Query 021529
Match_columns 311
No_of_seqs 246 out of 1691
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 03:43:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021529.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021529hhsearch_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 9.5E-70 2.1E-74 518.7 35.4 297 2-299 55-351 (393)
2 PRK03980 flap endonuclease-1; 100.0 1.8E-68 3.9E-73 492.0 33.0 282 3-294 1-292 (292)
3 TIGR03674 fen_arch flap struct 100.0 7.1E-63 1.5E-67 464.6 32.3 283 2-294 47-338 (338)
4 cd00128 XPG Xeroderma pigmento 100.0 1.9E-54 4.1E-59 405.6 30.2 268 5-276 48-315 (316)
5 KOG2519 5'-3' exonuclease [Rep 100.0 2.3E-54 5.1E-59 406.3 25.1 304 4-307 51-355 (449)
6 PRK14976 5'-3' exonuclease; Pr 100.0 2.6E-47 5.7E-52 350.1 22.2 238 2-267 28-281 (281)
7 smart00475 53EXOc 5'-3' exonuc 100.0 1.7E-46 3.7E-51 341.0 19.5 215 2-242 22-246 (259)
8 TIGR00593 pola DNA polymerase 100.0 5E-44 1.1E-48 370.6 23.9 238 2-268 22-277 (887)
9 TIGR00600 rad2 DNA excision re 100.0 3.2E-43 6.9E-48 363.2 24.4 218 76-298 763-1006(1034)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 4.8E-43 1E-47 316.0 19.2 193 3-224 23-225 (240)
11 PRK09482 flap endonuclease-lik 100.0 3.1E-42 6.8E-47 310.6 18.5 189 4-224 23-224 (256)
12 PRK05755 DNA polymerase I; Pro 100.0 8.1E-42 1.8E-46 357.6 22.6 238 2-268 24-278 (880)
13 KOG2518 5'-3' exonuclease [Rep 100.0 9.5E-42 2.1E-46 324.3 20.5 233 6-242 48-288 (556)
14 COG0258 Exo 5'-3' exonuclease 100.0 3.7E-40 8.1E-45 308.0 23.8 262 2-294 33-309 (310)
15 KOG2520 5'-3' exonuclease [Rep 100.0 4.3E-33 9.3E-38 279.9 15.5 213 80-297 461-702 (815)
16 PHA00439 exonuclease 100.0 1.3E-30 2.8E-35 237.0 15.0 169 2-211 34-219 (286)
17 PHA02567 rnh RnaseH; Provision 99.9 6.7E-27 1.5E-31 213.6 16.4 161 2-191 33-206 (304)
18 PF02739 5_3_exonuc_N: 5'-3' e 99.9 4.2E-26 9.2E-31 195.0 11.2 138 2-165 24-169 (169)
19 PF00867 XPG_I: XPG I-region; 99.9 3.2E-24 6.9E-29 166.3 7.2 88 95-182 1-94 (94)
20 smart00484 XPGI Xeroderma pigm 99.8 1.2E-18 2.6E-23 128.1 7.8 72 96-167 2-73 (73)
21 cd00080 HhH2_motif Helix-hairp 99.6 1.8E-15 3.9E-20 112.2 6.3 52 164-215 2-55 (75)
22 PF01367 5_3_exonuc: 5'-3' exo 99.6 8.6E-18 1.9E-22 131.0 -6.7 91 167-258 1-101 (101)
23 smart00279 HhH2 Helix-hairpin- 99.3 4.6E-12 9.9E-17 80.1 3.8 33 169-202 1-36 (36)
24 PF12813 XPG_I_2: XPG domain c 98.9 9.7E-09 2.1E-13 93.1 9.0 89 86-177 5-107 (246)
25 smart00485 XPGN Xeroderma pigm 98.6 6E-08 1.3E-12 75.6 5.9 47 9-55 51-98 (99)
26 PF00752 XPG_N: XPG N-terminal 98.6 4.7E-08 1E-12 76.4 5.1 46 10-55 55-100 (101)
27 TIGR00600 rad2 DNA excision re 98.2 2.5E-06 5.5E-11 90.2 8.3 52 9-60 51-102 (1034)
28 COG5366 Protein involved in pr 96.8 0.00077 1.7E-08 64.9 2.9 101 88-190 132-233 (531)
29 PF12826 HHH_2: Helix-hairpin- 96.3 0.0032 6.9E-08 45.0 2.4 26 185-210 6-31 (64)
30 TIGR00084 ruvA Holliday juncti 96.2 0.052 1.1E-06 47.4 10.4 112 159-279 54-172 (191)
31 PF03159 XRN_N: XRN 5'-3' exon 96.1 0.048 1E-06 49.2 9.8 38 98-135 172-222 (237)
32 PRK00116 ruvA Holliday junctio 95.3 0.077 1.7E-06 46.3 7.6 91 186-279 77-174 (192)
33 KOG2045 5'-3' exonuclease XRN1 95.2 0.31 6.8E-06 51.2 12.5 183 16-199 64-307 (1493)
34 COG5049 XRN1 5'-3' exonuclease 95.1 0.47 1E-05 48.6 13.2 95 98-192 176-328 (953)
35 PRK14605 ruvA Holliday junctio 94.9 0.12 2.7E-06 45.1 7.7 110 159-279 55-173 (194)
36 PRK13901 ruvA Holliday junctio 94.1 0.36 7.8E-06 42.3 8.8 109 159-279 54-169 (196)
37 PRK14600 ruvA Holliday junctio 94.0 0.31 6.7E-06 42.4 8.2 110 158-279 54-170 (186)
38 KOG2044 5'-3' exonuclease HKE1 93.9 0.76 1.6E-05 47.6 11.7 188 11-199 79-360 (931)
39 PRK14671 uvrC excinuclease ABC 93.8 0.38 8.3E-06 49.4 9.7 26 185-210 572-597 (621)
40 PRK14602 ruvA Holliday junctio 93.8 0.56 1.2E-05 41.3 9.5 111 160-279 57-180 (203)
41 PRK14604 ruvA Holliday junctio 93.7 0.43 9.3E-06 41.8 8.6 109 160-279 56-174 (195)
42 PRK14606 ruvA Holliday junctio 93.7 0.36 7.8E-06 42.0 8.0 107 159-279 55-168 (188)
43 COG0632 RuvA Holliday junction 93.5 1.7 3.6E-05 38.3 11.9 117 156-280 52-182 (201)
44 PRK14603 ruvA Holliday junctio 93.5 0.67 1.5E-05 40.7 9.4 111 160-279 55-177 (197)
45 PRK14601 ruvA Holliday junctio 93.5 0.37 8.1E-06 41.8 7.7 105 159-278 55-166 (183)
46 PF04599 Pox_G5: Poxvirus G5 p 93.2 2 4.3E-05 41.8 12.7 110 89-213 147-273 (425)
47 PRK14667 uvrC excinuclease ABC 93.0 0.075 1.6E-06 53.9 3.1 30 182-211 514-543 (567)
48 PF00633 HHH: Helix-hairpin-he 93.0 0.084 1.8E-06 31.8 2.1 15 186-200 15-29 (30)
49 TIGR00194 uvrC excinuclease AB 92.9 0.075 1.6E-06 54.0 3.0 30 182-211 541-570 (574)
50 PF10391 DNA_pol_lambd_f: Fing 92.8 0.095 2.1E-06 35.8 2.4 24 186-209 6-30 (52)
51 PF14520 HHH_5: Helix-hairpin- 92.8 0.1 2.2E-06 36.5 2.7 25 186-210 9-34 (60)
52 PRK14670 uvrC excinuclease ABC 92.7 0.09 1.9E-06 53.4 3.1 30 182-211 514-543 (574)
53 PRK14669 uvrC excinuclease ABC 92.6 0.086 1.9E-06 54.0 2.9 29 183-211 553-581 (624)
54 PRK14672 uvrC excinuclease ABC 91.2 0.17 3.6E-06 52.1 3.1 30 182-211 608-637 (691)
55 PHA03065 Hypothetical protein; 88.9 5.3 0.00012 38.8 11.0 110 89-213 149-275 (438)
56 smart00278 HhH1 Helix-hairpin- 88.7 0.37 8E-06 27.7 2.0 17 185-201 4-20 (26)
57 PRK00558 uvrC excinuclease ABC 88.4 0.34 7.5E-06 49.6 2.9 27 185-211 546-572 (598)
58 PRK14668 uvrC excinuclease ABC 88.3 0.37 8.1E-06 49.1 3.0 30 182-211 525-554 (577)
59 PRK12766 50S ribosomal protein 88.0 0.41 8.8E-06 42.8 2.6 28 184-211 5-33 (232)
60 PRK14666 uvrC excinuclease ABC 87.9 0.41 8.9E-06 49.4 3.0 29 183-211 638-666 (694)
61 PF02371 Transposase_20: Trans 86.7 0.58 1.3E-05 35.2 2.5 25 183-207 3-27 (87)
62 COG0322 UvrC Nuclease subunit 85.8 0.62 1.3E-05 47.4 3.0 47 164-211 513-559 (581)
63 COG1948 MUS81 ERCC4-type nucle 84.8 0.82 1.8E-05 41.5 2.9 26 186-211 186-211 (254)
64 PRK14601 ruvA Holliday junctio 84.5 0.9 2E-05 39.4 3.0 46 155-202 80-128 (183)
65 TIGR01448 recD_rel helicase, p 84.1 3.3 7.1E-05 43.5 7.4 39 167-213 75-113 (720)
66 PF05991 NYN_YacP: YacP-like N 82.9 3.9 8.5E-05 34.7 6.2 39 97-135 66-110 (166)
67 PRK14603 ruvA Holliday junctio 81.3 1.8 4E-05 37.9 3.7 47 155-203 79-128 (197)
68 PRK14600 ruvA Holliday junctio 80.9 2.3 5.1E-05 36.9 4.2 46 155-202 80-127 (186)
69 PRK13901 ruvA Holliday junctio 79.9 1.7 3.7E-05 38.1 3.0 45 156-202 80-127 (196)
70 PRK02515 psbU photosystem II c 79.5 1.7 3.6E-05 35.5 2.6 24 187-210 66-91 (132)
71 PRK14606 ruvA Holliday junctio 78.8 2.4 5.3E-05 36.9 3.6 46 155-202 80-128 (188)
72 PRK14604 ruvA Holliday junctio 78.7 1.7 3.6E-05 38.1 2.6 47 155-203 80-129 (195)
73 TIGR00575 dnlj DNA ligase, NAD 77.8 2 4.4E-05 44.5 3.3 25 186-210 502-526 (652)
74 PF11798 IMS_HHH: IMS family H 77.8 1.7 3.6E-05 26.4 1.6 13 186-198 15-27 (32)
75 PF01927 Mut7-C: Mut7-C RNAse 76.9 3.4 7.4E-05 34.3 3.9 88 86-181 8-99 (147)
76 PRK14602 ruvA Holliday junctio 76.6 2.9 6.3E-05 36.8 3.5 47 155-203 81-130 (203)
77 PRK14351 ligA NAD-dependent DN 76.0 2.5 5.5E-05 44.0 3.4 25 186-210 532-556 (689)
78 TIGR00596 rad1 DNA repair prot 75.7 2.4 5.1E-05 45.1 3.2 25 186-210 761-785 (814)
79 TIGR01259 comE comEA protein. 74.6 3.2 6.9E-05 33.3 3.0 17 186-202 72-88 (120)
80 cd00141 NT_POLXc Nucleotidyltr 73.1 3.7 8E-05 38.5 3.5 26 186-212 89-116 (307)
81 smart00483 POLXc DNA polymeras 73.0 3.1 6.7E-05 39.5 3.0 25 186-211 93-119 (334)
82 COG0632 RuvA Holliday junction 72.1 4 8.8E-05 35.9 3.3 72 121-202 49-128 (201)
83 TIGR00305 probable toxin-antit 71.2 5.7 0.00012 31.1 3.7 29 105-133 85-113 (114)
84 PRK13766 Hef nuclease; Provisi 70.2 4 8.7E-05 43.0 3.3 26 186-211 719-744 (773)
85 PRK07956 ligA NAD-dependent DN 69.6 3.4 7.4E-05 42.9 2.6 23 187-209 516-538 (665)
86 PF00875 DNA_photolyase: DNA p 68.5 11 0.00023 31.5 5.0 44 84-127 52-96 (165)
87 COG1555 ComEA DNA uptake prote 67.2 6.2 0.00014 33.0 3.3 24 186-209 101-130 (149)
88 TIGR00426 competence protein C 66.4 7.1 0.00015 27.8 3.0 15 187-201 22-36 (69)
89 PRK08609 hypothetical protein; 65.5 11 0.00023 38.6 5.2 28 186-213 92-121 (570)
90 COG0272 Lig NAD-dependent DNA 65.3 4.6 0.0001 41.6 2.5 26 186-211 515-540 (667)
91 PF11731 Cdd1: Pathogenicity l 64.7 6.2 0.00013 30.3 2.5 32 186-217 16-56 (93)
92 PF14520 HHH_5: Helix-hairpin- 64.4 6.1 0.00013 27.3 2.3 17 186-202 42-58 (60)
93 TIGR00084 ruvA Holliday juncti 64.0 9 0.00019 33.4 3.7 44 156-201 80-126 (191)
94 PTZ00134 40S ribosomal protein 60.5 11 0.00023 31.8 3.4 35 169-203 8-51 (154)
95 PRK13844 recombination protein 59.6 8.5 0.00018 33.8 2.8 16 186-201 19-34 (200)
96 PF12826 HHH_2: Helix-hairpin- 58.6 7.9 0.00017 27.3 2.0 22 186-207 39-60 (64)
97 PRK13482 DNA integrity scannin 58.3 9.6 0.00021 36.4 3.1 25 187-211 292-316 (352)
98 COG0353 RecR Recombinational D 54.0 7.3 0.00016 34.0 1.4 15 186-200 16-30 (198)
99 PRK14605 ruvA Holliday junctio 53.9 9.5 0.00021 33.3 2.2 45 156-202 81-128 (194)
100 TIGR00615 recR recombination p 53.6 8.6 0.00019 33.6 1.8 16 186-201 15-30 (195)
101 PRK00076 recR recombination pr 53.5 8.6 0.00019 33.7 1.8 16 186-201 15-30 (196)
102 KOG2841 Structure-specific end 52.5 11 0.00023 33.9 2.3 29 183-211 196-224 (254)
103 TIGR00288 conserved hypothetic 49.8 22 0.00048 30.1 3.7 47 89-135 70-122 (160)
104 PF01850 PIN: PIN domain; Int 49.6 18 0.00039 27.7 3.0 49 80-134 70-118 (121)
105 TIGR02765 crypto_DASH cryptoch 49.5 58 0.0013 31.8 7.2 31 87-117 63-93 (429)
106 PRK01229 N-glycosylase/DNA lya 46.5 15 0.00032 32.5 2.2 18 186-203 123-140 (208)
107 COG1656 Uncharacterized conser 46.2 71 0.0015 27.2 6.1 50 84-134 12-61 (165)
108 TIGR00114 lumazine-synth 6,7-d 46.0 40 0.00086 27.8 4.6 55 83-137 15-82 (138)
109 PRK04053 rps13p 30S ribosomal 45.6 31 0.00066 28.9 3.9 34 170-203 4-46 (149)
110 PF00416 Ribosomal_S13: Riboso 45.6 19 0.00041 28.2 2.5 17 187-203 20-36 (107)
111 cd06167 LabA_like LabA_like pr 44.1 50 0.0011 26.7 5.0 49 87-135 54-116 (149)
112 TIGR00591 phr2 photolyase PhrI 41.9 79 0.0017 31.1 6.8 31 87-117 80-110 (454)
113 PF14229 DUF4332: Domain of un 41.7 68 0.0015 25.6 5.3 50 156-208 30-80 (122)
114 PF01936 NYN: NYN domain; Int 41.1 71 0.0015 25.4 5.4 49 87-135 49-112 (146)
115 PF14716 HHH_8: Helix-hairpin- 40.8 21 0.00046 25.3 2.0 14 185-198 50-63 (68)
116 PRK12419 riboflavin synthase s 40.1 48 0.001 28.0 4.2 55 83-137 25-92 (158)
117 PF11977 RNase_Zc3h12a: Zc3h12 39.9 81 0.0018 26.2 5.7 33 96-129 69-110 (155)
118 PF04919 DUF655: Protein of un 38.9 58 0.0013 28.1 4.6 46 166-212 95-151 (181)
119 TIGR03252 uncharacterized HhH- 38.7 21 0.00045 30.8 1.9 18 186-203 119-136 (177)
120 PF00885 DMRL_synthase: 6,7-di 38.5 61 0.0013 26.8 4.6 42 84-125 19-67 (144)
121 PF12482 DUF3701: Phage integr 38.1 42 0.0009 25.9 3.3 41 162-202 29-70 (96)
122 PRK10702 endonuclease III; Pro 37.6 21 0.00045 31.6 1.8 14 187-200 114-127 (211)
123 cd00056 ENDO3c endonuclease II 37.4 22 0.00048 29.3 1.9 15 186-200 87-101 (158)
124 TIGR02766 crypt_chrom_pln cryp 36.6 1.2E+02 0.0026 30.0 7.3 13 190-202 201-213 (475)
125 PRK14350 ligA NAD-dependent DN 36.4 32 0.00069 35.9 3.1 25 186-210 506-531 (669)
126 COG1412 Uncharacterized protei 36.3 44 0.00096 27.5 3.4 41 93-134 71-112 (136)
127 COG1948 MUS81 ERCC4-type nucle 35.8 1.3E+02 0.0028 27.5 6.5 24 187-210 219-242 (254)
128 PF14490 HHH_4: Helix-hairpin- 35.4 89 0.0019 23.6 4.8 31 189-221 19-49 (94)
129 PRK00061 ribH 6,7-dimethyl-8-r 35.2 62 0.0014 27.2 4.2 55 84-138 28-95 (154)
130 PF14579 HHH_6: Helix-hairpin- 35.0 49 0.0011 24.8 3.3 26 187-212 32-62 (90)
131 PF04760 IF2_N: Translation in 34.7 36 0.00079 22.8 2.3 48 156-203 4-52 (54)
132 PRK00116 ruvA Holliday junctio 34.6 28 0.00061 30.2 2.1 18 186-203 112-129 (192)
133 TIGR02236 recomb_radA DNA repa 34.5 34 0.00073 31.8 2.7 24 186-209 3-27 (310)
134 TIGR02990 ectoine_eutA ectoine 33.9 2.5E+02 0.0055 25.2 8.2 106 87-192 108-235 (239)
135 PF10454 DUF2458: Protein of u 33.9 1.2E+02 0.0026 25.4 5.6 34 73-106 93-126 (150)
136 TIGR03631 bact_S13 30S ribosom 33.5 38 0.00083 26.9 2.5 17 187-203 20-36 (113)
137 COG1647 Esterase/lipase [Gener 33.3 22 0.00047 31.9 1.2 57 84-140 167-224 (243)
138 cd04246 AAK_AK-DapG-like AAK_A 33.0 3.5E+02 0.0075 23.9 11.3 30 12-41 16-45 (239)
139 smart00478 ENDO3c endonuclease 32.9 30 0.00065 28.3 1.9 15 186-200 76-90 (149)
140 PLN02404 6,7-dimethyl-8-ribity 32.8 78 0.0017 26.2 4.3 56 83-138 22-90 (141)
141 PRK13913 3-methyladenine DNA g 32.7 29 0.00063 30.9 1.9 15 186-200 125-139 (218)
142 PRK10674 deoxyribodipyrimidine 31.9 1.6E+02 0.0034 29.3 7.1 33 86-118 58-94 (472)
143 PF14635 HHH_7: Helix-hairpin- 31.5 37 0.00079 26.6 2.1 44 156-202 15-70 (104)
144 COG4277 Predicted DNA-binding 31.2 57 0.0012 30.7 3.5 48 154-201 276-349 (404)
145 PF05687 DUF822: Plant protein 31.2 1.9E+02 0.0041 24.1 6.2 47 86-135 25-72 (150)
146 COG1491 Predicted RNA-binding 31.0 57 0.0012 28.3 3.3 46 167-213 110-166 (202)
147 TIGR01083 nth endonuclease III 30.7 32 0.0007 29.7 1.8 15 186-200 110-124 (191)
148 PRK05179 rpsM 30S ribosomal pr 30.7 44 0.00095 26.9 2.5 17 187-203 22-38 (122)
149 PF04900 Fcf1: Fcf1; InterPro 30.7 52 0.0011 25.1 2.8 38 97-134 42-79 (101)
150 PRK00124 hypothetical protein; 30.4 35 0.00075 28.6 1.9 91 107-211 56-146 (151)
151 CHL00137 rps13 ribosomal prote 30.2 46 0.001 26.8 2.5 17 187-203 22-38 (122)
152 PRK00254 ski2-like helicase; P 29.9 42 0.00091 35.2 2.9 26 186-211 649-675 (720)
153 cd04261 AAK_AKii-LysC-BS AAK_A 29.7 4E+02 0.0086 23.6 11.5 30 12-41 16-45 (239)
154 PF04019 DUF359: Protein of un 29.4 39 0.00086 27.2 2.0 29 81-109 45-73 (121)
155 PF02639 DUF188: Uncharacteriz 28.1 40 0.00087 27.5 1.8 82 107-199 40-121 (130)
156 TIGR00028 Mtu_PIN_fam Mycobact 28.0 59 0.0013 25.7 2.9 31 107-138 105-135 (142)
157 PF12836 HHH_3: Helix-hairpin- 27.6 49 0.0011 23.2 2.0 16 186-201 18-33 (65)
158 COG1569 Predicted nucleic acid 27.3 50 0.0011 27.3 2.2 32 107-138 91-122 (142)
159 PRK13910 DNA glycosylase MutY; 27.1 39 0.00084 31.5 1.8 18 186-203 76-94 (289)
160 COG0177 Nth Predicted EndoIII- 26.4 47 0.001 29.4 2.1 17 187-203 114-131 (211)
161 TIGR01084 mutY A/G-specific ad 24.9 46 0.00099 30.7 1.8 15 186-200 109-123 (275)
162 TIGR03629 arch_S13P archaeal r 24.9 61 0.0013 26.9 2.4 17 187-203 26-42 (144)
163 KOG2534 DNA polymerase IV (fam 24.1 46 0.001 31.4 1.7 25 186-210 101-126 (353)
164 PF12244 DUF3606: Protein of u 24.0 87 0.0019 21.6 2.7 28 155-182 20-47 (57)
165 TIGR00315 cdhB CO dehydrogenas 23.6 2.4E+02 0.0051 23.9 5.8 47 16-105 16-62 (162)
166 PRK07956 ligA NAD-dependent DN 23.6 1.7E+02 0.0038 30.5 5.9 26 184-209 447-474 (665)
167 cd05212 NAD_bind_m-THF_DH_Cycl 23.3 1.9E+02 0.004 23.8 5.0 41 86-126 11-59 (140)
168 PRK01189 V-type ATP synthase s 22.5 1E+02 0.0022 24.0 3.1 36 92-127 15-53 (104)
169 COG2266 GTP:adenosylcobinamide 22.5 2E+02 0.0042 24.8 5.0 43 86-128 51-95 (177)
170 PRK04301 radA DNA repair and r 21.7 77 0.0017 29.5 2.7 24 186-209 10-34 (317)
171 PRK10308 3-methyl-adenine DNA 21.7 57 0.0012 30.2 1.8 18 187-204 212-230 (283)
172 TIGR00289 conserved hypothetic 21.6 1.6E+02 0.0035 26.2 4.6 42 88-130 48-95 (222)
173 PTZ00349 dehydrodolichyl dipho 21.5 1.3E+02 0.0028 28.5 4.0 19 86-104 51-69 (322)
174 COG1476 Predicted transcriptio 21.4 2.6E+02 0.0057 20.1 4.8 48 156-211 15-63 (68)
175 PRK10736 hypothetical protein; 21.3 75 0.0016 30.8 2.5 21 187-207 13-33 (374)
176 PF09288 UBA_3: Fungal ubiquit 21.2 1.2E+02 0.0026 21.0 2.8 31 247-279 4-34 (55)
177 COG1671 Uncharacterized protei 21.1 87 0.0019 26.2 2.5 57 101-165 47-105 (150)
178 PRK10880 adenine DNA glycosyla 20.5 66 0.0014 30.8 2.0 18 186-203 113-131 (350)
179 PRK05234 mgsA methylglyoxal sy 20.3 1.2E+02 0.0026 25.0 3.2 35 91-125 42-80 (142)
180 PF10087 DUF2325: Uncharacteri 20.1 2.6E+02 0.0056 21.0 4.9 35 81-115 58-93 (97)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=9.5e-70 Score=518.65 Aligned_cols=297 Identities=59% Similarity=1.017 Sum_probs=281.7
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhcc
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~ 81 (311)
|+|++|.+|++++||++++++|+++||+|+|||||.+|++|++++++||++|+++++.+..+.+.|+.+++.+++++++.
T Consensus 55 l~~~~G~~t~~l~g~~~r~~~Ll~~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~ 134 (393)
T PTZ00217 55 LTNEAGEVTSHISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVR 134 (393)
T ss_pred chhccCCccHHHHHHHHHHHHHHHCCCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhccc
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHH
Q 021529 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (311)
Q Consensus 82 v~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v 161 (311)
+|++|++.++++|+.+||||++||||||||||+|++.|++++|+|+|+|+|+||++.+++++...+....++++++.+.+
T Consensus 135 vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v 214 (393)
T PTZ00217 135 VTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTV 214 (393)
T ss_pred CCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998887654333445788999999
Q ss_pred HHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhcCCCCCCcc
Q 021529 162 LEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (311)
Q Consensus 162 ~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~ 241 (311)
++.+|++|+||+|+|+|+||||++||||||+|||++||++||++|+|+++++..+..+|++|++.+++.+|++|.|..+.
T Consensus 215 ~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~~k~~~p~~~~~~~~~~~f~~p~V~~~~ 294 (393)
T PTZ00217 215 LEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPENFDYKEARELFLNPEVTPAE 294 (393)
T ss_pred HHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCCChHHHHHHhcCCCcCCCC
Confidence 99999999999999999999999999999999999999999999999999999888999999999999999999998765
Q ss_pred ccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhccCCCCCcccccCcCCC
Q 021529 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVAN 299 (311)
Q Consensus 242 ~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~~~~~~~~q~~l~~ff~~~~~ 299 (311)
+. +|.|+.||.++|++||+++++|+.+||.+.++|+.++....+|+|||+||..+..
T Consensus 295 ~~-~l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~ 351 (393)
T PTZ00217 295 EI-DLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKK 351 (393)
T ss_pred CC-CCCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhccCccCCHHHhcCCCCC
Confidence 65 7999999999999999999999999999999999988888899999999997743
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.8e-68 Score=491.99 Aligned_cols=282 Identities=45% Similarity=0.807 Sum_probs=263.0
Q ss_pred CCCCCCcchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhccC
Q 021529 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (311)
Q Consensus 3 ~~~~G~~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v 82 (311)
+|++|++|+|++||++++++|+++||+|+|||||.+|++|++++++||++|+++++.+..+.+.|+.+++.++++++.++
T Consensus 1 ~~~~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~v 80 (292)
T PRK03980 1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRL 80 (292)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCC---------ccc
Q 021529 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRK---------IPV 153 (311)
Q Consensus 83 ~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~---------~~~ 153 (311)
|++|++.++++|+.+||||++||||||||||+|++.|++++|+|+|+|+|+||++++++++...++++ ...
T Consensus 81 t~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~ 160 (292)
T PRK03980 81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKP 160 (292)
T ss_pred CHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999998886543221 134
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc-hHHHHHHh
Q 021529 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP-YQEARRLF 232 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~-~~~~~~~~ 232 (311)
+.++.+.+++.+|++++||+|+|+|+||||++||||||+|||++||++||++|+|+++++ .+++ +.+++.+|
T Consensus 161 e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~-------~~~~~~~~~r~~f 233 (292)
T PRK03980 161 ELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG-------FEIENYDEIREFF 233 (292)
T ss_pred eeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc-------CCCCCHHHHHHHh
Confidence 579999999999999999999999999999999999999999999999999999998643 2344 58999999
Q ss_pred cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhccCCCCCccccc
Q 021529 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (311)
Q Consensus 233 ~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~~~~~~~~q~~l~~ff 294 (311)
++|.|+. +. ++.|+.||.++|++||+++.+|+.+||.+.++|+.+..++.+|+|||+||
T Consensus 234 ~~p~v~~--~~-~~~~~~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~~~~~~~~q~~l~~ff 292 (292)
T PRK03980 234 LNPPVTD--DY-ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292 (292)
T ss_pred cCCCCCC--CC-CccCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccCcccchhhcC
Confidence 9999985 33 78999999999999999999999999999999999888878999999998
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=7.1e-63 Score=464.61 Aligned_cols=283 Identities=46% Similarity=0.809 Sum_probs=260.7
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhcc
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~ 81 (311)
|++++|.||++++||+.++++|+++|++|+|||||.+|++|++++++|++.|+++++.+..+.+.|+.+++.++++++.+
T Consensus 47 l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~ 126 (338)
T TIGR03674 47 LMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSR 126 (338)
T ss_pred hhhccCCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCC
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCc---------c
Q 021529 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------P 152 (311)
Q Consensus 82 v~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~---------~ 152 (311)
+|.+|++.++++|+.+|||+++||||||||||+|++.|.+++|+|+|+|+||||++++++++...+++.. .
T Consensus 127 ~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~ 206 (338)
T TIGR03674 127 LTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVK 206 (338)
T ss_pred CCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999888765432111 3
Q ss_pred cEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHh
Q 021529 153 VMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (311)
Q Consensus 153 ~~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~~~~~~~ 232 (311)
.+.++.+.+++.+|++|+||+|+|+|+||||++||||||+|||++||++||++|+|+++++.. +. + ..+++.+|
T Consensus 207 ~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~~---~~-~--~~~~~~~f 280 (338)
T TIGR03674 207 PELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGED---IE-N--YDEIREFF 280 (338)
T ss_pred ceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcCC---CC-C--HHHHHHHh
Confidence 456999999999999999999999999999999999999999999999999999999997532 22 2 47889999
Q ss_pred cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhccCCCCCccccc
Q 021529 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (311)
Q Consensus 233 ~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~~~~~~~~q~~l~~ff 294 (311)
.+|.|+.. . ++.|..||.++|.+|++++++|+.+||.+.++|+++.. +.+|+|||+||
T Consensus 281 ~~~~v~~~--~-~~~~~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~~-~~~q~~l~~ff 338 (338)
T TIGR03674 281 LNPPVTDD--Y-ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAY-KSKQKTLDRWF 338 (338)
T ss_pred CCCCCCCC--C-CccCCCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHhh-cccccchhhcC
Confidence 99998753 3 78999999999999888999999999999999998776 78999999998
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=1.9e-54 Score=405.55 Aligned_cols=268 Identities=52% Similarity=0.890 Sum_probs=248.8
Q ss_pred CCCCcchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhccCCH
Q 021529 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTK 84 (311)
Q Consensus 5 ~~G~~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v~~ 84 (311)
+.|.+|+++++|++++.+|+++|++|+|||||.++++|.++..+|+.+|++..+....++++|+.+++.++.+++..+++
T Consensus 48 ~~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (316)
T cd00128 48 SGGETTSHLQGFFYRTCRLLELGIKPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTP 127 (316)
T ss_pred CCCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCH
Confidence 57999999999999999999999999999999999999999999999999998888899999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHH
Q 021529 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 164 (311)
Q Consensus 85 ~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~ 164 (311)
.+++.++++|+.+|||+++||+|||||||+|+++|.+++|+|+|+|+++||++++++++...+. ..++.++.+.+.+.
T Consensus 128 ~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~--~~~~~~~~~~~~~~ 205 (316)
T cd00128 128 QMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGA--KPVEEIDLEKILKE 205 (316)
T ss_pred HHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCC--CceEEEEHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999887764321 24678999999999
Q ss_pred cCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhcCCCCCCccccc
Q 021529 165 LNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQL 244 (311)
Q Consensus 165 ~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~ 244 (311)
+|++++||+|+|+|+||||++||||||+|||++||++||+++++++++.+....++++|++.+++++|.+|.|... ..
T Consensus 206 lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~--~~ 283 (316)
T cd00128 206 LGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDD--FI 283 (316)
T ss_pred cCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCC--CC
Confidence 9999999999999999999999999999999999999999999999998777778899999999999999988753 23
Q ss_pred cCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHH
Q 021529 245 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIE 276 (311)
Q Consensus 245 ~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~ 276 (311)
.+.|..||.+.|+.|+..+.+|+.+||.+.+.
T Consensus 284 ~~~~~~p~~~~l~~~~~~~~~~~~~rv~~~~~ 315 (316)
T cd00128 284 DLRWRDPDEEGIIEFLCKEHGFNEDRVLKPLE 315 (316)
T ss_pred ceeecCCCHHHHHHHccCCCCCCHHHHHhhhc
Confidence 68899999999999999999999999987763
No 5
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-54 Score=406.26 Aligned_cols=304 Identities=61% Similarity=0.998 Sum_probs=285.7
Q ss_pred CCCCCcchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhccCC
Q 021529 4 NEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVT 83 (311)
Q Consensus 4 ~~~G~~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v~ 83 (311)
+..|++|+++.|+|.|+++|+++|++|||||||.+|..|.+++.+|..+|....+......+.|......+++.+.+.||
T Consensus 51 ~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvt 130 (449)
T KOG2519|consen 51 NEAGEPTSHLMGMFYRTIRLIENGIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVT 130 (449)
T ss_pred ccCCCchHHHHHHHHHHHHHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhc
Confidence 56899999999999999999999999999999999999999999999999988888888889999999999999999999
Q ss_pred HHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHH
Q 021529 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILE 163 (311)
Q Consensus 84 ~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~ 163 (311)
.++.+.++.+|..|||||+.||+||+||||.|+++|.|++++|+|+|.+.|+++.+++++..+.....++..|+.+.+++
T Consensus 131 k~~~dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~ 210 (449)
T KOG2519|consen 131 KQHNDEAKRLLSLMGIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILE 210 (449)
T ss_pred chhhHHHHHHHHHcCCeeecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999888876545567899999999999
Q ss_pred HcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCchHHHHHHhcCCCCCCccc
Q 021529 164 ELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWPYQEARRLFKEPEVVTDEE 242 (311)
Q Consensus 164 ~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 242 (311)
.++++.++|+|+|+|+|||||++|.|||+++|++||++|++++++++ +.+..++.+|++|++..++.+|..|.++.+..
T Consensus 211 ~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~~i~~ile~~~~~~~~~ip~~w~~~~~r~~f~~p~~~~~~~ 290 (449)
T KOG2519|consen 211 GLGLSRESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHGDIENILEINSDLKEYPIPEDWSYKLARKLFLEPEFPNPES 290 (449)
T ss_pred HhcccHHHHHHHHHHhcCcccccccccChHHHHHHHHHhcCHHHHhhhccchhhcCCCCCccHHHHHHHhcCcccCCccc
Confidence 99999999999999999999999999999999999999999999999 77667889999999999999999999987666
Q ss_pred cccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhccCCCCCcccccCcCCCCCccchhh
Q 021529 243 QLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVANTSAPIKRK 307 (311)
Q Consensus 243 ~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~~~~~~~~q~~l~~ff~~~~~~~~~~~~~ 307 (311)
.-++.|..||.+.+.+|+..+.+|+.+|+++.++++....+...|+++++||+.+...+.+.+.+
T Consensus 291 ~~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~~~~~~~~ 355 (449)
T KOG2519|consen 291 ILDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKGSPVRKLK 355 (449)
T ss_pred eeecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCCCCcchhH
Confidence 34899999999999999988999999999999999999999999999999999999887666655
No 6
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=2.6e-47 Score=350.11 Aligned_cols=238 Identities=24% Similarity=0.288 Sum_probs=198.2
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcC--CceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~--i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~ 79 (311)
++|++|.+|+|++||++++.++++.. -.+++|||+.+++||++.+++||++|+++|+.+
T Consensus 28 l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p~~l------------------- 88 (281)
T PRK14976 28 LKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKKTPESL------------------- 88 (281)
T ss_pred ccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCCCCHHH-------------------
Confidence 67899999999999999999999741 245779999989999999999999999999999
Q ss_pred ccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHHc----CceEEEecCCCccccccCCeeEEEeecCCCCCcccE
Q 021529 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (311)
Q Consensus 80 ~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~~----g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~ 154 (311)
..|++.++++|+.+|||++.+|| ||||+||+|+++ |..++|+|+|+|++|++++++... ...+. ....
T Consensus 89 ----~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~--~~~~~-~~~~ 161 (281)
T PRK14976 89 ----ISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVL--LKKKG-TSHF 161 (281)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEE--EecCC-CCcE
Confidence 78999999999999999999998 999999999873 665679999999999999886432 22221 1246
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchH-HHHH
Q 021529 155 EFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQ-EARR 230 (311)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~---ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~-~~~~ 230 (311)
.++.+.+.+++|++|+||+|+++|+| |.+|| |||||||||.+||++|||+|+|++++++++.++++++... +...
T Consensus 162 ~~~~~~v~~~~gv~p~q~~d~~aL~G-D~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~~ 240 (281)
T PRK14976 162 ILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKAL 240 (281)
T ss_pred EEcHHHHHHHhCcCHHHHHHHHHHhC-CccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHHH
Confidence 79999999999999999999999999 66665 5799999999999999999999999998865555555432 2221
Q ss_pred Hh-----cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCC
Q 021529 231 LF-----KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN 267 (311)
Q Consensus 231 ~~-----~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~ 267 (311)
+. ++.++++..+++++.+.++|.++|.++| ++++|+
T Consensus 241 ~s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~-~~~e~~ 281 (281)
T PRK14976 241 LSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIF-EELELK 281 (281)
T ss_pred HhhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHH-HHcCCC
Confidence 21 3556666666667888899999999999 788873
No 7
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.7e-46 Score=341.01 Aligned_cols=215 Identities=27% Similarity=0.404 Sum_probs=177.4
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
|+|++|.||+|++||++++.++++. .+| ++|||+.+++||++.+++||++|+++|+++
T Consensus 22 l~~~~G~~t~a~~g~~~~l~~l~~~-~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe~L------------------ 82 (259)
T smart00475 22 LKNSKGEPTNAVYGFLRMLLKLIKE-EKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPDEL------------------ 82 (259)
T ss_pred ccCCCCCcccHHHHHHHHHHHHHHH-cCCCeEEEEEeCCCCccccchhHHHHhCCCCCCHHH------------------
Confidence 6789999999999999999999984 567 779999889999999999999999999999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHHc----CceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~~----g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.++++|+++|||++.+|| ||||+||+|+++ |..++|+|+|+|++|++++++.+.. ..+.....
T Consensus 83 -----~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~--~~~~~~~~ 155 (259)
T smart00475 83 -----LEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLD--PTKGIKEF 155 (259)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEe--ccCCCCcc
Confidence 78899999999999999999998 999999999984 6777899999999999998865322 22212224
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHH
Q 021529 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~~~L~G--~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~~~~~~ 231 (311)
..++.+.+.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|++++++++.++.+.+........
T Consensus 156 ~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~~~~~~~~l~~~~~~~~ 235 (259)
T smart00475 156 ELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKKLREKLLAHKEDAK 235 (259)
T ss_pred EEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcHHHHH
Confidence 679999999999999999999999999 444445689999999999999999999999999876555554443222222
Q ss_pred hcCCCCCCccc
Q 021529 232 FKEPEVVTDEE 242 (311)
Q Consensus 232 ~~~~~v~~~~~ 242 (311)
..+..+++.++
T Consensus 236 ls~~L~~l~~d 246 (259)
T smart00475 236 LSRKLATIETD 246 (259)
T ss_pred HhhhhheeeeC
Confidence 33344444433
No 8
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5e-44 Score=370.63 Aligned_cols=238 Identities=30% Similarity=0.452 Sum_probs=202.5
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
|+|++|.||||++||++++.++++. .+| ++|||+.+++||++.+++||++|+++|+++
T Consensus 22 l~~~~G~~t~av~Gf~~~l~~ll~~-~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~Pe~l------------------ 82 (887)
T TIGR00593 22 LTNSKGEPTNAVYGFTKMLLKLLKE-EKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPEEL------------------ 82 (887)
T ss_pred CcCCCCCEecHHHHHHHHHHHHHHh-cCCCEEEEEEcCCCCcchHHHHHHHHhCCCCChHHH------------------
Confidence 7899999999999999999999984 677 668999999999999999999999999999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.++++|+++|||++.+|| ||||+||+|++ .|+.++|+|+|+|++|+++++|.. +...+. ...
T Consensus 83 -----~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~--~~~~~~-~~~ 154 (887)
T TIGR00593 83 -----IEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKV--LIPKGK-TSF 154 (887)
T ss_pred -----HHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEE--EeccCC-CCc
Confidence 78999999999999999999999 99999999987 377778999999999999998642 222211 124
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCchH-HH
Q 021529 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQ-EA 228 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~---ipgiG~ktA~~li~~~gsle~i~~~~~~~~~-~~~~~~~~~-~~ 228 (311)
..++.+.|.+++|++|+||+|+++|+| |.||| |||||||||.+||++|||+|+|++++++++. ++.+++... +.
T Consensus 155 ~~~~~~~v~~~~Gv~p~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~ 233 (887)
T TIGR00593 155 TEITPEYVVEKYGVTPDQLVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKED 233 (887)
T ss_pred eEEcHHHHHHHhCCCHHHHHHHHHHcC-CcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHH
Confidence 579999999999999999999999999 77776 5789999999999999999999999998864 466666532 22
Q ss_pred HHHh-----cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCH
Q 021529 229 RRLF-----KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 268 (311)
Q Consensus 229 ~~~~-----~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~ 268 (311)
..+. ++.+++++.+++++++..||.++|.+|| ++++|+.
T Consensus 234 a~ls~~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~-~~lef~~ 277 (887)
T TIGR00593 234 AFLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL-QELEFKS 277 (887)
T ss_pred HHHHHHhheeecCCCCCCCHHHhccCCCCHHHHHHHH-HHhCCcc
Confidence 2222 3566666666667888899999999999 7999963
No 9
>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=3.2e-43 Score=363.19 Aligned_cols=218 Identities=25% Similarity=0.430 Sum_probs=194.0
Q ss_pred hhhhccCCHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEE
Q 021529 76 SKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 155 (311)
Q Consensus 76 ~~~~~~v~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~ 155 (311)
.+++..||..++..++++|+.||||||+||||||||||+|++.|+|++|+|+|+|+|+||+++|+++++.. +..+..
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~---~~~ve~ 839 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQ---NKFVEY 839 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCC---CCceEE
Confidence 44578999999999999999999999999999999999999999999999999999999999999988642 345788
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHH---HHHhh---------------
Q 021529 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG--SIETILE---NINRE--------------- 215 (311)
Q Consensus 156 ~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~g--sle~i~~---~~~~~--------------- 215 (311)
|+...+++.+|++++||+++|+|+||||++||||||||||++||++|| +++++++ +++..
T Consensus 840 ~~~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~~~~~~~~~~~~ 919 (1034)
T TIGR00600 840 YQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKV 919 (1034)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhccccccccchhhh
Confidence 999999999999999999999999999999999999999999999999 4777764 33221
Q ss_pred -----cCCCCCCCchHHHHHHhcCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH-HhhccCCCCC
Q 021529 216 -----RYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK-AAKNKSSQGR 289 (311)
Q Consensus 216 -----~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~-~~~~~~~q~~ 289 (311)
+..+|++||+..++.+|++|.|+... ..|.|+.||.++|+.||++++||+.+||.+.|.++. +...+.+|+|
T Consensus 920 ~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~--~~f~W~~PD~e~L~~Fl~~~~gws~eRv~~~l~plikk~~~~~~Q~~ 997 (1034)
T TIGR00600 920 KKKLRLLQLTPGFPNPAVADAYLRPVVDDSK--GSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLR 997 (1034)
T ss_pred hhcccccccCCCCCcHHHHHHhcCCCCCCCc--CCCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHccCCccC
Confidence 14689999999999999999998543 379999999999999999999999999999999984 4556788999
Q ss_pred cccccCcCC
Q 021529 290 LESFFKPVA 298 (311)
Q Consensus 290 l~~ff~~~~ 298 (311)
|++||....
T Consensus 998 ld~FF~~~~ 1006 (1034)
T TIGR00600 998 IDSFFRLAQ 1006 (1034)
T ss_pred HHHhhCccc
Confidence 999997543
No 10
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=100.00 E-value=4.8e-43 Score=315.99 Aligned_cols=193 Identities=26% Similarity=0.383 Sum_probs=167.9
Q ss_pred CCC-CCCcchHHHHHHHHHHHHHHcC--CceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhh
Q 021529 3 TNE-AGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (311)
Q Consensus 3 ~~~-~G~~t~a~~g~~~~l~~ll~~~--i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~ 79 (311)
.++ +|.||+|++||+.++.++++.. ..+++||||.+++||++.+++||++|+++|+.+
T Consensus 23 ~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p~~l------------------- 83 (240)
T cd00008 23 KNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMPEEL------------------- 83 (240)
T ss_pred CCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCCHHH-------------------
Confidence 355 8999999999999999999742 456889999989999999999999999999999
Q ss_pred ccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCcccE
Q 021529 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (311)
Q Consensus 80 ~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~ 154 (311)
..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..++|+|+|+|++|++++++.. .... ...
T Consensus 84 ----~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~--~~~~----~~~ 153 (240)
T cd00008 84 ----REQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKV--VSPM----KKK 153 (240)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEE--EeCC----Cce
Confidence 78999999999999999999998 99999999986 577778999999999999887642 3222 135
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc
Q 021529 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP 224 (311)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~~d~~~L~G--~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~ 224 (311)
.++.+.+.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++..+.++.+.+.
T Consensus 154 ~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~ 225 (240)
T cd00008 154 LVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKGKLREKLE 225 (240)
T ss_pred EEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhHHHHHHHH
Confidence 79999999999999999999999999 55555678999999999999999999999999876554444443
No 11
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=3.1e-42 Score=310.65 Aligned_cols=189 Identities=21% Similarity=0.241 Sum_probs=164.8
Q ss_pred CCCCCcchHHHHHHHHHHHHHHcCCce---EEEEeCCCCc--hhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhh
Q 021529 4 NEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPD--LKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 4 ~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~VFDG~~~~--~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
+++|. |||++||++++.++++. ..| +++||+..++ ||++.+++||++|.++|+++
T Consensus 23 ~~~g~-t~av~gf~~~l~~ll~~-~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe~l------------------ 82 (256)
T PRK09482 23 SPNDI-NACVETCQHALDKLIRH-SQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEAL------------------ 82 (256)
T ss_pred CCCCc-chHHHHHHHHHHHHHHH-cCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcHHH------------------
Confidence 36788 99999999999999974 566 3479998776 99999999999999999999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.++++|+++||+++..|| ||||+||+|++ .|.-+.|+|+|+|++|+..+++.. +.... .
T Consensus 83 -----~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~--~~~~~----~ 151 (256)
T PRK09482 83 -----QQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQI--RDYFQ----K 151 (256)
T ss_pred -----HHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEE--Eeccc----c
Confidence 78999999999999999999999 99999999987 366567999999999999988643 22221 2
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc
Q 021529 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP 224 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~i---pgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~ 224 (311)
++++.+.+.+++|++|+|++|+++|+| |.+||| ||||||||.+||++|||+|+|++++++++.++.+.+.
T Consensus 152 ~~~~~~~v~~~~Gv~P~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~ 224 (256)
T PRK09482 152 RWLDAPFIEQEFGVEPQQLPDYWGLAG-ISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLE 224 (256)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHhC-CCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHH
Confidence 468999999999999999999999999 888875 6899999999999999999999999887655555554
No 12
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=8.1e-42 Score=357.56 Aligned_cols=238 Identities=26% Similarity=0.397 Sum_probs=199.0
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
++|++|.||+|++||++++.++++ ..+| ++|||+.+++||++.+++||++|.++|+++
T Consensus 24 ~~~~~g~~~~a~~g~~~~l~~~~~-~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~p~~l------------------ 84 (880)
T PRK05755 24 LRNSDGLPTGAVYGFLNMLLKLLK-EEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMPEDL------------------ 84 (880)
T ss_pred ccCCCCCcccHHHHHHHHHHHHHH-hcCCCEEEEEEECCCCccccccCHHHhCCCCCCcHHH------------------
Confidence 678999999999999999999996 4777 679999889999999999999999999999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.++++|+.+||+++.+|| ||||+||+|++ .|..++|+|+|+|++|++++++.. +.... ....
T Consensus 85 -----~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~--~~~~~-~~~~ 156 (880)
T PRK05755 85 -----REQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTL--LDTMG-VSKN 156 (880)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEE--eeccC-CCCC
Confidence 78999999999999999999998 99999999986 477788999999999999987632 22211 1124
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCC---CCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchH-HHH
Q 021529 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQ-EAR 229 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d---~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~-~~~ 229 (311)
..++.+.+.+++|++|+||+|+++|+| |.+| ||||||||||.+||++|||+|+|+++++.++.++++++... +..
T Consensus 157 ~~~~~~~v~~~~g~~p~q~~d~~~L~G-D~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~ 235 (880)
T PRK05755 157 EELDPEEVVEKYGVTPEQIIDYLALMG-DSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQA 235 (880)
T ss_pred eEEcHHHHHHHHCcCHHHHHHHHHHhC-CccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhchHHHHHHHHhHHHH
Confidence 679999999999999999999999999 6555 56899999999999999999999999998776666665532 211
Q ss_pred HHh-----cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCH
Q 021529 230 RLF-----KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 268 (311)
Q Consensus 230 ~~~-----~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~ 268 (311)
.++ ++.+++++.++.++.+..||.++|.+|| ++++|+.
T Consensus 236 ~ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~ 278 (880)
T PRK05755 236 FLSRKLATIKTDVPLEVDLEDLELQPPDREKLIALF-KELEFKS 278 (880)
T ss_pred HhhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHH-HHhCcHH
Confidence 121 2344444444557888899999999999 8999953
No 13
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=9.5e-42 Score=324.27 Aligned_cols=233 Identities=30% Similarity=0.486 Sum_probs=207.9
Q ss_pred CCCcchHHHHHHHHHHHHH-HcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhccCCH
Q 021529 6 AGEVTSHLQGMFTRTIRLL-EAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTK 84 (311)
Q Consensus 6 ~G~~t~a~~g~~~~l~~ll-~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v~~ 84 (311)
.|.||.....||..-++|| .+||+|+.||||.+.+.|.++..+|+.+|++..+....+|..|+...|..+|++|+.||+
T Consensus 48 ~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~ 127 (556)
T KOG2518|consen 48 KGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITP 127 (556)
T ss_pred cCCChHHHHHHHHHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcH
Confidence 5899998888888777776 589999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHH
Q 021529 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 164 (311)
Q Consensus 85 ~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~ 164 (311)
+|...++++|+..||+||+||||||||+|||.+.|.+++|||+|||+++|||..|+..+...|. ...++...+-+.
T Consensus 128 ~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~----~le~~~~~l~~~ 203 (556)
T KOG2518|consen 128 EMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGN----GLEINRSKLPEC 203 (556)
T ss_pred HHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCC----cccccHhhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999988876543 245666666554
Q ss_pred c----CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCc--hHHHHHHhcCCCC
Q 021529 165 L----NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWP--YQEARRLFKEPEV 237 (311)
Q Consensus 165 ~----gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~-~~~~~~~~~~~~~~--~~~~~~~~~~~~v 237 (311)
+ +++.++|..+|+|.||||.++|||||.+||.++|++|.+.|.++. +....+..+|++|. +..|...|+|..|
T Consensus 204 ~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~tF~hQrV 283 (556)
T KOG2518|consen 204 KPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLTFLHQRV 283 (556)
T ss_pred cccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHhhhhhhe
Confidence 4 357899999999999999999999999999999999999999875 44445667888887 4678899999999
Q ss_pred CCccc
Q 021529 238 VTDEE 242 (311)
Q Consensus 238 ~~~~~ 242 (311)
.++.+
T Consensus 284 ydP~~ 288 (556)
T KOG2518|consen 284 YDPIE 288 (556)
T ss_pred eCchH
Confidence 87653
No 14
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.7e-40 Score=307.99 Aligned_cols=262 Identities=28% Similarity=0.465 Sum_probs=200.8
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHH--cCCceEEEEeCCCCchhhHHHHHHHhchhc-cHHHHHHHHHcCCHHHHHHHhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLE--AGMKPIYVFDGQPPDLKKQELAKRYSKRAD-ATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~--~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~-~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
+.++.|.+|++++||..++.++++ ..++|++||||.+++||++++++||++|++ +|+++
T Consensus 33 ~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~~l------------------ 94 (310)
T COG0258 33 LGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMPDEL------------------ 94 (310)
T ss_pred cCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCHHHH------------------
Confidence 578999999999999999999885 248899999999999999999999999999 99999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.+.+++.++|++++..+| ||||.++++++ .|.+++|+|+|+|++||+++++..... .. ..+.
T Consensus 95 -----~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~--~~-~~~~ 166 (310)
T COG0258 95 -----APQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVING--KK-GEPE 166 (310)
T ss_pred -----HHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCcEEEec--cC-CCCc
Confidence 78999999999999999999999 99999999987 588999999999999999998543222 11 1111
Q ss_pred EEEeHHHHHHHc-CCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHH
Q 021529 154 MEFEVAKILEEL-NLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (311)
Q Consensus 154 ~~~~~~~v~~~~-gl~~~q~~d~~~L~G--~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~~~~~~~ 230 (311)
..++...+.+++ |++|+|++|+++|+| ||+.+||||||||||++||++||++|.++++++.++.+.++.+. .....
T Consensus 167 ~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l~-~~~~~ 245 (310)
T COG0258 167 KFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLL-EDKEK 245 (310)
T ss_pred ccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHHH-HHHHH
Confidence 158999999999 999999999999999 88888999999999999999999999999999865555555443 33444
Q ss_pred HhcC-CCCCCccccccCCCCCCCHHHHHHHHHhhcCCC---HHHHHHHHHHHHHhhccCCCCCccccc
Q 021529 231 LFKE-PEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN---SDRVTKAIEKIKAAKNKSSQGRLESFF 294 (311)
Q Consensus 231 ~~~~-~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~---~~~v~~~~~~~~~~~~~~~q~~l~~ff 294 (311)
+|++ +.+++..++ .+.+..++. ..+...+..+. ..++...++++.+......|.+++.||
T Consensus 246 afl~~~l~t~~~d~-~l~~~~~~~---~~~~~~~~d~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 309 (310)
T COG0258 246 AFLSKPLATIKTDV-PLEFDLEDI---LELLVPEHDFSKLLEERVELGFKRLLKAIGSVEQATLDEFF 309 (310)
T ss_pred HhcCcccccccccc-cCCcCccch---hhhccCcccHHHHHHHHHHHhHHHHHHHHhhhccccccccc
Confidence 5554 777765554 333443332 12221222332 233333444443332222566666654
No 15
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=4.3e-33 Score=279.92 Aligned_cols=213 Identities=27% Similarity=0.518 Sum_probs=183.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHH
Q 021529 80 VKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVA 159 (311)
Q Consensus 80 ~~v~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~ 159 (311)
-++|..|+..|+++|+.+|||||+||+|||||||.|...+++++|+|.|||.++||+.+||++++..+ ..+..|...
T Consensus 461 ~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~kn---k~ve~y~~~ 537 (815)
T KOG2520|consen 461 DEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKN---KYVEKYQLD 537 (815)
T ss_pred chhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcC---ccceeeehH
Confidence 46778999999999999999999999999999999999999999999999999999999999998643 347889999
Q ss_pred HHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHHHh-------------------h--
Q 021529 160 KILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG---SIETILENINR-------------------E-- 215 (311)
Q Consensus 160 ~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~g---sle~i~~~~~~-------------------~-- 215 (311)
.+...||+++..+|.+|.|+|+||+.||+||||++|+++|.+|+ ++..+-+++.+ .
T Consensus 538 di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~~~~~~~s~~~~~lrkkl~n 617 (815)
T KOG2520|consen 538 DIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGPADKEVGSTQQKMLRKKLKN 617 (815)
T ss_pred HHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCccccccccHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999 44443333331 0
Q ss_pred -cCCCCCCCchHHHHHHhcCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHH----HHHHHhhccCCCCCc
Q 021529 216 -RYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAI----EKIKAAKNKSSQGRL 290 (311)
Q Consensus 216 -~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~----~~~~~~~~~~~q~~l 290 (311)
+..++..||+..+..+|++|.|....+ .|.|+.||.+.|++||...+||+..+....+ +++.+..+..+|+++
T Consensus 618 ~~~~l~~~fP~~~v~~AYLrP~VD~sk~--~f~WG~pdl~~lRef~~~~fgW~~~kT~~~l~p~~~~~~~~~~~~~~~~~ 695 (815)
T KOG2520|consen 618 PKIILPSDFPNPNVIEAYLRPEVDDSKE--KFRWGKPDLDILREFMKRLFGWPDEKTDEELIPVIKRLEKKKTQLKQDRI 695 (815)
T ss_pred cccccCcCCCchhHHHHhhCCccCCCcc--cccCCCCCHHHHHHHHHHHcCCCccccchhhhhhHHHHHHHhhhhccccH
Confidence 146788999999999999999986654 6999999999999999999999998877665 444444556667777
Q ss_pred ccccCcC
Q 021529 291 ESFFKPV 297 (311)
Q Consensus 291 ~~ff~~~ 297 (311)
-+||...
T Consensus 696 ~~~f~~~ 702 (815)
T KOG2520|consen 696 SQFFEDE 702 (815)
T ss_pred HHHHHhh
Confidence 7777653
No 16
>PHA00439 exonuclease
Probab=99.97 E-value=1.3e-30 Score=237.00 Aligned_cols=169 Identities=15% Similarity=0.152 Sum_probs=134.3
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHc--CCce---EEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEA--GMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFS 76 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~--~i~P---v~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~ 76 (311)
|+|++|.||+|++||++++.++++. ..+| +++|| ..++||++.|+.||++|+++|+..
T Consensus 34 l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~~tfR~elyp~YKanR~~~p~~~---------------- 96 (286)
T PHA00439 34 IWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DSVNWRKEVVPTYKANRKAKRKPV---------------- 96 (286)
T ss_pred CCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CCCChHhhhhhHhcCCCCCCCCch----------------
Confidence 5789999999999999999999963 1455 34699 568999999999999999988775
Q ss_pred hhhccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCc-eEEEecCCCccccccCCeeEEEeecCCCCC
Q 021529 77 KRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ-VYAVASEDMDSLTFGAPRFLRHLMDPSSRK 150 (311)
Q Consensus 77 ~~~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~-v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~ 150 (311)
.+.+.+++++..+||+++..|| ||||.||+|++ .|. -.+|+|+|+|++|+....++ +...+
T Consensus 97 --------~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~---~~~~~-- 163 (286)
T PHA00439 97 --------GYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFL---WCTTG-- 163 (286)
T ss_pred --------hhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEE---EccCC--
Confidence 3567889999999999999999 99999999986 365 56799999999999865332 21111
Q ss_pred cccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHH---cCCHHHHHHH
Q 021529 151 IPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQ---HGSIETILEN 211 (311)
Q Consensus 151 ~~~~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~i---pgiG~ktA~~li~~---~gsle~i~~~ 211 (311)
....++.+ .|+|++++.+|+| |.+||| |||| |||.+||++ |-.++.++++
T Consensus 164 -~~~~~~~~--------~p~~~~d~~AL~G-DsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 164 -NILTQTPE--------TADRWHLFQTIKG-DSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred -ceEEcCcc--------cHHHHHhhhhccc-ccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 11113322 3999999999999 999986 6899 999999998 4445554444
No 17
>PHA02567 rnh RnaseH; Provisional
Probab=99.95 E-value=6.7e-27 Score=213.56 Aligned_cols=161 Identities=14% Similarity=0.112 Sum_probs=126.6
Q ss_pred CCCCCCCcchHHHH-HHHHHHHHHHc--CCc--eEEEEeCCC-CchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHH
Q 021529 2 LTNEAGEVTSHLQG-MFTRTIRLLEA--GMK--PIYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKF 75 (311)
Q Consensus 2 l~~~~G~~t~a~~g-~~~~l~~ll~~--~i~--Pv~VFDG~~-~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~ 75 (311)
|++++|.+|+++++ +++++.++.+. ... .+++||+.. ++||++.++.||++|+++|+++...++ .+
T Consensus 33 l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~~Peel~~q~~--------~l 104 (304)
T PHA02567 33 FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDREESPWDWE--------GL 104 (304)
T ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCCCChHHHHHHH--------Hh
Confidence 67899999999955 77777776651 222 256899975 789999999999999999998721110 00
Q ss_pred hhhhccCCHHHH-HHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccC-CeeEEEeecCCC
Q 021529 76 SKRTVKVTKQHN-DDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGA-PRFLRHLMDPSS 148 (311)
Q Consensus 76 ~~~~~~v~~~~~-~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~-~~v~~~l~~~~~ 148 (311)
.+++ +.+++++..+||+++..|| ||||.||+|++ .|..++|+|+|+|++|+.. +++.. +..
T Consensus 105 --------~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~--~~~-- 172 (304)
T PHA02567 105 --------FEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQ--WSP-- 172 (304)
T ss_pred --------hhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEE--eec--
Confidence 2223 5678889999999999999 99999999997 4666679999999999984 66532 221
Q ss_pred CCcccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCcc
Q 021529 149 RKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIG 191 (311)
Q Consensus 149 ~~~~~~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG 191 (311)
++.+.+.+++| .|+|++|+.+|+| |.+||||||-
T Consensus 173 -------~~~~~V~~k~G-~P~q~iD~kaL~G-DsSDNIPGVp 206 (304)
T PHA02567 173 -------MQKKWVKPKYG-SPEKDLMTKIIKG-DKKDGVASIK 206 (304)
T ss_pred -------CCHHHHHHHhC-CHHHHHHHHHhCC-cccCCcCCCC
Confidence 34577889999 5999999999999 9999999984
No 18
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.93 E-value=4.2e-26 Score=195.05 Aligned_cols=138 Identities=28% Similarity=0.449 Sum_probs=113.0
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHcCCce---EEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhh
Q 021529 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (311)
Q Consensus 2 l~~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~ 78 (311)
|++++|.||++++||+.++.++++. .+| ++|||+..++||++.+|+||++|.++|+++
T Consensus 24 l~~~~G~~t~ai~g~~~~l~~l~~~-~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~~p~~l------------------ 84 (169)
T PF02739_consen 24 LRNSDGEPTNAIYGFLRMLLKLLKD-FKPDYVVVAFDSKGPTFRKELYPEYKANRKPMPEEL------------------ 84 (169)
T ss_dssp -BETTSEB-HHHHHHHHHHHHHHHH-TTEEEEEEEEEBSSCHHHHHCCTTTTHHHHHHHHHH------------------
T ss_pred CcCCCCCChHHHHHHHHHHHHHHHH-cCCceEEEEecCCCcchHHHHHHHHHhCCCCCCHHH------------------
Confidence 6789999999999999999999974 555 558999988999999999999999999999
Q ss_pred hccCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHHHH----cCceEEEecCCCccccccCCeeEEEeecCCCCCccc
Q 021529 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (311)
Q Consensus 79 ~~~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L~~----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~ 153 (311)
..|++.++++|+.+||+++..|| ||||.||+|++ +|.-+.|+|+|+|++|+..+++-..++.++ ....
T Consensus 85 -----~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~~~~~--~~~~ 157 (169)
T PF02739_consen 85 -----IPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVYLLDPG--KKKF 157 (169)
T ss_dssp -----HHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEEEEETT--TTCS
T ss_pred -----HHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEEEeecC--CCCC
Confidence 78999999999999999999999 99999999987 466667999999999999994322334432 2345
Q ss_pred EEEeHHHHHHHc
Q 021529 154 MEFEVAKILEEL 165 (311)
Q Consensus 154 ~~~~~~~v~~~~ 165 (311)
..++.+.|.++|
T Consensus 158 ~~~~~~~v~eky 169 (169)
T PF02739_consen 158 KVYDPEEVEEKY 169 (169)
T ss_dssp -EB-HHHHHHHT
T ss_pred EEEcHHHHhhcC
Confidence 789999998875
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=99.90 E-value=3.2e-24 Score=166.34 Aligned_cols=88 Identities=53% Similarity=0.839 Sum_probs=74.6
Q ss_pred HHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEee-cC-CCC----CcccEEEeHHHHHHHcCCC
Q 021529 95 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLM-DP-SSR----KIPVMEFEVAKILEELNLT 168 (311)
Q Consensus 95 ~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~-~~-~~~----~~~~~~~~~~~v~~~~gl~ 168 (311)
+++||||++||||||+|||+|+++|.+++|+|+|||+|+||+++|++++. .. +.. ...+.+++.+.+++.+|++
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 57999999999999999999999999999999999999999999999886 22 211 2457899999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 021529 169 MDQFIDLCILSGCD 182 (311)
Q Consensus 169 ~~q~~d~~~L~G~D 182 (311)
++||+++|+|+|||
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
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.77 E-value=1.2e-18 Score=128.05 Aligned_cols=72 Identities=49% Similarity=0.750 Sum_probs=65.6
Q ss_pred HhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHHcCC
Q 021529 96 LMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNL 167 (311)
Q Consensus 96 ~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl 167 (311)
.+||||++||+|||+|||+|+++|++++|+|+|+|+|+||++++++++...++...+++.++...+++++|+
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 589999999999999999999999999999999999999999999998776544447899999999999885
No 21
>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=99.59 E-value=1.8e-15 Score=112.19 Aligned_cols=52 Identities=50% Similarity=0.809 Sum_probs=49.5
Q ss_pred HcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhh
Q 021529 164 ELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRE 215 (311)
Q Consensus 164 ~~gl~~~q~~d~~~L~G--~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~ 215 (311)
++|++|+||+++|+|+| |||.+||||||+|||.+||++|+++++++++++..
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~ 55 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 58999999999999999 99999999999999999999999999999998765
No 22
>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=99.59 E-value=8.6e-18 Score=131.04 Aligned_cols=91 Identities=33% Similarity=0.448 Sum_probs=53.0
Q ss_pred CCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCch-----HHHHHHh-cCCC
Q 021529 167 LTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPY-----QEARRLF-KEPE 236 (311)
Q Consensus 167 l~~~q~~d~~~L~G~D~~d~i---pgiG~ktA~~li~~~gsle~i~~~~~~~~~-~~~~~~~~-----~~~~~~~-~~~~ 236 (311)
|+|+|++||.+|+| |.+||| ||||+|||.+||++|||+|+|+++++.++. ++++.+.. ..++.+. ++.+
T Consensus 1 V~P~q~~D~~aL~G-D~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~d 79 (101)
T PF01367_consen 1 VPPEQIADYKALVG-DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTD 79 (101)
T ss_dssp --GHHHHHHCCCC--CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S-
T ss_pred CCHHHHHHHHHHcC-CcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcC
Confidence 57999999999999 999986 589999999999999999999999988765 55544331 1133333 4678
Q ss_pred CCCccccccCCCCCCCHHHHHH
Q 021529 237 VVTDEEQLQIKWSAPDEEGLIN 258 (311)
Q Consensus 237 v~~~~~~~~~~~~~~d~~~l~~ 258 (311)
++++.+++++++..+|.++|.+
T Consensus 80 v~l~~~l~~l~~~~~d~~~l~~ 101 (101)
T PF01367_consen 80 VPLPFSLEDLRLQPPDREKLIE 101 (101)
T ss_dssp ----------------HHHH--
T ss_pred CCCCCCcchhccCCCCHHHhcC
Confidence 8887888899999999998864
No 23
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.27 E-value=4.6e-12 Score=80.09 Aligned_cols=33 Identities=55% Similarity=0.945 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCccHHHHHHHHHHc
Q 021529 169 MDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 169 ~~q~~d~~~L~G~D~~d---~ipgiG~ktA~~li~~~ 202 (311)
|+||+++|+|+| ||+| ||||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 689999999999 9999 56899999999999986
No 24
>PF12813 XPG_I_2: XPG domain containing
Probab=98.86 E-value=9.7e-09 Score=93.07 Aligned_cols=89 Identities=28% Similarity=0.292 Sum_probs=67.9
Q ss_pred HHHHHHHHHHHh---CCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccC--CeeEEEeec---CC------CCCc
Q 021529 86 HNDDCKRLLKLM---GVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA--PRFLRHLMD---PS------SRKI 151 (311)
Q Consensus 86 ~~~~i~~lL~~~---gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~--~~v~~~l~~---~~------~~~~ 151 (311)
+.+.+.+.|+.+ |++++.+|||||..||.++++.-+ .|+|+|||+++|.. +.-+..+.+ .. ....
T Consensus 5 ~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i 83 (246)
T PF12813_consen 5 LVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYI 83 (246)
T ss_pred hHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCee
Confidence 456788999999 999999999999999999986555 69999999999976 332333321 11 0112
Q ss_pred ccEEEeHHHHHHHcCCCHHHHHHHHH
Q 021529 152 PVMEFEVAKILEELNLTMDQFIDLCI 177 (311)
Q Consensus 152 ~~~~~~~~~v~~~~gl~~~q~~d~~~ 177 (311)
....|+.+.++..+|+. .++.+|.
T Consensus 84 ~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 84 SAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 45679999999999999 6666666
No 25
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=98.63 E-value=6e-08 Score=75.58 Aligned_cols=47 Identities=60% Similarity=1.013 Sum_probs=42.9
Q ss_pred cch-HHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhc
Q 021529 9 VTS-HLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRAD 55 (311)
Q Consensus 9 ~t~-a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~ 55 (311)
+++ ++.+++.++..|+++||+|+|||||..++.|.++..+|+.+|++
T Consensus 51 ~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 51 PNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred CchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 344 99999999999999999999999999999999999999888875
No 26
>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=98.62 E-value=4.7e-08 Score=76.42 Aligned_cols=46 Identities=54% Similarity=1.060 Sum_probs=40.3
Q ss_pred chHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhc
Q 021529 10 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRAD 55 (311)
Q Consensus 10 t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~ 55 (311)
+..+.+++.++..|+.+||+|+|||||.+++.|.++..+|+.+|++
T Consensus 55 ~~~~~~~~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~r~~ 100 (101)
T PF00752_consen 55 DSHLRGLFSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKRREE 100 (101)
T ss_dssp -HHHHHHHHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 5899999999999999999999999999999999999999888865
No 27
>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=98.25 E-value=2.5e-06 Score=90.15 Aligned_cols=52 Identities=46% Similarity=0.722 Sum_probs=48.1
Q ss_pred cchHHHHHHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHH
Q 021529 9 VTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60 (311)
Q Consensus 9 ~t~a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l 60 (311)
.++++.|||+|+++|+.+||+|||||||.+|+.|+++..+|+.+|.++.+.+
T Consensus 51 ~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a~~~a 102 (1034)
T TIGR00600 51 KNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDA 102 (1034)
T ss_pred CCHHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999999999999999999999998876654
No 28
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=96.83 E-value=0.00077 Score=64.89 Aligned_cols=101 Identities=31% Similarity=0.441 Sum_probs=79.9
Q ss_pred HHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccC-CeeEEEeecCCCCCcccEEEeHHHHHHHcC
Q 021529 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA-PRFLRHLMDPSSRKIPVMEFEVAKILEELN 166 (311)
Q Consensus 88 ~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~-~~v~~~l~~~~~~~~~~~~~~~~~v~~~~g 166 (311)
..+-.++..-|+.|+++|+-|+.|||||+...+++++. +-+|.+.+.+ ++.+..+... ....++..+.....++-.-
T Consensus 132 d~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~-gp~d~l~ld~vdr~il~m~fg-~d~Ppl~~~~vp~~lem~l 209 (531)
T COG5366 132 DVASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAF-GPSDILLLDGVDRIILDMSFG-SDKPPLDVFHVPRFLEMFL 209 (531)
T ss_pred ccccccccccceEEEehhhHHHHHHHHHHHHHHHHhcC-CchHhHHHhhhhhheeecccC-CCCCCCcccccchHHHhcc
Confidence 35677888999999999999999999999988888665 5588888854 6666555433 3345667777777777777
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCc
Q 021529 167 LTMDQFIDLCILSGCDYCDSIRGI 190 (311)
Q Consensus 167 l~~~q~~d~~~L~G~D~~d~ipgi 190 (311)
.+-..|..+..+.|||.+..+|.+
T Consensus 210 ~s~~lFya~~ll~~c~~~s~~~~C 233 (531)
T COG5366 210 LSSRLFYALGLLLGCDFCSTIPRC 233 (531)
T ss_pred cccchhhhhccccccccccccccc
Confidence 788999999999999999988764
No 29
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.25 E-value=0.0032 Score=44.99 Aligned_cols=26 Identities=35% Similarity=0.597 Sum_probs=21.6
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 021529 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 185 d~ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
-||||||+++|..|+++|||++++.+
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~ 31 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMN 31 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Confidence 37999999999999999999998764
No 30
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.25 E-value=0.052 Score=47.41 Aligned_cols=112 Identities=20% Similarity=0.274 Sum_probs=65.5
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhc---C-CCCCCCchHHHHHHh-
Q 021529 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER---Y-QIPEDWPYQEARRLF- 232 (311)
Q Consensus 159 ~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~---~-~~~~~~~~~~~~~~~- 232 (311)
++-...||+ +.+.--.|..|++ |||||||+|+.++..+ +++++.+.+.... . ++| .+-.+.|..+.
T Consensus 54 ed~~~LyGF~~~~Er~lF~~L~~------V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ip-GiGkKtAerIil 125 (191)
T TIGR00084 54 EDAELLFGFNTLEERELFKELIK------VNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIP-GVGKKTAERLLL 125 (191)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC------CCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHHH
Confidence 334456887 6777777777765 8999999999999865 5788887776311 1 122 12223333333
Q ss_pred -cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 233 -KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 233 -~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
++..+.....+..-....+..+.+.+-| ..+||+...+.++++++.
T Consensus 126 eLk~k~~~~~~~~~~~~~~~~~~e~~~aL-~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 126 ELKGKLKGNKNLEMFTPTEAARDELFEAL-VSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHhhhcccccccccccccchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1111110000000001123446677777 589999999999998774
No 31
>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=96.13 E-value=0.048 Score=49.25 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=25.5
Q ss_pred CCceEec----cCcHHHHHHHHHH---------cCceEEEecCCCcccccc
Q 021529 98 GVPVVEA----PSEAEAQCAALCK---------SGQVYAVASEDMDSLTFG 135 (311)
Q Consensus 98 gi~~i~a----pgEADa~iA~L~~---------~g~v~~V~S~DsD~l~~~ 135 (311)
++.++.+ |||+|--|..+.+ .+..++|+|.|+|+++++
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 5667766 7999976665544 245788999999999986
No 32
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.27 E-value=0.077 Score=46.32 Aligned_cols=91 Identities=19% Similarity=0.317 Sum_probs=48.9
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHhhc----CCCCCCCchHHHHHHh--cCCCCC-CccccccCCCCCCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILENINRER----YQIPEDWPYQEARRLF--KEPEVV-TDEEQLQIKWSAPDEEGLIN 258 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~v~-~~~~~~~~~~~~~d~~~l~~ 258 (311)
+|||||||+|.+++..||+ +.+.+.+.... .++| .+....|..++ ++.... .......-.-.....+.+..
T Consensus 77 ~i~GIGpk~A~~il~~fg~-~~l~~~i~~~d~~~L~~v~-Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~ 154 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSP-EELVQAIANGDVKALTKVP-GIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVS 154 (192)
T ss_pred cCCCCCHHHHHHHHHhCCH-HHHHHHHHhCCHHHHHhCC-CCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHH
Confidence 3899999999999999987 33433332110 0111 12222222222 111110 00000000111223678888
Q ss_pred HHHhhcCCCHHHHHHHHHHHH
Q 021529 259 FLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 259 ~~~~~~~f~~~~v~~~~~~~~ 279 (311)
+| ..+||+...+.+.++.+.
T Consensus 155 aL-~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 155 AL-VALGYKPKEASKAVAKIL 174 (192)
T ss_pred HH-HHcCCCHHHHHHHHHHHh
Confidence 88 699999999988888775
No 33
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=95.20 E-value=0.31 Score=51.22 Aligned_cols=183 Identities=22% Similarity=0.331 Sum_probs=100.8
Q ss_pred HHHHHHHHHHcCCce--EE--EEeCCCCchhhHHHHHHHhc-hhccHHHHHHHHHcCCHHHHHHHhhhhccCCHHHHHHH
Q 021529 16 MFTRTIRLLEAGMKP--IY--VFDGQPPDLKKQELAKRYSK-RADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDC 90 (311)
Q Consensus 16 ~~~~l~~ll~~~i~P--v~--VFDG~~~~~K~~~~~~yk~~-R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v~~~~~~~i 90 (311)
+|+-+-.|.. -|+| +| .-||..|-.|......|+-+ -..+...+.++.+.|+.-..+.|=+.|+..-...+..+
T Consensus 64 IfnYIdhLf~-~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~rl 142 (1493)
T KOG2045|consen 64 IFNYIDHLFY-LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMVRL 142 (1493)
T ss_pred HHHHHHHHHH-hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHHHH
Confidence 3443444555 3777 33 47999886655544433322 22334566788888876555666666665433444444
Q ss_pred HHHHHH------------hCCceEe----ccCcHHHHHHHHHHc---------CceEEEecCCCccccccC----Cee--
Q 021529 91 KRLLKL------------MGVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PRF-- 139 (311)
Q Consensus 91 ~~lL~~------------~gi~~i~----apgEADa~iA~L~~~---------g~v~~V~S~DsD~l~~~~----~~v-- 139 (311)
.+-|+. .++.+|- +|||++.-|--..+. +--++++.=|-|++++|- ++.
T Consensus 143 ~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~l 222 (1493)
T KOG2045|consen 143 QEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVL 222 (1493)
T ss_pred HHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceee
Confidence 444433 4677764 599999766555441 335678889999999983 322
Q ss_pred EEEeecCCCCCc-------ccEEEeH-----------HHHHHH--cCCCH----HHHHHHHHHhCCCCCCCCCCccH-HH
Q 021529 140 LRHLMDPSSRKI-------PVMEFEV-----------AKILEE--LNLTM----DQFIDLCILSGCDYCDSIRGIGG-QT 194 (311)
Q Consensus 140 ~~~l~~~~~~~~-------~~~~~~~-----------~~v~~~--~gl~~----~q~~d~~~L~G~D~~d~ipgiG~-kt 194 (311)
+|--..-++++. .+-.... +++.+. +..+- +.|+.++.|+|+|+.+++|++-+ +.
T Consensus 223 LREEVtFgrrn~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~g 302 (1493)
T KOG2045|consen 223 LREEVTFGRRNKRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSG 302 (1493)
T ss_pred eeeeeecccccccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCC
Confidence 221001111111 0111111 222222 22232 56778888999999999998754 23
Q ss_pred HHHHH
Q 021529 195 ALKLI 199 (311)
Q Consensus 195 A~~li 199 (311)
|+-|+
T Consensus 303 Alpll 307 (1493)
T KOG2045|consen 303 ALPLL 307 (1493)
T ss_pred hHHHH
Confidence 55444
No 34
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=95.10 E-value=0.47 Score=48.58 Aligned_cols=95 Identities=23% Similarity=0.447 Sum_probs=60.6
Q ss_pred CCceEec----cCcHHHHHHHHHHc---------CceEEEecCCCccccccC----Cee--EE-E-eecCCCC-------
Q 021529 98 GVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PRF--LR-H-LMDPSSR------- 149 (311)
Q Consensus 98 gi~~i~a----pgEADa~iA~L~~~---------g~v~~V~S~DsD~l~~~~----~~v--~~-~-l~~~~~~------- 149 (311)
++.+|.+ |||++.-|-.+.+. +-.++|++-|-|++.+|- |++ +| . ++..+++
T Consensus 176 nl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~ 255 (953)
T COG5049 176 NLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTK 255 (953)
T ss_pred eEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCccccccccccc
Confidence 5566654 89999988877662 457889999999999983 432 22 1 1111110
Q ss_pred ---------------CcccEEEeHHHHHHH----c---CCC--------HHHHHHHHHHhCCCCCCCCCCccH
Q 021529 150 ---------------KIPVMEFEVAKILEE----L---NLT--------MDQFIDLCILSGCDYCDSIRGIGG 192 (311)
Q Consensus 150 ---------------~~~~~~~~~~~v~~~----~---gl~--------~~q~~d~~~L~G~D~~d~ipgiG~ 192 (311)
..++-+++.+.+.+. | +++ -+.|+.+|-++|+|+.+++|++-.
T Consensus 256 ~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldi 328 (953)
T COG5049 256 CGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDI 328 (953)
T ss_pred ccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCcccc
Confidence 113445665554432 1 222 256778899999999999997653
No 35
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.85 E-value=0.12 Score=45.14 Aligned_cols=110 Identities=17% Similarity=0.265 Sum_probs=62.1
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhc
Q 021529 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (311)
Q Consensus 159 ~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~~ 233 (311)
++-...||+ +.+.--.|..|++ |+|||||+|+.++..|+ .+.+.+.+..... ++|- +-.+.|..+..
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vpG-IGkKtAerIil 126 (194)
T PRK14605 55 EDALSLFGFATTEELSLFETLID------VSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIPG-IGKKTASRIVL 126 (194)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC------CCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCCC-CCHHHHHHHHH
Confidence 344456887 6677767777765 89999999999999886 6777766632110 1111 11222333221
Q ss_pred --CCCCC--CccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 234 --EPEVV--TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 234 --~~~v~--~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
+..+. ..... ... .....+.+...| ..+||+...+.+.++.+.
T Consensus 127 ELk~Ki~~~~~~~~-~~~-~~~~~~e~~~aL-~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 127 ELKDKIAKNWEAGV-LSQ-VTEANSDILATL-TALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHhhhhccc-ccc-ccchHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 00010 00000 000 011235666777 689999999998887763
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.10 E-value=0.36 Score=42.25 Aligned_cols=109 Identities=21% Similarity=0.281 Sum_probs=61.6
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh-
Q 021529 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF- 232 (311)
Q Consensus 159 ~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~- 232 (311)
++-...||+ +.+.---|..|++ |+|||||+|+.+|..+ +++++.+.+..... ++|- .-.+-|.++.
T Consensus 54 ED~~~LYGF~t~~Er~lF~~Lis------VsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIIl 125 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELIG------VDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKG-IGNKMAGKIFL 125 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 334456887 6666666777765 8899999999999876 57888777653211 1221 1122333333
Q ss_pred -cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 233 -KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 233 -~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
++..+...... . -.....+...+-| ..+||+...+.+++..+.
T Consensus 126 ELkdKl~~~~~~-~--~~~~~~~ea~~AL-~~LGy~~~ea~~al~~v~ 169 (196)
T PRK13901 126 KLRGKLVKNDEL-E--SSLFKFKELEQSI-VNMGFDRKLVNSAIKEIM 169 (196)
T ss_pred HHHHhhcccccc-c--cCcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 11111100000 0 0111234444555 489999999999987754
No 37
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.04 E-value=0.31 Score=42.38 Aligned_cols=110 Identities=15% Similarity=0.190 Sum_probs=64.0
Q ss_pred HHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc---hHHHHHHhc
Q 021529 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARRLFK 233 (311)
Q Consensus 158 ~~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~---~~~~~~~~~ 233 (311)
+++-...||+ +++.---|-.|++ |+|||||+|+.++..+ +.+++...+.....+.- ..| .+-|.++..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Lis------V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLVK------VSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 4444567887 6666666666654 8899999999999876 57888887764322111 233 233444441
Q ss_pred --CCCCC-CccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 234 --EPEVV-TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 234 --~~~v~-~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
+..+. ..... . . .....+.+..-| ..+||+...+.+++.++.
T Consensus 126 ELk~K~~~~~~~~-~-~-~~~~~~e~~~aL-~~LGy~~~ea~~al~~v~ 170 (186)
T PRK14600 126 ELQYKVSKLEINE-T-N-FIIINDDALAAL-ISLGYEKTKAFNAIQKIK 170 (186)
T ss_pred HHHHHhhcccccc-c-c-ccccHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 11111 00000 0 0 111234444555 589999999999998763
No 38
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=93.89 E-value=0.76 Score=47.64 Aligned_cols=188 Identities=20% Similarity=0.350 Sum_probs=101.7
Q ss_pred hHHHHHHHHHHHHHHcCCceEE-EEeCCCCchhhHHHHHH--HhchhccHHHH--H----HHHHcCCH---H-HHHHHhh
Q 021529 11 SHLQGMFTRTIRLLEAGMKPIY-VFDGQPPDLKKQELAKR--YSKRADATDDL--A----EAVEAGNK---E-DIEKFSK 77 (311)
Q Consensus 11 ~a~~g~~~~l~~ll~~~i~Pv~-VFDG~~~~~K~~~~~~y--k~~R~~~~~~l--~----~~~~~g~~---~-~~~~~~~ 77 (311)
-+++-++.|++.|.+- -+-.| ..||..|-.|.....+| ++.|+.+.++. + ....+|.. . ..+.|=.
T Consensus 79 ~avFeyiDrlf~mvRP-RkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDS 157 (931)
T KOG2044|consen 79 VAVFEYIDRLFSMVRP-RKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDS 157 (931)
T ss_pred HHHHHHHHHHHHhccc-hheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhcccccc
Confidence 4566666666666652 23344 69999886555443333 33343332222 1 11223321 1 1112222
Q ss_pred hhccCCHHHHHHHHHHHHH------------hCCceEec----cCcHHHHHHHHHHc---------CceEEEecCCCccc
Q 021529 78 RTVKVTKQHNDDCKRLLKL------------MGVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSL 132 (311)
Q Consensus 78 ~~~~v~~~~~~~i~~lL~~------------~gi~~i~a----pgEADa~iA~L~~~---------g~v~~V~S~DsD~l 132 (311)
.|+..-.+.++.+-..|+. -+|.+|.+ |||++.-|-...+. +..+++++-|-|++
T Consensus 158 NcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLI 237 (931)
T KOG2044|consen 158 NCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLI 237 (931)
T ss_pred CccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccce
Confidence 3443322344555554543 36777765 89999877776651 34788999999999
Q ss_pred cccC----Ce--eEEEeecCCC----------------------------------CCcccEEEeHHHHHH----HcCC-
Q 021529 133 TFGA----PR--FLRHLMDPSS----------------------------------RKIPVMEFEVAKILE----ELNL- 167 (311)
Q Consensus 133 ~~~~----~~--v~~~l~~~~~----------------------------------~~~~~~~~~~~~v~~----~~gl- 167 (311)
++|- ++ ++|-.+.+++ .+.++.+++...+.+ ++-+
T Consensus 238 mLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p 317 (931)
T KOG2044|consen 238 MLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMP 317 (931)
T ss_pred eeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCC
Confidence 9983 22 3333222210 012345556544433 2222
Q ss_pred ------CH----HHHHHHHHHhCCCCCCCCCCccHH-HHHHHH
Q 021529 168 ------TM----DQFIDLCILSGCDYCDSIRGIGGQ-TALKLI 199 (311)
Q Consensus 168 ------~~----~q~~d~~~L~G~D~~d~ipgiG~k-tA~~li 199 (311)
+- +.|+-+|-.+|+||.+.+|-+-+. .|+++|
T Consensus 318 ~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeIRegAId~L 360 (931)
T KOG2044|consen 318 NLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEIREGAIDRL 360 (931)
T ss_pred CCCccccHHhhhcceEEEEeeecCccCCCCCchhhhhcHHHHH
Confidence 22 456668999999999999976543 244443
No 39
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=93.83 E-value=0.38 Score=49.44 Aligned_cols=26 Identities=42% Similarity=0.694 Sum_probs=23.6
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 021529 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 185 d~ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
++|||||+|+|..|++.|||+++|..
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 47999999999999999999988754
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.76 E-value=0.56 Score=41.33 Aligned_cols=111 Identities=14% Similarity=0.194 Sum_probs=61.3
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh--
Q 021529 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF-- 232 (311)
Q Consensus 160 ~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~-- 232 (311)
+-...||+ +.++--.|..|++ |+|||||+|+.+|..+ +.+++.+.+..... ++|- +-.+-|.++.
T Consensus 57 d~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~~ipG-IGkKtAerIilE 128 (203)
T PRK14602 57 DALELFGFATWDERQTFIVLIS------ISKVGAKTALAILSQF-RPDDLRRLVAEEDVAALTRVSG-IGKKTAQHIFLE 128 (203)
T ss_pred CcceeeCCCCHHHHHHHHHHhC------CCCcCHHHHHHHHhhC-CHHHHHHHHHhCCHHHHhcCCC-cCHHHHHHHHHH
Confidence 33456887 6777777777765 8999999999999976 57888877753211 1221 1112233322
Q ss_pred cCCCCC---Ccc--cccc-CCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 233 KEPEVV---TDE--EQLQ-IKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 233 ~~~~v~---~~~--~~~~-~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
++..+. ... .... ........+...+-| ..+||+...+.++++++.
T Consensus 129 LkdK~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL-~~LGy~~~ea~~av~~~~ 180 (203)
T PRK14602 129 LKYKLKVEGLPAAAVLAGTGAVPGSVFRDALAGL-ANLGYGEEEARPVLKEVL 180 (203)
T ss_pred HHHhhccccccccccccccccCCCchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 111111 000 0000 001111123444445 589999999999998764
No 41
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.73 E-value=0.43 Score=41.82 Aligned_cols=109 Identities=17% Similarity=0.226 Sum_probs=59.8
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhc-
Q 021529 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (311)
Q Consensus 160 ~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~~- 233 (311)
+....||+ +.+.--.|..|++ |+|||||+|+.+|..+ +.+++.+.+..... ++|- +-.+-|.++..
T Consensus 56 d~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpG-IGkKtAerIilE 127 (195)
T PRK14604 56 DALTLYGFSTPAQRQLFELLIG------VSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPG-IGKKTAERIVLE 127 (195)
T ss_pred CCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33456786 5666666666654 7899999999999864 57888877753211 1111 11122333221
Q ss_pred -CCCCC---CccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 234 -EPEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 234 -~~~v~---~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
+..+. ....... ......+.+.+-| ..+||+...+.+++.++.
T Consensus 128 Lk~K~~~~~~~~~~~~--~~~~~~~e~~~aL-~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 128 LKGKIDVRQLSGSTSP--AVSALDRELSEIL-ISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHHhccccccccccc--cccccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 11110 0000000 0111124455555 489999999999998774
No 42
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.70 E-value=0.36 Score=42.02 Aligned_cols=107 Identities=16% Similarity=0.201 Sum_probs=62.3
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh-
Q 021529 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF- 232 (311)
Q Consensus 159 ~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~- 232 (311)
++-...||+ +.++--.|..|++ |.|||||+|+.+|..+ +.+++.+.+..... ++|- .-.+-|.++.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAerIil 126 (188)
T PRK14606 55 QDGITLYGFSNERKKELFLSLTK------VSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPG-ISKKTAERIVM 126 (188)
T ss_pred cCCceeeCCCCHHHHHHHHHHhc------cCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 344557887 5666666666664 8899999999999875 57888877753211 1221 1122333333
Q ss_pred -cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 233 -KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 233 -~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
++..+.. .... .....+.+.+-| ..+||++..+.++++++.
T Consensus 127 ELkdK~~~-~~~~----~~~~~~e~~~AL-~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 127 ELKDEFES-AGIK----DMRIYHESLEAL-VSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHhhcc-ccCC----CcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1221210 0010 011234455555 489999999999998764
No 43
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.54 E-value=1.7 Score=38.30 Aligned_cols=117 Identities=17% Similarity=0.241 Sum_probs=63.4
Q ss_pred EeHHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc---hHHHHHH
Q 021529 156 FEVAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARRL 231 (311)
Q Consensus 156 ~~~~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~~~~~~~~---~~~~~~~ 231 (311)
+-+++....||+ +.+.=..|..|.. |.|||||+|+.+|.. .+++++.+.+..-....-..+| .+-|.++
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~Lis------VnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLLIS------VNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHHHc------cCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHH
Confidence 445666778998 4444444555543 788999999999974 5688888887643322222233 2233343
Q ss_pred hc--CCCCCC------ccccccCCCC--CCCHHHHHHHHHhhcCCCHHHHHHHHHHHHH
Q 021529 232 FK--EPEVVT------DEEQLQIKWS--APDEEGLINFLVSENGFNSDRVTKAIEKIKA 280 (311)
Q Consensus 232 ~~--~~~v~~------~~~~~~~~~~--~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~~ 280 (311)
.. +-.+.. .....+.... .+-.+.-.+-| ..+||++.++.+++..+..
T Consensus 125 vleLk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~AL-~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 125 VLELKGKLAAFLKGDGGSPAEDLSLDESSPALEEAVEAL-VALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred HHHHhhhhhhhcccccccccccccccccchhhhHHHHHH-HHcCCCHHHHHHHHHHHHh
Confidence 32 111100 0000011111 11111213334 4899999999998877654
No 44
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.49 E-value=0.67 Score=40.65 Aligned_cols=111 Identities=17% Similarity=0.158 Sum_probs=58.4
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh--
Q 021529 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF-- 232 (311)
Q Consensus 160 ~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~-- 232 (311)
+-...||+ +.+.---|-.|.+ |.|||||+|+.+|..+ +.+++.+.+..... ++|- +-.+-|.++.
T Consensus 55 d~~~LyGF~~~~Er~lF~~L~~------V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpG-IGkKtAerIilE 126 (197)
T PRK14603 55 DALSLYGFPDEDSLELFELLLG------VSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASG-VGKKLAERIALE 126 (197)
T ss_pred CCceeeCcCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33456787 5555555555554 7889999999999865 57777777653211 1111 1112222222
Q ss_pred cCCCCC---Cccc--cccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 233 KEPEVV---TDEE--QLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 233 ~~~~v~---~~~~--~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
++..+. .... ...-.......+.+.+-| ..+||+...+.++++++.
T Consensus 127 LkdK~~~~~~~~~~~~~~~~~~~~~~~ea~~AL-~~LGy~~~ea~~al~~i~ 177 (197)
T PRK14603 127 LKGKVPEHLLAGPAGGGGTKVSSTAAEDAVLAL-LALGFREAQVRSVVAELL 177 (197)
T ss_pred HHHHhhhhcccccccccccccCCccHHHHHHHH-HHcCCCHHHHHHHHHHHH
Confidence 111110 0000 000001112234455555 589999999999998764
No 45
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.48 E-value=0.37 Score=41.75 Aligned_cols=105 Identities=14% Similarity=0.234 Sum_probs=60.3
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh-
Q 021529 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF- 232 (311)
Q Consensus 159 ~~v~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~~~~~----~~~~~~~~~~~~~~~- 232 (311)
++-...||+ +.+.--.|..|.+ |+|||||+|+.++..+ +.+++.+.+..... ++|- .-.+-|.++.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~------VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIil 126 (183)
T PRK14601 55 EDSNKLYGFLDKDEQKMFEMLLK------VNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPG-IGPKSAKRIIA 126 (183)
T ss_pred cCCceeeCCCCHHHHHHHHHHhc------cCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 334456887 6666666666665 8899999999999875 57888877753211 2221 1122333333
Q ss_pred -cCCCCCCccccccCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHH
Q 021529 233 -KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKI 278 (311)
Q Consensus 233 -~~~~v~~~~~~~~~~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~ 278 (311)
++..+. ... . .....+...+-| ..+||+...+.++++.+
T Consensus 127 ELkdK~~---~~~--~-~~~~~~ea~~AL-~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 127 ELSDAKT---KLE--N-VSDDKSEALAAL-LTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHhh---ccC--C-CCccHHHHHHHH-HHcCCCHHHHHHHHHhc
Confidence 111111 000 0 011223444444 48999999999998765
No 46
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=93.15 E-value=2 Score=41.79 Aligned_cols=110 Identities=21% Similarity=0.329 Sum_probs=66.2
Q ss_pred HHHHHHHHh--CCceEeccC-cHHHHHHHHHH-----cCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHH
Q 021529 89 DCKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAK 160 (311)
Q Consensus 89 ~i~~lL~~~--gi~~i~apg-EADa~iA~L~~-----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~ 160 (311)
.+.++|..+ +|.++...| .||-++..-++ .|.=..++|.|-|.++|.+-.....+...
T Consensus 147 ~l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t-------------- 212 (425)
T PF04599_consen 147 ILESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKT-------------- 212 (425)
T ss_pred HHHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHh--------------
Confidence 345555555 899999999 99988777665 46555789999999999864311111100
Q ss_pred HHHHcCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHHH--HHHHHHcCCHHHHHHHHH
Q 021529 161 ILEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQTA--LKLIRQHGSIETILENIN 213 (311)
Q Consensus 161 v~~~~gl~~----~q~-~d~~~L~G~D~~d~ipgiG--~ktA--~~li~~~gsle~i~~~~~ 213 (311)
+-+.+-+-| .-+ ...++.=||||-+|+-|+- .++- .+|...| +++++++.+-
T Consensus 213 ~~~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~ 273 (425)
T PF04599_consen 213 MNQLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLA 273 (425)
T ss_pred HHhHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHh
Confidence 011122211 112 2345566999999998854 3331 3333333 4777777664
No 47
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=93.01 E-value=0.075 Score=53.88 Aligned_cols=30 Identities=27% Similarity=0.418 Sum_probs=26.6
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 182 D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
.-.|+|||||+|+..+||+.|||+++|.++
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 455799999999999999999999998753
No 48
>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=92.97 E-value=0.084 Score=31.76 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.7
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||++||-.++.
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 479999999988764
No 49
>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=92.95 E-value=0.075 Score=54.02 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=26.5
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 182 D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
.-.|+|||||+|+..+||+.|||+++|.++
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 456799999999999999999999998653
No 50
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=92.84 E-value=0.095 Score=35.80 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=17.4
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~ 209 (311)
+|.||||+||.++..+ +.|++++-
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl~Dl~ 30 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTLEDLR 30 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SHHHHH
T ss_pred hcccccHHHHHHHHHhCCCCHHHHh
Confidence 5899999999999984 67898883
No 51
>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=92.78 E-value=0.1 Score=36.46 Aligned_cols=25 Identities=36% Similarity=0.476 Sum_probs=22.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~~ 210 (311)
+|||||+++|..|... |++++++..
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 5899999999999998 899988865
No 52
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=92.66 E-value=0.09 Score=53.37 Aligned_cols=30 Identities=30% Similarity=0.443 Sum_probs=26.5
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 182 D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
.-.++|||||+++..+||+.|||+++|.++
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 355799999999999999999999998754
No 53
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=92.64 E-value=0.086 Score=54.02 Aligned_cols=29 Identities=28% Similarity=0.499 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 183 ~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
-.++|||||++++.+|+++|||+++|...
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 45689999999999999999999998753
No 54
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=91.21 E-value=0.17 Score=52.13 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=26.7
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 182 D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
.-.++|||||++++.+||+.|||+++|.++
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 456799999999999999999999998754
No 55
>PHA03065 Hypothetical protein; Provisional
Probab=88.95 E-value=5.3 Score=38.76 Aligned_cols=110 Identities=19% Similarity=0.326 Sum_probs=65.7
Q ss_pred HHHHHHHHh--CCceEeccC-cHHHHHHHHHH-----cCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHH
Q 021529 89 DCKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAK 160 (311)
Q Consensus 89 ~i~~lL~~~--gi~~i~apg-EADa~iA~L~~-----~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~ 160 (311)
.+-+.|..+ +|.++.+.| .|+-++..-++ .|.=..++|.|.|.+.|.+-.-.-.+. ..
T Consensus 149 ~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI--------------~t 214 (438)
T PHA03065 149 LLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKII--------------KT 214 (438)
T ss_pred HHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHH--------------Hh
Confidence 344567777 999999999 99987776665 465557899999999997643110000 01
Q ss_pred HHHHcCCCH----HHHH-HHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHH
Q 021529 161 ILEELNLTM----DQFI-DLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENIN 213 (311)
Q Consensus 161 v~~~~gl~~----~q~~-d~~~L~G~D~~d~ipgiG--~kt--A~~li~~~gsle~i~~~~~ 213 (311)
+-+.|.+-| .-+. ..++.=||||-+|+-|+- +++ -.+|...| +.+++++.+-
T Consensus 215 ~~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~ 275 (438)
T PHA03065 215 ANQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLA 275 (438)
T ss_pred HHHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHH
Confidence 112222222 1122 234555999999998854 443 23344443 3566666554
No 56
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=88.72 E-value=0.37 Score=27.74 Aligned_cols=17 Identities=35% Similarity=0.520 Sum_probs=14.5
Q ss_pred CCCCCccHHHHHHHHHH
Q 021529 185 DSIRGIGGQTALKLIRQ 201 (311)
Q Consensus 185 d~ipgiG~ktA~~li~~ 201 (311)
..|||||+++|.+++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 36899999999999863
No 57
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=88.44 E-value=0.34 Score=49.58 Aligned_cols=27 Identities=37% Similarity=0.634 Sum_probs=24.6
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 185 d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
++|||||++++.+|++.|||+++|.++
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 579999999999999999999998753
No 58
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=88.29 E-value=0.37 Score=49.06 Aligned_cols=30 Identities=33% Similarity=0.614 Sum_probs=26.4
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 182 D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
...+.|||||++++.+|++.|||+++|.++
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 344679999999999999999999999864
No 59
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=87.97 E-value=0.41 Score=42.82 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=24.7
Q ss_pred CCCCCCccHHHHHHHHHH-cCCHHHHHHH
Q 021529 184 CDSIRGIGGQTALKLIRQ-HGSIETILEN 211 (311)
Q Consensus 184 ~d~ipgiG~ktA~~li~~-~gsle~i~~~ 211 (311)
.+.|||||+++|.+|++. |+|+++|...
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 457899999999999999 9999988653
No 60
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=87.88 E-value=0.41 Score=49.44 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=26.0
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 183 ~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
-.+.|||||++++.+|++.|||+++|.+.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 45679999999999999999999999874
No 61
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=86.69 E-value=0.58 Score=35.25 Aligned_cols=25 Identities=40% Similarity=0.509 Sum_probs=21.2
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHH
Q 021529 183 YCDSIRGIGGQTALKLIRQHGSIET 207 (311)
Q Consensus 183 ~~d~ipgiG~ktA~~li~~~gsle~ 207 (311)
....|||||+.+|..|+.+.|+++.
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchh
Confidence 3457899999999999999988654
No 62
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=85.82 E-value=0.62 Score=47.39 Aligned_cols=47 Identities=21% Similarity=0.290 Sum_probs=33.0
Q ss_pred HcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 164 ELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 164 ~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
.|.++...=.--....= ...|+|||||+++..+||+.|||+++|.++
T Consensus 513 rfAi~~hR~~R~k~~~~-s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 513 RFAITYHRKKRSKAMLQ-SSLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred HHHHHHHHHHhhhhhhc-CccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 45554332222333333 356899999999999999999999988754
No 63
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=84.78 E-value=0.82 Score=41.54 Aligned_cols=26 Identities=42% Similarity=0.724 Sum_probs=23.7
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
++||||++.|..|+..|||++++...
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 47999999999999999999998765
No 64
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.54 E-value=0.9 Score=39.38 Aligned_cols=46 Identities=20% Similarity=0.352 Sum_probs=33.3
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 021529 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 155 ~~~~~~v~~~~-gl~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~ 202 (311)
-+.+..-+.-+ +++|+++.. ++..| |..- .+||||+|||.+++-+-
T Consensus 80 GIGpK~Al~ILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 80 GIGANTAMAVCSSLDVNSFYK-ALSLG-DESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 35566556666 578888864 45556 6663 68999999999999763
No 65
>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=84.12 E-value=3.3 Score=43.53 Aligned_cols=39 Identities=21% Similarity=0.480 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 021529 167 LTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (311)
Q Consensus 167 l~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~gsle~i~~~~~ 213 (311)
-+.+.++.|.. .| .|||||+++|.+++..|| ++.++.+.
T Consensus 75 ~~~~~i~~yL~-s~-----~~~GIG~~~A~~iv~~fg--~~~~~~i~ 113 (720)
T TIGR01448 75 TSKEGIVAYLS-SR-----SIKGVGKKLAQRIVKTFG--EAAFDVLD 113 (720)
T ss_pred CCHHHHHHHHh-cC-----CCCCcCHHHHHHHHHHhC--HhHHHHHH
Confidence 35677777765 44 699999999999999999 34555544
No 66
>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=82.88 E-value=3.9 Score=34.74 Aligned_cols=39 Identities=18% Similarity=0.184 Sum_probs=29.7
Q ss_pred hCCceEecc-C-cHHHHHHHHHH---c-CceEEEecCCCcccccc
Q 021529 97 MGVPVVEAP-S-EAEAQCAALCK---S-GQVYAVASEDMDSLTFG 135 (311)
Q Consensus 97 ~gi~~i~ap-g-EADa~iA~L~~---~-g~v~~V~S~DsD~l~~~ 135 (311)
-||.++.++ | .||+.|-.++. . +.-..|+|+|...-...
T Consensus 66 ~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~ 110 (166)
T PF05991_consen 66 GGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAA 110 (166)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHH
Confidence 578888887 4 99999998876 2 45667999988766553
No 67
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.28 E-value=1.8 Score=37.92 Aligned_cols=47 Identities=21% Similarity=0.200 Sum_probs=34.4
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHcC
Q 021529 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~g 203 (311)
-+.+..-+.-++ ++|+++.. ++..| |..- .+||||+|||-+++-+..
T Consensus 79 GIGpK~AL~iLs~~~~~~l~~-aI~~~-D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 79 GVGPKLALALLSALPPALLAR-ALLEG-DARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHHH
Confidence 366666666675 78988865 34455 6663 689999999999997743
No 68
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.88 E-value=2.3 Score=36.91 Aligned_cols=46 Identities=22% Similarity=0.357 Sum_probs=33.4
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC-CCCCccHHHHHHHHHHc
Q 021529 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD-SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d-~ipgiG~ktA~~li~~~ 202 (311)
-+.+..-+.-+. ++|+++... +-.| |..- .+||||.|||.+++-+.
T Consensus 80 GIGpK~Al~iLs~~~~~~l~~a-I~~~-D~~~L~vpGIGkKtAerIilEL 127 (186)
T PRK14600 80 GVNYKTAMSILSKLTPEQLFSA-IVNE-DKAALKVNGIGEKLINRIITEL 127 (186)
T ss_pred CcCHHHHHHHHccCCHHHHHHH-HHcC-CHhheECCCCcHHHHHHHHHHH
Confidence 366666666665 789988764 4445 6542 68999999999999764
No 69
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.91 E-value=1.7 Score=38.08 Aligned_cols=45 Identities=24% Similarity=0.305 Sum_probs=32.8
Q ss_pred EeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 021529 156 FEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 156 ~~~~~v~~~~-gl~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~ 202 (311)
+.+..-+.-+ .++|+++... +..| |..- .+||||+|||.+++-+.
T Consensus 80 IGPK~ALaILs~~~~~el~~a-I~~~-D~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 80 IGPRAALRVLSGIKYNEFRDA-IDRE-DIELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred cCHHHHHHHHcCCCHHHHHHH-HHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 5555556666 4788888653 4555 7663 68999999999999764
No 70
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=79.47 E-value=1.7 Score=35.45 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=19.0
Q ss_pred CCCccHHHHHHHHHH--cCCHHHHHH
Q 021529 187 IRGIGGQTALKLIRQ--HGSIETILE 210 (311)
Q Consensus 187 ipgiG~ktA~~li~~--~gsle~i~~ 210 (311)
+|||||+.|.++++. |.++|++++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 589999999999963 567777754
No 71
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.79 E-value=2.4 Score=36.86 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=33.8
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 021529 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 155 ~~~~~~v~~~~-gl~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~ 202 (311)
-+.+..-+.-+ +++|+++.. ++..| |..- .+||||+|||.+++-+.
T Consensus 80 GIGpK~AL~iLs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 80 RLGPKTALKIISNEDAETLVT-MIASQ-DVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 35666666666 578888865 45556 6653 68999999999999764
No 72
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.72 E-value=1.7 Score=38.12 Aligned_cols=47 Identities=26% Similarity=0.282 Sum_probs=33.4
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHcC
Q 021529 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~g 203 (311)
-+.+..-+.-++ ++|++|... +..| |..- .+||||+|||.+++-+..
T Consensus 80 GIGpK~Al~iLs~~~~~el~~a-I~~~-D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 80 GVGPKAALNLLSSGTPDELQLA-IAGG-DVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CcCHHHHHHHHcCCCHHHHHHH-HHhC-CHHHHhhCCCCCHHHHHHHHHHHH
Confidence 355665566665 688888653 4445 6653 689999999999998743
No 73
>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=77.85 E-value=2 Score=44.49 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=20.3
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
+|||||+++|..|++.|+|++++..
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~ 526 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKA 526 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4788888888888888888887754
No 74
>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=77.78 E-value=1.7 Score=26.43 Aligned_cols=13 Identities=54% Similarity=0.695 Sum_probs=10.3
Q ss_pred CCCCccHHHHHHH
Q 021529 186 SIRGIGGQTALKL 198 (311)
Q Consensus 186 ~ipgiG~ktA~~l 198 (311)
.++|||.+|+.+|
T Consensus 15 ~~~GIG~kt~~kL 27 (32)
T PF11798_consen 15 KFWGIGKKTAKKL 27 (32)
T ss_dssp GSTTS-HHHHHHH
T ss_pred hhCCccHHHHHHH
Confidence 5799999999885
No 75
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=76.92 E-value=3.4 Score=34.31 Aligned_cols=88 Identities=16% Similarity=0.223 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccccCCe--eEEEeecCCCCCcccEEEeHHHHHH
Q 021529 86 HNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPR--FLRHLMDPSSRKIPVMEFEVAKILE 163 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~--v~~~l~~~~~~~~~~~~~~~~~v~~ 163 (311)
++..+-+.|+.+|+.++.++...|+.+..+|.+..- +|+|.|++++...... ++. + ... . ..-...++.+
T Consensus 8 ~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~~~~~~~~~~~l-i-~~~-~----~~~QL~ev~~ 79 (147)
T PF01927_consen 8 MLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLLKRRRVSGGVIL-I-RSD-D----PEEQLREVLE 79 (147)
T ss_pred CHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHHHhhccCCEEE-E-cCC-C----HHHHHHHHHH
Confidence 456688899999999999998888899988875433 3799999988764322 221 2 111 0 1123456667
Q ss_pred HcCCCH--HHHHHHHHHhCC
Q 021529 164 ELNLTM--DQFIDLCILSGC 181 (311)
Q Consensus 164 ~~gl~~--~q~~d~~~L~G~ 181 (311)
.+|+.+ +.+..-|..|++
T Consensus 80 ~~~l~~~~~~~~sRC~~CN~ 99 (147)
T PF01927_consen 80 RFGLKLRLDPIFSRCPKCNG 99 (147)
T ss_pred HcCCccccCCCCCccCCCCc
Confidence 777655 333345555553
No 76
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.61 E-value=2.9 Score=36.80 Aligned_cols=47 Identities=19% Similarity=0.272 Sum_probs=33.6
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHcC
Q 021529 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~g 203 (311)
-+.+..-+.-++ +++++|.. ++..| |..- .+||||+|||-+++-+..
T Consensus 81 GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 81 KVGAKTALAILSQFRPDDLRR-LVAEE-DVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CcCHHHHHHHHhhCCHHHHHH-HHHhC-CHHHHhcCCCcCHHHHHHHHHHHH
Confidence 356666666665 68888764 34555 6663 689999999999997643
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=75.97 E-value=2.5 Score=44.03 Aligned_cols=25 Identities=36% Similarity=0.622 Sum_probs=22.4
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
+|||||+++|..|++.|+|++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4799999999999999999998764
No 78
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=75.71 E-value=2.4 Score=45.08 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
++||||++.|..|+.+|||++++..
T Consensus 761 ~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred HCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 3799999999999999999999875
No 79
>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=74.63 E-value=3.2 Score=33.34 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=14.4
Q ss_pred CCCCccHHHHHHHHHHc
Q 021529 186 SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~ 202 (311)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 46899999999999874
No 80
>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=73.09 E-value=3.7 Score=38.50 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=21.2
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQH--GSIETILENI 212 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~--gsle~i~~~~ 212 (311)
+|||||||||.+|. +. .|++++....
T Consensus 89 ~i~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 89 RVPGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred cCCCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 57999999999999 54 4888887764
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=73.00 E-value=3.1 Score=39.51 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=20.9
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHG--SIETILEN 211 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~g--sle~i~~~ 211 (311)
+|||||||||..|.+ .| |++++.++
T Consensus 93 ~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 93 NVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred ccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 579999999999988 65 88888654
No 82
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=72.14 E-value=4 Score=35.88 Aligned_cols=72 Identities=26% Similarity=0.337 Sum_probs=44.1
Q ss_pred eEEEecCCCccccccCCe-----eEEEeecCCCCCcccEEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccH
Q 021529 121 VYAVASEDMDSLTFGAPR-----FLRHLMDPSSRKIPVMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGG 192 (311)
Q Consensus 121 v~~V~S~DsD~l~~~~~~-----v~~~l~~~~~~~~~~~~~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~--d~ipgiG~ 192 (311)
+.-++.+|. ..+||-.. +++.+. .+.-+....-+.-+. ++++.|... +-.+ |.. -.+||||.
T Consensus 49 t~~~vREd~-~~LyGF~~~~ER~lF~~Li-------sVnGIGpK~ALaiLs~~~~~~l~~a-I~~~-d~~~L~k~PGIGk 118 (201)
T COG0632 49 THLVVREDA-HLLYGFLTEEERELFRLLI-------SVNGIGPKLALAILSNLDPEELAQA-IANE-DVKALSKIPGIGK 118 (201)
T ss_pred EEEeehhhH-HHHcCCCCHHHHHHHHHHH-------ccCCccHHHHHHHHcCCCHHHHHHH-HHhc-ChHhhhcCCCCCH
Confidence 556677777 66776422 111111 122355555566664 588888764 3344 655 36899999
Q ss_pred HHHHHHHHHc
Q 021529 193 QTALKLIRQH 202 (311)
Q Consensus 193 ktA~~li~~~ 202 (311)
|||-+++-+-
T Consensus 119 KtAerivleL 128 (201)
T COG0632 119 KTAERIVLEL 128 (201)
T ss_pred HHHHHHHHHH
Confidence 9999998764
No 83
>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=71.22 E-value=5.7 Score=31.12 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=23.6
Q ss_pred cCcHHHHHHHHHHcCceEEEecCCCcccc
Q 021529 105 PSEAEAQCAALCKSGQVYAVASEDMDSLT 133 (311)
Q Consensus 105 pgEADa~iA~L~~~g~v~~V~S~DsD~l~ 133 (311)
+-..|+-+..++..+.+++++|+|+|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 44667777778888888899999999875
No 84
>PRK13766 Hef nuclease; Provisional
Probab=70.17 E-value=4 Score=43.01 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=23.6
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
+|||||+++|.+|+++||++++++..
T Consensus 719 ~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 719 SLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 58999999999999999999988753
No 85
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=69.56 E-value=3.4 Score=42.93 Aligned_cols=23 Identities=39% Similarity=0.632 Sum_probs=14.0
Q ss_pred CCCccHHHHHHHHHHcCCHHHHH
Q 021529 187 IRGIGGQTALKLIRQHGSIETIL 209 (311)
Q Consensus 187 ipgiG~ktA~~li~~~gsle~i~ 209 (311)
|||||+++|..|++.|+|++++.
T Consensus 516 i~~IG~~~ak~L~~~f~sl~~l~ 538 (665)
T PRK07956 516 IRHVGEKAAKALARHFGSLEALR 538 (665)
T ss_pred ccCcCHHHHHHHHHHcCCHHHHH
Confidence 45666666666666666666554
No 86
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=68.50 E-value=11 Score=31.55 Aligned_cols=44 Identities=20% Similarity=0.312 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHc-CceEEEecC
Q 021529 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS-GQVYAVASE 127 (311)
Q Consensus 84 ~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~-g~v~~V~S~ 127 (311)
.+.+..+.+-|+.+|++.++-.|++.+.+..|+++ |...+++..
T Consensus 52 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~V~~~~ 96 (165)
T PF00875_consen 52 LESLADLQESLRKLGIPLLVLRGDPEEVLPELAKEYGATAVYFNE 96 (165)
T ss_dssp HHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHHHTESEEEEE-
T ss_pred HHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHhcCcCeeEecc
Confidence 34567788888999999999999999988888774 544333333
No 87
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=67.24 E-value=6.2 Score=32.97 Aligned_cols=24 Identities=25% Similarity=0.470 Sum_probs=17.7
Q ss_pred CCCCccHHHHHHHHHH------cCCHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ------HGSIETIL 209 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~------~gsle~i~ 209 (311)
.+||||+++|.+++.. |.++|++.
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~ 130 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDLA 130 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence 3588999999999873 35666654
No 88
>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=66.38 E-value=7.1 Score=27.77 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.7
Q ss_pred CCCccHHHHHHHHHH
Q 021529 187 IRGIGGQTALKLIRQ 201 (311)
Q Consensus 187 ipgiG~ktA~~li~~ 201 (311)
+||||+++|.++|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 688898888888887
No 89
>PRK08609 hypothetical protein; Provisional
Probab=65.49 E-value=11 Score=38.57 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=21.0
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHG--SIETILENIN 213 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~g--sle~i~~~~~ 213 (311)
.|||||||||.+|-++.| |++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 578999999999887654 7777766554
No 90
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=65.32 E-value=4.6 Score=41.58 Aligned_cols=26 Identities=38% Similarity=0.643 Sum_probs=23.6
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
|||+||+++|..|.+.|+|++++++.
T Consensus 515 GIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 515 GIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred CCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 58999999999999999999998764
No 91
>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=64.75 E-value=6.2 Score=30.32 Aligned_cols=32 Identities=28% Similarity=0.145 Sum_probs=21.6
Q ss_pred CCCCccHHHHHHHHHH-cCC--------HHHHHHHHHhhcC
Q 021529 186 SIRGIGGQTALKLIRQ-HGS--------IETILENINRERY 217 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gs--------le~i~~~~~~~~~ 217 (311)
.|||||+.+|..|..- +.+ .+++++.+....+
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~G 56 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALTG 56 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHcC
Confidence 4899999999999852 334 4455666655443
No 92
>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=64.40 E-value=6.1 Score=27.33 Aligned_cols=17 Identities=47% Similarity=0.642 Sum_probs=14.8
Q ss_pred CCCCccHHHHHHHHHHc
Q 021529 186 SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~ 202 (311)
.|||||+++|-+|+...
T Consensus 42 ~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 42 EIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp TSTTSSHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 58999999999998763
No 93
>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=63.97 E-value=9 Score=33.38 Aligned_cols=44 Identities=23% Similarity=0.336 Sum_probs=29.6
Q ss_pred EeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 021529 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (311)
Q Consensus 156 ~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~ 201 (311)
+.+...+.-++ ++++++... +..| |..- .+||||+|||.+++-+
T Consensus 80 IGpK~Al~iL~~~~~~el~~a-I~~~-d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 80 VGPKLALAILSNMSPEEFVYA-IETE-EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCHHHHHHHHhcCCHHHHHHH-HHhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 55555555666 477777553 3334 5553 6899999999999844
No 94
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=60.48 E-value=11 Score=31.82 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 021529 169 MDQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 169 ~~q~~d~~~L~G~D~~d~---------ipgiG~ktA~~li~~~g 203 (311)
+++|-.+.-++|+|..++ |.|||..+|..++.+.|
T Consensus 8 ~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 8 ADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 357777888889887765 57999999999999987
No 95
>PRK13844 recombination protein RecR; Provisional
Probab=59.55 E-value=8.5 Score=33.82 Aligned_cols=16 Identities=19% Similarity=0.312 Sum_probs=13.3
Q ss_pred CCCCccHHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ 201 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~ 201 (311)
.+||||+|+|.++.-.
T Consensus 19 ~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 19 KLPTIGKKSSQRLALY 34 (200)
T ss_pred HCCCCCHHHHHHHHHH
Confidence 5799999999988653
No 96
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=58.61 E-value=7.9 Score=27.29 Aligned_cols=22 Identities=27% Similarity=0.341 Sum_probs=15.1
Q ss_pred CCCCccHHHHHHHHHHcCCHHH
Q 021529 186 SIRGIGGQTALKLIRQHGSIET 207 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~gsle~ 207 (311)
.|||||+++|..+..-|...++
T Consensus 39 ~i~gIG~~~A~si~~ff~~~~n 60 (64)
T PF12826_consen 39 AIPGIGPKIAQSIYEFFQDPEN 60 (64)
T ss_dssp TSTT--HHHHHHHHHHHH-HHH
T ss_pred ccCCcCHHHHHHHHHHHCCHHh
Confidence 6899999999998877665443
No 97
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=58.28 E-value=9.6 Score=36.38 Aligned_cols=25 Identities=20% Similarity=0.375 Sum_probs=22.9
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 187 IRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 187 ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
||+++...|.+|+.+|||+.+++..
T Consensus 292 IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 292 IPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred CCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 5899999999999999999999863
No 98
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=54.00 E-value=7.3 Score=34.00 Aligned_cols=15 Identities=27% Similarity=0.516 Sum_probs=12.6
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||+|+|.++.-
T Consensus 16 kLPGvG~KsA~R~Af 30 (198)
T COG0353 16 KLPGVGPKSAQRLAF 30 (198)
T ss_pred hCCCCChhHHHHHHH
Confidence 579999999988754
No 99
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.86 E-value=9.5 Score=33.31 Aligned_cols=45 Identities=24% Similarity=0.325 Sum_probs=28.1
Q ss_pred EeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 021529 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (311)
Q Consensus 156 ~~~~~v~~~~g-l~~~q~~d~~~L~G~D~~d--~ipgiG~ktA~~li~~~ 202 (311)
+.+..-+.-+. +++++|+.. +..+ |..- .+||||+|||.+++-+-
T Consensus 81 IGpK~Al~ILs~~~~~~l~~a-I~~~-D~~~L~~vpGIGkKtAerIilEL 128 (194)
T PRK14605 81 IGPKLGLAMLSAMNAEALASA-IISG-NAELLSTIPGIGKKTASRIVLEL 128 (194)
T ss_pred CCHHHHHHHHHhCCHHHHHHH-HHhC-CHHHHHhCCCCCHHHHHHHHHHH
Confidence 33333333332 567776543 3345 6653 58999999999988763
No 100
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.60 E-value=8.6 Score=33.64 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=13.1
Q ss_pred CCCCccHHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ 201 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~ 201 (311)
.+||||+|+|.++.-.
T Consensus 15 ~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 15 KLPGIGPKSAQRLAFH 30 (195)
T ss_pred HCCCCCHHHHHHHHHH
Confidence 5799999999988543
No 101
>PRK00076 recR recombination protein RecR; Reviewed
Probab=53.49 E-value=8.6 Score=33.69 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=13.3
Q ss_pred CCCCccHHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ 201 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~ 201 (311)
.+||||+|+|.++.-.
T Consensus 15 ~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 15 KLPGIGPKSAQRLAFH 30 (196)
T ss_pred HCCCCCHHHHHHHHHH
Confidence 5799999999988654
No 102
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=52.48 E-value=11 Score=33.94 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=25.3
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 183 ~~d~ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
+.-+||||+...|..|+.+|||++.++.+
T Consensus 196 ~Lt~i~~VnKtda~~LL~~FgsLq~~~~A 224 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLLQKFGSLQQISNA 224 (254)
T ss_pred HHHhCCCCCcccHHHHHHhcccHHHHHhc
Confidence 44578999999999999999999998754
No 103
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=49.82 E-value=22 Score=30.09 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=34.1
Q ss_pred HHHHHHHHhCCceEeccCcHHHHHHH--HHH--cC--ceEEEecCCCcccccc
Q 021529 89 DCKRLLKLMGVPVVEAPSEAEAQCAA--LCK--SG--QVYAVASEDMDSLTFG 135 (311)
Q Consensus 89 ~i~~lL~~~gi~~i~apgEADa~iA~--L~~--~g--~v~~V~S~DsD~l~~~ 135 (311)
.+++.|..+|+..+...|..|-.++- |.- .+ .+.+++|+|+|+.-+.
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv 122 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVI 122 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHH
Confidence 46789999999998888876654442 211 23 3567899999998876
No 104
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=49.60 E-value=18 Score=27.67 Aligned_cols=49 Identities=22% Similarity=0.180 Sum_probs=36.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccc
Q 021529 80 VKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (311)
Q Consensus 80 ~~v~~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~ 134 (311)
.+++.+....+.++....+ .+-+|+.++.++....+..++|.|+|+..+
T Consensus 70 ~~~~~~~~~~~~~~~~~~~------~~~~Da~~~a~A~~~~~~~v~T~D~~f~~~ 118 (121)
T PF01850_consen 70 LPITSEVFERAAELMRKYG------LDFADALIAATAKENGAPLVVTFDKDFRKV 118 (121)
T ss_dssp EEBCHHHHHHHHHHHHHHH------SSHHHHHHHHHHHHHT-EEE-ESSHHHHHH
T ss_pred ccchhHHHHHHHHHHHhcc------CChhHHHHHHHHHHcCCEEEEECCcCHHhc
Confidence 3566777888888888877 557999999999865566677999997654
No 105
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=49.53 E-value=58 Score=31.75 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhCCceEeccCcHHHHHHHHHH
Q 021529 87 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCK 117 (311)
Q Consensus 87 ~~~i~~lL~~~gi~~i~apgEADa~iA~L~~ 117 (311)
+..+.+-|+++|++.++.-|++.+.+..|++
T Consensus 63 L~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~ 93 (429)
T TIGR02765 63 LKDLRTSLRKLGSDLLVRSGKPEDVLPELIK 93 (429)
T ss_pred HHHHHHHHHHcCCCeEEEeCCHHHHHHHHHH
Confidence 4455555566666666666666666666655
No 106
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=46.49 E-value=15 Score=32.52 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=14.8
Q ss_pred CCCCccHHHHHHHHHHcC
Q 021529 186 SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~g 203 (311)
++||||+|||--++.-.+
T Consensus 123 ~lpGIG~KTAd~vL~~~~ 140 (208)
T PRK01229 123 NIKGIGYKEASHFLRNVG 140 (208)
T ss_pred cCCCCcHHHHHHHHHHcc
Confidence 789999999999886433
No 107
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.23 E-value=71 Score=27.15 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccc
Q 021529 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (311)
Q Consensus 84 ~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~ 134 (311)
..++-.+-++|+.+|.+....-.+.|+.+..++.+.-. +++|.|.-++.-
T Consensus 12 D~mLG~LARwLRllGydt~~~~~~~d~~i~~i~~~e~r-IllTRDr~L~~r 61 (165)
T COG1656 12 DAMLGKLARWLRLLGYDTVYSSNESDDEIILIAKKEGR-ILLTRDRELYKR 61 (165)
T ss_pred HHhHHHHHHHHHHcCCceeeeccCCcHHHHHHHhcCCe-EEEeccHHHHHH
Confidence 45677889999999999999888889999888875323 478999998887
No 108
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=46.04 E-value=40 Score=27.80 Aligned_cols=55 Identities=22% Similarity=0.232 Sum_probs=37.8
Q ss_pred CHHHHHHHHHHHHHhCCc-----eEeccC--cHHHHHHHHHHcCceEEE------ecCCCccccccCC
Q 021529 83 TKQHNDDCKRLLKLMGVP-----VVEAPS--EAEAQCAALCKSGQVYAV------ASEDMDSLTFGAP 137 (311)
Q Consensus 83 ~~~~~~~i~~lL~~~gi~-----~i~apg--EADa~iA~L~~~g~v~~V------~S~DsD~l~~~~~ 137 (311)
+..+++-+.+.|+..|+. ++..|| |-=-.+..|++.|..|+| +-++++-+.+.+.
T Consensus 15 ~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~LG~VIrG~T~H~e~v~~ 82 (138)
T TIGR00114 15 TDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIALGCVIRGGTPHFEYVAD 82 (138)
T ss_pred HHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEeeEEeCCCchhHHHHH
Confidence 356778888899998865 888999 777777788886644444 3455555555443
No 109
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=45.62 E-value=31 Score=28.90 Aligned_cols=34 Identities=32% Similarity=0.585 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 021529 170 DQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 170 ~q~~d~~~L~G~D~~d~---------ipgiG~ktA~~li~~~g 203 (311)
++|-.+.=++|+|..++ |-|||..+|..++++.|
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 45666777888887775 46999999999999986
No 110
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=45.59 E-value=19 Score=28.18 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=15.3
Q ss_pred CCCccHHHHHHHHHHcC
Q 021529 187 IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~~g 203 (311)
|.|||+.+|..++.+.|
T Consensus 20 IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 20 IYGIGRRKAKQICKKLG 36 (107)
T ss_dssp STTBCHHHHHHHHHHTT
T ss_pred hhccCHHHHHHHHHHcC
Confidence 68999999999999876
No 111
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=44.10 E-value=50 Score=26.68 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhCCceEeccC--------cHHHHHHHHH-----HcC-ceEEEecCCCcccccc
Q 021529 87 NDDCKRLLKLMGVPVVEAPS--------EAEAQCAALC-----KSG-QVYAVASEDMDSLTFG 135 (311)
Q Consensus 87 ~~~i~~lL~~~gi~~i~apg--------EADa~iA~L~-----~~g-~v~~V~S~DsD~l~~~ 135 (311)
.....+.|+..|+.++..|. .+|-.++.-+ .++ .+.+++|+|+|+....
T Consensus 54 ~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i 116 (149)
T cd06167 54 QRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLV 116 (149)
T ss_pred HHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHH
Confidence 35577888999999998873 4776555322 223 3667999999999774
No 112
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.94 E-value=79 Score=31.14 Aligned_cols=31 Identities=6% Similarity=0.006 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhCCceEeccCcHHHHHHHHHH
Q 021529 87 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCK 117 (311)
Q Consensus 87 ~~~i~~lL~~~gi~~i~apgEADa~iA~L~~ 117 (311)
+..+.+-|+.+|++.++.-|+....+..|++
T Consensus 80 L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~ 110 (454)
T TIGR00591 80 LDEVANECERLIIPFHLLDGPPKELLPYFVD 110 (454)
T ss_pred HHHHHHHHHHcCCceEEeecChHHHHHHHHH
Confidence 4445555556666666666655555555555
No 113
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=41.72 E-value=68 Score=25.64 Aligned_cols=50 Identities=20% Similarity=0.282 Sum_probs=36.3
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHH-cCCHHHH
Q 021529 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ-HGSIETI 208 (311)
Q Consensus 156 ~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~-~gsle~i 208 (311)
.+...+.+..|++...+..+..++ |.. -|||||+..|.=|... +.|++++
T Consensus 30 ~~r~~La~~~~i~~~~l~~w~~~A--dL~-ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 30 LGRKALAKKLGISERNLLKWVNQA--DLM-RIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred HHHHHHHHhcCCCHHHHHHHHhHH--Hhh-hcCCCCHHHHHHHHHhCcCcHHHH
Confidence 445567888999999998887775 677 8999999987655543 2355443
No 114
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=41.11 E-value=71 Score=25.40 Aligned_cols=49 Identities=16% Similarity=0.147 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhCCceEeccC---------cHHHHHHHH----HH-c-CceEEEecCCCcccccc
Q 021529 87 NDDCKRLLKLMGVPVVEAPS---------EAEAQCAAL----CK-S-GQVYAVASEDMDSLTFG 135 (311)
Q Consensus 87 ~~~i~~lL~~~gi~~i~apg---------EADa~iA~L----~~-~-g~v~~V~S~DsD~l~~~ 135 (311)
...+.+.|+..|+++...|. .+|-.++.= +. . -...+++|+|+|+.-..
T Consensus 49 ~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v 112 (146)
T PF01936_consen 49 QKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLV 112 (146)
T ss_dssp HHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHH
T ss_pred hhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHH
Confidence 45566888999998876653 366555421 21 1 24667999999988764
No 115
>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=40.79 E-value=21 Score=25.30 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=11.9
Q ss_pred CCCCCccHHHHHHH
Q 021529 185 DSIRGIGGQTALKL 198 (311)
Q Consensus 185 d~ipgiG~ktA~~l 198 (311)
..|||||.++|.++
T Consensus 50 ~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 50 KKLPGIGKSIAKKI 63 (68)
T ss_dssp CTSTTTTHHHHHHH
T ss_pred hhCCCCCHHHHHHH
Confidence 46899999998876
No 116
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=40.13 E-value=48 Score=28.03 Aligned_cols=55 Identities=22% Similarity=0.283 Sum_probs=38.6
Q ss_pred CHHHHHHHHHHHHHhC-----CceEeccC--cHHHHHHHHHHcCceEE------EecCCCccccccCC
Q 021529 83 TKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYA------VASEDMDSLTFGAP 137 (311)
Q Consensus 83 ~~~~~~~i~~lL~~~g-----i~~i~apg--EADa~iA~L~~~g~v~~------V~S~DsD~l~~~~~ 137 (311)
+..+++-+.+.|+..| |.++..|| |-=-.+..|++.|..|+ |+-++++-+-+.+.
T Consensus 25 t~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIaLG~VIrGeT~H~e~V~~ 92 (158)
T PRK12419 25 VDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVAAALVVDGGIYRHEFVAQ 92 (158)
T ss_pred HHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEEEEEcCCCchhHHHHH
Confidence 4567778888889988 67899999 77777778888664333 44555555555543
No 117
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=39.91 E-value=81 Score=26.16 Aligned_cols=33 Identities=9% Similarity=0.115 Sum_probs=19.0
Q ss_pred HhCCceEeccC-c--------HHHHHHHHHHcCceEEEecCCC
Q 021529 96 LMGVPVVEAPS-E--------AEAQCAALCKSGQVYAVASEDM 129 (311)
Q Consensus 96 ~~gi~~i~apg-E--------ADa~iA~L~~~g~v~~V~S~Ds 129 (311)
..|+=++..++ . +|..+.++|.+.-. +|+|+|.
T Consensus 69 ~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~~~a-~IVSND~ 110 (155)
T PF11977_consen 69 RKGIIYFTPSGSNYGSRSRNYDDRYILYYAEEKDA-VIVSNDR 110 (155)
T ss_dssp HTTSEEEE-EEEETTEEEEB-HHHHHHHHHHHTT--EEE-S--
T ss_pred HCCeEEEcCCCCCCCCcccccchHHHHHHHHHcCC-EEEeCch
Confidence 37775665555 5 88888888875434 4779984
No 118
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=38.92 E-value=58 Score=28.12 Aligned_cols=46 Identities=24% Similarity=0.369 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHhCCCCCCC------CCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 021529 166 NLTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENI 212 (311)
Q Consensus 166 gl~~~q~~d~~~L~G~D~~d~------ipgiG~ktA~~li~~-----~gsle~i~~~~ 212 (311)
.=..+.|+++.--+| --+.. +||||-|+..++|.+ |.|.++|-+.+
T Consensus 95 ~~~E~~FV~FfN~A~-PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 95 KENEERFVDFFNEAQ-PITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp HTTHHHHHHHH------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred HhChHHHHHHhhcCC-CChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 346789999999988 33332 599999999999986 67888876665
No 119
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=38.69 E-value=21 Score=30.76 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=14.3
Q ss_pred CCCCccHHHHHHHHHHcC
Q 021529 186 SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~g 203 (311)
.+||||+|||-=.+...|
T Consensus 119 ~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 119 ALPGFGKQKAKIFLALLG 136 (177)
T ss_pred cCCCCCHHHHHHHHHHHH
Confidence 479999999987776544
No 120
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=38.54 E-value=61 Score=26.84 Aligned_cols=42 Identities=29% Similarity=0.328 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHhCC-----ceEeccC--cHHHHHHHHHHcCceEEEe
Q 021529 84 KQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (311)
Q Consensus 84 ~~~~~~i~~lL~~~gi-----~~i~apg--EADa~iA~L~~~g~v~~V~ 125 (311)
..+++.+.+.|...|+ .++..|| |-=-.+..|.+.+..|+|+
T Consensus 19 ~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi 67 (144)
T PF00885_consen 19 DRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVI 67 (144)
T ss_dssp HHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEE
T ss_pred HHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEE
Confidence 5567778888888876 7899999 8888888898887655554
No 121
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=38.15 E-value=42 Score=25.93 Aligned_cols=41 Identities=17% Similarity=0.299 Sum_probs=33.5
Q ss_pred HHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHc
Q 021529 162 LEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQH 202 (311)
Q Consensus 162 ~~~~gl-~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~ 202 (311)
+..-|+ |-..+++.+...|.----.|||||++.|..+..=+
T Consensus 29 L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awL 70 (96)
T PF12482_consen 29 LAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWL 70 (96)
T ss_pred HHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHH
Confidence 445687 78999999999997777889999999998876533
No 122
>PRK10702 endonuclease III; Provisional
Probab=37.59 E-value=21 Score=31.58 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=12.0
Q ss_pred CCCccHHHHHHHHH
Q 021529 187 IRGIGGQTALKLIR 200 (311)
Q Consensus 187 ipgiG~ktA~~li~ 200 (311)
+||||+|||--++.
T Consensus 114 lpGVG~ktA~~ill 127 (211)
T PRK10702 114 LPGVGRKTANVVLN 127 (211)
T ss_pred CCcccHHHHHHHHH
Confidence 69999999988764
No 123
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=37.45 E-value=22 Score=29.30 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.5
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.|||||++||--++.
T Consensus 87 ~l~GIG~~tA~~~l~ 101 (158)
T cd00056 87 ALPGVGRKTANVVLL 101 (158)
T ss_pred cCCCCCHHHHHHHHH
Confidence 479999999887765
No 124
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=36.57 E-value=1.2e+02 Score=30.00 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=10.8
Q ss_pred ccHHHHHHHHHHc
Q 021529 190 IGGQTALKLIRQH 202 (311)
Q Consensus 190 iG~ktA~~li~~~ 202 (311)
.|...|.+.|+.|
T Consensus 201 gGe~~A~~~L~~F 213 (475)
T TIGR02766 201 PGWSNADKALTEF 213 (475)
T ss_pred CccHHHHHHHHHH
Confidence 4888899988887
No 125
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=36.38 E-value=32 Score=35.90 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=19.1
Q ss_pred CCCCccHHHHHHHH-HHcCCHHHHHH
Q 021529 186 SIRGIGGQTALKLI-RQHGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li-~~~gsle~i~~ 210 (311)
|||+||.++|..|. +.|++++++.+
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 46788888888888 77888887654
No 126
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=36.27 E-value=44 Score=27.49 Aligned_cols=41 Identities=17% Similarity=0.089 Sum_probs=29.9
Q ss_pred HHHHhCCceEeccCcHHHHHHHHHH-cCceEEEecCCCccccc
Q 021529 93 LLKLMGVPVVEAPSEAEAQCAALCK-SGQVYAVASEDMDSLTF 134 (311)
Q Consensus 93 lL~~~gi~~i~apgEADa~iA~L~~-~g~v~~V~S~DsD~l~~ 134 (311)
+....+.+++..-..||+.+-..+. +| +++|+|+|..+-+-
T Consensus 71 ~~~~er~~~~~~~~~aDe~i~~~a~~~~-~~iVaTnD~eLk~r 112 (136)
T COG1412 71 LKYAERLECIHKGRYADECLLEAALKHG-RYIVATNDKELKRR 112 (136)
T ss_pred HHHhhccCccccCCChHHHHHHHHHHcC-CEEEEeCCHHHHHH
Confidence 3445678888884489887777765 55 55799999998755
No 127
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=35.80 E-value=1.3e+02 Score=27.54 Aligned_cols=24 Identities=25% Similarity=0.444 Sum_probs=18.5
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHH
Q 021529 187 IRGIGGQTALKLIRQHGSIETILE 210 (311)
Q Consensus 187 ipgiG~ktA~~li~~~gsle~i~~ 210 (311)
+.|||+++|.++=+-|.+.-....
T Consensus 219 v~gig~k~A~~I~~~~~t~~~~~~ 242 (254)
T COG1948 219 VKGIGEKKAREIYRFLRTEYKLIE 242 (254)
T ss_pred hcCccHHHHHHHHHHHhchhhhhc
Confidence 589999999998887777554443
No 128
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=35.45 E-value=89 Score=23.58 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=18.5
Q ss_pred CccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCC
Q 021529 189 GIGGQTALKLIRQHGSIETILENINRERYQIPE 221 (311)
Q Consensus 189 giG~ktA~~li~~~gsle~i~~~~~~~~~~~~~ 221 (311)
||+++.|.+|.+.||+ +.++.+++-++.+-.
T Consensus 19 gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD--DAIEILKENPYRLIE 49 (94)
T ss_dssp T--HHHHHHHHHHH-T--THHHHHHH-STCCCB
T ss_pred CCCHHHHHHHHHHHhH--HHHHHHHHChHHHHH
Confidence 5788888888888886 455666655655444
No 129
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=35.18 E-value=62 Score=27.16 Aligned_cols=55 Identities=24% Similarity=0.285 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhC-----CceEeccC--cHHHHHHHHHHcCceEE------EecCCCccccccCCe
Q 021529 84 KQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYA------VASEDMDSLTFGAPR 138 (311)
Q Consensus 84 ~~~~~~i~~lL~~~g-----i~~i~apg--EADa~iA~L~~~g~v~~------V~S~DsD~l~~~~~~ 138 (311)
..+++-+.+.|+..| |.++..|| |-=-.+..|++.+..|+ |+-++++-+.+.+..
T Consensus 28 ~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~VIrG~T~H~e~V~~~ 95 (154)
T PRK00061 28 DALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAVIRGETPHFDYVANE 95 (154)
T ss_pred HHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeEEcCCCchHHHHHHH
Confidence 567788888999888 56788899 77677778887654443 344555555555443
No 130
>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=35.01 E-value=49 Score=24.79 Aligned_cols=26 Identities=27% Similarity=0.647 Sum_probs=19.8
Q ss_pred CCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 021529 187 IRGIGGQTALKLIRQ-----HGSIETILENI 212 (311)
Q Consensus 187 ipgiG~ktA~~li~~-----~gsle~i~~~~ 212 (311)
|+|||...|.+++.. |.|++++++.+
T Consensus 32 Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 32 IKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp STTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred cCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 689999999999975 56777777765
No 131
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=34.72 E-value=36 Score=22.79 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=31.0
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHH-hCCCCCCCCCCccHHHHHHHHHHcC
Q 021529 156 FEVAKILEELNLTMDQFIDLCIL-SGCDYCDSIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 156 ~~~~~v~~~~gl~~~q~~d~~~L-~G~D~~d~ipgiG~ktA~~li~~~g 203 (311)
++..++.+.+|+++..++..+.- .|-.....-..|....|..+...|+
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 55678899999999999999966 8855122224566667777666665
No 132
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=34.65 E-value=28 Score=30.20 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=15.8
Q ss_pred CCCCccHHHHHHHHHHcC
Q 021529 186 SIRGIGGQTALKLIRQHG 203 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~~g 203 (311)
.+||||+|+|.+++..+.
T Consensus 112 ~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 112 KVPGIGKKTAERIVLELK 129 (192)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 489999999999998764
No 133
>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=34.47 E-value=34 Score=31.75 Aligned_cols=24 Identities=33% Similarity=0.437 Sum_probs=20.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~ 209 (311)
.+||||+++|.+|.+. |.+++++.
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~ 27 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIA 27 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHH
Confidence 4799999999999998 88887764
No 134
>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=33.91 E-value=2.5e+02 Score=25.20 Aligned_cols=106 Identities=17% Similarity=0.160 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhCCce--EeccCcHH---HHHHHHHHcCceEEEecC--CCcccccc--CC-ee---EEEeecCCCCCc--
Q 021529 87 NDDCKRLLKLMGVPV--VEAPSEAE---AQCAALCKSGQVYAVASE--DMDSLTFG--AP-RF---LRHLMDPSSRKI-- 151 (311)
Q Consensus 87 ~~~i~~lL~~~gi~~--i~apgEAD---a~iA~L~~~g~v~~V~S~--DsD~l~~~--~~-~v---~~~l~~~~~~~~-- 151 (311)
...+.+.|+++|+.= +..||-.| ...++|...|+-+..+.+ ..|-..++ .+ .+ ++.+..++....
T Consensus 108 ~~A~~~AL~alg~~RIalvTPY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifi 187 (239)
T TIGR02990 108 SSAAVDGLAALGVRRISLLTPYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFL 187 (239)
T ss_pred HHHHHHHHHHcCCCEEEEECCCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEE
Confidence 456788888899884 67798333 456677778864322211 11111111 00 00 000000000000
Q ss_pred ---ccEEEe-HHHHHHHcCC---CHHHHHHHHHHhCCCCCCCCCCccH
Q 021529 152 ---PVMEFE-VAKILEELNL---TMDQFIDLCILSGCDYCDSIRGIGG 192 (311)
Q Consensus 152 ---~~~~~~-~~~v~~~~gl---~~~q~~d~~~L~G~D~~d~ipgiG~ 192 (311)
....++ .+.+.+.+|. +..|..-+.+|--++..+.+||.|-
T Consensus 188 sCTnLrt~~vi~~lE~~lGkPVlsSNqat~W~~Lr~~G~~~~~~g~G~ 235 (239)
T TIGR02990 188 SCTALRAATCAQRIEQAIGKPVVTSNQATAWRCLRLCGDPDMRPGYGR 235 (239)
T ss_pred eCCCchhHHHHHHHHHHHCCCEEEHHHHHHHHHHHHcCCCCCCCCCcC
Confidence 001111 2345567884 6888888888876677778898873
No 135
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=33.86 E-value=1.2e+02 Score=25.37 Aligned_cols=34 Identities=29% Similarity=0.457 Sum_probs=22.7
Q ss_pred HHHhhhhccCCHHHHHHHHHHHHHhCCceEeccC
Q 021529 73 EKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (311)
Q Consensus 73 ~~~~~~~~~v~~~~~~~i~~lL~~~gi~~i~apg 106 (311)
..|=.+...-...+......-|+.+|||++....
T Consensus 93 ~~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 93 DKFDEKVYKASKQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeCCC
Confidence 3343333333356777888899999999987754
No 136
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=33.47 E-value=38 Score=26.88 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=15.1
Q ss_pred CCCccHHHHHHHHHHcC
Q 021529 187 IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~~g 203 (311)
|.|||..+|..++.+.|
T Consensus 20 i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 20 IYGIGRTRARKILEKAG 36 (113)
T ss_pred eecccHHHHHHHHHHhC
Confidence 57999999999999877
No 137
>COG1647 Esterase/lipase [General function prediction only]
Probab=33.26 E-value=22 Score=31.94 Aligned_cols=57 Identities=18% Similarity=0.163 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccc-cCCeeE
Q 021529 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF-GAPRFL 140 (311)
Q Consensus 84 ~~~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~-~~~~v~ 140 (311)
...++.++.-++..-+|.++.-++.|..+-.=+.+-+-+-|.|+|+++..| ++.+||
T Consensus 167 ~~~i~~~~~~~~~I~~pt~vvq~~~D~mv~~~sA~~Iy~~v~s~~KeL~~~e~SgHVI 224 (243)
T COG1647 167 KKLIKDARRSLDKIYSPTLVVQGRQDEMVPAESANFIYDHVESDDKELKWLEGSGHVI 224 (243)
T ss_pred HHHHHHHHhhhhhcccchhheecccCCCCCHHHHHHHHHhccCCcceeEEEccCCcee
Confidence 456677888888889999999888886544333333344588999999988 455665
No 138
>cd04246 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulati
Probab=32.97 E-value=3.5e+02 Score=23.92 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHcCCceEEEEeCCCCch
Q 021529 12 HLQGMFTRTIRLLEAGMKPIYVFDGQPPDL 41 (311)
Q Consensus 12 a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~ 41 (311)
.+..++.-+..+.+.|.+|++|--|..+..
T Consensus 16 ~~~~~~~~i~~l~~~g~~~viV~sg~g~~~ 45 (239)
T cd04246 16 RIKRVAERIKKAVKKGYQVVVVVSAMGGTT 45 (239)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEECCCCchH
Confidence 456666666666667899999999765443
No 139
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=32.86 E-value=30 Score=28.25 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.9
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||++||--++.
T Consensus 76 ~l~GIG~~tA~~~l~ 90 (149)
T smart00478 76 KLPGVGRKTANAVLS 90 (149)
T ss_pred cCCCCcHHHHHHHHH
Confidence 589999999866554
No 140
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=32.84 E-value=78 Score=26.21 Aligned_cols=56 Identities=29% Similarity=0.220 Sum_probs=38.8
Q ss_pred CHHHHHHHHHHHHHhCC-----ceEeccC--cHHHHHHHHHHcCceEE------EecCCCccccccCCe
Q 021529 83 TKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYA------VASEDMDSLTFGAPR 138 (311)
Q Consensus 83 ~~~~~~~i~~lL~~~gi-----~~i~apg--EADa~iA~L~~~g~v~~------V~S~DsD~l~~~~~~ 138 (311)
+..+++-+.+.|...|+ .++..|| |-=-.+..|++.+..|+ |+-++++-+.+.+..
T Consensus 22 ~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIaLG~VIrGeT~H~e~V~~~ 90 (141)
T PLN02404 22 TKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVIRGDTTHYDAVANS 90 (141)
T ss_pred HHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEEEEEEeCCCchhHHHHHH
Confidence 35677788888888985 6788999 77777778887654333 455666666665543
No 141
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=32.75 E-value=29 Score=30.92 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=12.8
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||++||--++-
T Consensus 125 ~l~GIG~kTAd~iLl 139 (218)
T PRK13913 125 DQKGIGKESADAILC 139 (218)
T ss_pred cCCCccHHHHHHHHH
Confidence 479999999988775
No 142
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=31.89 E-value=1.6e+02 Score=29.34 Aligned_cols=33 Identities=12% Similarity=0.206 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHhCCceEeccC----cHHHHHHHHHHc
Q 021529 86 HNDDCKRLLKLMGVPVVEAPS----EAEAQCAALCKS 118 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~i~apg----EADa~iA~L~~~ 118 (311)
-+..+.+-|+.+|++.++.-| +..+++..|+++
T Consensus 58 sL~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~ 94 (472)
T PRK10674 58 QLNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQ 94 (472)
T ss_pred HHHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHH
Confidence 345556666667777666643 466666666653
No 143
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=31.50 E-value=37 Score=26.64 Aligned_cols=44 Identities=27% Similarity=0.456 Sum_probs=27.7
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC------------CCCccHHHHHHHHHHc
Q 021529 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDS------------IRGIGGQTALKLIRQH 202 (311)
Q Consensus 156 ~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~------------ipgiG~ktA~~li~~~ 202 (311)
+..+.+.+.+ ...|+|.-..+|.|-..- |+|.||.+|..|++..
T Consensus 15 l~~d~L~~~l---e~~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l 70 (104)
T PF14635_consen 15 LPKDKLLEAL---ERAFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKAL 70 (104)
T ss_dssp S-HHHHHHHH---HHHHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHH---HHHHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHH
Confidence 4445544444 456788888888775531 5799999999998864
No 144
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=31.19 E-value=57 Score=30.67 Aligned_cols=48 Identities=17% Similarity=0.289 Sum_probs=32.0
Q ss_pred EEEeHHHHHHHcCCCHHHHHHH--------------HHHhCCCCCC---C---------CCCccHHHHHHHHHH
Q 021529 154 MEFEVAKILEELNLTMDQFIDL--------------CILSGCDYCD---S---------IRGIGGQTALKLIRQ 201 (311)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~~d~--------------~~L~G~D~~d---~---------ipgiG~ktA~~li~~ 201 (311)
+.|..+.++..||+.++.+.+- ++|--.|.-+ | |||||+|+|..++..
T Consensus 276 RLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 276 RLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 4577888899999999887653 2222222222 1 488999988888764
No 145
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=31.16 E-value=1.9e+02 Score=24.09 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhCCceEeccCcHHHHHHHHHHc-CceEEEecCCCcccccc
Q 021529 86 HNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS-GQVYAVASEDMDSLTFG 135 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~i~apgEADa~iA~L~~~-g~v~~V~S~DsD~l~~~ 135 (311)
+...|..-|+..|---+-.-..-.++|+.||.+ |.+ |-.|-..+--+
T Consensus 25 IaakIfaGLR~~Gny~Lp~~aD~NeVLkALc~eAGw~---Ve~DGTtyr~~ 72 (150)
T PF05687_consen 25 IAAKIFAGLRAHGNYKLPKHADNNEVLKALCREAGWT---VEPDGTTYRKG 72 (150)
T ss_pred HHHHHHHHHHHhcCCCCCCcCCHHHHHHHHHHhCCEE---EccCCCeeccC
Confidence 334455666666654333333555777777774 543 34555544433
No 146
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.00 E-value=57 Score=28.32 Aligned_cols=46 Identities=22% Similarity=0.333 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHhCCCCCCC------CCCccHHHHHHHHHH-----cCCHHHHHHHHH
Q 021529 167 LTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENIN 213 (311)
Q Consensus 167 l~~~q~~d~~~L~G~D~~d~------ipgiG~ktA~~li~~-----~gsle~i~~~~~ 213 (311)
-..+.|+++.-=++ --+-. +||||.|++..+|.+ |.|.++|-+.+.
T Consensus 110 ~~E~rFV~fFN~A~-PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~Rv~ 166 (202)
T COG1491 110 ENEDRFVKFFNEAE-PITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKERVK 166 (202)
T ss_pred hhhhHHHHHhcccC-cchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHHHhc
Confidence 34566777765555 22221 499999999999986 678888776653
No 147
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=30.72 E-value=32 Score=29.67 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.5
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||++||--++.
T Consensus 110 ~l~GIG~ktA~~ill 124 (191)
T TIGR01083 110 KLPGVGRKTANVVLN 124 (191)
T ss_pred hCCCCcHHHHHHHHH
Confidence 479999999988764
No 148
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=30.71 E-value=44 Score=26.94 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 021529 187 IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~~g 203 (311)
|.|||+.+|..++.+.|
T Consensus 22 I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 22 IYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccHHHHHHHHHHhC
Confidence 57999999999999877
No 149
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=30.68 E-value=52 Score=25.13 Aligned_cols=38 Identities=21% Similarity=0.195 Sum_probs=26.2
Q ss_pred hCCceEeccCcHHHHHHHHHHcCceEEEecCCCccccc
Q 021529 97 MGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (311)
Q Consensus 97 ~gi~~i~apgEADa~iA~L~~~g~v~~V~S~DsD~l~~ 134 (311)
........+..||+.+..++..+-..+|+|.|.++-.-
T Consensus 42 ~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~ 79 (101)
T PF04900_consen 42 RKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRR 79 (101)
T ss_pred hcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHH
Confidence 33333333668999999999654436789999988643
No 150
>PRK00124 hypothetical protein; Validated
Probab=30.35 E-value=35 Score=28.63 Aligned_cols=91 Identities=13% Similarity=0.139 Sum_probs=51.6
Q ss_pred cHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC
Q 021529 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (311)
Q Consensus 107 EADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ 186 (311)
.||..|+.+++.| |+|+|.|.=+--..-.+-...+...| ..|+.+.+-..+.. +...-++- =.| -.+.|
T Consensus 56 ~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~Kga~vl~prG------~~yt~~nI~~~L~~-R~~~~~lR-~~G-~~t~G 124 (151)
T PRK00124 56 AADNEIVQLAEKG--DIVITQDYGLAALALEKGAIVLNPRG------YIYTNDNIDQLLAM-RDLMATLR-RSG-IRTGG 124 (151)
T ss_pred hHHHHHHHhCCCC--CEEEeCCHHHHHHHHHCCCEEECCCC------cCCCHHHHHHHHHH-HHHHHHHH-HcC-CCCCC
Confidence 8999999999998 56899987776554333222233222 45777776555422 22222221 224 24445
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHH
Q 021529 187 IRGIGGQTALKLIRQHGSIETILEN 211 (311)
Q Consensus 187 ipgiG~ktA~~li~~~gsle~i~~~ 211 (311)
=+..+.+.-....+. ++.++..
T Consensus 125 p~~~~~~Dr~~F~~~---L~~~l~~ 146 (151)
T PRK00124 125 PKPFTQEDRSRFEAE---LDKLIRR 146 (151)
T ss_pred CCCCCHHHHHHHHHH---HHHHHHH
Confidence 556777766555553 5666654
No 151
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=30.15 E-value=46 Score=26.82 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 021529 187 IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~~g 203 (311)
|.|||+.+|..++.+.|
T Consensus 22 i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 22 IYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccHHHHHHHHHHcC
Confidence 57999999999999876
No 152
>PRK00254 ski2-like helicase; Provisional
Probab=29.91 E-value=42 Score=35.21 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETILEN 211 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~~~ 211 (311)
.|||||+++|.+|++. |+|+++|.+.
T Consensus 649 ~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 649 RLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred cCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 3699999999999999 9999988654
No 153
>cd04261 AAK_AKii-LysC-BS AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase isoenzyme type, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In this organism and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and
Probab=29.70 E-value=4e+02 Score=23.57 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHcCCceEEEEeCCCCch
Q 021529 12 HLQGMFTRTIRLLEAGMKPIYVFDGQPPDL 41 (311)
Q Consensus 12 a~~g~~~~l~~ll~~~i~Pv~VFDG~~~~~ 41 (311)
.+..++..+..+.+.|.+|++|--|....-
T Consensus 16 ~~~~~~~~i~~l~~~g~~~vvV~sg~g~~~ 45 (239)
T cd04261 16 RIKRVAERIKKRKKKGNQVVVVVSAMGGTT 45 (239)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEECCCCchh
Confidence 455666666666667899999999865443
No 154
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=29.39 E-value=39 Score=27.18 Aligned_cols=29 Identities=17% Similarity=0.157 Sum_probs=18.9
Q ss_pred cCCHHHHHHHHHHHHHhCCceEeccCcHH
Q 021529 81 KVTKQHNDDCKRLLKLMGVPVVEAPSEAE 109 (311)
Q Consensus 81 ~v~~~~~~~i~~lL~~~gi~~i~apgEAD 109 (311)
.+|.+.+..+++.+..-+=-.|...||=|
T Consensus 45 ~It~el~~ai~~a~~~~~~~~I~V~GEED 73 (121)
T PF04019_consen 45 TITEELIEAIKKALESGKPVVIFVDGEED 73 (121)
T ss_pred cccHHHHHHHHHHHhCCCCEEEEEeChHH
Confidence 45677777788777654444566677655
No 155
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=28.12 E-value=40 Score=27.47 Aligned_cols=82 Identities=13% Similarity=0.129 Sum_probs=44.4
Q ss_pred cHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC
Q 021529 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (311)
Q Consensus 107 EADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ 186 (311)
.||..|+..++.|.+ |||.|-=+-.+.-.+-...+...| ..|+.+.+-+.+..- . +-.=.--.| -+..|
T Consensus 40 aaD~~I~~~~~~gDi--VITqDigLA~~~l~Kga~vl~~rG------~~yt~~nI~~~L~~R-~-~~~~lR~~G-~~~~g 108 (130)
T PF02639_consen 40 AADFYIVNHAKPGDI--VITQDIGLASLLLAKGAYVLNPRG------KEYTKENIDELLAMR-H-LMAKLRRAG-KRTKG 108 (130)
T ss_pred hHHHHHHHcCCCCCE--EEECCHHHHHHHHHCCCEEECCCC------CCCCHHHHHHHHHHH-H-HHHHHHHhC-CCCCC
Confidence 889999998888865 789988776654433222333322 357777665544221 1 111111124 34445
Q ss_pred CCCccHHHHHHHH
Q 021529 187 IRGIGGQTALKLI 199 (311)
Q Consensus 187 ipgiG~ktA~~li 199 (311)
-+..+++.=....
T Consensus 109 pk~~~~~d~~~F~ 121 (130)
T PF02639_consen 109 PKKFTKKDRQRFA 121 (130)
T ss_pred CCCCCHHHHHHHH
Confidence 5566665544433
No 156
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=27.99 E-value=59 Score=25.67 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=21.9
Q ss_pred cHHHHHHHHHHcCceEEEecCCCccccccCCe
Q 021529 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (311)
Q Consensus 107 EADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~ 138 (311)
-+|+.++..+...-+ .++|.|.|+-.++.-.
T Consensus 105 ~~D~~i~a~A~~~~~-~lvT~D~~f~~~~~~~ 135 (142)
T TIGR00028 105 VTDAHLAALAREHGA-ELVTFDRGFARFAGIR 135 (142)
T ss_pred chHHHHHHHHHHcCC-EEEecCCCccccCCCe
Confidence 589988888775434 5779999976555433
No 157
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=27.61 E-value=49 Score=23.17 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=11.6
Q ss_pred CCCCccHHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ 201 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~ 201 (311)
.+||||++.|.++++.
T Consensus 18 ~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 18 ALPGIGPKQAKAIVEY 33 (65)
T ss_dssp TSTT--HHHHHHHHHH
T ss_pred HcCCCCHHHHHHHHHH
Confidence 4699999999999873
No 158
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=27.29 E-value=50 Score=27.31 Aligned_cols=32 Identities=16% Similarity=0.166 Sum_probs=23.8
Q ss_pred cHHHHHHHHHHcCceEEEecCCCccccccCCe
Q 021529 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (311)
Q Consensus 107 EADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~ 138 (311)
+=|.-.-.++-.|.+++++|+|+|+|.+-..+
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~~n 122 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRDEN 122 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheecccC
Confidence 44555555677788888999999999876543
No 159
>PRK13910 DNA glycosylase MutY; Provisional
Probab=27.11 E-value=39 Score=31.46 Aligned_cols=18 Identities=28% Similarity=0.386 Sum_probs=14.1
Q ss_pred CCCCccHHHHHHHHH-HcC
Q 021529 186 SIRGIGGQTALKLIR-QHG 203 (311)
Q Consensus 186 ~ipgiG~ktA~~li~-~~g 203 (311)
.+||||++||--++. .|+
T Consensus 76 ~LpGIG~kTA~aIl~~af~ 94 (289)
T PRK13910 76 KLPGIGAYTANAILCFGFR 94 (289)
T ss_pred hCCCCCHHHHHHHHHHHCC
Confidence 469999999988776 344
No 160
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=26.39 E-value=47 Score=29.44 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=13.8
Q ss_pred CCCccHHHHHHHHHH-cC
Q 021529 187 IRGIGGQTALKLIRQ-HG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~-~g 203 (311)
+||||.|||-=.|.. ||
T Consensus 114 LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 114 LPGVGRKTANVVLSFAFG 131 (211)
T ss_pred CCCcchHHHHHHHHhhcC
Confidence 489999999888775 55
No 161
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=24.94 E-value=46 Score=30.72 Aligned_cols=15 Identities=27% Similarity=0.492 Sum_probs=12.2
Q ss_pred CCCCccHHHHHHHHH
Q 021529 186 SIRGIGGQTALKLIR 200 (311)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (311)
.+||||++||--++.
T Consensus 109 ~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 109 ALPGVGRYTAGAILS 123 (275)
T ss_pred hCCCCCHHHHHHHHH
Confidence 379999999977665
No 162
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.87 E-value=61 Score=26.92 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.7
Q ss_pred CCCccHHHHHHHHHHcC
Q 021529 187 IRGIGGQTALKLIRQHG 203 (311)
Q Consensus 187 ipgiG~ktA~~li~~~g 203 (311)
|.|||+.+|..++++.|
T Consensus 26 I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 26 IKGIGRRFARAIARKLG 42 (144)
T ss_pred eeccCHHHHHHHHHHcC
Confidence 57999999999998876
No 163
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=24.13 E-value=46 Score=31.37 Aligned_cols=25 Identities=32% Similarity=0.458 Sum_probs=20.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~~ 210 (311)
||-|||.+||.++.++ |.+++++-+
T Consensus 101 nifGvG~ktA~~Wy~~GfrTled~Rk 126 (353)
T KOG2534|consen 101 NIFGVGLKTAEKWYREGFRTLEDVRK 126 (353)
T ss_pred HHhccCHHHHHHHHHhhhhHHHHHHh
Confidence 5779999999999885 678877653
No 164
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=24.00 E-value=87 Score=21.56 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=23.3
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhCCC
Q 021529 155 EFEVAKILEELNLTMDQFIDLCILSGCD 182 (311)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~~d~~~L~G~D 182 (311)
.+......++||++++|+...-.-+|++
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~AV~~vG~~ 47 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLREAVRAVGNS 47 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHCcC
Confidence 3556777889999999999999999944
No 165
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=23.62 E-value=2.4e+02 Score=23.90 Aligned_cols=47 Identities=9% Similarity=0.227 Sum_probs=33.3
Q ss_pred HHHHHHHHHHcCCceEEEEeCCCCchhhHHHHHHHhchhccHHHHHHHHHcCCHHHHHHHhhhhccCCHHHHHHHHHHHH
Q 021529 16 MFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLK 95 (311)
Q Consensus 16 ~~~~l~~ll~~~i~Pv~VFDG~~~~~K~~~~~~yk~~R~~~~~~l~~~~~~g~~~~~~~~~~~~~~v~~~~~~~i~~lL~ 95 (311)
--..+..+++..-+|++++.+..... ...+.+.++.+
T Consensus 16 ~p~~aa~lLk~AKRPvIivG~ga~~~-------------------------------------------~a~e~l~~laE 52 (162)
T TIGR00315 16 SPKLVAMMIKRAKRPLLIVGPENLED-------------------------------------------EEKELIVKFIE 52 (162)
T ss_pred CHHHHHHHHHcCCCcEEEECCCcCcc-------------------------------------------cHHHHHHHHHH
Confidence 34567777876789999988765210 11245788888
Q ss_pred HhCCceEecc
Q 021529 96 LMGVPVVEAP 105 (311)
Q Consensus 96 ~~gi~~i~ap 105 (311)
.+|+|++..+
T Consensus 53 klgiPVvtT~ 62 (162)
T TIGR00315 53 KFDLPVVATA 62 (162)
T ss_pred HHCCCEEEcC
Confidence 8999999887
No 166
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=23.57 E-value=1.7e+02 Score=30.54 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=20.1
Q ss_pred CCCCCCccHHHHHHHHHHc--CCHHHHH
Q 021529 184 CDSIRGIGGQTALKLIRQH--GSIETIL 209 (311)
Q Consensus 184 ~d~ipgiG~ktA~~li~~~--gsle~i~ 209 (311)
+-+|||+|++++.+|.... .++++++
T Consensus 447 al~I~GLG~k~i~~L~~~g~I~~i~DL~ 474 (665)
T PRK07956 447 AMDIDGLGEKIIEQLFEKGLIHDPADLF 474 (665)
T ss_pred ccCCCCcCHHHHHHHHHcCCCCCHHHHH
Confidence 3468999999999998864 3677666
No 167
>cd05212 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional
Probab=23.32 E-value=1.9e+02 Score=23.77 Aligned_cols=41 Identities=22% Similarity=0.185 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhCCce------EeccC--cHHHHHHHHHHcCceEEEec
Q 021529 86 HNDDCKRLLKLMGVPV------VEAPS--EAEAQCAALCKSGQVYAVAS 126 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~------i~apg--EADa~iA~L~~~g~v~~V~S 126 (311)
...-+.++|+..|+++ ++-.. -+......|.++|....++.
T Consensus 11 t~~a~~~ll~~~~~~~~gk~v~VvGrs~~vG~pla~lL~~~gatV~~~~ 59 (140)
T cd05212 11 VAKAVKELLNKEGVRLDGKKVLVVGRSGIVGAPLQCLLQRDGATVYSCD 59 (140)
T ss_pred HHHHHHHHHHHcCCCCCCCEEEEECCCchHHHHHHHHHHHCCCEEEEeC
Confidence 4456778888887764 22222 45555566666776554554
No 168
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=22.51 E-value=1e+02 Score=24.00 Aligned_cols=36 Identities=19% Similarity=0.228 Sum_probs=27.0
Q ss_pred HHHHHhCCc-eEeccC--cHHHHHHHHHHcCceEEEecC
Q 021529 92 RLLKLMGVP-VVEAPS--EAEAQCAALCKSGQVYAVASE 127 (311)
Q Consensus 92 ~lL~~~gi~-~i~apg--EADa~iA~L~~~g~v~~V~S~ 127 (311)
--++..||. ++.+.. ||.+....|+..++-.+++|+
T Consensus 15 lGFrlaGi~~v~~~~~~e~~~~~~~~l~~~~~gII~iTE 53 (104)
T PRK01189 15 LGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSE 53 (104)
T ss_pred HHHHHcCCceEEEcCCHHHHHHHHHHHhcCCeEEEEEEH
Confidence 356889996 666644 777888888888887667776
No 169
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=22.47 E-value=2e+02 Score=24.85 Aligned_cols=43 Identities=37% Similarity=0.449 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhCCceEeccCc--HHHHHHHHHHcCceEEEecCC
Q 021529 86 HNDDCKRLLKLMGVPVVEAPSE--AEAQCAALCKSGQVYAVASED 128 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~i~apgE--ADa~iA~L~~~g~v~~V~S~D 128 (311)
.-+.++.++.+.||++|..||| -.|.-..+..-|--..|+|.|
T Consensus 51 ~tp~t~~~~~~~gv~vi~tpG~GYv~Dl~~al~~l~~P~lvvsaD 95 (177)
T COG2266 51 HTPKTKEYLESVGVKVIETPGEGYVEDLRFALESLGTPILVVSAD 95 (177)
T ss_pred CCHhHHHHHHhcCceEEEcCCCChHHHHHHHHHhcCCceEEEecc
Confidence 3467889999999999999975 334444455556444566654
No 170
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=21.74 E-value=77 Score=29.54 Aligned_cols=24 Identities=33% Similarity=0.466 Sum_probs=17.3
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 021529 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (311)
Q Consensus 186 ~ipgiG~ktA~~li~~-~gsle~i~ 209 (311)
.+||||+++|.+|.+. +.+++++.
T Consensus 10 ~l~gIg~~~a~~L~~~Gi~t~~dl~ 34 (317)
T PRK04301 10 DLPGVGPATAEKLREAGYDTVEAIA 34 (317)
T ss_pred hcCCCCHHHHHHHHHcCCCCHHHHH
Confidence 4688888888887775 56666654
No 171
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=21.68 E-value=57 Score=30.18 Aligned_cols=18 Identities=33% Similarity=0.327 Sum_probs=13.0
Q ss_pred CCCccHHHHHHHH-HHcCC
Q 021529 187 IRGIGGQTALKLI-RQHGS 204 (311)
Q Consensus 187 ipgiG~ktA~~li-~~~gs 204 (311)
|||||++||--++ ..+|.
T Consensus 212 LpGIGpwTA~~vllr~lg~ 230 (283)
T PRK10308 212 FPGIGRWTANYFALRGWQA 230 (283)
T ss_pred CCCcCHHHHHHHHHHhCCC
Confidence 6999999986554 44554
No 172
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=21.58 E-value=1.6e+02 Score=26.21 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCceEec--cCcHHHHH----HHHHHcCceEEEecCCCc
Q 021529 88 DDCKRLLKLMGVPVVEA--PSEAEAQC----AALCKSGQVYAVASEDMD 130 (311)
Q Consensus 88 ~~i~~lL~~~gi~~i~a--pgEADa~i----A~L~~~g~v~~V~S~DsD 130 (311)
+.+....+++|||.+.. +++-++.. ..|.+.| +.+|+++|-+
T Consensus 48 ~~~~~qA~algiPl~~~~~~~~~e~~~~~l~~~l~~~g-v~~vv~GdI~ 95 (222)
T TIGR00289 48 HLTDLVAEAVGIPLIKLYTSGEEEKEVEDLAGQLGELD-VEALCIGAIE 95 (222)
T ss_pred HHHHHHHHHcCCCeEEEEcCCchhHHHHHHHHHHHHcC-CCEEEECccc
Confidence 55677888999997644 45434333 3333345 6678888655
No 173
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=21.52 E-value=1.3e+02 Score=28.53 Aligned_cols=19 Identities=0% Similarity=-0.050 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHhCCceEec
Q 021529 86 HNDDCKRLLKLMGVPVVEA 104 (311)
Q Consensus 86 ~~~~i~~lL~~~gi~~i~a 104 (311)
.+..+.+.+..+||+++..
T Consensus 51 ~l~~il~~c~~lGIk~lTl 69 (322)
T PTZ00349 51 ALIQIIEICIKLKIKILSV 69 (322)
T ss_pred HHHHHHHHHHHcCCCEEEE
Confidence 3455677777888888764
No 174
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=21.44 E-value=2.6e+02 Score=20.10 Aligned_cols=48 Identities=27% Similarity=0.459 Sum_probs=32.5
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC-CHHHHHHH
Q 021529 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG-SIETILEN 211 (311)
Q Consensus 156 ~~~~~v~~~~gl~~~q~~d~~~L~G~D~~d~ipgiG~ktA~~li~~~g-sle~i~~~ 211 (311)
++-+++.+..|+++.-+. ++=-| +|.|++ ..|.++.+.|+ ++|+|+..
T Consensus 15 ltQ~elA~~vgVsRQTi~--~iEkg-ky~Psl-----~La~kia~~f~~~iedIF~~ 63 (68)
T COG1476 15 LTQEELAKLVGVSRQTII--AIEKG-KYNPSL-----ELALKIARVFGKTIEDIFQL 63 (68)
T ss_pred cCHHHHHHHcCcCHHHHH--HHHcC-CCCchH-----HHHHHHHHHhCCCHHHHHhh
Confidence 445566666777776653 44556 888774 48899998887 67777643
No 175
>PRK10736 hypothetical protein; Provisional
Probab=21.30 E-value=75 Score=30.76 Aligned_cols=21 Identities=5% Similarity=0.172 Sum_probs=19.0
Q ss_pred CCCccHHHHHHHHHHcCCHHH
Q 021529 187 IRGIGGQTALKLIRQHGSIET 207 (311)
Q Consensus 187 ipgiG~ktA~~li~~~gsle~ 207 (311)
+||||+++..+|+..||+.++
T Consensus 13 ~~giG~~~~~~L~~~~~~~~~ 33 (374)
T PRK10736 13 VSSLYGDKMVRIAHRLLAQSQ 33 (374)
T ss_pred CCCCCHHHHHHHHHHhcChhh
Confidence 589999999999999998774
No 176
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=21.16 E-value=1.2e+02 Score=20.95 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=20.2
Q ss_pred CCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 021529 247 KWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (311)
Q Consensus 247 ~~~~~d~~~l~~~~~~~~~f~~~~v~~~~~~~~ 279 (311)
.+..+|.+-+..|. .+||..++|...++++.
T Consensus 4 ~~~Gi~~~lVd~F~--~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 4 ALYGIDKDLVDQFE--NMGFERDKVVEVLRRLG 34 (55)
T ss_dssp S----SHHHHHHHH--HHT--HHHHHHHHHHS-
T ss_pred HHcCCCHHHHHHHH--HcCCcHHHHHHHHHHhC
Confidence 44567888888886 78999999999998864
No 177
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.07 E-value=87 Score=26.22 Aligned_cols=57 Identities=19% Similarity=0.165 Sum_probs=34.2
Q ss_pred eEeccC--cHHHHHHHHHHcCceEEEecCCCccccccCCeeEEEeecCCCCCcccEEEeHHHHHHHc
Q 021529 101 VVEAPS--EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEEL 165 (311)
Q Consensus 101 ~i~apg--EADa~iA~L~~~g~v~~V~S~DsD~l~~~~~~v~~~l~~~~~~~~~~~~~~~~~v~~~~ 165 (311)
+++++| -||+-|+.+++.|.+ |+|.|-=+--....+....+...| +.|+.+.+-+.+
T Consensus 47 v~V~~g~DaaD~~Iv~~a~~gDl--VVT~Di~LA~~ll~kg~~v~~prG------r~y~~~nI~~~L 105 (150)
T COG1671 47 VVVDAGFDAADDWIVNLAEKGDL--VVTADIPLASLLLDKGAAVLNPRG------RLYTEENIGERL 105 (150)
T ss_pred EEecCCcchHHHHHHHhCCCCCE--EEECchHHHHHHHhcCCEEECCCC------cccCHhHHHHHH
Confidence 345566 788999999999875 678876554443222121233222 457776665444
No 178
>PRK10880 adenine DNA glycosylase; Provisional
Probab=20.46 E-value=66 Score=30.80 Aligned_cols=18 Identities=28% Similarity=0.536 Sum_probs=13.9
Q ss_pred CCCCccHHHHHHHHH-HcC
Q 021529 186 SIRGIGGQTALKLIR-QHG 203 (311)
Q Consensus 186 ~ipgiG~ktA~~li~-~~g 203 (311)
.+||||++||--++. .|+
T Consensus 113 ~LpGIG~~TA~aIl~~af~ 131 (350)
T PRK10880 113 ALPGVGRSTAGAILSLSLG 131 (350)
T ss_pred cCCCccHHHHHHHHHHHCC
Confidence 369999999988776 344
No 179
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=20.29 E-value=1.2e+02 Score=25.01 Aligned_cols=35 Identities=23% Similarity=0.297 Sum_probs=21.1
Q ss_pred HHHHHHh-CCceEeccCc---HHHHHHHHHHcCceEEEe
Q 021529 91 KRLLKLM-GVPVVEAPSE---AEAQCAALCKSGQVYAVA 125 (311)
Q Consensus 91 ~~lL~~~-gi~~i~apgE---ADa~iA~L~~~g~v~~V~ 125 (311)
-++|+.. |+++-....| ++.+++.+.++|.++.|+
T Consensus 42 a~~L~~~~Gi~v~~vi~~~~gg~~~i~~~I~~g~i~lVI 80 (142)
T PRK05234 42 GGLIQEATGLDVTRLLSGPLGGDQQIGALIAEGKIDMLI 80 (142)
T ss_pred HHHHHhccCCeeEEEEcCCCCCchhHHHHHHcCceeEEE
Confidence 4445556 7765433333 567777777777766654
No 180
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.06 E-value=2.6e+02 Score=20.97 Aligned_cols=35 Identities=23% Similarity=0.248 Sum_probs=27.4
Q ss_pred cCCHHHHHHHHHHHHHhCCceEeccC-cHHHHHHHH
Q 021529 81 KVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAAL 115 (311)
Q Consensus 81 ~v~~~~~~~i~~lL~~~gi~~i~apg-EADa~iA~L 115 (311)
.+++.....+++.++..|+|++.+.. -..+....|
T Consensus 58 ~vsH~~~~~vk~~akk~~ip~~~~~~~~~~~l~~~l 93 (97)
T PF10087_consen 58 YVSHNAMWKVKKAAKKYGIPIIYSRSRGVSSLERAL 93 (97)
T ss_pred CcChHHHHHHHHHHHHcCCcEEEECCCCHHHHHHHH
Confidence 45688899999999999999999985 554444443
Done!