK14671 uvrC excinuclease ABC 22.1 1.7E+02 0.0036 29.7 5.3 37 104-145 582-618 (621)
209 KOG2336 Molybdopterin biosynth 22.0 1.8E+02 0.0039 26.6 4.9 76 141-217 48-132 (422)
210 PF06781 UPF0233: Uncharacteri 21.9 76 0.0016 23.5 2.1 16 1-16 1-16 (87)
211 PF07900 DUF1670: Protein of u 21.8 2.4E+02 0.0052 24.6 5.4 52 120-171 70-124 (220)
212 PRK14467 ribosomal RNA large s 21.8 2.4E+02 0.0052 26.4 5.9 55 117-176 4-58 (348)
213 PF14199 DUF4317: Domain of un 21.4 2.6E+02 0.0056 26.5 6.0 71 79-150 235-310 (371)
214 cd08332 CARD_CASP2 Caspase act 21.3 3.2E+02 0.0069 20.0 5.5 44 86-129 39-87 (90)
215 PF10264 Stork_head: Winged he 21.2 1.7E+02 0.0037 21.3 3.8 31 83-113 13-45 (80)
216 PRK14455 ribosomal RNA large s 21.2 2.3E+02 0.0049 26.5 5.7 54 117-175 13-66 (356)
217 PRK07757 acetyltransferase; Pr 21.1 81 0.0018 24.7 2.4 38 177-214 80-119 (152)
218 KOG0662 Cyclin-dependent kinas 21.1 80 0.0017 27.1 2.4 37 177-213 181-222 (292)
219 smart00845 GatB_Yqey GatB doma 21.1 2.2E+02 0.0047 22.8 4.9 63 79-152 40-103 (147)
220 PRK14466 ribosomal RNA large s 21.0 2.1E+02 0.0046 26.7 5.4 55 117-176 7-61 (345)
221 TIGR01896 cas_AF1879 CRISPR-as 20.9 77 0.0017 28.6 2.4 10 266-275 260-270 (271)
222 PRK14671 uvrC excinuclease ABC 20.9 73 0.0016 32.3 2.5 26 168-194 566-591 (621)
223 PRK14457 ribosomal RNA large s 20.9 2.4E+02 0.0052 26.3 5.8 54 117-175 4-57 (345)
224 PF04919 DUF655: Protein of un 20.8 69 0.0015 27.1 1.9 20 172-191 117-136 (181)
225 PRK14459 ribosomal RNA large s 20.7 2.5E+02 0.0055 26.5 5.9 55 116-175 23-77 (373)
226 PRK14465 ribosomal RNA large s 20.5 2.4E+02 0.0051 26.4 5.6 55 117-176 7-61 (342)
227 PRK03980 flap endonuclease-1; 20.5 63 0.0014 29.4 1.8 16 174-189 192-207 (292)
228 TIGR02249 integrase_gron integ 20.5 4.1E+02 0.0089 23.5 7.2 65 123-187 3-67 (315)
229 COG0237 CoaE Dephospho-CoA kin 20.3 3.9E+02 0.0085 22.8 6.6 40 173-213 7-57 (201)
230 PRK03100 sec-independent trans 20.2 2.4E+02 0.0052 22.7 4.8 59 117-184 18-80 (136)
231 PF06992 Phage_lambda_P: Repli 20.1 4.2E+02 0.009 23.4 6.6 95 98-212 38-139 (233)
232 PHA00439 exonuclease 20.1 63 0.0014 29.4 1.7 19 171-190 188-206 (286)
No 1
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-52 Score=357.91 Aligned_cols=206 Identities=32% Similarity=0.449 Sum_probs=193.4
Q ss_pred HHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHH
Q 023471 28 AEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASL 107 (281)
Q Consensus 28 ~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L 107 (281)
.....++.+.|.+.|+...... ...|||++||++||||||+++.+.+++.+|
T Consensus 3 ~~~~~~i~~~l~~~~p~~~~~l----------------------------~~~~pf~lLva~iLSaqttD~~vn~at~~L 54 (211)
T COG0177 3 KKKALEILDRLRELYPEPKTEL----------------------------DFKDPFELLVAVILSAQTTDEVVNKATPAL 54 (211)
T ss_pred HhhHHHHHHHHHHHCCCCCCcc----------------------------CcCCcHHHHHHHHHhccCchHHHHHHHHHH
Confidence 3567888889988888766411 258999999999999999999999999999
Q ss_pred HhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 108 KSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 108 ~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
++.|+||++|+++++++|++.|+.+||+++||++|+++++.|.++||| .+|+.+++|++|||||+|||++|
T Consensus 55 f~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g---------~vP~~~~eL~~LPGVGrKTAnvV 125 (211)
T COG0177 55 FKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG---------EVPDTREELLSLPGVGRKTANVV 125 (211)
T ss_pred HHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC---------CCCchHHHHHhCCCcchHHHHHH
Confidence 999999999999999999999999999999999999999999999999 78999999999999999999999
Q ss_pred HHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCC
Q 023471 188 LMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGN 267 (281)
Q Consensus 188 l~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~ 267 (281)
|.++||.++|+|||||+|+++|+||++ ..+++++++.|.+++|++.|..+|.+||.|||. +|++++ | + |+
T Consensus 126 L~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~--iC~ar~-P---~---C~ 195 (211)
T COG0177 126 LSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIPKELWTDLHHWLILHGRY--ICKARK-P---R---CE 195 (211)
T ss_pred HHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhh--hccCCC-C---C---cC
Confidence 999999999999999999999999987 789999999999999999999999999999999 999984 4 3 99
Q ss_pred CCCChhhcccccC
Q 023471 268 LCPLLNYCEKSNK 280 (281)
Q Consensus 268 ~Cpl~~~C~~~~~ 280 (281)
.|||+++|+++++
T Consensus 196 ~C~l~~~C~~~~~ 208 (211)
T COG0177 196 ECPLADLCPSAGK 208 (211)
T ss_pred cccchhhCchhcc
Confidence 9999999999976
No 2
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.8e-49 Score=342.48 Aligned_cols=205 Identities=25% Similarity=0.328 Sum_probs=189.6
Q ss_pred HHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHH
Q 023471 29 EECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLK 108 (281)
Q Consensus 29 ~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~ 108 (281)
.+...+++.|.+.||...- | ...++||++||++||||||++.++.+++.+|+
T Consensus 4 ~~~~~i~~~l~~~~~~~~~---~-------------------------~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~ 55 (211)
T PRK10702 4 AKRLEILTRLRDNNPHPTT---E-------------------------LNFSSPFELLIAVLLSAQATDVSVNKATAKLY 55 (211)
T ss_pred HHHHHHHHHHHHHCCCCCC---C-------------------------CCCCChHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 4678999999999986431 1 13689999999999999999999999999999
Q ss_pred hhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471 109 STFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL 188 (281)
Q Consensus 109 ~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il 188 (281)
.+||||++|++++.++|+++|+++||+++||++|+++|+.+.+++|+ +.++.+++|++|||||+|||++||
T Consensus 56 ~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~---------~~p~~~~~Ll~lpGVG~ktA~~il 126 (211)
T PRK10702 56 PVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG---------EVPEDRAALEALPGVGRKTANVVL 126 (211)
T ss_pred HHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC---------CCCchHHHHhcCCcccHHHHHHHH
Confidence 99999999999999999999999999999999999999999998887 578899999999999999999999
Q ss_pred HHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCCC
Q 023471 189 MFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNL 268 (281)
Q Consensus 189 ~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~~ 268 (281)
+|+||+++|+||+||+||+.|+|+.+ ..+++++++.++..+|.+.+.++|.+||+||+. +|++++ | + |+.
T Consensus 127 l~a~~~~~~~VDt~v~Rv~~r~g~~~-~~~~~~~~~~l~~~lp~~~~~~~~~~li~~Gr~--~C~~~~-P---~---C~~ 196 (211)
T PRK10702 127 NTAFGWPTIAVDTHIFRVCNRTQFAP-GKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRY--TCIARK-P---R---CGS 196 (211)
T ss_pred HHHcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHhCCchHHHHHHHHHHHHhHH--HcCCCC-C---C---CCC
Confidence 99999999999999999999999976 478999999999999999999999999999999 999884 4 3 999
Q ss_pred CCChhhcccccC
Q 023471 269 CPLLNYCEKSNK 280 (281)
Q Consensus 269 Cpl~~~C~~~~~ 280 (281)
|||++.|++|++
T Consensus 197 Cpl~~~C~~~~~ 208 (211)
T PRK10702 197 CIIEDLCEYKEK 208 (211)
T ss_pred CcChhhcCcccc
Confidence 999999999875
No 3
>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=2.8e-44 Score=321.27 Aligned_cols=184 Identities=21% Similarity=0.266 Sum_probs=168.9
Q ss_pred CCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCC
Q 023471 77 GEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKL 156 (281)
Q Consensus 77 ~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~ 156 (281)
....|||++||++||+|||+++++..++.+|.++|||+++|+++++++|.++|+++||+ +||++|+++|+.|.+++|+
T Consensus 21 r~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g- 98 (275)
T TIGR01084 21 RQNKTPYRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGG- 98 (275)
T ss_pred CCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCC-
Confidence 45789999999999999999999999999999999999999999999999999999999 4999999999999998887
Q ss_pred chHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHH----HHhhCCc
Q 023471 157 CLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLH----LNQRIPK 232 (281)
Q Consensus 157 ~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~----l~~~~p~ 232 (281)
..++.+++|++|||||+|||++|++|+||++.++||+||+|++.|++.+....+..++++. ++..+|.
T Consensus 99 --------~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~lp~ 170 (275)
T TIGR01084 99 --------EFPQDFEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLPK 170 (275)
T ss_pred --------CCcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHCCh
Confidence 4677899999999999999999999999999999999999999998776655666666655 7889999
Q ss_pred ccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCCCCCChhhccccc
Q 023471 233 ELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSN 279 (281)
Q Consensus 233 ~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~~Cpl~~~C~~~~ 279 (281)
+.+.+||++||+||+. +|++++ | + |+.|||++.|.+|.
T Consensus 171 ~~~~~~n~alm~lG~~--vC~~~~-P---~---C~~Cpl~~~C~~~~ 208 (275)
T TIGR01084 171 ADPEAFNQALMDLGAM--ICTRKK-P---K---CDLCPLQDFCLAYQ 208 (275)
T ss_pred hhHHHHHHHHHHHhHH--HcCCCC-C---C---CCCCCChhhCHHHH
Confidence 9999999999999999 999874 4 3 99999999999875
No 4
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=6.6e-44 Score=327.59 Aligned_cols=205 Identities=17% Similarity=0.179 Sum_probs=180.5
Q ss_pred HHHHHHHHHhhCCChh-hhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhh
Q 023471 32 RGIRDELLALHGFPPE-FVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKST 110 (281)
Q Consensus 32 ~~v~~~L~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~ 110 (281)
+.+.+.|.+||...++ ..+| ....|||++||++||+|||++++|..++.+|+++
T Consensus 4 ~~~~~~ll~W~~~~~r~~lpW-------------------------r~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~ 58 (350)
T PRK10880 4 SQFSAQVLDWYDKYGRKTLPW-------------------------QIDKTPYKVWLSEVMLQQTQVATVIPYFERFMAR 58 (350)
T ss_pred HHHHHHHHHHHHHcCCCCCCC-------------------------CCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 5678899999876553 2233 4578999999999999999999999999999999
Q ss_pred CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 111 FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 111 ~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
|||+++|+++++++|.++|+++||++ ||++|+++|+.+.++||| ..++.+++|++|||||+|||++|++|
T Consensus 59 fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g---------~~p~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 59 FPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGG---------EFPETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred CcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCC---------CchhhHHHHhcCCCccHHHHHHHHHH
Confidence 99999999999999999999999996 999999999999998887 56889999999999999999999999
Q ss_pred hcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHH----HHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCC
Q 023471 191 HLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLH----LNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAG 266 (281)
Q Consensus 191 ~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~----l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C 266 (281)
+||+++++||+||+|++.|++.+....++.++++. ++..+|.+.+.+||++||+||+. +|++++ | + |
T Consensus 129 af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~~l~p~~~~~~~nqalm~lGa~--vC~p~~-P---~---C 199 (350)
T PRK10880 129 SLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSEQVTPAVGVERFNQAMMDLGAM--VCTRSK-P---K---C 199 (350)
T ss_pred HCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCChhHHHHHHHHHHHhhHH--hccCCC-C---C---C
Confidence 99999999999999999997555544555555544 45778888999999999999999 999874 4 3 9
Q ss_pred CCCCChhhcccccC
Q 023471 267 NLCPLLNYCEKSNK 280 (281)
Q Consensus 267 ~~Cpl~~~C~~~~~ 280 (281)
+.|||++.|.+|..
T Consensus 200 ~~Cpl~~~C~~~~~ 213 (350)
T PRK10880 200 ELCPLQNGCIAYAN 213 (350)
T ss_pred CCCccHhhhHHHHc
Confidence 99999999999863
No 5
>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=2e-43 Score=301.67 Aligned_cols=187 Identities=28% Similarity=0.375 Sum_probs=172.4
Q ss_pred HHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHh
Q 023471 30 ECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKS 109 (281)
Q Consensus 30 ~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~ 109 (281)
+++++++.|.+.||....+. ...|||++||++||||||+++++.+++.+|++
T Consensus 2 ~~~~i~~~l~~~~~~~~~~~----------------------------~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~ 53 (191)
T TIGR01083 2 KAQEILERLRKNYPHPTTEL----------------------------DYNNPFELLVATILSAQATDKSVNKATKKLFE 53 (191)
T ss_pred hHHHHHHHHHHHCCCCCccc----------------------------CCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHH
Confidence 36789999999998654211 24789999999999999999999999999999
Q ss_pred hCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHH
Q 023471 110 TFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 110 ~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.||||++|+++++++|+++|+++||+++||++|+++|+.+.+++++ +.++.++.|++|||||+|||++||+
T Consensus 54 ~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~---------~~~~~~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 54 VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG---------EVPEDREELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCC---------CCchHHHHHHhCCCCcHHHHHHHHH
Confidence 9999999999999999999999999999999999999999998776 4567899999999999999999999
Q ss_pred HhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCC
Q 023471 190 FHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKG 256 (281)
Q Consensus 190 ~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~ 256 (281)
|++|+++||||+|++|++.|+|+.. ..+++++++.++.++|.+.+.+||.+||+||+. +|++++
T Consensus 125 ~~~~~~~~~vD~~v~Ri~~r~g~~~-~~~~~~~~~~l~~~~p~~~~~~~h~~li~~G~~--~C~~~~ 188 (191)
T TIGR01083 125 VAFGIPAIAVDTHVFRVSNRLGLSK-GKDPDKVEEELLKLIPREFWTKLHHWLILHGRY--TCKARK 188 (191)
T ss_pred HHcCCCccccchhHHHHHHHcCCCC-CCCHHHHHHHHHHHCCchhHHHHHHHHHHHhHH--hcCCCC
Confidence 9999999999999999999999975 468999999999999999999999999999999 999874
No 6
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.6e-43 Score=295.26 Aligned_cols=207 Identities=25% Similarity=0.347 Sum_probs=184.8
Q ss_pred HHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHH
Q 023471 28 AEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASL 107 (281)
Q Consensus 28 ~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L 107 (281)
.....++++.|...||+++||+ ..+.+|++|++||+|||+|++|.+++++|
T Consensus 5 ~~~~~~iy~~L~~~yg~q~WWp-----------------------------~~~~~EiiigAILtQNT~WknvekAlenL 55 (215)
T COG2231 5 MENITKIYKELLRLYGDQGWWP-----------------------------ADNKDEIIIGAILTQNTSWKNVEKALENL 55 (215)
T ss_pred hHHHHHHHHHHHHHcCCccCCC-----------------------------CCCchhHHHHHHHhccccHHHHHHHHHHH
Confidence 3567899999999999999944 45566999999999999999999999999
Q ss_pred HhhC-CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHH
Q 023471 108 KSTF-PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVAC 186 (281)
Q Consensus 108 ~~~~-pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~ 186 (281)
+... .++++|..++.++|+++|++.|||+|||++|+.+...+...+.++ +.+ ....+|++|++|+|||+.|||+
T Consensus 56 k~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~--~~~---~~~~~R~~LL~iKGIG~ETaDs 130 (215)
T COG2231 56 KNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL--ESF---KSEVLREELLSIKGIGKETADS 130 (215)
T ss_pred HHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh--hcc---chHHHHHHHHccCCcchhhHHH
Confidence 9987 589999999999999999999999999999988888888755433 322 2333799999999999999999
Q ss_pred HHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCccc--HHHHHHHHHHhcccCCCCcCCCCCCCcCCC
Q 023471 187 VLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKEL--KFDLNCLLYTHGKLCRNCIKKGGNRQRKES 264 (281)
Q Consensus 187 il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~--~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~ 264 (281)
||+|++++++|+||.+++|++.|+|.+..+ +|+++++.++..+|.+. +.+||++|+.||+. +|+.+ |.
T Consensus 131 ILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k-~ydeik~~fe~~l~~~~~lyqe~HAlIv~~~K~--f~~k~--~~----- 200 (215)
T COG2231 131 ILLYALDRPVFVVDKYTRRLLSRLGGIEEK-KYDEIKELFEENLPENLRLYQEFHALIVEHAKH--FCKKK--PL----- 200 (215)
T ss_pred HHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHH--HccCC--cC-----
Confidence 999999999999999999999999998754 89999999999999875 68999999999999 99988 43
Q ss_pred CCCCCCChhhccccc
Q 023471 265 AGNLCPLLNYCEKSN 279 (281)
Q Consensus 265 ~C~~Cpl~~~C~~~~ 279 (281)
|+.|||+..|.+|.
T Consensus 201 -~~~cpL~~~~~~~~ 214 (215)
T COG2231 201 -CEKCPLKEKCKKYR 214 (215)
T ss_pred -CCCchHHHHHhhcc
Confidence 99999999998875
No 7
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=8.4e-44 Score=302.60 Aligned_cols=212 Identities=27% Similarity=0.358 Sum_probs=195.8
Q ss_pred hHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC-CCHHHHHhCCHHHHHH
Q 023471 49 VKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTF-PTWEHVLAAEQKCIEN 127 (281)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~-pt~~~la~~~~eel~~ 127 (281)
+.+|.||++..+|||.+||.- .+.....+....|++||+.+||.||.++....++.+|.+.. .|+++|.++++..|.+
T Consensus 46 ~~ir~mR~k~~APVD~mGc~~-~~~~~~~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~ 124 (286)
T KOG1921|consen 46 ERIRKMRSKIVAPVDTMGCSR-IPSLKADPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNE 124 (286)
T ss_pred HHHHHHhhcccCCcccccccc-CccccCChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHh
Confidence 457889999999999999974 33335556677899999999999999999999999999998 6999999999999999
Q ss_pred HhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC-CccccchHHHHH
Q 023471 128 AIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEI 206 (281)
Q Consensus 128 ~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri 206 (281)
+|.++||+++||+||+..|+.+.++|+| |+|...+.|++|||||||+|..+|..|+|. ..+.||+||+|+
T Consensus 125 LI~~VgFy~rKA~ylkkta~IL~d~f~g---------DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi 195 (286)
T KOG1921|consen 125 LIYPVGFYTRKAKYLKKTAKILQDKFDG---------DIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRI 195 (286)
T ss_pred hhhhccchHHHHHHHHHHHHHHHHHhCC---------CCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHH
Confidence 9999999999999999999999999999 899999999999999999999999999999 999999999999
Q ss_pred HHHhCCCCC-CCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCCCCCC-hhhccccc
Q 023471 207 SKAIGWVPT-AADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPL-LNYCEKSN 279 (281)
Q Consensus 207 ~~rlG~~~~-~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~~Cpl-~~~C~~~~ 279 (281)
++||||++. ..++++++.+|+.|+|+..|.++|.+||.||+. +|.++. |+ |+.|-+ +++|++..
T Consensus 196 ~nrlgWv~~ktkspE~TR~aLq~wLPk~lW~eIN~lLVGFGQ~--iC~p~~-pr------C~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 196 CNRLGWVDTKTKSPEQTRVALQQWLPKSLWVEINHLLVGFGQT--ICTPRR-PR------CGLCLLSRDLCPSSF 261 (286)
T ss_pred HHHhcccccccCCHHHHHHHHHHhCcHHHHhhhhceeecccce--eeecCC-CC------ccccccCcccCchhh
Confidence 999999974 345999999999999999999999999999999 999995 43 999999 69999854
No 8
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.1e-42 Score=300.04 Aligned_cols=188 Identities=16% Similarity=0.191 Sum_probs=167.8
Q ss_pred HHHHHHHHHHH----hhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHH
Q 023471 30 ECRGIRDELLA----LHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFA 105 (281)
Q Consensus 30 ~~~~v~~~L~~----~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~ 105 (281)
...+++..|.+ .+|++.| | +..++|++||++||+|||+|+++.+++.
T Consensus 3 ~~~~l~~~l~~~~~~~~~~~~W---W--------------------------p~~~~fevLV~aILsQqT~~~~v~~a~~ 53 (218)
T PRK13913 3 DSFELLKALKSLDLLKNAPAWW---W--------------------------PNALKFEALLGAVLTQNTKFEAVEKSLE 53 (218)
T ss_pred cHHHHHHHHHhhhhhhcCCCCC---C--------------------------cCcCHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 45688999999 8999888 4 2689999999999999999999999999
Q ss_pred HHHhh-------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcC
Q 023471 106 SLKST-------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRG 178 (281)
Q Consensus 106 ~L~~~-------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~G 178 (281)
+|+++ +|||++|++++.++|+++|+++||+++||++|+++|+.+.+++|++ +.+ ..++++++|+++||
T Consensus 54 ~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~--~~~---~~~~~re~Ll~l~G 128 (218)
T PRK13913 54 NLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSF--ENF---KQEVTREWLLDQKG 128 (218)
T ss_pred HHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCc--hhc---cCchHHHHHHcCCC
Confidence 99985 5699999999999999999999999999999999999999988763 222 34678999999999
Q ss_pred ccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCC-----------c-----ccHHHHHHHH
Q 023471 179 IGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIP-----------K-----ELKFDLNCLL 242 (281)
Q Consensus 179 IG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p-----------~-----~~~~~~h~~l 242 (281)
||+||||+||+|++|+++|+||+|++|++.|+|+.. .+|++++..++..++ . ..+.+||++|
T Consensus 129 IG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Hali 206 (218)
T PRK13913 129 IGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKI 206 (218)
T ss_pred ccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhhhhhhhhhccccccchHHHHHHHHHHHH
Confidence 999999999999999999999999999999999964 579999999998762 1 2478999999
Q ss_pred HHhcccCCCCcCC
Q 023471 243 YTHGKLCRNCIKK 255 (281)
Q Consensus 243 v~~G~~c~~C~~~ 255 (281)
|+||+. +|.-+
T Consensus 207 ve~~k~--~~~~~ 217 (218)
T PRK13913 207 VEFSKQ--KLELK 217 (218)
T ss_pred HHHHHH--hhhcc
Confidence 999999 88643
No 9
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=1.5e-38 Score=285.30 Aligned_cols=169 Identities=21% Similarity=0.306 Sum_probs=154.4
Q ss_pred HhhhccHHHHHH-HHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHH
Q 023471 91 LSQNTTEANSLK-AFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEI 169 (281)
Q Consensus 91 Lsqqts~~~a~~-~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~ 169 (281)
|+|||+.+++.. .+.+|+++|||+++|++++++||.++|+++||++ ||++|+++|+.+.++|+| ..+..
T Consensus 1 mlQQT~v~~v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g---------~~P~~ 70 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS---------QLPND 70 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC---------CCChh
Confidence 589999999975 9999999999999999999999999999999995 999999999999998877 45678
Q ss_pred HHHHhcCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHh-CCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhccc
Q 023471 170 KAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAI-GWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKL 248 (281)
Q Consensus 170 ~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rl-G~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~ 248 (281)
+++|++|||||+|||++||+|+||+++++||+||+|++.|+ |+. ...++.+++...+.++|.+.+.++|++||+||+.
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~af~~~~~~VD~nV~RVl~Rl~g~~-~~~~~~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~ 149 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGLD-PNIHAKDLQIKANDFLNLNESFNHNQALIDLGAL 149 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHCCCCcCcccHHHHHHHHHHhcCC-CCccHHHHHHHHHHhCCccchHHHHHHHHHHhHH
Confidence 99999999999999999999999999999999999999996 664 4566777777778899999999999999999999
Q ss_pred CCCCcCCCCCCCcCCCCCCCCCChhhcccccC
Q 023471 249 CRNCIKKGGNRQRKESAGNLCPLLNYCEKSNK 280 (281)
Q Consensus 249 c~~C~~~~~p~~p~~~~C~~Cpl~~~C~~~~~ 280 (281)
+|+++ |. |+.|||++.|.+|+.
T Consensus 150 --iC~~~--P~------C~~CPl~~~C~~~~~ 171 (289)
T PRK13910 150 --ICSPK--PK------CAICPLNPYCLGKNN 171 (289)
T ss_pred --HcCCC--CC------CCCCcChhhhhhhhc
Confidence 99984 54 999999999999864
No 10
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-36 Score=273.15 Aligned_cols=206 Identities=19% Similarity=0.277 Sum_probs=181.0
Q ss_pred HHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHh
Q 023471 30 ECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKS 109 (281)
Q Consensus 30 ~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~ 109 (281)
+...+.+.|++||...++..+| +...+||.++|++||+|||+.+.|...+.++.+
T Consensus 7 ~~~~~~~~ll~Wy~~~~R~LPW-------------------------R~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~ 61 (342)
T COG1194 7 DIEKFQEALLDWYDKNGRDLPW-------------------------RETKDPYRVWVSEIMLQQTQVATVIPYYERFLE 61 (342)
T ss_pred hhHHHHHHHHHHHHHhCCcCCC-------------------------CCCCCcceehhHHHHhhhccHhhhhhhHHHHHH
Confidence 3455688999999888875666 346779999999999999999999999999999
Q ss_pred hCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHH
Q 023471 110 TFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 110 ~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
+|||+++||+++.+||..++.++||+. ||+.|++.|+.+.++||| ..|+..+.|.+|||||++||..|+.
T Consensus 62 rfPti~~LA~A~~~evl~~W~gLGYys-RArnL~~~A~~v~~~~~G---------~~P~~~~~l~~LpGiG~yTa~Ail~ 131 (342)
T COG1194 62 RFPTIKALAAAPEDEVLKAWEGLGYYS-RARNLHKAAQEVVERHGG---------EFPDDEEELAALPGVGPYTAGAILS 131 (342)
T ss_pred hCCCHHHHhcCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCC---------CCCCCHHHHHhCCCCcHHHHHHHHH
Confidence 999999999999999999999999775 999999999999999999 4788899999999999999999999
Q ss_pred HhcCCCccccchHHHHHHHHhCCCCCC----CCHHHHHHHHHhhCCccc-HHHHHHHHHHhcccCCCCcCCCCCCCcCCC
Q 023471 190 FHLQQDDFPVDTHVFEISKAIGWVPTA----ADRNKTYLHLNQRIPKEL-KFDLNCLLYTHGKLCRNCIKKGGNRQRKES 264 (281)
Q Consensus 190 ~~~~~~~~~vD~~v~Ri~~rlG~~~~~----~~~~~~~~~l~~~~p~~~-~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~ 264 (281)
|++|.+...||+||.|++.|+.-+... .+...+...++..+..+. ..+|+++||++|.. +|++++ | +
T Consensus 132 ~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~p~~~~~~fnqammdlGA~--ICt~~~-P---~-- 203 (342)
T COG1194 132 FAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAMMDLGAT--ICTAKK-P---K-- 203 (342)
T ss_pred HHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHHhcCCCCChHHHHHHHHHhhhH--hhcCCC-C---C--
Confidence 999999999999999999997554432 245566777788555554 89999999999999 999984 4 3
Q ss_pred CCCCCCChhhccccc
Q 023471 265 AGNLCPLLNYCEKSN 279 (281)
Q Consensus 265 ~C~~Cpl~~~C~~~~ 279 (281)
|+.|||++.|..|.
T Consensus 204 -C~~CPl~~~c~a~~ 217 (342)
T COG1194 204 -CSLCPLRDNCAAYR 217 (342)
T ss_pred -CCcCcchHHHHHHH
Confidence 99999999998764
No 11
>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=1e-32 Score=228.60 Aligned_cols=157 Identities=33% Similarity=0.466 Sum_probs=148.0
Q ss_pred HHHHHHHHHhhhccHHHHHHHHHHHHhhC-CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHH
Q 023471 83 LDGLVKTVLSQNTTEANSLKAFASLKSTF-PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYL 161 (281)
Q Consensus 83 fe~Lv~~ILsqqts~~~a~~~~~~L~~~~-pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l 161 (281)
||+||++||+|||+++++..++.+|.++| |||++|+.+++++|.+++.++| +++||++|+++++.+.+.+++...
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~--- 76 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVL--- 76 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccC---
Confidence 68999999999999999999999999999 9999999999999999999999 788999999999999997776432
Q ss_pred hcCChHHHHHHHhcCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHH
Q 023471 162 RGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCL 241 (281)
Q Consensus 162 ~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~ 241 (281)
+.+++++.|++|||||+|||++|++|+++.++||+|+|+.|++.|+|+++...+++++++.++.++|......+|.+
T Consensus 77 ---~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (158)
T cd00056 77 ---DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLPKPYWGEANQA 153 (158)
T ss_pred ---CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH
Confidence 56889999999999999999999999999999999999999999999977778999999999999998888999999
Q ss_pred HHHhc
Q 023471 242 LYTHG 246 (281)
Q Consensus 242 lv~~G 246 (281)
|++||
T Consensus 154 l~~~g 158 (158)
T cd00056 154 LMDLG 158 (158)
T ss_pred HHHcC
Confidence 99997
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=1.3e-32 Score=225.80 Aligned_cols=149 Identities=34% Similarity=0.453 Sum_probs=141.4
Q ss_pred HhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHH
Q 023471 91 LSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIK 170 (281)
Q Consensus 91 Lsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~ 170 (281)
|+|||+++++..++.+|.+.||||++|+.+++++|.++|+++||+++||++|+++++.+.+.+++ +.++.+
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~---------~~~~~~ 71 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG---------EVPDDR 71 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC---------CccHHH
Confidence 68999999999999999999999999999999999999999999999999999999999987765 356789
Q ss_pred HHHhcCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhccc
Q 023471 171 AELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKL 248 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~ 248 (281)
+.|++|||||+|||++|++|+++++++++|+|+.|++.|+|+++...+++++++.++.++|.+.|..+|.+++.||+.
T Consensus 72 ~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 72 EELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPKEDWRELNLLLIDFGRT 149 (149)
T ss_pred HHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHcCC
Confidence 999999999999999999999999999999999999999999887788999999999999999999999999999973
No 13
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.97 E-value=1.2e-29 Score=217.08 Aligned_cols=142 Identities=18% Similarity=0.157 Sum_probs=123.8
Q ss_pred CCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCC--CchHHHHHHHHHHHHH---HHH
Q 023471 78 EEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGG--LAPTKAACIKNILKCL---LES 152 (281)
Q Consensus 78 ~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G--~~~~KA~~I~~~a~~i---~~~ 152 (281)
...++|+.||++||||||+|+++.+++.+|. ++.+ .++.++|+++|+++| |+++||++|+++++.+ .+.
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~ 106 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEIG-----DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEI 106 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-----HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999994 4556 899999999999995 9999999999999984 222
Q ss_pred cCCCchHHHhcCChHHHHHHHh-cCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCC------CCCHHHHHHH
Q 023471 153 KGKLCLEYLRGLSIDEIKAELS-RFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPT------AADRNKTYLH 225 (281)
Q Consensus 153 ~g~~~l~~l~~~~~~~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~------~~~~~~~~~~ 225 (281)
+ . .+.+.++++++|+ ++||||+|||++||++...+++|+||+|++|++.|+|+++. ..+|.+++..
T Consensus 107 ~------~-~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~ 179 (208)
T PRK01229 107 I------K-ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEI 179 (208)
T ss_pred H------h-ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHH
Confidence 2 0 1336789999999 99999999999999866558999999999999999999875 2689999999
Q ss_pred HHhhCCc
Q 023471 226 LNQRIPK 232 (281)
Q Consensus 226 l~~~~p~ 232 (281)
|.+..+.
T Consensus 180 l~~~~~~ 186 (208)
T PRK01229 180 LREIAEE 186 (208)
T ss_pred HHHHHHH
Confidence 9887764
No 14
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.96 E-value=1.2e-29 Score=228.26 Aligned_cols=216 Identities=17% Similarity=0.201 Sum_probs=182.1
Q ss_pred HHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHH
Q 023471 29 EECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLK 108 (281)
Q Consensus 29 ~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~ 108 (281)
.+++.++.-|++||....+-.+||+-+.+- . ..-....|+++|+.||+|||+.+.+.+.+.+++
T Consensus 88 ~Ev~~fR~sLl~wYD~~KRdLPWR~r~sEd-----e-----------~DwerRaYeVwVSEiMLQQTrV~TV~~YYt~WM 151 (555)
T KOG2457|consen 88 NEVQKFRMSLLDWYDVNKRDLPWRNRRSED-----E-----------KDWERRAYEVWVSEIMLQQTRVQTVMKYYTRWM 151 (555)
T ss_pred HHHHHHHHHHHHHhhhhcccCccccCCccc-----h-----------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 366888999999999998888886543220 0 011346899999999999999999999999999
Q ss_pred hhCCCHHHHHhCCH-HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc-CcCccHHHHHH
Q 023471 109 STFPTWEHVLAAEQ-KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR-FRGIGPKTVAC 186 (281)
Q Consensus 109 ~~~pt~~~la~~~~-eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~-l~GIG~~tA~~ 186 (281)
+.+||..+++.++. ++|.++|.++|||. |+++|++.|+.+++..+| ..|..-+.|.+ +||||+|||..
T Consensus 152 qkwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~g---------e~Prta~~l~kgvpGVG~YTAGA 221 (555)
T KOG2457|consen 152 QKWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEG---------EFPRTASSLMKGVPGVGQYTAGA 221 (555)
T ss_pred HhCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCC---------CCCChHHHHHhhCCCCCccchhh
Confidence 99999999999998 79999999999996 999999999999998777 46777788876 99999999999
Q ss_pred HHHHhcCCCccccchHHHHHHHHhCCCCCCCCH----HHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcC
Q 023471 187 VLMFHLQQDDFPVDTHVFEISKAIGWVPTAADR----NKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRK 262 (281)
Q Consensus 187 il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~----~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~ 262 (281)
|+..|||...=+||.||.|++.|.--+..+.+. ...-...++++.+..+++||++||++|.. .|++.+ |.
T Consensus 222 iaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~~wkLA~qLVDP~RPGDFNQalMELGAt--~CTpq~-P~--- 295 (555)
T KOG2457|consen 222 IASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQSSWKLAAQLVDPSRPGDFNQALMELGAT--LCTPQK-PS--- 295 (555)
T ss_pred hhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHHHHHHHHHhcCCCCCCcHHHHHHHhcCe--eccCCC-CC---
Confidence 999999999999999999999985443333332 22334456788888999999999999999 999984 43
Q ss_pred CCCCCCCCChhhccccc
Q 023471 263 ESAGNLCPLLNYCEKSN 279 (281)
Q Consensus 263 ~~~C~~Cpl~~~C~~~~ 279 (281)
|+.||+...|..|+
T Consensus 296 ---CS~CPvss~CrA~q 309 (555)
T KOG2457|consen 296 ---CSSCPVSSQCRAFQ 309 (555)
T ss_pred ---cCCCCcHHHHHHHh
Confidence 99999999999875
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=1.6e-26 Score=210.85 Aligned_cols=148 Identities=25% Similarity=0.449 Sum_probs=126.5
Q ss_pred CCHHHHHHHHHHhhhccHHHHHHHHHHHHhh---------------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHH
Q 023471 80 ESVLDGLVKTVLSQNTTEANSLKAFASLKST---------------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKN 144 (281)
Q Consensus 80 ~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~---------------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~ 144 (281)
.|+||+||++|++||+++.++.+++.+|.++ ||||++|+.++.+ +.|+.+||++ ||++|++
T Consensus 117 ~d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e---~~Lr~~G~g~-Ra~~I~~ 192 (310)
T TIGR00588 117 QDPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAE---AHLRKLGLGY-RARYIRE 192 (310)
T ss_pred CCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChH---HHHHHcCCHH-HHHHHHH
Confidence 4999999999999999999999999999763 7889999986643 4688899965 8999999
Q ss_pred HHHHHHHHcCCC-chHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC-CccccchHHHHHHHHh-CCCC-------
Q 023471 145 ILKCLLESKGKL-CLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEISKAI-GWVP------- 214 (281)
Q Consensus 145 ~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri~~rl-G~~~------- 214 (281)
+|+.+.+.+++. +++.+.+++.++++++|++|||||+|||++|++|++|+ ++||||+|++|++.|+ |+.+
T Consensus 193 ~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~ 272 (310)
T TIGR00588 193 TARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKG 272 (310)
T ss_pred HHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhccccccccccc
Confidence 999999976655 78888999999999999999999999999999999999 7999999999999996 5532
Q ss_pred -CCCCHHHHHHHHHhhCC
Q 023471 215 -TAADRNKTYLHLNQRIP 231 (281)
Q Consensus 215 -~~~~~~~~~~~l~~~~p 231 (281)
...++++++....+.+.
T Consensus 273 ~~~~~~~~i~~~~~~~~g 290 (310)
T TIGR00588 273 PSPFARKELGNFFRSLWG 290 (310)
T ss_pred CChhHHHHHHHHHHHHhc
Confidence 12345666666666555
No 16
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.94 E-value=3e-25 Score=199.63 Aligned_cols=165 Identities=30% Similarity=0.386 Sum_probs=142.0
Q ss_pred CCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhh----------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHH
Q 023471 77 GEEESVLDGLVKTVLSQNTTEANSLKAFASLKST----------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNIL 146 (281)
Q Consensus 77 ~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~----------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a 146 (281)
....|+||.||++|++||.|.+.|.+++.+|.+. ||||++|+.++++. ++.+|++..|++||+++|
T Consensus 100 ~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~----l~~~g~s~~Ka~yi~~~A 175 (285)
T COG0122 100 PLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEA----LRRCGLSGRKAEYIISLA 175 (285)
T ss_pred CCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHH----HHHhCCcHHHHHHHHHHH
Confidence 3468999999999999999999999999999985 57899999999865 457999999999999999
Q ss_pred HHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC-CccccchH-HHHHHHHhCCCCCCCCHHHHHH
Q 023471 147 KCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTH-VFEISKAIGWVPTAADRNKTYL 224 (281)
Q Consensus 147 ~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~-v~Ri~~rlG~~~~~~~~~~~~~ 224 (281)
+.+.+ |.++++.+.+++.+++++.|++|+|||+|||++||+|++|+ ++||+|++ +++..++++..+...+...+..
T Consensus 176 ~~~~~--g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~ 253 (285)
T COG0122 176 RAAAE--GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRE 253 (285)
T ss_pred HHHHc--CCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCchHHHHHH
Confidence 99998 77899999999999999999999999999999999999999 99997555 5556777763344445555678
Q ss_pred HHHhhCCcccHHHHHHHHHHhcc
Q 023471 225 HLNQRIPKELKFDLNCLLYTHGK 247 (281)
Q Consensus 225 ~l~~~~p~~~~~~~h~~lv~~G~ 247 (281)
..+.+-|...+..+|.|-...+.
T Consensus 254 ~~e~w~p~rs~A~~yLw~~~~~~ 276 (285)
T COG0122 254 LAERWGPYRSYAALYLWRYARAT 276 (285)
T ss_pred HHhcccCHHHHHHHHHHHhhhcc
Confidence 88899999988888888665443
No 17
>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=99.93 E-value=4e-25 Score=183.51 Aligned_cols=119 Identities=10% Similarity=0.073 Sum_probs=106.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhC----CCchHHHHHHHHHHH
Q 023471 74 YDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCG----GLAPTKAACIKNILK 147 (281)
Q Consensus 74 ~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~----G~~~~KA~~I~~~a~ 147 (281)
+......+||++||++||||||+|++|.+++.+|++++ +||++|+.++.++|+++|++. ||+++||++|+++++
T Consensus 10 ~~~l~~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~ 89 (177)
T TIGR03252 10 ADELLSSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQ 89 (177)
T ss_pred ccccccCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHH
Confidence 34445789999999999999999999999999998765 699999999999999999865 999999999999999
Q ss_pred HHHHHcCCCchHHHhc---CChHHHHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 148 CLLESKGKLCLEYLRG---LSIDEIKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 148 ~i~~~~g~~~l~~l~~---~~~~~~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
.|.++|+| +++.|.. .+..+++++|++|||||+|||++||.+...
T Consensus 90 ~iie~y~G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 90 YVVDTYDG-DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHHHHhCC-ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 99999998 8888876 456678999999999999999999985433
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.92 E-value=3.6e-24 Score=192.81 Aligned_cols=186 Identities=18% Similarity=0.135 Sum_probs=149.7
Q ss_pred HHHHHHHHHHhhCCChhhhHHHH-hhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHHh
Q 023471 31 CRGIRDELLALHGFPPEFVKYRN-QRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKS 109 (281)
Q Consensus 31 ~~~v~~~L~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~ 109 (281)
...+...+..+++....+..+.. ++.. +. ..++.+.....|+||.+|++|++||+|...+.+...+|.+
T Consensus 71 ~~~~~~~vrr~fdLd~d~~~i~~~L~~~----~~------~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~ 140 (283)
T PRK10308 71 AAECLAKMSRLFDLQCNPQIVNGALGKL----GA------ARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQ 140 (283)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHH----HH------hCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 44678888888888877665521 1100 00 1123334457999999999999999999999999999987
Q ss_pred h-------------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 110 T-------------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 110 ~-------------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
+ ||||++|+++++++|. .+|++++|+++|+++|+.+.+ |.++++... +.+++++.|++|
T Consensus 141 ~~G~~l~~~~~~~~FPtpe~La~~~~~eL~----~~Gl~~~Ra~~L~~lA~~i~~--g~l~l~~~~--~~~~~~~~L~~L 212 (283)
T PRK10308 141 LYGERLDDFPEYVCFPTPERLAAADPQALK----ALGMPLKRAEALIHLANAALE--GTLPLTIPG--DVEQAMKTLQTF 212 (283)
T ss_pred HhCccccCCCCccCCCCHHHHHcCCHHHHH----HCCCCHHHHHHHHHHHHHHHc--CCCCccccC--CHHHHHHHHhcC
Confidence 5 5789999999988754 689999999999999999998 777766543 568899999999
Q ss_pred cCccHHHHHHHHHHhcCC-Ccc-ccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHH
Q 023471 177 RGIGPKTVACVLMFHLQQ-DDF-PVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCL 241 (281)
Q Consensus 177 ~GIG~~tA~~il~~~~~~-~~~-~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~ 241 (281)
||||+|||++|++|++|+ ++| +.|.++++.+ + ..++++++...+.|-|+..+..+|.|
T Consensus 213 pGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----~~~~~~~~~~a~~w~P~rsya~~~LW 272 (283)
T PRK10308 213 PGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----GMTPAQIRRYAERWKPWRSYALLHIW 272 (283)
T ss_pred CCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----cCCHHHHHHHHHhcCCHHHHHHHHHH
Confidence 999999999999999999 999 5577777633 2 24788899999999999999999988
No 19
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.87 E-value=8.6e-22 Score=165.79 Aligned_cols=158 Identities=20% Similarity=0.252 Sum_probs=134.6
Q ss_pred CCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhh------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 78 EEESVLDGLVKTVLSQNTTEANSLKAFASLKST------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 78 ~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
+.+.||+.|+++|++||.+.++|..+++++... |++|+.+..++.++ |+.|||+.+|+.||+.+|.+..+
T Consensus 71 ~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~----lrkcG~S~rK~~yLh~lA~~~~n 146 (254)
T KOG1918|consen 71 ETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEE----LRKCGFSKRKASYLHSLAEAYTN 146 (254)
T ss_pred cccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHH----HHHhCcchhhHHHHHHHHHHHhc
Confidence 578899999999999999999999999999975 57899999999876 56699999999999999999997
Q ss_pred HcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC-CccccchHHHHH-HHH-hCCCCCCCCHHHHHHHHHh
Q 023471 152 SKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEI-SKA-IGWVPTAADRNKTYLHLNQ 228 (281)
Q Consensus 152 ~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri-~~r-lG~~~~~~~~~~~~~~l~~ 228 (281)
.| -.+.+.+.+|+.+++.+.|+.++|||+||+.++|.|.++| |++|+|+...|- .+. +|+ ++-+.+.++++..+.
T Consensus 147 g~-I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl-~~~p~~~evekl~e~ 224 (254)
T KOG1918|consen 147 GY-IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGL-KPLPLPKEVEKLCEK 224 (254)
T ss_pred CC-CCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCC-CCCCchHHHHHHhhh
Confidence 22 3377788899999999999999999999999999999999 999999987773 333 566 445678889999888
Q ss_pred hCCcccHHHHHHH
Q 023471 229 RIPKELKFDLNCL 241 (281)
Q Consensus 229 ~~p~~~~~~~h~~ 241 (281)
+-|....+.|..|
T Consensus 225 ~kpyRtvaawYlW 237 (254)
T KOG1918|consen 225 CKPYRTVAAWYLW 237 (254)
T ss_pred ccchHHHHHHHHH
Confidence 8887665544433
No 20
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.87 E-value=2.3e-21 Score=168.56 Aligned_cols=128 Identities=25% Similarity=0.442 Sum_probs=117.9
Q ss_pred CCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhh---------------CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHH
Q 023471 78 EEESVLDGLVKTVLSQNTTEANSLKAFASLKST---------------FPTWEHVLAAEQKCIENAIRCGGLAPTKAACI 142 (281)
Q Consensus 78 ~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~---------------~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I 142 (281)
...+|+|.|++.|+|+|.+.++...+.++|... ||+.++++. .++++.+|.+||.+ ||+||
T Consensus 113 LrQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGY-RAkYI 188 (323)
T KOG2875|consen 113 LRQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGY-RAKYI 188 (323)
T ss_pred HhcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcch-hHHHH
Confidence 468999999999999999999999999998885 567888775 67788999999998 99999
Q ss_pred HHHHHHHHHHcCCC-chHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC-CccccchHHHHHHHH
Q 023471 143 KNILKCLLESKGKL-CLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEISKA 209 (281)
Q Consensus 143 ~~~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri~~r 209 (281)
...|++|.++.|+. .|..+++++.+++++.|..+||||+|+||||++++++. .++|||+|+.|++.-
T Consensus 189 ~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~ 257 (323)
T KOG2875|consen 189 SATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQD 257 (323)
T ss_pred HHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhc
Confidence 99999999998884 67788899999999999999999999999999999999 899999999999994
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=99.81 E-value=4.7e-19 Score=137.47 Aligned_cols=103 Identities=28% Similarity=0.392 Sum_probs=93.6
Q ss_pred HHHHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcC
Q 023471 87 VKTVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGL 164 (281)
Q Consensus 87 v~~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~ 164 (281)
|++||+|||+++++.+++.+|.++| |||++|+.+++++|.++|+++||+++||++|+++++.+.
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 7899999999999999999999994 899999999999999999999999999999999999987
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcCC--CccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQQ--DDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIP 231 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~--~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p 231 (281)
|+ .++++|.|+.|++.|+|+++...+++++++.+++.++
T Consensus 67 ----------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~ 107 (108)
T PF00730_consen 67 ----------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWP 107 (108)
T ss_dssp ----------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGT
T ss_pred ----------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCc
Confidence 65 4899999999999999998877899999999977765
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.36 E-value=3.9e-12 Score=105.40 Aligned_cols=127 Identities=18% Similarity=0.197 Sum_probs=105.1
Q ss_pred CCCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCC--CchHHHHHHHHHHHHHHHHcCC
Q 023471 78 EEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGG--LAPTKAACIKNILKCLLESKGK 155 (281)
Q Consensus 78 ~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G--~~~~KA~~I~~~a~~i~~~~g~ 155 (281)
...+.|.-|..+||+.|+|...+.++...|-+. +..++.+||.+.++.+| |+++||+||.+.-+.+.
T Consensus 35 ~~e~lf~ELsFCILTANsSA~~~~~~q~~lG~g------fly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~----- 103 (210)
T COG1059 35 TKEDLFKELSFCILTANSSATMGLRAQNELGDG------FLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD----- 103 (210)
T ss_pred cHHHHHHHHHHHhccccchHHHHHHHHHHhccc------cccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH-----
Confidence 357789999999999999999999999988755 45668999999999995 78999999999777663
Q ss_pred CchHHHhcCChHH--HHHHHh-cCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCCC
Q 023471 156 LCLEYLRGLSIDE--IKAELS-RFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTA 216 (281)
Q Consensus 156 ~~l~~l~~~~~~~--~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~ 216 (281)
++..+-+.+..+ +|+.|. .++|||-|-|+++|....-.|+..+|.|+.|.+.|.|.+.+.
T Consensus 104 -~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~ 166 (210)
T COG1059 104 -DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDEN 166 (210)
T ss_pred -HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccC
Confidence 334444333222 889988 999999999999998665569999999999999999998643
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=98.09 E-value=1.5e-06 Score=51.37 Aligned_cols=25 Identities=44% Similarity=0.705 Sum_probs=21.0
Q ss_pred hHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 166 IDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 166 ~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.+..+++|+++||||++||+.|+.|
T Consensus 6 ~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 6 IPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 3556899999999999999999876
No 24
>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=97.17 E-value=0.016 Score=48.78 Aligned_cols=110 Identities=13% Similarity=0.154 Sum_probs=83.6
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchH--HHHHHHHHHHHHHHHcC
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPT--KAACIKNILKCLLESKG 154 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~--KA~~I~~~a~~i~~~~g 154 (281)
....||.|+-.++-.-.||..+.+-...+.++| -+++.|+..+++++++++..-|+-+. |.+.+.+-|+.+.+-..
T Consensus 27 d~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~i~~ 106 (179)
T TIGR00624 27 SVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQLEQ 106 (179)
T ss_pred CHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999998 48999999999999999999998654 45567777777765222
Q ss_pred CCchHHHh-c----C---------------C--hHHHHHHHh--cCcCccHHHHHHHHH
Q 023471 155 KLCLEYLR-G----L---------------S--IDEIKAELS--RFRGIGPKTVACVLM 189 (281)
Q Consensus 155 ~~~l~~l~-~----~---------------~--~~~~~~~L~--~l~GIG~~tA~~il~ 189 (281)
. ++...- . . + ...+-+.|. .++-|||-|+.++|+
T Consensus 107 e-sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~~lskdLKkrGfkFvGpt~~ysfmq 164 (179)
T TIGR00624 107 N-DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESKAMSKELKKRGFRFVGPTICYALMQ 164 (179)
T ss_pred c-cHHHHHHhccCCCCccCCccccccCCCCCHHHHHHHHHHHHcCCeecChHHHHHHHH
Confidence 2 333221 1 1 1 344555665 378899999988887
No 25
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=97.09 E-value=0.012 Score=49.81 Aligned_cols=110 Identities=13% Similarity=0.196 Sum_probs=83.6
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCc--hHHHHHHHHHHHHHHH---
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLA--PTKAACIKNILKCLLE--- 151 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~--~~KA~~I~~~a~~i~~--- 151 (281)
....||.|+-+.+-.-.||..+.+-...+.++| -+++.|+..++++|++++..-|+- +.|.+.+.+-|+.+.+
T Consensus 28 d~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~ 107 (187)
T PRK10353 28 SKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQ 107 (187)
T ss_pred cHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999998 489999999999999999999984 4566677777777653
Q ss_pred HcCCCchHHHh----------------cC---C--hHHHHHHHh--cCcCccHHHHHHHHH
Q 023471 152 SKGKLCLEYLR----------------GL---S--IDEIKAELS--RFRGIGPKTVACVLM 189 (281)
Q Consensus 152 ~~g~~~l~~l~----------------~~---~--~~~~~~~L~--~l~GIG~~tA~~il~ 189 (281)
++|+++ +.+. +. + ...+-+.|. .++-|||-|+.++|+
T Consensus 108 e~gSf~-~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrGFkFvGpt~~ysfmq 167 (187)
T PRK10353 108 NGEPFA-DFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRGFKFVGTTICYSFMQ 167 (187)
T ss_pred hcCCHH-HHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcCCcccCcHHHHHHHH
Confidence 444431 1221 11 1 124455665 378899999988887
No 26
>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=96.95 E-value=0.018 Score=48.54 Aligned_cols=113 Identities=20% Similarity=0.326 Sum_probs=79.2
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCC--CHHHHHhCCHHHHHHHhhhCCC--chHHHHHHHHHHHHHHH---
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTFP--TWEHVLAAEQKCIENAIRCGGL--APTKAACIKNILKCLLE--- 151 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~p--t~~~la~~~~eel~~~i~~~G~--~~~KA~~I~~~a~~i~~--- 151 (281)
....||.|+-.++-.--||..+.+-...+.++|- +++.|+..++++|++++..-|+ .+.|.+.+.+-|+.+.+
T Consensus 23 D~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~ 102 (179)
T PF03352_consen 23 DRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQE 102 (179)
T ss_dssp HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999999999999999994 7999999999999999999998 56788888888888753
Q ss_pred HcCCCchHHHhc----------------C-----ChHHHHHHHh--cCcCccHHHHHHHHHHhcC
Q 023471 152 SKGKLCLEYLRG----------------L-----SIDEIKAELS--RFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 152 ~~g~~~l~~l~~----------------~-----~~~~~~~~L~--~l~GIG~~tA~~il~~~~~ 193 (281)
++|+++ +.+.+ + -...+-+.|. .++-|||.|+.++|. |.|
T Consensus 103 e~gsF~-~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vysflq-A~G 165 (179)
T PF03352_consen 103 EFGSFS-DYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYSFLQ-AIG 165 (179)
T ss_dssp TTS-HH-HHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHHHHH-HTT
T ss_pred hcCCHH-HHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHHHHH-HhC
Confidence 345431 11111 0 0234455565 478899999999888 444
No 27
>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=96.45 E-value=0.0011 Score=33.84 Aligned_cols=17 Identities=41% Similarity=1.107 Sum_probs=10.2
Q ss_pred CcCCCCCCCcCCCCCCCCCChhhc
Q 023471 252 CIKKGGNRQRKESAGNLCPLLNYC 275 (281)
Q Consensus 252 C~~~~~p~~p~~~~C~~Cpl~~~C 275 (281)
|+++ +|+ |+.|||+++|
T Consensus 1 Ctar----~P~---C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTAR----KPK---CEECPLADYC 17 (17)
T ss_dssp S-SS----S-----GGG-TTGGG-
T ss_pred CcCC----CCc---cccCCCcccC
Confidence 6676 344 9999999998
No 28
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=96.43 E-value=0.09 Score=44.30 Aligned_cols=77 Identities=17% Similarity=0.184 Sum_probs=64.0
Q ss_pred CCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCch--HHHHHHHHHHHHHH---HH
Q 023471 80 ESVLDGLVKTVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAP--TKAACIKNILKCLL---ES 152 (281)
Q Consensus 80 ~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~--~KA~~I~~~a~~i~---~~ 152 (281)
...||.|+-.+.-.-.||..+.+-..++.+.| -+|+.|+..+.++++.++...|+-+ .|.+.+..-|+.+. ++
T Consensus 30 ~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e 109 (188)
T COG2818 30 QRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKE 109 (188)
T ss_pred HHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 35799999999999999999999999999998 4899999999999999999999855 55556666666654 44
Q ss_pred cCCC
Q 023471 153 KGKL 156 (281)
Q Consensus 153 ~g~~ 156 (281)
+|++
T Consensus 110 ~Gsf 113 (188)
T COG2818 110 FGSF 113 (188)
T ss_pred cCCH
Confidence 5653
No 29
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.49 E-value=0.0081 Score=34.04 Aligned_cols=22 Identities=23% Similarity=0.608 Sum_probs=17.4
Q ss_pred CCcCCCCCCCcCCCCCCCCCChhhccccc
Q 023471 251 NCIKKGGNRQRKESAGNLCPLLNYCEKSN 279 (281)
Q Consensus 251 ~C~~~~~p~~p~~~~C~~Cpl~~~C~~~~ 279 (281)
+|++++ |+ |+.|||++.|.+|.
T Consensus 1 vC~ar~----P~---C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARK----PR---CDECPLKDLCPAYX 22 (26)
T ss_pred CccCCC----CC---CCCCcCHHHhhhhh
Confidence 588874 33 99999999999753
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=95.33 E-value=0.013 Score=33.18 Aligned_cols=20 Identities=45% Similarity=0.620 Sum_probs=17.4
Q ss_pred HHhcCcCccHHHHHHHHHHh
Q 023471 172 ELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 172 ~L~~l~GIG~~tA~~il~~~ 191 (281)
.|.+++|||+++|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999998743
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=95.13 E-value=0.14 Score=36.07 Aligned_cols=58 Identities=14% Similarity=0.165 Sum_probs=39.0
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+++.+.....|-...|+....+.+..|.. ++ .. +....+.|.+|||||+.+|.-|--|
T Consensus 9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~-~~--------i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 9 EELADLYELQGGDPFRARAYRRAAAAIKA-LP-YP--------ITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHHTSTSHHHHHHHHHHHHHHHH-SS-S---------HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCcHHHHHHHHHHHHHHh-CC-Hh--------HhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 34455555554445699999999999877 33 22 3333225999999999999987543
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.08 E-value=0.045 Score=38.12 Aligned_cols=40 Identities=38% Similarity=0.462 Sum_probs=27.1
Q ss_pred HHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 145 ILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 145 ~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.|+.+.+.|| +++.+... ..++|.+++|||+.+|..|..|
T Consensus 15 ~ak~L~~~f~--sl~~l~~a----~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFG--SLEALMNA----SVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCS--CHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcC--CHHHHHHc----CHHHHhccCCcCHHHHHHHHHH
Confidence 3455566666 56777654 3567999999999999999875
No 33
>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=93.89 E-value=2.4 Score=37.27 Aligned_cols=161 Identities=17% Similarity=0.244 Sum_probs=82.4
Q ss_pred HHHHHHHHHhhhccHHHHHHHHHHHHhhC-CCHH-HHHhCCHHHHHHHhhhCCCch---HHHHHHHHHHHHHHHHcCCCc
Q 023471 83 LDGLVKTVLSQNTTEANSLKAFASLKSTF-PTWE-HVLAAEQKCIENAIRCGGLAP---TKAACIKNILKCLLESKGKLC 157 (281)
Q Consensus 83 fe~Lv~~ILsqqts~~~a~~~~~~L~~~~-pt~~-~la~~~~eel~~~i~~~G~~~---~KA~~I~~~a~~i~~~~g~~~ 157 (281)
.-.+|+++|+=- +.++..+..+.|.+.. ++|. -|.+.+.+++.......-+.- .-...+....+.+..+||++
T Consensus 17 i~afiaA~lAyG-~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL- 94 (232)
T PF09674_consen 17 IAAFIAALLAYG-NRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL- 94 (232)
T ss_pred HHHHHHHHHHcc-CHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH-
Confidence 445556655544 4455555555665554 3444 455666666666666543322 23334445555556666653
Q ss_pred hHHHh------cCCh----HHHHHHHhcC------------------cCccHHHHHHHHHHhcCC-C-------------
Q 023471 158 LEYLR------GLSI----DEIKAELSRF------------------RGIGPKTVACVLMFHLQQ-D------------- 195 (281)
Q Consensus 158 l~~l~------~~~~----~~~~~~L~~l------------------~GIG~~tA~~il~~~~~~-~------------- 195 (281)
+.+- .-+. ....+.+.++ +|-.-|=..++|.---.+ .
T Consensus 95 -e~~f~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~p~~~SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps 173 (232)
T PF09674_consen 95 -EEAFAKGYNKSEDVLEAICAFIEEFFELPHSSRGYKHLFGLLPPPEKGSACKRLNMFLRWMVRKDSPVDFGLWSSIDPS 173 (232)
T ss_pred -HHHHHhhccCCCCHHHHHHHHHHHHHHhhcccccccccccccCCCCCCcHHHHHHHHHHhhccCCCCCCCcCCCCCCHH
Confidence 3222 1122 2233333331 111223344555432222 1
Q ss_pred --ccccchHHHHHHHHhCCCCCCC-C---HHHHHHHHHhhCCcccHHHHHHHHHHhcc
Q 023471 196 --DFPVDTHVFEISKAIGWVPTAA-D---RNKTYLHLNQRIPKELKFDLNCLLYTHGK 247 (281)
Q Consensus 196 --~~~vD~~v~Ri~~rlG~~~~~~-~---~~~~~~~l~~~~p~~~~~~~h~~lv~~G~ 247 (281)
++|+|+||.|++.+||++..+. + ..++.+.+.+..|.| +..+.-+|-.+|.
T Consensus 174 ~LiiPLDtHv~~var~LGL~~rk~~d~k~A~elT~~lr~~~p~D-PvKYDFAL~~~Gi 230 (232)
T PF09674_consen 174 DLIIPLDTHVFRVARKLGLLKRKSADWKAARELTEALREFDPDD-PVKYDFALFRLGI 230 (232)
T ss_pred HccccchHhHHHHHHHcCCccCCCccHHHHHHHHHHHHhcCCCC-CcchhhhcccCCc
Confidence 6899999999999999986432 2 234455566666644 3333334555553
No 34
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=93.53 E-value=0.28 Score=45.51 Aligned_cols=56 Identities=20% Similarity=0.196 Sum_probs=38.2
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCCc-hHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 132 GGLAPTKAACIKNILKCLLESKGKLC-LEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 132 ~G~~~~KA~~I~~~a~~i~~~~g~~~-l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
-|+...=|+.|.++.+ .|.+. +.....-+.+....+|++++||||+||..+-. +|.
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi 110 (334)
T smart00483 54 PGIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGI 110 (334)
T ss_pred CCccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCC
Confidence 3566555555655533 26655 44444557888999999999999999976644 554
No 35
>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=93.51 E-value=1.6 Score=38.28 Aligned_cols=157 Identities=19% Similarity=0.237 Sum_probs=77.0
Q ss_pred HHHHhhhccHHHHHHHHHHHHhh----C-CCHHH-HHhCCHHHHH-HHhhhCCCch---HHHHHHHHHHHHHHHHcCCCc
Q 023471 88 KTVLSQNTTEANSLKAFASLKST----F-PTWEH-VLAAEQKCIE-NAIRCGGLAP---TKAACIKNILKCLLESKGKLC 157 (281)
Q Consensus 88 ~~ILsqqts~~~a~~~~~~L~~~----~-pt~~~-la~~~~eel~-~~i~~~G~~~---~KA~~I~~~a~~i~~~~g~~~ 157 (281)
.+++..-.++-++..++..+..- . ++|.+ |..-+++++. +.+...-+.- .-...+...++.+.++||++
T Consensus 22 ~aliaA~~AyGn~k~I~~~l~~ld~~~~~~sp~~fv~~~~~~~~~~~~~~~f~yRf~~~~D~~~~~~~l~~~~~~~~sl- 100 (229)
T TIGR02757 22 SGLICALFSYGNRKAILKSLDKLDFSLLGNSPYAYLLSSTWAQLKNAGFKTFYYRFQNEKDIQAIFKTLYRIYESHGSL- 100 (229)
T ss_pred HHHHHHHHHccCHHHHHHHHHHhChhhccCCHHHHHHccCHhhhhhhhhcCCcccCCCHHHHHHHHHHHHHHHHhcCCH-
Confidence 44445555565655555554443 2 35553 4444444443 3343332221 23334455555566666653
Q ss_pred hHHHh-c----CChHH----HHHHHhcCcC--------ccH---HHHHHHHHHhcCCC---------------ccccchH
Q 023471 158 LEYLR-G----LSIDE----IKAELSRFRG--------IGP---KTVACVLMFHLQQD---------------DFPVDTH 202 (281)
Q Consensus 158 l~~l~-~----~~~~~----~~~~L~~l~G--------IG~---~tA~~il~~~~~~~---------------~~~vD~~ 202 (281)
+..- . .+... ..+.+.+++| -+. |=-+++|..--..+ ++|+|+|
T Consensus 101 -e~~f~~~~~~~~~~~~i~~f~~~~~~~~~~~~~~~~~~~~Sa~KR~nMFLRWMVR~d~VD~GlW~~i~ps~LiiPLDtH 179 (229)
T TIGR02757 101 -EELFYAAYYKGPPIERLSSFRKHIIKLNSYNNTIADPSGGSPLKRLNMFLRWMIRKDEVDLGIWESFKPSDLILPLDTH 179 (229)
T ss_pred -HHHHHhccccccHHHHHHHHHHHHHhccccccccCCCCCCchHHHHHHHHHhhccCCCCCCcCCCCCCHHHceeechHh
Confidence 3222 1 12222 2233333322 222 55566665433221 6899999
Q ss_pred HHHHHHHhCCCCCCC-C---HHHHHHHHHhhCCcccHHHHHHHHHHhcc
Q 023471 203 VFEISKAIGWVPTAA-D---RNKTYLHLNQRIPKELKFDLNCLLYTHGK 247 (281)
Q Consensus 203 v~Ri~~rlG~~~~~~-~---~~~~~~~l~~~~p~~~~~~~h~~lv~~G~ 247 (281)
|.|++.+||++.-+. + ..++-..|.++-|.| +..+.-+|-.+|.
T Consensus 180 ~~rvar~LgL~~Rk~~d~kaa~ElT~~Lr~~dp~D-PvKYDFAL~~lGi 227 (229)
T TIGR02757 180 VFRIAKKLKLLKRKSYDLKAAIEITEALRELNPED-PIKYDFALFRLGQ 227 (229)
T ss_pred HHHHHHHhCCcccCchhHHHHHHHHHHHHhcCCCC-CcchhhhcccCCc
Confidence 999999999986322 1 233444455555544 3333445555553
No 36
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=93.17 E-value=0.52 Score=32.08 Aligned_cols=49 Identities=31% Similarity=0.399 Sum_probs=32.4
Q ss_pred hhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 130 RCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 130 ~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.--|+....++.| .+ .|-.+++++... ..+.|.+++|||+++|+-+...
T Consensus 9 ~I~Gig~~~a~~L-------~~-~G~~t~~~l~~a----~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 9 SIPGIGPKRAEKL-------YE-AGIKTLEDLANA----DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp TSTTCHHHHHHHH-------HH-TTCSSHHHHHTS----HHHHHHTSTTSSHHHHHHHHHH
T ss_pred cCCCCCHHHHHHH-------Hh-cCCCcHHHHHcC----CHHHHhcCCCCCHHHHHHHHHH
Confidence 3346666555444 43 243367777654 3467999999999999988754
No 37
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.75 E-value=0.41 Score=40.96 Aligned_cols=51 Identities=20% Similarity=0.271 Sum_probs=33.6
Q ss_pred HHhhhCCCchHHHHHHH------HHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 127 NAIRCGGLAPTKAACIK------NILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 127 ~~i~~~G~~~~KA~~I~------~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
.+|.--|...+.|-.|. ++.++|.+ +..+.|.++||||+|||.-|.+---+
T Consensus 73 ~LisVsGIGPK~ALaILs~~~~~el~~aI~~----------------~D~~~L~~vpGIGkKtAeRIIlELkd 129 (196)
T PRK13901 73 ELIGVDGIGPRAALRVLSGIKYNEFRDAIDR----------------EDIELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred HHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh----------------CCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 34455567765555554 34444443 23578999999999999999864433
No 38
>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=92.70 E-value=0.41 Score=43.88 Aligned_cols=55 Identities=36% Similarity=0.405 Sum_probs=38.2
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCC-chHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 132 GGLAPTKAACIKNILKCLLESKGKL-CLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 132 ~G~~~~KA~~I~~~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
-|....-|+.|.++.+. |.+ .++.+..- .+....+|++++||||++|..+- .+|.
T Consensus 51 pgiG~~ia~kI~E~~~t-----G~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~--~lGi 106 (307)
T cd00141 51 PGIGKKIAEKIEEILET-----GKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY--ELGI 106 (307)
T ss_pred CCccHHHHHHHHHHHHc-----CCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH--HcCC
Confidence 36666666666665442 544 45555543 78889999999999999997665 5554
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=91.67 E-value=0.27 Score=41.99 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=9.6
Q ss_pred HHhcCcCccHHHHHHHHH
Q 023471 172 ELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 172 ~L~~l~GIG~~tA~~il~ 189 (281)
.|.++||||+++|+.|+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~ 126 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVL 126 (192)
T ss_pred HHHhCCCCCHHHHHHHHH
Confidence 455555555555555543
No 40
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=91.61 E-value=0.36 Score=38.39 Aligned_cols=62 Identities=15% Similarity=0.191 Sum_probs=44.4
Q ss_pred HHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHH
Q 023471 105 ASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTV 184 (281)
Q Consensus 105 ~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA 184 (281)
.+|. .+...-+|-.++.+++.. --|++..+|+.|.. +|.+ ...+.|.+++|||+++.
T Consensus 44 ~kl~-~~~~kIdiN~A~~~el~~---lpGigP~~A~~IV~--------nGpf-----------~sveDL~~V~GIgekqk 100 (132)
T PRK02515 44 AKLG-EFGEKIDLNNSSVRAFRQ---FPGMYPTLAGKIVK--------NAPY-----------DSVEDVLNLPGLSERQK 100 (132)
T ss_pred HHHH-hcCCcccCCccCHHHHHH---CCCCCHHHHHHHHH--------CCCC-----------CCHHHHHcCCCCCHHHH
Confidence 3444 456666778888887765 35788888988872 4654 24678899999999987
Q ss_pred HHHHH
Q 023471 185 ACVLM 189 (281)
Q Consensus 185 ~~il~ 189 (281)
..+--
T Consensus 101 ~~l~k 105 (132)
T PRK02515 101 ELLEA 105 (132)
T ss_pred HHHHH
Confidence 76654
No 41
>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=90.92 E-value=0.33 Score=34.02 Aligned_cols=58 Identities=21% Similarity=0.273 Sum_probs=36.7
Q ss_pred HHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 116 HVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+|-.++.++|..++.. ++..+|+.|.+.-. .+|++ +..++|.+++|||.++++-+..+
T Consensus 9 nvNta~~~~L~~~ipg--ig~~~a~~Il~~R~----~~g~~-----------~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNG--VGLKKAEAIVSYRE----EYGPF-----------KTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCC--CCHHHHHHHHHHHH----HcCCc-----------CCHHHHHcCCCCCHHHHHHHHhh
Confidence 3445677777665544 44445555443221 24543 14677899999999999988765
No 42
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.89 E-value=0.31 Score=41.70 Aligned_cols=30 Identities=30% Similarity=0.581 Sum_probs=24.6
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
+.+++.+.|.+|||||+|+|.-+..+-+..
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~ 34 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQR 34 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 357889999999999999998777655544
No 43
>PRK13844 recombination protein RecR; Provisional
Probab=90.72 E-value=0.33 Score=41.60 Aligned_cols=30 Identities=20% Similarity=0.408 Sum_probs=24.5
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
..+++.+.|.+|||||+|+|.-+..+-+..
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 367889999999999999998777655544
No 44
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.70 E-value=0.34 Score=41.40 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=24.0
Q ss_pred hHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 166 IDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 166 ~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
.+++.+.|.+|||||+|||.-+..+-+..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~ 34 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKR 34 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 67889999999999999998776655544
No 45
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=90.44 E-value=0.35 Score=41.14 Aligned_cols=30 Identities=27% Similarity=0.571 Sum_probs=24.2
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
..+.+.+.|.+|||||+|+|.-+..+-+.+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 357889999999999999998776655544
No 46
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=89.76 E-value=0.34 Score=41.66 Aligned_cols=39 Identities=28% Similarity=0.236 Sum_probs=26.4
Q ss_pred CchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 156 LCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 156 ~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
++.+.+...=..+..+.|.++||||.|||+-+++---++
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K 131 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGK 131 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhh
Confidence 344444433233457889999999999999988744433
No 47
>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=89.75 E-value=0.44 Score=40.67 Aligned_cols=55 Identities=24% Similarity=0.294 Sum_probs=33.9
Q ss_pred HHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 126 ENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 126 ~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
..+++--|...++|..|.+ .++.+.+...=..+....|.++||||+|||.-|++-
T Consensus 72 ~~L~~V~GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHhCCCCCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 4455666888777766622 223333321111123467999999999999999853
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.65 E-value=0.34 Score=41.07 Aligned_cols=56 Identities=18% Similarity=0.275 Sum_probs=33.6
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcCC-Ccc-ccc---hHHHHHHHHhCCCCCCCCHHHHHHHHHhh
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQQ-DDF-PVD---THVFEISKAIGWVPTAADRNKTYLHLNQR 229 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~~-~~~-~vD---~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~ 229 (281)
..+.|.++||||+|||.-+++---++ ... ... .-+...+.-||+- ..++.+.+...
T Consensus 106 D~~~L~~vpGIGkKtAeRIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~-----~~ea~~a~~~~ 166 (183)
T PRK14601 106 DESVLKKVPGIGPKSAKRIIAELSDAKTKLENVSDDKSEALAALLTLGFK-----QEKIIKVLASC 166 (183)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHHhhccCCCCccHHHHHHHHHHcCCC-----HHHHHHHHHhc
Confidence 46789999999999999998654333 111 111 1234455567773 34455555443
No 49
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=89.16 E-value=0.54 Score=38.51 Aligned_cols=54 Identities=30% Similarity=0.533 Sum_probs=36.8
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL 188 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il 188 (281)
|-.++.+|| +.|. |.+..||+.|.+. .+++|.| ...+.|...+|||+++.+-..
T Consensus 91 iNtAs~eeL-~~lp--gIG~~kA~aIi~y----Re~~G~f-----------~sv~dL~~v~GiG~~~~ekl~ 144 (149)
T COG1555 91 INTASAEEL-QALP--GIGPKKAQAIIDY----REENGPF-----------KSVDDLAKVKGIGPKTLEKLK 144 (149)
T ss_pred ccccCHHHH-HHCC--CCCHHHHHHHHHH----HHHcCCC-----------CcHHHHHhccCCCHHHHHHHH
Confidence 455677777 4454 4555688888663 4455654 246779999999999987554
No 50
>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=89.11 E-value=3.1 Score=42.16 Aligned_cols=80 Identities=20% Similarity=0.285 Sum_probs=48.3
Q ss_pred HHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH-------------------------HHHcCC
Q 023471 103 AFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL-------------------------LESKGK 155 (281)
Q Consensus 103 ~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i-------------------------~~~~g~ 155 (281)
.+..|.+.. -++.+|..+..++|.++ -||....+..|.+..+.- .+.|+
T Consensus 444 ~i~~L~~~g~I~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~- 519 (652)
T TIGR00575 444 VIEQLFEKKLVRSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFG- 519 (652)
T ss_pred HHHHHHHcCCcCCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhC-
Confidence 445566554 37788887776665542 356665666555443322 12222
Q ss_pred CchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 156 LCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 156 ~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
+++.+...+ .++|.+++|||+++|..|..|-
T Consensus 520 -sl~~l~~As----~eeL~~i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 520 -TLDKLKAAS----LEELLSVEGVGPKVAESIVNFF 550 (652)
T ss_pred -CHHHHHhCC----HHHHhcCCCcCHHHHHHHHHHH
Confidence 344554332 3478999999999999998763
No 51
>PRK08609 hypothetical protein; Provisional
Probab=88.58 E-value=1 Score=44.94 Aligned_cols=50 Identities=24% Similarity=0.365 Sum_probs=27.7
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCC-chHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 132 GGLAPTKAACIKNILKCLLESKGKL-CLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 132 ~G~~~~KA~~I~~~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
-|+...=|+.|.++.+ .|.+ -++.|.. +.++...+|++++||||+||..+
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~le~l~~-~~p~~~~~l~~i~GiGpk~a~~l 104 (570)
T PRK08609 54 KGIGKGTAEVIQEYRE-----TGESSVLQELKK-EVPEGLLPLLKLPGLGGKKIAKL 104 (570)
T ss_pred CCcCHHHHHHHHHHHH-----hCChHHHHHHHh-hCcHHHHHHhcCCCCCHHHHHHH
Confidence 3455444444444332 1443 3455554 34555667788888888887543
No 52
>PRK00024 hypothetical protein; Reviewed
Probab=88.13 E-value=0.96 Score=39.57 Aligned_cols=62 Identities=24% Similarity=0.276 Sum_probs=43.2
Q ss_pred HhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471 118 LAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL 188 (281)
Q Consensus 118 a~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il 188 (281)
..++..||.++|=..|..+ +-.+.+|+.+.++||+ +..+...+ .++|.+++|||+..|..++
T Consensus 22 ~~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as----~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 22 AALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDAS----LEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred ccCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCC----HHHHhhccCccHHHHHHHH
Confidence 3456677777665555544 3456788899888874 56665544 4568899999999886654
No 53
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.08 E-value=0.5 Score=40.20 Aligned_cols=57 Identities=18% Similarity=0.239 Sum_probs=34.6
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcCC-Ccccc-c----hHHHHHHHHhCCCCCCCCHHHHHHHHHhhC
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQQ-DDFPV-D----THVFEISKAIGWVPTAADRNKTYLHLNQRI 230 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~v-D----~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~ 230 (281)
..+.|.++||||+|||.-+.+---++ ..+.+ + .-+...+.-||+- ..++...+....
T Consensus 106 D~~~L~~vpGIGkKtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~-----~~ea~~av~~~~ 168 (188)
T PRK14606 106 DVEGLSKLPGISKKTAERIVMELKDEFESAGIKDMRIYHESLEALVSLGYP-----EKQAREAVKHVY 168 (188)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCC-----HHHHHHHHHHHh
Confidence 35789999999999999998644333 21111 1 1233456668883 345555555543
No 54
>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=87.97 E-value=1.3 Score=30.16 Aligned_cols=42 Identities=17% Similarity=0.186 Sum_probs=33.4
Q ss_pred HHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH
Q 023471 103 AFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK 147 (281)
Q Consensus 103 ~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~ 147 (281)
...+|.+. |.|+++|+.++.++|.+ --|++..+|+.|.+.++
T Consensus 17 ~a~~L~~~G~~t~~~l~~a~~~~L~~---i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 17 RAEKLYEAGIKTLEDLANADPEELAE---IPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHTTCSSHHHHHTSHHHHHHT---STTSSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCcHHHHHcCCHHHHhc---CCCCCHHHHHHHHHHHh
Confidence 34567777 88999999999988766 36788889999887665
No 55
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.95 E-value=0.51 Score=40.46 Aligned_cols=22 Identities=18% Similarity=0.176 Sum_probs=19.0
Q ss_pred HHHHHhcCcCccHHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~ 190 (281)
..+.|.++||||+|||.-|++-
T Consensus 105 D~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 105 DARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred CHHHHhhCCCCCHHHHHHHHHH
Confidence 3678999999999999998853
No 56
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.42 E-value=2.1 Score=36.64 Aligned_cols=21 Identities=33% Similarity=0.463 Sum_probs=17.9
Q ss_pred HHHHHhcCcCccHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~ 189 (281)
..+.|.++||||+|||.-+++
T Consensus 106 D~~~L~~vpGIGkKtAerIil 126 (194)
T PRK14605 106 NAELLSTIPGIGKKTASRIVL 126 (194)
T ss_pred CHHHHHhCCCCCHHHHHHHHH
Confidence 457799999999999999664
No 57
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.30 E-value=0.75 Score=39.32 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=22.4
Q ss_pred HHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 167 DEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
-++.+.|++++||||++|-.||. .++-
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs-~~~~ 95 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLS-AMNA 95 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHH-hCCH
Confidence 46788899999999999999987 3444
No 58
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.22 E-value=0.6 Score=39.97 Aligned_cols=25 Identities=32% Similarity=0.339 Sum_probs=20.3
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
..+.|.++||||+|||+-+++---+
T Consensus 106 D~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 106 DVARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 3678999999999999998864333
No 59
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.96 E-value=0.56 Score=40.43 Aligned_cols=22 Identities=36% Similarity=0.484 Sum_probs=19.1
Q ss_pred HHHHHhcCcCccHHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~ 190 (281)
..+.|.++||||+|||.-+++-
T Consensus 107 D~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 107 DVAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred CHHHHhcCCCcCHHHHHHHHHH
Confidence 3578999999999999998864
No 60
>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=86.31 E-value=0.62 Score=34.31 Aligned_cols=41 Identities=27% Similarity=0.356 Sum_probs=29.9
Q ss_pred HHHhcCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCC
Q 023471 171 AELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVP 214 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~ 214 (281)
+.|++|||||+-||..++....+...|+-..++ ...+|+.+
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l---~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQL---ASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhh---hhcccccc
Confidence 458899999999999998877443566655444 45678865
No 61
>PRK07945 hypothetical protein; Provisional
Probab=86.21 E-value=2 Score=39.93 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=42.9
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCc-hHHHhcCChHHHHH-HHhcCcCccHHHHHHHHHHhc
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLC-LEYLRGLSIDEIKA-ELSRFRGIGPKTVACVLMFHL 192 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~-l~~l~~~~~~~~~~-~L~~l~GIG~~tA~~il~~~~ 192 (281)
++++.+|.-.|-..-|++..++.|+.|.. .+ .+ ++.+. .+ .|.+|||||.-+|..|.-+.-
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~-~~~~~~~~-------~~g~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA-LD-AAERARRA-------RAGSLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cC-hhHHHHHH-------hcCCcccCCCcCHHHHHHHHHHHh
Confidence 45566677777776799999999999975 22 12 22221 11 688999999999998876643
No 62
>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=85.63 E-value=1.7 Score=38.44 Aligned_cols=160 Identities=15% Similarity=0.189 Sum_probs=87.6
Q ss_pred HHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhC----CCchHHHHHHHHHHHHHHHHcCCCchHHH
Q 023471 86 LVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCG----GLAPTKAACIKNILKCLLESKGKLCLEYL 161 (281)
Q Consensus 86 Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~----G~~~~KA~~I~~~a~~i~~~~g~~~l~~l 161 (281)
++-++.|-|-+... +..|..|.+.|-+- .+ .-..+++.+.|... .+.++|.++|..+...+.+ +.+...
T Consensus 43 i~NaLvSYqLs~kG-Ee~W~~Fs~yfs~~-~~-~~~~~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~----l~l~~~ 115 (246)
T PF09171_consen 43 IANALVSYQLSGKG-EEYWWEFSEYFSKR-PI-EDICEAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLEN----LSLQDN 115 (246)
T ss_dssp HHHHHT-SS-TT-H-HHHHHHHHHHHCTS----SSHHHHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHT----T-HHHH
T ss_pred HHHHHHHHhcCCch-HHHHHHHHHHHhcC-Cc-hhHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHH----hhhhhh
Confidence 34466777777665 45777777766321 00 11234555666543 3466899999998887643 233333
Q ss_pred hc--CChHHHHHHHhcCcCccH---------HHHHHHHHHhcCC--C-----ccccchHHHHHHHHhCCCCCC-----CC
Q 023471 162 RG--LSIDEIKAELSRFRGIGP---------KTVACVLMFHLQQ--D-----DFPVDTHVFEISKAIGWVPTA-----AD 218 (281)
Q Consensus 162 ~~--~~~~~~~~~L~~l~GIG~---------~tA~~il~~~~~~--~-----~~~vD~~v~Ri~~rlG~~~~~-----~~ 218 (281)
.. -+...+++.|.++=|-.+ |+..+....++|. + -+|||.|+.++..+.|++... .+
T Consensus 116 ~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~~~~~~~~~ 195 (246)
T PF09171_consen 116 PLYYEDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIECEREEMMRT 195 (246)
T ss_dssp HHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS-----TTS-----HHHHHHHHCTTS-SS-HHHHHCT
T ss_pred hhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCcccCCCCccHHHHHHHHHhccccccHHhhhcc
Confidence 22 466778888887655442 3444455556565 2 489999999999999997531 23
Q ss_pred HHHHHHHHHhhCCc--ccHHHHHHHHH-HhcccCCCCcC
Q 023471 219 RNKTYLHLNQRIPK--ELKFDLNCLLY-THGKLCRNCIK 254 (281)
Q Consensus 219 ~~~~~~~l~~~~p~--~~~~~~h~~lv-~~G~~c~~C~~ 254 (281)
+++++..+....-. --+-.++..|+ -+|+. ....
T Consensus 196 ~~~v~~~W~~Va~~sgIpplhLDs~lW~l~G~~--~~~~ 232 (246)
T PF09171_consen 196 REEVQKAWREVAKESGIPPLHLDSLLWPLLGRA--RDVK 232 (246)
T ss_dssp CCHHHHHHHHHHHHHT--HHHHHHHHHHHHCCH--HCCT
T ss_pred HHHHHHHHHHHHhhcCCCchhhhhHHHHhcccc--hhhh
Confidence 34444444432211 12458888888 88887 5443
No 63
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.43 E-value=2.5 Score=36.81 Aligned_cols=62 Identities=23% Similarity=0.163 Sum_probs=43.2
Q ss_pred hCCHHHHHHHhhhCCCchHHHH-HHHHHHHHHHHHc---CCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHH
Q 023471 119 AAEQKCIENAIRCGGLAPTKAA-CIKNILKCLLESK---GKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 119 ~~~~eel~~~i~~~G~~~~KA~-~I~~~a~~i~~~~---g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.++..||.++|=..|..+ + -...+|+.+.++| | ++..+...+ .++|.+++|||+..|..++.
T Consensus 13 ~Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g--~l~~l~~a~----~~eL~~i~GiG~aka~~l~a 78 (218)
T TIGR00608 13 ALSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQD--SLGHLLSAP----PEELSSVPGIGEAKAIQLKA 78 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccC--CHHHHHhCC----HHHHHhCcCCcHHHHHHHHH
Confidence 456677777665555544 2 4678899999887 5 466776554 45688999999977766543
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=85.33 E-value=6.1 Score=40.22 Aligned_cols=79 Identities=18% Similarity=0.217 Sum_probs=47.9
Q ss_pred HHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH-------------------------HHHcCC
Q 023471 103 AFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL-------------------------LESKGK 155 (281)
Q Consensus 103 ~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i-------------------------~~~~g~ 155 (281)
.+..|.+.. .++.+|..+..++|..+ -||...++..|.+..+.. .+.|+
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---EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFG- 532 (665)
T ss_pred HHHHHHHcCCCCCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcC-
Confidence 345566554 47888888876665442 367666665554433221 22222
Q ss_pred CchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 156 LCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 156 ~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+++.+...+ .++|.+++|||+++|..|..|
T Consensus 533 -sl~~l~~As----~eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 533 -SLEALRAAS----EEELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred -CHHHHHhCC----HHHHhccCCcCHHHHHHHHHH
Confidence 344444332 457999999999999999876
No 65
>PRK00024 hypothetical protein; Reviewed
Probab=85.26 E-value=2.7 Score=36.79 Aligned_cols=61 Identities=26% Similarity=0.353 Sum_probs=47.3
Q ss_pred HHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHH
Q 023471 85 GLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKC 148 (281)
Q Consensus 85 ~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~ 148 (281)
.|+..+|..-+....+.....+|.++|++..++..++.++|.. + -|....||..|..+.+.
T Consensus 28 ELLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~-i--~GIG~akA~~L~a~~El 88 (224)
T PRK00024 28 ELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQS-I--KGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhh-c--cCccHHHHHHHHHHHHH
Confidence 4667777777788888888899999999999999999998775 3 46666777766554444
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=85.19 E-value=1.5 Score=37.40 Aligned_cols=77 Identities=19% Similarity=0.270 Sum_probs=43.7
Q ss_pred HHHHHHhcCcCccHHHHHHHHHHhcCCCcc---ccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCC------------c
Q 023471 168 EIKAELSRFRGIGPKTVACVLMFHLQQDDF---PVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIP------------K 232 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~---~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p------------~ 232 (281)
+....|..++||||++|..++. .||.+.+ ..+....++..--|+- ..+.+.+...+...+. .
T Consensus 70 ~~f~~L~~i~GIGpk~A~~il~-~fg~~~l~~~i~~~d~~~L~~v~Gig--~k~A~~I~~~l~~~~~~~~~~~~~~~~~~ 146 (192)
T PRK00116 70 ELFRLLISVSGVGPKLALAILS-GLSPEELVQAIANGDVKALTKVPGIG--KKTAERIVLELKDKLAAAASAAAAAAAAS 146 (192)
T ss_pred HHHHHHhcCCCCCHHHHHHHHH-hCCHHHHHHHHHhCCHHHHHhCCCCC--HHHHHHHHHHHHHHhhccccccccccccc
Confidence 4467889999999999988865 5665322 3344444443333542 2333444444433332 1
Q ss_pred ccHHHHHHHHHHhcc
Q 023471 233 ELKFDLNCLLYTHGK 247 (281)
Q Consensus 233 ~~~~~~h~~lv~~G~ 247 (281)
....++...|..||-
T Consensus 147 ~~~~ev~~aL~~LG~ 161 (192)
T PRK00116 147 SALEEAVSALVALGY 161 (192)
T ss_pred chHHHHHHHHHHcCC
Confidence 114577777777774
No 67
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=84.69 E-value=1 Score=31.22 Aligned_cols=52 Identities=25% Similarity=0.389 Sum_probs=29.8
Q ss_pred HhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 118 LAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 118 a~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
-.++.+||.. --|++...|+.|.+.-+. .|++ ...++|..++|||+.+.+-+
T Consensus 9 N~as~~eL~~---lpgi~~~~A~~Iv~~R~~----~G~f-----------~s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 9 NTASAEELQA---LPGIGPKQAKAIVEYREK----NGPF-----------KSLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTS-HHHHHT---STT--HHHHHHHHHHHHH----H-S------------SSGGGGGGSTT--HHHHHHH
T ss_pred ccCCHHHHHH---cCCCCHHHHHHHHHHHHh----CcCC-----------CCHHHHhhCCCCCHHHHHHH
Confidence 3456655443 238888888888775443 3654 13567899999999998765
No 68
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.62 E-value=2.4 Score=35.97 Aligned_cols=55 Identities=16% Similarity=0.307 Sum_probs=32.2
Q ss_pred HHHHhcCcCccHHHHHHHHHHhcCC-Ccccc-----c---hHHHHHHHHhCCCCCCCCHHHHHHHHHhhC
Q 023471 170 KAELSRFRGIGPKTVACVLMFHLQQ-DDFPV-----D---THVFEISKAIGWVPTAADRNKTYLHLNQRI 230 (281)
Q Consensus 170 ~~~L~~l~GIG~~tA~~il~~~~~~-~~~~v-----D---~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~ 230 (281)
.+.| ++||||+|||.-+++---++ ..+.. + .-+.-.+..||+- ..+++..+.+..
T Consensus 107 ~~~L-~vpGIGkKtAerIilELk~K~~~~~~~~~~~~~~~~e~~~aL~~LGy~-----~~ea~~al~~v~ 170 (186)
T PRK14600 107 KAAL-KVNGIGEKLINRIITELQYKVSKLEINETNFIIINDDALAALISLGYE-----KTKAFNAIQKIK 170 (186)
T ss_pred Hhhe-ECCCCcHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHcCCC-----HHHHHHHHHHhh
Confidence 4778 99999999999998643333 11110 0 1233455567772 345555555543
No 69
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=84.26 E-value=14 Score=32.27 Aligned_cols=61 Identities=25% Similarity=0.244 Sum_probs=42.6
Q ss_pred HhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 118 LAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 118 a~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
..++..||.+++=..|.. -.....+|+.+.++||+ |..+.+.+ .++|++++|||+..|--+
T Consensus 22 ~~Lsd~ELLailLrtG~~---~~~~~~la~~lL~~fg~--L~~l~~a~----~~el~~v~GiG~aka~~l 82 (224)
T COG2003 22 EALSDAELLAILLRTGTK---GESVLDLAKELLQEFGS--LAELLKAS----VEELSSVKGIGLAKAIQI 82 (224)
T ss_pred hhcchHHHHHHHHhcCCC---CCCHHHHHHHHHHHccc--HHHHHhCC----HHHHhhCCCccHHHHHHH
Confidence 345666777766555543 45578999999999986 55665443 578999999997665433
No 70
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=84.24 E-value=2.6 Score=38.59 Aligned_cols=59 Identities=19% Similarity=0.277 Sum_probs=43.5
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHH--HhcCcCccHHHHHHHHHHh
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAE--LSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~--L~~l~GIG~~tA~~il~~~ 191 (281)
++++..+.-.|-...|++.-...|+.+.+ ... +.+++.+. ++.|||||+-+|+.|.-|.
T Consensus 13 e~iA~~me~~Gen~fk~~aYr~Aa~sle~--~~e--------~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 13 ERIADYMELEGENPFKIRAYRKAAQSLEN--LTE--------DLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred HHHHHHHHhcCCCccchHHHHHHHHhhhh--ccc--------chHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 44556666667665688888899999876 333 34555555 9999999999999987654
No 71
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=83.36 E-value=2.2 Score=37.43 Aligned_cols=42 Identities=24% Similarity=0.345 Sum_probs=36.1
Q ss_pred HHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH
Q 023471 105 ASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL 149 (281)
Q Consensus 105 ~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i 149 (281)
..|...||+.++|..++.+||+.+ -|++.+||++|+++.+..
T Consensus 209 ~~LL~~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~p 250 (254)
T KOG2841|consen 209 QLLLQKFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQP 250 (254)
T ss_pred HHHHHhcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhcc
Confidence 457788999999999999998874 689999999999887654
No 72
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=82.57 E-value=3.8 Score=38.24 Aligned_cols=47 Identities=23% Similarity=0.347 Sum_probs=40.1
Q ss_pred HHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 102 KAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 102 ~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
....+|.++|++.+.|..++.++|.++ -|++..||+.|++.++.+.+
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~V---eGIGe~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEV---EGIGEVRARAIREGLSRLAE 344 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhC---CCcCHHHHHHHHHHHHHHHH
Confidence 566889999999999999999987763 36678899999999998876
No 73
>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=82.53 E-value=1.7 Score=32.63 Aligned_cols=28 Identities=14% Similarity=0.229 Sum_probs=21.7
Q ss_pred HHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 167 DEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
.+....|+.|||||+.+|.-+...++..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 3456789999999999998877655443
No 74
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.32 E-value=4 Score=35.58 Aligned_cols=61 Identities=21% Similarity=0.340 Sum_probs=47.1
Q ss_pred HHHHHHHhhhccHH-HHHHHHHHHHhhC---CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHH
Q 023471 85 GLVKTVLSQNTTEA-NSLKAFASLKSTF---PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKC 148 (281)
Q Consensus 85 ~Lv~~ILsqqts~~-~a~~~~~~L~~~~---pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~ 148 (281)
.|+..+|..-+... .+....++|.++| ++...|..++.+||.+ + -|....||..|..+.+.
T Consensus 18 ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~-i--~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 18 ELLAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSS-V--PGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHh-C--cCCcHHHHHHHHHHHHH
Confidence 46677777777777 8888888999999 9999999999998776 3 46666688777655443
No 75
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=81.88 E-value=11 Score=38.48 Aligned_cols=23 Identities=22% Similarity=0.372 Sum_probs=19.6
Q ss_pred HHHHHhcCcCccHHHHHHHHHHh
Q 023471 169 IKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
..++|++++|||+.+|..|..|-
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 34579999999999999998864
No 76
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=81.54 E-value=3.6 Score=38.18 Aligned_cols=56 Identities=14% Similarity=0.164 Sum_probs=37.6
Q ss_pred HHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 124 CIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 124 el~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
++.+++.-.|-...|+.+..+.+..|.. + ..+++ + .+.|.+|||||+.+|+-|--+
T Consensus 12 ~la~l~el~gen~~k~~ay~~Aa~~i~~-l-~~~i~--------~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 12 ILAENYEVFGENKRKCSYFRKAASVLKS-L-PFPIN--------S-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHHh-C-CCCCC--------C-HHHHhcCCCccHHHHHHHHHH
Confidence 3444444456555688888888888865 2 22322 1 247889999999999998644
No 77
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=81.42 E-value=2.4 Score=29.33 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=29.0
Q ss_pred HHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH
Q 023471 102 KAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK 147 (281)
Q Consensus 102 ~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~ 147 (281)
..-..|.++|++++.|.+++.++|.+ --|+....|+.|.+..+
T Consensus 14 ~~ak~L~~~f~sl~~l~~a~~e~L~~---i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 14 KTAKLLAKHFGSLEALMNASVEELSA---IPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp HHHHHHHHCCSCHHHHCC--HHHHCT---STT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHcCHHHHhc---cCCcCHHHHHHHHHHHC
Confidence 34567889999999999999987654 24777778877766544
No 78
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=80.76 E-value=13 Score=38.10 Aligned_cols=79 Identities=15% Similarity=0.178 Sum_probs=45.1
Q ss_pred HHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHH-------------------------HHHHHHcCC
Q 023471 103 AFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNIL-------------------------KCLLESKGK 155 (281)
Q Consensus 103 ~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a-------------------------~~i~~~~g~ 155 (281)
.+..|.+.. -++.+|..+..++|..+ -||...++..|.+.. +.+...|+
T Consensus 474 ~i~~L~~~g~V~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~- 549 (689)
T PRK14351 474 RVQQLVDAGLVESLADLYDLTVADLAEL---EGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFG- 549 (689)
T ss_pred HHHHHHHcCCCCCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhC-
Confidence 345555554 36777777776654432 356555554433221 12222333
Q ss_pred CchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 156 LCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 156 ~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+++.+...+ .++|.+++|||+++|..|..|
T Consensus 550 -si~~L~~As----~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 550 -TFEAIMDAD----EEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred -CHHHHHhCC----HHHHhccCCcCHHHHHHHHHH
Confidence 244444333 356889999999999988776
No 79
>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=80.57 E-value=1.5 Score=37.36 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=19.8
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++...|++++||||++|-.+|.
T Consensus 68 r~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 68 RELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHh
Confidence 46788899999999999988855
No 80
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=80.53 E-value=1.8 Score=29.95 Aligned_cols=23 Identities=30% Similarity=0.622 Sum_probs=17.6
Q ss_pred HHHHHhcCcCccHHHHHHHHHHh
Q 023471 169 IKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
..++|.++||||++.|..|+.|-
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHH
Confidence 46789999999999999998764
No 81
>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=80.41 E-value=3 Score=42.80 Aligned_cols=28 Identities=25% Similarity=0.390 Sum_probs=16.3
Q ss_pred hHHHHHHHhc--CcCccHHHHHHHHHHhcCC
Q 023471 166 IDEIKAELSR--FRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 166 ~~~~~~~L~~--l~GIG~~tA~~il~~~~~~ 194 (281)
.+.+..+|.+ |+|||++||.-|.. .||.
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv~-~fg~ 106 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIVK-TFGE 106 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHH-HhCH
Confidence 3455566654 66777766665553 4554
No 82
>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=80.36 E-value=1.8 Score=28.87 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=15.5
Q ss_pred HHHhcCcCccHHHHHHHHHHhcC
Q 023471 171 AELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
+.+.++.|||+.||.-....++.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--
T ss_pred cchhhcccccHHHHHHHHHhCCC
Confidence 57889999999999977664444
No 83
>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=80.09 E-value=4.4 Score=31.81 Aligned_cols=60 Identities=22% Similarity=0.337 Sum_probs=40.6
Q ss_pred CHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 113 TWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 113 t~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.+-.|-.++.++|.. --|++..+|+.|.+.-.. +|.+ ...++|..++|||+++++-+.-|
T Consensus 58 ~~iniNtA~~~eL~~---lpGIG~~~A~~Ii~~R~~----~g~f-----------~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 58 AAVNINAASLEELQA---LPGIGPAKAKAIIEYREE----NGAF-----------KSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CCEeCCcCCHHHHhc---CCCCCHHHHHHHHHHHHh----cCCc-----------CCHHHHHcCCCCCHHHHHHHHhc
Confidence 345566777777654 346777788777654332 3543 23578899999999999887654
No 84
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=80.03 E-value=12 Score=32.62 Aligned_cols=62 Identities=21% Similarity=0.274 Sum_probs=49.8
Q ss_pred HHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHH
Q 023471 84 DGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKC 148 (281)
Q Consensus 84 e~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~ 148 (281)
.-|++.+|-.-|....+...-..|.++|++...+..++.+++.. + -|++..|+-.|+.+.+.
T Consensus 27 ~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~-v--~GiG~aka~~l~a~~El 88 (224)
T COG2003 27 AELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSS-V--KGIGLAKAIQIKAAIEL 88 (224)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhh-C--CCccHHHHHHHHHHHHH
Confidence 35778888889999999999999999999999999999988776 4 45555677666655544
No 85
>PRK14973 DNA topoisomerase I; Provisional
Probab=79.26 E-value=6.7 Score=41.49 Aligned_cols=99 Identities=16% Similarity=0.177 Sum_probs=59.2
Q ss_pred HHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH-HHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHH
Q 023471 106 SLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK-CLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKT 183 (281)
Q Consensus 106 ~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~-~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~t 183 (281)
++.+. |-++++++.+++++|.. --|++.-.+..+...+. .+.. -+-+.......+.-+.+|++++|||++|
T Consensus 817 ~~~~~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~t 889 (936)
T PRK14973 817 KYQEAGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGETT 889 (936)
T ss_pred HHHHhcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHHH
Confidence 34333 56899999999998776 46888766666655444 3322 1112222223344455699999999999
Q ss_pred HHHHHHHhcCC-CccccchHHHHHHHHhCC
Q 023471 184 VACVLMFHLQQ-DDFPVDTHVFEISKAIGW 212 (281)
Q Consensus 184 A~~il~~~~~~-~~~~vD~~v~Ri~~rlG~ 212 (281)
++-.-.-+.-. +.+.-. -..+++.+-|+
T Consensus 890 ~~~l~~ag~~~~e~l~~~-d~~~la~~~~i 918 (936)
T PRK14973 890 LEKLYLAGVYDGDLLVSA-DPKKLAKVTGI 918 (936)
T ss_pred HHHHHHcCCCCHHHhccC-CHHHHhhhcCC
Confidence 96554433333 233333 45556666565
No 86
>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=78.91 E-value=1.7 Score=25.81 Aligned_cols=15 Identities=40% Similarity=0.705 Sum_probs=11.4
Q ss_pred HhcCcCccHHHHHHH
Q 023471 173 LSRFRGIGPKTVACV 187 (281)
Q Consensus 173 L~~l~GIG~~tA~~i 187 (281)
+.+++|||++|+.-+
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 467999999999753
No 87
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=78.36 E-value=12 Score=37.29 Aligned_cols=79 Identities=16% Similarity=0.207 Sum_probs=47.7
Q ss_pred HHHHHHhhC--CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH----------------------HcCCCch
Q 023471 103 AFASLKSTF--PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE----------------------SKGKLCL 158 (281)
Q Consensus 103 ~~~~L~~~~--pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~----------------------~~g~~~l 158 (281)
.+..|.+.. -++.+|..+..++|.++ -||...+++.|.+..+.-.+ .++ ++
T Consensus 437 ~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~--~i 511 (562)
T PRK08097 437 TWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR--SW 511 (562)
T ss_pred HHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcC--CH
Confidence 445566654 47888888886655442 36666666655443221110 111 34
Q ss_pred HHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 159 EYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 159 ~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+.|...+ .+.|.+++|||+.+|+.|..|
T Consensus 512 ~~l~~a~----~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 512 QQLLSRS----EQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHcCC----HHHHhcCCCchHHHHHHHHHH
Confidence 4444333 356999999999999999886
No 88
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=77.98 E-value=4.9 Score=29.95 Aligned_cols=57 Identities=23% Similarity=0.279 Sum_probs=34.8
Q ss_pred CHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc-CcCccHHHHHHHHH
Q 023471 121 EQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR-FRGIGPKTVACVLM 189 (281)
Q Consensus 121 ~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~-l~GIG~~tA~~il~ 189 (281)
+..++...|...|++...+..| .+.||.-.++.+.+-++ .|.. +.|||-++||.|.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl-------~~~yg~~ai~~l~~nPY-----~L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKL-------YKKYGDDAIEILKENPY-----RLIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHH-------HHHH-TTHHHHHHH-ST-----CCCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHH-------HHHHhHHHHHHHHHChH-----HHHHHccCCCHHHHHHHHH
Confidence 3456677788899997555444 45567655554443222 3555 89999999998877
No 89
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=77.80 E-value=1.7 Score=26.55 Aligned_cols=17 Identities=41% Similarity=0.700 Sum_probs=13.8
Q ss_pred HhcCcCccHHHHHHHHH
Q 023471 173 LSRFRGIGPKTVACVLM 189 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~ 189 (281)
+-.+||||++||--++.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 45789999999987664
No 90
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.59 E-value=2.2 Score=36.62 Aligned_cols=23 Identities=30% Similarity=0.388 Sum_probs=20.3
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.||.
T Consensus 68 r~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 68 LELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 45788899999999999988887
No 91
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.57 E-value=2.1 Score=36.81 Aligned_cols=23 Identities=22% Similarity=0.252 Sum_probs=20.4
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.+|.
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHh
Confidence 46788899999999999988887
No 92
>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=76.52 E-value=2.6 Score=33.10 Aligned_cols=23 Identities=26% Similarity=0.561 Sum_probs=20.0
Q ss_pred HHHHHhcCcCccHHHHHHHHHHh
Q 023471 169 IKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
..++|.++||||++.|..|+.+-
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 46789999999999999999864
No 93
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=76.42 E-value=26 Score=32.27 Aligned_cols=57 Identities=28% Similarity=0.310 Sum_probs=38.2
Q ss_pred CCchHHHHHHHHHHHHHHHHcCCC-chHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 133 GLAPTKAACIKNILKCLLESKGKL-CLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 133 G~~~~KA~~I~~~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
|+...-|+-|++++ + .|.+ .+++..+-+.....+.+.++-|||.+||+..-.-+|.-
T Consensus 63 ~iG~kia~ki~Eil----e-tG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrT 120 (353)
T KOG2534|consen 63 GIGPKIAEKIQEIL----E-TGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRT 120 (353)
T ss_pred CCCHHHHHHHHHHH----H-cCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhH
Confidence 44444555555544 3 2443 34555544556778889999999999999988877765
No 94
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=76.08 E-value=2.4 Score=34.66 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=24.4
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcCC-Cccccch
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDT 201 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~ 201 (281)
..++|..|||||++.|..|..+--.. +.--+|+
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d 128 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVDD 128 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence 34667999999999999999875333 4545555
No 95
>PRK07758 hypothetical protein; Provisional
Probab=75.14 E-value=7.8 Score=29.14 Aligned_cols=31 Identities=26% Similarity=0.468 Sum_probs=23.4
Q ss_pred CCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471 154 GKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL 188 (281)
Q Consensus 154 g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il 188 (281)
|--++++|..++ .++|++|+|+|+++.+-|-
T Consensus 54 GI~TL~dLv~~t----e~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 54 GIHTVEELSKYS----EKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCCcHHHHHcCC----HHHHHHccCCCHHHHHHHH
Confidence 333677776554 5679999999999998764
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=74.94 E-value=7.2 Score=35.76 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=21.3
Q ss_pred HHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 167 DEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
++..++|+.++||||.|..++.+.+
T Consensus 265 p~~feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 265 PSDFEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred ccCHHHHHhcCCCCHHHHHHHHHHH
Confidence 5678999999999999998877654
No 97
>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=72.49 E-value=11 Score=26.26 Aligned_cols=48 Identities=25% Similarity=0.308 Sum_probs=31.5
Q ss_pred hhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471 129 IRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL 188 (281)
Q Consensus 129 i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il 188 (281)
|..+|++. |+.. .+. +.|-..+.+|..++. +.|.+++|+|.++.+-|.
T Consensus 14 I~~L~LS~-Ra~n------~L~-~~~I~tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 14 IEDLGLSV-RAYN------CLK-RAGIHTVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGGSTSBH-HHHH------HHH-CTT--BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred HHHhCCCH-HHHH------HHH-HhCCcCHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 66789986 4332 222 234447777876653 579999999999998764
No 98
>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=71.30 E-value=9.3 Score=35.01 Aligned_cols=57 Identities=16% Similarity=0.163 Sum_probs=37.5
Q ss_pred HHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 124 CIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 124 el~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
++..++.-.|-..-|++...+.|..+.. . ..++. ..+++.+|||||+.+|+.|--+.
T Consensus 9 ~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l-~~~i~---------~~~~~~~ipgiG~~ia~kI~E~~ 65 (307)
T cd00141 9 ELADLLELLGGNPFRVRAYRKAARALES-L-PEPIE---------SLEEAKKLPGIGKKIAEKIEEIL 65 (307)
T ss_pred HHHHHHHhccCCcchHHHHHHHHHHHHh-C-CcccC---------CHHHhcCCCCccHHHHHHHHHHH
Confidence 3444444444334588888888888875 2 22221 13366899999999999987654
No 99
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.17 E-value=3.9 Score=35.06 Aligned_cols=23 Identities=39% Similarity=0.559 Sum_probs=20.3
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.||.
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 46788899999999999988886
No 100
>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=70.76 E-value=2.4 Score=30.37 Aligned_cols=20 Identities=35% Similarity=0.486 Sum_probs=16.4
Q ss_pred HHHhcCcCccHHHHHHHHHH
Q 023471 171 AELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~ 190 (281)
+.+..+||||++||.-++.-
T Consensus 22 D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred ccCCCCCcccHHHHHHHHHH
Confidence 44668999999999988863
No 101
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.53 E-value=3.9 Score=34.73 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=20.3
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.+|.
T Consensus 69 r~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 69 QDCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 45778899999999999988887
No 102
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.51 E-value=4 Score=34.58 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=20.2
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.||.
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHc
Confidence 46788899999999999988886
No 103
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=70.03 E-value=12 Score=26.13 Aligned_cols=39 Identities=18% Similarity=0.161 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhh
Q 023471 27 TAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQN 94 (281)
Q Consensus 27 ~~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqq 94 (281)
....+..+...|++.||.. | +.+ ..+-|.+|+.+||..+
T Consensus 24 ~~~~v~~vl~~LL~lY~~n-W-~lI---------------------------Eed~Y~~L~dai~e~~ 62 (65)
T PF10440_consen 24 SKKQVRPVLKNLLKLYDGN-W-ELI---------------------------EEDNYRVLADAIFEEQ 62 (65)
T ss_pred CHHHHHHHHHHHHHHHcCC-c-hhh---------------------------hcccHHHHHHHHHHHh
Confidence 3467889999999999977 5 433 5789999999998765
No 104
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.31 E-value=4.4 Score=34.46 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=20.5
Q ss_pred hHHHHHHHhcCcCccHHHHHHHHH
Q 023471 166 IDEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 166 ~~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.-++.+.|+++.||||++|=.+|.
T Consensus 68 Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 68 KKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHhccCCccHHHHHHHHc
Confidence 346788899999999999988885
No 105
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=69.25 E-value=4.3 Score=32.34 Aligned_cols=20 Identities=15% Similarity=0.333 Sum_probs=17.5
Q ss_pred HHHHhcCcCccHHHHHHHHH
Q 023471 170 KAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 170 ~~~L~~l~GIG~~tA~~il~ 189 (281)
.++|.++|||||..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45688999999999999984
No 106
>PRK08609 hypothetical protein; Provisional
Probab=68.04 E-value=13 Score=37.22 Aligned_cols=58 Identities=19% Similarity=0.354 Sum_probs=39.5
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
+++++++.-.|-..-|++.-++.|+.|... ..++ .+ ...|.+|||||+.+|+.|--+.
T Consensus 11 ~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l--~~~i--------~~-~~~l~~ipgIG~~ia~kI~Eil 68 (570)
T PRK08609 11 ETIATYMELKGENPFKISAFRKAAQALELD--ERSL--------SE-IDDFTKLKGIGKGTAEVIQEYR 68 (570)
T ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHHHHhC--chhh--------hh-hhhhccCCCcCHHHHHHHHHHH
Confidence 344555555665445888889999988762 2222 22 2478999999999999886543
No 107
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.34 E-value=4.9 Score=34.36 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=20.4
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-++.+.|+++.||||++|=.+|.
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 46788899999999999988887
No 108
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=64.93 E-value=7.5 Score=27.01 Aligned_cols=21 Identities=29% Similarity=0.643 Sum_probs=18.1
Q ss_pred HHHHhc-CcCccHHHHHHHHHH
Q 023471 170 KAELSR-FRGIGPKTVACVLMF 190 (281)
Q Consensus 170 ~~~L~~-l~GIG~~tA~~il~~ 190 (281)
.+.|.. ++|||+.+|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457878 999999999999886
No 109
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=64.73 E-value=13 Score=34.79 Aligned_cols=39 Identities=26% Similarity=0.399 Sum_probs=28.0
Q ss_pred HHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 143 KNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 143 ~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
+.+|+.+.++||+ +..+.+.+ .++|.+++|||+..|..|
T Consensus 297 k~iAk~Ll~~FGS--L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 297 SAVIENLVEHFGS--LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHHcCC--HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 3577888888874 55554433 456889999999998764
No 110
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=64.01 E-value=17 Score=37.15 Aligned_cols=42 Identities=26% Similarity=0.399 Sum_probs=33.3
Q ss_pred HHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH
Q 023471 105 ASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL 149 (281)
Q Consensus 105 ~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i 149 (281)
.+|.++|+++++|..++.++|.++ -|++..+|+.|.+..+.+
T Consensus 651 k~LL~~FGSle~I~~AS~eELa~V---~Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 651 RLLWERFGSLQAMAAAGEEGLAAV---PGIGPARAAALHEHLKTL 692 (694)
T ss_pred HHHHHHhCCHHHHHhcCHHHHHhc---CCcCHHHHHHHHHHHHHh
Confidence 446667999999999999887663 588888998888776654
No 111
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=63.95 E-value=15 Score=37.10 Aligned_cols=29 Identities=31% Similarity=0.461 Sum_probs=22.0
Q ss_pred hHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 158 LEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 158 l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
++.+... ..++|.+++|||...|..|..|
T Consensus 534 l~~l~~a----~~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 534 LEALLAA----SEEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HHHHHhc----CHHHHhhccchhHHHHHHHHHH
Confidence 4555433 3567888999999999999875
No 112
>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=63.13 E-value=32 Score=24.78 Aligned_cols=52 Identities=17% Similarity=0.215 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhhCC-CHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 99 NSLKAFASLKSTFP-TWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 99 ~a~~~~~~L~~~~p-t~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
+-...+..|.+..+ +.+.|..+.++|+.+++.-+|+.. |--.++++-+++.+
T Consensus 20 nLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~s-KPLHVrRlqKAL~e 72 (82)
T PF04904_consen 20 NLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMAS-KPLHVRRLQKALQE 72 (82)
T ss_pred hHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccC-ccHHHHHHHHHHHH
Confidence 33457788888876 799999999999999999999986 65555555555443
No 113
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=62.28 E-value=88 Score=28.19 Aligned_cols=125 Identities=18% Similarity=0.194 Sum_probs=75.3
Q ss_pred HHHHHHH--HHHhhhccHHHHHHHHHHHHhhC--CCHHHHHhCCHHHHHHHhhhC----CCchHHHHHHHHHHHHHHHHc
Q 023471 82 VLDGLVK--TVLSQNTTEANSLKAFASLKSTF--PTWEHVLAAEQKCIENAIRCG----GLAPTKAACIKNILKCLLESK 153 (281)
Q Consensus 82 ~fe~Lv~--~ILsqqts~~~a~~~~~~L~~~~--pt~~~la~~~~eel~~~i~~~----G~~~~KA~~I~~~a~~i~~~~ 153 (281)
.|-.||- ++.|-|-+..--. .|..|.+.| .+++++ .+++...|... .+..+|-++|+.+..++.+
T Consensus 47 ~~~~Lvi~NaLvSYqLsgkGEe-~W~eFs~yf~~~~~~~~----~~~~~~Fl~~s~~nrrl~e~KikRi~r~~~fl~~-- 119 (269)
T PRK13280 47 LFAKLVIANALVSYQLSGKGEE-WWWEFSKYFSEKGVEDI----VEAYIEFLKNSKGNRRLLEQKIKRIEKVEPFLES-- 119 (269)
T ss_pred HHHHHHHHHHHHHHhcCCcHHH-HHHHHHHHhcccCchhH----HHHHHHHHhcCchhHHHHHHHHHHHHHHHHHhhh--
Confidence 3544444 7778887765444 777777776 233332 23444455544 2345788888888776543
Q ss_pred CCCchHHHhc--CChHHHHHHHhcCcCcc---------HHHHHHHHHHhcCC--C-----ccccchHHHHHHHHhCCCCC
Q 023471 154 GKLCLEYLRG--LSIDEIKAELSRFRGIG---------PKTVACVLMFHLQQ--D-----DFPVDTHVFEISKAIGWVPT 215 (281)
Q Consensus 154 g~~~l~~l~~--~~~~~~~~~L~~l~GIG---------~~tA~~il~~~~~~--~-----~~~vD~~v~Ri~~rlG~~~~ 215 (281)
+.+.++.. .+.+++++.|..+=|-- -|++.+....+++. + -+|||.-+..+....|++..
T Consensus 120 --L~l~~~~~~y~~l~~l~~~La~~L~s~~~~KTiVFAvKM~~Ya~r~~~~~~~p~p~~IpIPvD~Ria~~T~~sglv~~ 197 (269)
T PRK13280 120 --LTLLDLPLYYEDLEELLEQLAKILGAKKESKTVVFAVKMFGYACRAAFGEFRPYPMEIPIPVDYRIAKLTKCSGLVEG 197 (269)
T ss_pred --hccchhhhhHhhHHHHHHHHHHHhCCCCCcceeeeHHHHHHHHHHHhccccCCCCcCCCCcccHHHHHHHHHhccccC
Confidence 22222221 34567777777654433 35555555555554 3 37899999999999999864
No 114
>PF10343 DUF2419: Protein of unknown function (DUF2419); InterPro: IPR019438 This entry contains proteins that have no known function.
Probab=61.83 E-value=77 Score=28.86 Aligned_cols=123 Identities=15% Similarity=0.153 Sum_probs=82.0
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCC--CHHHHHhCCHHHHHHHhhhC-----CCchHHHHHHHHHHHHHHH
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTFP--TWEHVLAAEQKCIENAIRCG-----GLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~p--t~~~la~~~~eel~~~i~~~-----G~~~~KA~~I~~~a~~i~~ 151 (281)
..+.|..|+++| -+.|.+..| +|+-+..++.++|..++++- -+-..|++.|+++.+.+.+
T Consensus 44 ~~tgY~~L~aal-------------~rAl~~~~pi~~~~~~~~~t~~~l~~if~s~~~~~iPll~eR~~~L~E~G~vL~~ 110 (287)
T PF10343_consen 44 TYTGYWSLCAAL-------------KRALDEGIPITDPKYYAKMTDEELRHIFRSDTEEEIPLLEERARLLREVGRVLLE 110 (287)
T ss_pred CcchHHHHHHHH-------------HHHHhcCCCCcCHHHHHhCCHHHHHHHhcCCCCCcCCCHHHHHHHHHHHHHHHHH
Confidence 446677776554 122333344 79999999999999999864 3445899999999999999
Q ss_pred HcCCCchHHHh--cCChHHHHHHHh-cCcCccHH-----------------HHHHHHHHh---cCC----C--ccccchH
Q 023471 152 SKGKLCLEYLR--GLSIDEIKAELS-RFRGIGPK-----------------TVACVLMFH---LQQ----D--DFPVDTH 202 (281)
Q Consensus 152 ~~g~~~l~~l~--~~~~~~~~~~L~-~l~GIG~~-----------------tA~~il~~~---~~~----~--~~~vD~~ 202 (281)
+|+|--.+-+. +.+...+.+.|. .|||.-.. +||....|. .|. + .+-.|--
T Consensus 111 ~f~gs~~~~i~~a~~sA~~Lv~~l~~~Fp~FrD~~~y~G~~V~~~KRAQIlvaDlw~~f~g~~~g~F~Did~lTmFADyr 190 (287)
T PF10343_consen 111 KFDGSFANCIKSANGSAAKLVRLLVENFPSFRDEATYKGRQVYFYKRAQILVADLWACFKGQGLGEFPDIDQLTMFADYR 190 (287)
T ss_pred HHhhhHHHHHHhcccCHHHHHHHHHHhCCCcccceEECCcEEEeeHHHHHHHHHHHHHhCCCCCCCcCCHhhcccccCCc
Confidence 88874222222 456777778777 48885543 355555552 111 1 3445777
Q ss_pred HHHHHHHhCCCC
Q 023471 203 VFEISKAIGWVP 214 (281)
Q Consensus 203 v~Ri~~rlG~~~ 214 (281)
|-.++..+|.+.
T Consensus 191 VPqvL~~lG~L~ 202 (287)
T PF10343_consen 191 VPQVLRHLGVLR 202 (287)
T ss_pred hHHHHHHCCcEE
Confidence 778888888863
No 115
>PRK14973 DNA topoisomerase I; Provisional
Probab=61.83 E-value=47 Score=35.35 Aligned_cols=73 Identities=19% Similarity=0.138 Sum_probs=49.4
Q ss_pred CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHH-----c------------CCC-chHHHhcCChHHHHHHH
Q 023471 112 PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLES-----K------------GKL-CLEYLRGLSIDEIKAEL 173 (281)
Q Consensus 112 pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~-----~------------g~~-~l~~l~~~~~~~~~~~L 173 (281)
.+.++|+.+++.. |+..|++..+++.+.+.|+.+..+ . +|+ +++++.. ...++|
T Consensus 766 ~~~~~~~~~~~~~----~~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~----a~p~~L 837 (936)
T PRK14973 766 NDIAALARADPAD----LKKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCS----VHPAYL 837 (936)
T ss_pred chHHHHhhCCHHH----HHHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHh----cCHHHH
Confidence 3688888888865 556899999999999988544321 1 223 3444432 234689
Q ss_pred hcCcCccHHHHHHHHHHhc
Q 023471 174 SRFRGIGPKTVACVLMFHL 192 (281)
Q Consensus 174 ~~l~GIG~~tA~~il~~~~ 192 (281)
..++||++-|+......+.
T Consensus 838 a~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 838 ALKTGISPETICRHAKLVC 856 (936)
T ss_pred hcCCCCChhhHHHHHHHHH
Confidence 9999999988876644333
No 116
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=60.82 E-value=14 Score=36.95 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=28.0
Q ss_pred HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHH
Q 023471 107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNI 145 (281)
Q Consensus 107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~ 145 (281)
|.++|+|.+.|..||.|||.+ +|++...|+.|.+.
T Consensus 530 Ll~~Fgs~~~ik~As~eeL~~----vgi~~~~A~~I~~~ 564 (567)
T PRK14667 530 IYRNFKTLYDFLKADDEELKK----LGIPPSVKQEVKKY 564 (567)
T ss_pred HHHHhCCHHHHHhCCHHHHHH----cCCCHHHHHHHHHH
Confidence 444689999999999999877 38888888877654
No 117
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=60.61 E-value=23 Score=31.09 Aligned_cols=44 Identities=30% Similarity=0.331 Sum_probs=35.5
Q ss_pred HHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH
Q 023471 103 AFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL 149 (281)
Q Consensus 103 ~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i 149 (281)
....|.+. |.|.++|..++.++|.+ --|++..+|..|++.+..+
T Consensus 15 rakkLl~~GF~Sve~Ik~AS~eEL~~---V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 15 KAEALREAGFESVEDVRAADQSELAE---VDGIGNALAARIKADVGGL 59 (232)
T ss_pred HHHHHHHcCCCCHHHHHhCCHHHHHH---ccCCCHHHHHHHHHHhccc
Confidence 34667888 99999999999988766 3588888999998876644
No 118
>PRK00254 ski2-like helicase; Provisional
Probab=59.63 E-value=29 Score=35.63 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=8.0
Q ss_pred HhcCcCccHHHHHHHHH
Q 023471 173 LSRFRGIGPKTVACVLM 189 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~ 189 (281)
|.+++|||+++|..|..
T Consensus 680 l~~~~gi~~~~a~~i~~ 696 (720)
T PRK00254 680 LLKVEGIGAKIVEGIFK 696 (720)
T ss_pred HhcCCCCCHHHHHHHHH
Confidence 34444444444444433
No 119
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=59.35 E-value=8.5 Score=33.13 Aligned_cols=23 Identities=35% Similarity=0.488 Sum_probs=19.9
Q ss_pred HHHHHHHhcCcCccHHHHHHHHH
Q 023471 167 DEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
-+....|+++.||||++|=.||.
T Consensus 69 R~lF~~LisVnGIGpK~ALaiLs 91 (201)
T COG0632 69 RELFRLLISVNGIGPKLALAILS 91 (201)
T ss_pred HHHHHHHHccCCccHHHHHHHHc
Confidence 45778899999999999988776
No 120
>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=58.96 E-value=11 Score=28.80 Aligned_cols=22 Identities=23% Similarity=0.374 Sum_probs=19.1
Q ss_pred HHHHHHhcCcCccHHHHHHHHH
Q 023471 168 EIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.+.-.|.+|.|||+.+|..|+.
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~ 33 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICK 33 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHH
Confidence 3678899999999999997776
No 121
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=57.86 E-value=28 Score=30.58 Aligned_cols=48 Identities=29% Similarity=0.438 Sum_probs=32.3
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 132 GGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 132 ~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
-|.+..+++.|. + +|=-+++.+...+ .++|.+++|||..+|.-|..+.
T Consensus 9 pGIG~krakkLl-------~-~GF~Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 9 SGVGPSKAEALR-------E-AGFESVEDVRAAD----QSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred CCcCHHHHHHHH-------H-cCCCCHHHHHhCC----HHHHHHccCCCHHHHHHHHHHh
Confidence 466666666553 3 1212556665433 5778999999999999998764
No 122
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=57.71 E-value=19 Score=33.32 Aligned_cols=50 Identities=14% Similarity=0.165 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCC-HHHHHhCCHHHHHHHh
Q 023471 80 ESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPT-WEHVLAAEQKCIENAI 129 (281)
Q Consensus 80 ~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt-~~~la~~~~eel~~~i 129 (281)
.-|++.+++..+.--+..+.+..+|++|.++|+| .+.|..++.|+|..+.
T Consensus 303 liPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi~vLi~a~~e~La~V~ 353 (403)
T COG1379 303 LIPLAEIISMALGKGITTKAVKRTWERLVRAFGTEIDVLIDAPIEELARVD 353 (403)
T ss_pred cccHHHHHHHHhccceechhHHHHHHHHHHHhcchhhhHhcCCHHHHhhhh
Confidence 3467888888888889999999999999999985 7777888888877644
No 123
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=56.71 E-value=8.2 Score=35.30 Aligned_cols=21 Identities=38% Similarity=0.491 Sum_probs=18.8
Q ss_pred HHHHHhcCcCccHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~ 189 (281)
..++|+.+||||.++|.-|++
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~ 348 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVM 348 (404)
T ss_pred CHHHhcccCCCChHHHHHHHH
Confidence 478999999999999998876
No 124
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=53.88 E-value=56 Score=29.16 Aligned_cols=87 Identities=20% Similarity=0.233 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHcCC-CchHHHh-cCChHHHHHH-HhcCcCccHHHHHHHHHHhcCC-CccccchHHHHHHHHhCC
Q 023471 137 TKAACIKNILKCLLESKGK-LCLEYLR-GLSIDEIKAE-LSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEISKAIGW 212 (281)
Q Consensus 137 ~KA~~I~~~a~~i~~~~g~-~~l~~l~-~~~~~~~~~~-L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri~~rlG~ 212 (281)
.-+..|+.+++....+... +...... ..+..+.... |.+|||||+..|.-++..-... +++-++.+ .+..-.|.
T Consensus 145 ~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~--eL~~v~gi 222 (254)
T COG1948 145 ETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEE--ELMKVKGI 222 (254)
T ss_pred HHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCHH--HHHHhcCc
Confidence 5677888888888742221 1111111 2345555554 5689999999999888755444 77777662 22233344
Q ss_pred CCCCCCHHHHHHHHH
Q 023471 213 VPTAADRNKTYLHLN 227 (281)
Q Consensus 213 ~~~~~~~~~~~~~l~ 227 (281)
.. .....+++.+.
T Consensus 223 g~--k~A~~I~~~~~ 235 (254)
T COG1948 223 GE--KKAREIYRFLR 235 (254)
T ss_pred cH--HHHHHHHHHHh
Confidence 21 23344555543
No 125
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=53.58 E-value=78 Score=24.74 Aligned_cols=24 Identities=29% Similarity=0.469 Sum_probs=18.1
Q ss_pred HHHHhcCcCccHHHHHHHHHHhcC
Q 023471 170 KAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 170 ~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
+..|..++|||+..|..++.-++.
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHHhCcC
Confidence 566889999999999866654443
No 126
>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=52.74 E-value=22 Score=33.59 Aligned_cols=50 Identities=12% Similarity=0.074 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCC-HHHHHhCCHHHHHHH
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPT-WEHVLAAEQKCIENA 128 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt-~~~la~~~~eel~~~ 128 (281)
..=|++.+++.++.-....+.+...+++|.++|++ .+-|.+++.|||.++
T Consensus 295 ~~iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E~~iL~~~~~eel~~~ 345 (374)
T TIGR00375 295 HLIPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTEIAVLHEAAEEDLARV 345 (374)
T ss_pred eeCCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccHHHHHhcCCHHHHHHH
Confidence 34478999999998888899999999999999975 777788888887654
No 127
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=51.53 E-value=80 Score=32.40 Aligned_cols=46 Identities=26% Similarity=0.444 Sum_probs=30.5
Q ss_pred CCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 132 GGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 132 ~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
-|++..+++.| .+.|| +++.+...+ .++|.+++|||+++|..|+.+
T Consensus 643 PGIGpkr~k~L-------L~~FG--Sle~I~~AS----~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 643 EGIGPATARLL-------WERFG--SLQAMAAAG----EEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred CCCCHHHHHHH-------HHHhC--CHHHHHhcC----HHHHHhcCCcCHHHHHHHHHH
Confidence 46666555444 34466 456665444 355888999999999988653
No 128
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=51.44 E-value=43 Score=22.40 Aligned_cols=49 Identities=12% Similarity=0.141 Sum_probs=33.4
Q ss_pred CHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccH
Q 023471 121 EQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGP 181 (281)
Q Consensus 121 ~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~ 181 (281)
+.++|.+.|+.+|+.. .+..+.+ +.+|.+.|..++.+++.+ +.+.-+|+
T Consensus 4 ~~~~V~~WL~~~~l~~--------y~~~F~~--~~i~g~~L~~lt~~dL~~--lgi~~~gh 52 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQ--------YAENFEK--NYIDGEDLLSLTEEDLEE--LGITKLGH 52 (64)
T ss_dssp SHHHHHHHHHHTTGGG--------GHHHHHH--TTSSHHHHTTSCHHHHHH--TT-SSHHH
T ss_pred CHHHHHHHHHHCCCHH--------HHHHHHc--CCchHHHHHhcCHHHHHH--cCCCCHHH
Confidence 5788899999999865 2334433 667889998888776544 55555554
No 129
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=50.13 E-value=29 Score=23.38 Aligned_cols=34 Identities=9% Similarity=0.265 Sum_probs=27.8
Q ss_pred HHHHhhCCCHHHHH---hCCHHHHHHHhhhCCCchHH
Q 023471 105 ASLKSTFPTWEHVL---AAEQKCIENAIRCGGLAPTK 138 (281)
Q Consensus 105 ~~L~~~~pt~~~la---~~~~eel~~~i~~~G~~~~K 138 (281)
.+|+..|++.+++. .++.++|.+-|+.+||.+..
T Consensus 14 ~kLRD~~~sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~ 50 (55)
T PF14056_consen 14 MKLRDEYSSLDELCYDYDIDKEELEEKLASIGYEYDE 50 (55)
T ss_pred HHHHhccCCHHHHHHHhCCCHHHHHHHHHHcCCeEch
Confidence 46788888888875 48899999999999997643
No 130
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=49.81 E-value=1.7e+02 Score=25.33 Aligned_cols=130 Identities=15% Similarity=0.095 Sum_probs=79.4
Q ss_pred CHHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHH
Q 023471 27 TAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFAS 106 (281)
Q Consensus 27 ~~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~ 106 (281)
|-+....+...|.+.|+.... +. ....+..+.+|..|=.-+...++....-+.
T Consensus 43 tD~~vn~at~~Lf~~~~t~e~---l~------------------------~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~ 95 (211)
T COG0177 43 TDEVVNKATPALFKRYPTPED---LL------------------------NADEEELEELIKSIGLYRNKAKNIKELARI 95 (211)
T ss_pred chHHHHHHHHHHHHHcCCHHH---HH------------------------cCCHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence 445667778888888874332 20 024667888999998899999999999999
Q ss_pred HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH------------HHHHHcCCCchHHHhcCChHHHHHHHh
Q 023471 107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK------------CLLESKGKLCLEYLRGLSIDEIKAELS 174 (281)
Q Consensus 107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~------------~i~~~~g~~~l~~l~~~~~~~~~~~L~ 174 (281)
|.+.|.. --+++.+++++--|.++.-|.-+...+- .+..+.|-.+ ..+.+++.++|.
T Consensus 96 l~e~~~g------~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-----~~~p~~ve~~L~ 164 (211)
T COG0177 96 LLEKFGG------EVPDTREELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-----GKTPEEVEEALM 164 (211)
T ss_pred HHHHcCC------CCCchHHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-----CCCHHHHHHHHH
Confidence 9999964 1233444555556777633333222211 1111112110 235667777777
Q ss_pred cCcCccHHHHHHHHHHhcCC
Q 023471 175 RFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 175 ~l~GIG~~tA~~il~~~~~~ 194 (281)
++=.=.-|+--+..+..+|+
T Consensus 165 ~~iP~~~~~~~h~~lI~~GR 184 (211)
T COG0177 165 KLIPKELWTDLHHWLILHGR 184 (211)
T ss_pred HHCCHHHHHHHHHHHHHhhh
Confidence 76556667766667767776
No 131
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=49.06 E-value=35 Score=18.91 Aligned_cols=27 Identities=11% Similarity=0.231 Sum_probs=21.7
Q ss_pred HHHHHhhhccHHHHHHHHHHHHhhCCC
Q 023471 87 VKTVLSQNTTEANSLKAFASLKSTFPT 113 (281)
Q Consensus 87 v~~ILsqqts~~~a~~~~~~L~~~~pt 113 (281)
++.+.-++.....|...++++.+.||+
T Consensus 6 ~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 6 LARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 445556667889999999999999984
No 132
>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=47.97 E-value=4 Score=31.13 Aligned_cols=19 Identities=42% Similarity=0.532 Sum_probs=12.8
Q ss_pred HhcCcCccHHHHHHHHHHh
Q 023471 173 LSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~~~ 191 (281)
+-.+||||+|||.-++...
T Consensus 20 IPGV~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEY 38 (101)
T ss_dssp B---TTSTCHCCCCCHHHH
T ss_pred CCCCCCCCHHHHHHHHHHc
Confidence 5578999999998776633
No 133
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=47.05 E-value=35 Score=35.65 Aligned_cols=40 Identities=13% Similarity=0.223 Sum_probs=32.4
Q ss_pred HHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH
Q 023471 104 FASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK 147 (281)
Q Consensus 104 ~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~ 147 (281)
+.+|.++|++.++|++++.++|.++ +| ...+|+.|.++.+
T Consensus 770 a~~ll~~f~si~~l~~as~eeL~~~---iG-~~~~A~~i~~fl~ 809 (814)
T TIGR00596 770 YRNLRKKVKSIRELAKLSQNELNEL---IG-DEEAAKRLYDFLR 809 (814)
T ss_pred HHHHHHHcCCHHHHHhCCHHHHHHH---hC-CHHHHHHHHHHhc
Confidence 4567778999999999999999985 55 4668998888765
No 134
>PF13592 HTH_33: Winged helix-turn helix
Probab=47.01 E-value=31 Score=23.26 Aligned_cols=34 Identities=12% Similarity=0.115 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhcCC-CccccchHHHHHHHHhCCCC
Q 023471 181 PKTVACVLMFHLQQ-DDFPVDTHVFEISKAIGWVP 214 (281)
Q Consensus 181 ~~tA~~il~~~~~~-~~~~vD~~v~Ri~~rlG~~~ 214 (281)
.||+..|..+.... .+-.-...+.+++.|+|+..
T Consensus 4 ~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~ 38 (60)
T PF13592_consen 4 RWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSY 38 (60)
T ss_pred cccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCcc
Confidence 45555554443333 33336788999999999964
No 135
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=46.89 E-value=36 Score=34.12 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=29.1
Q ss_pred HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHH
Q 023471 107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNIL 146 (281)
Q Consensus 107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a 146 (281)
|.++|++.+.|..||.+||.++ -|++...|+.|.+..
T Consensus 530 LL~~Fgs~~~I~~As~eeL~~v---~gi~~~~A~~I~~~l 566 (574)
T PRK14670 530 ILKSLGTYKDILLLNEDEIAEK---MKINIKMAKKIKKFA 566 (574)
T ss_pred HHHHhCCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHH
Confidence 4556899999999999987662 488887888776654
No 136
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=46.59 E-value=49 Score=29.51 Aligned_cols=47 Identities=23% Similarity=0.249 Sum_probs=38.9
Q ss_pred HHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHH
Q 023471 103 AFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLES 152 (281)
Q Consensus 103 ~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~ 152 (281)
...+|+..|++.+++..++.+||.. .-|.+..||..|+.+.....+.
T Consensus 194 ~a~~ll~~fgS~~~~~tas~~eL~~---v~gig~k~A~~I~~~~~t~~~~ 240 (254)
T COG1948 194 LAERLLKKFGSVEDVLTASEEELMK---VKGIGEKKAREIYRFLRTEYKL 240 (254)
T ss_pred HHHHHHHHhcCHHHHhhcCHHHHHH---hcCccHHHHHHHHHHHhchhhh
Confidence 4567888999999999999976655 4688888999999998887653
No 137
>KOG0495 consensus HAT repeat protein [RNA processing and modification]
Probab=45.47 E-value=1.2e+02 Score=31.11 Aligned_cols=157 Identities=15% Similarity=0.093 Sum_probs=96.9
Q ss_pred HHHHHHHHHHhhhccHHHHHHHHHHHHhhCCC--HHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchH
Q 023471 82 VLDGLVKTVLSQNTTEANSLKAFASLKSTFPT--WEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLE 159 (281)
Q Consensus 82 ~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt--~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~ 159 (281)
-|-++.+-|.-|+-..+.+..+|..=....|. |--|.-+..||. .| .-.||+.|.+-++.=.-+...+.|+
T Consensus 686 Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk------~~-~~~rAR~ildrarlkNPk~~~lwle 758 (913)
T KOG0495|consen 686 KLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEK------DG-QLVRARSILDRARLKNPKNALLWLE 758 (913)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHH------hc-chhhHHHHHHHHHhcCCCcchhHHH
Confidence 45677888888888888888888765666663 333333333321 22 2358887776555322111122333
Q ss_pred HHh----cCChH----HHHHHHhcCcCccHHHHHHHHHHhcCC-Ccccc--------chHHHHHHHHhCCCCCCCCHHHH
Q 023471 160 YLR----GLSID----EIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPV--------DTHVFEISKAIGWVPTAADRNKT 222 (281)
Q Consensus 160 ~l~----~~~~~----~~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~v--------D~~v~Ri~~rlG~~~~~~~~~~~ 222 (281)
.++ ....+ -.-+.|+..|+-|---|+.|-++.-+. ....+ |.||.=...++.|. ...+++.
T Consensus 759 ~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~--e~k~~ka 836 (913)
T KOG0495|consen 759 SIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWS--EKKIEKA 836 (913)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHH--HHHHHHH
Confidence 322 11111 234578899999987788888877655 55554 45776667777774 3567888
Q ss_pred HHHHHhhCCc-----ccHHHHHHHHHHhcc
Q 023471 223 YLHLNQRIPK-----ELKFDLNCLLYTHGK 247 (281)
Q Consensus 223 ~~~l~~~~p~-----~~~~~~h~~lv~~G~ 247 (281)
+.++++.+.. |.|..|..--..||.
T Consensus 837 r~Wf~Ravk~d~d~GD~wa~fykfel~hG~ 866 (913)
T KOG0495|consen 837 REWFERAVKKDPDNGDAWAWFYKFELRHGT 866 (913)
T ss_pred HHHHHHHHccCCccchHHHHHHHHHHHhCC
Confidence 8899888753 346677776778883
No 138
>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=45.25 E-value=77 Score=19.94 Aligned_cols=41 Identities=17% Similarity=0.101 Sum_probs=31.5
Q ss_pred HHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH
Q 023471 104 FASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK 147 (281)
Q Consensus 104 ~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~ 147 (281)
...|.+. |-|.++++.+++++|.+. -|+...++..|+..++
T Consensus 6 ~~~L~~~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHH
Confidence 3445544 579999999999998873 6788888888877665
No 139
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=44.60 E-value=38 Score=30.91 Aligned_cols=44 Identities=23% Similarity=0.331 Sum_probs=34.6
Q ss_pred HHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHH
Q 023471 102 KAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKC 148 (281)
Q Consensus 102 ~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~ 148 (281)
....+|...|.+..+|.+++.++|.++ =|.+..||+.|++-...
T Consensus 304 ~iv~nlV~~F~~l~~il~As~edL~~V---eGIGe~rAr~i~~Gl~r 347 (349)
T COG1623 304 AIVENLVRAFGTLDGILEASAEDLDAV---EGIGEARARAIKEGLSR 347 (349)
T ss_pred HHHHHHHHHHhhHHHHHHhcHhHHhhh---cchhHHHHHHHHHhHhh
Confidence 456778888999999999999998773 46777788888775543
No 140
>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=43.46 E-value=83 Score=32.43 Aligned_cols=19 Identities=26% Similarity=0.214 Sum_probs=15.1
Q ss_pred cCcCccHHHHHHHHHHhcCC
Q 023471 175 RFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 175 ~l~GIG~~tA~~il~~~~~~ 194 (281)
.++|||-++||.|... +|.
T Consensus 185 ~i~gigF~~aD~iA~~-~g~ 203 (720)
T TIGR01448 185 DVKGIGFLTADQLAQA-LGI 203 (720)
T ss_pred hcCCCCHHHHHHHHHH-cCC
Confidence 5899999999998653 443
No 141
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=43.40 E-value=45 Score=33.74 Aligned_cols=35 Identities=23% Similarity=0.248 Sum_probs=26.7
Q ss_pred HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHH
Q 023471 107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNIL 146 (281)
Q Consensus 107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a 146 (281)
|.++|++.++|..|+.+||..+ ++...|+.|.+..
T Consensus 568 LL~~FgSi~~I~~As~eeL~~v-----i~~k~A~~I~~~l 602 (624)
T PRK14669 568 LLKHFGSLERVRAATETQLAAV-----VGRAAAEAIIAHF 602 (624)
T ss_pred HHHHcCCHHHHHhCCHHHHHHH-----hCHHHHHHHHHHh
Confidence 4456899999999999999875 4556777776654
No 142
>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=43.22 E-value=72 Score=21.62 Aligned_cols=42 Identities=14% Similarity=0.246 Sum_probs=30.1
Q ss_pred HHHHhhCCC-HHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHH
Q 023471 105 ASLKSTFPT-WEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLL 150 (281)
Q Consensus 105 ~~L~~~~pt-~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~ 150 (281)
....+.|++ |+++..++..+ ++..|.+-+--+||....+.+.
T Consensus 13 ~~~~~kf~~~w~~lf~~~s~~----LK~~GIp~r~RryiL~~~ek~r 55 (57)
T PF09597_consen 13 EEHAEKFESDWEKLFTTSSKQ----LKELGIPVRQRRYILRWREKYR 55 (57)
T ss_pred HHHHHHHHHHHHHHHhcCHHH----HHHCCCCHHHHHHHHHHHHHHh
Confidence 445566777 99999999765 5568998766677777666553
No 143
>PRK14976 5'-3' exonuclease; Provisional
Probab=41.68 E-value=16 Score=33.05 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=16.4
Q ss_pred HHhcCcCccHHHHHHHHHHhcCC
Q 023471 172 ELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 172 ~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
.+-.+||||+|||.-++. -+|.
T Consensus 192 nipGVpGIG~KtA~~LL~-~~gs 213 (281)
T PRK14976 192 NIKGVKGIGPKTAIKLLN-KYGN 213 (281)
T ss_pred CCCCCCcccHHHHHHHHH-HcCC
Confidence 455689999999987775 4443
No 144
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=40.97 E-value=47 Score=33.93 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=31.4
Q ss_pred HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHH
Q 023471 107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKC 148 (281)
Q Consensus 107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~ 148 (281)
|.++|++.+.|..|+.+||.++ .|++...|+.|...|..
T Consensus 624 LL~~FgS~~~i~~As~eel~~v---~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 624 LLAHFGSFRSLQSATPQDIATA---IHIPLTQAHTILHAATR 662 (691)
T ss_pred HHHHhcCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHhhc
Confidence 4446899999999999998763 48888888888887654
No 145
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=40.33 E-value=59 Score=20.82 Aligned_cols=35 Identities=20% Similarity=0.178 Sum_probs=27.4
Q ss_pred HHHhCCHHHHHHHhhhCCCch------HHHHHHHHHHHHHH
Q 023471 116 HVLAAEQKCIENAIRCGGLAP------TKAACIKNILKCLL 150 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~------~KA~~I~~~a~~i~ 150 (281)
++..++.+||.+.+...|+.. .|.-|++.+.+.+.
T Consensus 2 d~~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~~ 42 (44)
T smart00540 2 DVDRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRKLRR 42 (44)
T ss_pred chhHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHHc
Confidence 466788999999999999853 67778877776653
No 146
>PRK09482 flap endonuclease-like protein; Provisional
Probab=39.79 E-value=18 Score=32.25 Aligned_cols=18 Identities=39% Similarity=0.658 Sum_probs=14.7
Q ss_pred HHhcCcCccHHHHHHHHH
Q 023471 172 ELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 172 ~L~~l~GIG~~tA~~il~ 189 (281)
-+-.+||||++||.-++.
T Consensus 183 nIpGVpGIG~KtA~~LL~ 200 (256)
T PRK09482 183 KIPGVAGIGPKSAAELLN 200 (256)
T ss_pred CCCCCCCcChHHHHHHHH
Confidence 355689999999987776
No 147
>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=38.23 E-value=20 Score=31.49 Aligned_cols=19 Identities=37% Similarity=0.501 Sum_probs=15.0
Q ss_pred HHHhcCcCccHHHHHHHHH
Q 023471 171 AELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~ 189 (281)
+.+..+||||++||.-++.
T Consensus 183 DnipGv~GiG~ktA~~Ll~ 201 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLK 201 (240)
T ss_pred cCCCCCCccCHHHHHHHHH
Confidence 3456789999999977665
No 148
>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=37.81 E-value=1.2e+02 Score=22.50 Aligned_cols=54 Identities=19% Similarity=0.246 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHh
Q 023471 137 TKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 137 ~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~ 191 (281)
...+....+...+.+.||..+.+.+...+.+++.+.+.. -|.+..-|..|...+
T Consensus 9 ~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~-~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 9 TSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRP-LGFSRRKAKYIIELA 62 (108)
T ss_dssp S-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTT-STSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhc-cCCCHHHHHHHHHHH
Confidence 456667777888888888679999998887666555544 788877777776544
No 149
>smart00475 53EXOc 5'-3' exonuclease.
Probab=37.67 E-value=21 Score=31.88 Aligned_cols=19 Identities=37% Similarity=0.501 Sum_probs=15.2
Q ss_pred HHHhcCcCccHHHHHHHHH
Q 023471 171 AELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~ 189 (281)
+.+-.+||||++||.-++.
T Consensus 186 DnipGV~GIG~KtA~~Ll~ 204 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLK 204 (259)
T ss_pred cCCCCCCCCCHHHHHHHHH
Confidence 3456789999999987775
No 150
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=37.15 E-value=1.4e+02 Score=26.67 Aligned_cols=91 Identities=12% Similarity=0.156 Sum_probs=52.2
Q ss_pred hCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHH---------
Q 023471 119 AAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLM--------- 189 (281)
Q Consensus 119 ~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~--------- 189 (281)
..+.++|.+.+..-||+-.++ +|-++.+.+.- -.+.....| -+|||.--+..++.
T Consensus 136 ~ltq~ela~~lgk~g~~isrs-~Isn~lrll~~-------------L~~~i~~~l--~~glGr~~~~~L~~L~~~a~~~w 199 (258)
T TIGR03764 136 SLSQRELARRLSADGYPISQS-HISRMGDTVEY-------------LYPAIPNLL--YSGLGRPQIEKLLSLRKAAEKIW 199 (258)
T ss_pred CCCHHHHHHHhcccCCCCCHH-HHHHHHHHHHh-------------ChHHHHHHH--HccCChHHHHHHHHHHHHHHHHH
Confidence 367788888887777776554 55555555432 123344444 68898765555432
Q ss_pred --HhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHH
Q 023471 190 --FHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLN 227 (281)
Q Consensus 190 --~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~ 227 (281)
++++.. ...|+--..++.++. .++..+++.++..|.
T Consensus 200 ~~~~~~~~-~~f~~~f~~~~~~~d-~~~~~~~~~~~deli 237 (258)
T TIGR03764 200 NRYSSGVE-VDFEEVFQEVLARFD-DPEEFSLERFRDELI 237 (258)
T ss_pred HHHccccC-CCHHHHHHHHHHhcC-CcccCCHHHHHHHHH
Confidence 233332 445666666666665 344556666666553
No 151
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=37.12 E-value=2.9e+02 Score=27.06 Aligned_cols=112 Identities=14% Similarity=0.174 Sum_probs=62.6
Q ss_pred HHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCcc
Q 023471 101 LKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIG 180 (281)
Q Consensus 101 ~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG 180 (281)
..+++.|.++.|...+|..+|.+-|.+ . | .+.-++-.+..+-+. +-+.|-= -...+.-.|.-+.|+|
T Consensus 421 l~virk~aekiPgf~el~paDq~lLle---s-------a-flelfvlRlAyRs~~-~e~kliF-csG~vlhr~qC~rgfg 487 (605)
T KOG4217|consen 421 LEVIRKWAEKIPGFAELPPADQDLLLE---S-------A-FLELFVLRLAYRSNP-SEDKLIF-CSGLVLHRLQCLRGFG 487 (605)
T ss_pred HHHHHHHHHhCcCcccCChhhHHHHHH---H-------H-HHHHHHHHHHHhcCC-CCCeEEE-ecchhhhHHHHHHHHH
Confidence 356778888888777776666543322 1 1 121222222221121 1111110 0124556688899999
Q ss_pred HHHHHHHHHHhcCCCccccchHHHH-------HHHHhCCCCCCCCHHHHHHHHH
Q 023471 181 PKTVACVLMFHLQQDDFPVDTHVFE-------ISKAIGWVPTAADRNKTYLHLN 227 (281)
Q Consensus 181 ~~tA~~il~~~~~~~~~~vD~~v~R-------i~~rlG~~~~~~~~~~~~~~l~ 227 (281)
.| .|.|+-|....+-..+|.-..- |..|+|+- +....++++..+.
T Consensus 488 ew-idsi~~FS~~l~~l~idi~AfacL~aLa~iTErhGL~-epkrVeelqnkIi 539 (605)
T KOG4217|consen 488 EW-IDSIREFSRSLHSLNIDISAFACLSALALITERHGLK-EPKRVEELQNKII 539 (605)
T ss_pred HH-HHHHHHHHHHhhhchhhHHHHHHHHHHHhhhhhhcCC-CcchHHHHHHHHH
Confidence 55 4889999888887788876654 34567774 3455666665543
No 152
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=36.75 E-value=1.2e+02 Score=25.83 Aligned_cols=31 Identities=26% Similarity=0.259 Sum_probs=22.8
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcCCC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQQD 195 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~ 195 (281)
++..-.-.|.-|||||.|+...||----.++
T Consensus 124 PIt~RLH~LELLpGiGkK~m~~ILeERkkkp 154 (202)
T COG1491 124 PITLRLHQLELLPGIGKKTMWAILEERKKKP 154 (202)
T ss_pred cchHHHHHHHhcccccHHHHHHHHHHHhcCC
Confidence 3444455788899999999999998554444
No 153
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=36.69 E-value=23 Score=27.88 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=18.8
Q ss_pred HHHHHHhcCcCccHHHHHHHHHH
Q 023471 168 EIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.+.-.|..|.|||+.+|..|+..
T Consensus 14 ~v~~aLt~i~GIG~~~A~~ic~~ 36 (122)
T CHL00137 14 RIEYALTYIYGIGLTSAKEILEK 36 (122)
T ss_pred EeeeeecccccccHHHHHHHHHH
Confidence 34567899999999999987763
No 154
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=36.30 E-value=1.3e+02 Score=23.98 Aligned_cols=58 Identities=12% Similarity=0.100 Sum_probs=40.4
Q ss_pred CHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHH
Q 023471 81 SVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNI 145 (281)
Q Consensus 81 ~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~ 145 (281)
.-+..++..|=....+.+. +....-|.+++.+++.++|.+++..+|.+.---+++...
T Consensus 67 P~l~~WL~vVgl~~~~i~~-------i~~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~A 124 (129)
T PF13543_consen 67 PSLRQWLRVVGLRPESIQA-------ILSKVLTLEALLEMSDEELKEILNRCGAREEECRRLCRA 124 (129)
T ss_pred CcHHHHhhhcCCCHHHHHH-------HHHhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 4577777777554444433 333456899999999999999999999876444444443
No 155
>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=36.08 E-value=91 Score=28.20 Aligned_cols=45 Identities=20% Similarity=0.278 Sum_probs=35.4
Q ss_pred HHHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH
Q 023471 102 KAFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL 149 (281)
Q Consensus 102 ~~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i 149 (281)
....+|.+. |.|.++|+.++.++|.+. .|+...++..|.+.+...
T Consensus 10 ~~~~~L~~~Gi~ti~dl~~~~~~~L~~~---~g~~~~~a~~l~~~~~~~ 55 (310)
T TIGR02236 10 ATAEKLREAGYDTFEAIAVASPKELSEI---AGISEGTAAKIIQAARKA 55 (310)
T ss_pred HHHHHHHHcCCCCHHHHHcCCHHHHHhc---cCCCHHHHHHHHHHHHHH
Confidence 345677777 789999999999988774 488877888888877633
No 156
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=34.57 E-value=27 Score=27.56 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=18.3
Q ss_pred HHHHHhcCcCccHHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+.-.|..|.|||+.+|..|+..
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~ 36 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAA 36 (122)
T ss_pred EEeeecccccccHHHHHHHHHH
Confidence 4567899999999999987763
No 157
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=34.45 E-value=1e+02 Score=21.19 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=25.5
Q ss_pred hhCCCHHHHHhCCHHHHHHHhhhCCC-----chHHHHHH
Q 023471 109 STFPTWEHVLAAEQKCIENAIRCGGL-----APTKAACI 142 (281)
Q Consensus 109 ~~~pt~~~la~~~~eel~~~i~~~G~-----~~~KA~~I 142 (281)
..|.+++++..++.|.|.+.|...|+ -..||.++
T Consensus 4 ~~f~sa~eLe~lGldrLK~~L~a~GLKcGGTl~ERA~RL 42 (60)
T PF13297_consen 4 DAFSSAEELEALGLDRLKSALMALGLKCGGTLQERAARL 42 (60)
T ss_pred hhcCCHHHHHHhCHHHHHHHHHHcCCccCCCHHHHHHHH
Confidence 35778999999999999988877665 34555555
No 158
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=33.41 E-value=77 Score=26.77 Aligned_cols=42 Identities=24% Similarity=0.347 Sum_probs=33.2
Q ss_pred HhcCcCccHHHHHHHHHHhc-CCCccccchHHHHHHHHhCCCC
Q 023471 173 LSRFRGIGPKTVACVLMFHL-QQDDFPVDTHVFEISKAIGWVP 214 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~~~~-~~~~~~vD~~v~Ri~~rlG~~~ 214 (281)
+..+||||.-|.--++.--+ +...+-..+....++.+.|++.
T Consensus 9 itGVpGvGKTTVl~~~~~~l~~~~ivNyG~~Mle~A~k~glve 51 (189)
T COG2019 9 ITGVPGVGKTTVLKIALKELVKHKIVNYGDLMLEIAKKKGLVE 51 (189)
T ss_pred EEcCCCCChHHHHHHHHHHHhhceeeeHhHHHHHHHHHhCCcc
Confidence 45789999999776666555 4466777888999999999974
No 159
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=33.39 E-value=41 Score=24.63 Aligned_cols=37 Identities=14% Similarity=0.197 Sum_probs=22.7
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcCCCccccchHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFE 205 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~R 205 (281)
++--|..|+|||..+|..|+.---+.+.--+.+.+.|
T Consensus 25 Ir~gl~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R 61 (90)
T PF14579_consen 25 IRLGLSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR 61 (90)
T ss_dssp EE-BGGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH
T ss_pred EeehHhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH
Confidence 4445889999999999988864434454444444443
No 160
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=32.72 E-value=99 Score=28.61 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHH
Q 023471 137 TKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 137 ~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
-|+..-..++..+.. +. + ++ ...+++.+|||||+++|..|--+
T Consensus 33 ~r~~~y~~Aasvlk~-~p-~--------~I-~S~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 33 DRARAYRRAASVLKS-LP-F--------PI-TSGEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred HHHHHHHHHHHHHHh-CC-C--------Cc-ccHHHhcCCCCCCHHHHHHHHHH
Confidence 355555566666654 22 1 12 24678889999999999987654
No 161
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=32.57 E-value=2.9e+02 Score=22.99 Aligned_cols=100 Identities=13% Similarity=0.199 Sum_probs=59.1
Q ss_pred hCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHH---HHHHHhcCCC
Q 023471 119 AAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVA---CVLMFHLQQD 195 (281)
Q Consensus 119 ~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~---~il~~~~~~~ 195 (281)
.++.+||.-.++.+||...|....+-++..=.+..|.+ ..++.+......=|.+.---+ +|-+|-....
T Consensus 49 ~iD~~EL~vAmralGFE~~k~ei~kll~d~dk~~~g~i--------~fe~f~~~mt~k~~e~dt~eEi~~afrl~D~D~~ 120 (172)
T KOG0028|consen 49 KIDVEELKVAMRALGFEPKKEEILKLLADVDKEGSGKI--------TFEDFRRVMTVKLGERDTKEEIKKAFRLFDDDKT 120 (172)
T ss_pred cccHHHHHHHHHHcCCCcchHHHHHHHHhhhhccCcee--------chHHHHHHHHHHHhccCcHHHHHHHHHcccccCC
Confidence 46788898889999999867765555555433322333 344455554444444442222 2223333334
Q ss_pred ccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhh
Q 023471 196 DFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQR 229 (281)
Q Consensus 196 ~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~ 229 (281)
.-.-=.+..|++.+||- ..+.++++..+++.
T Consensus 121 Gkis~~~lkrvakeLge---nltD~El~eMIeEA 151 (172)
T KOG0028|consen 121 GKISQRNLKRVAKELGE---NLTDEELMEMIEEA 151 (172)
T ss_pred CCcCHHHHHHHHHHhCc---cccHHHHHHHHHHh
Confidence 55556788999999976 45666777665544
No 162
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=32.41 E-value=1.6e+02 Score=22.24 Aligned_cols=21 Identities=10% Similarity=0.101 Sum_probs=17.6
Q ss_pred HHHhcCcCccHHHHHHHHHHh
Q 023471 171 AELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~~ 191 (281)
.+-.++||||..-|..|..|-
T Consensus 50 ~Wwr~vpglG~~~A~~I~awL 70 (96)
T PF12482_consen 50 RWWRAVPGLGAAGARRIEAWL 70 (96)
T ss_pred hHHHhCcccchHHHHHHHHHH
Confidence 678889999999999887753
No 163
>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=31.76 E-value=1e+02 Score=28.09 Aligned_cols=20 Identities=25% Similarity=0.311 Sum_probs=15.3
Q ss_pred HhcCcCccHHHHHHHHHHhcC
Q 023471 173 LSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~~~~~ 193 (281)
+..++|||++||--++.- +|
T Consensus 225 ~~gv~giG~k~A~~li~~-~~ 244 (316)
T cd00128 225 TEGIPGIGPVTALKLIKK-YG 244 (316)
T ss_pred CCCCCCccHHHHHHHHHH-cC
Confidence 346999999999877753 44
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=30.91 E-value=31 Score=26.81 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=18.5
Q ss_pred HHHHHHhcCcCccHHHHHHHHHH
Q 023471 168 EIKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~~ 190 (281)
.+.-.|.+|.|||..+|..|+..
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~ 34 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEK 34 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHH
Confidence 34567899999999999877753
No 165
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=30.84 E-value=29 Score=28.58 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=18.4
Q ss_pred HHHHHHhcCcCccHHHHHHHHH
Q 023471 168 EIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.+.-.|..|.|||+.+|..|+.
T Consensus 27 ~v~~aLt~I~GIG~~~A~~I~~ 48 (154)
T PTZ00134 27 KVPYALTAIKGIGRRFAYLVCK 48 (154)
T ss_pred EEEEeecccccccHHHHHHHHH
Confidence 3556799999999999987775
No 166
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=30.60 E-value=38 Score=31.54 Aligned_cols=62 Identities=21% Similarity=0.241 Sum_probs=37.6
Q ss_pred HHHHHHHhcCcCccHHHHHHHHHHh---cCC-CccccchHHHHHHHHhCCCC------CCCCHHHHHHHHHhhCC
Q 023471 167 DEIKAELSRFRGIGPKTVACVLMFH---LQQ-DDFPVDTHVFEISKAIGWVP------TAADRNKTYLHLNQRIP 231 (281)
Q Consensus 167 ~~~~~~L~~l~GIG~~tA~~il~~~---~~~-~~~~vD~~v~Ri~~rlG~~~------~~~~~~~~~~~l~~~~p 231 (281)
++..++|+-+|||||.|+.+..+.| +|. +.|- |--. .+..+|.-+ +..+|+++-..+++.+.
T Consensus 274 p~Df~elLl~~GiGpstvRALalVAEvIyg~~~s~r-DP~~--yafA~GGKDgvP~pV~~~~yde~I~~l~~~ve 345 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVAEVIYGEPPSFR-DPVK--YAFAVGGKDGVPFPVNRKTYDELIEFLEELVE 345 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHHHHHhCCCCCcC-Cchh--hhhhhcCCCCCCCCcchhhHHHHHHHHHHHHH
Confidence 4567888999999999998877654 554 2221 2111 333445421 23467777777766654
No 167
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=30.52 E-value=1.3e+02 Score=27.72 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=15.8
Q ss_pred HhcCcCccHHHHHHHHHHh
Q 023471 173 LSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~~~ 191 (281)
+..|+|+|.+++.-|+.+.
T Consensus 130 ~~~l~GfG~kse~~il~~i 148 (326)
T COG1796 130 IRGLRGFGKKSEAKILENI 148 (326)
T ss_pred ccccCCccchhHHHHHHHH
Confidence 4579999999999998753
No 168
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=30.34 E-value=1.5e+02 Score=19.97 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=26.8
Q ss_pred cCcCccHHHHHHHHHHhcCCCccccchHHHHHHHHhCCCCC-CCCHHHHHHHHHhhC
Q 023471 175 RFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPT-AADRNKTYLHLNQRI 230 (281)
Q Consensus 175 ~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Ri~~rlG~~~~-~~~~~~~~~~l~~~~ 230 (281)
++.||-+-.++.+...+|.+ +.|..+++|+|+-.. +.+.....+.+++++
T Consensus 4 ~~~Gi~~~lVd~F~~mGF~~------dkVvevlrrlgik~~n~~dn~t~~~ilEELL 54 (55)
T PF09288_consen 4 ALYGIDKDLVDQFENMGFER------DKVVEVLRRLGIKSMNGVDNETENKILEELL 54 (55)
T ss_dssp S----SHHHHHHHHHHT--H------HHHHHHHHHS--SS--SS--HHHHHHHHHHT
T ss_pred HHcCCCHHHHHHHHHcCCcH------HHHHHHHHHhCCCCCCCccchhHHHHHHHHh
Confidence 46688888888888877776 346678999999542 244555556666654
No 169
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=30.20 E-value=1e+02 Score=31.08 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=13.6
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
....|..|||||++++..++. .||
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~-~Fg 564 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLK-HFG 564 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHH-HcC
Confidence 345566666666666664443 444
No 170
>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=29.39 E-value=34 Score=27.78 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=17.5
Q ss_pred HHHHHhcCcCccHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~ 189 (281)
+.-.|..|.|||+.+|..|+.
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~ 39 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIAR 39 (144)
T ss_pred EEEeecceeccCHHHHHHHHH
Confidence 455789999999999987765
No 171
>PRK01172 ski2-like helicase; Provisional
Probab=29.34 E-value=1.6e+02 Score=29.97 Aligned_cols=39 Identities=18% Similarity=0.111 Sum_probs=32.7
Q ss_pred CCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHc
Q 023471 112 PTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESK 153 (281)
Q Consensus 112 pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~ 153 (281)
-|+.+|+.++++++.++ .|++.+.++.|.+-|+.+.+.|
T Consensus 634 ~~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 634 KTVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred CCHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHHHh
Confidence 47999999999998776 4788899999999888887644
No 172
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=29.30 E-value=43 Score=26.32 Aligned_cols=22 Identities=18% Similarity=0.242 Sum_probs=18.4
Q ss_pred HHHHHhcCcCccHHHHHHHHHH
Q 023471 169 IKAELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~ 190 (281)
+.-.|..|.|||..+|..|+.-
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~ 36 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKK 36 (121)
T ss_pred EeehhhhhccccHHHHHHHHHH
Confidence 3456899999999999998873
No 173
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=29.26 E-value=14 Score=23.20 Aligned_cols=32 Identities=28% Similarity=0.401 Sum_probs=17.9
Q ss_pred HHHHHHHHhcccCCCCcCCCCCCCcCCCCCCCCCChhhccccc
Q 023471 237 DLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSN 279 (281)
Q Consensus 237 ~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~~Cpl~~~C~~~~ 279 (281)
.+..+|..|-..|.+|.+. +.|-|.+++..|+
T Consensus 4 ~lelll~~H~~dC~~C~~~-----------G~CeLQ~~~~~~g 35 (41)
T PF10588_consen 4 VLELLLANHPLDCPTCDKN-----------GNCELQDLAYEYG 35 (41)
T ss_dssp HHHHHHTT----TTT-TTG-----------GG-HHHHHHHHH-
T ss_pred HHHHHHhCCCCcCcCCCCC-----------CCCHHHHHHHHhC
Confidence 3556777788888888744 6788888777665
No 174
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=29.00 E-value=2.9e+02 Score=22.18 Aligned_cols=56 Identities=34% Similarity=0.433 Sum_probs=38.2
Q ss_pred HHHHHHHhhhCCC--chHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHh-cCcCccHHHHHHHHH
Q 023471 122 QKCIENAIRCGGL--APTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELS-RFRGIGPKTVACVLM 189 (281)
Q Consensus 122 ~eel~~~i~~~G~--~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~-~l~GIG~~tA~~il~ 189 (281)
.+++.+.++..|+ +.+|.. +++.+.+..+.+ +.+++.+.|. ..|+||.-|+.-.|-
T Consensus 5 ~~~~~~~lk~~glr~T~qR~~----vl~~L~~~~~~~--------sAeei~~~l~~~~p~islaTVYr~L~ 63 (145)
T COG0735 5 LEDAIERLKEAGLRLTPQRLA----VLELLLEADGHL--------SAEELYEELREEGPGISLATVYRTLK 63 (145)
T ss_pred HHHHHHHHHHcCCCcCHHHHH----HHHHHHhcCCCC--------CHHHHHHHHHHhCCCCCHhHHHHHHH
Confidence 4567778888887 444443 345555432333 6778888887 579999999987774
No 175
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=28.98 E-value=1.1e+02 Score=30.75 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=25.5
Q ss_pred HHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHH
Q 023471 106 SLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKN 144 (281)
Q Consensus 106 ~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~ 144 (281)
.|.++|+++++|..++.++|.. --|++...|+.|.+
T Consensus 540 ~LL~~FGS~~~I~~As~eeL~~---vpGi~~~~A~~I~~ 575 (577)
T PRK14668 540 RLLRRFGSVEGVREASVEDLRD---VPGVGEKTAETIRE 575 (577)
T ss_pred HHHHHcCCHHHHHhCCHHHHHh---CCCCCHHHHHHHHH
Confidence 4555688999999999887644 12777767766654
No 176
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=28.85 E-value=32 Score=28.14 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=18.2
Q ss_pred HHHHHHhcCcCccHHHHHHHHH
Q 023471 168 EIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.+.-.|..|.|||+.+|..|+.
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~ 43 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIAR 43 (149)
T ss_pred EEeeeccccccccHHHHHHHHH
Confidence 3566799999999999987765
No 177
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=28.42 E-value=1.2e+02 Score=30.50 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=28.2
Q ss_pred HHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHH
Q 023471 105 ASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNI 145 (281)
Q Consensus 105 ~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~ 145 (281)
..|.++|++++.|..++.++|.+ --|++...|+.|.+.
T Consensus 557 k~Ll~~FgS~~~i~~As~eeL~~---v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 557 KALLKHFGSLKAIKEASVEELAK---VPGISKKLAEAIYEA 594 (598)
T ss_pred HHHHHHcCCHHHHHhCCHHHHhh---cCCcCHHHHHHHHHH
Confidence 45667799999999999887654 237777777777654
No 178
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=28.40 E-value=62 Score=32.79 Aligned_cols=49 Identities=20% Similarity=0.430 Sum_probs=28.6
Q ss_pred HHHHHHHHHcCCCchHHHhcC-ChHHHHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 144 NILKCLLESKGKLCLEYLRGL-SIDEIKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 144 ~~a~~i~~~~g~~~l~~l~~~-~~~~~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
.+.+.|.++-..+-+..-++. +-......|.+|||||++++..+|. .||
T Consensus 524 ~lLq~iRDEaHRFAIt~hRk~R~k~~~~S~L~~IpGIG~kr~~~LL~-~Fg 573 (624)
T PRK14669 524 HLVQSIRDEAHRFAITFHRKRRETRDRTSELLEIPGVGAKTVQRLLK-HFG 573 (624)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhHHHHHHHHhcCCCCCHHHHHHHHH-HcC
Confidence 445555544222333333322 2234567788999999999987665 455
No 179
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=28.19 E-value=1.1e+02 Score=30.88 Aligned_cols=36 Identities=17% Similarity=0.222 Sum_probs=27.8
Q ss_pred HHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHH
Q 023471 105 ASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKN 144 (281)
Q Consensus 105 ~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~ 144 (281)
..|.++|++.+.|..|+.+||.++ |.+..-|..|++
T Consensus 544 ~~LL~~Fgs~~~i~~As~eel~~v----gi~~~~a~~i~~ 579 (581)
T COG0322 544 KALLKHFGSLKGIKSASVEELAKV----GISKKLAEKIYE 579 (581)
T ss_pred HHHHHHhhCHHHHHhcCHHHHHHc----CCCHHHHHHHHh
Confidence 446667999999999999987773 777766666654
No 180
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=27.59 E-value=57 Score=27.22 Aligned_cols=72 Identities=15% Similarity=0.109 Sum_probs=47.8
Q ss_pred HHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHHHhcCCCccccchHH
Q 023471 124 CIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHV 203 (281)
Q Consensus 124 el~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v 203 (281)
++.++|..-+ .+...|..+++.+.+.||-+ .+++.+.+.+.=||-+--+..|..|--....-|+..|+
T Consensus 23 ~i~~ii~~~~---~~~~~li~~L~~iQ~~~GyI---------p~e~~~~iA~~l~v~~a~V~gVatFY~~f~~~P~Gk~~ 90 (169)
T PRK07571 23 VLEATMKRNQ---YRQDALIEVLHKAQELFGYL---------ERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSGEHT 90 (169)
T ss_pred HHHHHHHHcC---CCHHHHHHHHHHHHHHcCCC---------CHHHHHHHHHHhCcCHHHHHHHHHHccccCcCCCCCEE
Confidence 3444444433 25567888999999988875 35677777777788887777788775444445556665
Q ss_pred HHHH
Q 023471 204 FEIS 207 (281)
Q Consensus 204 ~Ri~ 207 (281)
.+++
T Consensus 91 I~VC 94 (169)
T PRK07571 91 CVVC 94 (169)
T ss_pred EEEc
Confidence 5543
No 181
>PTZ00035 Rad51 protein; Provisional
Probab=27.57 E-value=1.8e+02 Score=27.02 Aligned_cols=47 Identities=28% Similarity=0.244 Sum_probs=38.7
Q ss_pred HHHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 102 KAFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 102 ~~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
....+|.++ |-|.++|+.++..+|.+ -.|++..+|.-|++.++.+..
T Consensus 34 ~~~~kL~~~g~~t~~~~~~~~~~~L~~---~~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 34 ADIKKLKEAGICTVESVAYATKKDLCN---IKGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHH---hhCCCHHHHHHHHHHHHHhcc
Confidence 345667766 57999999999988776 489999999999999888865
No 182
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=27.36 E-value=1.5e+02 Score=18.79 Aligned_cols=22 Identities=14% Similarity=0.010 Sum_probs=15.2
Q ss_pred HHHHHHhhhCCCchHHHHHHHH
Q 023471 123 KCIENAIRCGGLAPTKAACIKN 144 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~ 144 (281)
+|+.+.|-.+||...-+..+..
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~ 25 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVS 25 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 5677888899998866655443
No 183
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=26.94 E-value=1.7e+02 Score=26.61 Aligned_cols=44 Identities=23% Similarity=0.280 Sum_probs=34.3
Q ss_pred HHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHH
Q 023471 103 AFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCL 149 (281)
Q Consensus 103 ~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i 149 (281)
..++|.+. |-|.++|+.+++++|.+. .|+...++..|.+.++..
T Consensus 18 ~a~~L~~~Gi~t~~dl~~~~~~~L~~~---~g~~~~~a~~l~~~a~~~ 62 (317)
T PRK04301 18 TAEKLREAGYDTVEAIAVASPKELSEA---AGIGESTAAKIIEAAREA 62 (317)
T ss_pred HHHHHHHcCCCCHHHHHcCCHHHHHHh---cCCCHHHHHHHHHHHHHh
Confidence 34566666 679999999999888764 588778888888887753
No 184
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=26.90 E-value=83 Score=25.15 Aligned_cols=53 Identities=21% Similarity=0.431 Sum_probs=41.6
Q ss_pred cCChHHHHHHHhcC--cCccHHHHHHHHHHhcCC--CccccchHHHHHHHHhCCCCC
Q 023471 163 GLSIDEIKAELSRF--RGIGPKTVACVLMFHLQQ--DDFPVDTHVFEISKAIGWVPT 215 (281)
Q Consensus 163 ~~~~~~~~~~L~~l--~GIG~~tA~~il~~~~~~--~~~~vD~~v~Ri~~rlG~~~~ 215 (281)
+++.++..+.+.++ +|+-|--...+|.-+.|. -.++...-+.|++++-|+.++
T Consensus 27 K~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe 83 (151)
T KOG0400|consen 27 KLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE 83 (151)
T ss_pred hcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC
Confidence 44667777777765 899898888888766665 467778889999999999874
No 185
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=26.84 E-value=2.2e+02 Score=19.73 Aligned_cols=64 Identities=22% Similarity=0.261 Sum_probs=26.4
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHH---hcCcCccHHHHHHHHH
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAEL---SRFRGIGPKTVACVLM 189 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L---~~l~GIG~~tA~~il~ 189 (281)
++..+.++.-|++..-.+.=....+.+.+-++.-+++.+ +.+++...+ ..-.|+.+.|.+..+.
T Consensus 3 ~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~i---t~~~i~~y~~~l~~~~~~s~~T~~~~~~ 69 (85)
T PF13495_consen 3 EEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEI---TPEDIEQYLNYLQNERGLSPSTINQYLS 69 (85)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG-----HHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchh---HHHHHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 344555666777653333222222223332232233333 444555544 4457899999887654
No 186
>PRK00159 putative septation inhibitor protein; Reviewed
Probab=26.44 E-value=54 Score=24.27 Aligned_cols=11 Identities=45% Similarity=0.619 Sum_probs=9.2
Q ss_pred Ccccccccccc
Q 023471 1 MQKSRKRKQVE 11 (281)
Q Consensus 1 ~~~~~kr~~~~ 11 (281)
|+|++.||+.+
T Consensus 1 MPkSK~RKk~~ 11 (87)
T PRK00159 1 MPKSKVRKKND 11 (87)
T ss_pred CCCccccCCCC
Confidence 88999888866
No 187
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=26.20 E-value=1.1e+02 Score=27.12 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=8.0
Q ss_pred HHHHhcCcCccHHHHHH
Q 023471 170 KAELSRFRGIGPKTVAC 186 (281)
Q Consensus 170 ~~~L~~l~GIG~~tA~~ 186 (281)
+++|.+++|+|+-.|.-
T Consensus 226 ~~ele~~~G~G~~kak~ 242 (254)
T KOG2841|consen 226 EGELEQCPGLGPAKAKR 242 (254)
T ss_pred HhHHHhCcCcCHHHHHH
Confidence 34444455555544443
No 188
>PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=25.67 E-value=1.8e+02 Score=27.43 Aligned_cols=56 Identities=16% Similarity=0.192 Sum_probs=41.7
Q ss_pred HHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 116 HVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
.|..++.+||.+.+...|...-||+.| .+++..+ +..+.+.+.+++. ++++.|.+.
T Consensus 19 ~~~~~~~~el~~~~~~~g~~~~r~~qi---~~w~y~~-~~~~~~~m~~l~~-~~r~~l~~~ 74 (368)
T PRK14456 19 NIRNLRRQELTELLARLGEPAWRAAQL---HQWLFSH-RALSFEEMTTLSK-PLRRKLAES 74 (368)
T ss_pred CcccCCHHHHHHHHHHcCCCchHHHHH---HHHHHHc-CCCCHHHhccccH-HHHHHHhcc
Confidence 377889999999999999877666655 6677763 4568888888764 467777653
No 189
>PRK13766 Hef nuclease; Provisional
Probab=25.57 E-value=1.5e+02 Score=30.53 Aligned_cols=42 Identities=19% Similarity=0.303 Sum_probs=32.7
Q ss_pred HHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHH
Q 023471 103 AFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILK 147 (281)
Q Consensus 103 ~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~ 147 (281)
...+|.++|++++++..++.++|.++ -|++..+++.|.++.+
T Consensus 727 ~a~~Ll~~fgs~~~i~~as~~~L~~i---~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 727 LARNLLEHFGSVEAVMTASEEELMEV---EGIGEKTAKRIREVVT 768 (773)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHHh
Confidence 45678889999999999999887652 3777778888876543
No 190
>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=25.55 E-value=2e+02 Score=26.42 Aligned_cols=46 Identities=22% Similarity=0.282 Sum_probs=38.0
Q ss_pred HHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 103 AFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 103 ~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
..++|.++ |-|.++++.++..+|.+ -.|++..++..|++.+.....
T Consensus 13 ~~~~L~~~g~~t~~~~~~~~~~~L~~---~~gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 13 DIKKLKSAGICTVNGVIMTTRRALCK---IKGLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHH---hcCCCHHHHHHHHHHHHhhhc
Confidence 45667766 57999999999988766 489999999999998888765
No 191
>PRK14454 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=25.41 E-value=1.9e+02 Score=26.98 Aligned_cols=54 Identities=11% Similarity=0.224 Sum_probs=40.2
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR 175 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~ 175 (281)
|..++.+||.+.+...|+..-||+.| .+++..+ +..+.+.+.+++. +.++.|..
T Consensus 4 ~~~~~~~~l~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~m~~l~~-~~r~~l~~ 57 (342)
T PRK14454 4 ILDFTLEELKEWMKENGEKKFRAKQI---FDWIYKK-GVTDFDEMTNIPK-NLREKLKE 57 (342)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHHc-CCCCHHHhccccH-HHHHHHHh
Confidence 56788999999999999877777655 5677653 5568888887754 46777665
No 192
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=25.19 E-value=3.9e+02 Score=22.12 Aligned_cols=63 Identities=11% Similarity=0.182 Sum_probs=42.0
Q ss_pred CCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHHH
Q 023471 120 AEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLM 189 (281)
Q Consensus 120 ~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il~ 189 (281)
.+.+++..+....||...-.+.+.+...+|...-... +++.+.+.+.|..+ |+...-++.+..
T Consensus 22 ~~~~~~~kl~~~~~~~~~~lk~~va~l~fiL~~A~k~------n~~~~~l~~eL~~l-glp~e~~~~l~~ 84 (174)
T cd04752 22 IDYEKVLKLTADAKFESGDVKASIAVLSFILSSAAKY------NVDGESLSSELQQL-GLPKEHATSLCR 84 (174)
T ss_pred CCHHHHHHHHHHhCCCHhhHHHHHHHHHHHHHHHHHc------CCCHHHHHHHHHHc-CCCHHHHHHHHH
Confidence 4566777777777877766677777777666421111 23566777788887 888888877766
No 193
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=25.08 E-value=2.1e+02 Score=26.75 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=38.5
Q ss_pred HHHHHHHhh-CCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHH
Q 023471 102 KAFASLKST-FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLE 151 (281)
Q Consensus 102 ~~~~~L~~~-~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~ 151 (281)
....+|.++ |-|.++|+.++..+|.+ -.|++..++..|.+.++.+..
T Consensus 42 ~~~~kL~~~g~~tv~~~~~~~~~~L~~---~~g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 42 GDVKKLQDAGIYTCNGLMMHTKKNLTG---IKGLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred HHHHHHHHcCCCcHHHHHhCCHHHHHH---hcCCCHHHHHHHHHHHHHhhc
Confidence 345677776 57999999999988776 489999999999988888765
No 194
>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=24.77 E-value=75 Score=31.88 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=19.1
Q ss_pred HHHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 168 EIKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
.....|..|||||+++....|. .||
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~-~Fg 562 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLK-YFG 562 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHH-HcC
Confidence 3456788999999999986654 444
No 195
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=24.70 E-value=2.2e+02 Score=18.91 Aligned_cols=39 Identities=15% Similarity=0.150 Sum_probs=27.2
Q ss_pred CHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCch-HHHhcCChHHH
Q 023471 121 EQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCL-EYLRGLSIDEI 169 (281)
Q Consensus 121 ~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l-~~l~~~~~~~~ 169 (281)
+.++|.+.|+.+|+.. .+..+.+ .+++. +.|..++.+++
T Consensus 5 ~~~~v~~WL~~~gl~~--------y~~~f~~--~~i~g~~~L~~l~~~~L 44 (66)
T PF07647_consen 5 SPEDVAEWLKSLGLEQ--------YADNFRE--NGIDGLEDLLQLTEEDL 44 (66)
T ss_dssp CHHHHHHHHHHTTCGG--------GHHHHHH--TTCSHHHHHTTSCHHHH
T ss_pred CHHHHHHHHHHCCcHH--------HHHHHHH--cCCcHHHHHhhCCHHHH
Confidence 5788899999999954 3445555 45676 77777766554
No 196
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=24.39 E-value=35 Score=26.29 Aligned_cols=15 Identities=40% Similarity=0.738 Sum_probs=12.6
Q ss_pred CCCCCCChhhccccc
Q 023471 265 AGNLCPLLNYCEKSN 279 (281)
Q Consensus 265 ~C~~Cpl~~~C~~~~ 279 (281)
.|..||+++-|....
T Consensus 32 ~C~~Cp~r~~C~~~~ 46 (125)
T PF13751_consen 32 DCKNCPLREQCTKSK 46 (125)
T ss_pred hccCCCccccCCCcc
Confidence 399999999997653
No 197
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=23.77 E-value=44 Score=33.48 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=19.1
Q ss_pred HHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 169 IKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 169 ~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
....|..|||||+++....|. .||-
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~-~Fgs 536 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILK-SLGT 536 (574)
T ss_pred cccccccCCCCCHHHHHHHHH-HhCC
Confidence 556888999999999876554 5553
No 198
>TIGR00048 radical SAM enzyme, Cfr family. A Staphylococcus sciuri plasmid-borne member of this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol by an unknown mechanism. A 14-15 residue cluster with four perfectly conserved Cys residues suggests this protein may be an enzyme with an iron-sulfur cluster. The Cys cluster is part of the radical SAM domain, suggested to provide a general mechanism by which the Fe-S center cleaves S-adenosylmethionine to initiate radical-based catalysis. Members of this family lack apparent transmembrane domains.
Probab=23.63 E-value=1.8e+02 Score=27.16 Aligned_cols=56 Identities=21% Similarity=0.304 Sum_probs=41.3
Q ss_pred HHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 116 HVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
.|..++.+||++.+...|+..-||+.| .+++..+ +..+.+.+.+++. ++++.|...
T Consensus 8 ~~~~~~~~~l~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~m~~l~~-~~r~~l~~~ 63 (355)
T TIGR00048 8 SLYDLTLQELRQWLKDLGEKPFRAKQI---YKWLYHK-GKDSFDDMTNLSK-DLREKLNRV 63 (355)
T ss_pred CcccCCHHHHHHHHHHcCCCchhHHHH---HHHHHHc-CCCCHHHccccCH-HHHHHHhhc
Confidence 367789999999999999987777766 5666653 4457888887754 467777653
No 199
>PRK11194 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=23.48 E-value=2e+02 Score=27.11 Aligned_cols=54 Identities=13% Similarity=0.208 Sum_probs=39.7
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR 175 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~ 175 (281)
|..++.+||.+.+...|+..-||+.| .+++..+ +..|.+.+.+++. ++++.|..
T Consensus 8 l~~~~~~el~~~~~~~g~~~~ra~qi---~~w~y~~-~~~~~~~mt~l~~-~~r~~L~~ 61 (372)
T PRK11194 8 LLDLNRQQMREFFAELGEKPFRADQV---MKWIYHY-GCDDFDEMTNINK-VLREKLKE 61 (372)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHhc-CCCCHHHhccccH-HHHHHHhc
Confidence 67788999999999999877777665 5566653 4558888887753 46666654
No 200
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.36 E-value=2.1e+02 Score=25.27 Aligned_cols=16 Identities=38% Similarity=0.563 Sum_probs=15.1
Q ss_pred HhcCcCccHHHHHHHH
Q 023471 173 LSRFRGIGPKTVACVL 188 (281)
Q Consensus 173 L~~l~GIG~~tA~~il 188 (281)
|.++||||+-+|..|.
T Consensus 190 l~~~pgig~~~a~~i~ 205 (303)
T COG3547 190 LASIPGIGELTAAAIA 205 (303)
T ss_pred HHhCCCccHHHHHHHH
Confidence 8899999999999888
No 201
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=23.35 E-value=71 Score=33.45 Aligned_cols=28 Identities=14% Similarity=0.063 Sum_probs=22.8
Q ss_pred ChHHHHHHHhcCcCccHHHHHHHHHHhcC
Q 023471 165 SIDEIKAELSRFRGIGPKTVACVLMFHLQ 193 (281)
Q Consensus 165 ~~~~~~~~L~~l~GIG~~tA~~il~~~~~ 193 (281)
...+..+.|++|||||++.|..+|.. ||
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~-f~ 778 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKK-VK 778 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHH-cC
Confidence 34566788999999999999988875 44
No 202
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=23.30 E-value=91 Score=18.55 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=20.5
Q ss_pred hCCHHHHHHHhhhCCCch--HHHHHHHHHHHH
Q 023471 119 AAEQKCIENAIRCGGLAP--TKAACIKNILKC 148 (281)
Q Consensus 119 ~~~~eel~~~i~~~G~~~--~KA~~I~~~a~~ 148 (281)
.+...||.+.++..|++. .|+..|..+.++
T Consensus 3 ~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~ 34 (35)
T PF02037_consen 3 KLTVAELKEELKERGLSTSGKKAELIERLKEH 34 (35)
T ss_dssp TSHHHHHHHHHHHTTS-STSSHHHHHHHHHHH
T ss_pred cCcHHHHHHHHHHCCCCCCCCHHHHHHHHHHh
Confidence 345678888888888753 577777666554
No 203
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=22.50 E-value=42 Score=26.84 Aligned_cols=15 Identities=47% Similarity=0.840 Sum_probs=13.6
Q ss_pred HHHhcCcCccHHHHH
Q 023471 171 AELSRFRGIGPKTVA 185 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~ 185 (281)
+.|..|.||||+.+.
T Consensus 67 DDLt~I~GIGPk~e~ 81 (133)
T COG3743 67 DDLTRISGIGPKLEK 81 (133)
T ss_pred ccchhhcccCHHHHH
Confidence 689999999999876
No 204
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.42 E-value=2.1e+02 Score=26.50 Aligned_cols=55 Identities=22% Similarity=0.234 Sum_probs=40.3
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
|..++.++|.+.+...|+..-||+.| .+++..+ +..+.+.+.+++. ++++.|.+.
T Consensus 4 ~~~~~~~~~~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~~~~~~~-~~r~~l~~~ 58 (343)
T PRK14469 4 ILDLSYEELVSEITELGLEKYRADQI---LDWIYKK-KVFNFDEMTNLSK-DHRALLSEH 58 (343)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHhc-CCCCHHHhccccH-HHHHHHhhc
Confidence 56788999999999999977777655 5566653 4458888888764 467777653
No 205
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.37 E-value=1.9e+02 Score=26.94 Aligned_cols=56 Identities=20% Similarity=0.226 Sum_probs=41.1
Q ss_pred HHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 116 HVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
.|..++.++|.+.+...|+..-|++.| .+++..+ +..+.+.+.+++. ++++.|.+-
T Consensus 6 ~~~~~~~~~l~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~m~~l~~-~~r~~l~~~ 61 (349)
T PRK14463 6 DIKNLTLQELEAFLAGQGKERFRAKQI---FKWLYQR-DARSFAEMTNLSK-DLRAELEET 61 (349)
T ss_pred ccccCCHHHHHHHHHHcCCCchHHHHH---HHHHHHh-CCCCHHHhcccCH-HHHHhhcCC
Confidence 367788999999999999987777655 5566653 4458888887753 467777653
No 206
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=22.37 E-value=84 Score=24.05 Aligned_cols=44 Identities=32% Similarity=0.409 Sum_probs=25.5
Q ss_pred HHHhh-hCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHH
Q 023471 126 ENAIR-CGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKT 183 (281)
Q Consensus 126 ~~~i~-~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~t 183 (281)
...|. -+|++.+||..|.+..+. .|+ .=+.|+.|...-.+|+++
T Consensus 49 ~~~LqfV~GLGPRKA~~Ll~~l~~----~g~----------~l~~R~~Lv~~~~~g~~V 93 (104)
T PF14635_consen 49 ANLLQFVCGLGPRKAQALLKALKQ----NGG----------RLENRSQLVTKCLMGPKV 93 (104)
T ss_dssp HGGGGGSTT--HHHHHHHHHHHHH----C-S--------------TTHHHHTTSS-HHH
T ss_pred HhhHhHhcCCChHHHHHHHHHHHH----cCC----------ccccHHHHHhcCCCCCeE
Confidence 33443 379999999998876663 243 234678888877888865
No 207
>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=22.17 E-value=26 Score=24.35 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=11.2
Q ss_pred CCCCCChhhcccc
Q 023471 266 GNLCPLLNYCEKS 278 (281)
Q Consensus 266 C~~Cpl~~~C~~~ 278 (281)
|..||++..|..+
T Consensus 32 C~~CPVr~~C~~~ 44 (66)
T PF02467_consen 32 CARCPVRAECLEY 44 (66)
T ss_pred HcCChhHHHHHHH
Confidence 8899999999765
No 208
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=22.08 E-value=1.7e+02 Score=29.74 Aligned_cols=37 Identities=22% Similarity=0.202 Sum_probs=26.9
Q ss_pred HHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHH
Q 023471 104 FASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNI 145 (281)
Q Consensus 104 ~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~ 145 (281)
...|...|+|++.|..++.++|.++ ++...|..|.+.
T Consensus 582 a~~Ll~~Fgs~~~i~~As~eeL~~v-----ig~k~A~~I~~~ 618 (621)
T PRK14671 582 AEKLLEHFGSVEKVAKASLEELAAV-----AGPKTAETIYRY 618 (621)
T ss_pred HHHHHHHcCCHHHHHhCCHHHHHHH-----hCHHHHHHHHHH
Confidence 3456677999999999999998775 444566666543
No 209
>KOG2336 consensus Molybdopterin biosynthesis-related protein [Coenzyme transport and metabolism]
Probab=22.04 E-value=1.8e+02 Score=26.61 Aligned_cols=76 Identities=16% Similarity=0.169 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHcCCC-chHHHhcC----ChHHHHHHHh---cCcCccHHHHHHHHHHhcCC-CccccchHHHHHHHHhC
Q 023471 141 CIKNILKCLLESKGKL-CLEYLRGL----SIDEIKAELS---RFRGIGPKTVACVLMFHLQQ-DDFPVDTHVFEISKAIG 211 (281)
Q Consensus 141 ~I~~~a~~i~~~~g~~-~l~~l~~~----~~~~~~~~L~---~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Ri~~rlG 211 (281)
.|.+++..+++. +.+ .|=.|..| +++.+|+.-. .+-|||.-||++.-.-+.|+ -.|-.|.--..-++||.
T Consensus 48 kieklSsEVVDS-NPYSRLMALqRMgIV~dYErIR~~aVAiVGvGGVGSV~AeMLTRCGIGkLlLfDYDkVElANMNRLF 126 (422)
T KOG2336|consen 48 KIEKLSSEVVDS-NPYSRLMALQRMGIVDDYERIREFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVELANMNRLF 126 (422)
T ss_pred HHHHhhhhHhcC-ChHHHHHHHHHhcchhhHHHHhhheeEEEecCchhHHHHHHHHhcCcceEEEeecchhhhhcccccc
Confidence 455666666542 111 23333333 3455555433 45678899999998888888 77888887777788888
Q ss_pred CCCCCC
Q 023471 212 WVPTAA 217 (281)
Q Consensus 212 ~~~~~~ 217 (281)
+.+..+
T Consensus 127 f~P~Qa 132 (422)
T KOG2336|consen 127 FQPDQA 132 (422)
T ss_pred cCcccc
Confidence 866543
No 210
>PF06781 UPF0233: Uncharacterised protein family (UPF0233); InterPro: IPR009619 This is a group of proteins of unknown function.
Probab=21.86 E-value=76 Score=23.50 Aligned_cols=16 Identities=38% Similarity=0.420 Sum_probs=11.5
Q ss_pred CccccccccccccCCC
Q 023471 1 MQKSRKRKQVEVTETR 16 (281)
Q Consensus 1 ~~~~~kr~~~~~~~~~ 16 (281)
|+|++.||+.......
T Consensus 1 MPkSk~rKk~~~~~~~ 16 (87)
T PF06781_consen 1 MPKSKVRKKAAYTPPP 16 (87)
T ss_pred CCCccccccccCCCCC
Confidence 8898888888754333
No 211
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=21.81 E-value=2.4e+02 Score=24.64 Aligned_cols=52 Identities=23% Similarity=0.201 Sum_probs=32.7
Q ss_pred CCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCC---chHHHhcCChHHHHH
Q 023471 120 AEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKL---CLEYLRGLSIDEIKA 171 (281)
Q Consensus 120 ~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~---~l~~l~~~~~~~~~~ 171 (281)
.+.|+++......|....+..+|.++.+.-.++.|-+ |+..|-+.+...+++
T Consensus 70 ~~~ED~e~~~~~~~~~elr~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~ 124 (220)
T PF07900_consen 70 VDPEDIEMRNEKYGLSELRKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISK 124 (220)
T ss_pred cCHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHH
Confidence 3566777666667888888888888888877754444 333333444444333
No 212
>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.76 E-value=2.4e+02 Score=26.38 Aligned_cols=55 Identities=16% Similarity=0.068 Sum_probs=40.5
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
|..++.+||.+.+...|+..-||+.| .+++..+ +..+.+.+.+++. ++++.|.+.
T Consensus 4 l~~~~~~~l~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~m~~l~~-~~r~~l~~~ 58 (348)
T PRK14467 4 IKNYNLEELEEFVVELGWEKYRAKQI---AKWVYKK-KVTDFDEMTDLSK-EDRQLLKEN 58 (348)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHhc-CCCCHHHhccccH-HHHHHHhcC
Confidence 56788999999999999877777655 5666653 4458888888764 467777654
No 213
>PF14199 DUF4317: Domain of unknown function (DUF4317)
Probab=21.37 E-value=2.6e+02 Score=26.49 Aligned_cols=71 Identities=13% Similarity=0.178 Sum_probs=56.6
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhC---C--CHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHH
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTF---P--TWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLL 150 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~---p--t~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~ 150 (281)
....|+.+|..+++-....+.+..+..+|-+.. . +++. ..++..++..+|..+|....+...+...-..+.
T Consensus 235 qKe~F~~iv~~~lged~~~e~v~~i~E~l~~~ie~~~e~~~Ep-~~L~~~~v~~iL~~sGv~~e~~e~~e~~y~~~~ 310 (371)
T PF14199_consen 235 QKETFQEIVKEVLGEDCDYEVVQNIHEELNEMIEEHKEEEPEP-PTLDKKDVKRILEESGVEEEKLEKFEKAYEEVF 310 (371)
T ss_pred HHHHHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhccCCCCC-cccCHHHHHHHHHHcCCchHHHHHHHHHHHHHh
Confidence 456799999999999999998888888876642 1 2332 667889999999999999988887777666665
No 214
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=21.32 E-value=3.2e+02 Score=20.02 Aligned_cols=44 Identities=11% Similarity=0.227 Sum_probs=29.2
Q ss_pred HHHHHHhhhccHHHHHHHHHHHHhhCCC-----HHHHHhCCHHHHHHHh
Q 023471 86 LVKTVLSQNTTEANSLKAFASLKSTFPT-----WEHVLAAEQKCIENAI 129 (281)
Q Consensus 86 Lv~~ILsqqts~~~a~~~~~~L~~~~pt-----~~~la~~~~eel~~~i 129 (281)
....|.++.|+.+.+.+.+.-|..+.|. -++|...+...|+++|
T Consensus 39 ~~~~I~~~~t~~~k~~~Lld~L~~RG~~AF~~F~~aL~~~~~~~La~lL 87 (90)
T cd08332 39 MAESIMAKPTSFSQNVALLNLLPKRGPRAFSAFCEALRETSQEHLCDLL 87 (90)
T ss_pred HHHHHHcCCCcHHHHHHHHHHHHHhChhHHHHHHHHHHhcChHHHHHHH
Confidence 5667788889999998888888887664 3333333444444443
No 215
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=21.20 E-value=1.7e+02 Score=21.32 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=24.2
Q ss_pred HHHHHHHH--HhhhccHHHHHHHHHHHHhhCCC
Q 023471 83 LDGLVKTV--LSQNTTEANSLKAFASLKSTFPT 113 (281)
Q Consensus 83 fe~Lv~~I--Lsqqts~~~a~~~~~~L~~~~pt 113 (281)
-|+|..+| |.++......+...+.|.++||.
T Consensus 13 ~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~ 45 (80)
T PF10264_consen 13 PEVLCWVISDLNAAGQPATQETLREHLRKHYPG 45 (80)
T ss_pred HHHHHHHHHHHhccCCcchHHHHHHHHHHhCCC
Confidence 46777777 66666677778889999999985
No 216
>PRK14455 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.18 E-value=2.3e+02 Score=26.53 Aligned_cols=54 Identities=15% Similarity=0.177 Sum_probs=39.4
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR 175 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~ 175 (281)
|..++.+||++.+...|+..-||+.| .+++..+ +..|.+.|.+++. ++++.|.+
T Consensus 13 ~~~~~~~~l~~~~~~~g~~~~r~~qi---~~~~~~~-~~~~~~~m~~l~~-~~r~~l~~ 66 (356)
T PRK14455 13 IYSLTLDELQEWLVEQGEKKFRATQI---WDWLYRK-RVQSFEEMTNLSK-DLREKLND 66 (356)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHHc-CCCCHHHhcccCH-HHHHHHhc
Confidence 67889999999999999877776655 5566653 4458888887753 46666654
No 217
>PRK07757 acetyltransferase; Provisional
Probab=21.11 E-value=81 Score=24.68 Aligned_cols=38 Identities=21% Similarity=0.133 Sum_probs=27.3
Q ss_pred cCccHHHHHHHHHHhcCC--CccccchHHHHHHHHhCCCC
Q 023471 177 RGIGPKTVACVLMFHLQQ--DDFPVDTHVFEISKAIGWVP 214 (281)
Q Consensus 177 ~GIG~~tA~~il~~~~~~--~~~~vD~~v~Ri~~rlG~~~ 214 (281)
+|+|....+.+...+... ..+.+.+...++..++|+..
T Consensus 80 ~Glg~~Ll~~l~~~a~~~g~~~i~~~~~~~~~Y~k~GF~~ 119 (152)
T PRK07757 80 QGIGRMLVEACLEEARELGVKRVFALTYQPEFFEKLGFRE 119 (152)
T ss_pred CCHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHCCCEE
Confidence 788888888888777543 34444555678889999965
No 218
>KOG0662 consensus Cyclin-dependent kinase CDK5 [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=21.10 E-value=80 Score=27.09 Aligned_cols=37 Identities=22% Similarity=0.343 Sum_probs=29.2
Q ss_pred cCccHHHHHHHHHH--hcCCCccc---cchHHHHHHHHhCCC
Q 023471 177 RGIGPKTVACVLMF--HLQQDDFP---VDTHVFEISKAIGWV 213 (281)
Q Consensus 177 ~GIG~~tA~~il~~--~~~~~~~~---vD~~v~Ri~~rlG~~ 213 (281)
-.|..|+|.||... --|+|.|| ||+...||+..||-.
T Consensus 181 tsidmwsagcifaelanagrplfpg~dvddqlkrif~~lg~p 222 (292)
T KOG0662|consen 181 TSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTP 222 (292)
T ss_pred cchHhhhcchHHHHHhhcCCCCCCCCcHHHHHHHHHHHhCCC
Confidence 35788999999854 35667776 789999999999874
No 219
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=21.06 E-value=2.2e+02 Score=22.82 Aligned_cols=63 Identities=13% Similarity=0.127 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHhhhccHHHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHH-HHHHHHHHHHHHHH
Q 023471 79 EESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTK-AACIKNILKCLLES 152 (281)
Q Consensus 79 ~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~K-A~~I~~~a~~i~~~ 152 (281)
..+-|..|+..+-....+...+..++..+.+...++++ +++..|+...- ...|..+.+.+.++
T Consensus 40 ~~~~l~~li~lv~~g~It~~~ak~vl~~~~~~~~~~~~-----------ii~~~~l~~isd~~el~~~v~~vi~~ 103 (147)
T smart00845 40 TPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEE-----------IVEEKGLKQISDEGELEAIVDEVIAE 103 (147)
T ss_pred CHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCHHH-----------HHHHcCCccCCCHHHHHHHHHHHHHH
Confidence 45678899999999999999999999888766444433 33444544311 23566666666653
No 220
>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.99 E-value=2.1e+02 Score=26.75 Aligned_cols=55 Identities=13% Similarity=0.193 Sum_probs=40.4
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
|..++.+||++.+...|...-||+.| .+++..+ +..+.+.+.+++. ++++.|.+.
T Consensus 7 l~~l~~~el~~~~~~~g~~~fra~Qi---~~wi~~~-~~~~~~~mt~l~~-~~r~~L~~~ 61 (345)
T PRK14466 7 LLGMTLEELQSVAKRLGMPAFAAKQI---ASWLYDK-KVTSIDEMTNISL-AHREKLAEE 61 (345)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHhc-CCCCHHHHhhhhH-HHHHhhcCC
Confidence 67788999999999999877777665 5666653 4568888887753 467777653
No 221
>TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a particularly strongly conserved family found so only in the APERN subtype of CRISPR/Cas loci and represented by AF1879 from Archaeoglobus fulgidus. This family has four perfectly preserved Cys residues. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa1, for CRISPR/Cas Subtype Protein 1.
Probab=20.90 E-value=77 Score=28.61 Aligned_cols=10 Identities=40% Similarity=1.035 Sum_probs=9.5
Q ss_pred CC-CCCChhhc
Q 023471 266 GN-LCPLLNYC 275 (281)
Q Consensus 266 C~-~Cpl~~~C 275 (281)
|. .|++++.|
T Consensus 260 C~~~C~f~~vC 270 (271)
T TIGR01896 260 CPPTCPFLEHC 270 (271)
T ss_pred ccCCCCCcCcc
Confidence 97 99999999
No 222
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=20.88 E-value=73 Score=32.28 Aligned_cols=26 Identities=35% Similarity=0.574 Sum_probs=20.0
Q ss_pred HHHHHHhcCcCccHHHHHHHHHHhcCC
Q 023471 168 EIKAELSRFRGIGPKTVACVLMFHLQQ 194 (281)
Q Consensus 168 ~~~~~L~~l~GIG~~tA~~il~~~~~~ 194 (281)
.....|..|+|||++++..++. .||-
T Consensus 566 ~~~s~L~~I~GIG~k~a~~Ll~-~Fgs 591 (621)
T PRK14671 566 TLQTELTDIAGIGEKTAEKLLE-HFGS 591 (621)
T ss_pred HhhhhhhcCCCcCHHHHHHHHH-HcCC
Confidence 4566788999999999986665 5543
No 223
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.85 E-value=2.4e+02 Score=26.30 Aligned_cols=54 Identities=15% Similarity=0.156 Sum_probs=40.3
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR 175 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~ 175 (281)
|..++.+||++.+...|...-||+.| .+++..+ +..+.+.+.+++. ++++.|.+
T Consensus 4 ~~~~~~~~l~~~~~~~g~~~~r~~qi---~~w~~~~-~~~~~~~m~~l~~-~~r~~l~~ 57 (345)
T PRK14457 4 LLGRSLAELEDWAVAQGQPAFRGRQL---HDWLYNK-GVRSLDEISVLPK-AWRESLKD 57 (345)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHhc-CCCCHHHcCccCH-HHHHHHhh
Confidence 56788999999999999877777665 5666653 4458888887753 47777776
No 224
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=20.84 E-value=69 Score=27.07 Aligned_cols=20 Identities=35% Similarity=0.378 Sum_probs=14.4
Q ss_pred HHhcCcCccHHHHHHHHHHh
Q 023471 172 ELSRFRGIGPKTVACVLMFH 191 (281)
Q Consensus 172 ~L~~l~GIG~~tA~~il~~~ 191 (281)
.|.=|||||.|+...||---
T Consensus 117 ~LeLLPGIGKK~m~~ILeER 136 (181)
T PF04919_consen 117 SLELLPGIGKKTMWKILEER 136 (181)
T ss_dssp GGGGSTT--HHHHHHHHHHH
T ss_pred HHhhcccccHHHHHHHHHHH
Confidence 46668999999999998643
No 225
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.74 E-value=2.5e+02 Score=26.53 Aligned_cols=55 Identities=15% Similarity=0.109 Sum_probs=40.8
Q ss_pred HHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhc
Q 023471 116 HVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSR 175 (281)
Q Consensus 116 ~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~ 175 (281)
.|..++.+||.+.+...|...-||+.| .+++..+ +..|.+.+.+++. ++++.|.+
T Consensus 23 ~l~~l~~~el~~~~~~~g~~~~ra~Qi---~~wiy~~-~~~~~~~mt~l~k-~~r~~L~~ 77 (373)
T PRK14459 23 HLADLTPAERREAVAELGLPAFRAKQL---ARHYFGR-LTADPAQMTDLPA-AAREELAE 77 (373)
T ss_pred CcccCCHHHHHHHHHHcCCCcHHHHHH---HHHHHhc-CCCCHHHhcccCH-HHHHHHHh
Confidence 478889999999999999877777655 5666663 4458888888754 46666654
No 226
>PRK14465 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.52 E-value=2.4e+02 Score=26.35 Aligned_cols=55 Identities=16% Similarity=0.125 Sum_probs=40.4
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcC
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRF 176 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l 176 (281)
|..++.++|++.+...|...-||+.| .+++..+ +..|.+.|.+++. ++++.|.+.
T Consensus 7 ~~~~~~~~l~~~~~~~g~~~fra~Qi---~~wiy~~-~~~~~~~mt~l~~-~~r~~L~~~ 61 (342)
T PRK14465 7 LKGRTLKELSEIMVSLGEKKFRAKQI---YHGLYVN-RYETWDQFTTFSK-EVKEKLEEL 61 (342)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHH---HHHHHHc-CCCCHHHhccccH-HHHHHHhcc
Confidence 56788999999999999877666654 5677663 4568888888764 467777653
No 227
>PRK03980 flap endonuclease-1; Provisional
Probab=20.48 E-value=63 Score=29.42 Aligned_cols=16 Identities=38% Similarity=0.686 Sum_probs=13.4
Q ss_pred hcCcCccHHHHHHHHH
Q 023471 174 SRFRGIGPKTVACVLM 189 (281)
Q Consensus 174 ~~l~GIG~~tA~~il~ 189 (281)
..++|||++||--++.
T Consensus 192 ~GI~GIG~ktA~kLi~ 207 (292)
T PRK03980 192 PGIKGIGPKTALKLIK 207 (292)
T ss_pred CCCCCccHHHHHHHHH
Confidence 3799999999987765
No 228
>TIGR02249 integrase_gron integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.
Probab=20.48 E-value=4.1e+02 Score=23.45 Aligned_cols=65 Identities=9% Similarity=0.084 Sum_probs=35.8
Q ss_pred HHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471 123 KCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV 187 (281)
Q Consensus 123 eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i 187 (281)
+++.+.++..|++..-.+......+.+.+-+|..+++.+...++.+....|..-.++++.|.+..
T Consensus 3 ~~~~~~~~~~~~s~~T~~~y~~~~~~~~~~~g~~~~~~it~~~i~~~l~~l~~~~~~~~~t~~~~ 67 (315)
T TIGR02249 3 DQVREHMRTRHYAKRTEEAYLHWIKRFIRFHNKRHPSTMGDTEVEAFLSDLAVDGKVAASTQNQA 67 (315)
T ss_pred HHHHHHHHccCCcHHHHHHHHHHHHHHHHHhCCCChHhcCHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 35566677777765444444444444444456556666544444444445544457888877643
No 229
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=20.32 E-value=3.9e+02 Score=22.78 Aligned_cols=40 Identities=30% Similarity=0.226 Sum_probs=32.5
Q ss_pred HhcCcCccHHHHHHHHHHhcCCCccccchHHH-----------HHHHHhCCC
Q 023471 173 LSRFRGIGPKTVACVLMFHLQQDDFPVDTHVF-----------EISKAIGWV 213 (281)
Q Consensus 173 L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~-----------Ri~~rlG~~ 213 (281)
|+.-+|.|.-|+.-++.- +|.+++-.|.-++ .+..++|..
T Consensus 7 lTG~igsGKStva~~~~~-~G~~vidaD~v~r~~~~~~~~~~~~i~~~fG~~ 57 (201)
T COG0237 7 LTGGIGSGKSTVAKILAE-LGFPVIDADDVAREVVEPGGEALQEIAERFGLE 57 (201)
T ss_pred EecCCCCCHHHHHHHHHH-cCCeEEEccHHHHHHHhccchHHHHHHHHcCCc
Confidence 345589999999888887 8899999999999 566777764
No 230
>PRK03100 sec-independent translocase; Provisional
Probab=20.15 E-value=2.4e+02 Score=22.68 Aligned_cols=59 Identities=24% Similarity=0.347 Sum_probs=33.6
Q ss_pred HHhCCHHHHHHHhhhCCCchHHHHH-HHHHHHHHHHHcCCCchHHHhcCChHHHHH---HHhcCcCccHHHH
Q 023471 117 VLAAEQKCIENAIRCGGLAPTKAAC-IKNILKCLLESKGKLCLEYLRGLSIDEIKA---ELSRFRGIGPKTV 184 (281)
Q Consensus 117 la~~~~eel~~~i~~~G~~~~KA~~-I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~---~L~~l~GIG~~tA 184 (281)
|.-..++.|-++++.+|-.-.+++. ..++-+.+.++.|. + .+++++ +|.++.+..+..+
T Consensus 18 Lvv~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~elg~-e--------~~dlrk~l~el~~lr~l~Pr~~ 80 (136)
T PRK03100 18 LVILGPERLPGAIRWTARALRQARDYASGATSQLREELGP-E--------FDDLRKPLGELQKLRGMTPRAA 80 (136)
T ss_pred HhhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-h--------HHHHHHHHHHHHHHhcCChHHH
Confidence 4455677777888887766555543 33333344443332 2 334444 5566778888765
No 231
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=20.07 E-value=4.2e+02 Score=23.39 Aligned_cols=95 Identities=21% Similarity=0.293 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCC-chHHHhcCChHHHHHHHhc-
Q 023471 98 ANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKL-CLEYLRGLSIDEIKAELSR- 175 (281)
Q Consensus 98 ~~a~~~~~~L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~-~l~~l~~~~~~~~~~~L~~- 175 (281)
..+...|.+|...||-|. +.-+.+++.+ .|...|..+++ +|+ +.+.+.. ....++..-.-
T Consensus 38 ~~vd~lF~~L~aifPa~~--a~~~~~~~~~---------aKr~Wi~~f~e------ngI~t~eQv~~-Gm~~aR~~~spF 99 (233)
T PF06992_consen 38 KLVDRLFRQLKAIFPAWR--ANPDQEELNE---------AKRQWIKAFAE------NGITTMEQVRA-GMRRARASESPF 99 (233)
T ss_pred HHHHHHHHHHHHhCchhc--cCCCHHHHHH---------HHHHHHHHHHH------cCCCcHHHHHH-HHHHHHhcCCCC
Confidence 567788899999999764 4466666655 37777766544 344 4454442 13334444443
Q ss_pred CcCccHHHHHHHHHH--hcCCCccccchHHH---HHHHHhCC
Q 023471 176 FRGIGPKTVACVLMF--HLQQDDFPVDTHVF---EISKAIGW 212 (281)
Q Consensus 176 l~GIG~~tA~~il~~--~~~~~~~~vD~~v~---Ri~~rlG~ 212 (281)
+|.+|.+++-|--.- .+|.| -+|.... +.+.+-|+
T Consensus 100 ~PS~GqFI~WCk~~~~~~lGLP--~~del~~~~~~y~~~rg~ 139 (233)
T PF06992_consen 100 WPSPGQFIAWCKPGDYEALGLP--SVDELYQRYKRYCRYRGF 139 (233)
T ss_pred CCChhHHHHHHhcchHHhcCCC--CHHHHHHHHHHHHHHhCC
Confidence 599999998876332 34542 2344333 34444454
No 232
>PHA00439 exonuclease
Probab=20.05 E-value=63 Score=29.37 Aligned_cols=19 Identities=26% Similarity=0.251 Sum_probs=15.7
Q ss_pred HHHhcCcCccHHHHHHHHHH
Q 023471 171 AELSRFRGIGPKTVACVLMF 190 (281)
Q Consensus 171 ~~L~~l~GIG~~tA~~il~~ 190 (281)
+-+-.+|||| +||.-+|.-
T Consensus 188 DNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 188 DGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred cCCCCCCCcC-HHHHHHHhC
Confidence 4466799999 999998875
Done!