Query psy1206
Match_columns 531
No_of_seqs 411 out of 1977
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 17:36:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1206.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1206hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 1.1E-44 2.3E-49 383.3 25.1 245 12-463 83-352 (393)
2 PRK03980 flap endonuclease-1; 100.0 2.6E-41 5.6E-46 345.1 22.7 160 9-168 25-218 (292)
3 TIGR03674 fen_arch flap struct 100.0 7.2E-37 1.6E-41 318.4 24.3 158 12-169 75-266 (338)
4 cd00128 XPG Xeroderma pigmento 100.0 1.5E-35 3.2E-40 305.5 20.3 213 10-224 71-309 (316)
5 TIGR00600 rad2 DNA excision re 100.0 8.3E-35 1.8E-39 333.2 22.9 228 41-459 768-1004(1034)
6 KOG2519|consensus 100.0 7.8E-34 1.7E-38 298.0 17.3 250 9-463 74-348 (449)
7 KOG2518|consensus 100.0 4.1E-34 8.9E-39 303.0 12.8 188 34-225 117-314 (556)
8 smart00475 53EXOc 5'-3' exonuc 100.0 1.5E-29 3.3E-34 254.8 16.5 158 7-172 48-219 (259)
9 PTZ00217 flap endonuclease-1; 100.0 2.2E-28 4.7E-33 259.2 12.4 136 304-447 8-152 (393)
10 PRK14976 5'-3' exonuclease; Pr 100.0 1.4E-27 3.1E-32 243.1 16.4 157 7-172 54-224 (281)
11 KOG2519|consensus 99.9 2.7E-28 5.9E-33 256.4 9.3 133 304-448 8-147 (449)
12 cd00008 53EXOc 5'-3' exonuclea 99.9 3.3E-27 7.3E-32 235.3 16.4 154 7-172 49-216 (240)
13 PRK09482 flap endonuclease-lik 99.9 1.2E-26 2.7E-31 232.8 16.4 155 7-172 46-215 (256)
14 TIGR03674 fen_arch flap struct 99.9 5E-27 1.1E-31 244.7 12.3 128 312-447 16-144 (338)
15 KOG2520|consensus 99.9 2.3E-26 5E-31 256.9 12.5 184 41-227 462-674 (815)
16 TIGR00593 pola DNA polymerase 99.9 1.3E-25 2.7E-30 258.3 17.5 156 7-171 48-217 (887)
17 PRK05755 DNA polymerase I; Pro 99.9 1.9E-24 4.2E-29 249.8 16.0 156 7-171 50-219 (880)
18 COG0258 Exo 5'-3' exonuclease 99.9 6.7E-24 1.4E-28 218.7 16.1 180 7-196 59-255 (310)
19 PF00867 XPG_I: XPG I-region; 99.9 4.7E-24 1E-28 183.7 5.7 88 52-139 1-94 (94)
20 PRK03980 flap endonuclease-1; 99.9 2.1E-21 4.5E-26 198.9 10.8 96 343-446 1-96 (292)
21 cd00128 XPG Xeroderma pigmento 99.8 5E-21 1.1E-25 197.6 13.0 119 316-446 23-141 (316)
22 TIGR00600 rad2 DNA excision re 99.8 2E-20 4.4E-25 215.4 10.7 84 316-405 23-107 (1034)
23 PF00752 XPG_N: XPG N-terminal 99.8 5.3E-20 1.2E-24 159.7 7.8 80 313-396 22-101 (101)
24 smart00485 XPGN Xeroderma pigm 99.8 3.7E-20 8.1E-25 160.3 6.4 77 314-396 21-99 (99)
25 PHA00439 exonuclease 99.8 2.2E-19 4.7E-24 182.4 12.5 143 7-171 63-222 (286)
26 smart00484 XPGI Xeroderma pigm 99.8 9.1E-19 2E-23 144.6 7.6 73 52-124 1-73 (73)
27 KOG2518|consensus 99.7 3.6E-17 7.7E-22 174.7 10.6 117 317-446 24-141 (556)
28 PHA02567 rnh RnaseH; Provision 99.5 4.2E-14 9.2E-19 144.7 11.4 123 7-146 62-207 (304)
29 cd00080 HhH2_motif Helix-hairp 99.5 8E-14 1.7E-18 115.7 6.1 51 121-171 2-54 (75)
30 COG0258 Exo 5'-3' exonuclease 99.2 7.2E-12 1.6E-16 129.5 5.8 110 313-446 7-117 (310)
31 PF02739 5_3_exonuc_N: 5'-3' e 99.2 2.3E-11 4.9E-16 115.8 5.1 106 7-122 50-169 (169)
32 PF01367 5_3_exonuc: 5'-3' exo 99.1 1.4E-12 2.9E-17 114.3 -4.9 49 124-172 1-51 (101)
33 cd00080 HhH2_motif Helix-hairp 99.1 9.7E-11 2.1E-15 97.3 5.5 46 229-274 7-54 (75)
34 smart00279 HhH2 Helix-hairpin- 99.0 5.7E-10 1.2E-14 80.2 3.9 34 126-159 1-36 (36)
35 smart00279 HhH2 Helix-hairpin- 98.6 3.2E-08 6.9E-13 71.2 3.1 32 230-262 2-36 (36)
36 cd00008 53EXOc 5'-3' exonuclea 98.3 5.9E-07 1.3E-11 90.1 5.0 79 318-400 2-83 (240)
37 PF12813 XPG_I_2: XPG domain c 98.2 3.3E-06 7.2E-11 85.2 8.2 87 45-134 7-107 (246)
38 PRK14976 5'-3' exonuclease; Pr 98.2 2E-06 4.2E-11 88.4 5.1 84 318-401 4-89 (281)
39 smart00475 53EXOc 5'-3' exonuc 98.2 2.1E-06 4.5E-11 87.2 5.1 79 318-401 2-83 (259)
40 KOG2520|consensus 97.9 2.5E-05 5.3E-10 89.5 7.2 56 45-100 229-284 (815)
41 PRK09482 flap endonuclease-lik 97.8 2.7E-05 5.9E-10 79.0 4.9 46 229-274 167-214 (256)
42 PRK05755 DNA polymerase I; Pro 97.6 3.5E-05 7.6E-10 90.5 4.1 81 318-402 3-86 (880)
43 TIGR00593 pola DNA polymerase 97.6 7.1E-05 1.5E-09 87.8 6.0 79 320-401 2-83 (887)
44 PF01367 5_3_exonuc: 5'-3' exo 97.0 4.2E-05 9E-10 67.4 -4.1 45 230-274 4-50 (101)
45 PF12826 HHH_2: Helix-hairpin- 96.6 0.002 4.4E-08 51.9 3.5 24 143-166 7-30 (64)
46 PRK14602 ruvA Holliday junctio 96.2 0.007 1.5E-07 59.6 5.0 50 115-171 55-105 (203)
47 PRK13901 ruvA Holliday junctio 95.9 0.0078 1.7E-07 59.1 3.8 50 115-171 53-103 (196)
48 PRK14601 ruvA Holliday junctio 95.8 0.0087 1.9E-07 58.1 3.8 50 115-171 54-104 (183)
49 PRK14600 ruvA Holliday junctio 95.8 0.01 2.3E-07 57.7 4.3 50 115-171 54-104 (186)
50 PRK14603 ruvA Holliday junctio 95.7 0.0091 2E-07 58.6 3.7 50 115-171 53-103 (197)
51 PRK14606 ruvA Holliday junctio 95.7 0.0098 2.1E-07 58.0 3.7 50 115-171 54-104 (188)
52 PRK14604 ruvA Holliday junctio 95.7 0.0097 2.1E-07 58.3 3.7 50 115-171 54-104 (195)
53 COG0632 RuvA Holliday junction 95.6 0.032 6.9E-07 55.0 6.9 53 112-171 51-104 (201)
54 COG5366 Protein involved in pr 95.3 0.008 1.7E-07 65.0 1.8 122 46-169 133-258 (531)
55 PRK14605 ruvA Holliday junctio 95.1 0.023 4.9E-07 55.7 4.1 49 115-170 54-103 (194)
56 TIGR00084 ruvA Holliday juncti 95.0 0.029 6.3E-07 54.8 4.5 50 115-171 53-103 (191)
57 PRK00116 ruvA Holliday junctio 94.1 0.054 1.2E-06 52.8 4.0 47 116-169 55-102 (192)
58 PF02739 5_3_exonuc_N: 5'-3' e 93.9 0.055 1.2E-06 51.8 3.7 82 318-401 2-89 (169)
59 PRK07956 ligA NAD-dependent DN 91.1 0.8 1.7E-05 52.8 8.7 124 143-276 449-579 (665)
60 TIGR00575 dnlj DNA ligase, NAD 89.7 0.79 1.7E-05 52.8 7.2 27 143-170 436-464 (652)
61 PF10391 DNA_pol_lambd_f: Fing 89.0 0.36 7.7E-06 37.6 2.6 26 142-167 5-31 (52)
62 TIGR01448 recD_rel helicase, p 87.7 1.2 2.7E-05 51.8 7.2 39 124-170 75-113 (720)
63 PF12826 HHH_2: Helix-hairpin- 87.1 0.3 6.5E-06 39.3 1.2 26 246-271 7-32 (64)
64 PF14520 HHH_5: Helix-hairpin- 85.6 0.66 1.4E-05 36.6 2.4 25 143-167 9-34 (60)
65 PF00633 HHH: Helix-hairpin-he 84.4 0.8 1.7E-05 31.7 2.1 15 143-157 15-29 (30)
66 PF04599 Pox_G5: Poxvirus G5 p 84.1 2.6 5.5E-05 46.0 6.8 116 46-176 147-279 (425)
67 PRK14667 uvrC excinuclease ABC 83.8 0.93 2E-05 51.4 3.5 29 140-168 515-543 (567)
68 PHA00439 exonuclease 83.5 2.2 4.7E-05 44.4 5.8 60 318-377 7-74 (286)
69 PRK14669 uvrC excinuclease ABC 83.2 0.87 1.9E-05 52.2 3.0 28 141-168 554-581 (624)
70 PHA03065 Hypothetical protein; 82.4 2.9 6.3E-05 45.4 6.3 118 45-177 148-282 (438)
71 TIGR00194 uvrC excinuclease AB 81.6 1.1 2.3E-05 50.9 3.0 28 141-168 543-570 (574)
72 PRK14670 uvrC excinuclease ABC 81.5 1.2 2.6E-05 50.5 3.3 29 140-168 515-543 (574)
73 PF00633 HHH: Helix-hairpin-he 81.0 0.94 2E-05 31.4 1.4 17 244-260 13-29 (30)
74 PF14520 HHH_5: Helix-hairpin- 80.3 1.1 2.4E-05 35.2 1.8 27 244-270 7-34 (60)
75 COG0272 Lig NAD-dependent DNA 80.3 2.9 6.3E-05 48.0 5.7 33 244-276 545-579 (667)
76 PF00867 XPG_I: XPG I-region; 80.0 0.68 1.5E-05 39.8 0.6 14 229-242 81-94 (94)
77 smart00483 POLXc DNA polymeras 79.6 2.6 5.7E-05 44.6 4.9 27 244-271 91-119 (334)
78 PRK14671 uvrC excinuclease ABC 78.6 1.7 3.6E-05 49.9 3.3 26 142-167 572-597 (621)
79 PRK14351 ligA NAD-dependent DN 77.7 7.9 0.00017 45.1 8.4 25 143-167 466-492 (689)
80 PRK14672 uvrC excinuclease ABC 75.6 2.3 5.1E-05 49.0 3.3 28 141-168 610-637 (691)
81 smart00278 HhH1 Helix-hairpin- 74.8 2.3 5E-05 28.1 1.8 18 141-158 3-20 (26)
82 PRK14601 ruvA Holliday junctio 74.4 2.4 5.2E-05 41.3 2.6 46 113-159 81-128 (183)
83 PRK14668 uvrC excinuclease ABC 74.2 2.4 5.2E-05 48.2 3.0 31 139-169 525-555 (577)
84 PF02371 Transposase_20: Trans 74.1 2.6 5.7E-05 35.7 2.5 26 140-165 3-28 (87)
85 PRK00558 uvrC excinuclease ABC 74.0 2.4 5.2E-05 48.4 2.9 27 142-168 546-572 (598)
86 PRK12766 50S ribosomal protein 73.9 2.8 6E-05 42.3 3.0 28 141-168 5-33 (232)
87 PRK14350 ligA NAD-dependent DN 73.4 7.6 0.00016 45.0 6.7 35 244-278 543-579 (669)
88 PRK14669 uvrC excinuclease ABC 72.5 2.5 5.5E-05 48.5 2.6 29 243-271 553-581 (624)
89 TIGR00084 ruvA Holliday juncti 72.1 5.2 0.00011 39.2 4.4 53 229-292 68-124 (191)
90 PRK13901 ruvA Holliday junctio 71.9 3 6.4E-05 41.2 2.6 46 113-159 80-127 (196)
91 PRK14604 ruvA Holliday junctio 71.6 2.5 5.5E-05 41.5 2.1 76 77-160 48-129 (195)
92 PRK14606 ruvA Holliday junctio 71.5 2.6 5.6E-05 41.2 2.1 47 113-159 81-128 (188)
93 PRK14603 ruvA Holliday junctio 71.0 3.2 6.9E-05 40.9 2.6 76 77-160 47-128 (197)
94 PRK14600 ruvA Holliday junctio 71.0 4 8.7E-05 39.9 3.3 45 113-159 81-127 (186)
95 PRK02515 psbU photosystem II c 70.7 3.8 8.2E-05 38.0 2.8 25 143-167 65-91 (132)
96 PF02371 Transposase_20: Trans 69.9 3.5 7.5E-05 34.9 2.3 27 241-267 1-27 (87)
97 PRK14666 uvrC excinuclease ABC 69.5 3.8 8.3E-05 47.4 3.2 29 140-168 638-666 (694)
98 PRK00116 ruvA Holliday junctio 69.3 3.5 7.7E-05 40.2 2.5 20 245-264 76-95 (192)
99 TIGR00194 uvrC excinuclease AB 68.9 3.4 7.4E-05 47.0 2.6 29 243-271 542-570 (574)
100 PRK14667 uvrC excinuclease ABC 68.4 3.8 8.3E-05 46.5 2.9 29 243-271 515-543 (567)
101 PRK14602 ruvA Holliday junctio 68.3 4.1 8.8E-05 40.3 2.7 46 113-159 82-129 (203)
102 PRK14605 ruvA Holliday junctio 67.9 7.3 0.00016 38.2 4.4 35 229-273 69-103 (194)
103 PRK14670 uvrC excinuclease ABC 67.8 4 8.7E-05 46.4 2.9 29 243-271 515-543 (574)
104 PF10391 DNA_pol_lambd_f: Fing 67.8 5.1 0.00011 31.2 2.6 25 244-268 4-29 (52)
105 COG5049 XRN1 5'-3' exonuclease 67.7 14 0.0003 42.9 6.9 103 54-156 175-336 (953)
106 PF03159 XRN_N: XRN 5'-3' exon 66.4 10 0.00022 38.4 5.2 70 319-395 32-105 (237)
107 COG0322 UvrC Nuclease subunit 66.3 5.5 0.00012 45.4 3.6 28 142-169 533-560 (581)
108 PRK08609 hypothetical protein; 65.0 14 0.00031 42.0 6.6 23 141-163 50-74 (570)
109 COG0632 RuvA Holliday junction 64.3 7.2 0.00016 38.6 3.6 76 77-160 48-129 (201)
110 COG1948 MUS81 ERCC4-type nucle 63.6 6.1 0.00013 40.5 3.0 26 143-168 186-211 (254)
111 TIGR00596 rad1 DNA repair prot 61.8 4.3 9.4E-05 48.0 1.8 30 139-168 757-786 (814)
112 PRK14672 uvrC excinuclease ABC 61.5 6.3 0.00014 45.7 2.9 29 243-271 609-637 (691)
113 PRK14668 uvrC excinuclease ABC 61.4 5.7 0.00012 45.2 2.6 30 242-271 525-554 (577)
114 PRK14671 uvrC excinuclease ABC 60.2 6.2 0.00014 45.3 2.7 27 244-270 571-597 (621)
115 TIGR00575 dnlj DNA ligase, NAD 58.0 8.7 0.00019 44.4 3.3 34 245-278 533-568 (652)
116 COG1948 MUS81 ERCC4-type nucle 57.9 7.3 0.00016 39.9 2.4 28 244-271 184-211 (254)
117 PRK14351 ligA NAD-dependent DN 57.4 9.2 0.0002 44.5 3.4 33 245-277 563-597 (689)
118 PRK14666 uvrC excinuclease ABC 57.0 7.6 0.00017 45.1 2.6 30 243-272 638-667 (694)
119 PRK00558 uvrC excinuclease ABC 56.0 7.9 0.00017 44.3 2.5 29 243-271 544-572 (598)
120 PRK12766 50S ribosomal protein 55.5 9.2 0.0002 38.7 2.6 25 244-268 5-30 (232)
121 TIGR01259 comE comEA protein. 55.1 12 0.00026 33.9 3.1 24 142-165 71-100 (120)
122 TIGR00596 rad1 DNA repair prot 53.3 7.6 0.00016 46.0 1.9 30 242-271 757-786 (814)
123 COG1555 ComEA DNA uptake prote 53.2 14 0.0003 34.9 3.3 26 142-167 100-131 (149)
124 cd04236 AAK_NAGS-Urea AAK_NAGS 53.1 12 0.00025 38.7 3.0 69 287-381 3-81 (271)
125 cd00141 NT_POLXc Nucleotidyltr 50.1 16 0.00034 38.3 3.4 27 143-169 89-116 (307)
126 PRK13766 Hef nuclease; Provisi 49.8 14 0.0003 43.1 3.4 28 141-168 717-744 (773)
127 PF11798 IMS_HHH: IMS family H 49.0 12 0.00026 26.1 1.6 15 142-156 14-28 (32)
128 smart00483 POLXc DNA polymeras 48.4 15 0.00032 39.0 3.0 28 142-169 92-120 (334)
129 smart00685 DM14 Repeats in fly 48.1 32 0.00068 27.7 4.1 27 392-425 7-33 (59)
130 TIGR00305 probable toxin-antit 48.0 12 0.00026 32.8 1.9 29 62-90 85-113 (114)
131 PHA02567 rnh RnaseH; Provision 47.6 35 0.00075 36.0 5.5 55 318-378 15-74 (304)
132 PRK08609 hypothetical protein; 47.2 28 0.00062 39.6 5.2 30 143-172 92-123 (570)
133 PRK07956 ligA NAD-dependent DN 46.6 16 0.00034 42.5 3.0 18 141-158 481-498 (665)
134 PF11731 Cdd1: Pathogenicity l 45.2 20 0.00042 31.4 2.7 23 142-164 15-38 (93)
135 COG0322 UvrC Nuclease subunit 45.0 17 0.00037 41.5 3.0 29 244-272 532-560 (581)
136 PF06200 tify: tify domain; I 44.5 11 0.00024 27.3 0.9 16 370-386 15-30 (36)
137 TIGR00426 competence protein C 43.9 25 0.00054 28.2 3.0 15 144-158 22-36 (69)
138 PF14490 HHH_4: Helix-hairpin- 42.6 39 0.00084 29.0 4.2 45 248-294 18-65 (94)
139 PRK02515 psbU photosystem II c 40.5 19 0.00042 33.4 2.0 25 245-269 64-90 (132)
140 PF14863 Alkyl_sulf_dimr: Alky 38.6 76 0.0016 29.7 5.8 69 373-446 43-118 (141)
141 TIGR01259 comE comEA protein. 36.9 27 0.00059 31.6 2.5 18 245-262 71-88 (120)
142 cd00141 NT_POLXc Nucleotidyltr 36.9 34 0.00075 35.8 3.5 55 215-271 48-115 (307)
143 PF07864 DUF1651: Protein of u 35.3 17 0.00037 30.1 0.8 31 374-408 36-67 (75)
144 COG0177 Nth Predicted EndoIII- 34.5 23 0.0005 35.4 1.7 37 125-167 28-66 (211)
145 PRK13766 Hef nuclease; Provisi 34.1 27 0.00058 40.8 2.5 28 244-271 717-744 (773)
146 PHA02994 hypothetical protein; 34.0 24 0.00052 35.3 1.7 16 371-386 101-116 (218)
147 PRK13482 DNA integrity scannin 33.6 35 0.00075 36.7 3.0 54 115-168 243-316 (352)
148 TIGR03629 arch_S13P archaeal r 33.1 37 0.00081 31.9 2.8 50 232-281 2-73 (144)
149 PRK14350 ligA NAD-dependent DN 32.4 85 0.0018 36.7 6.0 25 246-270 506-531 (669)
150 PRK08097 ligB NAD-dependent DN 32.2 62 0.0013 37.0 4.8 33 244-276 522-556 (562)
151 TIGR00615 recR recombination p 31.2 30 0.00064 34.3 1.8 17 142-158 14-30 (195)
152 PRK00076 recR recombination pr 31.2 29 0.00064 34.3 1.8 17 142-158 14-30 (196)
153 COG0353 RecR Recombinational D 30.7 29 0.00062 34.4 1.6 19 140-158 13-31 (198)
154 PF05991 NYN_YacP: YacP-like N 30.7 48 0.001 31.6 3.1 49 320-377 1-53 (166)
155 TIGR00160 MGSA methylglyoxal s 30.1 57 0.0012 30.8 3.4 68 12-82 6-78 (143)
156 PTZ00134 40S ribosomal protein 30.0 45 0.00098 31.8 2.8 34 230-263 9-51 (154)
157 PF13052 DUF3913: Protein of u 29.8 27 0.00059 26.9 1.0 17 135-151 14-31 (57)
158 COG0353 RecR Recombinational D 29.5 22 0.00048 35.1 0.6 16 244-259 14-29 (198)
159 PF11438 N36: 36-mer N-termina 29.0 49 0.0011 23.6 2.1 20 385-404 2-21 (35)
160 PF04708 Pox_F16: Poxvirus F16 29.0 37 0.00081 34.1 2.1 19 369-387 99-117 (218)
161 KOG2841|consensus 28.6 41 0.00088 34.3 2.3 29 141-169 197-225 (254)
162 PRK13844 recombination protein 28.2 36 0.00078 33.8 1.8 17 142-158 18-34 (200)
163 COG4277 Predicted DNA-binding 27.7 75 0.0016 33.8 4.1 47 112-158 277-349 (404)
164 PF04919 DUF655: Protein of un 27.4 62 0.0013 31.7 3.2 48 123-170 95-152 (181)
165 TIGR00426 competence protein C 26.8 80 0.0017 25.2 3.4 15 247-261 22-36 (69)
166 PF03449 GreA_GreB_N: Transcri 26.7 1.6E+02 0.0035 24.5 5.2 48 384-436 16-64 (74)
167 PF12836 HHH_3: Helix-hairpin- 26.5 37 0.00081 27.1 1.4 24 143-166 18-47 (65)
168 PF14490 HHH_4: Helix-hairpin- 26.2 1.1E+02 0.0024 26.2 4.3 42 146-189 19-63 (94)
169 PF03159 XRN_N: XRN 5'-3' exon 25.8 42 0.0009 34.1 1.9 38 55-92 172-222 (237)
170 PF14579 HHH_6: Helix-hairpin- 25.3 83 0.0018 26.7 3.4 27 143-169 31-62 (90)
171 PRK05892 nucleoside diphosphat 24.9 1.6E+02 0.0036 27.9 5.6 55 384-443 18-72 (158)
172 TIGR00615 recR recombination p 24.8 36 0.00077 33.7 1.2 16 244-259 13-28 (195)
173 PRK00076 recR recombination pr 24.7 36 0.00078 33.7 1.2 17 244-260 13-29 (196)
174 PRK04053 rps13p 30S ribosomal 24.0 73 0.0016 30.2 3.0 34 230-263 4-46 (149)
175 TIGR02990 ectoine_eutA ectoine 23.8 4.5E+02 0.0097 26.6 8.8 37 45-81 109-150 (239)
176 COG1803 MgsA Methylglyoxal syn 23.3 87 0.0019 29.2 3.2 67 12-81 8-79 (142)
177 PF14716 HHH_8: Helix-hairpin- 23.1 56 0.0012 26.3 1.8 16 141-156 49-64 (68)
178 TIGR00322 diphth2_R diphthamid 23.0 1.7E+02 0.0036 31.2 5.8 71 363-447 191-263 (332)
179 PRK13482 DNA integrity scannin 22.9 57 0.0012 35.1 2.3 27 245-271 290-316 (352)
180 PRK13844 recombination protein 22.7 41 0.00088 33.4 1.1 55 244-313 17-73 (200)
181 COG1569 Predicted nucleic acid 22.6 59 0.0013 30.6 2.0 30 64-93 91-120 (142)
182 KOG2045|consensus 22.2 1.6E+02 0.0034 35.8 5.7 55 361-415 68-127 (1493)
183 TIGR02236 recomb_radA DNA repa 21.0 85 0.0018 32.4 3.1 26 142-167 2-28 (310)
184 PF11731 Cdd1: Pathogenicity l 20.9 59 0.0013 28.5 1.6 17 244-260 14-30 (93)
185 PRK01229 N-glycosylase/DNA lya 20.4 70 0.0015 31.9 2.2 16 143-158 123-138 (208)
186 KOG1247|consensus 20.2 1.1E+02 0.0024 33.9 3.7 105 319-437 359-472 (567)
187 TIGR01448 recD_rel helicase, p 20.1 79 0.0017 37.1 2.9 17 247-263 89-105 (720)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.1e-44 Score=383.25 Aligned_cols=245 Identities=51% Similarity=0.831 Sum_probs=212.7
Q ss_pred ceeecccCCCCCcchhH------HhHH----------------HHHHhhccCCCH---HHHHHHHhhcCCccccCCCchh
Q psy1206 12 GLVKYLCGDKNFAEDRI------RNGA----------------KKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEAE 66 (531)
Q Consensus 12 ~~~a~~~~~~~f~~~~~------R~~~----------------~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEAD 66 (531)
-++.||.+.++++..++ |..+ ..++++...+|+ +.++++|+++||||++||||||
T Consensus 83 Pv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAd 162 (393)
T PTZ00217 83 PVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAE 162 (393)
T ss_pred EEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHH
Confidence 46899998888876542 2222 123444455666 4578899999999999999999
Q ss_pred HHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCCCCC
Q psy1206 67 AQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG 146 (531)
Q Consensus 67 Aq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pGIpG 146 (531)
||||+|++.|++|+|+|+|+|+|+||++.|+++++.++..+.+++.++++.+++.+|++++||+|+|+|+||||+|||||
T Consensus 163 aq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~G 242 (393)
T PTZ00217 163 AQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKG 242 (393)
T ss_pred HHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCC
Confidence 99999999999999999999999999999999987654444467899999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccCCChhhhH
Q psy1206 147 IGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAI 226 (531)
Q Consensus 147 IG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~~ 226 (531)
||+|||++||++|+|+|+|+++++.
T Consensus 243 IG~ktA~~Li~~~gsle~il~~~~~------------------------------------------------------- 267 (393)
T PTZ00217 243 IGPKTAYKLIKKYKSIEEILEHLDK------------------------------------------------------- 267 (393)
T ss_pred ccHHHHHHHHHHcCCHHHHHHHHHh-------------------------------------------------------
Confidence 9999999999999999999987632
Q ss_pred hHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCccccccc
Q psy1206 227 ELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELV 306 (531)
Q Consensus 227 el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv 306 (531)
.++.+|++|+|.+|+.+|+||.|+||.+
T Consensus 268 ------------------------------------------------~k~~~p~~~~~~~~~~~f~~p~V~~~~~---- 295 (393)
T PTZ00217 268 ------------------------------------------------TKYPVPENFDYKEARELFLNPEVTPAEE---- 295 (393)
T ss_pred ------------------------------------------------cCCCCCCCCChHHHHHHhcCCCcCCCCC----
Confidence 1245799999999999999999999831
Q ss_pred cccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHH
Q psy1206 307 ADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGEL 386 (531)
Q Consensus 307 ~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~ 386 (531)
T Consensus 296 -------------------------------------------------------------------------------- 295 (393)
T PTZ00217 296 -------------------------------------------------------------------------------- 295 (393)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccccchhh
Q psy1206 387 NKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREE 463 (531)
Q Consensus 387 ~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~~~~~~ 463 (531)
-+++|+.||.+++++|++.+..|..++|.+.+.+|.+++++.+|+|||+||++.++.
T Consensus 296 --------------------~~l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~~ 352 (393)
T PTZ00217 296 --------------------IDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKP 352 (393)
T ss_pred --------------------CCCCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhccCccCCHHHhcCCCCCc
Confidence 136799999999999999999999999999999999999999999999999998664
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.6e-41 Score=345.11 Aligned_cols=160 Identities=35% Similarity=0.549 Sum_probs=134.7
Q ss_pred CccceeecccCCCCCcchhH------HhHHH----------------HHHhhccCCCH---HHHHHHHhhcCCccccCCC
Q psy1206 9 DEDGLVKYLCGDKNFAEDRI------RNGAK----------------KLLKARSSTTQ---GRLDSFFTIRREEKRKAPC 63 (531)
Q Consensus 9 d~~~~~a~~~~~~~f~~~~~------R~~~~----------------~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPy 63 (531)
...-++.||.+.++++.++. |..+. +++++...+|+ +.++++|+++||||++|||
T Consensus 25 gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~ 104 (292)
T PRK03980 25 GIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPS 104 (292)
T ss_pred CCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCc
Confidence 34458999999888875543 22221 22333445565 4578899999999999999
Q ss_pred chhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHHHh
Q psy1206 64 EAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDLCI 134 (531)
Q Consensus 64 EADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~~i 134 (531)
|||||||+|++.|++|+|+|+|+|+|+||+++|+++++..+.+++ ..+.++.+.+++.+|++++||+|+|+
T Consensus 105 EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~i 184 (292)
T PRK03980 105 EGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLIDIAI 184 (292)
T ss_pred hHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHHHhCCCHHHHHHHHH
Confidence 999999999999999999999999999999999999977654322 34579999999999999999999999
Q ss_pred HcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 135 LLGCDYCDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 135 L~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
|+||||+|||||||+|||++||++|+|+|+|+++
T Consensus 185 L~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~ 218 (292)
T PRK03980 185 LVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEE 218 (292)
T ss_pred hcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHh
Confidence 9999999999999999999999999999999873
No 3
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=7.2e-37 Score=318.41 Aligned_cols=158 Identities=34% Similarity=0.527 Sum_probs=133.3
Q ss_pred ceeecccCCCCCcchh------HHhHHHHH----------------HhhccCCCH---HHHHHHHhhcCCccccCCCchh
Q psy1206 12 GLVKYLCGDKNFAEDR------IRNGAKKL----------------LKARSSTTQ---GRLDSFFTIRREEKRKAPCEAE 66 (531)
Q Consensus 12 ~~~a~~~~~~~f~~~~------~R~~~~~~----------------~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEAD 66 (531)
-++.||.+.++|+..+ .|..+.+. .++...+|+ +.++++|+++||||++||+|||
T Consensus 75 Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAe 154 (338)
T TIGR03674 75 PVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGE 154 (338)
T ss_pred EEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHH
Confidence 4899999998886333 34443222 223344555 4578999999999999999999
Q ss_pred HHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHHHhHcC
Q psy1206 67 AQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDLCILLG 137 (531)
Q Consensus 67 Aq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~~iL~G 137 (531)
||||+|++.|.||+|+|+|+|+|+||+++|+++++..+.++. ..+.++.+.+++.+|++++||+|+|+|+|
T Consensus 155 aq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G 234 (338)
T TIGR03674 155 AQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVG 234 (338)
T ss_pred HHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcC
Confidence 999999999999999999999999999999999876553221 34568999999999999999999999999
Q ss_pred CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206 138 CDYCDSIRGIGPKRAIELIKEHRSIEKILENI 169 (531)
Q Consensus 138 ~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l 169 (531)
|||+|||||||+|||++||++|+|+|+|++++
T Consensus 235 ~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~ 266 (338)
T TIGR03674 235 TDYNEGVKGIGPKTALKLIKEHGDLEKVLKAR 266 (338)
T ss_pred CCCCCCCCCccHHHHHHHHHHcCCHHHHHHhh
Confidence 99999999999999999999999999998764
No 4
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=1.5e-35 Score=305.48 Aligned_cols=213 Identities=36% Similarity=0.492 Sum_probs=171.4
Q ss_pred ccceeecccCCCCCcchh------HHhHHHH----------------HHhhccCCCH---HHHHHHHhhcCCccccCCCc
Q psy1206 10 EDGLVKYLCGDKNFAEDR------IRNGAKK----------------LLKARSSTTQ---GRLDSFFTIRREEKRKAPCE 64 (531)
Q Consensus 10 ~~~~~a~~~~~~~f~~~~------~R~~~~~----------------~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyE 64 (531)
...++.||.+.+++++.+ .|.++.. +..+...+++ +.++++|+++||||++||||
T Consensus 71 i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~E 150 (316)
T cd00128 71 IKPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYE 150 (316)
T ss_pred CEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcC
Confidence 347889999888887433 2322211 1112223444 56788999999999999999
Q ss_pred hhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCCC
Q psy1206 65 AEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI 144 (531)
Q Consensus 65 ADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pGI 144 (531)
||||||+|+++|.+|+|+|+|||+|+||+++|+++++..+. ..++.++.+.+.+.+|++++||+|+|+|+||||+|||
T Consensus 151 Adaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~--~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv 228 (316)
T cd00128 151 AEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGA--KPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGI 228 (316)
T ss_pred HHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCC--CceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCC
Confidence 99999999999999999999999999999999999876441 2467899999999999999999999999999999999
Q ss_pred CCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCC-CCcccccccccccccccccccCCChh
Q psy1206 145 RGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADP-ETIEFIDLCILLGCDYCDSIRGIGPK 223 (531)
Q Consensus 145 pGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~-~~~~~v~Ls~~~~~d~cesl~~~Gp~ 223 (531)
||||+|||++||++|+|++.+++++......+|.+|++..++..|.+|.|.+. ....|..........++....+|.+.
T Consensus 229 ~giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~~p~~~~l~~~~~~~~~~~~~ 308 (316)
T cd00128 229 PGIGPVTALKLIKKYGDIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDDFIDLRWRDPDEEGIIEFLCKEHGFNED 308 (316)
T ss_pred CCccHHHHHHHHHHcCChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCCCCceeecCCCHHHHHHHccCCCCCCHH
Confidence 99999999999999999999999999887788899999999999999998875 44555444333333444445556543
Q ss_pred h
Q psy1206 224 R 224 (531)
Q Consensus 224 ~ 224 (531)
+
T Consensus 309 r 309 (316)
T cd00128 309 R 309 (316)
T ss_pred H
Confidence 3
No 5
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=8.3e-35 Score=333.23 Aligned_cols=228 Identities=22% Similarity=0.380 Sum_probs=184.6
Q ss_pred CCCHHH---HHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206 41 STTQGR---LDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK 117 (531)
Q Consensus 41 ~~t~~~---i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~ 117 (531)
.+|+.+ ++++|++||||||+||+|||||||+|++.|+||+|+|+|+|+|+||+++|++++...+ ..+..|+.++
T Consensus 768 ~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~---~~ve~~~~~~ 844 (1034)
T TIGR00600 768 EVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQN---KFVEYYQYVD 844 (1034)
T ss_pred cCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCC---CceEEeeHHH
Confidence 566654 5788999999999999999999999999999999999999999999999999985322 2578899999
Q ss_pred HHHhCCCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHH---hhhcCCCCCCCCcHHHHHHHhcCC
Q psy1206 118 VLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHR--SIEKILEN---IDTKKYTVPEGWLYKEARELFRHP 192 (531)
Q Consensus 118 i~~~lglt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~--sle~il~~---l~~~~~~ip~~f~~~~A~~~f~~p 192 (531)
+++.+|+++++|+++|+|+||||++||||||++||++||++|+ +++.+++. +... . ...
T Consensus 845 i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~-------------~---~~~ 908 (1034)
T TIGR00600 845 IHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEA-------------Q---KDK 908 (1034)
T ss_pred HHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHh-------------h---hcc
Confidence 9999999999999999999999999999999999999999999 47776642 2110 0 000
Q ss_pred CcCCCCCcccccccccccccccccccCCChhhhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHH
Q psy1206 193 EVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENI 272 (531)
Q Consensus 193 ~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l 272 (531)
.. .+. + . ++. ...
T Consensus 909 ~~-~~~-----------------------~-------------------------~--------~~~----------~~~ 921 (1034)
T TIGR00600 909 KK-REN-----------------------P-------------------------N--------DTK----------VKK 921 (1034)
T ss_pred cc-ccc-----------------------c-------------------------c--------hhh----------hhh
Confidence 00 000 0 0 000 000
Q ss_pred hhCCCCCCCcchHHHHHHHhcCCcccCccccccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcch
Q psy1206 273 DTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSH 352 (531)
Q Consensus 273 ~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tsh 352 (531)
+..++.+|++|++..++.+|++|.|-+.
T Consensus 922 ~~~~~~lp~~FP~~~V~~~yl~P~V~~~---------------------------------------------------- 949 (1034)
T TIGR00600 922 KLRLLQLTPGFPNPAVADAYLRPVVDDS---------------------------------------------------- 949 (1034)
T ss_pred cccccccCCCCCcHHHHHHhcCCCCCCC----------------------------------------------------
Confidence 1123569999999999999999998643
Q ss_pred hhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchH
Q psy1206 353 LMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAED 432 (531)
Q Consensus 353 l~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ 432 (531)
.+.+.|+.||.++++.|++.+..+..+
T Consensus 950 -----------------------------------------------------~~~f~W~~PD~e~L~~Fl~~~~gws~e 976 (1034)
T TIGR00600 950 -----------------------------------------------------KGSFLWGKPDLDKIREFCQRYFGWNRE 976 (1034)
T ss_pred -----------------------------------------------------cCCCCCCCCCHHHHHHHHHHccCCCHH
Confidence 134689999999999999999999999
Q ss_pred HHHHHHHHHHH-HhccCCcCcccccccc
Q psy1206 433 RIRNGAKKLLK-ARSTTTQGRLDSFFTI 459 (531)
Q Consensus 433 ~~~~~~~~ll~-~~~~~~~~rld~ff~~ 459 (531)
++.+.+.++++ +..+.+|+|||+||++
T Consensus 977 Rv~~~l~plikk~~~~~~Q~~ld~FF~~ 1004 (1034)
T TIGR00600 977 KTDEVLLPVLKKLNAQQTQLRIDSFFRL 1004 (1034)
T ss_pred HHHHHHHHHHHHHHccCCccCHHHhhCc
Confidence 99999999987 5567889999999995
No 6
>KOG2519|consensus
Probab=100.00 E-value=7.8e-34 Score=298.04 Aligned_cols=250 Identities=46% Similarity=0.798 Sum_probs=211.7
Q ss_pred CccceeecccCCCCCcchhHHhHHHHH----------------------HhhccCCCH---HHHHHHHhhcCCccccCCC
Q psy1206 9 DEDGLVKYLCGDKNFAEDRIRNGAKKL----------------------LKARSSTTQ---GRLDSFFTIRREEKRKAPC 63 (531)
Q Consensus 9 d~~~~~a~~~~~~~f~~~~~R~~~~~~----------------------~k~~~~~t~---~~i~~lL~~~gIp~vvAPy 63 (531)
+.+.++-||.+-+.++.++........ .++-..+|- .-.+.+|..|||||+.||+
T Consensus 74 gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~ 153 (449)
T KOG2519|consen 74 GIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPG 153 (449)
T ss_pred CCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCc
Confidence 455788899888888755432222111 111111111 2467899999999999999
Q ss_pred chhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCC
Q psy1206 64 EAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDS 143 (531)
Q Consensus 64 EADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pG 143 (531)
||+||||+|++.|.|++++|+|||.|.||++.+++++..+.+++.++.+|+++.+++.++++.++|+|+|+|+||||+++
T Consensus 154 EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~ 233 (449)
T KOG2519|consen 154 EAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPT 233 (449)
T ss_pred hHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCccccc
Confidence 99999999999999999999999999999999999987765666799999999999999999999999999999999999
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccCCChh
Q psy1206 144 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPK 223 (531)
Q Consensus 144 IpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~ 223 (531)
|.|||+++|++||++|++++++++-
T Consensus 234 I~Gig~~~al~lir~~~~i~~ile~------------------------------------------------------- 258 (449)
T KOG2519|consen 234 IRGIGPKKALKLIRQHGDIENILEI------------------------------------------------------- 258 (449)
T ss_pred ccccChHHHHHHHHHhcCHHHHhhh-------------------------------------------------------
Confidence 9999999999999999998888752
Q ss_pred hhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCcccc
Q psy1206 224 RAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETI 303 (531)
Q Consensus 224 ~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~ 303 (531)
....+.++||++|++..|+..|..+.|-+|+..
T Consensus 259 -----------------------------------------------~~~~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~ 291 (449)
T KOG2519|consen 259 -----------------------------------------------NSDLKEYPIPEDWSYKLARKLFLEPEFPNPESI 291 (449)
T ss_pred -----------------------------------------------ccchhhcCCCCCccHHHHHHHhcCcccCCccce
Confidence 001235789999999999999999999888421
Q ss_pred ccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcch
Q psy1206 304 ELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKS 383 (531)
Q Consensus 304 ~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~ 383 (531)
T Consensus 292 -------------------------------------------------------------------------------- 291 (449)
T KOG2519|consen 292 -------------------------------------------------------------------------------- 291 (449)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccccchhh
Q psy1206 384 GELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREE 463 (531)
Q Consensus 384 ~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~~~~~~ 463 (531)
=++.|..||++++.+|++.+..|..+++.....+++..++..+|||+|+||+..++-
T Consensus 292 -----------------------~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~ 348 (449)
T KOG2519|consen 292 -----------------------LDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKG 348 (449)
T ss_pred -----------------------eecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCC
Confidence 246899999999999999889999999999999999999999999999999997763
No 7
>KOG2518|consensus
Probab=100.00 E-value=4.1e-34 Score=303.03 Aligned_cols=188 Identities=28% Similarity=0.399 Sum_probs=159.5
Q ss_pred HHHhhccCCCHHHH---HHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCc
Q psy1206 34 KLLKARSSTTQGRL---DSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPV 110 (531)
Q Consensus 34 ~~~k~~~~~t~~~i---~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v 110 (531)
..|..+.++|++++ .++|+..||+|||||||||||||||++.|+|++|||||||+++|||++||++|+..|. .
T Consensus 117 ~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~----~ 192 (556)
T KOG2518|consen 117 ECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGN----G 192 (556)
T ss_pred HHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCC----c
Confidence 35888889999764 5567788999999999999999999999999999999999999999999999986553 2
Q ss_pred EEecHHHHHHhC----CCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HhhhcCCCCCCCCc--HH
Q psy1206 111 QEFHLEKVLEGM----ELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILE-NIDTKKYTVPEGWL--YK 183 (531)
Q Consensus 111 ~~~~~~~i~~~l----glt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~-~l~~~~~~ip~~f~--~~ 183 (531)
..++...+.+.. +++.++|+.||+|+||||++||||||.+||+++|++|.+.+.++. .+...+..+|++|. |.
T Consensus 193 le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~ 272 (556)
T KOG2518|consen 193 LEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFE 272 (556)
T ss_pred ccccHhhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHH
Confidence 344555554433 478999999999999999999999999999999999999999865 45566788999996 99
Q ss_pred HHHHHhcCCCcCCCCCcccccccccccccccccccCCChhhh
Q psy1206 184 EARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRA 225 (531)
Q Consensus 184 ~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~ 225 (531)
+|..+|+|+.||||..+++++|++.+....-+.+.+.|+...
T Consensus 273 ~A~~tF~hQrVydP~~k~~~~L~~~~~~l~~~~~~~~g~~~~ 314 (556)
T KOG2518|consen 273 RANLTFLHQRVYDPIEKKLIHLNPIEDELDNEDLEFLGPLKD 314 (556)
T ss_pred HHHHhhhhhheeCchHhhhhcCCchhhhcchhhHhhcccccC
Confidence 999999999999999999999999765443355566665443
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.96 E-value=1.5e-29 Score=254.80 Aligned_cols=158 Identities=27% Similarity=0.307 Sum_probs=136.4
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA--- 75 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~--- 75 (531)
+|++ ++++||.+.++| |++.++.||++|..+| +.++++|+++|||++.+| |||||+||+|+++
T Consensus 48 ~p~~-~~~~fD~~~~~~-----R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~ 121 (259)
T smart00475 48 KPTY-VAVVFDAKGKTF-----RHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA 121 (259)
T ss_pred CCCe-EEEEEeCCCCcc-----ccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHh
Confidence 7999 999999776666 5556788899998888 467899999999999887 6999999999974
Q ss_pred -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
|..++|+|+|+|++++++++|......++.. ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||+|||
T Consensus 122 ~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~--~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA 199 (259)
T smart00475 122 EGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIK--EFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTA 199 (259)
T ss_pred CCCeEEEEeCCCcHhhcCCCCEEEEeccCCCC--ccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHH
Confidence 7889999999999999998774322223221 24579999999999999999999999999 999999999999999
Q ss_pred HHHHHHcCCHHHHHHHhhhc
Q psy1206 153 IELIKEHRSIEKILENIDTK 172 (531)
Q Consensus 153 ~kLI~~~~sle~il~~l~~~ 172 (531)
.+||++|+|+|+|+++++..
T Consensus 200 ~~Ll~~ygsle~i~~~~~~~ 219 (259)
T smart00475 200 AKLLKEFGSLENILENLDKL 219 (259)
T ss_pred HHHHHHhCCHHHHHHHHHHH
Confidence 99999999999999998763
No 9
>PTZ00217 flap endonuclease-1; Provisional
Probab=99.95 E-value=2.2e-28 Score=259.19 Aligned_cols=136 Identities=51% Similarity=0.774 Sum_probs=127.1
Q ss_pred ccccccCCCcccc-------cceeeecccchHHHHHHHHhh--cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEee
Q psy1206 304 ELVADVAPSSIRE-------SRKICIDASMSLYQFLIAVRS--EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF 374 (531)
Q Consensus 304 ~Lv~~~aP~~i~~-------gk~iAIDa~~~lyqfl~~ir~--~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVF 374 (531)
.++.+++|.++.+ |++||||||+|||||++++|+ +|.+|+|+.|++|+||+|+|+|+++|+++||+|||||
T Consensus 8 ~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~gikPv~VF 87 (393)
T PTZ00217 8 KFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAGIKPVYVF 87 (393)
T ss_pred HHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCCCCEEEEE
Confidence 3556666666654 899999999999999999996 6889999999999999999999999999999999999
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206 375 DGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST 447 (531)
Q Consensus 375 DG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~ 447 (531)
||+||++|++++++|+++|+++.+++++|.++|+.+ +|++|++| +..++++|++.+++||++||=
T Consensus 88 DG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~-------~a~k~~~r-~~~vt~~~~~~~~~lL~~~Gi 152 (393)
T PTZ00217 88 DGKPPELKSGELEKRRERREEAEEELEKAIEEGDDE-------EIKKQSKR-TVRVTKEQNEDAKKLLRLMGI 152 (393)
T ss_pred cCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHH-------HHHHHHhh-cccCCHHHHHHHHHHHHHcCC
Confidence 999999999999999999999999999999999977 99999998 999999999999999999983
No 10
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.95 E-value=1.4e-27 Score=243.09 Aligned_cols=157 Identities=24% Similarity=0.302 Sum_probs=134.7
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA--- 75 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~--- 75 (531)
.|++ .+|+||.+.++| |++.++.||++|..+| +.++++|+++|||++.+| |||||+||+|+++
T Consensus 54 ~p~~-~~v~fD~~~~~~-----R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~ 127 (281)
T PRK14976 54 NPSY-ILIAFDAGRKTF-----RHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSK 127 (281)
T ss_pred CCCE-EEEEEECCCCcc-----cccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH
Confidence 7898 999999876665 4556788899998888 357889999999999999 6999999999864
Q ss_pred -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
|.-..|+|+|+|++++++++|.......+. ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||+|||
T Consensus 128 ~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~---~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA 204 (281)
T PRK14976 128 QNITVLIYSSDKDLLQLVNENTDVLLKKKGT---SHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTA 204 (281)
T ss_pred CCCeEEEEeCCCCcCccCCCCeEEEEecCCC---CcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHH
Confidence 666789999999999999876332222221 24679999999999999999999999999 999999999999999
Q ss_pred HHHHHHcCCHHHHHHHhhhc
Q psy1206 153 IELIKEHRSIEKILENIDTK 172 (531)
Q Consensus 153 ~kLI~~~~sle~il~~l~~~ 172 (531)
.+||++|||+|+|++++++.
T Consensus 205 ~~LL~~~gsle~i~~~~~~~ 224 (281)
T PRK14976 205 IKLLNKYGNIENIYENIDKI 224 (281)
T ss_pred HHHHHHcCCHHHHHHhHHHH
Confidence 99999999999999998764
No 11
>KOG2519|consensus
Probab=99.95 E-value=2.7e-28 Score=256.40 Aligned_cols=133 Identities=53% Similarity=0.822 Sum_probs=126.1
Q ss_pred ccccccCCCcccc-------cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecC
Q psy1206 304 ELVADVAPSSIRE-------SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376 (531)
Q Consensus 304 ~Lv~~~aP~~i~~-------gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG 376 (531)
+++++++|+++++ ||+||||||||||||++++|+. ++..|++|+||.|+||||++|+++||+|||||||
T Consensus 8 ~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~----~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG 83 (449)
T KOG2519|consen 8 KVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSC----RNEAGEPTSHLMGMFYRTIRLIENGIKPVYVFDG 83 (449)
T ss_pred HHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccc----cccCCCchHHHHHHHHHHHHHHHcCCcEEEEECC
Confidence 4678999999988 7999999999999999999975 6778999999999999999999999999999999
Q ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccC
Q psy1206 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTT 448 (531)
Q Consensus 377 ~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~ 448 (531)
+||+||+.+++||.++|.+|.+.++.+.+.|..+ ...+|+.| ..+++..-.+++++||..||--
T Consensus 84 ~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~-------~~~k~~~r-~vkvtk~~~dEak~LL~lmGIp 147 (449)
T KOG2519|consen 84 KPPDLKSQELAKRSERRSEADKELKPAKEAGAKE-------NMEKFFSR-LVKVTKQHNDEAKRLLSLMGIP 147 (449)
T ss_pred CCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHH-------HHHHHHHH-HhhhcchhhHHHHHHHHHcCCe
Confidence 9999999999999999999999999999999977 99999998 9999999999999999999975
No 12
>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=99.95 E-value=3.3e-27 Score=235.30 Aligned_cols=154 Identities=25% Similarity=0.273 Sum_probs=132.6
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK---- 74 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r---- 74 (531)
+|++ .+++||.+.++|+ ++..+.||++|..+| +.++++|+++|||++.+| +||||+||+|++
T Consensus 49 ~p~~-~~~~fD~~~~~~R-----~~l~p~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~ 122 (240)
T cd00008 49 KPTY-VAVVFDAGGKTFR-----HELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEA 122 (240)
T ss_pred CCCe-EEEEEeCCCCccc-----ccccHHHHcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH
Confidence 6888 9999998756664 445677899998777 457889999999999988 699999999985
Q ss_pred cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 75 AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 75 ~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
.|...+|+|+|+|++++++++|..... . ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||+|||
T Consensus 123 ~g~~~~I~S~DkD~~ql~~~~v~~~~~-~-----~~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA 196 (240)
T cd00008 123 EGYKVVIVSGDKDLLQLVSDNVKVVSP-M-----KKKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTA 196 (240)
T ss_pred cCCeEEEEeCCCChhhhCCCCEEEEeC-C-----CceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHH
Confidence 578889999999999998887643211 1 13568999999999999999999999999 999999999999999
Q ss_pred HHHHHHcCCHHHHHHHhhhc
Q psy1206 153 IELIKEHRSIEKILENIDTK 172 (531)
Q Consensus 153 ~kLI~~~~sle~il~~l~~~ 172 (531)
.+||++|+|+|+|+++++..
T Consensus 197 ~~Ll~~~gsle~i~~~~~~~ 216 (240)
T cd00008 197 AKLLKEYGSLEGILENLDKI 216 (240)
T ss_pred HHHHHHhCCHHHHHHhHHHH
Confidence 99999999999999998764
No 13
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.94 E-value=1.2e-26 Score=232.76 Aligned_cols=155 Identities=19% Similarity=0.227 Sum_probs=132.4
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA--- 75 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~--- 75 (531)
+|+| ++|+||.+.++ ..+|++.++.||++|..+| +.|++++.++|||++..| |||||+||+|+++
T Consensus 46 ~p~~-i~v~fD~~~~~---~~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~ 121 (256)
T PRK09482 46 QPTH-AVAVFDGDARS---SGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQ 121 (256)
T ss_pred CCCE-EEEEEeCCCCC---cccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHH
Confidence 7999 99999986554 1146667888999998888 467899999999999988 5999999999863
Q ss_pred -CCEEEEEcCCCccccccCCeEE-EeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHH
Q psy1206 76 -GKVYATATEDMDALTFGSNILL-RHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKR 151 (531)
Q Consensus 76 -G~vd~ViSeDsDlL~fg~~~Vi-~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~kt 151 (531)
|.-..|+|.|+|++++..++|. .+. .. .+.++.+.+.+.+|++|+|++|+.+|+| +||+|||||||+||
T Consensus 122 ~~~~v~I~S~DKDl~Qlv~~~v~~~~~--~~-----~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~Kt 194 (256)
T PRK09482 122 AGHQATIVSTDKGYCQLLSPTIQIRDY--FQ-----KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKS 194 (256)
T ss_pred CCCeEEEEECCCCccccCCCCeEEEec--cc-----cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHH
Confidence 6666789999999999988763 322 11 2358999999999999999999999999 99999999999999
Q ss_pred HHHHHHHcCCHHHHHHHhhhc
Q psy1206 152 AIELIKEHRSIEKILENIDTK 172 (531)
Q Consensus 152 A~kLI~~~~sle~il~~l~~~ 172 (531)
|.+||++|||+|+|++++++.
T Consensus 195 A~~LL~~~gsle~i~~~~~~~ 215 (256)
T PRK09482 195 AAELLNQFRSLENIYESLDAL 215 (256)
T ss_pred HHHHHHHhCCHHHHHHhHHHh
Confidence 999999999999999998653
No 14
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=99.94 E-value=5e-27 Score=244.72 Aligned_cols=128 Identities=42% Similarity=0.659 Sum_probs=122.3
Q ss_pred CcccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHH
Q psy1206 312 SSIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRM 390 (531)
Q Consensus 312 ~~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~ 390 (531)
-....|++||||||+|||||++++|+ +|.+++|++|++|+||+|+|+|+++|+++||+|||||||+||++|.+++++|+
T Consensus 16 l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~ 95 (338)
T TIGR03674 16 LEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERR 95 (338)
T ss_pred HHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHH
Confidence 34456999999999999999999998 79999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206 391 EKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST 447 (531)
Q Consensus 391 ~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~ 447 (531)
++|++|.+++++++++|+.+ +|++|++| +..++++|++.+++||++||=
T Consensus 96 ~~r~~a~~~~~~~~~~g~~~-------~a~~~~~r-~~~~~~~~~~~~k~lL~~~Gi 144 (338)
T TIGR03674 96 EIREEAEEKWEEALEKGDLE-------EARKYAQR-SSRLTSEIVESSKKLLDLMGI 144 (338)
T ss_pred HHHHHHHHHHHHHHHcCCHH-------HHHHHHhh-cCCCCHHHHHHHHHHHHHcCC
Confidence 99999999999999999987 99999998 899999999999999999983
No 15
>KOG2520|consensus
Probab=99.93 E-value=2.3e-26 Score=256.94 Aligned_cols=184 Identities=24% Similarity=0.408 Sum_probs=150.1
Q ss_pred CCCHHH---HHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206 41 STTQGR---LDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK 117 (531)
Q Consensus 41 ~~t~~~---i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~ 117 (531)
.+|+.+ ++++|+.+|||||+||+|||||||.|...++||+|||+|||+|+||+.+|++++. ..++ .+..|.+.+
T Consensus 462 evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F-~knk--~ve~y~~~d 538 (815)
T KOG2520|consen 462 EVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFF-NKNK--YVEKYQLDD 538 (815)
T ss_pred hhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHh-hcCc--cceeeehHH
Confidence 466654 5789999999999999999999999999999999999999999999999999984 3333 478899999
Q ss_pred HHHhCCCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHhh----------------------hc
Q psy1206 118 VLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHR---SIEKILENID----------------------TK 172 (531)
Q Consensus 118 i~~~lglt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~---sle~il~~l~----------------------~~ 172 (531)
+...||+++..+|-++.|+|+||+.||+|||+++|+.+|.+|+ ++..+-+++. ..
T Consensus 539 i~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~~~~~~~s~~~~~lrkkl~n~ 618 (815)
T KOG2520|consen 539 IEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGPADKEVGSTQQKMLRKKLKNP 618 (815)
T ss_pred HHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCccccccccHHHHHHHHHhcCc
Confidence 9999999999999999999999999999999999999999999 4333322222 12
Q ss_pred CCCCCCCCcHHHHHHHhcCCCcCCCCC-cccccccccccccccccccCCChhhhHh
Q psy1206 173 KYTVPEGWLYKEARELFRHPEVADPET-IEFIDLCILLGCDYCDSIRGIGPKRAIE 227 (531)
Q Consensus 173 ~~~ip~~f~~~~A~~~f~~p~V~d~~~-~~~v~Ls~~~~~d~cesl~~~Gp~~~~e 227 (531)
+..+|.+||...+..+|+||.|.+... ..|.-..-.....++...++|.-+++++
T Consensus 619 ~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~pdl~~lRef~~~~fgW~~~kT~~ 674 (815)
T KOG2520|consen 619 KIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGKPDLDILREFMKRLFGWPDEKTDE 674 (815)
T ss_pred ccccCcCCCchhHHHHhhCCccCCCcccccCCCCCHHHHHHHHHHHcCCCccccch
Confidence 367899999999999999999987544 3444332222345566677777666655
No 16
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=1.3e-25 Score=258.32 Aligned_cols=156 Identities=26% Similarity=0.333 Sum_probs=134.8
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA--- 75 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~--- 75 (531)
+|+| ++|+||.+.++| |++.++.||++|..+| +.++++|+++|||++.+| |||||+||+|+++
T Consensus 48 ~p~~-i~v~FD~~~~tf-----R~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~ 121 (887)
T TIGR00593 48 KPTY-VAVAFDSGTPTF-----RHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEK 121 (887)
T ss_pred CCCE-EEEEEcCCCCcc-----hHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHh
Confidence 7999 999999876666 5566888899998888 467899999999999888 6999999999974
Q ss_pred -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
|+.+.|+|+|+|++++++++|.......+. ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||+|||
T Consensus 122 ~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~---~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA 198 (887)
T TIGR00593 122 EGYEVRIISGDKDLLQLVSDNVKVLIPKGKT---SFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTA 198 (887)
T ss_pred CCCcEEEEECCCChhhcCCCCEEEEeccCCC---CceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHH
Confidence 888899999999999999876332112211 24569999999999999999999999999 899999999999999
Q ss_pred HHHHHHcCCHHHHHHHhhh
Q psy1206 153 IELIKEHRSIEKILENIDT 171 (531)
Q Consensus 153 ~kLI~~~~sle~il~~l~~ 171 (531)
.+||++|||+|+|+++++.
T Consensus 199 ~kLL~~ygsle~i~~~~~~ 217 (887)
T TIGR00593 199 AKLLQEFGSLENIYENLDQ 217 (887)
T ss_pred HHHHHHcCCHHHHHHHHHH
Confidence 9999999999999998765
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=99.91 E-value=1.9e-24 Score=249.82 Aligned_cols=156 Identities=25% Similarity=0.298 Sum_probs=134.1
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK---- 74 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r---- 74 (531)
.|+| ++|+||.+.++| |++.++.||++|..+| +.++++|+++|||++.+| |||||+||+|++
T Consensus 50 ~p~~-~~v~fD~~~~~~-----R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~ 123 (880)
T PRK05755 50 KPTH-VAVAFDAKGKTF-----RHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEA 123 (880)
T ss_pred CCCE-EEEEEECCCCcc-----ccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHh
Confidence 7999 999999876666 4456788899998877 468899999999999999 699999999985
Q ss_pred cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 75 AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 75 ~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
.|..++|+|+|+|++++++++|-......+. ....++.+.+.+.+|++|+||+|+++|+| |||+|||||||+|||
T Consensus 124 ~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~~---~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA 200 (880)
T PRK05755 124 AGYEVLIVTGDKDLLQLVDDNVTLLDTMGVS---KNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTA 200 (880)
T ss_pred CCCcEEEEcCCCChhhhCCCCEEEeeccCCC---CCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHH
Confidence 5888999999999999999876221111111 24579999999999999999999999999 899999999999999
Q ss_pred HHHHHHcCCHHHHHHHhhh
Q psy1206 153 IELIKEHRSIEKILENIDT 171 (531)
Q Consensus 153 ~kLI~~~~sle~il~~l~~ 171 (531)
.+||++|||+|+|+++++.
T Consensus 201 ~~Ll~~~gsle~i~~~~~~ 219 (880)
T PRK05755 201 AKLLQEYGSLEGLYENLDE 219 (880)
T ss_pred HHHHHHcCCHHHHHHhHHH
Confidence 9999999999999998875
No 18
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.91 E-value=6.7e-24 Score=218.73 Aligned_cols=180 Identities=26% Similarity=0.316 Sum_probs=144.2
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCC-CH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH---
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSST-TQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK--- 74 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~-t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r--- 74 (531)
.|.+ .+++||.+.++| |++..+.+|++|.. ++ +.|.+++.++|++++..+ +||||.++++++
T Consensus 59 ~~~~-~~~vFD~~~~tf-----R~~~~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~ 132 (310)
T COG0258 59 EPTH-PVVVFDGKPPTF-----RHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132 (310)
T ss_pred CCCc-EEEEEcCCCCcc-----hHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence 5667 999999866666 44457778888888 77 467888999999999766 699999999885
Q ss_pred -cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhC-CCCHHHHHHHHhHcC--CCCCCCCCCccHH
Q psy1206 75 -AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGM-ELSHEEFIDLCILLG--CDYCDSIRGIGPK 150 (531)
Q Consensus 75 -~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~l-glt~eqfid~~iL~G--~DY~pGIpGIG~k 150 (531)
.|.++.|+|+|+|+|+|+++++.......+. +...++...+.+.+ |++|+||+|+++|+| |||+|||||||+|
T Consensus 133 ~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~---~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~k 209 (310)
T COG0258 133 KKGDVVLIISGDKDLLQLVSPNVLVINGKKGE---PEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPK 209 (310)
T ss_pred hcCCeEEEEeCCcchhhhcCCCcEEEeccCCC---CcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHH
Confidence 6899999999999999999996543333321 11157889999999 999999999999999 9999999999999
Q ss_pred HHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcC-CCcCC
Q psy1206 151 RAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRH-PEVAD 196 (531)
Q Consensus 151 tA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~-p~V~d 196 (531)
||++||++|||+|.++++++..+ .............+|.+ +.|.+
T Consensus 210 tA~~Ll~~~gs~e~i~~~~~~~~-~~~~~~l~~~~~~afl~~~l~t~ 255 (310)
T COG0258 210 TALKLLQEYGSLEGLYENLDIIK-KKTREKLLEDKEKAFLSKPLATI 255 (310)
T ss_pred HHHHHHHHhCCHHHHHHhhhhhc-chhhHHHHHHHHHHhcCcccccc
Confidence 99999999999999999987322 11222335677888888 66655
No 19
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.89 E-value=4.7e-24 Score=183.72 Aligned_cols=88 Identities=41% Similarity=0.629 Sum_probs=75.2
Q ss_pred hhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEecc-cc-Ccc----cCCcEEecHHHHHHhCCCC
Q psy1206 52 TIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMT-FS-EAR----KLPVQEFHLEKVLEGMELS 125 (531)
Q Consensus 52 ~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~-~~-~~~----~~~v~~~~~~~i~~~lglt 125 (531)
+++||||++||||||||||+|+++|+||+|+|+|||+|+||+++||++++ .. +.. ...++.++.+.+++.++++
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~ 80 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT 80 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence 47899999999999999999999999999999999999999999999996 33 221 2458899999999999999
Q ss_pred HHHHHHHHhHcCCC
Q psy1206 126 HEEFIDLCILLGCD 139 (531)
Q Consensus 126 ~eqfid~~iL~G~D 139 (531)
+++|+++|+|+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 99999999999998
No 20
>PRK03980 flap endonuclease-1; Provisional
Probab=99.85 E-value=2.1e-21 Score=198.87 Aligned_cols=96 Identities=47% Similarity=0.750 Sum_probs=93.7
Q ss_pred cCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHH
Q psy1206 343 MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKY 422 (531)
Q Consensus 343 ~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~ 422 (531)
||++|++||||+|+|+|+++|+++||+|||||||+||++|.+++++|+++|++|.+++++|+++|+.+ +|++|
T Consensus 1 ~~~~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~-------~a~k~ 73 (292)
T PRK03980 1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLE-------EARKY 73 (292)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHH-------HHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999977 99999
Q ss_pred HhhccccchHHHHHHHHHHHHHhc
Q psy1206 423 LCGDKNFAEDRIRNGAKKLLKARS 446 (531)
Q Consensus 423 ~~~~~~~~~~~~~~~~~~ll~~~~ 446 (531)
+++ +.+++++|++.+++||++||
T Consensus 74 ~~~-~~~vt~~~~~~~k~lL~~~G 96 (292)
T PRK03980 74 AQR-SSRLTDEIVEDSKKLLDLMG 96 (292)
T ss_pred Hhc-cccCCHHHHHHHHHHHHHCC
Confidence 998 99999999999999999998
No 21
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=99.85 E-value=5e-21 Score=197.64 Aligned_cols=119 Identities=45% Similarity=0.657 Sum_probs=111.7
Q ss_pred ccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206 316 ESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395 (531)
Q Consensus 316 ~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~ 395 (531)
.|++|||||++||||++++++... .+.|.+|+|+.|+++|+.+|+++||+|||||||.+|++|.+|+.+|+++|++
T Consensus 23 ~gk~laID~~~~l~r~~~a~~~~~----~~~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~ 98 (316)
T cd00128 23 RGKKVAIDASIWLYQFLKACRQEL----GSGGETTSHLQGFFYRTCRLLELGIKPVFVFDGKPPPLKAETLAKRRERREE 98 (316)
T ss_pred CCcEEEecHHHHHHHHHHHhhhhc----cCCCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHH
Confidence 689999999999999999998632 2679999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206 396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS 446 (531)
Q Consensus 396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~ 446 (531)
+.+++..+.++|+.+ ++.++.++ ...+++.+++.+++||++||
T Consensus 99 ~~~~~~~~~~~~~~~-------~~~~~~~~-~~~~~~~~~~~~~~lL~~~g 141 (316)
T cd00128 99 AEEEAKEALEKGLEE-------EAKKLERR-AVRVTPQMIEEAKELLRLMG 141 (316)
T ss_pred HHHHHHHHHHhCCHH-------HHHHHHhc-cCcCCHHHHHHHHHHHHHcC
Confidence 999999999999876 99999887 88899999999999999996
No 22
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.82 E-value=2e-20 Score=215.44 Aligned_cols=84 Identities=39% Similarity=0.637 Sum_probs=77.7
Q ss_pred ccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHH
Q psy1206 316 ESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRE 394 (531)
Q Consensus 316 ~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~ 394 (531)
.||+||||||+|||||+.++|. .|++++| +||.|+|+|+++||++||+|||||||.||++|.+|+++|+++|+
T Consensus 23 ~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n------~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~ 96 (1034)
T TIGR00600 23 EGKRLAVDISIWLNQALKGVRDREGNAIKN------SHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRD 96 (1034)
T ss_pred CCeEEEechHHHHHHHHHHHHhccCCccCC------HHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHH
Confidence 4999999999999999999998 7888765 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH
Q psy1206 395 DAQKALAKAQE 405 (531)
Q Consensus 395 ~a~~~~~~a~~ 405 (531)
+|.+..++..+
T Consensus 97 ~a~~~a~~~~~ 107 (1034)
T TIGR00600 97 GASEDARKTAE 107 (1034)
T ss_pred HHHHHHHHHHH
Confidence 98877765554
No 23
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=99.81 E-value=5.3e-20 Score=159.67 Aligned_cols=80 Identities=50% Similarity=0.764 Sum_probs=66.0
Q ss_pred cccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206 313 SIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEK 392 (531)
Q Consensus 313 ~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~ 392 (531)
.-..|++|||||++||||++.+.+.. +. ..+..++|+.++++|+..|+.+||+|||||||.+|++|.+|.++|+++
T Consensus 22 ~~l~g~~vaID~s~wl~~~~~~~~~~---~~-~~~~~~~~~~~~~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~ 97 (101)
T PF00752_consen 22 SELRGKRVAIDASCWLHQFLFSCREE---LG-QGVGTDSHLRGLFSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKR 97 (101)
T ss_dssp GGGTTCEEEEEHHHHHHHHHHHSBCT---TS-CB-BS-HHHHHHHHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHH
T ss_pred HHhCCCEEEEEcHHHHHHHHHHhHHH---hc-cccchHHHHHHHHHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHH
Confidence 34568999999999999999988641 11 112227999999999999999999999999999999999999999999
Q ss_pred HHHH
Q psy1206 393 REDA 396 (531)
Q Consensus 393 r~~a 396 (531)
|++|
T Consensus 98 r~~~ 101 (101)
T PF00752_consen 98 REEA 101 (101)
T ss_dssp HHHH
T ss_pred HhcC
Confidence 9987
No 24
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.80 E-value=3.7e-20 Score=160.32 Aligned_cols=77 Identities=61% Similarity=0.991 Sum_probs=68.2
Q ss_pred ccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcc-hhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206 314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTS-HLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME 391 (531)
Q Consensus 314 i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~ts-hl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~ 391 (531)
...|++|||||++||||++.+++. .+..+ .++ |+.++|+|+.+|+++||+|||||||.+|++|.+|+++|++
T Consensus 21 ~l~g~~vaIDa~~wl~~~~~~~~~~~~~~~------~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~ 94 (99)
T smart00485 21 ALRGKTLAIDASIWLYQFLTACREKLGTPL------PNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRE 94 (99)
T ss_pred HhCCceEeccHHHHHHHHHHHHhhhhcCCC------CchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHH
Confidence 345999999999999999999976 34433 234 9999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy1206 392 KREDA 396 (531)
Q Consensus 392 ~r~~a 396 (531)
+|++|
T Consensus 95 ~r~~~ 99 (99)
T smart00485 95 RREEA 99 (99)
T ss_pred HHhcC
Confidence 99875
No 25
>PHA00439 exonuclease
Probab=99.80 E-value=2.2e-19 Score=182.37 Aligned_cols=143 Identities=15% Similarity=0.146 Sum_probs=111.9
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----c
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----A 75 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----~ 75 (531)
+||+ ++|+|| +.+ .+|++.++.||++|..++ +.+++++.++||+++..| +||||.+|+|++ .
T Consensus 63 ~p~~-i~vaFD-~~~-----tfR~elyp~YKanR~~~p~~~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~ 135 (286)
T PHA00439 63 KDAP-IVLAFT-DSV-----NWRKEVVPTYKANRKAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLF 135 (286)
T ss_pred CCCe-EEEEEC-CCC-----ChHhhhhhHhcCCCCCCCCchhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHC
Confidence 8999 999999 544 456777888999997765 578899999999999777 799999999986 3
Q ss_pred CC-EEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206 76 GK-VYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA 152 (531)
Q Consensus 76 G~-vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA 152 (531)
|+ -..|+|.|+|++++....++.. . .+ . +..++.+ .+++++|+.+|+| +||+||||||| |||
T Consensus 136 g~~~vvIvS~DKDl~QLv~~~~~~~-~-~~-~---~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA 200 (286)
T PHA00439 136 GFKKAVLVSCDKDFKTIPNCDFLWC-T-TG-N---ILTQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTA 200 (286)
T ss_pred CCCeEEEEeCCCCHhhcCcceEEEc-c-CC-c---eEEcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHH
Confidence 66 6678999999999976544422 1 11 1 1112322 2999999999999 99999999999 999
Q ss_pred HHHHHH---cCCHHHHHHHhhh
Q psy1206 153 IELIKE---HRSIEKILENIDT 171 (531)
Q Consensus 153 ~kLI~~---~~sle~il~~l~~ 171 (531)
.+||.+ |..++.++++-..
T Consensus 201 ~kLL~~~~~~~~~~~~~~sg~~ 222 (286)
T PHA00439 201 EAFLENPYIFEQVEKVLKSGKR 222 (286)
T ss_pred HHHHhCccccchhhHHhhcccc
Confidence 999998 5667777766533
No 26
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.76 E-value=9.1e-19 Score=144.58 Aligned_cols=73 Identities=42% Similarity=0.532 Sum_probs=67.5
Q ss_pred hhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCC
Q psy1206 52 TIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMEL 124 (531)
Q Consensus 52 ~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lgl 124 (531)
+.+||||++||||||||||+|+++|++|+|+|+|+|+|+||+++||++++++++++.+++.+++..+++.+|+
T Consensus 1 ~~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred CcCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 3689999999999999999999999999999999999999999999999887765567899999999998875
No 27
>KOG2518|consensus
Probab=99.70 E-value=3.6e-17 Score=174.73 Aligned_cols=117 Identities=22% Similarity=0.333 Sum_probs=105.5
Q ss_pred cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHH-HHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206 317 SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIR-LVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395 (531)
Q Consensus 317 gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~-ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~ 395 (531)
|++||||+|+|||+.+.++.. ....|++|+.+..+|....+ |+.+||+||.||||.|.+.|+.|..+||++|++
T Consensus 24 g~tvavD~y~WLhrg~~~Ca~-----el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~ 98 (556)
T KOG2518|consen 24 GKTVAVDGYCWLHRGALACAE-----KLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKK 98 (556)
T ss_pred CceEEEehhhHHhhhHHhHHH-----HHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHH
Confidence 899999999999999998865 33457888766666666666 589999999999999999999999999999999
Q ss_pred HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206 396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS 446 (531)
Q Consensus 396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~ 446 (531)
..+..++.+.+|+.. +|++|+++ +..|+++|++..++.++.+|
T Consensus 99 n~~~a~~ll~~G~~~-------~A~~~fqr-~VdIT~~ma~~lI~~~r~~n 141 (556)
T KOG2518|consen 99 NLDAAEQLLAEGKES-------NARECFQR-CVDITPEMAHKLIQYLRSQN 141 (556)
T ss_pred hHHHHHHHHHcCCHH-------HHHHHHHH-hccCcHHHHHHHHHHHHHcC
Confidence 999999999999987 99999999 99999999999999999885
No 28
>PHA02567 rnh RnaseH; Provisional
Probab=99.53 E-value=4.2e-14 Score=144.71 Aligned_cols=123 Identities=16% Similarity=0.058 Sum_probs=97.2
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCHH---------------HHHHHHhhcCCccccCC-CchhHHHH
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQG---------------RLDSFFTIRREEKRKAP-CEAEAQCA 70 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~~---------------~i~~lL~~~gIp~vvAP-yEADAq~A 70 (531)
.|++ ++++||.+. ...+|++.++.||++|..+|+ .+++++.++||+++..| +||||.+|
T Consensus 62 ~~~~-i~vaFD~~~----~~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIg 136 (304)
T PHA02567 62 EYPE-IVLAFDNSK----SGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIA 136 (304)
T ss_pred CCCe-EEEEEeCCC----CCCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHH
Confidence 4667 899999764 233567778999999987773 35667788999999877 69999999
Q ss_pred HHHH----cCCEEEEEcCCCccccccC-CeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCC
Q psy1206 71 AMVK----AGKVYATATEDMDALTFGS-NILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDS 143 (531)
Q Consensus 71 ~L~r----~G~vd~ViSeDsDlL~fg~-~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pG 143 (531)
+|++ .|.-..|+|+|+|++|+.. ++|-. ++. ++.+.+.+++| .|+|++|+.+|+| +|++||
T Consensus 137 TLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~-~~~----------~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPG 204 (304)
T PHA02567 137 VLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQ-WSP----------MQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVAS 204 (304)
T ss_pred HHHHHHHhCCCcEEEEeCCCChhhccCCCCeEE-eec----------CCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCC
Confidence 9986 4667789999999999974 55422 211 23466788999 5999999999999 999999
Q ss_pred CCC
Q psy1206 144 IRG 146 (531)
Q Consensus 144 IpG 146 (531)
||-
T Consensus 205 Vp~ 207 (304)
T PHA02567 205 IKV 207 (304)
T ss_pred CCC
Confidence 984
No 29
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.46 E-value=8e-14 Score=115.71 Aligned_cols=51 Identities=49% Similarity=0.831 Sum_probs=49.0
Q ss_pred hCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 121 GMELSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 121 ~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.+|++|++|+|+++|+| |||+|||||||+|||.+||++|+++++++++++.
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 58999999999999999 9999999999999999999999999999998865
No 30
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.24 E-value=7.2e-12 Score=129.54 Aligned_cols=110 Identities=30% Similarity=0.404 Sum_probs=91.4
Q ss_pred cccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206 313 SIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME 391 (531)
Q Consensus 313 ~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~ 391 (531)
....|+.++||+++|+|+++++++. .++++.++.| .++|+.++++|++++.+. ++||+||||+||.+|.++.++|+.
T Consensus 7 ~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~-~~~~~~~~l~~~~~~~~~-~~~~~vFD~~~~tfR~~~~~~yK~ 84 (310)
T COG0258 7 MNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTG-AVSGFLGMLYRLIRLLEP-THPVVVFDGKPPTFRHELLEEYKA 84 (310)
T ss_pred hhccCcEEEEechHHHHHHHHhcchhcCCCCCCCcc-HHHHHHHHHHHHHHhcCC-CcEEEEEcCCCCcchHHHHHHHHh
Confidence 3456899999999999999999988 6777777777 899999999999999999 999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206 392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS 446 (531)
Q Consensus 392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~ 446 (531)
.|++ +...+|..+ ...+++.|.+..+.+|+.+|
T Consensus 85 ~R~~---------------------~~p~~l~~q-~~~i~~~~~~~~~~~l~~~G 117 (310)
T COG0258 85 NREK---------------------EMPDELAPQ-IPILTELLVALGIPLLELMG 117 (310)
T ss_pred CCCc---------------------cCHHHHHHH-HHHHHHHHHHhCcHhhhcCC
Confidence 9988 134444444 55566666666666666665
No 31
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.17 E-value=2.3e-11 Score=115.83 Aligned_cols=106 Identities=17% Similarity=0.156 Sum_probs=81.0
Q ss_pred CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206 7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK---- 74 (531)
Q Consensus 7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r---- 74 (531)
+|++ ++++||.+.+ .+|++..+.||++|..++ +.++++++++||+++..| +||||.+|+|++
T Consensus 50 ~p~~-~vv~fD~~~~-----~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~ 123 (169)
T PF02739_consen 50 KPDY-VVVAFDSKGP-----TFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASE 123 (169)
T ss_dssp TEEE-EEEEEEBSSC-----HHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHH
T ss_pred CCce-EEEEecCCCc-----chHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhcc
Confidence 7888 9999997766 456667888899987777 467889999999999887 799999999986
Q ss_pred cCCEEEEEcCCCccccccCC--eEEEeccccCcccCCcEEecHHHHHHhC
Q psy1206 75 AGKVYATATEDMDALTFGSN--ILLRHMTFSEARKLPVQEFHLEKVLEGM 122 (531)
Q Consensus 75 ~G~vd~ViSeDsDlL~fg~~--~Vi~~l~~~~~~~~~v~~~~~~~i~~~l 122 (531)
.|.-..|+|+|+|++|+..+ +|.. ++..+. ....++.+.+.++|
T Consensus 124 ~~~~v~IvS~DkD~~QLv~~~~~V~~-~~~~~~---~~~~~~~~~v~eky 169 (169)
T PF02739_consen 124 EGFEVIIVSGDKDLLQLVDENVNVYL-LDPGKK---KFKVYDPEEVEEKY 169 (169)
T ss_dssp TTCEEEEE-SSGGGGGGTCS-TSEEE-EETTTT---CS-EB-HHHHHHHT
T ss_pred CCCEEEEEcCCCCHHHhcCCCceEEE-eecCCC---CCEEEcHHHHhhcC
Confidence 47778899999999999999 4433 332211 35789999988764
No 32
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=99.13 E-value=1.4e-12 Score=114.33 Aligned_cols=49 Identities=39% Similarity=0.613 Sum_probs=40.3
Q ss_pred CCHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhc
Q psy1206 124 LSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTK 172 (531)
Q Consensus 124 lt~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~ 172 (531)
++|+|++|+.+|+| +||+|||||||+|||.+||++|||+|+|+++++..
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~ 51 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI 51 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence 57999999999999 99999999999999999999999999999988764
No 33
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.10 E-value=9.7e-11 Score=97.27 Aligned_cols=46 Identities=50% Similarity=0.810 Sum_probs=43.8
Q ss_pred Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206 229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 274 (531)
Q Consensus 229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~ 274 (531)
.++|+++|+|+| |||+|+|||||+|+|.++|++|++++.++.+++.
T Consensus 7 ~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 7 PEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred HHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 579999999999 9999999999999999999999999999998864
No 34
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.96 E-value=5.7e-10 Score=80.15 Aligned_cols=34 Identities=44% Similarity=0.851 Sum_probs=30.7
Q ss_pred HHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHc
Q psy1206 126 HEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 126 ~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
|+||+++++|+| +|++|||||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 589999999999 5666699999999999999986
No 35
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.60 E-value=3.2e-08 Score=71.17 Aligned_cols=32 Identities=50% Similarity=0.997 Sum_probs=30.2
Q ss_pred hhhhhhhhhccCcccc---CCCCCchHHHHHHHHhh
Q psy1206 230 YSFIDLCILLGCDYCD---SIRGIGPKRAIELIKEH 262 (531)
Q Consensus 230 e~F~~~CiLsGCDY~~---~i~giG~k~A~kli~k~ 262 (531)
++|+++|+|+| ||.+ +|||||+|+|.++|++|
T Consensus 2 ~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 2 EQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred HHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 68999999999 9999 88899999999999986
No 36
>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=98.31 E-value=5.9e-07 Score=90.12 Aligned_cols=79 Identities=23% Similarity=0.298 Sum_probs=67.4
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCC-CCCCcchhhhHHHHHHHHHHcC--CeeEEeecCCCCCcchHHHHHHHHHHH
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSV-DGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDGKPPTLKSGELNKRMEKRE 394 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~-~g~~tshl~g~~~R~~~ll~~g--IkPVfVFDG~pp~lK~~~~~kR~~~r~ 394 (531)
+.++||+++.+|++..+++. +.++ +|++|+++.|++.++.++++.. ..||+||||.+|..+.+...+.+..|.
T Consensus 2 ~~llIDg~~l~yr~~~a~~~----~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~ 77 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPP----LKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRK 77 (240)
T ss_pred cEEEEEChHHHHHHHHCCCC----cCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCC
Confidence 47899999999999998753 3344 8999999999999999999888 899999999999999999988888886
Q ss_pred HHHHHH
Q psy1206 395 DAQKAL 400 (531)
Q Consensus 395 ~a~~~~ 400 (531)
+.-+.+
T Consensus 78 ~~p~~l 83 (240)
T cd00008 78 KMPEEL 83 (240)
T ss_pred CCCHHH
Confidence 544333
No 37
>PF12813 XPG_I_2: XPG domain containing
Probab=98.22 E-value=3.3e-06 Score=85.17 Aligned_cols=87 Identities=16% Similarity=0.217 Sum_probs=66.7
Q ss_pred HHHHHHHhhc---CCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccC----CeE-EEeccccC------cccCCc
Q psy1206 45 GRLDSFFTIR---REEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGS----NIL-LRHMTFSE------ARKLPV 110 (531)
Q Consensus 45 ~~i~~lL~~~---gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~----~~V-i~~l~~~~------~~~~~v 110 (531)
+.+.++|+.+ |+++++.|+|||+.||.++++.-. .|+|+|||+++|.. ..+ +..+.+.. ...+..
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i~~ 85 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYISA 85 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCeeEE
Confidence 5667888888 999999999999999999986444 78999999999998 233 33333322 123456
Q ss_pred EEecHHHHHHhCCCCHHHHHHHHh
Q psy1206 111 QEFHLEKVLEGMELSHEEFIDLCI 134 (531)
Q Consensus 111 ~~~~~~~i~~~lglt~eqfid~~i 134 (531)
..|+++.+.+.+|+. .+..++.
T Consensus 86 ~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 86 KVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEcHHHHHHHcCCc--hhHHHHH
Confidence 779999999999999 5555555
No 38
>PRK14976 5'-3' exonuclease; Provisional
Probab=98.16 E-value=2e-06 Score=88.42 Aligned_cols=84 Identities=15% Similarity=0.256 Sum_probs=70.2
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcC--CeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDGKPPTLKSGELNKRMEKRED 395 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~g--IkPVfVFDG~pp~lK~~~~~kR~~~r~~ 395 (531)
+.++||+++.||+...+...++..+++++|.+|+++.|++..+.++++.. -.+++||||+.|..+.+....++..|.+
T Consensus 4 ~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~ 83 (281)
T PRK14976 4 KALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKK 83 (281)
T ss_pred cEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCC
Confidence 57899999999998777543344688999999999999999999998765 6789999999999999999998888865
Q ss_pred HHHHHH
Q psy1206 396 AQKALA 401 (531)
Q Consensus 396 a~~~~~ 401 (531)
.-+.+.
T Consensus 84 ~p~~l~ 89 (281)
T PRK14976 84 TPESLI 89 (281)
T ss_pred CCHHHH
Confidence 444433
No 39
>smart00475 53EXOc 5'-3' exonuclease.
Probab=98.15 E-value=2.1e-06 Score=87.23 Aligned_cols=79 Identities=24% Similarity=0.386 Sum_probs=66.8
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHH
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKRE 394 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~ 394 (531)
+.++||+++.||++..+++ .+++++|++|+++.|++..+.+|++.- +| |+||||++|....+...+.+..|+
T Consensus 2 ~lllIDg~~~i~R~~~a~~----~l~~~~G~~t~a~~g~~~~l~~l~~~~-~p~~~~~~fD~~~~~~R~~l~p~YKa~R~ 76 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALP----PLKNSKGEPTNAVYGFLRMLLKLIKEE-KPTYVAVVFDAKGKTFRHELYPEYKANRP 76 (259)
T ss_pred cEEEEeCcHHHHHHHHCCC----cccCCCCCcccHHHHHHHHHHHHHHHc-CCCeEEEEEeCCCCccccchhHHHHhCCC
Confidence 3589999999999998874 378899999999999999999998864 67 999999999998888888888877
Q ss_pred HHHHHHH
Q psy1206 395 DAQKALA 401 (531)
Q Consensus 395 ~a~~~~~ 401 (531)
+..+.+.
T Consensus 77 ~~pe~L~ 83 (259)
T smart00475 77 KTPDELL 83 (259)
T ss_pred CCCHHHH
Confidence 5554443
No 40
>KOG2520|consensus
Probab=97.87 E-value=2.5e-05 Score=89.45 Aligned_cols=56 Identities=20% Similarity=0.268 Sum_probs=48.7
Q ss_pred HHHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEec
Q psy1206 45 GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHM 100 (531)
Q Consensus 45 ~~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l 100 (531)
.+.+.++..++...+.++.+...++-.....++++.++..|+|.+.|+....|.+.
T Consensus 229 k~~r~l~~~~~d~~~~~~~~~~~~~d~~~~~~~~~~~~e~~~~~~~~~~e~~i~~~ 284 (815)
T KOG2520|consen 229 KITRKLVDLENDAPIEAKDKSETLCDGNSVSGLVDFIIESDSDILKFGGENLIKED 284 (815)
T ss_pred HHHHHHHHhhccchhhhcccccccCCcccccchhhcccccchHHhhcccccccccc
Confidence 35677888999999999999889998888889999999999999999998776654
No 41
>PRK09482 flap endonuclease-like protein; Provisional
Probab=97.76 E-value=2.7e-05 Score=79.03 Aligned_cols=46 Identities=37% Similarity=0.556 Sum_probs=43.0
Q ss_pred Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206 229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 274 (531)
Q Consensus 229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~ 274 (531)
.++|.|+..|.| .|..|++||||+|||.+|+++|+|+++|++++..
T Consensus 167 P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~ 214 (256)
T PRK09482 167 PQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDA 214 (256)
T ss_pred HHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHH
Confidence 578999999999 8899999999999999999999999999999853
No 42
>PRK05755 DNA polymerase I; Provisional
Probab=97.64 E-value=3.5e-05 Score=90.46 Aligned_cols=81 Identities=25% Similarity=0.328 Sum_probs=69.8
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHH
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKRE 394 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~ 394 (531)
+.++||+++.+|++..++ +..+++++|.+|+++.|++..+.+|+ ++.+| |+|||++.|.++.+...+++..|.
T Consensus 3 ~~~liDg~~~~~r~~~a~---~~~~~~~~g~~~~a~~g~~~~l~~~~-~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~ 78 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYAL---LPTLRNSDGLPTGAVYGFLNMLLKLL-KEEKPTHVAVAFDAKGKTFRHELYPEYKANRP 78 (880)
T ss_pred eEEEEeCcHHHHHHHHCC---CCcccCCCCCcccHHHHHHHHHHHHH-HhcCCCEEEEEEECCCCccccccCHHHhCCCC
Confidence 468999999999999876 34678999999999999999999999 67888 999999999999999999999886
Q ss_pred HHHHHHHH
Q psy1206 395 DAQKALAK 402 (531)
Q Consensus 395 ~a~~~~~~ 402 (531)
+.-+.+..
T Consensus 79 ~~p~~l~~ 86 (880)
T PRK05755 79 PMPEDLRE 86 (880)
T ss_pred CCcHHHHH
Confidence 65554443
No 43
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.61 E-value=7.1e-05 Score=87.77 Aligned_cols=79 Identities=23% Similarity=0.402 Sum_probs=68.4
Q ss_pred eeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHHHH
Q psy1206 320 ICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKREDA 396 (531)
Q Consensus 320 iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~~a 396 (531)
+.||+++.||++..+++ +.++++++|++|+++.|++..+.+|++.. +| ++||||+.|.++.+...+.+..|.+.
T Consensus 2 ~lIDg~~l~~Ra~~a~~--~~~l~~~~G~~t~av~Gf~~~l~~ll~~~-~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~ 78 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALK--NKPLTNSKGEPTNAVYGFTKMLLKLLKEE-KPTYVAVAFDSGTPTFRHEAYAEYKANRAPT 78 (887)
T ss_pred EEEeCcHHHHHHHHCCC--cccCcCCCCCEecHHHHHHHHHHHHHHhc-CCCEEEEEEcCCCCcchHHHHHHHHhCCCCC
Confidence 68999999999998874 23588999999999999999999999864 78 99999999999999888888888766
Q ss_pred HHHHH
Q psy1206 397 QKALA 401 (531)
Q Consensus 397 ~~~~~ 401 (531)
-+.+.
T Consensus 79 Pe~l~ 83 (887)
T TIGR00593 79 PEELI 83 (887)
T ss_pred hHHHH
Confidence 65554
No 44
>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=96.97 E-value=4.2e-05 Score=67.36 Aligned_cols=45 Identities=40% Similarity=0.617 Sum_probs=34.5
Q ss_pred hhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206 230 YSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 274 (531)
Q Consensus 230 e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~ 274 (531)
++|.|+-.|.| .|-.|++||||+|||.+|+++|+|++.|+.++..
T Consensus 4 ~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~ 50 (101)
T PF01367_consen 4 EQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDE 50 (101)
T ss_dssp HHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SS
T ss_pred HHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHh
Confidence 57788877777 5777888999999999999999999999988753
No 45
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.61 E-value=0.002 Score=51.88 Aligned_cols=24 Identities=38% Similarity=0.546 Sum_probs=20.4
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHH
Q psy1206 143 SIRGIGPKRAIELIKEHRSIEKIL 166 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~~~sle~il 166 (531)
||||||+++|..|+++|+|++++.
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~ 30 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALM 30 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHC
T ss_pred CCCCccHHHHHHHHHHcCCHHHHH
Confidence 899999999999999999998765
No 46
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.16 E-value=0.007 Score=59.63 Aligned_cols=50 Identities=20% Similarity=0.303 Sum_probs=35.9
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++-...|||. .+.--.|-.| -+|+|||||+|+.++..+ +++++...+..
T Consensus 55 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~~l~~aI~~ 105 (203)
T PRK14602 55 REDALELFGFATWDERQTFIVL------ISISKVGAKTALAILSQF-RPDDLRRLVAE 105 (203)
T ss_pred ecCcceeeCCCCHHHHHHHHHH------hCCCCcCHHHHHHHHhhC-CHHHHHHHHHh
Confidence 34445678875 4555555555 468999999999999986 56888877744
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.86 E-value=0.0078 Score=59.05 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=35.3
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++-...|||. .+.--.|-.| -+|+|||||+|+.+++.+ +++++...+..
T Consensus 53 rED~~~LYGF~t~~Er~lF~~L------isVsGIGPK~ALaILs~~-~~~el~~aI~~ 103 (196)
T PRK13901 53 REDELKLFGFLNSSEREVFEEL------IGVDGIGPRAALRVLSGI-KYNEFRDAIDR 103 (196)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence 44445678874 4444445555 378999999999999986 66788777644
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.79 E-value=0.0087 Score=58.14 Aligned_cols=50 Identities=14% Similarity=0.192 Sum_probs=35.3
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++-...|||. .+.--.|-.| -+|+|||||+|+.+++.+ +++++...+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~VsGIGpK~Al~ILs~~-~~~el~~aI~~ 104 (183)
T PRK14601 54 KEDSNKLYGFLDKDEQKMFEML------LKVNGIGANTAMAVCSSL-DVNSFYKALSL 104 (183)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 44445678874 4444445555 368999999999999886 56788777644
No 49
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.78 E-value=0.01 Score=57.70 Aligned_cols=50 Identities=20% Similarity=0.246 Sum_probs=35.8
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++....|||. .+.--.|-.| -+|+|||||+|+.+++.+ +++++...+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------isV~GIGpK~Al~iLs~~-~~~~l~~aI~~ 104 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRML------VKVSGVNYKTAMSILSKL-TPEQLFSAIVN 104 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHccC-CHHHHHHHHHc
Confidence 45555678975 4444444444 378999999999999986 66888877754
No 50
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.73 E-value=0.0091 Score=58.59 Aligned_cols=50 Identities=20% Similarity=0.262 Sum_probs=34.6
Q ss_pred HHHHHHhCCCCHH-HHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELSHE-EFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt~e-qfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++-...|||... .-..|-.| -+|+|||||+|+.+++.+ +++++.+.+..
T Consensus 53 rEd~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~ 103 (197)
T PRK14603 53 REDALSLYGFPDEDSLELFELL------LGVSGVGPKLALALLSAL-PPALLARALLE 103 (197)
T ss_pred ccCCceeeCcCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence 3444567887533 33333444 378999999999999985 66888877754
No 51
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.69 E-value=0.0098 Score=57.96 Aligned_cols=50 Identities=18% Similarity=0.272 Sum_probs=35.2
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++....|||. .+.--.|-.| -+|+|||||+|+.++..+ +++++.+.+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~-~~~el~~aI~~ 104 (188)
T PRK14606 54 SQDGITLYGFSNERKKELFLSL------TKVSRLGPKTALKIISNE-DAETLVTMIAS 104 (188)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 44455678975 4444444455 368999999999999875 66788777644
No 52
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.69 E-value=0.0097 Score=58.32 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=34.9
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++....|||. .+.--.|-.| -+|+|||||+|+.++..+ +++++...+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~el~~aI~~ 104 (195)
T PRK14604 54 REDALTLYGFSTPAQRQLFELL------IGVSGVGPKAALNLLSSG-TPDELQLAIAG 104 (195)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence 34445678875 4444444444 368999999999999974 67888877754
No 53
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=95.59 E-value=0.032 Score=55.01 Aligned_cols=53 Identities=25% Similarity=0.281 Sum_probs=36.8
Q ss_pred EecHHHHHHhCCCCHHHHHH-HHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 112 EFHLEKVLEGMELSHEEFID-LCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 112 ~~~~~~i~~~lglt~eqfid-~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.+-.++....|||....=.+ |..| -+|.|||||+|+.+++.. +++++...+..
T Consensus 51 ~~vREd~~~LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~-~~~~l~~aI~~ 104 (201)
T COG0632 51 LVVREDAHLLYGFLTEEERELFRLL------ISVNGIGPKLALAILSNL-DPEELAQAIAN 104 (201)
T ss_pred EeehhhHHHHcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 45567778889986333333 3333 368899999999999863 56777777643
No 54
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=95.33 E-value=0.008 Score=65.00 Aligned_cols=122 Identities=25% Similarity=0.382 Sum_probs=91.9
Q ss_pred HHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccC-CeEEEeccccCcccCCcEEecHHHHHHhCCC
Q psy1206 46 RLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGS-NILLRHMTFSEARKLPVQEFHLEKVLEGMEL 124 (531)
Q Consensus 46 ~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~-~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lgl 124 (531)
.+..++...+|.|+++||-|..|||||....+++++ -+.+|.+++.+ +++|..+.+..+ +.++..++.....+-.-.
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~-~gp~d~l~ld~vdr~il~m~fg~d-~Ppl~~~~vp~~lem~l~ 210 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYA-FGPSDILLLDGVDRIILDMSFGSD-KPPLDVFHVPRFLEMFLL 210 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhc-CCchHhHHHhhhhhheeecccCCC-CCCCcccccchHHHhccc
Confidence 345578889999999999999999999999999975 77999998876 788888876533 356777777776666667
Q ss_pred CHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHc---CCHHHHHHHh
Q psy1206 125 SHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH---RSIEKILENI 169 (531)
Q Consensus 125 t~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~---~sle~il~~l 169 (531)
+-.-|...-.|.|||+++.+|.+-..-+..+.... ++-|.+...+
T Consensus 211 s~~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd~~~qElfs~ai 258 (531)
T COG5366 211 SSRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGDMKGQELFSKAI 258 (531)
T ss_pred ccchhhhhcccccccccccccccccchhHHHHHHHhccccHHHHHHHh
Confidence 78889999999999999999985443344444433 3344444443
No 55
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.09 E-value=0.023 Score=55.66 Aligned_cols=49 Identities=24% Similarity=0.333 Sum_probs=34.8
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID 170 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~ 170 (531)
.++....|||. .+.--.|-.| -+|+|||||+|+.++..++ .+.++..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~-~~~l~~aI~ 103 (194)
T PRK14605 54 REDALSLFGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMN-AEALASAII 103 (194)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCC-HHHHHHHHH
Confidence 44445678875 4444444555 4799999999999999875 577777663
No 56
>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=95.00 E-value=0.029 Score=54.78 Aligned_cols=50 Identities=26% Similarity=0.269 Sum_probs=34.7
Q ss_pred HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206 115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171 (531)
Q Consensus 115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~ 171 (531)
.++-...|||. .+.--.|..| -+|||||||+|+.++..+ +++++.+.+..
T Consensus 53 red~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~-~~~el~~aI~~ 103 (191)
T TIGR00084 53 REDAELLFGFNTLEERELFKEL------IKVNGVGPKLALAILSNM-SPEEFVYAIET 103 (191)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcC-CHHHHHHHHHh
Confidence 34445578874 4444444555 379999999999998764 57888777743
No 57
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.09 E-value=0.054 Score=52.83 Aligned_cols=47 Identities=23% Similarity=0.442 Sum_probs=30.2
Q ss_pred HHHHHhCCCCHHHHHH-HHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206 116 EKVLEGMELSHEEFID-LCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENI 169 (531)
Q Consensus 116 ~~i~~~lglt~eqfid-~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l 169 (531)
++....+|+....=.+ +..|. .|||||||+|.+++..|++ +.+.+.+
T Consensus 55 d~~~~l~gF~~~~ek~~f~~L~------~i~GIGpk~A~~il~~fg~-~~l~~~i 102 (192)
T PRK00116 55 EDAILLYGFLTKEERELFRLLI------SVSGVGPKLALAILSGLSP-EELVQAI 102 (192)
T ss_pred chhHHHcCcCCHHHHHHHHHHh------cCCCCCHHHHHHHHHhCCH-HHHHHHH
Confidence 3444557765222222 33443 4999999999999999987 5555444
No 58
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=93.94 E-value=0.055 Score=51.79 Aligned_cols=82 Identities=24% Similarity=0.357 Sum_probs=56.2
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCC--eeEEeecCCCCCcchHH----HHHHHH
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGL--KPIYVFDGKPPTLKSGE----LNKRME 391 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gI--kPVfVFDG~pp~lK~~~----~~kR~~ 391 (531)
+.+-||+++.+|+...+... .++.+++|.+|+-+.|++.-+.+++..-- ..|+|||++.+....+- -+.|..
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~--~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~ 79 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPK--DPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRKP 79 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTT--ST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHHH
T ss_pred eEEEEechHHHHHHHHhhcc--CCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCCC
Confidence 45789999999988776643 56889999999999999988888865543 67899999876222211 344555
Q ss_pred HHHHHHHHHH
Q psy1206 392 KREDAQKALA 401 (531)
Q Consensus 392 ~r~~a~~~~~ 401 (531)
..++-...+.
T Consensus 80 ~p~~l~~q~~ 89 (169)
T PF02739_consen 80 MPEELIPQLP 89 (169)
T ss_dssp HHHHHHHHHH
T ss_pred CCHHHHHHHH
Confidence 5555444333
No 59
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=91.05 E-value=0.8 Score=52.85 Aligned_cols=124 Identities=19% Similarity=0.274 Sum_probs=60.7
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHhhhcCC-CCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccC
Q psy1206 143 SIRGIGPKRAIELIKEH--RSIEKILENIDTKKY-TVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRG 219 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~~--~sle~il~~l~~~~~-~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~ 219 (531)
.|+|+|++++.+|+.+. .++++++ .+..... .+| +|--+.|.+++..-.-.- + .+|... .+.....+
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~-~L~~~~L~~l~-gfG~Ksa~~ll~~Ie~sk--~---~~l~R~---l~algi~~ 518 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLF-KLTAEDLLGLE-GFGEKSAQNLLDAIEKSK--E---TSLARF---LYALGIRH 518 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHH-hcCHHHHhcCc-CcchHHHHHHHHHHHHhh--c---CCHHHh---hHhhhccC
Confidence 58999999999999874 5888888 5543222 122 343333332222111000 0 011110 11222345
Q ss_pred CChhhhHhHHhhhhhhhhhc--cCccccCCCCCchHHHHHHHHhhccH--HHHHHHHhhCC
Q psy1206 220 IGPKRAIELLYSFIDLCILL--GCDYCDSIRGIGPKRAIELIKEHRSI--EKILENIDTKK 276 (531)
Q Consensus 220 ~Gp~~~~el~e~F~~~CiLs--GCDY~~~i~giG~k~A~kli~k~~s~--~~vi~~l~~~~ 276 (531)
.|+..+..|...|..+--|. .-+-+..++|||+++|..++.-+.+. ..++..|...|
T Consensus 519 IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~g 579 (665)
T PRK07956 519 VGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAG 579 (665)
T ss_pred cCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcC
Confidence 56655555555554432221 22334567777777776666655543 24455554333
No 60
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=89.74 E-value=0.79 Score=52.79 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=20.0
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHhh
Q psy1206 143 SIRGIGPKRAIELIKEH--RSIEKILENID 170 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~~--~sle~il~~l~ 170 (531)
.|+|+|++++.+|+.+. .++++++ .|.
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~-~L~ 464 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLY-ALK 464 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHH-hcC
Confidence 47889999988888764 4777777 443
No 61
>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=88.96 E-value=0.36 Score=37.63 Aligned_cols=26 Identities=31% Similarity=0.552 Sum_probs=18.8
Q ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE-HRSIEKILE 167 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~-~~sle~il~ 167 (531)
-+|.|||++||.+++.. ++|++++..
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 37899999999999985 789999944
No 62
>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=87.74 E-value=1.2 Score=51.75 Aligned_cols=39 Identities=28% Similarity=0.440 Sum_probs=27.6
Q ss_pred CCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhh
Q psy1206 124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID 170 (531)
Q Consensus 124 lt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~ 170 (531)
-+.+.++.+.. + +.+||||+++|-+|+..|| ++.++.+.
T Consensus 75 ~~~~~i~~yL~---s---~~~~GIG~~~A~~iv~~fg--~~~~~~i~ 113 (720)
T TIGR01448 75 TSKEGIVAYLS---S---RSIKGVGKKLAQRIVKTFG--EAAFDVLD 113 (720)
T ss_pred CCHHHHHHHHh---c---CCCCCcCHHHHHHHHHHhC--HhHHHHHH
Confidence 35667776543 2 2488999999999999998 35555553
No 63
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=87.11 E-value=0.3 Score=39.27 Aligned_cols=26 Identities=35% Similarity=0.512 Sum_probs=21.0
Q ss_pred CCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 246 SIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 246 ~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
+|||||.++|..|.++|+|++++..+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 79999999999999999999887643
No 64
>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=85.63 E-value=0.66 Score=36.55 Aligned_cols=25 Identities=44% Similarity=0.731 Sum_probs=22.4
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206 143 SIRGIGPKRAIELIKE-HRSIEKILE 167 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~-~~sle~il~ 167 (531)
.|||||+++|.+|... |+|++++..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~~~l~~ 34 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTLEDLAN 34 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred cCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence 6999999999999998 899888764
No 65
>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=84.38 E-value=0.8 Score=31.70 Aligned_cols=15 Identities=40% Similarity=0.780 Sum_probs=12.2
Q ss_pred CCCCccHHHHHHHHH
Q psy1206 143 SIRGIGPKRAIELIK 157 (531)
Q Consensus 143 GIpGIG~ktA~kLI~ 157 (531)
.|||||++||-.++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 689999999998864
No 66
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=84.06 E-value=2.6 Score=45.98 Aligned_cols=116 Identities=23% Similarity=0.255 Sum_probs=69.3
Q ss_pred HHHHHHhhc--CCcccc-CCCchhHHHHHHH-----HcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206 46 RLDSFFTIR--REEKRK-APCEAEAQCAAMV-----KAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK 117 (531)
Q Consensus 46 ~i~~lL~~~--gIp~vv-APyEADAq~A~L~-----r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~ 117 (531)
.+.++|..+ +|.++- ....||=.+-+=+ +.|.=-.++|.|-|.|+|.+..-..++- .+..
T Consensus 147 ~l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI-----------~t~~- 214 (425)
T PF04599_consen 147 ILESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKII-----------KTMN- 214 (425)
T ss_pred HHHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHH-----------HhHH-
Confidence 456667666 677774 5568887666544 3577778999999999999843222210 0111
Q ss_pred HHHhCCC-----CHHHHHHHHhHcCCCCCCCCCCcc--HHHHHHHHHHcC--CHHHHHHHhhhcCCCC
Q psy1206 118 VLEGMEL-----SHEEFIDLCILLGCDYCDSIRGIG--PKRAIELIKEHR--SIEKILENIDTKKYTV 176 (531)
Q Consensus 118 i~~~lgl-----t~eqfid~~iL~G~DY~pGIpGIG--~ktA~kLI~~~~--sle~il~~l~~~~~~i 176 (531)
+.+.+ +.---...++.-||||-||+-|+. .++--+ +.-|. +++++++.|.-+++..
T Consensus 215 --~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~-i~LF~dFti~Ni~~SL~~kny~~ 279 (425)
T PF04599_consen 215 --QLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNR-IKLFEDFTIDNILQSLAIKNYSL 279 (425)
T ss_pred --hHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccc-eeccccccHHHHHHHHhhhhhhh
Confidence 11211 222223345667899999999964 333222 33343 6789998886654433
No 67
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=83.82 E-value=0.93 Score=51.36 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=25.5
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 140 YCDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
=+.+|||||+|+..+|+++|||+++|.++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 34589999999999999999999998754
No 68
>PHA00439 exonuclease
Probab=83.55 E-value=2.2 Score=44.45 Aligned_cols=60 Identities=10% Similarity=0.158 Sum_probs=47.3
Q ss_pred ceeeecccchHHHHHHHHhh--c-CccccCCCCCCcchhhhHHHHHHHHHHc----CCee-EEeecCC
Q psy1206 318 RKICIDASMSLYQFLIAVRS--E-GNQLMSVDGEPTSHLMGTFYRTIRLVEH----GLKP-IYVFDGK 377 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~--~-g~~l~~~~g~~tshl~g~~~R~~~ll~~----gIkP-VfVFDG~ 377 (531)
..+-||++..+|+...++-. + +..+++++|..|+-+.|++.-+.++++. .-.+ |++||+.
T Consensus 7 ~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~~ 74 (286)
T PHA00439 7 GVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTDS 74 (286)
T ss_pred cEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECCC
Confidence 57889999999998888732 1 3457899999999999999999999865 3333 5669954
No 69
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=83.20 E-value=0.87 Score=52.15 Aligned_cols=28 Identities=29% Similarity=0.444 Sum_probs=25.1
Q ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
+.+|||||++++.+|+++|||+++|.+.
T Consensus 554 L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 554 LLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 3589999999999999999999998763
No 70
>PHA03065 Hypothetical protein; Provisional
Probab=82.38 E-value=2.9 Score=45.45 Aligned_cols=118 Identities=21% Similarity=0.266 Sum_probs=69.5
Q ss_pred HHHHHHHhhc--CCcccc-CCCchhHHHHHHH-----HcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHH
Q psy1206 45 GRLDSFFTIR--REEKRK-APCEAEAQCAAMV-----KAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLE 116 (531)
Q Consensus 45 ~~i~~lL~~~--gIp~vv-APyEADAq~A~L~-----r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~ 116 (531)
..+.+.|..+ +|.++- ..-.||=.+-.=+ +.|.=-.++|.|-|.|+|.+..-+-++ ..+.
T Consensus 148 ~~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki-----------I~t~- 215 (438)
T PHA03065 148 RLLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI-----------IKTA- 215 (438)
T ss_pred HHHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH-----------HHhH-
Confidence 4566677777 677774 4457776655433 357777899999999999874211111 0111
Q ss_pred HHHHhCCCC-----HHHHHHHHhHcCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHhhhcCCCCC
Q psy1206 117 KVLEGMELS-----HEEFIDLCILLGCDYCDSIRGIG--PKR--AIELIKEHRSIEKILENIDTKKYTVP 177 (531)
Q Consensus 117 ~i~~~lglt-----~eqfid~~iL~G~DY~pGIpGIG--~kt--A~kLI~~~~sle~il~~l~~~~~~ip 177 (531)
-+.+.+. .---...++.-||||.||+-|+. +++ -.+|...| +.+++++.|..+++.+.
T Consensus 216 --~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~kny~l~ 282 (438)
T PHA03065 216 --NQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLAIKNYSLK 282 (438)
T ss_pred --HHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHHhhhhhcc
Confidence 1122222 22222345557899999999975 333 12333333 66899988876655443
No 71
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=81.57 E-value=1.1 Score=50.92 Aligned_cols=28 Identities=32% Similarity=0.417 Sum_probs=25.1
Q ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
+.+|||||+|+..+|+++|||+++|.+.
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 3589999999999999999999998754
No 72
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=81.48 E-value=1.2 Score=50.53 Aligned_cols=29 Identities=31% Similarity=0.458 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 140 YCDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
-+..|||||+++..+|+++|||+++|.++
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 45699999999999999999999998764
No 73
>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=81.02 E-value=0.94 Score=31.37 Aligned_cols=17 Identities=35% Similarity=0.600 Sum_probs=12.8
Q ss_pred ccCCCCCchHHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIK 260 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~ 260 (531)
+.++||||+++|-.++.
T Consensus 13 L~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 13 LMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHTSTT-SHHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHHh
Confidence 45799999999987653
No 74
>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=80.30 E-value=1.1 Score=35.23 Aligned_cols=27 Identities=41% Similarity=0.609 Sum_probs=23.3
Q ss_pred ccCCCCCchHHHHHHHHh-hccHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKE-HRSIEKILE 270 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k-~~s~~~vi~ 270 (531)
+.+|||||+++|.+|+.. ++|++.+..
T Consensus 7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~ 34 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYEAGIKTLEDLAN 34 (60)
T ss_dssp HHTSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred hccCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence 457999999999999999 889887764
No 75
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=80.26 E-value=2.9 Score=47.98 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=25.5
Q ss_pred ccCCCCCchHHHHHHHHhhccH--HHHHHHHhhCC
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSI--EKILENIDTKK 276 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~--~~vi~~l~~~~ 276 (531)
+.+++|||.+.|..++.=+... ..+++.|...|
T Consensus 545 l~~i~giG~~vA~si~~ff~~~~~~~li~~L~~~g 579 (667)
T COG0272 545 LASIPGIGEVVARSIIEFFANEENRELIDELLAAG 579 (667)
T ss_pred HhhccchhHHHHHHHHHHHcCHHHHHHHHHHHHcC
Confidence 3459999999999999888765 45777776655
No 76
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=79.98 E-value=0.68 Score=39.81 Aligned_cols=14 Identities=71% Similarity=1.326 Sum_probs=13.4
Q ss_pred HhhhhhhhhhccCc
Q psy1206 229 LYSFIDLCILLGCD 242 (531)
Q Consensus 229 ~e~F~~~CiLsGCD 242 (531)
.++|+++|||+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 78999999999998
No 77
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=79.60 E-value=2.6 Score=44.57 Aligned_cols=27 Identities=26% Similarity=0.561 Sum_probs=20.9
Q ss_pred ccCCCCCchHHHHHHHHhhc--cHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKEHR--SIEKILEN 271 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~--s~~~vi~~ 271 (531)
+-+|||||||||.++.. .+ |++.+.++
T Consensus 91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 35799999999999987 55 67766554
No 78
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=78.65 E-value=1.7 Score=49.90 Aligned_cols=26 Identities=38% Similarity=0.603 Sum_probs=23.8
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKEHRSIEKILE 167 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~~~sle~il~ 167 (531)
.||||||+++|..|++.|+|+++|..
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 68999999999999999999988754
No 79
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=77.74 E-value=7.9 Score=45.05 Aligned_cols=25 Identities=24% Similarity=0.585 Sum_probs=17.8
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHH
Q psy1206 143 SIRGIGPKRAIELIKEH--RSIEKILE 167 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~~--~sle~il~ 167 (531)
.|+|+|+++..+|+... .++.+++.
T Consensus 466 ~I~GLG~k~i~~L~~~g~V~~~~Dl~~ 492 (689)
T PRK14351 466 DIEGLGEERVQQLVDAGLVESLADLYD 492 (689)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHH
Confidence 57888888888888763 46666654
No 80
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=75.57 E-value=2.3 Score=49.05 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=25.1
Q ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
+..|||||++++.+|+++|||+++|.+.
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 4589999999999999999999998754
No 81
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=74.79 E-value=2.3 Score=28.08 Aligned_cols=18 Identities=33% Similarity=0.599 Sum_probs=15.4
Q ss_pred CCCCCCccHHHHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKE 158 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~ 158 (531)
+..|||||+++|.+++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 457999999999999863
No 82
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.43 E-value=2.4 Score=41.35 Aligned_cols=46 Identities=26% Similarity=0.386 Sum_probs=31.7
Q ss_pred ecHHHHHHhC-CCCHHHHHHHHhHcC-CCCCCCCCCccHHHHHHHHHHc
Q psy1206 113 FHLEKVLEGM-ELSHEEFIDLCILLG-CDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 113 ~~~~~i~~~l-glt~eqfid~~iL~G-~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
+.+..-+.-+ ++++++|... +..| ...+..+||||+|||-++|-+.
T Consensus 81 IGpK~Al~ILs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 81 IGANTAMAVCSSLDVNSFYKA-LSLGDESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred ccHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 4444444444 5788887654 3344 4566799999999999999764
No 83
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=74.20 E-value=2.4 Score=48.20 Aligned_cols=31 Identities=26% Similarity=0.500 Sum_probs=26.9
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206 139 DYCDSIRGIGPKRAIELIKEHRSIEKILENI 169 (531)
Q Consensus 139 DY~pGIpGIG~ktA~kLI~~~~sle~il~~l 169 (531)
.-+..|||||++++.+|+++|||+++|..+-
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As 555 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREAS 555 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 3456899999999999999999999998753
No 84
>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=74.08 E-value=2.6 Score=35.67 Aligned_cols=26 Identities=38% Similarity=0.552 Sum_probs=21.7
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHH
Q psy1206 140 YCDSIRGIGPKRAIELIKEHRSIEKI 165 (531)
Q Consensus 140 Y~pGIpGIG~ktA~kLI~~~~sle~i 165 (531)
-+-.|||||+.+|..|+.+.++++.+
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~rF 28 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISRF 28 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchhc
Confidence 45689999999999999998876543
No 85
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=74.00 E-value=2.4 Score=48.40 Aligned_cols=27 Identities=48% Similarity=0.724 Sum_probs=24.5
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
.+|||||++++.+|++.|||+++|.+.
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 589999999999999999999988653
No 86
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=73.88 E-value=2.8 Score=42.35 Aligned_cols=28 Identities=29% Similarity=0.536 Sum_probs=24.8
Q ss_pred CCCCCCccHHHHHHHHHH-cCCHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKE-HRSIEKILEN 168 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~-~~sle~il~~ 168 (531)
+..|||||+++|.+|+.. |+|+++|...
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 458999999999999999 9999998654
No 87
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=73.41 E-value=7.6 Score=45.03 Aligned_cols=35 Identities=20% Similarity=0.297 Sum_probs=25.5
Q ss_pred ccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCC
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYT 278 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~ 278 (531)
+.+|+|||+++|..++.=+.+.+ .+++.|..-++.
T Consensus 543 l~~i~giG~~~a~si~~ff~~~~~~~~i~~l~~~gv~ 579 (669)
T PRK14350 543 LLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFK 579 (669)
T ss_pred HhhCCCccHHHHHHHHHHHcCHHHHHHHHHHHHcCCC
Confidence 45799999999999998887754 456656444443
No 88
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=72.50 E-value=2.5 Score=48.47 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=25.6
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+.+|||||++++.+|++.++|+++|..+
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 35689999999999999999999987753
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=72.13 E-value=5.2 Score=39.15 Aligned_cols=53 Identities=30% Similarity=0.480 Sum_probs=35.2
Q ss_pred HhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCC---C-CCCCcchHHHHHHHh
Q psy1206 229 LYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKK---Y-TVPEGWLYKEARELF 292 (531)
Q Consensus 229 ~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~---~-~vP~~y~~~~A~~~F 292 (531)
++.|+.| -+++|||||+|..++..+ +++.+++++..+. + ++| ++-=+.|..+.
T Consensus 68 r~lF~~L---------~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ip-GiGkKtAerIi 124 (191)
T TIGR00084 68 RELFKEL---------IKVNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIP-GVGKKTAERLL 124 (191)
T ss_pred HHHHHHH---------hCCCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHH
Confidence 6678777 378999999999998765 5777777775421 1 333 23245555555
No 90
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.87 E-value=3 Score=41.18 Aligned_cols=46 Identities=20% Similarity=0.223 Sum_probs=31.8
Q ss_pred ecHHHHHHhC-CCCHHHHHHHHhHcC-CCCCCCCCCccHHHHHHHHHHc
Q psy1206 113 FHLEKVLEGM-ELSHEEFIDLCILLG-CDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 113 ~~~~~i~~~l-glt~eqfid~~iL~G-~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
+.+..-+.-+ .+++++|+..- ..| ...+..+||||+|||-++|-+.
T Consensus 80 IGPK~ALaILs~~~~~el~~aI-~~~D~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 80 IGPRAALRVLSGIKYNEFRDAI-DREDIELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred cCHHHHHHHHcCCCHHHHHHHH-HhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 4444434444 47888877653 344 4566799999999999999764
No 91
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.64 E-value=2.5 Score=41.52 Aligned_cols=76 Identities=17% Similarity=0.142 Sum_probs=44.9
Q ss_pred CEEEEEcCCCccccccCCe-----EEEeccccCcccCCcEEecHHHHHHhCC-CCHHHHHHHHhHcCCCCCCCCCCccHH
Q psy1206 77 KVYATATEDMDALTFGSNI-----LLRHMTFSEARKLPVQEFHLEKVLEGME-LSHEEFIDLCILLGCDYCDSIRGIGPK 150 (531)
Q Consensus 77 ~vd~ViSeDsDlL~fg~~~-----Vi~~l~~~~~~~~~v~~~~~~~i~~~lg-lt~eqfid~~iL~G~DY~pGIpGIG~k 150 (531)
++..++.|| +..+||-.. +++.+ +.+.-+.+..-+.-++ +++++|+..-.---..-+..+||||+|
T Consensus 48 ~t~~~vrEd-~~~LyGF~~~~Er~lF~~L-------i~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkK 119 (195)
T PRK14604 48 YTHLIVRED-ALTLYGFSTPAQRQLFELL-------IGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKK 119 (195)
T ss_pred EEEEEEecC-CceeeCCCCHHHHHHHHHH-------hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHH
Confidence 456777777 355566421 11111 0122344444444444 788888765433224566799999999
Q ss_pred HHHHHHHHcC
Q psy1206 151 RAIELIKEHR 160 (531)
Q Consensus 151 tA~kLI~~~~ 160 (531)
||-+++-+.+
T Consensus 120 tAerIilELk 129 (195)
T PRK14604 120 TAERIVLELK 129 (195)
T ss_pred HHHHHHHHHH
Confidence 9999998643
No 92
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.47 E-value=2.6 Score=41.23 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=33.1
Q ss_pred ecHHHHHHhC-CCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHc
Q psy1206 113 FHLEKVLEGM-ELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 113 ~~~~~i~~~l-glt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
+.+..-+.-+ ++++++|+..-.---...+..+||||+|||-+++-+.
T Consensus 81 IGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 81 LGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred ccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 4455445555 5788888765433225566799999999999999764
No 93
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.98 E-value=3.2 Score=40.86 Aligned_cols=76 Identities=17% Similarity=0.107 Sum_probs=44.9
Q ss_pred CEEEEEcCCCccccccCCeE-----EEeccccCcccCCcEEecHHHHHHhCC-CCHHHHHHHHhHcCCCCCCCCCCccHH
Q psy1206 77 KVYATATEDMDALTFGSNIL-----LRHMTFSEARKLPVQEFHLEKVLEGME-LSHEEFIDLCILLGCDYCDSIRGIGPK 150 (531)
Q Consensus 77 ~vd~ViSeDsDlL~fg~~~V-----i~~l~~~~~~~~~v~~~~~~~i~~~lg-lt~eqfid~~iL~G~DY~pGIpGIG~k 150 (531)
++..++.||. ..+||-... ++.+ ..+.-+.+..-+.-++ +++++|+..-.---..-+..+||||+|
T Consensus 47 ~t~~~vrEd~-~~LyGF~~~~Er~lF~~L-------~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkK 118 (197)
T PRK14603 47 HTRLVVREDA-LSLYGFPDEDSLELFELL-------LGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKK 118 (197)
T ss_pred EEEEEEccCC-ceeeCcCCHHHHHHHHHH-------hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHH
Confidence 4567777774 555664311 1111 1122344554455554 788887764322113455699999999
Q ss_pred HHHHHHHHcC
Q psy1206 151 RAIELIKEHR 160 (531)
Q Consensus 151 tA~kLI~~~~ 160 (531)
||-++|-+.+
T Consensus 119 tAerIilELk 128 (197)
T PRK14603 119 LAERIALELK 128 (197)
T ss_pred HHHHHHHHHH
Confidence 9999998743
No 94
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.97 E-value=4 Score=39.85 Aligned_cols=45 Identities=18% Similarity=0.255 Sum_probs=32.1
Q ss_pred ecHHHHHHhCC-CCHHHHHHHHhHcC-CCCCCCCCCccHHHHHHHHHHc
Q psy1206 113 FHLEKVLEGME-LSHEEFIDLCILLG-CDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 113 ~~~~~i~~~lg-lt~eqfid~~iL~G-~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
+.+..-+.-++ +++++|+..-. .| ..-+ .+||||.|||-+++-+.
T Consensus 81 IGpK~Al~iLs~~~~~~l~~aI~-~~D~~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 81 VNYKTAMSILSKLTPEQLFSAIV-NEDKAAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred cCHHHHHHHHccCCHHHHHHHHH-cCCHhhe-ECCCCcHHHHHHHHHHH
Confidence 44544455554 78888876543 34 5567 99999999999999764
No 95
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=70.70 E-value=3.8 Score=37.97 Aligned_cols=25 Identities=28% Similarity=0.466 Sum_probs=21.4
Q ss_pred CCCCccHHHHHHHHHH--cCCHHHHHH
Q psy1206 143 SIRGIGPKRAIELIKE--HRSIEKILE 167 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~--~~sle~il~ 167 (531)
.+|||||+.|-++|.. |.|+|++++
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4799999999999974 779998875
No 96
>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=69.88 E-value=3.5 Score=34.92 Aligned_cols=27 Identities=37% Similarity=0.559 Sum_probs=22.9
Q ss_pred CccccCCCCCchHHHHHHHHhhccHHH
Q psy1206 241 CDYCDSIRGIGPKRAIELIKEHRSIEK 267 (531)
Q Consensus 241 CDY~~~i~giG~k~A~kli~k~~s~~~ 267 (531)
|+-+.+|||||+.+|..++...+++++
T Consensus 1 ~~~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 1 AELLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred CchhcCCCCccHHHHHHHHHHHcCchh
Confidence 456789999999999999998888743
No 97
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=69.47 E-value=3.8 Score=47.45 Aligned_cols=29 Identities=24% Similarity=0.362 Sum_probs=25.7
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 140 YCDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
-+..|||||++++.+|+++|||+++|.+.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 34589999999999999999999998874
No 98
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=69.26 E-value=3.5 Score=40.19 Aligned_cols=20 Identities=30% Similarity=0.577 Sum_probs=18.2
Q ss_pred cCCCCCchHHHHHHHHhhcc
Q psy1206 245 DSIRGIGPKRAIELIKEHRS 264 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k~~s 264 (531)
.++||||||+|.+++..+++
T Consensus 76 ~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 76 ISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred hcCCCCCHHHHHHHHHhCCH
Confidence 46999999999999999987
No 99
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=68.90 E-value=3.4 Score=46.98 Aligned_cols=29 Identities=31% Similarity=0.367 Sum_probs=25.4
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+..|||||+|+..+|++.++|+++|-.+
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 35689999999999999999999887653
No 100
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=68.43 E-value=3.8 Score=46.52 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=25.6
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+..|||||+|+..+|++.++|+++|-.+
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 46689999999999999999999887654
No 101
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.33 E-value=4.1 Score=40.29 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=31.9
Q ss_pred ecHHHHHHhCC-CCHHHHHHHHhHcC-CCCCCCCCCccHHHHHHHHHHc
Q psy1206 113 FHLEKVLEGME-LSHEEFIDLCILLG-CDYCDSIRGIGPKRAIELIKEH 159 (531)
Q Consensus 113 ~~~~~i~~~lg-lt~eqfid~~iL~G-~DY~pGIpGIG~ktA~kLI~~~ 159 (531)
+.+..-+.-++ +++++|+.. +..| .+-+..+||||+|||-++|-+.
T Consensus 82 IGpK~Al~iLs~~~~~~l~~a-I~~~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 82 VGAKTALAILSQFRPDDLRRL-VAEEDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred cCHHHHHHHHhhCCHHHHHHH-HHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 44444445554 688877654 3344 4566799999999999999864
No 102
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.88 E-value=7.3 Score=38.23 Aligned_cols=35 Identities=29% Similarity=0.437 Sum_probs=27.1
Q ss_pred HhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHh
Q psy1206 229 LYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID 273 (531)
Q Consensus 229 ~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~ 273 (531)
++.|+.+ -+++|||||+|..++..++ ++.++..+.
T Consensus 69 r~lF~~L---------i~V~GIGpK~Al~ILs~~~-~~~l~~aI~ 103 (194)
T PRK14605 69 LSLFETL---------IDVSGIGPKLGLAMLSAMN-AEALASAII 103 (194)
T ss_pred HHHHHHH---------hCCCCCCHHHHHHHHHhCC-HHHHHHHHH
Confidence 5667666 3789999999999999875 666666663
No 103
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=67.80 E-value=4 Score=46.41 Aligned_cols=29 Identities=31% Similarity=0.458 Sum_probs=25.8
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+..|||||+++..+|++.++|+++|-.+
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 46689999999999999999999987754
No 104
>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=67.76 E-value=5.1 Score=31.22 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=17.9
Q ss_pred ccCCCCCchHHHHHHHHh-hccHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKE-HRSIEKI 268 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k-~~s~~~v 268 (531)
..+|.|||++||.+++.+ ++|++.+
T Consensus 4 f~~I~GVG~~tA~~w~~~G~rtl~Dl 29 (52)
T PF10391_consen 4 FTGIWGVGPKTARKWYAKGIRTLEDL 29 (52)
T ss_dssp HHTSTT--HHHHHHHHHTT--SHHHH
T ss_pred hhhcccccHHHHHHHHHhCCCCHHHH
Confidence 357999999999999975 7788877
No 105
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=67.67 E-value=14 Score=42.88 Aligned_cols=103 Identities=21% Similarity=0.352 Sum_probs=65.5
Q ss_pred cCCcccc----CCCchhHHHHHHHHcC---------CEEEEEcCCCccccccC----Ce--EEE-eccccCc----c---
Q psy1206 54 RREEKRK----APCEAEAQCAAMVKAG---------KVYATATEDMDALTFGS----NI--LLR-HMTFSEA----R--- 106 (531)
Q Consensus 54 ~gIp~vv----APyEADAq~A~L~r~G---------~vd~ViSeDsDlL~fg~----~~--Vi~-~l~~~~~----~--- 106 (531)
.+|.+|. -|+|+|.-+-...|.. -..+|.+-|.|++++|- |+ |+| .+.+..+ +
T Consensus 175 rnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~ 254 (953)
T COG5049 175 RNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCT 254 (953)
T ss_pred eeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCcccccccccc
Confidence 3567764 3899999998887743 45789999999999994 33 455 3322210 0
Q ss_pred ----------------cCCcEEecHHHHHHhC-----------CCC----HHHHHHHHhHcCCCCCCCCCCccHH-HHHH
Q psy1206 107 ----------------KLPVQEFHLEKVLEGM-----------ELS----HEEFIDLCILLGCDYCDSIRGIGPK-RAIE 154 (531)
Q Consensus 107 ----------------~~~v~~~~~~~i~~~l-----------glt----~eqfid~~iL~G~DY~pGIpGIG~k-tA~k 154 (531)
..++-+++++-+++-+ .++ -+.|+.+|-++|.|++|.+|++-+. .|+.
T Consensus 255 ~~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~ 334 (953)
T COG5049 255 KCGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIE 334 (953)
T ss_pred cccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHH
Confidence 0134456666554421 133 3456667888999999999998642 3444
Q ss_pred HH
Q psy1206 155 LI 156 (531)
Q Consensus 155 LI 156 (531)
+|
T Consensus 335 ~l 336 (953)
T COG5049 335 TL 336 (953)
T ss_pred HH
Confidence 33
No 106
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=66.37 E-value=10 Score=38.39 Aligned_cols=70 Identities=14% Similarity=0.187 Sum_probs=36.4
Q ss_pred eeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee----EEeecCCCCCcchHHHHHHHHHHH
Q psy1206 319 KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP----IYVFDGKPPTLKSGELNKRMEKRE 394 (531)
Q Consensus 319 ~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP----VfVFDG~pp~lK~~~~~kR~~~r~ 394 (531)
-+=||....||.....-. + +.-.+...+..-+++.+..|-+-++| ++.+||.+|-.|-.+...||-+..
T Consensus 32 ~LYiDmN~IIH~~~~~~~--~-----~~~~~~~~~~~~i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~ 104 (237)
T PF03159_consen 32 NLYIDMNGIIHNCIHPND--S-----SIPKTEEEIFQRIFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSA 104 (237)
T ss_dssp EEEEETHHHHHHHHS-SS--S---------SHHHHHHHHHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHH
T ss_pred EEEEEcchhhhHhcCCcc--c-----CCCccHHHHHHHHHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHh
Confidence 467889999998654221 1 11112233333334444444456666 688999999999988888776644
Q ss_pred H
Q psy1206 395 D 395 (531)
Q Consensus 395 ~ 395 (531)
.
T Consensus 105 ~ 105 (237)
T PF03159_consen 105 K 105 (237)
T ss_dssp H
T ss_pred h
Confidence 3
No 107
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=66.26 E-value=5.5 Score=45.40 Aligned_cols=28 Identities=43% Similarity=0.628 Sum_probs=24.9
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206 142 DSIRGIGPKRAIELIKEHRSIEKILENI 169 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~~~sle~il~~l 169 (531)
.+|||||+++..+|+++|||+++|.+..
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i~~As 560 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGIKSAS 560 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence 5899999999999999999999887654
No 108
>PRK08609 hypothetical protein; Provisional
Probab=65.03 E-value=14 Score=42.00 Aligned_cols=23 Identities=22% Similarity=0.304 Sum_probs=15.9
Q ss_pred CCCCCCccHHHHHHHHH--HcCCHH
Q psy1206 141 CDSIRGIGPKRAIELIK--EHRSIE 163 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~--~~~sle 163 (531)
...|||||.+.|.++-. +.|++.
T Consensus 50 l~~ipgIG~~ia~kI~Eil~tG~~~ 74 (570)
T PRK08609 50 FTKLKGIGKGTAEVIQEYRETGESS 74 (570)
T ss_pred hccCCCcCHHHHHHHHHHHHhCChH
Confidence 46899999999876432 345543
No 109
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=64.33 E-value=7.2 Score=38.64 Aligned_cols=76 Identities=22% Similarity=0.227 Sum_probs=49.6
Q ss_pred CEEEEEcCCCccccccCCeE-----EEeccccCcccCCcEEecHHHHHHhC-CCCHHHHHHHHhHcCCCCCCCCCCccHH
Q psy1206 77 KVYATATEDMDALTFGSNIL-----LRHMTFSEARKLPVQEFHLEKVLEGM-ELSHEEFIDLCILLGCDYCDSIRGIGPK 150 (531)
Q Consensus 77 ~vd~ViSeDsDlL~fg~~~V-----i~~l~~~~~~~~~v~~~~~~~i~~~l-glt~eqfid~~iL~G~DY~pGIpGIG~k 150 (531)
++..++.||. ..+||-... ++.+ +.+.-+.+..-+.-+ .++++.|+..-..---.++-.+||||.|
T Consensus 48 ~t~~~vREd~-~~LyGF~~~~ER~lF~~L-------isVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkK 119 (201)
T COG0632 48 FTHLVVREDA-HLLYGFLTEEERELFRLL-------ISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKK 119 (201)
T ss_pred EEEEeehhhH-HHHcCCCCHHHHHHHHHH-------HccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHH
Confidence 4567888998 888886421 1111 012224444444444 4688888876665556677899999999
Q ss_pred HHHHHHHHcC
Q psy1206 151 RAIELIKEHR 160 (531)
Q Consensus 151 tA~kLI~~~~ 160 (531)
||-+++-+-.
T Consensus 120 tAerivleLk 129 (201)
T COG0632 120 TAERIVLELK 129 (201)
T ss_pred HHHHHHHHHh
Confidence 9999998643
No 110
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=63.64 E-value=6.1 Score=40.51 Aligned_cols=26 Identities=50% Similarity=0.736 Sum_probs=24.0
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 143 SIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
++||||.+.|..|+.+|+|++++...
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 78999999999999999999988764
No 111
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=61.80 E-value=4.3 Score=48.02 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=25.9
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 139 DYCDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 139 DY~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
||+-++||||++.|..|+.+|+|++++...
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 344579999999999999999999998763
No 112
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=61.53 E-value=6.3 Score=45.66 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=25.6
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+..|||||++++.+|++.++|+++|-.+
T Consensus 609 ~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred ccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 46689999999999999999999887654
No 113
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=61.44 E-value=5.7 Score=45.24 Aligned_cols=30 Identities=27% Similarity=0.536 Sum_probs=26.7
Q ss_pred ccccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 242 DYCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 242 DY~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
.-+.+|||||++++.+|++.++|+++|..+
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 346789999999999999999999998864
No 114
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=60.24 E-value=6.2 Score=45.33 Aligned_cols=27 Identities=37% Similarity=0.562 Sum_probs=24.0
Q ss_pred ccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIEKILE 270 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~~vi~ 270 (531)
+.+|||||+|+|..|++.++|++.|..
T Consensus 571 L~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 571 LTDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hhcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 457999999999999999999987754
No 115
>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=57.98 E-value=8.7 Score=44.42 Aligned_cols=34 Identities=18% Similarity=0.383 Sum_probs=25.4
Q ss_pred cCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCC
Q psy1206 245 DSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYT 278 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~ 278 (531)
..++|||.++|..++.-+.+.+ .++..|...|+.
T Consensus 533 ~~i~GIG~~~A~~I~~ff~~~~~~~~i~~L~~~gv~ 568 (652)
T TIGR00575 533 LSVEGVGPKVAESIVNFFHDPNNRQLIKKLEELGVE 568 (652)
T ss_pred hcCCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCC
Confidence 4689999999999998776643 567777655544
No 116
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=57.89 E-value=7.3 Score=39.92 Aligned_cols=28 Identities=46% Similarity=0.698 Sum_probs=25.3
Q ss_pred ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
+.++||||.+.|.+++.+++|+++++.+
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred HHcCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 4589999999999999999999998865
No 117
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=57.38 E-value=9.2 Score=44.53 Aligned_cols=33 Identities=15% Similarity=0.276 Sum_probs=23.4
Q ss_pred cCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCC
Q psy1206 245 DSIRGIGPKRAIELIKEHRSIE--KILENIDTKKY 277 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~ 277 (531)
..++|||.++|..++.-+.+.+ .++..|...|+
T Consensus 563 ~~i~GIG~k~A~sI~~ff~~~~n~~~i~~L~~~Gv 597 (689)
T PRK14351 563 RAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGV 597 (689)
T ss_pred hccCCcCHHHHHHHHHHHhhhHHHHHHHHHHhccc
Confidence 4688999999998888777654 45555544443
No 118
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=56.99 E-value=7.6 Score=45.06 Aligned_cols=30 Identities=23% Similarity=0.300 Sum_probs=26.2
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILENI 272 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~l 272 (531)
-+.+|||||++++.+|++.++|++.|..+-
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~AS 667 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAAG 667 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhcC
Confidence 356799999999999999999999888643
No 119
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=56.03 E-value=7.9 Score=44.32 Aligned_cols=29 Identities=45% Similarity=0.631 Sum_probs=25.5
Q ss_pred cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 243 YCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
-+.+|||||++++.+|++.++|++.|..+
T Consensus 544 ~L~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 544 ALDDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred hHhhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 35689999999999999999999888753
No 120
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=55.46 E-value=9.2 Score=38.69 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=16.3
Q ss_pred ccCCCCCchHHHHHHHHh-hccHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKE-HRSIEKI 268 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k-~~s~~~v 268 (531)
+..|||||+++|.+|+.. |+|++.|
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~I 30 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDV 30 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHH
Confidence 345677777777777776 6666654
No 121
>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=55.09 E-value=12 Score=33.87 Aligned_cols=24 Identities=29% Similarity=0.702 Sum_probs=18.7
Q ss_pred CCCCCccHHHHHHHHHH------cCCHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE------HRSIEKI 165 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~------~~sle~i 165 (531)
..+||||+++|.++|.. |.|++++
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL 100 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYREENGAFKSVDDL 100 (120)
T ss_pred hcCCCCCHHHHHHHHHHHHhcCCcCCHHHH
Confidence 36899999999999976 3556655
No 122
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=53.31 E-value=7.6 Score=46.03 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=26.5
Q ss_pred ccccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 242 DYCDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 242 DY~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
+|+-++||||++.|.+++.+++|+++++.+
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 556689999999999999999999988763
No 123
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=53.19 E-value=14 Score=34.86 Aligned_cols=26 Identities=31% Similarity=0.687 Sum_probs=20.3
Q ss_pred CCCCCccHHHHHHHHHH------cCCHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE------HRSIEKILE 167 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~------~~sle~il~ 167 (531)
..+||||+++|-++|.. |.|++++.+
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 35799999999999962 568777654
No 124
>cd04236 AAK_NAGS-Urea AAK_NAGS-Urea: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the urea cycle found in animals. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate; NAG is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Ureogenic NAGS activity is dependent on the concentration of glutamate (substrate) and arginine (activator). Domain architecture of ureogenic NAGS consists of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal DUF619 domain. Members of this CD belong to the protein superfamily, the Amino Acid Kinase Family (AAKF).
Probab=53.09 E-value=12 Score=38.74 Aligned_cols=69 Identities=22% Similarity=0.227 Sum_probs=50.2
Q ss_pred HHHHHhcCCcccCccccccccccCCCcccccceeeecccchHHHHHHHHhh----------cCccccCCCCCCcchhhhH
Q psy1206 287 EARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRS----------EGNQLMSVDGEPTSHLMGT 356 (531)
Q Consensus 287 ~A~~~F~~~~V~dP~~~~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~----------~g~~l~~~~g~~tshl~g~ 356 (531)
+..+.|+|+.-+||++ +..||-+|-++-.. .|..+.++ .++..+
T Consensus 3 ~~~~~~~~~~~~~~~e---------------------~~~~l~~f~~~~~~~~~~f~VIK~GG~~~~~~-----~~~~~l 56 (271)
T cd04236 3 RDVKAFLHQKGGDPRE---------------------ARYWLTQFQIAMPNDWPAFAVLEVDHSVFRSL-----EMVQSL 56 (271)
T ss_pred chHHHHHHHhCCCHHH---------------------HHHHHHHhhccCCCCCCCEEEEEEChhhhcCc-----hhHHHH
Confidence 4567899999888864 56788888875421 34444322 356777
Q ss_pred HHHHHHHHHcCCeeEEeecCCCCCc
Q psy1206 357 FYRTIRLVEHGLKPIYVFDGKPPTL 381 (531)
Q Consensus 357 ~~R~~~ll~~gIkPVfVFDG~pp~l 381 (531)
..=+.-|-..|++||.|.-|.|+.-
T Consensus 57 ~~dla~L~~lGl~~VlVHGggp~i~ 81 (271)
T cd04236 57 SFGLAFLQRMDMKLLVVMGLSAPDG 81 (271)
T ss_pred HHHHHHHHHCCCeEEEEeCCChHHh
Confidence 7777888999999999999988544
No 125
>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=50.09 E-value=16 Score=38.31 Aligned_cols=27 Identities=30% Similarity=0.561 Sum_probs=22.7
Q ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHHh
Q psy1206 143 SIRGIGPKRAIELIK-EHRSIEKILENI 169 (531)
Q Consensus 143 GIpGIG~ktA~kLI~-~~~sle~il~~l 169 (531)
+||||||+||.+|.. ...|++++....
T Consensus 89 ~i~GiGpk~a~~l~~lGi~sl~dL~~a~ 116 (307)
T cd00141 89 RVPGVGPKTARKLYELGIRTLEDLRKAA 116 (307)
T ss_pred cCCCCCHHHHHHHHHcCCCCHHHHHHHh
Confidence 689999999999993 256999998864
No 126
>PRK13766 Hef nuclease; Provisional
Probab=49.83 E-value=14 Score=43.09 Aligned_cols=28 Identities=25% Similarity=0.507 Sum_probs=24.9
Q ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
+.+|||||+++|.+|+.+|+|+++++..
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4589999999999999999999988753
No 127
>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=48.97 E-value=12 Score=26.13 Aligned_cols=15 Identities=40% Similarity=0.479 Sum_probs=11.6
Q ss_pred CCCCCccHHHHHHHH
Q psy1206 142 DSIRGIGPKRAIELI 156 (531)
Q Consensus 142 pGIpGIG~ktA~kLI 156 (531)
..++|||.+|+.+|-
T Consensus 14 ~~~~GIG~kt~~kL~ 28 (32)
T PF11798_consen 14 RKFWGIGKKTAKKLN 28 (32)
T ss_dssp GGSTTS-HHHHHHHH
T ss_pred HhhCCccHHHHHHHH
Confidence 378999999999863
No 128
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=48.44 E-value=15 Score=38.96 Aligned_cols=28 Identities=29% Similarity=0.574 Sum_probs=22.6
Q ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHHh
Q psy1206 142 DSIRGIGPKRAIELIKE-HRSIEKILENI 169 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~-~~sle~il~~l 169 (531)
-.|||||||||.+|... ..|++++.+..
T Consensus 92 ~~i~GiGpk~a~~l~~lGi~tl~eL~~a~ 120 (334)
T smart00483 92 TNVFGVGPKTAAKWYRKGIRTLEELKKNK 120 (334)
T ss_pred HccCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence 37899999999999982 35999987654
No 129
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=48.08 E-value=32 Score=27.72 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhh
Q psy1206 392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCG 425 (531)
Q Consensus 392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~ 425 (531)
|.++.++....|+.+||++ .|+.|+.-
T Consensus 7 R~~~yk~Aa~~AK~~gd~~-------kAr~~~R~ 33 (59)
T smart00685 7 RQEQYKQAALQAKRAGDEE-------KARRHLRI 33 (59)
T ss_pred HHHHHHHHHHHHHHcCCHH-------HHHHHHHH
Confidence 4455666667799999988 99999875
No 130
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=48.00 E-value=12 Score=32.80 Aligned_cols=29 Identities=24% Similarity=0.163 Sum_probs=25.0
Q ss_pred CCchhHHHHHHHHcCCEEEEEcCCCcccc
Q psy1206 62 PCEAEAQCAAMVKAGKVYATATEDMDALT 90 (531)
Q Consensus 62 PyEADAq~A~L~r~G~vd~ViSeDsDlL~ 90 (531)
|-..|+....++..+-+|+++|+|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 55678888889999999999999999874
No 131
>PHA02567 rnh RnaseH; Provisional
Probab=47.59 E-value=35 Score=36.00 Aligned_cols=55 Identities=16% Similarity=0.123 Sum_probs=42.3
Q ss_pred ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcC---C--eeEEeecCCC
Q psy1206 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG---L--KPIYVFDGKP 378 (531)
Q Consensus 318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~g---I--kPVfVFDG~p 378 (531)
..+-||+|..++....+ .+++++|-.|+-+.+++..+++-+... . ..|++||++-
T Consensus 15 ~~~LiDgs~i~~~~~~a------~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~ 74 (304)
T PHA02567 15 GVNLIDFSQIIIATIMA------NFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSK 74 (304)
T ss_pred CEEEEehHHHHHHHHHh------hCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence 46889999999988876 278888999998888888888854333 2 2478999963
No 132
>PRK08609 hypothetical protein; Provisional
Probab=47.20 E-value=28 Score=39.59 Aligned_cols=30 Identities=27% Similarity=0.391 Sum_probs=24.5
Q ss_pred CCCCccHHHHHHHHHH--cCCHHHHHHHhhhc
Q psy1206 143 SIRGIGPKRAIELIKE--HRSIEKILENIDTK 172 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~--~~sle~il~~l~~~ 172 (531)
.|||||||||.+|-.+ ..|++++.+..+..
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~ 123 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACENG 123 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhC
Confidence 7999999999999976 45898888766543
No 133
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=46.57 E-value=16 Score=42.52 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=11.2
Q ss_pred CCCCCCccHHHHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELIKE 158 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~ 158 (531)
+-.+||+|.|+|.+|+..
T Consensus 481 L~~l~gfG~Ksa~~ll~~ 498 (665)
T PRK07956 481 LLGLEGFGEKSAQNLLDA 498 (665)
T ss_pred HhcCcCcchHHHHHHHHH
Confidence 345666777776666653
No 134
>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=45.24 E-value=20 Score=31.44 Aligned_cols=23 Identities=30% Similarity=0.250 Sum_probs=17.8
Q ss_pred CCCCCccHHHHHHHHH-HcCCHHH
Q psy1206 142 DSIRGIGPKRAIELIK-EHRSIEK 164 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~-~~~sle~ 164 (531)
..|||||+++|..|+. .+.|+++
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s~~~ 38 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRSPAD 38 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCCHHH
Confidence 4799999999999996 3555543
No 135
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=45.03 E-value=17 Score=41.49 Aligned_cols=29 Identities=41% Similarity=0.589 Sum_probs=25.6
Q ss_pred ccCCCCCchHHHHHHHHhhccHHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIEKILENI 272 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~~vi~~l 272 (531)
+..|||||+++.-+|++.++|++.|..+-
T Consensus 532 Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As 560 (581)
T COG0322 532 LDDIPGIGPKRRKALLKHFGSLKGIKSAS 560 (581)
T ss_pred cccCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence 56799999999999999999998887654
No 136
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=44.51 E-value=11 Score=27.34 Aligned_cols=16 Identities=44% Similarity=0.850 Sum_probs=11.9
Q ss_pred eEEeecCCCCCcchHHH
Q psy1206 370 PIYVFDGKPPTLKSGEL 386 (531)
Q Consensus 370 PVfVFDG~pp~lK~~~~ 386 (531)
-|+|||+-||+ |.+++
T Consensus 15 ~V~Vfd~v~~~-Ka~~i 30 (36)
T PF06200_consen 15 QVCVFDDVPPD-KAQEI 30 (36)
T ss_pred EEEEeCCCCHH-HHHHH
Confidence 38999998876 55544
No 137
>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=43.94 E-value=25 Score=28.22 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=13.2
Q ss_pred CCCccHHHHHHHHHH
Q psy1206 144 IRGIGPKRAIELIKE 158 (531)
Q Consensus 144 IpGIG~ktA~kLI~~ 158 (531)
+||||+++|.++|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 788999999999976
No 138
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=42.63 E-value=39 Score=29.02 Aligned_cols=45 Identities=27% Similarity=0.413 Sum_probs=31.9
Q ss_pred CCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCC---cchHHHHHHHhcC
Q psy1206 248 RGIGPKRAIELIKEHRSIEKILENIDTKKYTVPE---GWLYKEARELFRH 294 (531)
Q Consensus 248 ~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~---~y~~~~A~~~F~~ 294 (531)
-|++++.|.++.+.|++ ..++.|+...|.+=. +..|+.|+.+=+.
T Consensus 18 ~gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 18 YGLSPKLAMKLYKKYGD--DAIEILKENPYRLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp TT--HHHHHHHHHHH-T--THHHHHHH-STCCCB-SSSSBHHHHHHHHHT
T ss_pred cCCCHHHHHHHHHHHhH--HHHHHHHHChHHHHHHccCCCHHHHHHHHHH
Confidence 47999999999999997 667888877776444 4459999887665
No 139
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=40.47 E-value=19 Score=33.40 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=17.3
Q ss_pred cCCCCCchHHHHHHHHh--hccHHHHH
Q psy1206 245 DSIRGIGPKRAIELIKE--HRSIEKIL 269 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k--~~s~~~vi 269 (531)
..+|||||++|-++|.. |++++.++
T Consensus 64 ~~lpGigP~~A~~IV~nGpf~sveDL~ 90 (132)
T PRK02515 64 RQFPGMYPTLAGKIVKNAPYDSVEDVL 90 (132)
T ss_pred HHCCCCCHHHHHHHHHCCCCCCHHHHH
Confidence 35799999999999952 44555443
No 140
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=38.64 E-value=76 Score=29.70 Aligned_cols=69 Identities=17% Similarity=0.278 Sum_probs=36.0
Q ss_pred eecCCCCCcchHHHHHHHHH-------HHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHh
Q psy1206 373 VFDGKPPTLKSGELNKRMEK-------REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKAR 445 (531)
Q Consensus 373 VFDG~pp~lK~~~~~kR~~~-------r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~ 445 (531)
=|||.|-.|..-.-++.-++ .+...++.+++..+|+..| --++-+++.. ....+.+...-....|+.|
T Consensus 43 WfDgnP~~L~pl~p~~~A~~~v~l~GG~d~vl~~A~~~~~~gd~~w----A~~L~d~l~~-adp~n~~ar~l~A~al~~l 117 (141)
T PF14863_consen 43 WFDGNPANLNPLPPEEEAKRYVELAGGADKVLERAQAALAAGDYQW----AAELLDHLVF-ADPDNEEARQLKADALEQL 117 (141)
T ss_dssp S--S-GGGTS---HHHHHHHHHHHTTCHHHHHHHHHHHHHCT-HHH----HHHHHHHHHH-H-TT-HHHHHHHHHHHHHH
T ss_pred ccCCCccccCCCChHHHHHHHHHHcCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHH-cCCCcHHHHHHHHHHHHHH
Confidence 39999999987544443333 5566677778888999775 2345555554 3333444555455555555
Q ss_pred c
Q psy1206 446 S 446 (531)
Q Consensus 446 ~ 446 (531)
+
T Consensus 118 g 118 (141)
T PF14863_consen 118 G 118 (141)
T ss_dssp H
T ss_pred H
Confidence 4
No 141
>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=36.90 E-value=27 Score=31.55 Aligned_cols=18 Identities=33% Similarity=0.689 Sum_probs=13.3
Q ss_pred cCCCCCchHHHHHHHHhh
Q psy1206 245 DSIRGIGPKRAIELIKEH 262 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k~ 262 (531)
.++||||+++|.++|...
T Consensus 71 ~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYR 88 (120)
T ss_pred hcCCCCCHHHHHHHHHHH
Confidence 467888888888877664
No 142
>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=36.88 E-value=34 Score=35.77 Aligned_cols=55 Identities=29% Similarity=0.407 Sum_probs=33.3
Q ss_pred ccccCCChhhhHhH-----------HhhhhhhhhhccCccccCCCCCchHHHHHHHHh--hccHHHHHHH
Q psy1206 215 DSIRGIGPKRAIEL-----------LYSFIDLCILLGCDYCDSIRGIGPKRAIELIKE--HRSIEKILEN 271 (531)
Q Consensus 215 esl~~~Gp~~~~el-----------~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k--~~s~~~vi~~ 271 (531)
.++.+.|+..+.++ ++.++.= ...|--.+-+|+|||||||.++. . .+|++.+..+
T Consensus 48 ~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 48 KKLPGIGKKIAEKIEEILETGKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred cCCCCccHHHHHHHHHHHHcCCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 45667787665532 2222221 22333445589999999999999 5 3366666554
No 143
>PF07864 DUF1651: Protein of unknown function (DUF1651); InterPro: IPR012447 The proteins in this entry have not been characterised.
Probab=35.26 E-value=17 Score=30.12 Aligned_cols=31 Identities=35% Similarity=0.554 Sum_probs=25.6
Q ss_pred ec-CCCCCcchHHHHHHHHHHHHHHHHHHHHHHccc
Q psy1206 374 FD-GKPPTLKSGELNKRMEKREDAQKALAKAQEQGK 408 (531)
Q Consensus 374 FD-G~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~ 408 (531)
.- |.||.||.. |+..+++|.+.|++.++.|=
T Consensus 36 ~~~g~pp~lk~r----r~l~~~~A~e~W~~L~~~GW 67 (75)
T PF07864_consen 36 MPLGEPPLLKTR----RRLTREEARELWKELQKTGW 67 (75)
T ss_pred cCCCCCCcceEE----EEEEHHHHHHHHHHHHHcCC
Confidence 55 899999974 56678999999999999873
No 144
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=34.53 E-value=23 Score=35.43 Aligned_cols=37 Identities=24% Similarity=0.213 Sum_probs=26.0
Q ss_pred CHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206 125 SHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILE 167 (531)
Q Consensus 125 t~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~ 167 (531)
+|-+++-..+|+. +|- .--+...+|...|+++|++++
T Consensus 28 ~pf~lLva~iLSaqttD~------~vn~at~~Lf~~~~t~e~l~~ 66 (211)
T COG0177 28 DPFELLVAVILSAQTTDE------VVNKATPALFKRYPTPEDLLN 66 (211)
T ss_pred CcHHHHHHHHHhccCchH------HHHHHHHHHHHHcCCHHHHHc
Confidence 5667777778877 563 234566778889999888764
No 145
>PRK13766 Hef nuclease; Provisional
Probab=34.11 E-value=27 Score=40.78 Aligned_cols=28 Identities=25% Similarity=0.507 Sum_probs=25.1
Q ss_pred ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
+.+|||||+++|.+|+.+++|++.++.+
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 5689999999999999999999988753
No 146
>PHA02994 hypothetical protein; Provisional
Probab=33.99 E-value=24 Score=35.28 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=13.4
Q ss_pred EEeecCCCCCcchHHH
Q psy1206 371 IYVFDGKPPTLKSGEL 386 (531)
Q Consensus 371 VfVFDG~pp~lK~~~~ 386 (531)
-++|||-||.+|.-.+
T Consensus 101 ~l~fDG~PPsFr~v~~ 116 (218)
T PHA02994 101 NLAFDGIPPSFRMVNI 116 (218)
T ss_pred ceeeccCCCcceeecc
Confidence 4689999999998654
No 147
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=33.59 E-value=35 Score=36.70 Aligned_cols=54 Identities=33% Similarity=0.486 Sum_probs=38.0
Q ss_pred HHHHHHhC-CCCHHHHHHHH---hHcC----C---CC--CC-------CCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206 115 LEKVLEGM-ELSHEEFIDLC---ILLG----C---DY--CD-------SIRGIGPKRAIELIKEHRSIEKILEN 168 (531)
Q Consensus 115 ~~~i~~~l-glt~eqfid~~---iL~G----~---DY--~p-------GIpGIG~ktA~kLI~~~~sle~il~~ 168 (531)
.+++.+.+ .++.+.++|.. -++| . |. .| +||++|...|.+|+.+|||+.+++..
T Consensus 243 ~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 243 PEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred HHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 45555544 57777776663 3344 1 11 12 58999999999999999999999864
No 148
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=33.12 E-value=37 Score=31.94 Aligned_cols=50 Identities=26% Similarity=0.450 Sum_probs=33.3
Q ss_pred hhhhhhhccCcccc---------CCCCCchHHHHHHHHhhcc-------------HHHHHHHHhhCCCCCCC
Q psy1206 232 FIDLCILLGCDYCD---------SIRGIGPKRAIELIKEHRS-------------IEKILENIDTKKYTVPE 281 (531)
Q Consensus 232 F~~~CiLsGCDY~~---------~i~giG~k~A~kli~k~~s-------------~~~vi~~l~~~~~~vP~ 281 (531)
|.+|.-++|.|--+ .|.|||..+|..++.+.+= ++.|...|...++.+|+
T Consensus 2 ~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~ 73 (144)
T TIGR03629 2 FKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPS 73 (144)
T ss_pred cceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCH
Confidence 45555566665543 5889999999999998761 33455555444566774
No 149
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=32.40 E-value=85 Score=36.67 Aligned_cols=25 Identities=28% Similarity=0.466 Sum_probs=22.2
Q ss_pred CCCCCchHHHHHHH-HhhccHHHHHH
Q psy1206 246 SIRGIGPKRAIELI-KEHRSIEKILE 270 (531)
Q Consensus 246 ~i~giG~k~A~kli-~k~~s~~~vi~ 270 (531)
+||+||.++|-.|. +.+++++++..
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 59999999999999 89999988765
No 150
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=32.19 E-value=62 Score=37.00 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=25.3
Q ss_pred ccCCCCCchHHHHHHHHhhccH--HHHHHHHhhCC
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSI--EKILENIDTKK 276 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~--~~vi~~l~~~~ 276 (531)
+..|+|||++.|..++.=+.+. .++++.|..-|
T Consensus 522 l~~i~gIG~~~a~si~~~f~~~~~~~~i~~L~~~g 556 (562)
T PRK08097 522 WQQLPGIGEGRARQLIAFLQHPEVKALADWLAAQG 556 (562)
T ss_pred HhcCCCchHHHHHHHHHHHcCHHHHHHHHHHHHcC
Confidence 5689999999999999998764 45666665433
No 151
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.21 E-value=30 Score=34.26 Aligned_cols=17 Identities=41% Similarity=0.618 Sum_probs=14.6
Q ss_pred CCCCCccHHHHHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE 158 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~ 158 (531)
..+||||+|+|.++.-.
T Consensus 14 ~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 46899999999998764
No 152
>PRK00076 recR recombination protein RecR; Reviewed
Probab=31.19 E-value=29 Score=34.28 Aligned_cols=17 Identities=41% Similarity=0.602 Sum_probs=14.7
Q ss_pred CCCCCccHHHHHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE 158 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~ 158 (531)
..+||||+|+|.++.-.
T Consensus 14 ~~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFH 30 (196)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 46899999999998865
No 153
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=30.67 E-value=29 Score=34.40 Aligned_cols=19 Identities=32% Similarity=0.473 Sum_probs=15.3
Q ss_pred CCCCCCCccHHHHHHHHHH
Q psy1206 140 YCDSIRGIGPKRAIELIKE 158 (531)
Q Consensus 140 Y~pGIpGIG~ktA~kLI~~ 158 (531)
.+.-+||||+|+|.++.-.
T Consensus 13 ~l~kLPGvG~KsA~R~Afh 31 (198)
T COG0353 13 ALKKLPGVGPKSAQRLAFH 31 (198)
T ss_pred HHhhCCCCChhHHHHHHHH
Confidence 3457899999999988754
No 154
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=30.66 E-value=48 Score=31.58 Aligned_cols=49 Identities=18% Similarity=0.165 Sum_probs=26.2
Q ss_pred eeecccchHHHHHH--HHhhcCccccCCCCCCcchhh-hHHHHHHHH-HHcCCeeEEeecCC
Q psy1206 320 ICIDASMSLYQFLI--AVRSEGNQLMSVDGEPTSHLM-GTFYRTIRL-VEHGLKPIYVFDGK 377 (531)
Q Consensus 320 iAIDa~~~lyqfl~--~ir~~g~~l~~~~g~~tshl~-g~~~R~~~l-l~~gIkPVfVFDG~ 377 (531)
|-||+||.||+.-. .+..++. | .+.. .|...+.+. -..|.+-+.||||.
T Consensus 1 LlIDGYNli~~~~~l~~~~~~~~-l--------~~aR~~Li~~L~~y~~~~~~~v~VVFDa~ 53 (166)
T PF05991_consen 1 LLIDGYNLIHAWPELRSLAERGD-L--------EAARERLIEMLSEYAQFSGYEVIVVFDAY 53 (166)
T ss_pred CeEcchhhhCCCHHHHhhcCcCC-H--------HHHHHHHHHHHHHHhcccCCEEEEEEeCC
Confidence 46999999998322 2211110 1 1111 222223332 35679999999995
No 155
>TIGR00160 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars.
Probab=30.08 E-value=57 Score=30.80 Aligned_cols=68 Identities=15% Similarity=0.115 Sum_probs=40.8
Q ss_pred ceeecccCCCCCcchhHHhHHHHHHhhccCCCH----HHHHHHHhhcCCc-cccCCCchhHHHHHHHHcCCEEEEE
Q psy1206 12 GLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ----GRLDSFFTIRREE-KRKAPCEAEAQCAAMVKAGKVYATA 82 (531)
Q Consensus 12 ~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~----~~i~~lL~~~gIp-~vvAPyEADAq~A~L~r~G~vd~Vi 82 (531)
+++|-|.++... -.+-......++....... .+|.+.. .+.|. +...|.=+|.|+|.+...|-+|+||
T Consensus 6 ALIAHD~kK~~l--~~f~~~~~~~L~~h~L~ATgTTG~~i~~~t-gL~V~~~~SGplGGDqQIga~Ia~g~id~vI 78 (143)
T TIGR00160 6 ALIAHDKKKQDL--VNFVQQHKPLLSQHDLYATGTTGNLISRAT-GLNINAMLSGPMGGDQQIGALIAEGKIDAVI 78 (143)
T ss_pred EEEecccchHHH--HHHHHHHHHHHcCCCEEECccHHHHHHHHH-CCCeEEeccCCccHHHHHHHHHHhCCCCEEE
Confidence 567777665544 2233334445555553333 3444432 23333 3356889999999999999999873
No 156
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=29.99 E-value=45 Score=31.79 Aligned_cols=34 Identities=24% Similarity=0.321 Sum_probs=28.7
Q ss_pred hhhhhhhhhccCcccc---------CCCCCchHHHHHHHHhhc
Q psy1206 230 YSFIDLCILLGCDYCD---------SIRGIGPKRAIELIKEHR 263 (531)
Q Consensus 230 e~F~~~CiLsGCDY~~---------~i~giG~k~A~kli~k~~ 263 (531)
+.|.+|.-++|.|.-. .|.|||+.+|..++.+.+
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 3688998888988654 488999999999999876
No 157
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=29.83 E-value=27 Score=26.90 Aligned_cols=17 Identities=47% Similarity=0.610 Sum_probs=14.3
Q ss_pred HcC-CCCCCCCCCccHHH
Q psy1206 135 LLG-CDYCDSIRGIGPKR 151 (531)
Q Consensus 135 L~G-~DY~pGIpGIG~kt 151 (531)
|+| -|+.|.||.||.|.
T Consensus 14 llgiwdnvptiprigekv 31 (57)
T PF13052_consen 14 LLGIWDNVPTIPRIGEKV 31 (57)
T ss_pred hhhhhccCCCccccchhh
Confidence 566 69999999999873
No 158
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=29.52 E-value=22 Score=35.15 Aligned_cols=16 Identities=38% Similarity=0.667 Sum_probs=13.5
Q ss_pred ccCCCCCchHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELI 259 (531)
Q Consensus 244 ~~~i~giG~k~A~kli 259 (531)
+..+||||+|+|.++-
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 5678999999998864
No 159
>PF11438 N36: 36-mer N-terminal peptide of the N protein (N36); InterPro: IPR020952 Antitermination proteins positively regulate expression of bacteriophage early and late gene operons []. Bacterial host RNA polymerase is modified by these antitermination proteins to a terminator-resistant form that transcribes through termination sites that would otherwise prevent expression of the regulated genes. Enterobacteria phage lambda antitermination protein N is essential for the expression of two phage early operons which are critical for phage development. This entry represents the RNA-binding arginine-rich motif (also known as N36) which forms a complex with boxB RNA by binding tightly to the major groove of the boxB hairpin via hydrophobic and electrostatic interactions forming a bent alpha helix []. ; PDB: 1QFQ_B.
Probab=29.03 E-value=49 Score=23.56 Aligned_cols=20 Identities=25% Similarity=0.361 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy1206 385 ELNKRMEKREDAQKALAKAQ 404 (531)
Q Consensus 385 ~~~kR~~~r~~a~~~~~~a~ 404 (531)
...+||++|.+.+++|+.+-
T Consensus 2 AQ~RRRErRaeKQa~WKa~n 21 (35)
T PF11438_consen 2 AQTRRRERRAEKQAQWKAAN 21 (35)
T ss_dssp -HHHHHHHTHHHHHHHHHT-
T ss_pred hhHHHHHHHHHHHHHHhhcC
Confidence 35789999999999998764
No 160
>PF04708 Pox_F16: Poxvirus F16 protein; InterPro: IPR006798 This entry represents the Poxvirus F16 proteins.
Probab=29.02 E-value=37 Score=34.05 Aligned_cols=19 Identities=32% Similarity=0.747 Sum_probs=14.8
Q ss_pred eeEEeecCCCCCcchHHHH
Q psy1206 369 KPIYVFDGKPPTLKSGELN 387 (531)
Q Consensus 369 kPVfVFDG~pp~lK~~~~~ 387 (531)
|--++|||-||.+|.-...
T Consensus 99 kD~L~fDG~pP~Fr~v~~d 117 (218)
T PF04708_consen 99 KDNLAFDGSPPSFRPVNMD 117 (218)
T ss_pred ecceEecccCCcceEecch
Confidence 3346899999999996653
No 161
>KOG2841|consensus
Probab=28.62 E-value=41 Score=34.33 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.6
Q ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206 141 CDSIRGIGPKRAIELIKEHRSIEKILENI 169 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI~~~~sle~il~~l 169 (531)
+-.||||+...|..|+.+||||+.++.+-
T Consensus 197 Lt~i~~VnKtda~~LL~~FgsLq~~~~AS 225 (254)
T KOG2841|consen 197 LTTIPGVNKTDAQLLLQKFGSLQQISNAS 225 (254)
T ss_pred HHhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence 34799999999999999999999988654
No 162
>PRK13844 recombination protein RecR; Provisional
Probab=28.19 E-value=36 Score=33.82 Aligned_cols=17 Identities=24% Similarity=0.229 Sum_probs=14.7
Q ss_pred CCCCCccHHHHHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE 158 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~ 158 (531)
..+||||+|+|.++.-.
T Consensus 18 ~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 56899999999998865
No 163
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=27.72 E-value=75 Score=33.77 Aligned_cols=47 Identities=21% Similarity=0.264 Sum_probs=34.0
Q ss_pred EecHHHHHHhCCCCHHHHHHH--------------HhHcCCCCCC------------CCCCccHHHHHHHHHH
Q psy1206 112 EFHLEKVLEGMELSHEEFIDL--------------CILLGCDYCD------------SIRGIGPKRAIELIKE 158 (531)
Q Consensus 112 ~~~~~~i~~~lglt~eqfid~--------------~iL~G~DY~p------------GIpGIG~ktA~kLI~~ 158 (531)
.|..+.++..+|+.++.+++. ++|--.|..| .|||||+|+|..++..
T Consensus 277 LYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 277 LYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 356677788899988877653 3444445444 4899999999999964
No 164
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=27.41 E-value=62 Score=31.71 Aligned_cols=48 Identities=25% Similarity=0.322 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHhHcCCCCCC-----CCCCccHHHHHHHHHH-----cCCHHHHHHHhh
Q psy1206 123 ELSHEEFIDLCILLGCDYCD-----SIRGIGPKRAIELIKE-----HRSIEKILENID 170 (531)
Q Consensus 123 glt~eqfid~~iL~G~DY~p-----GIpGIG~ktA~kLI~~-----~~sle~il~~l~ 170 (531)
.-+.+.|++|.--+|.-.+. =+||||.|+.-++|.+ |.|.++|-+.+.
T Consensus 95 ~~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~ 152 (181)
T PF04919_consen 95 KENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVK 152 (181)
T ss_dssp HTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST
T ss_pred HhChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhc
Confidence 35788999999888844333 5899999999999964 889998887764
No 165
>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=26.80 E-value=80 Score=25.24 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=12.0
Q ss_pred CCCCchHHHHHHHHh
Q psy1206 247 IRGIGPKRAIELIKE 261 (531)
Q Consensus 247 i~giG~k~A~kli~k 261 (531)
+||||.++|.++|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 788888888888766
No 166
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=26.68 E-value=1.6e+02 Score=24.45 Aligned_cols=48 Identities=31% Similarity=0.421 Sum_probs=32.6
Q ss_pred HHHHHHH-HHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHH
Q psy1206 384 GELNKRM-EKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRN 436 (531)
Q Consensus 384 ~~~~kR~-~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 (531)
.+++..+ ..|.+..+.+.+|.+.||+. +..-...+...-.+++.+|.+
T Consensus 16 ~EL~~L~~~~rpe~~~~i~~Ar~~GDls-----ENaeY~aAke~q~~le~rI~~ 64 (74)
T PF03449_consen 16 AELEHLKNVERPEIAEEIAEAREQGDLS-----ENAEYHAAKERQAFLEARIRE 64 (74)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCSSST-----SSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHcCCcc-----cchhHHHHHHHHHHHHHHHHH
Confidence 4555544 47889999999999999987 445555555544455555544
No 167
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=26.45 E-value=37 Score=27.09 Aligned_cols=24 Identities=33% Similarity=0.689 Sum_probs=15.3
Q ss_pred CCCCccHHHHHHHHHH------cCCHHHHH
Q psy1206 143 SIRGIGPKRAIELIKE------HRSIEKIL 166 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~------~~sle~il 166 (531)
.+||||++.|.++|.. |.|++++.
T Consensus 18 ~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~ 47 (65)
T PF12836_consen 18 ALPGIGPKQAKAIVEYREKNGPFKSLEDLK 47 (65)
T ss_dssp TSTT--HHHHHHHHHHHHHH-S-SSGGGGG
T ss_pred HcCCCCHHHHHHHHHHHHhCcCCCCHHHHh
Confidence 6799999999999962 44555443
No 168
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=26.23 E-value=1.1e+02 Score=26.20 Aligned_cols=42 Identities=29% Similarity=0.469 Sum_probs=22.1
Q ss_pred CccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCC---CCcHHHHHHHh
Q psy1206 146 GIGPKRAIELIKEHRSIEKILENIDTKKYTVPE---GWLYKEARELF 189 (531)
Q Consensus 146 GIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~---~f~~~~A~~~f 189 (531)
||+++.|.+|.+.||+ +.++.++++++.+-. +..|..|...-
T Consensus 19 gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~~~i~gi~F~~aD~iA 63 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD--DAIEILKENPYRLIEDIDGIGFKTADKIA 63 (94)
T ss_dssp T--HHHHHHHHHHH-T--THHHHHHH-STCCCB-SSSSBHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhH--HHHHHHHHChHHHHHHccCCCHHHHHHHH
Confidence 5667777777777775 445666666655443 33455555443
No 169
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=25.84 E-value=42 Score=34.08 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=26.2
Q ss_pred CCccccC----CCchhHHHHHHHHc---------CCEEEEEcCCCcccccc
Q psy1206 55 REEKRKA----PCEAEAQCAAMVKA---------GKVYATATEDMDALTFG 92 (531)
Q Consensus 55 gIp~vvA----PyEADAq~A~L~r~---------G~vd~ViSeDsDlL~fg 92 (531)
++.++.+ |+|+|--+....|. ....+|++.|+|+++++
T Consensus 172 ~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 172 NLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp CSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred ceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 4666653 79999888776542 46789999999999887
No 170
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=25.32 E-value=83 Score=26.67 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=21.8
Q ss_pred CCCCccHHHHHHHHHH-----cCCHHHHHHHh
Q psy1206 143 SIRGIGPKRAIELIKE-----HRSIEKILENI 169 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~-----~~sle~il~~l 169 (531)
.|+|||...|.+++.. |.|+++++..+
T Consensus 31 ~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 31 AIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred hcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 6899999999999963 77999998877
No 171
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=24.85 E-value=1.6e+02 Score=27.89 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHH
Q psy1206 384 GELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLK 443 (531)
Q Consensus 384 ~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~ 443 (531)
.+++..+..|.+..+...+|.+.||+. |..-...++++-..++.+|..=-.+|-.
T Consensus 18 ~EL~~L~~~r~~i~~~i~~Ar~~GDls-----ENaey~aak~~q~~~e~RI~~L~~~L~~ 72 (158)
T PRK05892 18 AELARLRARRDRLAVEVNDRGMIGDHG-----DQAEAIQRADELARLDDRINELDRRLRT 72 (158)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhCCCcc-----hhhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456777777888889999999999987 2333444454444456666554444443
No 172
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.84 E-value=36 Score=33.70 Aligned_cols=16 Identities=44% Similarity=0.686 Sum_probs=13.5
Q ss_pred ccCCCCCchHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELI 259 (531)
Q Consensus 244 ~~~i~giG~k~A~kli 259 (531)
+..+||||+|+|.++.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4578999999998875
No 173
>PRK00076 recR recombination protein RecR; Reviewed
Probab=24.75 E-value=36 Score=33.69 Aligned_cols=17 Identities=41% Similarity=0.565 Sum_probs=13.9
Q ss_pred ccCCCCCchHHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIK 260 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~ 260 (531)
+..+||||+|+|.++.-
T Consensus 13 l~~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 13 LRKLPGIGPKSAQRLAF 29 (196)
T ss_pred HHHCCCCCHHHHHHHHH
Confidence 45789999999988753
No 174
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=23.99 E-value=73 Score=30.22 Aligned_cols=34 Identities=24% Similarity=0.376 Sum_probs=28.3
Q ss_pred hhhhhhhhhccCcccc---------CCCCCchHHHHHHHHhhc
Q psy1206 230 YSFIDLCILLGCDYCD---------SIRGIGPKRAIELIKEHR 263 (531)
Q Consensus 230 e~F~~~CiLsGCDY~~---------~i~giG~k~A~kli~k~~ 263 (531)
+.|.+|.-+.|+|--. .|.|||..+|..+..+.+
T Consensus 4 ~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 4 EEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 4688888888887654 488999999999999866
No 175
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=23.76 E-value=4.5e+02 Score=26.61 Aligned_cols=37 Identities=5% Similarity=-0.063 Sum_probs=27.8
Q ss_pred HHHHHHHhhcCCccc--cCCCch---hHHHHHHHHcCCEEEE
Q psy1206 45 GRLDSFFTIRREEKR--KAPCEA---EAQCAAMVKAGKVYAT 81 (531)
Q Consensus 45 ~~i~~lL~~~gIp~v--vAPyEA---DAq~A~L~r~G~vd~V 81 (531)
.-+.+.|+++|+.=| +.||-. +...++|+..|+-...
T Consensus 109 ~A~~~AL~alg~~RIalvTPY~~~v~~~~~~~l~~~G~eV~~ 150 (239)
T TIGR02990 109 SAAVDGLAALGVRRISLLTPYTPETSRPMAQYFAVRGFEIVN 150 (239)
T ss_pred HHHHHHHHHcCCCEEEEECCCcHHHHHHHHHHHHhCCcEEee
Confidence 567889999999865 789944 3666789999976443
No 176
>COG1803 MgsA Methylglyoxal synthase [Carbohydrate transport and metabolism]
Probab=23.32 E-value=87 Score=29.21 Aligned_cols=67 Identities=18% Similarity=0.203 Sum_probs=39.8
Q ss_pred ceeecccCCCCCcchhHHhHHHHHHhhccC----CCHHHHHHHHhhcCC-ccccCCCchhHHHHHHHHcCCEEEE
Q psy1206 12 GLVKYLCGDKNFAEDRIRNGAKKLLKARSS----TTQGRLDSFFTIRRE-EKRKAPCEAEAQCAAMVKAGKVYAT 81 (531)
Q Consensus 12 ~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~----~t~~~i~~lL~~~gI-p~vvAPyEADAq~A~L~r~G~vd~V 81 (531)
+++|-|.++... =.+-...+..++.... +|-.+|++.. .+.| .+...|.-.|-|++.|...|.+|++
T Consensus 8 ALIAHD~kK~~l--v~f~~~~~~~L~~h~L~ATGTTG~~i~~at-gL~v~~~~SGPmGGDQQiGa~Iaeg~id~l 79 (142)
T COG1803 8 ALIAHDHKKDDL--VNFVQAHKELLSRHDLYATGTTGGLIQEAT-GLNVHRLKSGPMGGDQQIGALIAEGKIDVL 79 (142)
T ss_pred EEEecchhHHHH--HHHHHHHHHHhhhceEEEecCchHHHHHHh-CCceEEeecCCCCccHHHHHHHhcCcceEE
Confidence 566666554433 1122223344444442 2335666555 2333 3446799999999999999999986
No 177
>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=23.12 E-value=56 Score=26.32 Aligned_cols=16 Identities=25% Similarity=0.331 Sum_probs=13.5
Q ss_pred CCCCCCccHHHHHHHH
Q psy1206 141 CDSIRGIGPKRAIELI 156 (531)
Q Consensus 141 ~pGIpGIG~ktA~kLI 156 (531)
..+|||||.++|.++.
T Consensus 49 ~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKID 64 (68)
T ss_dssp HCTSTTTTHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHH
Confidence 3799999999998873
No 178
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=22.95 E-value=1.7e+02 Score=31.21 Aligned_cols=71 Identities=14% Similarity=0.135 Sum_probs=43.3
Q ss_pred HHHcCCeeEEeecCCCCCcchHH--HHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHH
Q psy1206 363 LVEHGLKPIYVFDGKPPTLKSGE--LNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKK 440 (531)
Q Consensus 363 ll~~gIkPVfVFDG~pp~lK~~~--~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 (531)
+|.++ +|||.||--.-.+-..+ .++=.++|..+-++.+.|..-|=+- ..-+.-....+++..++
T Consensus 191 ~l~~~-~~v~~~DP~s~~~~~~~~~~~~~l~rR~~~I~ka~~A~~vGIlv-------------gTl~~q~~~~~~~~l~~ 256 (332)
T TIGR00322 191 AIHTE-KEVFKYDPYSGEFTRIGEDAKQFVKVRALAISKARKGKKFGVVL-------------SSKGGQGRLRLAKNLKK 256 (332)
T ss_pred HHHcC-CcEEEECCCCCceeEccccHHHHHHHHHHHHHHHhcCCEEEEEE-------------ecCccCCCHHHHHHHHH
Confidence 45554 89999997766665543 3333444555555555555544322 00133456899999999
Q ss_pred HHHHhcc
Q psy1206 441 LLKARST 447 (531)
Q Consensus 441 ll~~~~~ 447 (531)
+|+..|+
T Consensus 257 ll~~~gk 263 (332)
T TIGR00322 257 NLEEAGK 263 (332)
T ss_pred HHHHcCC
Confidence 9999664
No 179
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=22.89 E-value=57 Score=35.11 Aligned_cols=27 Identities=15% Similarity=0.236 Sum_probs=24.6
Q ss_pred cCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206 245 DSIRGIGPKRAIELIKEHRSIEKILEN 271 (531)
Q Consensus 245 ~~i~giG~k~A~kli~k~~s~~~vi~~ 271 (531)
.+||+++...|.+|+.+|+|+.+|+.+
T Consensus 290 s~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 290 SKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 469999999999999999999998864
No 180
>PRK13844 recombination protein RecR; Provisional
Probab=22.70 E-value=41 Score=33.43 Aligned_cols=55 Identities=9% Similarity=-0.122 Sum_probs=30.4
Q ss_pred ccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcch--HHHHHHHhcCCcccCccccccccccCCCc
Q psy1206 244 CDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWL--YKEARELFRHPEIADPETIELVADVAPSS 313 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~--~~~A~~~F~~~~V~dP~~~~Lv~~~aP~~ 313 (531)
+.++||||+|+|.++.-.- | .-|+++. +-+|....+....+|+.=.-+ .++.|..
T Consensus 17 l~~LPGIG~KsA~Rla~~l---------L-----~~~~~~~~~la~~i~~~~~~i~~C~~C~~l-te~~~C~ 73 (200)
T PRK13844 17 LRKLPTIGKKSSQRLALYL---------L-----DKSPETAIAIANSLLDATANIKKCVYCQAL-TEDDVCN 73 (200)
T ss_pred HHHCCCCCHHHHHHHHHHH---------H-----cCCHHHHHHHHHHHHHHHHhCCcCCCCCCC-CCCCCCC
Confidence 5678999999998875321 1 1133332 455555555556666644333 3444443
No 181
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=22.64 E-value=59 Score=30.63 Aligned_cols=30 Identities=20% Similarity=0.173 Sum_probs=25.0
Q ss_pred chhHHHHHHHHcCCEEEEEcCCCccccccC
Q psy1206 64 EAEAQCAAMVKAGKVYATATEDMDALTFGS 93 (531)
Q Consensus 64 EADAq~A~L~r~G~vd~ViSeDsDlL~fg~ 93 (531)
+=|+-.-.++-.|.+++++|+|.|+|.+..
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~ 120 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRD 120 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheecc
Confidence 447777788889999999999999986544
No 182
>KOG2045|consensus
Probab=22.22 E-value=1.6e+02 Score=35.81 Aligned_cols=55 Identities=33% Similarity=0.404 Sum_probs=41.8
Q ss_pred HHHHHcCCeeEEee----cCCCCCcchHHHHHHH-HHHHHHHHHHHHHHHcccccCCCCC
Q psy1206 361 IRLVEHGLKPIYVF----DGKPPTLKSGELNKRM-EKREDAQKALAKAQEQGKLKWSDPD 415 (531)
Q Consensus 361 ~~ll~~gIkPVfVF----DG~pp~lK~~~~~kR~-~~r~~a~~~~~~a~~~G~~~~~~~~ 415 (531)
|.=|.+-|||==+| ||.+|-.|-.....|| ....+|+..+++|.+.|++--.++|
T Consensus 68 IdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erF 127 (1493)
T KOG2045|consen 68 IDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERF 127 (1493)
T ss_pred HHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCccccc
Confidence 33477889997666 9999999996655444 5567899999999999997644444
No 183
>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=21.03 E-value=85 Score=32.35 Aligned_cols=26 Identities=27% Similarity=0.465 Sum_probs=23.0
Q ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206 142 DSIRGIGPKRAIELIKE-HRSIEKILE 167 (531)
Q Consensus 142 pGIpGIG~ktA~kLI~~-~~sle~il~ 167 (531)
..+||||+++|.+|.+. +.|++++..
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~ 28 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAV 28 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 46899999999999998 999988865
No 184
>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=20.92 E-value=59 Score=28.49 Aligned_cols=17 Identities=29% Similarity=0.272 Sum_probs=14.4
Q ss_pred ccCCCCCchHHHHHHHH
Q psy1206 244 CDSIRGIGPKRAIELIK 260 (531)
Q Consensus 244 ~~~i~giG~k~A~kli~ 260 (531)
+..|||||+++|-.|+.
T Consensus 14 L~~iP~IG~a~a~DL~~ 30 (93)
T PF11731_consen 14 LTDIPNIGKATAEDLRL 30 (93)
T ss_pred HhcCCCccHHHHHHHHH
Confidence 45799999999998874
No 185
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=20.36 E-value=70 Score=31.90 Aligned_cols=16 Identities=38% Similarity=0.723 Sum_probs=14.2
Q ss_pred CCCCccHHHHHHHHHH
Q psy1206 143 SIRGIGPKRAIELIKE 158 (531)
Q Consensus 143 GIpGIG~ktA~kLI~~ 158 (531)
.+||||+|||--++..
T Consensus 123 ~lpGIG~KTAd~vL~~ 138 (208)
T PRK01229 123 NIKGIGYKEASHFLRN 138 (208)
T ss_pred cCCCCcHHHHHHHHHH
Confidence 8999999999988853
No 186
>KOG1247|consensus
Probab=20.24 E-value=1.1e+02 Score=33.94 Aligned_cols=105 Identities=20% Similarity=0.281 Sum_probs=63.0
Q ss_pred eeeecccchHHHHHHHHhhc--Cccc------cCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHH-
Q psy1206 319 KICIDASMSLYQFLIAVRSE--GNQL------MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKR- 389 (531)
Q Consensus 319 ~iAIDa~~~lyqfl~~ir~~--g~~l------~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR- 389 (531)
-..|-+++|=|-.|+ +|-+ ++.. .--++|..+.|-.+.+|+.+++.++ |-|..|+++...-.++
T Consensus 359 d~gi~~~vWRyYLl~-~RPEssDs~Fsw~df~~k~nseLl~NLGNFvNR~l~fv~~~------~~g~Vp~~~~~~~~~~~ 431 (567)
T KOG1247|consen 359 DTGIPASVWRYYLLY-IRPESSDSAFSWDDFVLKVNSELLNNLGNFVNRVLKFVAAK------YNGVVPEMELTSGDKKL 431 (567)
T ss_pred cCCCCHHHHHHHHhh-ccCcccCCcCcHHHHHHHhhHHHHHHHHHHHHHHHHHHHHh------hCCcccceeecCChHHH
Confidence 345778899997776 5532 2221 1234566778889999999998876 5677777754332222
Q ss_pred HHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHH
Q psy1206 390 MEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNG 437 (531)
Q Consensus 390 ~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 (531)
-+.-.+.-.++.++.|++.++ ++.+-+..-+.+-+..|-++
T Consensus 432 ~~dv~~~~~~y~~~me~vklr-------~~l~~~m~is~~GNqylQ~~ 472 (567)
T KOG1247|consen 432 LEDVNELLAKYVAAMEKVKLR-------EALKTAMEISRRGNQYLQEN 472 (567)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhhhHHHhcc
Confidence 122334455677777777766 55554444344445555444
No 187
>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=20.07 E-value=79 Score=37.11 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=9.8
Q ss_pred CCCCchHHHHHHHHhhc
Q psy1206 247 IRGIGPKRAIELIKEHR 263 (531)
Q Consensus 247 i~giG~k~A~kli~k~~ 263 (531)
+||||+++|-+++..++
T Consensus 89 ~~GIG~~~A~~iv~~fg 105 (720)
T TIGR01448 89 IKGVGKKLAQRIVKTFG 105 (720)
T ss_pred CCCcCHHHHHHHHHHhC
Confidence 55555555555555555
Done!