Query psy4002
Match_columns 378
No_of_seqs 239 out of 2174
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:54:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4002hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1921|consensus 100.0 2.6E-55 5.5E-60 411.2 19.6 245 84-363 12-262 (286)
2 COG0177 Nth Predicted EndoIII- 100.0 3.7E-51 8.1E-56 380.8 22.0 206 108-364 4-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1.6E-45 3.5E-50 344.4 23.1 184 143-363 25-208 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 1.2E-43 2.5E-48 343.7 21.8 197 143-376 22-223 (275)
5 PRK10880 adenine DNA glycosyla 100.0 1.4E-42 3E-47 345.7 23.3 196 144-376 27-227 (350)
6 TIGR01083 nth endonuclease III 100.0 5.3E-40 1.1E-44 302.0 22.2 168 145-349 24-191 (191)
7 PRK13910 DNA glycosylase MutY; 100.0 2.9E-38 6.4E-43 307.7 18.4 174 156-367 1-175 (289)
8 COG1194 MutY A/G-specific DNA 100.0 6.3E-36 1.4E-40 294.4 17.4 195 146-377 33-233 (342)
9 PRK13913 3-methyladenine DNA g 100.0 1.7E-34 3.7E-39 271.2 19.2 167 140-344 23-216 (218)
10 COG2231 Uncharacterized protei 100.0 1.4E-31 3.1E-36 246.5 17.5 184 141-362 24-214 (215)
11 smart00478 ENDO3c endonuclease 100.0 2.3E-29 5.1E-34 221.0 16.5 149 156-340 1-149 (149)
12 cd00056 ENDO3c endonuclease II 100.0 7.2E-29 1.6E-33 219.6 17.2 154 148-338 1-158 (158)
13 KOG2457|consensus 99.9 6.7E-28 1.5E-32 238.3 10.3 185 145-366 123-313 (555)
14 PRK01229 N-glycosylase/DNA lya 99.9 7E-26 1.5E-30 211.5 15.4 151 145-337 35-201 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 99.9 5.3E-22 1.2E-26 195.6 16.4 121 146-305 118-263 (310)
16 COG0122 AlkA 3-methyladenine D 99.9 7.4E-22 1.6E-26 192.5 16.9 193 106-336 61-273 (285)
17 TIGR03252 uncharacterized HhH- 99.9 8.5E-22 1.8E-26 179.5 12.5 106 144-249 15-137 (177)
18 PRK10308 3-methyl-adenine DNA 99.9 1E-20 2.2E-25 184.4 18.6 145 145-334 111-273 (283)
19 KOG1918|consensus 99.8 2.6E-19 5.5E-24 166.7 11.9 178 108-328 41-232 (254)
20 PF00730 HhH-GPD: HhH-GPD supe 99.7 3.3E-17 7E-22 136.4 12.5 106 152-324 1-108 (108)
21 KOG2875|consensus 99.6 5.8E-16 1.3E-20 148.8 10.9 120 144-302 114-258 (323)
22 COG1059 Thermostable 8-oxoguan 98.9 1.3E-08 2.8E-13 93.7 9.8 118 146-306 38-164 (210)
23 PF00633 HHH: Helix-hairpin-he 98.3 2.4E-07 5.2E-12 61.5 0.5 29 218-246 2-30 (30)
24 PF10576 EndIII_4Fe-2S: Iron-s 97.2 9.9E-05 2.1E-09 43.0 0.4 17 342-358 1-17 (17)
25 smart00525 FES FES domain. iro 96.5 0.001 2.2E-08 42.4 0.7 22 341-362 1-22 (26)
26 PF03352 Adenine_glyco: Methyl 95.9 0.073 1.6E-06 49.3 10.4 101 146-246 25-163 (179)
27 COG2818 Tag 3-methyladenine DN 95.3 0.19 4.1E-06 46.9 10.5 101 146-246 31-169 (188)
28 PF14716 HHH_8: Helix-hairpin- 93.0 0.4 8.6E-06 37.1 6.5 56 189-246 10-66 (68)
29 PF09674 DUF2400: Protein of u 92.9 0.047 1E-06 52.5 1.4 53 287-340 175-231 (232)
30 PF12826 HHH_2: Helix-hairpin- 92.6 0.17 3.7E-06 38.9 3.9 37 210-247 15-55 (64)
31 smart00278 HhH1 Helix-hairpin- 92.6 0.085 1.8E-06 33.5 1.9 20 228-247 2-21 (26)
32 TIGR00624 tag DNA-3-methyladen 92.5 0.79 1.7E-05 42.6 8.8 72 145-216 28-103 (179)
33 PRK10353 3-methyl-adenine DNA 92.3 0.74 1.6E-05 43.0 8.4 72 145-216 29-104 (187)
34 TIGR02757 conserved hypothetic 91.6 0.089 1.9E-06 50.5 1.5 53 287-340 172-228 (229)
35 PF09171 DUF1886: Domain of un 89.0 1 2.2E-05 43.9 6.3 163 147-344 37-232 (246)
36 TIGR00426 competence protein C 87.3 1.1 2.4E-05 34.5 4.5 58 181-246 9-66 (69)
37 PRK13901 ruvA Holliday junctio 86.3 1.9 4.2E-05 40.6 6.3 47 197-250 78-130 (196)
38 PF14520 HHH_5: Helix-hairpin- 85.0 2 4.2E-05 32.2 4.7 22 225-246 36-57 (60)
39 PF12836 HHH_3: Helix-hairpin- 85.0 1.2 2.5E-05 34.2 3.5 53 182-243 8-60 (65)
40 COG0353 RecR Recombinational D 84.5 1.2 2.5E-05 42.0 3.9 30 221-250 6-35 (198)
41 TIGR00608 radc DNA repair prot 83.2 1.5 3.2E-05 41.8 4.1 63 185-250 14-84 (218)
42 PRK14606 ruvA Holliday junctio 83.0 1.4 2.9E-05 41.2 3.7 26 225-250 106-131 (188)
43 PRK14601 ruvA Holliday junctio 82.3 1.5 3.3E-05 40.8 3.7 26 225-250 106-131 (183)
44 PRK14602 ruvA Holliday junctio 82.1 1.7 3.7E-05 40.9 4.1 27 224-250 106-132 (203)
45 TIGR00575 dnlj DNA ligase, NAD 81.8 5.2 0.00011 44.0 8.2 78 165-246 441-549 (652)
46 PRK14604 ruvA Holliday junctio 81.3 1.9 4.1E-05 40.4 4.0 26 225-250 106-131 (195)
47 PRK14603 ruvA Holliday junctio 81.2 1.9 4.2E-05 40.4 4.0 35 209-250 96-130 (197)
48 PRK00116 ruvA Holliday junctio 80.9 2.4 5.2E-05 39.4 4.5 24 224-247 105-128 (192)
49 PRK02515 psbU photosystem II c 80.7 2.4 5.2E-05 37.6 4.2 57 177-246 50-106 (132)
50 COG0632 RuvA Holliday junction 80.5 2 4.4E-05 40.6 3.9 30 224-253 105-134 (201)
51 PRK00076 recR recombination pr 79.9 2.2 4.8E-05 40.2 3.9 29 222-250 6-34 (196)
52 PRK13844 recombination protein 79.8 2.1 4.6E-05 40.5 3.8 29 222-250 10-38 (200)
53 COG2003 RadC DNA repair protei 79.8 8.9 0.00019 36.9 8.0 55 185-242 24-81 (224)
54 PRK00024 hypothetical protein; 79.7 2.7 5.8E-05 40.2 4.5 63 184-249 23-89 (224)
55 PRK07956 ligA NAD-dependent DN 78.4 7.3 0.00016 43.0 8.0 77 166-246 455-562 (665)
56 PRK00116 ruvA Holliday junctio 78.2 7.7 0.00017 36.0 7.0 20 226-245 72-91 (192)
57 PF12836 HHH_3: Helix-hairpin- 77.7 2.2 4.8E-05 32.6 2.8 24 224-247 11-34 (65)
58 PF11731 Cdd1: Pathogenicity l 77.6 2 4.3E-05 35.9 2.6 27 225-251 10-36 (93)
59 TIGR00615 recR recombination p 76.8 2.2 4.8E-05 40.2 3.0 30 222-251 6-35 (195)
60 cd00141 NT_POLXc Nucleotidyltr 76.6 4.2 9.1E-05 40.5 5.1 48 198-245 52-103 (307)
61 smart00483 POLXc DNA polymeras 76.1 6.3 0.00014 39.8 6.2 55 190-246 13-67 (334)
62 PRK14605 ruvA Holliday junctio 75.7 7.2 0.00016 36.4 6.1 27 224-250 105-131 (194)
63 TIGR01259 comE comEA protein. 75.5 5.1 0.00011 34.6 4.7 59 179-246 59-117 (120)
64 PRK14350 ligA NAD-dependent DN 74.9 14 0.0003 40.9 8.9 79 165-247 445-561 (669)
65 PRK08097 ligB NAD-dependent DN 74.6 11 0.00024 40.9 7.9 79 165-247 434-540 (562)
66 PF14520 HHH_5: Helix-hairpin- 74.3 10 0.00022 28.4 5.5 43 167-212 16-59 (60)
67 PRK14600 ruvA Holliday junctio 74.3 3.3 7.1E-05 38.6 3.4 25 225-250 106-130 (186)
68 smart00483 POLXc DNA polymeras 73.1 5.9 0.00013 39.9 5.2 50 198-247 55-109 (334)
69 COG1555 ComEA DNA uptake prote 72.3 4.2 9.1E-05 36.5 3.5 55 181-244 90-144 (149)
70 PRK14351 ligA NAD-dependent DN 72.0 16 0.00034 40.7 8.5 77 166-246 472-579 (689)
71 COG1555 ComEA DNA uptake prote 71.6 3.2 7E-05 37.3 2.6 24 224-247 94-117 (149)
72 PRK00024 hypothetical protein; 71.5 11 0.00024 35.9 6.4 62 149-213 27-88 (224)
73 PF14229 DUF4332: Domain of un 71.3 13 0.00027 32.2 6.1 66 169-250 8-76 (122)
74 TIGR00084 ruvA Holliday juncti 69.8 8.3 0.00018 36.0 5.0 26 225-250 105-130 (191)
75 TIGR01259 comE comEA protein. 68.4 4.4 9.6E-05 34.9 2.7 23 224-246 65-87 (120)
76 PF10391 DNA_pol_lambd_f: Fing 67.4 5 0.00011 29.9 2.4 24 226-249 1-24 (52)
77 PF02371 Transposase_20: Trans 66.6 4.8 0.0001 32.4 2.4 27 227-254 2-28 (87)
78 PRK14973 DNA topoisomerase I; 65.6 17 0.00037 41.8 7.3 83 165-250 811-900 (936)
79 PRK07945 hypothetical protein; 65.4 12 0.00025 37.8 5.4 58 189-247 9-69 (335)
80 TIGR00608 radc DNA repair prot 65.0 19 0.00041 34.4 6.4 61 149-212 17-81 (218)
81 PRK08609 hypothetical protein; 64.7 12 0.00026 40.5 5.6 47 198-244 55-105 (570)
82 TIGR01954 nusA_Cterm_rpt trans 64.6 30 0.00065 24.3 6.0 43 168-213 5-48 (50)
83 PRK13482 DNA integrity scannin 63.1 19 0.00042 36.9 6.4 47 167-216 298-344 (352)
84 PRK02515 psbU photosystem II c 62.8 5.6 0.00012 35.3 2.2 23 224-246 58-80 (132)
85 cd00141 NT_POLXc Nucleotidyltr 62.8 16 0.00034 36.4 5.7 43 203-247 23-65 (307)
86 PF11798 IMS_HHH: IMS family H 61.9 6.5 0.00014 26.2 1.9 15 229-243 13-27 (32)
87 COG2003 RadC DNA repair protei 59.6 22 0.00047 34.3 5.8 62 149-213 27-88 (224)
88 PF10343 DUF2419: Protein of u 57.0 41 0.00089 33.6 7.4 54 170-223 57-117 (287)
89 TIGR00084 ruvA Holliday juncti 56.7 9.1 0.0002 35.7 2.7 21 225-245 70-90 (191)
90 PF05559 DUF763: Protein of un 56.7 17 0.00036 36.8 4.6 26 222-247 264-289 (319)
91 PRK14605 ruvA Holliday junctio 56.5 9.5 0.00021 35.7 2.8 22 225-246 71-92 (194)
92 KOG2534|consensus 56.4 21 0.00045 36.3 5.2 43 203-247 34-76 (353)
93 KOG2841|consensus 55.9 18 0.00038 35.3 4.5 34 175-211 214-247 (254)
94 COG0272 Lig NAD-dependent DNA 55.4 11 0.00023 41.6 3.3 80 164-246 453-562 (667)
95 PF14490 HHH_4: Helix-hairpin- 55.1 26 0.00056 28.6 4.9 54 186-246 7-65 (94)
96 smart00279 HhH2 Helix-hairpin- 53.4 11 0.00023 26.0 1.9 17 229-245 18-34 (36)
97 PF04904 NCD1: NAB conserved r 51.9 33 0.00073 27.9 4.7 51 165-216 21-72 (82)
98 COG1796 POL4 DNA polymerase IV 51.8 25 0.00054 35.6 5.0 44 203-247 28-73 (326)
99 PRK13482 DNA integrity scannin 51.6 15 0.00033 37.6 3.5 38 208-245 297-337 (352)
100 PRK13280 N-glycosylase/DNA lya 51.2 1.1E+02 0.0025 30.3 9.3 125 147-306 47-196 (269)
101 PRK08609 hypothetical protein; 49.1 29 0.00064 37.6 5.4 56 189-246 12-67 (570)
102 PF12826 HHH_2: Helix-hairpin- 48.3 41 0.0009 25.6 4.7 43 166-211 13-55 (64)
103 TIGR00426 competence protein C 47.5 18 0.00038 27.7 2.6 22 225-246 14-36 (69)
104 PRK14973 DNA topoisomerase I; 45.2 60 0.0013 37.5 7.3 46 166-215 754-800 (936)
105 cd00080 HhH2_motif Helix-hairp 45.0 12 0.00026 29.6 1.3 24 225-249 20-43 (75)
106 COG0272 Lig NAD-dependent DNA 42.8 1E+02 0.0022 34.3 8.3 21 231-252 515-535 (667)
107 PRK01172 ski2-like helicase; P 42.5 57 0.0012 35.7 6.4 37 178-217 635-671 (674)
108 PRK12766 50S ribosomal protein 41.3 48 0.001 32.2 4.9 22 225-246 34-55 (232)
109 PRK14600 ruvA Holliday junctio 40.6 21 0.00045 33.3 2.4 22 225-246 71-92 (186)
110 PRK13901 ruvA Holliday junctio 39.6 23 0.00049 33.4 2.5 21 225-245 70-90 (196)
111 PRK14601 ruvA Holliday junctio 39.4 23 0.00049 33.0 2.4 21 225-245 71-91 (183)
112 smart00845 GatB_Yqey GatB doma 39.1 1.3E+02 0.0028 26.5 7.0 39 146-184 42-80 (147)
113 COG1948 MUS81 ERCC4-type nucle 37.5 69 0.0015 31.5 5.5 48 167-217 193-240 (254)
114 PRK14606 ruvA Holliday junctio 37.1 28 0.0006 32.5 2.6 21 225-245 71-91 (188)
115 PRK14602 ruvA Holliday junctio 36.9 28 0.00062 32.7 2.7 22 225-246 72-93 (203)
116 PRK14604 ruvA Holliday junctio 35.9 27 0.00059 32.7 2.3 22 225-246 71-92 (195)
117 PRK14603 ruvA Holliday junctio 35.7 28 0.0006 32.7 2.4 21 225-245 70-90 (197)
118 PF13710 ACT_5: ACT domain; PD 34.3 49 0.0011 25.1 3.1 46 3-50 15-60 (63)
119 COG1796 POL4 DNA polymerase IV 33.2 1.4E+02 0.003 30.5 6.9 29 220-248 86-115 (326)
120 PRK00254 ski2-like helicase; P 32.5 99 0.0021 34.2 6.4 22 225-246 676-697 (720)
121 TIGR02238 recomb_DMC1 meiotic 31.5 1E+02 0.0023 30.8 5.8 48 166-216 11-59 (313)
122 TIGR01448 recD_rel helicase, p 30.9 97 0.0021 34.6 6.0 62 180-245 70-135 (720)
123 COG1379 PHP family phosphoeste 30.2 2.2E+02 0.0047 29.4 7.7 48 146-193 304-352 (403)
124 PTZ00035 Rad51 protein; Provis 29.4 1.1E+02 0.0025 30.8 5.8 48 166-216 33-81 (337)
125 PF00416 Ribosomal_S13: Riboso 29.0 48 0.001 27.9 2.5 22 226-247 14-35 (107)
126 PRK11152 ilvM acetolactate syn 28.8 61 0.0013 26.0 2.9 45 3-50 26-70 (76)
127 COG0632 RuvA Holliday junction 28.4 42 0.0009 31.8 2.2 22 225-246 71-92 (201)
128 TIGR00375 conserved hypothetic 27.8 1.9E+02 0.0042 29.9 7.1 46 146-191 297-343 (374)
129 PF00570 HRDC: HRDC domain Blo 27.7 1.1E+02 0.0024 22.7 4.1 21 222-242 39-59 (68)
130 PRK14666 uvrC excinuclease ABC 27.7 1.2E+02 0.0026 34.0 5.9 23 224-246 666-688 (694)
131 PF13543 KSR1-SAM: SAM like do 27.6 1.3E+02 0.0029 26.6 5.1 36 174-209 88-123 (129)
132 PRK12766 50S ribosomal protein 27.4 1.2E+02 0.0026 29.5 5.1 43 167-212 14-57 (232)
133 PLN03187 meiotic recombination 27.0 1.3E+02 0.0029 30.6 5.8 48 166-216 41-89 (344)
134 COG1415 Uncharacterized conser 26.9 51 0.0011 33.9 2.6 25 223-247 274-298 (373)
135 PRK14667 uvrC excinuclease ABC 26.8 79 0.0017 34.5 4.3 22 224-246 543-564 (567)
136 PRK04301 radA DNA repair and r 26.7 1.4E+02 0.003 29.4 5.8 44 167-213 17-61 (317)
137 TIGR02236 recomb_radA DNA repa 25.9 1.5E+02 0.0033 28.9 5.9 44 166-212 9-53 (310)
138 PRK00254 ski2-like helicase; P 24.8 1.1E+02 0.0024 33.9 5.0 32 222-253 640-671 (720)
139 PF01367 5_3_exonuc: 5'-3' exo 24.7 18 0.0004 30.5 -0.8 30 224-254 15-44 (101)
140 PF14056 DUF4250: Domain of un 23.6 84 0.0018 23.9 2.7 33 169-201 13-48 (55)
141 PRK00558 uvrC excinuclease ABC 23.0 79 0.0017 34.6 3.5 20 226-245 574-593 (598)
142 PF03118 RNA_pol_A_CTD: Bacter 23.0 70 0.0015 24.7 2.3 20 225-244 42-61 (66)
143 PRK14976 5'-3' exonuclease; Pr 22.7 54 0.0012 32.4 1.9 25 225-250 189-213 (281)
144 COG1468 CRISPR-associated prot 22.7 75 0.0016 29.6 2.8 32 312-360 157-188 (190)
145 PRK14670 uvrC excinuclease ABC 22.2 1.3E+02 0.0029 32.8 4.9 75 154-247 487-566 (574)
146 PRK06737 acetolactate synthase 21.9 94 0.002 24.9 2.9 46 4-51 26-71 (76)
147 TIGR00596 rad1 DNA repair prot 21.8 1.3E+02 0.0029 34.2 5.0 41 168-212 769-809 (814)
148 PRK14672 uvrC excinuclease ABC 21.5 1.2E+02 0.0027 33.8 4.6 26 224-249 637-662 (691)
149 PF04891 NifQ: NifQ; InterPro 20.9 2.5E+02 0.0055 25.9 5.8 51 302-358 105-165 (167)
150 cd00008 53EXOc 5'-3' exonuclea 20.7 64 0.0014 30.9 2.0 25 225-250 181-205 (240)
151 smart00475 53EXOc 5'-3' exonuc 20.6 65 0.0014 31.4 2.0 21 225-245 184-204 (259)
152 COG2406 Protein distantly rela 20.4 2.9E+02 0.0064 25.3 5.9 31 206-237 65-95 (172)
153 PF01930 Cas_Cas4: Domain of u 20.0 1.1E+02 0.0023 26.9 3.2 15 345-359 147-161 (162)
No 1
>KOG1921|consensus
Probab=100.00 E-value=2.6e-55 Score=411.25 Aligned_cols=245 Identities=51% Similarity=0.883 Sum_probs=224.9
Q ss_pred cccccCCCCCCCCCCCCC---CCCCChhhHHHHHHHHHHHhccCCCcccccCCCCCCCCCCCcccChHHHHHHHHHhccc
Q psy4002 84 KKQNVHNKDPIPDENDTK---KTKWEPAHWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQT 160 (378)
Q Consensus 84 ~~~~~~~~~~~p~~~~~~---~~~~~p~~~~e~~~~l~~~~~~~~apvd~~G~~~~~~~~~~~~~~pF~~Lv~~iLsqqt 160 (378)
+..++++.+..|...+.. .....|+.|.++|++|+.||....+|||.|||+..++....|...+|++||+.|||+||
T Consensus 12 ~r~~~~~~~~~~~~~~~~~~~~~~~ppe~w~~~y~~ir~mR~k~~APVD~mGc~~~~~~~~~pk~~RfqvLv~lmLSSQT 91 (286)
T KOG1921|consen 12 RRVNVPNTWSTPADPSEPMGSASGKPPENWLEVYERIRKMRSKIVAPVDTMGCSRIPSLKADPKERRFQVLVGLMLSSQT 91 (286)
T ss_pred hhccCCccccCcCCccccccCCCCCCCccHHHHHHHHHHHhhcccCCccccccccCccccCChhhHhHHHHHHHHHhcch
Confidence 335666666555443322 22345668999999999999999999999999999998888999999999999999999
Q ss_pred cHHHHHHHHHHHHHhC-CCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHH
Q psy4002 161 KDEVNHAAMGRLKEHG-LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKM 239 (378)
Q Consensus 161 ~~~~~~~~~~~L~~~~-pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpkt 239 (378)
+|+++.+++.||.+.+ +|+|++.++++..|.++|.++|||++||.||+..|+.+.++|+||||+++++|++||||||||
T Consensus 92 KDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKM 171 (286)
T KOG1921|consen 92 KDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKM 171 (286)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCCCchHH
Confidence 9999999999999997 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCC-CCCCHHHHHHHH
Q psy4002 240 AHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTK-VFKTPEDTRKEL 318 (378)
Q Consensus 240 A~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~-~~~~~~~~~~~l 318 (378)
|.++|..|||+..||+ ||+||||+++||||++ ..+++++++.+|
T Consensus 172 a~L~m~~AWn~i~GI~-----------------------------------VDtHVHRi~nrlgWv~~ktkspE~TR~aL 216 (286)
T KOG1921|consen 172 AHLTMQVAWNKIVGIC-----------------------------------VDTHVHRICNRLGWVDTKTKSPEQTRVAL 216 (286)
T ss_pred HHHHHHHHhccceeEE-----------------------------------eehHHHHHHHHhcccccccCCHHHHHHHH
Confidence 9999999999999997 9999999999999998 345699999999
Q ss_pred HhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCC-ccCCccccc
Q psy4002 319 ESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLN-KDLCPQGKK 363 (378)
Q Consensus 319 e~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl-~~~C~~~~~ 363 (378)
+.|+|.+.|.++|.+|++|||.||.|++|+|+.|.+ ++.||+...
T Consensus 217 q~wLPk~lW~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~~ 262 (286)
T KOG1921|consen 217 QQWLPKSLWVEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSFK 262 (286)
T ss_pred HHhCcHHHHhhhhceeecccceeeecCCCCccccccCcccCchhhh
Confidence 999999999999999999999999999999999999 699999653
No 2
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.7e-51 Score=380.84 Aligned_cols=206 Identities=38% Similarity=0.663 Sum_probs=190.9
Q ss_pred hhHHHHHHHHHHHhccCCCcccccCCCCCCCCCCCcccChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCH
Q psy4002 108 AHWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSE 187 (378)
Q Consensus 108 ~~~~e~~~~l~~~~~~~~apvd~~G~~~~~~~~~~~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~ 187 (378)
....+++..+.++.+......+ ..+||++||+.||||||+|+++..++.+|++.++|||+|+++++
T Consensus 4 ~~~~~i~~~l~~~~p~~~~~l~--------------~~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~ 69 (211)
T COG0177 4 KKALEILDRLRELYPEPKTELD--------------FKDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADE 69 (211)
T ss_pred hhHHHHHHHHHHHCCCCCCccC--------------cCCcHHHHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCH
Confidence 3457788888777655442221 24699999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcc
Q psy4002 188 DVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPS 267 (378)
Q Consensus 188 e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~ 267 (378)
++|+++|+.+|||++||++|+.+|+.|.++|+|++|+++++|.+|||||+|||+++|+++||.+ +|+
T Consensus 70 ~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~------------ 136 (211)
T COG0177 70 EELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFAFGIP-AIA------------ 136 (211)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHHHHHHHhhcCCC-ccc------------
Confidence 9999999999999999999999999999999999999999999999999999999999999986 554
Q ss_pred hhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhcCCcccHHHHHHHHHHhcchhccCCCC
Q psy4002 268 SRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWSEVNHLLVGFGQQICKSQRP 347 (378)
Q Consensus 268 ~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P 347 (378)
|||||+|+++|+||.+ ..+++++++.|.+++|++.|..+|++|+.|||.+|++++|
T Consensus 137 -----------------------VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~iC~ar~P 192 (211)
T COG0177 137 -----------------------VDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIPKELWTDLHHWLILHGRYICKARKP 192 (211)
T ss_pred -----------------------ccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhhhccCCCC
Confidence 9999999999999999 8999999999999999999999999999999999999999
Q ss_pred CCCCCCCccCCcccccc
Q psy4002 348 SCETCLNKDLCPQGKKE 364 (378)
Q Consensus 348 ~C~~Cpl~~~C~~~~~~ 364 (378)
+|+.||+++.|+++...
T Consensus 193 ~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 193 RCEECPLADLCPSAGKT 209 (211)
T ss_pred CcCcccchhhCchhccc
Confidence 99999999999998754
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.6e-45 Score=344.38 Aligned_cols=184 Identities=27% Similarity=0.483 Sum_probs=175.6
Q ss_pred cccChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCc
Q psy4002 143 PEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDI 222 (378)
Q Consensus 143 ~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~i 222 (378)
+..+||++||++||||||+++++..++.+|+..|||+++|+++++++|+++|+++|||++||++|+++|+.+.++|+|++
T Consensus 25 ~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~ 104 (211)
T PRK10702 25 NFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEV 104 (211)
T ss_pred CCCChHHHHHHHHHHhhcCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 34569999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHh
Q psy4002 223 PNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL 302 (378)
Q Consensus 223 p~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rl 302 (378)
|+++++|++|||||+|||+++|+|+||+ ++|+||+||+|++.|+
T Consensus 105 p~~~~~Ll~lpGVG~ktA~~ill~a~~~------------------------------------~~~~VDt~v~Rv~~r~ 148 (211)
T PRK10702 105 PEDRAALEALPGVGRKTANVVLNTAFGW------------------------------------PTIAVDTHIFRVCNRT 148 (211)
T ss_pred CchHHHHhcCCcccHHHHHHHHHHHcCC------------------------------------CcccccchHHHHHHHh
Confidence 9999999999999999999999999997 4556999999999999
Q ss_pred CCCCCCCCHHHHHHHHHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCccccc
Q psy4002 303 GWTKVFKTPEDTRKELESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKK 363 (378)
Q Consensus 303 g~~~~~~~~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~ 363 (378)
||.. ..+++++++.++.++|.+.|..+|++|++||+.+|++++|+|+.|||++.|+++.+
T Consensus 149 g~~~-~~~~~~~~~~l~~~lp~~~~~~~~~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 149 QFAP-GKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred CCCC-CCCHHHHHHHHHHhCCchHHHHHHHHHHHHhHHHcCCCCCCCCCCcChhhcCcccc
Confidence 9987 67899999999999999999999999999999999999999999999999998754
No 4
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=100.00 E-value=1.2e-43 Score=343.65 Aligned_cols=197 Identities=24% Similarity=0.368 Sum_probs=179.4
Q ss_pred cccChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCc
Q psy4002 143 PEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDI 222 (378)
Q Consensus 143 ~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~i 222 (378)
...+||++||++||+|||+++++..++.+|.+.|||+++|+++++++|.++|+++|||+ ||++|+++|+.|.+.|+|.+
T Consensus 22 ~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y~-RAr~L~~~A~~i~~~~~g~~ 100 (275)
T TIGR01084 22 QNKTPYRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYYA-RARNLHKAAQEVVEEFGGEF 100 (275)
T ss_pred CCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcHH-HHHHHHHHHHHHHHHcCCCC
Confidence 34569999999999999999999999999999999999999999999999999999995 99999999999999999999
Q ss_pred hhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHh
Q psy4002 223 PNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL 302 (378)
Q Consensus 223 p~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rl 302 (378)
|.++++|++|||||+|||+++|+|+||++ .++||+||+|++.|+
T Consensus 101 p~~~~~L~~LpGIG~~TA~~Il~~a~~~~------------------------------------~~~vD~~v~RVl~Rl 144 (275)
T TIGR01084 101 PQDFEDLAALPGVGRYTAGAILSFALNKP------------------------------------YPILDGNVKRVLSRL 144 (275)
T ss_pred cHHHHHHHhCCCCCHHHHHHHHHHHCCCC------------------------------------CCcchHhHHHHHHHH
Confidence 99999999999999999999999999974 345999999999999
Q ss_pred CCCCCCCCHHHHHHH----HHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcccccccc-cccCCCCCCC
Q psy4002 303 GWTKVFKTPEDTRKE----LESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELA-ERVKKSPKKR 376 (378)
Q Consensus 303 g~~~~~~~~~~~~~~----le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~-~~~~k~~~~~ 376 (378)
+++....+..++++. ++.++|.+.|+.+|++||+||+.+|++++|+|+.||+++.|.++..+.. +++.|++|++
T Consensus 145 ~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~~~~~ 223 (275)
T TIGR01084 145 FAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAA 223 (275)
T ss_pred ccCcCCCCHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCHhhcCCCCCCCC
Confidence 877644555555554 7899999999999999999999999999999999999999999987765 6777776654
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.4e-42 Score=345.73 Aligned_cols=196 Identities=20% Similarity=0.294 Sum_probs=176.7
Q ss_pred ccChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCch
Q psy4002 144 EVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIP 223 (378)
Q Consensus 144 ~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip 223 (378)
..+||++||++||+|||+++++..++.+|.+.|||+++|+++++++|.++|+++|||+ ||++|+.+|+.|.++|+|.+|
T Consensus 27 ~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~p 105 (350)
T PRK10880 27 DKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGGEFP 105 (350)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCCCch
Confidence 4469999999999999999999999999999999999999999999999999999996 999999999999999999999
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhC
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLG 303 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg 303 (378)
.++++|++|||||+|||+++|+|+||++ .++||+||+|++.|++
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~af~~~------------------------------------~~iVD~nV~RV~~Rl~ 149 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLSLGKH------------------------------------FPILDGNVKRVLARCY 149 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHHCCCC------------------------------------eecccHHHHHHHHHHh
Confidence 9999999999999999999999999973 3459999999999987
Q ss_pred CCCCCCCHHHHHH----HHHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcccccccc-cccCCCCCCC
Q psy4002 304 WTKVFKTPEDTRK----ELESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELA-ERVKKSPKKR 376 (378)
Q Consensus 304 ~~~~~~~~~~~~~----~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~-~~~~k~~~~~ 376 (378)
.+....++.++++ .++.++|.+.|+.+|++||+||+.+|+|++|+|+.|||++.|+++..+.. .+|.|++|++
T Consensus 150 ~i~~~~~~~~~~~~l~~~~~~l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~~~~P~k~~k~~ 227 (350)
T PRK10880 150 AVSGWPGKKEVENRLWQLSEQVTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQT 227 (350)
T ss_pred cccCCCChHHHHHHHHHHHHHhCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCHhhCCCCCCCCC
Confidence 6653344444443 45678899999999999999999999999999999999999999998775 6777766654
No 6
>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=5.3e-40 Score=301.97 Aligned_cols=168 Identities=34% Similarity=0.611 Sum_probs=161.6
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchh
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPN 224 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~ 224 (378)
.+||++||++||+|||+++++..++.+|++.|||+++|+++++++|.++|+++||+++||++|+++|+.+.++|+|++|+
T Consensus 24 ~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~~~ 103 (191)
T TIGR01083 24 NNPFELLVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPE 103 (191)
T ss_pred CCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCCch
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCC
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGW 304 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~ 304 (378)
++++|++|||||+|||+++|+|+++++ .|+||+||+|++.|+|+
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~~~~~------------------------------------~~~vD~~v~Ri~~r~g~ 147 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVAFGIP------------------------------------AIAVDTHVFRVSNRLGL 147 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHHcCCC------------------------------------ccccchhHHHHHHHcCC
Confidence 999999999999999999999999973 45699999999999999
Q ss_pred CCCCCCHHHHHHHHHhcCCcccHHHHHHHHHHhcchhccCCCCCC
Q psy4002 305 TKVFKTPEDTRKELESWLPESLWSEVNHLLVGFGQQICKSQRPSC 349 (378)
Q Consensus 305 ~~~~~~~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C 349 (378)
.. ..+++++++.++.++|.+.|.++|.+|+.||+.+|++++|+|
T Consensus 148 ~~-~~~~~~~~~~l~~~~p~~~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 148 SK-GKDPDKVEEELLKLIPREFWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred CC-CCCHHHHHHHHHHHCCchhHHHHHHHHHHHhHHhcCCCCCCC
Confidence 87 578999999999999999999999999999999999999999
No 7
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=2.9e-38 Score=307.66 Aligned_cols=174 Identities=22% Similarity=0.346 Sum_probs=159.7
Q ss_pred HhccccHHHHHH-HHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCC
Q psy4002 156 LSSQTKDEVNHA-AMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPG 234 (378)
Q Consensus 156 Lsqqt~~~~~~~-~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpG 234 (378)
|+|||+++.+.. .|.+|.+.|||+++|+++++++|.++|+++|||+ ||++|+.+|+.|.++|+|.+|.++++|++|||
T Consensus 1 mlQQT~v~~v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpG 79 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPG 79 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCC
Confidence 589999998865 9999999999999999999999999999999995 99999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCCCHHHH
Q psy4002 235 VGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDT 314 (378)
Q Consensus 235 VGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~ 314 (378)
||+|||+++|+|+||+ ++++||+||+||+.|++++....+.+++
T Consensus 80 IG~kTA~aIl~~af~~------------------------------------~~~~VD~nV~RVl~Rl~g~~~~~~~~~l 123 (289)
T PRK13910 80 IGAYTANAILCFGFRE------------------------------------KSACVDANIKRVLLRLFGLDPNIHAKDL 123 (289)
T ss_pred CCHHHHHHHHHHHCCC------------------------------------CcCcccHHHHHHHHHHhcCCCCccHHHH
Confidence 9999999999999997 4456999999999997444435666777
Q ss_pred HHHHHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCccccccccc
Q psy4002 315 RKELESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELAE 367 (378)
Q Consensus 315 ~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~~ 367 (378)
+...+.++|.+.|+.+|++||+||+.+|++ +|+|+.||+++.|.++..+...
T Consensus 124 ~~~~~~~l~~~~~~~~nqaLm~~Ga~iC~~-~P~C~~CPl~~~C~~~~~~~~~ 175 (289)
T PRK13910 124 QIKANDFLNLNESFNHNQALIDLGALICSP-KPKCAICPLNPYCLGKNNPEKH 175 (289)
T ss_pred HHHHHHhCCccchHHHHHHHHHHhHHHcCC-CCCCCCCcChhhhhhhhcCCcc
Confidence 777888999999999999999999999999 7999999999999999987774
No 8
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.3e-36 Score=294.44 Aligned_cols=195 Identities=25% Similarity=0.359 Sum_probs=178.4
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhh
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNT 225 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~ 225 (378)
+||.++||+||+|||..+.+...|.+|.++|||+++||+++++++..++.++|||. ||++|+.+|+.+.++|+|.+|++
T Consensus 33 ~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYys-RArnL~~~A~~v~~~~~G~~P~~ 111 (342)
T COG1194 33 DPYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYYS-RARNLHKAAQEVVERHGGEFPDD 111 (342)
T ss_pred CcceehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCCCCCCC
Confidence 39999999999999999999999999999999999999999999999999999765 99999999999999999999999
Q ss_pred HHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCC
Q psy4002 226 IELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWT 305 (378)
Q Consensus 226 ~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~ 305 (378)
.+.|.+|||||++||..+|.|+||++.+ +||+||.||+.|+..+
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~------------------------------------~lDgNV~RVl~R~f~i 155 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEP------------------------------------VLDGNVKRVLSRLFAI 155 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCc------------------------------------eeecchheeehhhhcc
Confidence 9999999999999999999999998543 5999999999999777
Q ss_pred CC----CCCHHHHHHHHHhcCCcc-cHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcccccccc-cccCCCCCCCC
Q psy4002 306 KV----FKTPEDTRKELESWLPES-LWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELA-ERVKKSPKKRK 377 (378)
Q Consensus 306 ~~----~~~~~~~~~~le~~lP~~-~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~-~~~~k~~~~~~ 377 (378)
.. ..+...++..++.++.++ ..+.|+++||++|+.||++.+|+|+.|||++.|..+..+.. .++.|++|+++
T Consensus 156 ~~~~~~~~~~~~~~~~~~~ll~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~ 233 (342)
T COG1194 156 SGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKL 233 (342)
T ss_pred cccccccchhHHHHHHHHHhcCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCcccCCCcCccccc
Confidence 63 234567788888855554 49999999999999999999999999999999999999888 68888888765
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.7e-34 Score=271.21 Aligned_cols=167 Identities=20% Similarity=0.264 Sum_probs=151.2
Q ss_pred CCCcccChHHHHHHHHHhccccHHHHHHHHHHHHHh-------CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 140 DIAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEH-------GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 140 ~~~~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~-------~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
.++|..+||++||++||+|||+++++.+++.+|.+. ++||+.|+++++++|+++|+++||+++||++|+++|+
T Consensus 23 ~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~ 102 (218)
T PRK13913 23 WWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSE 102 (218)
T ss_pred CCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 346677899999999999999999999999999985 4599999999999999999999999999999999999
Q ss_pred HHHHhcCC----CchhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCc
Q psy4002 213 ILKKNYNN----DIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQ 288 (378)
Q Consensus 213 ~i~e~y~g----~ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 (378)
.+.+.|++ ..+.++++|++|||||+|||+++|+|++++ |+
T Consensus 103 ~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r------------------------------------p~ 146 (218)
T PRK13913 103 NILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAK------------------------------------EV 146 (218)
T ss_pred HHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCC------------------------------------Cc
Confidence 99999987 357889999999999999999999999997 66
Q ss_pred cccchHHHHHHHHhCCCCCCCCHHHHHHHHHhcC-----------Cc-----ccHHHHHHHHHHhcchhccC
Q psy4002 289 LCVDVHVHRISHRLGWTKVFKTPEDTRKELESWL-----------PE-----SLWSEVNHLLVGFGQQICKS 344 (378)
Q Consensus 289 ~~VD~hv~Ri~~Rlg~~~~~~~~~~~~~~le~~l-----------P~-----~~~~~~~~~Lv~~G~~iC~~ 344 (378)
|+||+|++|++.|+||.. .++++++..++..+ |. ..+.+||.+|++||+..|..
T Consensus 147 fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 147 MVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred cccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 789999999999999965 47999999998866 21 26899999999999999964
No 10
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.98 E-value=1.4e-31 Score=246.50 Aligned_cols=184 Identities=30% Similarity=0.472 Sum_probs=166.4
Q ss_pred CCcccChHHHHHHHHHhccccHHHHHHHHHHHHHhC-CCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcC
Q psy4002 141 IAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHG-LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYN 219 (378)
Q Consensus 141 ~~~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~-pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~ 219 (378)
+||....++++|++||.|+|+|++|..++++|...+ .+++.|..++.++|+++|++.|||++||.||+++...+...|.
T Consensus 24 WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~ 103 (215)
T COG2231 24 WWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFI 103 (215)
T ss_pred CCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhh
Confidence 566777899999999999999999999999999987 4899999999999999999999999999999888888887655
Q ss_pred C--Cc-hh-hHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHH
Q psy4002 220 N--DI-PN-TIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHV 295 (378)
Q Consensus 220 g--~i-p~-~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv 295 (378)
+ .+ +. .+++|++++|||+-|||.+|++++++ |+|+||.+.
T Consensus 104 ~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r------------------------------------p~FVvD~Yt 147 (215)
T COG2231 104 NLESFKSEVLREELLSIKGIGKETADSILLYALDR------------------------------------PVFVVDKYT 147 (215)
T ss_pred hhhccchHHHHHHHHccCCcchhhHHHHHHHHhcC------------------------------------cccchhHHH
Confidence 4 12 22 58999999999999999999999986 788999999
Q ss_pred HHHHHHhCCCCCCCCHHHHHHHHHhcCCcc--cHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcccc
Q psy4002 296 HRISHRLGWTKVFKTPEDTRKELESWLPES--LWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGK 362 (378)
Q Consensus 296 ~Ri~~Rlg~~~~~~~~~~~~~~le~~lP~~--~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~ 362 (378)
+|++.|+|.+. .++++++++..+.-+|.+ .+.++|.+++.||+.+|+-. |.|+.|||...|.++.
T Consensus 148 ~R~l~rlg~i~-~k~ydeik~~fe~~l~~~~~lyqe~HAlIv~~~K~f~~k~-~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 148 RRLLSRLGGIE-EKKYDEIKELFEENLPENLRLYQEFHALIVEHAKHFCKKK-PLCEKCPLKEKCKKYR 214 (215)
T ss_pred HHHHHHhcccc-cccHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHccCC-cCCCCchHHHHHhhcc
Confidence 99999999998 459999999999989875 58999999999999999974 9999999999998764
No 11
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.96 E-value=2.3e-29 Score=221.00 Aligned_cols=149 Identities=42% Similarity=0.629 Sum_probs=141.5
Q ss_pred HhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCc
Q psy4002 156 LSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGV 235 (378)
Q Consensus 156 Lsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGV 235 (378)
|+|||+++++..++.+|.+.||||++|+++++++|.++|+++||+++||++|+++|+.+.+.|++++|+.+++|++||||
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GI 80 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGV 80 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCCCHHHHH
Q psy4002 236 GPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTR 315 (378)
Q Consensus 236 GpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~~ 315 (378)
|+|||+++++|++++ +++++|+|+.|++.|+|+.+...++++++
T Consensus 81 G~~tA~~~l~~~~~~------------------------------------~~~~~D~~v~r~~~rl~~~~~~~~~~~~~ 124 (149)
T smart00478 81 GRKTANAVLSFALGK------------------------------------PFIPVDTHVLRIAKRLGLVDKKSTPEEVE 124 (149)
T ss_pred cHHHHHHHHHHHCCC------------------------------------CCCccchHHHHHHHHhCCCCCCCCHHHHH
Confidence 999999999999997 23469999999999999998667799999
Q ss_pred HHHHhcCCcccHHHHHHHHHHhcch
Q psy4002 316 KELESWLPESLWSEVNHLLVGFGQQ 340 (378)
Q Consensus 316 ~~le~~lP~~~~~~~~~~Lv~~G~~ 340 (378)
+.++.|+|...|+.+|.+++.+|+.
T Consensus 125 ~~~~~~~p~~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 125 KLLEKLLPKEDWRELNLLLIDFGRT 149 (149)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999973
No 12
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.96 E-value=7.2e-29 Score=219.65 Aligned_cols=154 Identities=36% Similarity=0.545 Sum_probs=144.8
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHhC-CCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCc---h
Q psy4002 148 YHVLISLMLSSQTKDEVNHAAMGRLKEHG-LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDI---P 223 (378)
Q Consensus 148 F~~Lv~~iLsqqt~~~~~~~~~~~L~~~~-pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~i---p 223 (378)
|++|+++||+|||+++++..++.+|.+.+ ||+++|+.+++++|.+++.++| +++||++|+++|+.+.+.|++.. +
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~~~~ 79 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVLDDP 79 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccCCCc
Confidence 78999999999999999999999999999 9999999999999999999999 78899999999999999998876 8
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhC
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLG 303 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg 303 (378)
+.++.|++|||||+|||+++++|+++ .+. |++|+|++|++.|+|
T Consensus 80 ~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~-----------------------------------~pvD~~v~r~~~~~~ 123 (158)
T cd00056 80 DAREELLALPGVGRKTANVVLLFALG-PDA-----------------------------------FPVDTHVRRVLKRLG 123 (158)
T ss_pred ccHHHHHcCCCCCHHHHHHHHHHHCC-CCC-----------------------------------CccchhHHHHHHHhC
Confidence 89999999999999999999999999 544 458999999999999
Q ss_pred CCCCCCCHHHHHHHHHhcCCcccHHHHHHHHHHhc
Q psy4002 304 WTKVFKTPEDTRKELESWLPESLWSEVNHLLVGFG 338 (378)
Q Consensus 304 ~~~~~~~~~~~~~~le~~lP~~~~~~~~~~Lv~~G 338 (378)
++....+++++++.++.|.|...+..+|++|+.||
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g 158 (158)
T cd00056 124 LIPKKKTPEELEELLEELLPKPYWGEANQALMDLG 158 (158)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHcC
Confidence 97667899999999999999888999999999987
No 13
>KOG2457|consensus
Probab=99.95 E-value=6.7e-28 Score=238.33 Aligned_cols=185 Identities=24% Similarity=0.333 Sum_probs=170.2
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCH-HHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCch
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSE-DVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIP 223 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~-e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip 223 (378)
...|+++|++||.|||..+.+...|.++...+||..+++.++. +++.+++.++|||+ |+++|++.|+.+.+..+|.+|
T Consensus 123 rRaYeVwVSEiMLQQTrV~TV~~YYt~WMqkwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~ge~P 201 (555)
T KOG2457|consen 123 RRAYEVWVSEIMLQQTRVQTVMKYYTRWMQKWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEGEFP 201 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCCCCC
Confidence 4689999999999999999999999999999999999999998 88999999999997 999999999999999999999
Q ss_pred hhHHHHhc-CCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHh
Q psy4002 224 NTIELLCK-LPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRL 302 (378)
Q Consensus 224 ~~~e~L~~-LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rl 302 (378)
.+-+.|.+ +||||++||..++..||+++.|| ||.+|.|++.|.
T Consensus 202 rta~~l~kgvpGVG~YTAGAiaSIAf~q~tGi------------------------------------VDGNVirvlsRa 245 (555)
T KOG2457|consen 202 RTASSLMKGVPGVGQYTAGAIASIAFNQVTGI------------------------------------VDGNVIRVLSRA 245 (555)
T ss_pred ChHHHHHhhCCCCCccchhhhhhhhhcCcccc------------------------------------cccchHHHhHHh
Confidence 99999998 99999999999999999999887 999999999998
Q ss_pred CCCCC----CCCHHHHHHHHHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcccccccc
Q psy4002 303 GWTKV----FKTPEDTRKELESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQGKKELA 366 (378)
Q Consensus 303 g~~~~----~~~~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~~~~~~~ 366 (378)
--+.. ++-...+.+....++.+..+++||++||++|...|+|.+|.|+.||+...|..+....+
T Consensus 246 lAIhsDcSkgk~~q~~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~~Eq 313 (555)
T KOG2457|consen 246 LAIHSDCSKGKFFQSSWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQLSEQ 313 (555)
T ss_pred HhhcCCcchhhHHHHHHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhHhhh
Confidence 55542 22345677888889999999999999999999999999999999999999999985444
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.94 E-value=7e-26 Score=211.54 Aligned_cols=151 Identities=21% Similarity=0.183 Sum_probs=128.6
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccC--ChHHHHHHHHHHHHH---HHHhc-
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVG--FWKTKAKHIKMASDI---LKKNY- 218 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~G--f~~~KA~~I~~lA~~---i~e~y- 218 (378)
.+||+.||++||||||+++++.+++.+|. ++.+ +++.++|+++|+++| |+++||++|+++++. +.+.+
T Consensus 35 ~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~ 108 (208)
T PRK01229 35 EDLFSELSFCILTANSSAEGGIKAQKEIG-----DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIK 108 (208)
T ss_pred CChHHHHHHHHhcCcCcHHHHHHHHHhcC-----HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45999999999999999999999999994 3456 899999999999995 999999999999987 66666
Q ss_pred -CCCchhhHHHHh-cCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHH
Q psy4002 219 -NNDIPNTIELLC-KLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVH 296 (378)
Q Consensus 219 -~g~ip~~~e~L~-~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~ 296 (378)
++++|.++++|+ +|||||+|||+++|+....+ |+|+||+||+
T Consensus 109 ~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~------------------------------------~~~iVDtHv~ 152 (208)
T PRK01229 109 ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE------------------------------------DLAILDRHIL 152 (208)
T ss_pred ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC------------------------------------CeeeeeHHHH
Confidence 889999999999 99999999999999654333 5667999999
Q ss_pred HHHHHhCCCCC------CCCHHHHHHHHHhcCCcc--cHHHHHHHHHHh
Q psy4002 297 RISHRLGWTKV------FKTPEDTRKELESWLPES--LWSEVNHLLVGF 337 (378)
Q Consensus 297 Ri~~Rlg~~~~------~~~~~~~~~~le~~lP~~--~~~~~~~~Lv~~ 337 (378)
|++.|+|+++. ..+|.+++..+.+..+.- ..+.+..+||..
T Consensus 153 Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~~~~~Ldl~~w~~ 201 (208)
T PRK01229 153 RFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGISLGELDLYIWYK 201 (208)
T ss_pred HHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 99999999884 268999999998887642 355666666643
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=99.88 E-value=5.3e-22 Score=195.55 Aligned_cols=121 Identities=25% Similarity=0.306 Sum_probs=105.6
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHH---------------hCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHH
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKE---------------HGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMA 210 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~---------------~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~l 210 (378)
+||++||++|++||++.+++.+++.+|.+ .|||+++|+.++.++ .|+.+||.. ||++|+.+
T Consensus 118 d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g~-Ra~~I~~~ 193 (310)
T TIGR00588 118 DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLGY-RARYIRET 193 (310)
T ss_pred CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCHH-HHHHHHHH
Confidence 69999999999999999999999999965 378999999876442 347789954 89999999
Q ss_pred HHHHHHhcCCC----------chhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhh
Q psy4002 211 SDILKKNYNND----------IPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVR 280 (378)
Q Consensus 211 A~~i~e~y~g~----------ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 280 (378)
|+.+.+++++. .++.+++|++|||||+|||+++++|+++++++||
T Consensus 194 A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P------------------------- 248 (310)
T TIGR00588 194 ARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVP------------------------- 248 (310)
T ss_pred HHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee-------------------------
Confidence 99999987654 5678999999999999999999999999976665
Q ss_pred hccccCCccccchHHHHHHHHhCCC
Q psy4002 281 KCEKKIPQLCVDVHVHRISHRLGWT 305 (378)
Q Consensus 281 ~~~~~~~~~~VD~hv~Ri~~Rlg~~ 305 (378)
||+||+|++.|++..
T Consensus 249 ----------vD~~v~r~~~r~y~~ 263 (310)
T TIGR00588 249 ----------VDVHVWRIANRDYPW 263 (310)
T ss_pred ----------ecHHHHHHHHHHhcc
Confidence 999999999998543
No 16
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.88 E-value=7.4e-22 Score=192.54 Aligned_cols=193 Identities=18% Similarity=0.167 Sum_probs=153.9
Q ss_pred ChhhHHHHHHHHHHHhccCCCcccccCCCCCCCC-C--CCcccChHHHHHHHHHhccccHHHHHHHHHHHHHh-------
Q psy4002 106 EPAHWKEVLNNIREMRKHGDAPVDAMGWDHSANV-D--IAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKEH------- 175 (378)
Q Consensus 106 ~p~~~~e~~~~l~~~~~~~~apvd~~G~~~~~~~-~--~~~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~------- 175 (378)
........+.++-..+......++..|....... + .....++|+.||++|++||.+.+.+.+++.+|...
T Consensus 61 ~~~~~~~~~~~~~~lD~~l~~i~~~~~~~~~~~~~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~ 140 (285)
T COG0122 61 VAEDIEAALRRLFDLDPDLAPIIDALGPLPLLRAPGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEI 140 (285)
T ss_pred hhHHHHHHHHHHHhcCCcHHHHHHhcCccccccccCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCcccc
Confidence 3344566777777777777766676666554331 1 12246799999999999999999999999999872
Q ss_pred ---CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhc-------CCCchhhHHHHhcCCCccHHHHHHHHH
Q psy4002 176 ---GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNY-------NNDIPNTIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 176 ---~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y-------~g~ip~~~e~L~~LpGVGpktA~~~l~ 245 (378)
|||||+|+.++++.| +.+|++..||+||+++|+.+.+.. +.+..+.++.|++|+|||||||+|+|+
T Consensus 141 ~~~fptpe~l~~~~~~~l----~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~ll 216 (285)
T COG0122 141 YHSFPTPEQLAAADEEAL----RRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLL 216 (285)
T ss_pred ccCCCCHHHHHhcCHHHH----HHhCCcHHHHHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHH
Confidence 689999999999998 578999999999999999999842 112345789999999999999999999
Q ss_pred HHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhcCCcc
Q psy4002 246 HAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPES 325 (378)
Q Consensus 246 ~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~~~~le~~lP~~ 325 (378)
|++|+++.+| +.|.++++.+.+++..+...+....+...+.|-|+.
T Consensus 217 f~lgr~dvfP----------------------------------~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w~p~r 262 (285)
T COG0122 217 FGLGRPDVFP----------------------------------ADDLGLRRAIKKLYRLPTRPTEKEVRELAERWGPYR 262 (285)
T ss_pred HcCCCCCCCC----------------------------------hHHHHHHHHHHHHhcCCCCchHHHHHHHHhcccCHH
Confidence 9999988776 588888899999884444555566788999999998
Q ss_pred cHHHHHHHHHH
Q psy4002 326 LWSEVNHLLVG 336 (378)
Q Consensus 326 ~~~~~~~~Lv~ 336 (378)
.+..+|.|-..
T Consensus 263 s~A~~yLw~~~ 273 (285)
T COG0122 263 SYAALYLWRYA 273 (285)
T ss_pred HHHHHHHHHhh
Confidence 88777766543
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=99.87 E-value=8.5e-22 Score=179.51 Aligned_cols=106 Identities=20% Similarity=0.292 Sum_probs=97.1
Q ss_pred ccChHHHHHHHHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhccc----CChHHHHHHHHHHHHHHHHh
Q psy4002 144 EVRRYHVLISLMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPV----GFWKTKAKHIKMASDILKKN 217 (378)
Q Consensus 144 ~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~----Gf~~~KA~~I~~lA~~i~e~ 217 (378)
..+||++||++||||||+|+++..++.+|++.. +|++.|+++++++|+++|++. |||++||++|+++|+.|.++
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~ 94 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDT 94 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHH
Confidence 346999999999999999999999999997643 699999999999999999765 99999999999999999999
Q ss_pred cCCCc--------hhh---HHHHhcCCCccHHHHHHHHHHHhc
Q psy4002 218 YNNDI--------PNT---IELLCKLPGVGPKMAHLCMNHAWG 249 (378)
Q Consensus 218 y~g~i--------p~~---~e~L~~LpGVGpktA~~~l~~a~~ 249 (378)
|+|++ |++ +++|++|||||++||++||.+.-.
T Consensus 95 y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 95 YDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred hCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 99987 666 689999999999999999997544
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.86 E-value=1e-20 Score=184.44 Aligned_cols=145 Identities=14% Similarity=0.172 Sum_probs=125.0
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHh-------------CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHH
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEH-------------GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMAS 211 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~-------------~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA 211 (378)
.++|+.+|++|++||.+...+.....+|.+. |||++.|+++++++| +.+|++++||++|+.+|
T Consensus 111 ~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL----~~~Gl~~~Ra~~L~~lA 186 (283)
T PRK10308 111 VDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQAL----KALGMPLKRAEALIHLA 186 (283)
T ss_pred CCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHH----HHCCCCHHHHHHHHHHH
Confidence 4699999999999999999999999998653 589999999999998 46899999999999999
Q ss_pred HHHHHh-cCC----CchhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccC
Q psy4002 212 DILKKN-YNN----DIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKI 286 (378)
Q Consensus 212 ~~i~e~-y~g----~ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 286 (378)
+.+.+. +.. +..+.+++|++|||||+|||+++++|++|++++||
T Consensus 187 ~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp------------------------------- 235 (283)
T PRK10308 187 NAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL------------------------------- 235 (283)
T ss_pred HHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-------------------------------
Confidence 999882 221 23456899999999999999999999999998886
Q ss_pred CccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhcCCcccHHHHHHHH
Q psy4002 287 PQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWSEVNHLL 334 (378)
Q Consensus 287 ~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~~~~le~~lP~~~~~~~~~~L 334 (378)
+.|.+++|.+ + ..+++++.+..+.|.|++.|..+|.|=
T Consensus 236 ---~~D~~l~~~~---~----~~~~~~~~~~a~~w~P~rsya~~~LW~ 273 (283)
T PRK10308 236 ---PDDYLIKQRF---P----GMTPAQIRRYAERWKPWRSYALLHIWY 273 (283)
T ss_pred ---cccHHHHHhc---c----cCCHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 6999998844 1 347788999999999999999888773
No 19
>KOG1918|consensus
Probab=99.80 E-value=2.6e-19 Score=166.75 Aligned_cols=178 Identities=17% Similarity=0.137 Sum_probs=143.4
Q ss_pred hhHHHHHHHHHHHhccCCCcccccCCCCCCCCCCCcccChHHHHHHHHHhccccHHHHHHHHHHHHH------hCCCHHH
Q psy4002 108 AHWKEVLNNIREMRKHGDAPVDAMGWDHSANVDIAPEVRRYHVLISLMLSSQTKDEVNHAAMGRLKE------HGLTIEN 181 (378)
Q Consensus 108 ~~~~e~~~~l~~~~~~~~apvd~~G~~~~~~~~~~~~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~------~~pt~e~ 181 (378)
...+-++.+|.+.++.+...+.. +.. ....+...||+.|+++||+||.+++++..++.||.. .|++||.
T Consensus 41 ~k~e~al~hl~~kd~~L~~lv~~---~~p--~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~ 115 (254)
T KOG1918|consen 41 EKAEIALSHLDEKDPSLVKLVGN---HEP--LTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEF 115 (254)
T ss_pred HHHHHHHHhhhhcchHHHHHhcC---CCC--CCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchh
Confidence 34566677777666665555443 331 122345669999999999999999999999999986 4789999
Q ss_pred HhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCC--------CchhhHHHHhcCCCccHHHHHHHHHHHhccccc
Q psy4002 182 ICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNN--------DIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTG 253 (378)
Q Consensus 182 la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g--------~ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~ 253 (378)
+..++.++| +.+||+.+|+.||+.+|++..+.|=- +-+..++.|+.++|||+||++|||.|+++|++.
T Consensus 116 i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DV 191 (254)
T KOG1918|consen 116 IDPLDCEEL----RKCGFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDV 191 (254)
T ss_pred cCcCCHHHH----HHhCcchhhHHHHHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcc
Confidence 999999998 68899999999999999999885411 123456789999999999999999999999988
Q ss_pred cCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhcCCcccHH
Q psy4002 254 IGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFKTPEDTRKELESWLPESLWS 328 (378)
Q Consensus 254 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~~~~~~~~~le~~lP~~~~~ 328 (378)
+| +-|..|++-+..+........+.++.+..+.|-|.+.-+
T Consensus 192 mp----------------------------------~dDlgir~g~k~l~gl~~~p~~~evekl~e~~kpyRtva 232 (254)
T KOG1918|consen 192 MP----------------------------------ADDLGIRNGVKKLLGLKPLPLPKEVEKLCEKCKPYRTVA 232 (254)
T ss_pred cC----------------------------------chhhhHHHHHHHHhCCCCCCchHHHHHHhhhccchHHHH
Confidence 87 577888888888877776688899999999999976433
No 20
>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=99.73 E-value=3.3e-17 Score=136.42 Aligned_cols=106 Identities=37% Similarity=0.410 Sum_probs=93.7
Q ss_pred HHHHHhccccHHHHHHHHHHHHHh--CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHH
Q psy4002 152 ISLMLSSQTKDEVNHAAMGRLKEH--GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELL 229 (378)
Q Consensus 152 v~~iLsqqt~~~~~~~~~~~L~~~--~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L 229 (378)
|++||+|||+++++..++.+|.+. ||||++|+++++++|.++|+++||++.||++|+++|+.+.
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 689999999999999999999998 5899999999999999999999999999999999999987
Q ss_pred hcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHHHHHHHhCCCCCCC
Q psy4002 230 CKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVHRISHRLGWTKVFK 309 (378)
Q Consensus 230 ~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~Ri~~Rlg~~~~~~ 309 (378)
|+++ +.+++|+|++|++.|+|++....
T Consensus 67 -------------------~~~d----------------------------------~~~~~D~~v~r~~~r~~~~~~~~ 93 (108)
T PF00730_consen 67 -------------------GRPD----------------------------------PFPPVDTHVRRVLQRLGGIPEKK 93 (108)
T ss_dssp -------------------C-SS----------------------------------SS-TTSHHHHHHHHHHTSSSSST
T ss_pred -------------------hccc----------------------------------ceecCcHHHHHHHHHHcCCCCCC
Confidence 4433 24579999999999999999668
Q ss_pred CHHHHHHHHHhcCCc
Q psy4002 310 TPEDTRKELESWLPE 324 (378)
Q Consensus 310 ~~~~~~~~le~~lP~ 324 (378)
+++++++.++++.|+
T Consensus 94 ~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 94 TKEETEKKLEELWPP 108 (108)
T ss_dssp THHHHHHHHHHHGTT
T ss_pred CHHHHHHHHHhhCcC
Confidence 999999999776653
No 21
>KOG2875|consensus
Probab=99.65 E-value=5.8e-16 Score=148.81 Aligned_cols=120 Identities=23% Similarity=0.332 Sum_probs=104.7
Q ss_pred ccChHHHHHHHHHhccccHHHHHHHHHHHHH---------------hCCCHHHHhccCHHHHHHhhcccCChHHHHHHHH
Q psy4002 144 EVRRYHVLISLMLSSQTKDEVNHAAMGRLKE---------------HGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIK 208 (378)
Q Consensus 144 ~~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~---------------~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~ 208 (378)
..+||+.|++.|.|++.+.+.+....++|.. .|||.++|+. ++++.-+|.+||.. ||+||.
T Consensus 114 rQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGY-RAkYI~ 189 (323)
T KOG2875|consen 114 RQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGY-RAKYIS 189 (323)
T ss_pred hcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcch-hHHHHH
Confidence 4579999999999999999999999998865 4799999985 44555558889876 999999
Q ss_pred HHHHHHHHhcCC----------CchhhHHHHhcCCCccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHH
Q psy4002 209 MASDILKKNYNN----------DIPNTIELLCKLPGVGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELIC 278 (378)
Q Consensus 209 ~lA~~i~e~y~g----------~ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 278 (378)
..|++|.++++| .+++.++.|+.|||||+|+|||+++++++....+|
T Consensus 190 ~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP----------------------- 246 (323)
T KOG2875|consen 190 ATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVP----------------------- 246 (323)
T ss_pred HHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc-----------------------
Confidence 999999999988 34678899999999999999999999999876665
Q ss_pred hhhccccCCccccchHHHHHHHHh
Q psy4002 279 VRKCEKKIPQLCVDVHVHRISHRL 302 (378)
Q Consensus 279 ~~~~~~~~~~~~VD~hv~Ri~~Rl 302 (378)
||+||.|+++..
T Consensus 247 ------------VDvHi~ria~~y 258 (323)
T KOG2875|consen 247 ------------VDVHIWRIAQDY 258 (323)
T ss_pred ------------chhhHHHHhhcc
Confidence 999999999943
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.86 E-value=1.3e-08 Score=93.73 Aligned_cols=118 Identities=22% Similarity=0.285 Sum_probs=93.9
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccC--ChHHHHHHHHHHHHHHHHh---cCC
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVG--FWKTKAKHIKMASDILKKN---YNN 220 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~G--f~~~KA~~I~~lA~~i~e~---y~g 220 (378)
+-|..|..|||+.|++...+..+...|-+.|. .++.|+|++.++.+| |++.||+||..+-+.+-+- -..
T Consensus 38 ~lf~ELsFCILTANsSA~~~~~~q~~lG~gfl------y~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v~~ 111 (210)
T COG1059 38 DLFKELSFCILTANSSATMGLRAQNELGDGFL------YLSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIVKA 111 (210)
T ss_pred HHHHHHHHHhccccchHHHHHHHHHHhccccc------cCCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHHhc
Confidence 47999999999999999999999988886554 357899999999985 7999999999987665321 001
Q ss_pred -Cchh-hHHHHh-cCCCccHHHHHHHHHH-HhccccccCCCCCCCCCCCcchhhhhhhhhHHhhhccccCCccccchHHH
Q psy4002 221 -DIPN-TIELLC-KLPGVGPKMAHLCMNH-AWGIVTGIGKDESRQPILSPSSRQISRSELICVRKCEKKIPQLCVDVHVH 296 (378)
Q Consensus 221 -~ip~-~~e~L~-~LpGVGpktA~~~l~~-a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VD~hv~ 296 (378)
..+. .++.|. +++|+|.|-|..||.. ++. +.-++|.|+.
T Consensus 112 ~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~-------------------------------------D~AIlDrHIl 154 (210)
T COG1059 112 DENEKVARELLVENIKGIGYKEASHFLRNVGFE-------------------------------------DLAILDRHIL 154 (210)
T ss_pred CcchHHHHHHHHHHcccccHHHHHHHHHhcChh-------------------------------------HHHHHHHHHH
Confidence 1222 678888 8999999999999965 332 2225999999
Q ss_pred HHHHHhCCCC
Q psy4002 297 RISHRLGWTK 306 (378)
Q Consensus 297 Ri~~Rlg~~~ 306 (378)
|.+.|.|.+.
T Consensus 155 r~l~r~g~i~ 164 (210)
T COG1059 155 RWLVRYGLID 164 (210)
T ss_pred HHHHHhcccc
Confidence 9999999987
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=98.26 E-value=2.4e-07 Score=61.54 Aligned_cols=29 Identities=45% Similarity=0.753 Sum_probs=25.4
Q ss_pred cCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 218 YNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 218 y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
|+|.+|.++++|++|||||++||+.++.|
T Consensus 2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 2 LDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 55778999999999999999999999875
No 24
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=97.20 E-value=9.9e-05 Score=43.02 Aligned_cols=17 Identities=41% Similarity=1.206 Sum_probs=11.5
Q ss_pred ccCCCCCCCCCCCccCC
Q psy4002 342 CKSQRPSCETCLNKDLC 358 (378)
Q Consensus 342 C~~~~P~C~~Cpl~~~C 358 (378)
|++++|+|+.|||+++|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999988
No 25
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=96.46 E-value=0.001 Score=42.41 Aligned_cols=22 Identities=45% Similarity=1.130 Sum_probs=19.9
Q ss_pred hccCCCCCCCCCCCccCCcccc
Q psy4002 341 ICKSQRPSCETCLNKDLCPQGK 362 (378)
Q Consensus 341 iC~~~~P~C~~Cpl~~~C~~~~ 362 (378)
+|++++|+|+.||++..|+++.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999998754
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=95.95 E-value=0.073 Score=49.35 Aligned_cols=101 Identities=14% Similarity=0.181 Sum_probs=73.6
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhcccCC--hHHHHHHHHHHHHHHHH---hc
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPVGF--WKTKAKHIKMASDILKK---NY 218 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~Gf--~~~KA~~I~~lA~~i~e---~y 218 (378)
.-|+.|+-+++-.-.++..+.+-...|++.| ++++.|+.++++++++++..-|. +++|.+.+..=|+.+++ +|
T Consensus 25 ~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~ 104 (179)
T PF03352_consen 25 KLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEF 104 (179)
T ss_dssp HHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 4799999999999999999999999999987 69999999999999999998887 66788888877777654 34
Q ss_pred CC----------------------Cchhh-------HHHHh--cCCCccHHHHHHHHHH
Q psy4002 219 NN----------------------DIPNT-------IELLC--KLPGVGPKMAHLCMNH 246 (378)
Q Consensus 219 ~g----------------------~ip~~-------~e~L~--~LpGVGpktA~~~l~~ 246 (378)
|+ ++|.. ..+|. .++-|||.|+..+|.-
T Consensus 105 gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vysflqA 163 (179)
T PF03352_consen 105 GSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYSFLQA 163 (179)
T ss_dssp S-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHHHHHH
T ss_pred CCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHHHHHH
Confidence 33 11211 23454 4677999999999974
No 27
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.32 E-value=0.19 Score=46.88 Aligned_cols=101 Identities=16% Similarity=0.193 Sum_probs=77.9
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhcccCCh--HHHHHHHHHHHHHHHH---hc
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPVGFW--KTKAKHIKMASDILKK---NY 218 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~Gf~--~~KA~~I~~lA~~i~e---~y 218 (378)
.-|+.|+-++.-.-.++..+.+-.+.+++.| ++++.|+.+++++++.++...|.- +.|.+.+..=|+++.+ +|
T Consensus 31 ~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~ 110 (188)
T COG2818 31 RLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEF 110 (188)
T ss_pred HHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHc
Confidence 4799999999999999999999999999986 799999999999999999999974 4565666666666443 45
Q ss_pred CC----------------------Cchhh-------HHHHhc--CCCccHHHHHHHHHH
Q psy4002 219 NN----------------------DIPNT-------IELLCK--LPGVGPKMAHLCMNH 246 (378)
Q Consensus 219 ~g----------------------~ip~~-------~e~L~~--LpGVGpktA~~~l~~ 246 (378)
|+ ++|.. ...|.+ ++=|||.|+..+|..
T Consensus 111 Gsf~~flWsf~~~~~~~~~~~~~~~~pa~t~~S~~mskaLKkrGf~fvGpTt~yafmqA 169 (188)
T COG2818 111 GSFSEFLWSFVGGKPSRNQVNDGSEVPASTELSDAMSKALKKRGFKFVGPTTVYAFMQA 169 (188)
T ss_pred CCHHHHHHHhcCCCcccccccchhhccccchhHHHHHHHHHHccCeecCcHHHHHHHHH
Confidence 43 11211 134553 677999999998874
No 28
>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=93.04 E-value=0.4 Score=37.12 Aligned_cols=56 Identities=27% Similarity=0.240 Sum_probs=37.4
Q ss_pred HHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHH-HhcCCCccHHHHHHHHHH
Q psy4002 189 VLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIEL-LCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 189 ~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~-L~~LpGVGpktA~~~l~~ 246 (378)
++.++..-.|=..-|+.....++..|.. +...+... ++ |.+|||||+.+|..+.-|
T Consensus 10 ~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~~i~~~-~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 10 ELADLYELQGGDPFRARAYRRAAAAIKA-LPYPITSG-EEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS-HHSH-HHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCHhHhhH-HHHHhhCCCCCHHHHHHHHHH
Confidence 3334333443333488888888888877 44445433 65 999999999999987644
No 29
>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=92.91 E-value=0.047 Score=52.50 Aligned_cols=53 Identities=21% Similarity=0.294 Sum_probs=38.3
Q ss_pred CccccchHHHHHHHHhCCCCCC-CC---HHHHHHHHHhcCCcccHHHHHHHHHHhcch
Q psy4002 287 PQLCVDVHVHRISHRLGWTKVF-KT---PEDTRKELESWLPESLWSEVNHLLVGFGQQ 340 (378)
Q Consensus 287 ~~~~VD~hv~Ri~~Rlg~~~~~-~~---~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~ 340 (378)
-.+|+|+||.|++.+||++... .+ ..++-+.+.++.| +++-.+..+|-++|..
T Consensus 175 LiiPLDtHv~~var~LGL~~rk~~d~k~A~elT~~lr~~~p-~DPvKYDFAL~~~Gi~ 231 (232)
T PF09674_consen 175 LIIPLDTHVFRVARKLGLLKRKSADWKAARELTEALREFDP-DDPVKYDFALFRLGIN 231 (232)
T ss_pred ccccchHhHHHHHHHcCCccCCCccHHHHHHHHHHHHhcCC-CCCcchhhhcccCCcC
Confidence 3578999999999999999833 22 2334445556666 4578888888888863
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=92.64 E-value=0.17 Score=38.88 Aligned_cols=37 Identities=27% Similarity=0.620 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCCc----hhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 210 ASDILKKNYNNDI----PNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 210 lA~~i~e~y~g~i----p~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
.|+.|.+.|+. + ..+.++|.+++|||+.+|+.+..|-
T Consensus 15 ~ak~L~~~f~s-l~~l~~a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 15 TAKLLAKHFGS-LEALMNASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp HHHHHHHCCSC-HHHHCC--HHHHCTSTT--HHHHHHHHHHH
T ss_pred HHHHHHHHcCC-HHHHHHcCHHHHhccCCcCHHHHHHHHHHH
Confidence 34556666763 3 3578999999999999999988763
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.62 E-value=0.085 Score=33.48 Aligned_cols=20 Identities=40% Similarity=0.679 Sum_probs=17.5
Q ss_pred HHhcCCCccHHHHHHHHHHH
Q psy4002 228 LLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 228 ~L~~LpGVGpktA~~~l~~a 247 (378)
.|.++||||+++|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999998754
No 32
>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=92.48 E-value=0.79 Score=42.58 Aligned_cols=72 Identities=7% Similarity=-0.004 Sum_probs=61.7
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhcccCChH--HHHHHHHHHHHHHHH
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPVGFWK--TKAKHIKMASDILKK 216 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~Gf~~--~KA~~I~~lA~~i~e 216 (378)
..-|+.|+-+++-.-.++..+..-...|++.| ++++.++..+++++++++..-|.-+ .|.+.+..=|+.+++
T Consensus 28 ~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 28 VALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 34799999999999999999999999999986 7999999999999999999888744 455557776777665
No 33
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=92.34 E-value=0.74 Score=43.04 Aligned_cols=72 Identities=7% Similarity=0.002 Sum_probs=62.3
Q ss_pred cChHHHHHHHHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhcccCC--hHHHHHHHHHHHHHHHH
Q psy4002 145 VRRYHVLISLMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPVGF--WKTKAKHIKMASDILKK 216 (378)
Q Consensus 145 ~~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~Gf--~~~KA~~I~~lA~~i~e 216 (378)
..-|+.|+-+.+-.-.++..+..-...|++.| ++++.++..+++++++++..-|. ++.|.+.+..=|+.+.+
T Consensus 29 ~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 29 KKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred HHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 34799999999999999999999999999986 79999999999999999999887 55666677776666554
No 34
>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=91.55 E-value=0.089 Score=50.55 Aligned_cols=53 Identities=25% Similarity=0.248 Sum_probs=37.7
Q ss_pred CccccchHHHHHHHHhCCCCCCC-C---HHHHHHHHHhcCCcccHHHHHHHHHHhcch
Q psy4002 287 PQLCVDVHVHRISHRLGWTKVFK-T---PEDTRKELESWLPESLWSEVNHLLVGFGQQ 340 (378)
Q Consensus 287 ~~~~VD~hv~Ri~~Rlg~~~~~~-~---~~~~~~~le~~lP~~~~~~~~~~Lv~~G~~ 340 (378)
-++|+|+|+.|++.+||++.... + ..++-+.+.++.| +.+-.+..+|.++|+.
T Consensus 172 LiiPLDtH~~rvar~LgL~~Rk~~d~kaa~ElT~~Lr~~dp-~DPvKYDFAL~~lGi~ 228 (229)
T TIGR02757 172 LILPLDTHVFRIAKKLKLLKRKSYDLKAAIEITEALRELNP-EDPIKYDFALFRLGQN 228 (229)
T ss_pred ceeechHhHHHHHHHhCCcccCchhHHHHHHHHHHHHhcCC-CCCcchhhhcccCCcC
Confidence 35789999999999999998322 1 2333445555555 5678888888888863
No 35
>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=88.95 E-value=1 Score=43.87 Aligned_cols=163 Identities=17% Similarity=0.167 Sum_probs=83.5
Q ss_pred hHHH--HHHHHHhccccHHHHHHHHHHHHHhCC--CHHHHhccCHHHHHHhhccc----CChHHHHHHHHHHHHHHHHh-
Q psy4002 147 RYHV--LISLMLSSQTKDEVNHAAMGRLKEHGL--TIENICNTSEDVLGKLIIPV----GFWKTKAKHIKMASDILKKN- 217 (378)
Q Consensus 147 pF~~--Lv~~iLsqqt~~~~~~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~----Gf~~~KA~~I~~lA~~i~e~- 217 (378)
.|.. ++.++.|-|.+.+- +.-|..|.+.|- +++++ .+++.+.+... .+.++|.++|..+...+..-
T Consensus 37 ~~~~Lvi~NaLvSYqLs~kG-Ee~W~~Fs~yfs~~~~~~~----~~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~l~ 111 (246)
T PF09171_consen 37 LFAKLVIANALVSYQLSGKG-EEYWWEFSEYFSKRPIEDI----CEAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLENLS 111 (246)
T ss_dssp HHHHHHHHHHHT-SS-TT-H-HHHHHHHHHHHCTS--SSH----HHHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHTT-
T ss_pred HHHHHHHHHHHHHHhcCCch-HHHHHHHHHHHhcCCchhH----HHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHhh
Confidence 4553 34478888888765 567777766553 22222 24555566543 34678999998887665432
Q ss_pred -------cCCCchhhHHHHhcCCCcc---HHHHH------HHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhh
Q psy4002 218 -------YNNDIPNTIELLCKLPGVG---PKMAH------LCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRK 281 (378)
Q Consensus 218 -------y~g~ip~~~e~L~~LpGVG---pktA~------~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 (378)
| .++...+++|.++=|-. ..++- .....++|.....| ...|
T Consensus 112 l~~~~~~y-~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p---~~Ip------------------- 168 (246)
T PF09171_consen 112 LQDNPLYY-EDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYP---EEIP------------------- 168 (246)
T ss_dssp HHHHHHHH-CTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS--------TTS--------------------
T ss_pred hhhhhhhh-hhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCc---ccCC-------------------
Confidence 3 56677777776543322 22333 33444444322111 1122
Q ss_pred ccccCCccccchHHHHHHHHhCCCCCC-----CCHHHHHHHHHhcCC--cccHHHHHHHHH-HhcchhccC
Q psy4002 282 CEKKIPQLCVDVHVHRISHRLGWTKVF-----KTPEDTRKELESWLP--ESLWSEVNHLLV-GFGQQICKS 344 (378)
Q Consensus 282 ~~~~~~~~~VD~hv~Ri~~Rlg~~~~~-----~~~~~~~~~le~~lP--~~~~~~~~~~Lv-~~G~~iC~~ 344 (378)
+|||.|+.++..+.|+++.. .+.+++........- .-.+-+++..|| -+|+..+..
T Consensus 169 -------IPvD~Rva~~T~~sGi~~~~~~~~~~~~~~v~~~W~~Va~~sgIpplhLDs~lW~l~G~~~~~~ 232 (246)
T PF09171_consen 169 -------IPVDYRVAKLTKRSGIIECEREEMMRTREEVQKAWREVAKESGIPPLHLDSLLWPLLGRARDVK 232 (246)
T ss_dssp -----------HHHHHHHHCTTS-SS-HHHHHCTCCHHHHHHHHHHHHHT--HHHHHHHHHHHHCCHHCCT
T ss_pred -------CCccHHHHHHHHHhccccccHHhhhccHHHHHHHHHHHHhhcCCCchhhhhHHHHhcccchhhh
Confidence 37999999999999998721 222222222221110 113457888999 999987654
No 36
>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=87.33 E-value=1.1 Score=34.46 Aligned_cols=58 Identities=26% Similarity=0.426 Sum_probs=38.6
Q ss_pred HHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 181 NICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 181 ~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+|..++.++|..++..+|. .+|+.|.+--. .+++ + .+.++|.+++|||.++++-++.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R~----~~g~-~-~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYRE----EYGP-F-KTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHHH----HcCC-c-CCHHHHHcCCCCCHHHHHHHHhh
Confidence 5666888888776555555 34444443321 1221 2 37899999999999999988765
No 37
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.33 E-value=1.9 Score=40.57 Aligned_cols=47 Identities=28% Similarity=0.343 Sum_probs=33.9
Q ss_pred cCChHHHHHHHH------HHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 197 VGFWKTKAKHIK------MASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 197 ~Gf~~~KA~~I~------~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
-|-..+.|-.|. +++++|.+ .+.+.|+++||||+|||+-+..---++
T Consensus 78 sGIGPK~ALaILs~~~~~el~~aI~~-------~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 78 DGIGPRAALRVLSGIKYNEFRDAIDR-------EDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred CCcCHHHHHHHHcCCCHHHHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 444444555554 56666666 378999999999999999988766555
No 38
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=85.02 E-value=2 Score=32.24 Aligned_cols=22 Identities=32% Similarity=0.530 Sum_probs=15.9
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+.++|.+++|||+++|+-+...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4567888888888888776643
No 39
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=84.97 E-value=1.2 Score=34.16 Aligned_cols=53 Identities=28% Similarity=0.358 Sum_probs=31.7
Q ss_pred HhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHH
Q psy4002 182 ICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLC 243 (378)
Q Consensus 182 la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~ 243 (378)
|..++.++|..+ -|+....|+.|...-+.. -.|. ++++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL~~l---pgi~~~~A~~Iv~~R~~~-G~f~-----s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQAL---PGIGPKQAKAIVEYREKN-GPFK-----SLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTS---TT--HHHHHHHHHHHHHH--S-S-----SGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHc---CCCCHHHHHHHHHHHHhC-cCCC-----CHHHHhhCCCCCHHHHHHH
Confidence 456777777422 277777888887764432 2233 6889999999999887754
No 40
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=84.46 E-value=1.2 Score=42.01 Aligned_cols=30 Identities=43% Similarity=0.519 Sum_probs=25.3
Q ss_pred CchhhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 221 DIPNTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 221 ~ip~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
.+...++.|.+|||||+|+|.=+..+.+.+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 345678899999999999999988887765
No 41
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.16 E-value=1.5 Score=41.83 Aligned_cols=63 Identities=21% Similarity=0.194 Sum_probs=43.1
Q ss_pred cCHHHHHHhhcccCChHHHHH-HHHHHHHHHHHhcC--CCc----hhhHHHHhcCCCccHHHHHHH-HHHHhcc
Q psy4002 185 TSEDVLGKLIIPVGFWKTKAK-HIKMASDILKKNYN--NDI----PNTIELLCKLPGVGPKMAHLC-MNHAWGI 250 (378)
Q Consensus 185 a~~e~L~~~i~~~Gf~~~KA~-~I~~lA~~i~e~y~--g~i----p~~~e~L~~LpGVGpktA~~~-l~~a~~r 250 (378)
++..||-++|=..|..+ + -...+|+.|.++|+ |.+ ..+.++|++++|||+..|-.+ +.+.+++
T Consensus 14 Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~El~r 84 (218)
T TIGR00608 14 LSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVELAK 84 (218)
T ss_pred CCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHHHHH
Confidence 45666666655566643 3 57889999999983 344 356789999999999655444 4445554
No 42
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.00 E-value=1.4 Score=41.16 Aligned_cols=26 Identities=31% Similarity=0.326 Sum_probs=22.8
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...|+++||||+|||+-+..---++
T Consensus 106 D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 106 DVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 78999999999999999998765555
No 43
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.32 E-value=1.5 Score=40.77 Aligned_cols=26 Identities=31% Similarity=0.461 Sum_probs=22.7
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...|+++||||+|||+-++.---++
T Consensus 106 D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 106 DESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 78999999999999999988765554
No 44
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.09 E-value=1.7 Score=40.90 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=23.1
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
.+.+.|+++||||+|||+-++.---++
T Consensus 106 ~D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 106 EDVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred CCHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 378999999999999999998765555
No 45
>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=81.85 E-value=5.2 Score=44.05 Aligned_cols=78 Identities=24% Similarity=0.390 Sum_probs=49.8
Q ss_pred HHHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHH-------------------------HHh
Q psy4002 165 NHAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDIL-------------------------KKN 217 (378)
Q Consensus 165 ~~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i-------------------------~e~ 217 (378)
..+.+..|.+.+. ++++|..+..++|.++ -||....|..|.+..+.- .+.
T Consensus 441 G~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~ 517 (652)
T TIGR00575 441 GDKVIEQLFEKKLVRSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKH 517 (652)
T ss_pred CHHHHHHHHHcCCcCCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHH
Confidence 3344566777654 8888888888877543 367666777666555432 222
Q ss_pred cCCCch----hhHHHHhcCCCccHHHHHHHHHH
Q psy4002 218 YNNDIP----NTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 218 y~g~ip----~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
|+ ++. .+.++|.+++|||+++|..+..|
T Consensus 518 f~-sl~~l~~As~eeL~~i~GIG~~~A~~I~~f 549 (652)
T TIGR00575 518 FG-TLDKLKAASLEELLSVEGVGPKVAESIVNF 549 (652)
T ss_pred hC-CHHHHHhCCHHHHhcCCCcCHHHHHHHHHH
Confidence 32 221 24567888888888888888776
No 46
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.34 E-value=1.9 Score=40.42 Aligned_cols=26 Identities=27% Similarity=0.438 Sum_probs=22.9
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...|+++||||+|||+-++.---++
T Consensus 106 D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 106 DVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 78999999999999999998766555
No 47
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.23 E-value=1.9 Score=40.41 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 209 MASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 209 ~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+++++|.+ .+...|+++||||+|||+-++.---++
T Consensus 96 ~l~~aI~~-------~D~~~L~kvpGIGkKtAerIilELkdK 130 (197)
T PRK14603 96 LLARALLE-------GDARLLTSASGVGKKLAERIALELKGK 130 (197)
T ss_pred HHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 34455555 378999999999999999988665554
No 48
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=80.88 E-value=2.4 Score=39.39 Aligned_cols=24 Identities=29% Similarity=0.490 Sum_probs=20.7
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
.+.+.|.++||||+++|+.++..-
T Consensus 105 ~d~~~L~~v~Gig~k~A~~I~~~l 128 (192)
T PRK00116 105 GDVKALTKVPGIGKKTAERIVLEL 128 (192)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHH
Confidence 467899999999999999998653
No 49
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=80.72 E-value=2.4 Score=37.59 Aligned_cols=57 Identities=21% Similarity=0.291 Sum_probs=41.4
Q ss_pred CCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 177 LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 177 pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
...=+|..++.+++..+ =|++..+|+.|.. +|.+ .++|+|.++||||+++...+-.+
T Consensus 50 ~~kIdiN~A~~~el~~l---pGigP~~A~~IV~---------nGpf-~sveDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 50 GEKIDLNNSSVRAFRQF---PGMYPTLAGKIVK---------NAPY-DSVEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred CCcccCCccCHHHHHHC---CCCCHHHHHHHHH---------CCCC-CCHHHHHcCCCCCHHHHHHHHHh
Confidence 34446778888888653 4777788888872 2322 37999999999999988776654
No 50
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=80.46 E-value=2 Score=40.58 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=24.9
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhccccc
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGIVTG 253 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r~~~ 253 (378)
.++..|+++||||.|||+-++.---++...
T Consensus 105 ~d~~~L~k~PGIGkKtAerivleLk~K~~~ 134 (201)
T COG0632 105 EDVKALSKIPGIGKKTAERIVLELKGKLAA 134 (201)
T ss_pred cChHhhhcCCCCCHHHHHHHHHHHhhhhhh
Confidence 378899999999999999998876666443
No 51
>PRK00076 recR recombination protein RecR; Reviewed
Probab=79.90 E-value=2.2 Score=40.21 Aligned_cols=29 Identities=45% Similarity=0.558 Sum_probs=24.4
Q ss_pred chhhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 222 IPNTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...++.|.+|||||+|+|.=+..+-+..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~ 34 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQR 34 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 34567889999999999999988887764
No 52
>PRK13844 recombination protein RecR; Provisional
Probab=79.83 E-value=2.1 Score=40.46 Aligned_cols=29 Identities=31% Similarity=0.287 Sum_probs=24.4
Q ss_pred chhhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 222 IPNTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...++.|.+|||||+|+|.=+..+-+..
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 34567889999999999999988887765
No 53
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.79 E-value=8.9 Score=36.92 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=40.5
Q ss_pred cCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCC---CchhhHHHHhcCCCccHHHHHH
Q psy4002 185 TSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNN---DIPNTIELLCKLPGVGPKMAHL 242 (378)
Q Consensus 185 a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g---~ip~~~e~L~~LpGVGpktA~~ 242 (378)
.+..||-+++=..|-. -.....+|+.+..+||+ -...+.++|++++|||+..|--
T Consensus 24 Lsd~ELLailLrtG~~---~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~ 81 (224)
T COG2003 24 LSDAELLAILLRTGTK---GESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQ 81 (224)
T ss_pred cchHHHHHHHHhcCCC---CCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHH
Confidence 3456666666556663 35688999999999986 2356789999999999875543
No 54
>PRK00024 hypothetical protein; Reviewed
Probab=79.74 E-value=2.7 Score=40.18 Aligned_cols=63 Identities=17% Similarity=0.209 Sum_probs=42.7
Q ss_pred ccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCC---chhhHHHHhcCCCccHHHHHHHH-HHHhc
Q psy4002 184 NTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNND---IPNTIELLCKLPGVGPKMAHLCM-NHAWG 249 (378)
Q Consensus 184 ~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~---ip~~~e~L~~LpGVGpktA~~~l-~~a~~ 249 (378)
.++..||-++|=..|..+ +-...+|+.+.++||+- ...+.++|.+++|||+..|-.++ .+.++
T Consensus 23 ~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~ 89 (224)
T PRK00024 23 ALSDAELLAILLRTGTKG---KSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELA 89 (224)
T ss_pred cCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHH
Confidence 345666666654566644 45678899999988751 23467899999999999775544 33444
No 55
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=78.45 E-value=7.3 Score=43.02 Aligned_cols=77 Identities=22% Similarity=0.330 Sum_probs=50.1
Q ss_pred HHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH-------------------------HHHhc
Q psy4002 166 HAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI-------------------------LKKNY 218 (378)
Q Consensus 166 ~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~-------------------------i~e~y 218 (378)
.+.+..|.+.+. ++++|..+..++|..+ -||...++..|.+..+. |...|
T Consensus 455 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f 531 (665)
T PRK07956 455 EKIIEQLFEKGLIHDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHF 531 (665)
T ss_pred HHHHHHHHHcCCCCCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHc
Confidence 344566776653 8889988888777543 37766666665544332 22233
Q ss_pred CCCc----hhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 219 NNDI----PNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 219 ~g~i----p~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+ ++ ..+.++|.+++|||+++|..+..|
T Consensus 532 ~-sl~~l~~As~eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 532 G-SLEALRAASEEELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred C-CHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 2 22 234678999999999999988776
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=78.17 E-value=7.7 Score=36.03 Aligned_cols=20 Identities=40% Similarity=0.712 Sum_probs=17.2
Q ss_pred HHHHhcCCCccHHHHHHHHH
Q psy4002 226 IELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 226 ~e~L~~LpGVGpktA~~~l~ 245 (378)
...|..+|||||++|..++.
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 55788899999999998875
No 57
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=77.75 E-value=2.2 Score=32.60 Aligned_cols=24 Identities=38% Similarity=0.563 Sum_probs=18.8
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
.+.++|.++||||++.|..++.+-
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHH
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHH
Confidence 468999999999999999999873
No 58
>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=77.58 E-value=2 Score=35.94 Aligned_cols=27 Identities=15% Similarity=0.071 Sum_probs=23.2
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhccc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGIV 251 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r~ 251 (378)
.+.+|+.|||||+.+|.-+...++..+
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 578899999999999999988877653
No 59
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.81 E-value=2.2 Score=40.16 Aligned_cols=30 Identities=43% Similarity=0.500 Sum_probs=24.4
Q ss_pred chhhHHHHhcCCCccHHHHHHHHHHHhccc
Q psy4002 222 IPNTIELLCKLPGVGPKMAHLCMNHAWGIV 251 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~~l~~a~~r~ 251 (378)
+...++.|.+|||||+|+|.=+..+-+..+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 345678899999999999998888877643
No 60
>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=76.64 E-value=4.2 Score=40.49 Aligned_cols=48 Identities=31% Similarity=0.483 Sum_probs=33.8
Q ss_pred CChHHHHHHHHHHHHH----HHHhcCCCchhhHHHHhcCCCccHHHHHHHHH
Q psy4002 198 GFWKTKAKHIKMASDI----LKKNYNNDIPNTIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 198 Gf~~~KA~~I~~lA~~----i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~ 245 (378)
|....-|..|.++.+. ..++...+.|..+.+|++++||||++|..+-.
T Consensus 52 giG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~~ 103 (307)
T cd00141 52 GIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYE 103 (307)
T ss_pred CccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHHH
Confidence 4445566677766554 22223345788899999999999999988773
No 61
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=76.07 E-value=6.3 Score=39.75 Aligned_cols=55 Identities=27% Similarity=0.299 Sum_probs=37.7
Q ss_pred HHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 190 LGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 190 L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+.+++.-.|=...|+.+...+|..|.. +..++ .++++|.+|||||+.+|+-+--+
T Consensus 13 la~l~el~gen~~k~~ay~~Aa~~i~~-l~~~i-~~~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 13 LAENYEVFGENKRKCSYFRKAASVLKS-LPFPI-NSMKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHhcccHHHHHHHHHHHHHHHh-CCCCC-CCHHHHhcCCCccHHHHHHHHHH
Confidence 333333345434477778888887765 44444 34578999999999999988865
No 62
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.71 E-value=7.2 Score=36.43 Aligned_cols=27 Identities=30% Similarity=0.394 Sum_probs=21.8
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
.+.+.|+++||||+|||+-++.---++
T Consensus 105 ~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 105 GNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 378899999999999999977654443
No 63
>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=75.50 E-value=5.1 Score=34.57 Aligned_cols=59 Identities=27% Similarity=0.265 Sum_probs=40.8
Q ss_pred HHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 179 IENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 179 ~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+-+|..++.++|..+ - |....+|+.|.+--+. .|.+ .++++|..++|||+++++-+..+
T Consensus 59 ~iniNtA~~~eL~~l-p--GIG~~~A~~Ii~~R~~-----~g~f-~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 59 AVNINAASLEELQAL-P--GIGPAKAKAIIEYREE-----NGAF-KSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhcC-C--CCCHHHHHHHHHHHHh-----cCCc-CCHHHHHcCCCCCHHHHHHHHhc
Confidence 446778888888643 3 4445577766655432 1222 57899999999999999887654
No 64
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=74.92 E-value=14 Score=40.93 Aligned_cols=79 Identities=22% Similarity=0.283 Sum_probs=48.2
Q ss_pred HHHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH-------------------------HHH-H
Q psy4002 165 NHAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD-------------------------ILK-K 216 (378)
Q Consensus 165 ~~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~-------------------------~i~-e 216 (378)
..+.+..|.+.+. ++.+|..+..++|.++ =||...+|..|.+..+ .|. .
T Consensus 445 G~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l---~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~ 521 (669)
T PRK14350 445 SDKTIEFLFEKKFISSEIDLYTFNFDRLINL---KGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINN 521 (669)
T ss_pred CHHHHHHHHHcCCcCCHHHHhhCCHHHHhhc---cCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHH
Confidence 3445667777664 6777777777666443 2565555555544322 222 2
Q ss_pred hcCCCch----------hhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 217 NYNNDIP----------NTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 217 ~y~g~ip----------~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
.|+. +. .+.++|++++|||+.+|..+..|-
T Consensus 522 ~f~~-~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 522 NLNS-FDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred hhCC-HHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHH
Confidence 2321 11 255679999999999999988763
No 65
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=74.55 E-value=11 Score=40.92 Aligned_cols=79 Identities=15% Similarity=0.232 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH----------------------hcCC
Q psy4002 165 NHAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK----------------------NYNN 220 (378)
Q Consensus 165 ~~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e----------------------~y~g 220 (378)
..+.+..|.+.+. ++.+|..+..++|.++ -||...++..|.+..+.-.+ .|+
T Consensus 434 Ge~~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~- 509 (562)
T PRK08097 434 GEGTWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR- 509 (562)
T ss_pred CHHHHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcC-
Confidence 3345666777764 8888988888777543 37777777766555432111 121
Q ss_pred Cc----hhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 221 DI----PNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 221 ~i----p~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
++ ..+.++|.+++|||+.+|+.+..|-
T Consensus 510 ~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f 540 (562)
T PRK08097 510 SWQQLLSRSEQQWQQLPGIGEGRARQLIAFL 540 (562)
T ss_pred CHHHHHcCCHHHHhcCCCchHHHHHHHHHHH
Confidence 12 2356789999999999999998773
No 66
>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=74.35 E-value=10 Score=28.36 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=34.0
Q ss_pred HHHHHHHHh-CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 167 AAMGRLKEH-GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 167 ~~~~~L~~~-~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
....+|.+. +.|+++|+.++.++|.++ -|+...+|+.|...++
T Consensus 16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i---~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 16 KRAEKLYEAGIKTLEDLANADPEELAEI---PGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHHTTCSSHHHHHTSHHHHHHTS---TTSSHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCcHHHHHcCCHHHHhcC---CCCCHHHHHHHHHHHh
Confidence 345667777 679999999999998653 5788889999887765
No 67
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.30 E-value=3.3 Score=38.59 Aligned_cols=25 Identities=20% Similarity=0.230 Sum_probs=21.3
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...| ++||||+|||+-++.---++
T Consensus 106 D~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 106 DKAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CHhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 67889 99999999999998766555
No 68
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=73.15 E-value=5.9 Score=39.94 Aligned_cols=50 Identities=22% Similarity=0.349 Sum_probs=35.3
Q ss_pred CChHHHHHHHHHHHHH-----HHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 198 GFWKTKAKHIKMASDI-----LKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 198 Gf~~~KA~~I~~lA~~-----i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
|....=|..|.++.+. +.+.....+|..+.+|++++||||++|..+-..+
T Consensus 55 gIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~lG 109 (334)
T smart00483 55 GIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKG 109 (334)
T ss_pred CccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHHhC
Confidence 4444456666666543 3344455778899999999999999998876633
No 69
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=72.28 E-value=4.2 Score=36.53 Aligned_cols=55 Identities=25% Similarity=0.315 Sum_probs=38.4
Q ss_pred HHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHH
Q psy4002 181 NICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCM 244 (378)
Q Consensus 181 ~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l 244 (378)
+|..++.++| +.|-.+|- .||..|.+--+ .+| -=.++++|...+|||+++.+-..
T Consensus 90 NiNtAs~eeL-~~lpgIG~--~kA~aIi~yRe----~~G--~f~sv~dL~~v~GiG~~~~ekl~ 144 (149)
T COG1555 90 NINTASAEEL-QALPGIGP--KKAQAIIDYRE----ENG--PFKSVDDLAKVKGIGPKTLEKLK 144 (149)
T ss_pred cccccCHHHH-HHCCCCCH--HHHHHHHHHHH----HcC--CCCcHHHHHhccCCCHHHHHHHH
Confidence 4667888888 55565665 47777766533 233 12479999999999999887654
No 70
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=72.05 E-value=16 Score=40.66 Aligned_cols=77 Identities=19% Similarity=0.328 Sum_probs=48.4
Q ss_pred HHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH-------------------------HHHHhc
Q psy4002 166 HAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD-------------------------ILKKNY 218 (378)
Q Consensus 166 ~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~-------------------------~i~e~y 218 (378)
.+.+..|.+.+. ++.+|..+..++|.++ -||...+|..|.+..+ .|...|
T Consensus 472 ~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F 548 (689)
T PRK14351 472 EERVQQLVDAGLVESLADLYDLTVADLAEL---EGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREF 548 (689)
T ss_pred HHHHHHHHHcCCCCCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHh
Confidence 344566777664 7888888888776443 3666666655544332 233334
Q ss_pred CCCc----hhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 219 NNDI----PNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 219 ~g~i----p~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+ ++ ..+.++|.+++|||+++|..+..|
T Consensus 549 ~-si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 549 G-TFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred C-CHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 3 22 234577888888888888887766
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=71.56 E-value=3.2 Score=37.28 Aligned_cols=24 Identities=38% Similarity=0.596 Sum_probs=21.0
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
.+.++|..|||||++.|..+..+-
T Consensus 94 As~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 94 ASAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred cCHHHHHHCCCCCHHHHHHHHHHH
Confidence 457899999999999999998763
No 72
>PRK00024 hypothetical protein; Reviewed
Probab=71.50 E-value=11 Score=35.91 Aligned_cols=62 Identities=19% Similarity=0.233 Sum_probs=49.7
Q ss_pred HHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH
Q psy4002 149 HVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI 213 (378)
Q Consensus 149 ~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~ 213 (378)
..|++.+|..-++.+.+.....+|.++|.++..+..++.++|.++ . |....||..|..+.+.
T Consensus 27 ~ELLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i-~--GIG~akA~~L~a~~El 88 (224)
T PRK00024 27 AELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSI-K--GIGPAKAAQLKAALEL 88 (224)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhc-c--CccHHHHHHHHHHHHH
Confidence 568888999888888888999999999999999999999999753 4 4445677776555443
No 73
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=71.30 E-value=13 Score=32.21 Aligned_cols=66 Identities=23% Similarity=0.397 Sum_probs=45.7
Q ss_pred HHHHHHhCC-CHHHHhccCHHHHHH--hhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHH
Q psy4002 169 MGRLKEHGL-TIENICNTSEDVLGK--LIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 169 ~~~L~~~~p-t~e~la~a~~e~L~~--~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~ 245 (378)
..+|.+.+. |+++|.+.+.+.+.. +....|...+....+. .+.+|..++|||+..|.+++.
T Consensus 8 ~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~----------------~~AdL~ri~gi~~~~a~LL~~ 71 (122)
T PF14229_consen 8 AAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWV----------------NQADLMRIPGIGPQYAELLEH 71 (122)
T ss_pred HHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHH----------------hHHHhhhcCCCCHHHHHHHHH
Confidence 345666665 899999888777766 6566677543322222 245677889999999999888
Q ss_pred HHhcc
Q psy4002 246 HAWGI 250 (378)
Q Consensus 246 ~a~~r 250 (378)
-++.-
T Consensus 72 AGv~T 76 (122)
T PF14229_consen 72 AGVDT 76 (122)
T ss_pred hCcCc
Confidence 76653
No 74
>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=69.75 E-value=8.3 Score=35.95 Aligned_cols=26 Identities=35% Similarity=0.492 Sum_probs=21.6
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+...|.++||||+|||+-++.---++
T Consensus 105 d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 105 EVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred CHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 67789999999999999998654444
No 75
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=68.40 E-value=4.4 Score=34.94 Aligned_cols=23 Identities=35% Similarity=0.603 Sum_probs=20.6
Q ss_pred hhHHHHhcCCCccHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.+.++|.+|||||++.|..++.+
T Consensus 65 A~~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 65 ASLEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHH
Confidence 45789999999999999999876
No 76
>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=67.39 E-value=5 Score=29.89 Aligned_cols=24 Identities=29% Similarity=0.427 Sum_probs=17.1
Q ss_pred HHHHhcCCCccHHHHHHHHHHHhc
Q psy4002 226 IELLCKLPGVGPKMAHLCMNHAWG 249 (378)
Q Consensus 226 ~e~L~~LpGVGpktA~~~l~~a~~ 249 (378)
+..|+++.|||+.||.-+...++.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--
T ss_pred CcchhhcccccHHHHHHHHHhCCC
Confidence 357899999999999998876654
No 77
>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=66.62 E-value=4.8 Score=32.44 Aligned_cols=27 Identities=33% Similarity=0.631 Sum_probs=21.1
Q ss_pred HHHhcCCCccHHHHHHHHHHHhcccccc
Q psy4002 227 ELLCKLPGVGPKMAHLCMNHAWGIVTGI 254 (378)
Q Consensus 227 e~L~~LpGVGpktA~~~l~~a~~r~~~i 254 (378)
+.|+++||||+-+|..++... +.+..|
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF 28 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRF 28 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhc
Confidence 468899999999999998876 554434
No 78
>PRK14973 DNA topoisomerase I; Provisional
Probab=65.61 E-value=17 Score=41.77 Aligned_cols=83 Identities=14% Similarity=0.145 Sum_probs=53.0
Q ss_pred HHHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH-HHHHhc-----CCCchhhHHHHhcCCCccH
Q psy4002 165 NHAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD-ILKKNY-----NNDIPNTIELLCKLPGVGP 237 (378)
Q Consensus 165 ~~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~-~i~e~y-----~g~ip~~~e~L~~LpGVGp 237 (378)
.+....+++++|+ ++++++.+++++|. ...|+...-+..+...|. .+...- .........+|.+++|||+
T Consensus 811 ~~~~~~~~~~~G~~~~~d~~~a~p~~La---~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge 887 (936)
T PRK14973 811 PAVSLKKYQEAGFDTPEDFCSVHPAYLA---LKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGE 887 (936)
T ss_pred CHHHHHHHHHhcCCCHHHHHhcCHHHHh---cCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCH
Confidence 3444556666665 89999999999996 457888766666644444 322210 0111223456999999999
Q ss_pred HHHHHHHHHHhcc
Q psy4002 238 KMAHLCMNHAWGI 250 (378)
Q Consensus 238 ktA~~~l~~a~~r 250 (378)
+|++..-.-+.-.
T Consensus 888 ~t~~~l~~ag~~~ 900 (936)
T PRK14973 888 TTLEKLYLAGVYD 900 (936)
T ss_pred HHHHHHHHcCCCC
Confidence 9997765544433
No 79
>PRK07945 hypothetical protein; Provisional
Probab=65.44 E-value=12 Score=37.80 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=37.2
Q ss_pred HHHHhhcccCChHHHHHHHHHHHHHHHHhcCCC-chhhHH--HHhcCCCccHHHHHHHHHHH
Q psy4002 189 VLGKLIIPVGFWKTKAKHIKMASDILKKNYNND-IPNTIE--LLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 189 ~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~-ip~~~e--~L~~LpGVGpktA~~~l~~a 247 (378)
++..++.-.|-..=|++..+.+|+.|.. .+-+ +.+..+ .|.+|||||..+|..+.-+.
T Consensus 9 ~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~ 69 (335)
T PRK07945 9 RIAFLLERARADTYRVRAFRRAADVVEA-LDAAERARRARAGSLTSLPGIGPKTAKVIAQAL 69 (335)
T ss_pred HHHHHHHHcCCChhhHHHHHHHHHHHHh-cChhHHHHHHhcCCcccCCCcCHHHHHHHHHHH
Confidence 3344444444333377778888888865 3333 322222 68899999999999888764
No 80
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.04 E-value=19 Score=34.39 Aligned_cols=61 Identities=18% Similarity=0.193 Sum_probs=49.0
Q ss_pred HHHHHHHHhccccHH-HHHHHHHHHHHhC---CCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 149 HVLISLMLSSQTKDE-VNHAAMGRLKEHG---LTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 149 ~~Lv~~iLsqqt~~~-~~~~~~~~L~~~~---pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
..|++.+|..-++.+ .+.....+|.++| .+...|..++.++|.++ . |....||..|..+.+
T Consensus 17 ~ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i-~--GiG~aka~~l~a~~E 81 (218)
T TIGR00608 17 YELLAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSV-P--GIGEAKAIQLKAAVE 81 (218)
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhC-c--CCcHHHHHHHHHHHH
Confidence 568888999888888 8888889999998 89999999999999753 4 454567877765543
No 81
>PRK08609 hypothetical protein; Provisional
Probab=64.71 E-value=12 Score=40.52 Aligned_cols=47 Identities=26% Similarity=0.372 Sum_probs=28.5
Q ss_pred CChHHHHHHHHHHHHH----HHHhcCCCchhhHHHHhcCCCccHHHHHHHH
Q psy4002 198 GFWKTKAKHIKMASDI----LKKNYNNDIPNTIELLCKLPGVGPKMAHLCM 244 (378)
Q Consensus 198 Gf~~~KA~~I~~lA~~----i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l 244 (378)
|....=|..|.++.+. ..++...++|..+.+|+++|||||++|..+-
T Consensus 55 gIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 55 GIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred CcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHH
Confidence 3433445556655543 1222233567778888899999998876653
No 82
>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=64.59 E-value=30 Score=24.31 Aligned_cols=43 Identities=26% Similarity=0.281 Sum_probs=34.0
Q ss_pred HHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH
Q psy4002 168 AMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI 213 (378)
Q Consensus 168 ~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~ 213 (378)
...+|.+.+. |.++++.++.++|.++ .|+...++..|+..++.
T Consensus 5 ~~~~L~~~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 5 IAQLLVEEGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred HHHHHHHcCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 4556777665 9999999999999754 67888888888887764
No 83
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=63.09 E-value=19 Score=36.86 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=38.3
Q ss_pred HHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH
Q psy4002 167 AAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK 216 (378)
Q Consensus 167 ~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e 216 (378)
....+|.++|.+.+.|.+++.++|.++ . |....||+.|++.++.+.+
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~V-e--GIGe~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEV-E--GIGEVRARAIREGLSRLAE 344 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhC-C--CcCHHHHHHHHHHHHHHHH
Confidence 456778899999999999999999655 4 4446788889999888776
No 84
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=62.84 E-value=5.6 Score=35.28 Aligned_cols=23 Identities=17% Similarity=0.460 Sum_probs=20.3
Q ss_pred hhHHHHhcCCCccHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.+.++|.+||||||..|..+...
T Consensus 58 A~~~el~~lpGigP~~A~~IV~n 80 (132)
T PRK02515 58 SSVRAFRQFPGMYPTLAGKIVKN 80 (132)
T ss_pred cCHHHHHHCCCCCHHHHHHHHHC
Confidence 46789999999999999999953
No 85
>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=62.81 E-value=16 Score=36.41 Aligned_cols=43 Identities=26% Similarity=0.386 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 203 KAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 203 KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
|++..+.+|..|.. +.-++ .+.+++.+|||||+++|+.+--+.
T Consensus 23 r~~aY~~Aa~~l~~-l~~~i-~~~~~~~~ipgiG~~ia~kI~E~~ 65 (307)
T cd00141 23 RVRAYRKAARALES-LPEPI-ESLEEAKKLPGIGKKIAEKIEEIL 65 (307)
T ss_pred hHHHHHHHHHHHHh-CCccc-CCHHHhcCCCCccHHHHHHHHHHH
Confidence 67777888888765 33333 346788999999999999988663
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=61.94 E-value=6.5 Score=26.23 Aligned_cols=15 Identities=33% Similarity=0.412 Sum_probs=11.9
Q ss_pred HhcCCCccHHHHHHH
Q psy4002 229 LCKLPGVGPKMAHLC 243 (378)
Q Consensus 229 L~~LpGVGpktA~~~ 243 (378)
+.+++|||++|+.-+
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 668999999999874
No 87
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=59.58 E-value=22 Score=34.30 Aligned_cols=62 Identities=23% Similarity=0.282 Sum_probs=51.2
Q ss_pred HHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH
Q psy4002 149 HVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI 213 (378)
Q Consensus 149 ~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~ 213 (378)
..|++.+|..-++.+.+...-..|..+|.+...|..++.++|... .++|. .||-.|+.+.+.
T Consensus 27 ~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v-~GiG~--aka~~l~a~~El 88 (224)
T COG2003 27 AELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSV-KGIGL--AKAIQIKAAIEL 88 (224)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhC-CCccH--HHHHHHHHHHHH
Confidence 568999999999999999999999999999999999999999654 55664 466666655443
No 88
>PF10343 DUF2419: Protein of unknown function (DUF2419); InterPro: IPR019438 This entry contains proteins that have no known function.
Probab=57.00 E-value=41 Score=33.60 Aligned_cols=54 Identities=9% Similarity=0.187 Sum_probs=43.8
Q ss_pred HHHHHhCC--CHHHHhccCHHHHHHhhccc-----CChHHHHHHHHHHHHHHHHhcCCCch
Q psy4002 170 GRLKEHGL--TIENICNTSEDVLGKLIIPV-----GFWKTKAKHIKMASDILKKNYNNDIP 223 (378)
Q Consensus 170 ~~L~~~~p--t~e~la~a~~e~L~~~i~~~-----Gf~~~KA~~I~~lA~~i~e~y~g~ip 223 (378)
+.|.+..| +|+-+++++.++|..++++- -+-..|++.|+++.+.+.++|+|++-
T Consensus 57 rAl~~~~pi~~~~~~~~~t~~~l~~if~s~~~~~iPll~eR~~~L~E~G~vL~~~f~gs~~ 117 (287)
T PF10343_consen 57 RALDEGIPITDPKYYAKMTDEELRHIFRSDTEEEIPLLEERARLLREVGRVLLEKFDGSFA 117 (287)
T ss_pred HHHhcCCCCcCHHHHHhCCHHHHHHHhcCCCCCcCCCHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 34444444 89999999999999999864 24567999999999999999999753
No 89
>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=56.68 E-value=9.1 Score=35.68 Aligned_cols=21 Identities=38% Similarity=0.591 Sum_probs=18.0
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
.+..|.+++||||++|-.+|.
T Consensus 70 lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 70 LFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHhCCCCCCHHHHHHHHh
Confidence 467899999999999988865
No 90
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=56.66 E-value=17 Score=36.80 Aligned_cols=26 Identities=31% Similarity=0.361 Sum_probs=22.8
Q ss_pred chhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 222 IPNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
-|.++++|+.++||||.|...+.+.+
T Consensus 264 ~p~~feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 264 QPSDFEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred CccCHHHHHhcCCCCHHHHHHHHHHH
Confidence 47899999999999999998877764
No 91
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.47 E-value=9.5 Score=35.65 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=19.2
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.++.|.+++||||++|-.+|..
T Consensus 71 lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 71 LFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHhCCCCCCHHHHHHHHHh
Confidence 4678999999999999999873
No 92
>KOG2534|consensus
Probab=56.45 E-value=21 Score=36.29 Aligned_cols=43 Identities=33% Similarity=0.432 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 203 KAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 203 KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
|+.....+|..|.. |.-.| .+.+++.+|||||+++|..+--+.
T Consensus 34 r~~~y~~Aasvlk~-~p~~I-~S~~ea~~lP~iG~kia~ki~Eil 76 (353)
T KOG2534|consen 34 RARAYRRAASVLKS-LPFPI-TSGEEAEKLPGIGPKIAEKIQEIL 76 (353)
T ss_pred HHHHHHHHHHHHHh-CCCCc-ccHHHhcCCCCCCHHHHHHHHHHH
Confidence 66666666666654 32222 468999999999999999887663
No 93
>KOG2841|consensus
Probab=55.89 E-value=18 Score=35.30 Aligned_cols=34 Identities=26% Similarity=0.229 Sum_probs=17.9
Q ss_pred hCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHH
Q psy4002 175 HGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMAS 211 (378)
Q Consensus 175 ~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA 211 (378)
.|+|.+.+..+|+++|+.+ .|+..+||++|+...
T Consensus 214 ~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l 247 (254)
T KOG2841|consen 214 KFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFL 247 (254)
T ss_pred hcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHH
Confidence 4555555555555555433 344445555555443
No 94
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=55.43 E-value=11 Score=41.64 Aligned_cols=80 Identities=24% Similarity=0.400 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHhCC--CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH-------------------------HHH
Q psy4002 164 VNHAAMGRLKEHGL--TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI-------------------------LKK 216 (378)
Q Consensus 164 ~~~~~~~~L~~~~p--t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~-------------------------i~e 216 (378)
...+.+..|+++.. ++.+|..+..++|..+ -||...+|..|.+.-+. +..
T Consensus 453 LG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l---~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~ 529 (667)
T COG0272 453 LGEKIIEQLFEKGLIKDIADLYTLTEEDLLSL---EGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLAR 529 (667)
T ss_pred cCHHHHHHHHHcCccCCHHHHHhCCHHHHhhc---cchhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHH
Confidence 34556667777653 7777777777776543 23334455544443322 122
Q ss_pred hcCC---CchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 217 NYNN---DIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 217 ~y~g---~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.|+. -...+.++|.+++|||..+|..+..|
T Consensus 530 ~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 530 HFGTLEALLAASEEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HhhhHHHHHhcCHHHHhhccchhHHHHHHHHHH
Confidence 2221 11345689999999999999998876
No 95
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=55.08 E-value=26 Score=28.62 Aligned_cols=54 Identities=22% Similarity=0.210 Sum_probs=33.7
Q ss_pred CHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHH----Hhc-CCCccHHHHHHHHHH
Q psy4002 186 SEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIEL----LCK-LPGVGPKMAHLCMNH 246 (378)
Q Consensus 186 ~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~----L~~-LpGVGpktA~~~l~~ 246 (378)
+..++...|...|++...| ..|.+.||.+.-+.+++ |+. +.|||-++||-+...
T Consensus 7 ~~~~~~~~L~~~gl~~~~a-------~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLA-------MKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp --HHHHHHHHHTT--HHHH-------HHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHH-------HHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH
Confidence 3455666778899976444 44455577654444543 665 999999999998874
No 96
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=53.35 E-value=11 Score=25.99 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=13.8
Q ss_pred HhcCCCccHHHHHHHHH
Q psy4002 229 LCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 229 L~~LpGVGpktA~~~l~ 245 (378)
+-.+||||+++|--++.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 45789999999987664
No 97
>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=51.89 E-value=33 Score=27.89 Aligned_cols=51 Identities=16% Similarity=0.314 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH
Q psy4002 165 NHAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK 216 (378)
Q Consensus 165 ~~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e 216 (378)
-...|..|.+.+. +.+.|+.+.++|+.+++.-+|+.. |--+++++-+++.+
T Consensus 21 Ll~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~s-KPLHVrRlqKAL~e 72 (82)
T PF04904_consen 21 LLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMAS-KPLHVRRLQKALQE 72 (82)
T ss_pred HHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccC-ccHHHHHHHHHHHH
Confidence 3456777888765 899999999999999999999975 77788888777766
No 98
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=51.83 E-value=25 Score=35.64 Aligned_cols=44 Identities=25% Similarity=0.380 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHhcCCCchhhHHH--HhcCCCccHHHHHHHHHHH
Q psy4002 203 KAKHIKMASDILKKNYNNDIPNTIEL--LCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 203 KA~~I~~lA~~i~e~y~g~ip~~~e~--L~~LpGVGpktA~~~l~~a 247 (378)
|+..-+.+|+.|.. -+-+++...+. ++.|||||+.+|+.+.-+.
T Consensus 28 k~~aYr~Aa~sle~-~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 28 KIRAYRKAAQSLEN-LTEDLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred chHHHHHHHHhhhh-cccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 66667777777654 34567777777 9999999999999987663
No 99
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=51.58 E-value=15 Score=37.64 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=29.7
Q ss_pred HHHHHHHHHhcCC---CchhhHHHHhcCCCccHHHHHHHHH
Q psy4002 208 KMASDILKKNYNN---DIPNTIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 208 ~~lA~~i~e~y~g---~ip~~~e~L~~LpGVGpktA~~~l~ 245 (378)
+.+|+.+.++||+ -+..+.++|.+++|||++.|..+..
T Consensus 297 k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 297 SAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred HHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHH
Confidence 3578889999984 1245678999999999999988543
No 100
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=51.20 E-value=1.1e+02 Score=30.26 Aligned_cols=125 Identities=19% Similarity=0.242 Sum_probs=73.1
Q ss_pred hHHHHHH--HHHhccccHHHHHHHHHHHHHhC--CCHHHHhccCHHHHHHhhccc----CChHHHHHHHHHHHHHHHHh-
Q psy4002 147 RYHVLIS--LMLSSQTKDEVNHAAMGRLKEHG--LTIENICNTSEDVLGKLIIPV----GFWKTKAKHIKMASDILKKN- 217 (378)
Q Consensus 147 pF~~Lv~--~iLsqqt~~~~~~~~~~~L~~~~--pt~e~la~a~~e~L~~~i~~~----Gf~~~KA~~I~~lA~~i~e~- 217 (378)
.|..|+- +|.|-|.+.+-= .-|..|.+.| .+++++. +++...+... .+..+|.++|..++..+-+-
T Consensus 47 ~~~~Lvi~NaLvSYqLsgkGE-e~W~eFs~yf~~~~~~~~~----~~~~~Fl~~s~~nrrl~e~KikRi~r~~~fl~~L~ 121 (269)
T PRK13280 47 LFAKLVIANALVSYQLSGKGE-EWWWEFSKYFSEKGVEDIV----EAYIEFLKNSKGNRRLLEQKIKRIEKVEPFLESLT 121 (269)
T ss_pred HHHHHHHHHHHHHHhcCCcHH-HHHHHHHHHhcccCchhHH----HHHHHHHhcCchhHHHHHHHHHHHHHHHHHhhhhc
Confidence 3555444 788888876533 3676676665 3455554 3444444444 23457888888876543321
Q ss_pred -------cCCCchhhHHHHhcCCC---------ccHHHHHHHHHHHhccccccCCCCCCCCCCCcchhhhhhhhhHHhhh
Q psy4002 218 -------YNNDIPNTIELLCKLPG---------VGPKMAHLCMNHAWGIVTGIGKDESRQPILSPSSRQISRSELICVRK 281 (378)
Q Consensus 218 -------y~g~ip~~~e~L~~LpG---------VGpktA~~~l~~a~~r~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 (378)
| .++...++.|..+=| .--||+......+++...+.| ...||
T Consensus 122 l~~~~~~y-~~l~~l~~~La~~L~s~~~~KTiVFAvKM~~Ya~r~~~~~~~p~p---~~IpI------------------ 179 (269)
T PRK13280 122 LLDLPLYY-EDLEELLEQLAKILGAKKESKTVVFAVKMFGYACRAAFGEFRPYP---MEIPI------------------ 179 (269)
T ss_pred cchhhhhH-hhHHHHHHHHHHHhCCCCCcceeeeHHHHHHHHHHHhccccCCCC---cCCCC------------------
Confidence 2 344555555554433 223456666665665544443 22333
Q ss_pred ccccCCccccchHHHHHHHHhCCCC
Q psy4002 282 CEKKIPQLCVDVHVHRISHRLGWTK 306 (378)
Q Consensus 282 ~~~~~~~~~VD~hv~Ri~~Rlg~~~ 306 (378)
|||.-|..+....|+++
T Consensus 180 --------PvD~Ria~~T~~sglv~ 196 (269)
T PRK13280 180 --------PVDYRIAKLTKCSGLVE 196 (269)
T ss_pred --------cccHHHHHHHHHhcccc
Confidence 79999999999999987
No 101
>PRK08609 hypothetical protein; Provisional
Probab=49.08 E-value=29 Score=37.56 Aligned_cols=56 Identities=18% Similarity=0.235 Sum_probs=36.7
Q ss_pred HHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchhhHHHHhcCCCccHHHHHHHHHH
Q psy4002 189 VLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPNTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 189 ~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
++..++.-.|=..=|++.-+.+|+.|... ..++. ++.+|.+|||||..+|..+--+
T Consensus 12 ~~A~~le~~g~n~fr~~aYr~Aa~~i~~l-~~~i~-~~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 12 TIATYMELKGENPFKISAFRKAAQALELD-ERSLS-EIDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHhcCCCcHHHHHHHHHHHHHHhC-chhhh-hhhhhccCCCcCHHHHHHHHHH
Confidence 33444444442222777778888877663 33343 4568999999999999988765
No 102
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=48.26 E-value=41 Score=25.57 Aligned_cols=43 Identities=21% Similarity=0.130 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMAS 211 (378)
Q Consensus 166 ~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA 211 (378)
...-..|.++|.|+++|.+++.++|..+ . |+....|..|.+.-
T Consensus 13 ~~~ak~L~~~f~sl~~l~~a~~e~L~~i-~--gIG~~~A~si~~ff 55 (64)
T PF12826_consen 13 EKTAKLLAKHFGSLEALMNASVEELSAI-P--GIGPKIAQSIYEFF 55 (64)
T ss_dssp HHHHHHHHHCCSCHHHHCC--HHHHCTS-T--T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHcCHHHHhcc-C--CcCHHHHHHHHHHH
Confidence 3455678899999999999999998533 3 55566776666543
No 103
>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=47.50 E-value=18 Score=27.68 Aligned_cols=22 Identities=36% Similarity=0.389 Sum_probs=19.3
Q ss_pred hHHHHhc-CCCccHHHHHHHHHH
Q psy4002 225 TIELLCK-LPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~-LpGVGpktA~~~l~~ 246 (378)
..++|.. +||||+..|..++.+
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHH
Confidence 4678888 999999999999876
No 104
>PRK14973 DNA topoisomerase I; Provisional
Probab=45.15 E-value=60 Score=37.50 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=36.5
Q ss_pred HHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILK 215 (378)
Q Consensus 166 ~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~ 215 (378)
..++..|...+. ++++|+.+++..| +..|++..++..+.+-|+-++
T Consensus 754 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~sE~~~~~~~~~a~~~~ 800 (936)
T PRK14973 754 AKIMKALISSGINDIAALARADPADL----KKAGLSEAEAASLLAEAKSLC 800 (936)
T ss_pred HHHHHHHHhcCcchHHHHhhCCHHHH----HHcCCCHHHHHHHHHHHHHHH
Confidence 445666666665 8999999999988 578999999999998886554
No 105
>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=45.04 E-value=12 Score=29.56 Aligned_cols=24 Identities=29% Similarity=0.613 Sum_probs=18.3
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWG 249 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~ 249 (378)
+-+.+-.+||||+++|.-++.- |+
T Consensus 20 ~~D~i~gv~giG~k~A~~ll~~-~~ 43 (75)
T cd00080 20 KSDNIPGVPGIGPKTALKLLKE-YG 43 (75)
T ss_pred ccccCCCCCcccHHHHHHHHHH-hC
Confidence 3455668999999999988854 44
No 106
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=42.82 E-value=1e+02 Score=34.32 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=15.1
Q ss_pred cCCCccHHHHHHHHHHHhcccc
Q psy4002 231 KLPGVGPKMAHLCMNHAWGIVT 252 (378)
Q Consensus 231 ~LpGVGpktA~~~l~~a~~r~~ 252 (378)
.|+.||..+|..+.. .|+-.+
T Consensus 515 GIr~VG~~~Ak~La~-~f~sl~ 535 (667)
T COG0272 515 GIRHVGETTAKSLAR-HFGTLE 535 (667)
T ss_pred CCchhhHHHHHHHHH-HhhhHH
Confidence 578899988888776 555433
No 107
>PRK01172 ski2-like helicase; Provisional
Probab=42.54 E-value=57 Score=35.70 Aligned_cols=37 Identities=24% Similarity=0.323 Sum_probs=24.8
Q ss_pred CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHh
Q psy4002 178 TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKN 217 (378)
Q Consensus 178 t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~ 217 (378)
|+++|+.++.+++.++ +|+..+.|+.|..-|+.+.+-
T Consensus 635 ~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~~ 671 (674)
T PRK01172 635 TVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISSM 671 (674)
T ss_pred CHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHHH
Confidence 6777777777777554 366666777777776666654
No 108
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.28 E-value=48 Score=32.19 Aligned_cols=22 Identities=18% Similarity=0.261 Sum_probs=11.3
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+.++|.+++|||.++|.-+..+
T Consensus 34 S~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 34 DQSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred CHHHHHHccCCCHHHHHHHHHH
Confidence 3445555555555555555443
No 109
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.58 E-value=21 Score=33.25 Aligned_cols=22 Identities=27% Similarity=0.410 Sum_probs=19.0
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.++.|+++.||||++|=.+|..
T Consensus 71 lF~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 71 CLRMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHHHhCcCCcCHHHHHHHHcc
Confidence 4677999999999999998873
No 110
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.64 E-value=23 Score=33.43 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=18.5
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
.++.|+++.||||++|=.+|.
T Consensus 70 lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 70 VFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHhCcCCcCHHHHHHHHc
Confidence 467899999999999998885
No 111
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.41 E-value=23 Score=32.98 Aligned_cols=21 Identities=29% Similarity=0.478 Sum_probs=18.5
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
.++.|+++.||||++|=.+|.
T Consensus 71 lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 71 MFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHhccCCccHHHHHHHHc
Confidence 467899999999999998885
No 112
>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=39.05 E-value=1.3e+02 Score=26.53 Aligned_cols=39 Identities=18% Similarity=0.297 Sum_probs=32.3
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhCCCHHHHhc
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGLTIENICN 184 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~pt~e~la~ 184 (378)
.-|..|+..+-...++.+.+..++..+.+..-+++++.+
T Consensus 42 ~~l~~li~lv~~g~It~~~ak~vl~~~~~~~~~~~~ii~ 80 (147)
T smart00845 42 EHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVE 80 (147)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCHHHHHH
Confidence 369999999999999999999999999877666665543
No 113
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=37.49 E-value=69 Score=31.49 Aligned_cols=48 Identities=25% Similarity=0.162 Sum_probs=31.0
Q ss_pred HHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHh
Q psy4002 167 AAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKN 217 (378)
Q Consensus 167 ~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~ 217 (378)
...++|+++|.|.+++..+++++|..+ -|-...||..|+..-+...+.
T Consensus 193 ~~a~~ll~~fgS~~~~~tas~~eL~~v---~gig~k~A~~I~~~~~t~~~~ 240 (254)
T COG1948 193 KLAERLLKKFGSVEDVLTASEEELMKV---KGIGEKKAREIYRFLRTEYKL 240 (254)
T ss_pred HHHHHHHHHhcCHHHHhhcCHHHHHHh---cCccHHHHHHHHHHHhchhhh
Confidence 345667777777777777777776544 344445777777776665553
No 114
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.08 E-value=28 Score=32.49 Aligned_cols=21 Identities=29% Similarity=0.351 Sum_probs=18.3
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
.++.|+++.||||++|=.+|.
T Consensus 71 lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 71 LFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHhccCCccHHHHHHHHc
Confidence 457799999999999998885
No 115
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.94 E-value=28 Score=32.74 Aligned_cols=22 Identities=27% Similarity=0.360 Sum_probs=19.0
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.++.|.++.||||++|=.+|..
T Consensus 72 lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 72 TFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHhCCCCcCHHHHHHHHhh
Confidence 4677899999999999998874
No 116
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.86 E-value=27 Score=32.74 Aligned_cols=22 Identities=41% Similarity=0.569 Sum_probs=19.0
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.++.|+++.||||++|=.+|..
T Consensus 71 lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 71 LFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHhCcCCcCHHHHHHHHcC
Confidence 4678999999999999998873
No 117
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.71 E-value=28 Score=32.70 Aligned_cols=21 Identities=43% Similarity=0.676 Sum_probs=18.5
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
.++.|+++.||||++|=.+|.
T Consensus 70 lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 70 LFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHhCcCCcCHHHHHHHHc
Confidence 457799999999999999887
No 118
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=34.33 E-value=49 Score=25.13 Aligned_cols=46 Identities=33% Similarity=0.395 Sum_probs=34.4
Q ss_pred ccccCCcceeeeccccCCccceeeeeEEecccchhhhhhhhhcccccc
Q psy4002 3 RRSMKNKTLTVPVDTTKNGKQKRMHMVVKYDEPKFQQTRCQLEKNIAL 50 (378)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (378)
||...=.+|+|-. |.++...||-++|.-++....|.-+|++|=+.+
T Consensus 15 rRg~nI~sl~v~~--~~~~~~~riti~v~~~~~~i~~l~~Ql~KlidV 60 (63)
T PF13710_consen 15 RRGFNIESLSVGP--TEDPGISRITIVVSGDDREIEQLVKQLEKLIDV 60 (63)
T ss_dssp TTT-EECEEEEEE---SSTTEEEEEEEEES-CCHHHHHHHHHHCSTTE
T ss_pred cCCeEEeeEEeee--cCCCCEEEEEEEEeeCchhHHHHHHHHhccCCe
Confidence 4444455666655 788889999999999999999999999986654
No 119
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=33.22 E-value=1.4e+02 Score=30.49 Aligned_cols=29 Identities=34% Similarity=0.704 Sum_probs=21.7
Q ss_pred CCchhhHHHHhcCCCccH-HHHHHHHHHHh
Q psy4002 220 NDIPNTIELLCKLPGVGP-KMAHLCMNHAW 248 (378)
Q Consensus 220 g~ip~~~e~L~~LpGVGp-ktA~~~l~~a~ 248 (378)
+.+|..+..|+++||+|| +++.++..++.
T Consensus 86 ~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi 115 (326)
T COG1796 86 KEVPEGLEPLLKVPGLGPKKIVSLYKELGI 115 (326)
T ss_pred HhCCcchHHHhhCCCCCcHHHHHHHHHHCc
Confidence 456777888888899988 57777766643
No 120
>PRK00254 ski2-like helicase; Provisional
Probab=32.45 E-value=99 Score=34.25 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=15.6
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
+.++|.+++|||+++|..+..+
T Consensus 676 ~~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 676 KPSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4567777777777777777654
No 121
>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=31.47 E-value=1e+02 Score=30.76 Aligned_cols=48 Identities=27% Similarity=0.371 Sum_probs=39.8
Q ss_pred HHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK 216 (378)
Q Consensus 166 ~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e 216 (378)
.....+|.+++. |.++++.++.++|.+ ..|++..+|..|++.+..+..
T Consensus 11 ~~~~~~L~~~g~~t~~~~~~~~~~~L~~---~~gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 11 AADIKKLKSAGICTVNGVIMTTRRALCK---IKGLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred HHHHHHHHHcCCCcHHHHHhCCHHHHHH---hcCCCHHHHHHHHHHHHhhhc
Confidence 345678888865 999999999999964 479999999999998888755
No 122
>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=30.86 E-value=97 Score=34.63 Aligned_cols=62 Identities=15% Similarity=0.099 Sum_probs=42.0
Q ss_pred HHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHHhcCCCchh----hHHHHhcCCCccHHHHHHHHH
Q psy4002 180 ENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKKNYNNDIPN----TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 180 e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e~y~g~ip~----~~e~L~~LpGVGpktA~~~l~ 245 (378)
+.+.-.+.+.+...|.+.-|.. .=...|+.|.+.||.+.-+ ..+.|..+||||++.++.+..
T Consensus 70 ~~~~p~~~~~i~~yL~s~~~~G----IG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 70 ELEAPTSKEGIVAYLSSRSIKG----VGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred EEeCCCCHHHHHHHHhcCCCCC----cCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 3344457888888886543432 1123466777889877533 346799999999999998775
No 123
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=30.23 E-value=2.2e+02 Score=29.41 Aligned_cols=48 Identities=15% Similarity=0.137 Sum_probs=42.3
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhCC-CHHHHhccCHHHHHHh
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGL-TIENICNTSEDVLGKL 193 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~p-t~e~la~a~~e~L~~~ 193 (378)
-|.+.+++.-|..-+..+.+..+|++|.+.|. .++.|..++.|+|..+
T Consensus 304 iPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi~vLi~a~~e~La~V 352 (403)
T COG1379 304 IPLAEIISMALGKGITTKAVKRTWERLVRAFGTEIDVLIDAPIEELARV 352 (403)
T ss_pred ccHHHHHHHHhccceechhHHHHHHHHHHHhcchhhhHhcCCHHHHhhh
Confidence 48889999888999999999999999999997 5888999999998544
No 124
>PTZ00035 Rad51 protein; Provisional
Probab=29.37 E-value=1.1e+02 Score=30.77 Aligned_cols=48 Identities=29% Similarity=0.394 Sum_probs=39.9
Q ss_pred HHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK 216 (378)
Q Consensus 166 ~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e 216 (378)
.....+|.+++. |.++++.++..+|.+ ..|++..+|.-|...|+.+..
T Consensus 33 ~~~~~kL~~~g~~t~~~~~~~~~~~L~~---~~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 33 AADIKKLKEAGICTVESVAYATKKDLCN---IKGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred HHHHHHHHHcCCCcHHHHHhCCHHHHHH---hhCCCHHHHHHHHHHHHHhcc
Confidence 345677888865 999999999999964 479999999999999888764
No 125
>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=28.98 E-value=48 Score=27.91 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=18.9
Q ss_pred HHHHhcCCCccHHHHHHHHHHH
Q psy4002 226 IELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 226 ~e~L~~LpGVGpktA~~~l~~a 247 (378)
.-.|.++.|||+.+|..++...
T Consensus 14 ~~aLt~IyGIG~~~A~~Ic~~l 35 (107)
T PF00416_consen 14 YIALTKIYGIGRRKAKQICKKL 35 (107)
T ss_dssp HHHHTTSTTBCHHHHHHHHHHT
T ss_pred HhHHhhhhccCHHHHHHHHHHc
Confidence 5679999999999999988653
No 126
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=28.81 E-value=61 Score=25.95 Aligned_cols=45 Identities=13% Similarity=0.272 Sum_probs=32.8
Q ss_pred ccccCCcceeeeccccCCccceeeeeEEecccchhhhhhhhhcccccc
Q psy4002 3 RRSMKNKTLTVPVDTTKNGKQKRMHMVVKYDEPKFQQTRCQLEKNIAL 50 (378)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (378)
||...=..|++ ..|.++..-||-+||. ++-.+.|.-+|++|=+-+
T Consensus 26 rRGfnI~sl~v--~~t~~~~~sriti~v~-~~~~i~ql~kQL~KL~dV 70 (76)
T PRK11152 26 HRGFQVCSMNM--TQNTDAQNINIELTVA-SERPIDLLSSQLNKLVDV 70 (76)
T ss_pred cCCeeeeeEEe--eecCCCCEEEEEEEEC-CCchHHHHHHHHhcCcCe
Confidence 34333344554 4466888999999996 888899999999885543
No 127
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=28.38 E-value=42 Score=31.81 Aligned_cols=22 Identities=32% Similarity=0.622 Sum_probs=18.8
Q ss_pred hHHHHhcCCCccHHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.+..|+++.||||++|=.+|..
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHccCCccHHHHHHHHcC
Confidence 4578999999999999888864
No 128
>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=27.76 E-value=1.9e+02 Score=29.94 Aligned_cols=46 Identities=13% Similarity=0.034 Sum_probs=40.4
Q ss_pred ChHHHHHHHHHhccccHHHHHHHHHHHHHhCC-CHHHHhccCHHHHH
Q psy4002 146 RRYHVLISLMLSSQTKDEVNHAAMGRLKEHGL-TIENICNTSEDVLG 191 (378)
Q Consensus 146 ~pF~~Lv~~iLsqqt~~~~~~~~~~~L~~~~p-t~e~la~a~~e~L~ 191 (378)
-|++.+++..+.--...+.+...|.+|.++|. -.+-|.+++.|+|.
T Consensus 297 iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E~~iL~~~~~eel~ 343 (374)
T TIGR00375 297 IPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTEIAVLHEAAEEDLA 343 (374)
T ss_pred CCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccHHHHHhcCCHHHHH
Confidence 38899999999888889999999999999986 57888889999984
No 129
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=27.68 E-value=1.1e+02 Score=22.74 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=17.1
Q ss_pred chhhHHHHhcCCCccHHHHHH
Q psy4002 222 IPNTIELLCKLPGVGPKMAHL 242 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~ 242 (378)
.|.+.++|.+++|+|++.+.-
T Consensus 39 ~P~s~~~L~~i~g~~~~~~~~ 59 (68)
T PF00570_consen 39 LPTSIEELLQIPGMGKRKVRK 59 (68)
T ss_dssp --SSHHHHHTSTTCGHHHHHH
T ss_pred CCCCHHHHHHccCCCHHHHHH
Confidence 478999999999999987764
No 130
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=27.66 E-value=1.2e+02 Score=33.99 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=19.0
Q ss_pred hhHHHHhcCCCccHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
.+.++|.+++|||+++|..++.+
T Consensus 666 AS~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 666 AGEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred cCHHHHHhcCCcCHHHHHHHHHH
Confidence 47788889999999999888754
No 131
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=27.64 E-value=1.3e+02 Score=26.59 Aligned_cols=36 Identities=17% Similarity=0.284 Sum_probs=28.1
Q ss_pred HhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHH
Q psy4002 174 EHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKM 209 (378)
Q Consensus 174 ~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~ 209 (378)
....|.++|.++++++|.+++..+|++.-=-.+|..
T Consensus 88 ~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~ 123 (129)
T PF13543_consen 88 SKVLTLEALLEMSDEELKEILNRCGAREEECRRLCR 123 (129)
T ss_pred HhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence 346799999999999999999999986543344433
No 132
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=27.43 E-value=1.2e+02 Score=29.53 Aligned_cols=43 Identities=19% Similarity=0.218 Sum_probs=33.7
Q ss_pred HHHHHHHHh-CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 167 AAMGRLKEH-GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 167 ~~~~~L~~~-~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
.-...|.++ |.|+++|..++.++|.++ -|++..+|..|+....
T Consensus 14 krakkLl~~GF~Sve~Ik~AS~eEL~~V---~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 14 SKAEALREAGFESVEDVRAADQSELAEV---DGIGNALAARIKADVG 57 (232)
T ss_pred HHHHHHHHcCCCCHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHhc
Confidence 345667888 789999999999999533 4888888888877654
No 133
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=27.05 E-value=1.3e+02 Score=30.56 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=39.6
Q ss_pred HHHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDILKK 216 (378)
Q Consensus 166 ~~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~i~e 216 (378)
.....+|.+.++ |.++|+.++..+|.+ ..|++..+|..|...++.+..
T Consensus 41 ~~~~~kL~~~g~~tv~~~~~~~~~~L~~---~~g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 41 AGDVKKLQDAGIYTCNGLMMHTKKNLTG---IKGLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred HHHHHHHHHcCCCcHHHHHhCCHHHHHH---hcCCCHHHHHHHHHHHHHhhc
Confidence 345678888865 999999999999864 479999999999988887654
No 134
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=26.86 E-value=51 Score=33.92 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=21.8
Q ss_pred hhhHHHHhcCCCccHHHHHHHHHHH
Q psy4002 223 PNTIELLCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 223 p~~~e~L~~LpGVGpktA~~~l~~a 247 (378)
|.++++|+-.|||||.|+-++.+.|
T Consensus 274 p~Df~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHH
Confidence 6789999999999999998877664
No 135
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=26.79 E-value=79 Score=34.50 Aligned_cols=22 Identities=27% Similarity=0.270 Sum_probs=16.8
Q ss_pred hhHHHHhcCCCccHHHHHHHHHH
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNH 246 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~ 246 (378)
++.++|.++ |||.++|..+..+
T Consensus 543 As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 543 ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred CCHHHHHHc-CCCHHHHHHHHHH
Confidence 477888888 8888888877654
No 136
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=26.73 E-value=1.4e+02 Score=29.45 Aligned_cols=44 Identities=30% Similarity=0.352 Sum_probs=35.0
Q ss_pred HHHHHHHHhCC-CHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHHH
Q psy4002 167 AAMGRLKEHGL-TIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASDI 213 (378)
Q Consensus 167 ~~~~~L~~~~p-t~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~~ 213 (378)
....+|.+.++ |+++|+.+++++|.+. .|+...+|..|...++.
T Consensus 17 ~~a~~L~~~Gi~t~~dl~~~~~~~L~~~---~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 17 ATAEKLREAGYDTVEAIAVASPKELSEA---AGIGESTAAKIIEAARE 61 (317)
T ss_pred HHHHHHHHcCCCCHHHHHcCCHHHHHHh---cCCCHHHHHHHHHHHHH
Confidence 44677888754 9999999999999754 58877788888887765
No 137
>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=25.91 E-value=1.5e+02 Score=28.87 Aligned_cols=44 Identities=27% Similarity=0.261 Sum_probs=34.8
Q ss_pred HHHHHHHHHh-CCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 166 HAAMGRLKEH-GLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 166 ~~~~~~L~~~-~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
.....+|.+. +-|+++|+.++.++|.+. .|+....|..|...+.
T Consensus 9 ~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~---~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 9 PATAEKLREAGYDTFEAIAVASPKELSEI---AGISEGTAAKIIQAAR 53 (310)
T ss_pred HHHHHHHHHcCCCCHHHHHcCCHHHHHhc---cCCCHHHHHHHHHHHH
Confidence 3456778887 459999999999999754 4887778888887776
No 138
>PRK00254 ski2-like helicase; Provisional
Probab=24.79 E-value=1.1e+02 Score=33.93 Aligned_cols=32 Identities=22% Similarity=0.334 Sum_probs=25.2
Q ss_pred chhhHHHHhcCCCccHHHHHHHHHHHhccccc
Q psy4002 222 IPNTIELLCKLPGVGPKMAHLCMNHAWGIVTG 253 (378)
Q Consensus 222 ip~~~e~L~~LpGVGpktA~~~l~~a~~r~~~ 253 (378)
+++..-.|.++||||++.|..++..+++-...
T Consensus 640 ~~~~~~~L~~ipgig~~~~~~l~~~g~~s~~~ 671 (720)
T PRK00254 640 VREELLELMRLPMIGRKRARALYNAGFRSIED 671 (720)
T ss_pred CCHHHhhhhcCCCCCHHHHHHHHHccCCCHHH
Confidence 44556678899999999999999887775443
No 139
>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=24.70 E-value=18 Score=30.48 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=18.3
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhcccccc
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWGIVTGI 254 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~r~~~i 254 (378)
++.+-+-.+||||+|||.-++. -||-.++|
T Consensus 15 D~sDNIPGV~GIG~KtA~~LL~-~ygsle~i 44 (101)
T PF01367_consen 15 DSSDNIPGVPGIGPKTAAKLLQ-EYGSLENI 44 (101)
T ss_dssp CCCCTB---TTSTCHCCCCCHH-HHTSCHCC
T ss_pred CcccCCCCCCCCCHHHHHHHHH-HcCCHHHH
Confidence 3445566789999999987665 35555554
No 140
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=23.59 E-value=84 Score=23.86 Aligned_cols=33 Identities=12% Similarity=0.370 Sum_probs=27.7
Q ss_pred HHHHHHhCCCHHHHhc---cCHHHHHHhhcccCChH
Q psy4002 169 MGRLKEHGLTIENICN---TSEDVLGKLIIPVGFWK 201 (378)
Q Consensus 169 ~~~L~~~~pt~e~la~---a~~e~L~~~i~~~Gf~~ 201 (378)
=.+|++.+++.++|+. ++.++|.+-+..+||..
T Consensus 13 N~kLRD~~~sLd~Lc~~~~id~~~l~~kL~~~Gy~Y 48 (55)
T PF14056_consen 13 NMKLRDEYSSLDELCYDYDIDKEELEEKLASIGYEY 48 (55)
T ss_pred HHHHHhccCCHHHHHHHhCCCHHHHHHHHHHcCCeE
Confidence 3568888999999876 78999999999999954
No 141
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=23.04 E-value=79 Score=34.61 Aligned_cols=20 Identities=35% Similarity=0.629 Sum_probs=10.4
Q ss_pred HHHHhcCCCccHHHHHHHHH
Q psy4002 226 IELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 226 ~e~L~~LpGVGpktA~~~l~ 245 (378)
.++|.+++|||+++|..+..
T Consensus 574 ~eeL~~v~Gig~~~A~~I~~ 593 (598)
T PRK00558 574 VEELAKVPGISKKLAEAIYE 593 (598)
T ss_pred HHHHhhcCCcCHHHHHHHHH
Confidence 44555555555555555443
No 142
>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=22.96 E-value=70 Score=24.69 Aligned_cols=20 Identities=25% Similarity=0.144 Sum_probs=16.2
Q ss_pred hHHHHhcCCCccHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCM 244 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l 244 (378)
+.++|.+++|+|+++.+-+.
T Consensus 42 s~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 42 SEEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp -HHHHHTSTTSHHHHHHHHH
T ss_pred CHHHHHhCCCCCHhHHHHHH
Confidence 46789999999999987654
No 143
>PRK14976 5'-3' exonuclease; Provisional
Probab=22.71 E-value=54 Score=32.37 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=18.1
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+-+.+-.+||||+|||.-++. .||.
T Consensus 189 ~sDnipGVpGIG~KtA~~LL~-~~gs 213 (281)
T PRK14976 189 SSDNIKGVKGIGPKTAIKLLN-KYGN 213 (281)
T ss_pred ccCCCCCCCcccHHHHHHHHH-HcCC
Confidence 345566789999999998774 3454
No 144
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=22.66 E-value=75 Score=29.64 Aligned_cols=32 Identities=19% Similarity=0.544 Sum_probs=23.3
Q ss_pred HHHHHHHHhcCCcccHHHHHHHHHHhcchhccCCCCCCCCCCCccCCcc
Q psy4002 312 EDTRKELESWLPESLWSEVNHLLVGFGQQICKSQRPSCETCLNKDLCPQ 360 (378)
Q Consensus 312 ~~~~~~le~~lP~~~~~~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C~~ 360 (378)
++++..++...|+. ...++.|..|+++.+|..
T Consensus 157 ~ei~~ile~~~~p~-----------------~~~~~~C~~C~y~~iC~~ 188 (190)
T COG1468 157 KEIEEILEGGKPPP-----------------PKKKKKCKKCAYREICFP 188 (190)
T ss_pred HHHHHHHhCCCCCC-----------------CCCCCcCCCCCcceeccC
Confidence 45566666665554 336799999999999964
No 145
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=22.23 E-value=1.3e+02 Score=32.85 Aligned_cols=75 Identities=19% Similarity=0.135 Sum_probs=44.3
Q ss_pred HHHhccccHHHH---HHHHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHH--HHHHHhcCCCchhhHHH
Q psy4002 154 LMLSSQTKDEVN---HAAMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMAS--DILKKNYNNDIPNTIEL 228 (378)
Q Consensus 154 ~iLsqqt~~~~~---~~~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA--~~i~e~y~g~ip~~~e~ 228 (378)
..|.|+.+|++= ....++++.. .+ ..| +-|.++|-.+ |...|.... +.|.+ ++.++
T Consensus 487 l~lLq~iRDEaHRFAit~hRk~R~k-~~---------s~L-~~I~GiG~kr-~~~LL~~Fgs~~~I~~-------As~ee 547 (574)
T PRK14670 487 LRILQNVRDEAHRKANGFNKKLREN-IK---------LNY-TKIKGIGEKK-AKKILKSLGTYKDILL-------LNEDE 547 (574)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc-cc---------ccc-ccCCCCCHHH-HHHHHHHhCCHHHHHh-------CCHHH
Confidence 456788888753 3344455554 11 122 1235667644 333333332 22333 58999
Q ss_pred HhcCCCccHHHHHHHHHHH
Q psy4002 229 LCKLPGVGPKMAHLCMNHA 247 (378)
Q Consensus 229 L~~LpGVGpktA~~~l~~a 247 (378)
|.++||||.++|..+..+-
T Consensus 548 L~~v~gi~~~~A~~I~~~l 566 (574)
T PRK14670 548 IAEKMKINIKMAKKIKKFA 566 (574)
T ss_pred HHhCCCCCHHHHHHHHHHH
Confidence 9999999999999987663
No 146
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=21.94 E-value=94 Score=24.90 Aligned_cols=46 Identities=17% Similarity=0.162 Sum_probs=35.2
Q ss_pred cccCCcceeeeccccCCccceeeeeEEecccchhhhhhhhhccccccc
Q psy4002 4 RSMKNKTLTVPVDTTKNGKQKRMHMVVKYDEPKFQQTRCQLEKNIALN 51 (378)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (378)
|...=..|+ |..|.+...-||-++|.-++-...|.-+|++|=+.+.
T Consensus 26 RgfNI~Sl~--vg~te~~~~sriti~~~~~~~~i~qi~kQL~KLidV~ 71 (76)
T PRK06737 26 RGYYISSLN--LNERDTSGVSEMKLTAVCTENEATLLVSQLKKLINVL 71 (76)
T ss_pred cCcceEEEE--ecccCCCCeeEEEEEEECCHHHHHHHHHHHhCCcCEE
Confidence 333333444 5567788899999999899999999999999876543
No 147
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=21.84 E-value=1.3e+02 Score=34.24 Aligned_cols=41 Identities=20% Similarity=0.243 Sum_probs=31.7
Q ss_pred HHHHHHHhCCCHHHHhccCHHHHHHhhcccCChHHHHHHHHHHHH
Q psy4002 168 AMGRLKEHGLTIENICNTSEDVLGKLIIPVGFWKTKAKHIKMASD 212 (378)
Q Consensus 168 ~~~~L~~~~pt~e~la~a~~e~L~~~i~~~Gf~~~KA~~I~~lA~ 212 (378)
.+.+|..+|.|.++|++++.++|.+. +| ...+|+.|+++..
T Consensus 769 ~a~~ll~~f~si~~l~~as~eeL~~~---iG-~~~~A~~i~~fl~ 809 (814)
T TIGR00596 769 NYRNLRKKVKSIRELAKLSQNELNEL---IG-DEEAAKRLYDFLR 809 (814)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHHHHH---hC-CHHHHHHHHHHhc
Confidence 34566778999999999999999875 56 4667888877643
No 148
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=21.46 E-value=1.2e+02 Score=33.83 Aligned_cols=26 Identities=15% Similarity=0.014 Sum_probs=20.5
Q ss_pred hhHHHHhcCCCccHHHHHHHHHHHhc
Q psy4002 224 NTIELLCKLPGVGPKMAHLCMNHAWG 249 (378)
Q Consensus 224 ~~~e~L~~LpGVGpktA~~~l~~a~~ 249 (378)
++.++|.+++|||.++|..++-.+..
T Consensus 637 As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 637 ATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 47888888888888888888776654
No 149
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=20.92 E-value=2.5e+02 Score=25.86 Aligned_cols=51 Identities=25% Similarity=0.583 Sum_probs=36.7
Q ss_pred hCCCCCCCCHHHHHHHHHhcCCcc--------cHH--HHHHHHHHhcchhccCCCCCCCCCCCccCC
Q psy4002 302 LGWTKVFKTPEDTRKELESWLPES--------LWS--EVNHLLVGFGQQICKSQRPSCETCLNKDLC 358 (378)
Q Consensus 302 lg~~~~~~~~~~~~~~le~~lP~~--------~~~--~~~~~Lv~~G~~iC~~~~P~C~~Cpl~~~C 358 (378)
||+.. ..++...+.+++|.= .|. -+.++.-.-|-.+|++ |.|+.|.=...|
T Consensus 105 LGL~~----R~eLs~Lm~r~Fp~Laa~N~~~MrWKKFfYrqlCe~eG~~~C~a--PsC~~C~D~~~C 165 (167)
T PF04891_consen 105 LGLRS----RAELSALMRRHFPPLAARNTRNMRWKKFFYRQLCEREGLYLCRA--PSCEECSDYAVC 165 (167)
T ss_pred cCCCC----HHHHHHHHHHHhHHHHHhccCCCcHHHHHHHHHHHHcCCCcCCC--CCCCCcCCHhhc
Confidence 56644 466777888888751 454 4456777889999965 999999866666
No 150
>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=20.70 E-value=64 Score=30.86 Aligned_cols=25 Identities=24% Similarity=0.485 Sum_probs=18.1
Q ss_pred hHHHHhcCCCccHHHHHHHHHHHhcc
Q psy4002 225 TIELLCKLPGVGPKMAHLCMNHAWGI 250 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~~a~~r 250 (378)
+-+.+-.+|||||++|.-++. -||-
T Consensus 181 ~sDnipGv~GiG~ktA~~Ll~-~~gs 205 (240)
T cd00008 181 SSDNIPGVPGIGEKTAAKLLK-EYGS 205 (240)
T ss_pred cccCCCCCCccCHHHHHHHHH-HhCC
Confidence 345667889999999977664 3453
No 151
>smart00475 53EXOc 5'-3' exonuclease.
Probab=20.59 E-value=65 Score=31.39 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=16.5
Q ss_pred hHHHHhcCCCccHHHHHHHHH
Q psy4002 225 TIELLCKLPGVGPKMAHLCMN 245 (378)
Q Consensus 225 ~~e~L~~LpGVGpktA~~~l~ 245 (378)
+-+.+-.+||||++||.-++.
T Consensus 184 ~sDnipGV~GIG~KtA~~Ll~ 204 (259)
T smart00475 184 SSDNIPGVPGIGEKTAAKLLK 204 (259)
T ss_pred cccCCCCCCCCCHHHHHHHHH
Confidence 345567789999999998774
No 152
>COG2406 Protein distantly related to bacterial ferritins [General function prediction only]
Probab=20.45 E-value=2.9e+02 Score=25.34 Aligned_cols=31 Identities=19% Similarity=0.511 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCCchhhHHHHhcCCCccH
Q psy4002 206 HIKMASDILKKNYNNDIPNTIELLCKLPGVGP 237 (378)
Q Consensus 206 ~I~~lA~~i~e~y~g~ip~~~e~L~~LpGVGp 237 (378)
+...++..|.+ +||++|.++.+|..|.|.-+
T Consensus 65 H~e~i~~Ri~e-lg~~~Prd~~~l~dISgC~~ 95 (172)
T COG2406 65 HFELIAPRIYE-LGGDLPRDMKKLHDISGCKP 95 (172)
T ss_pred HHHHHHHHHHH-hCCCCchhHHHHHhhcCCCC
Confidence 46667777776 89999999999999998765
No 153
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=20.03 E-value=1.1e+02 Score=26.87 Aligned_cols=15 Identities=20% Similarity=0.747 Sum_probs=13.1
Q ss_pred CCCCCCCCCCccCCc
Q psy4002 345 QRPSCETCLNKDLCP 359 (378)
Q Consensus 345 ~~P~C~~Cpl~~~C~ 359 (378)
.+++|..|.+++.|.
T Consensus 147 ~~~~C~~C~y~~~C~ 161 (162)
T PF01930_consen 147 NSKKCRRCSYREFCW 161 (162)
T ss_pred CCCCCCCCCCcCcCC
Confidence 357999999999996
Done!