Query 020008
Match_columns 332
No_of_seqs 281 out of 1741
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 06:17:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020008hhsearch_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 2.5E-77 5.4E-82 582.7 36.5 297 2-299 55-351 (393)
2 PRK03980 flap endonuclease-1; 100.0 2.7E-75 5.9E-80 548.6 32.0 282 3-294 1-292 (292)
3 TIGR03674 fen_arch flap struct 100.0 1E-68 2.2E-73 514.6 31.4 283 2-294 47-338 (338)
4 KOG2519 5'-3' exonuclease [Rep 100.0 1.3E-64 2.9E-69 486.1 24.6 298 3-300 50-348 (449)
5 cd00128 XPG Xeroderma pigmento 100.0 3.2E-59 6.8E-64 446.3 29.3 268 5-276 48-315 (316)
6 TIGR00600 rad2 DNA excision re 100.0 1E-49 2.2E-54 419.9 22.4 218 76-298 763-1006(1034)
7 PRK14976 5'-3' exonuclease; Pr 100.0 2.2E-44 4.8E-49 337.7 22.3 239 2-267 28-281 (281)
8 smart00475 53EXOc 5'-3' exonuc 100.0 4.7E-44 1E-48 331.8 20.1 216 2-243 22-247 (259)
9 KOG2518 5'-3' exonuclease [Rep 100.0 2E-43 4.4E-48 343.2 20.7 234 5-242 47-288 (556)
10 TIGR00593 pola DNA polymerase 100.0 4.3E-41 9.3E-46 356.0 22.8 238 2-267 22-276 (887)
11 cd00008 53EXOc 5'-3' exonuclea 100.0 5.7E-41 1.2E-45 308.6 19.3 185 3-216 23-217 (240)
12 COG0258 Exo 5'-3' exonuclease 100.0 6.2E-40 1.3E-44 312.6 22.6 262 2-294 33-309 (310)
13 PRK05755 DNA polymerase I; Pro 100.0 1.2E-39 2.6E-44 347.9 22.9 239 2-268 24-278 (880)
14 PRK09482 flap endonuclease-lik 100.0 6.5E-38 1.4E-42 288.8 19.1 208 4-243 23-243 (256)
15 KOG2520 5'-3' exonuclease [Rep 100.0 1.7E-37 3.6E-42 318.4 15.9 212 79-295 460-700 (815)
16 PHA00439 exonuclease 99.9 1.7E-26 3.6E-31 214.8 14.9 210 2-272 34-260 (286)
17 PF00867 XPG_I: XPG I-region; 99.9 3E-26 6.5E-31 181.5 6.4 88 95-182 1-94 (94)
18 PHA02567 rnh RnaseH; Provision 99.9 4.6E-23 9.9E-28 192.7 16.3 161 2-191 33-206 (304)
19 PF02739 5_3_exonuc_N: 5'-3' e 99.9 1.9E-22 4.2E-27 176.2 12.5 138 2-165 24-169 (169)
20 smart00484 XPGI Xeroderma pigm 99.8 1.5E-20 3.2E-25 141.5 7.7 72 96-167 2-73 (73)
21 cd00080 HhH2_motif Helix-hairp 99.6 1.8E-15 3.9E-20 114.8 6.2 52 164-215 2-55 (75)
22 PF01367 5_3_exonuc: 5'-3' exo 99.4 1.7E-15 3.7E-20 121.0 -7.0 91 167-258 1-101 (101)
23 smart00279 HhH2 Helix-hairpin- 99.2 7.1E-12 1.5E-16 81.3 3.9 33 169-202 1-36 (36)
24 PF00752 XPG_N: XPG N-terminal 98.9 1.3E-09 2.7E-14 87.1 4.6 47 10-56 55-101 (101)
25 smart00485 XPGN Xeroderma pigm 98.9 2.8E-09 6.1E-14 84.9 5.4 49 8-56 50-99 (99)
26 PF12813 XPG_I_2: XPG domain c 98.8 8.8E-09 1.9E-13 95.3 8.4 89 86-177 5-107 (246)
27 TIGR00600 rad2 DNA excision re 98.7 2.7E-08 5.9E-13 106.9 6.6 68 9-76 51-122 (1034)
28 COG5366 Protein involved in pr 97.1 0.00054 1.2E-08 67.4 4.0 102 88-191 132-234 (531)
29 PF03159 XRN_N: XRN 5'-3' exon 96.7 0.0099 2.2E-07 54.8 8.9 38 98-135 172-222 (237)
30 COG5049 XRN1 5'-3' exonuclease 95.8 0.12 2.6E-06 53.8 12.2 118 75-192 141-328 (953)
31 KOG2045 5'-3' exonuclease XRN1 95.8 0.12 2.5E-06 55.4 12.3 185 14-199 62-307 (1493)
32 TIGR00084 ruvA Holliday juncti 95.8 0.06 1.3E-06 48.1 8.9 112 159-279 54-172 (191)
33 PF12826 HHH_2: Helix-hairpin- 95.7 0.0081 1.8E-07 43.9 2.4 27 185-211 6-32 (64)
34 PF04599 Pox_G5: Poxvirus G5 p 95.6 0.29 6.3E-06 48.4 13.6 110 90-214 148-274 (425)
35 KOG2044 5'-3' exonuclease HKE1 94.7 0.84 1.8E-05 48.4 14.2 187 12-199 80-360 (931)
36 PHA03065 Hypothetical protein; 94.6 0.67 1.4E-05 45.8 12.6 110 90-214 150-276 (438)
37 PRK00116 ruvA Holliday junctio 94.5 0.14 3.1E-06 45.6 7.3 91 186-279 77-174 (192)
38 PRK14671 uvrC excinuclease ABC 93.1 0.67 1.4E-05 48.7 10.3 26 185-210 572-597 (621)
39 PRK14605 ruvA Holliday junctio 93.0 0.3 6.4E-06 43.7 6.5 111 158-279 54-173 (194)
40 COG0632 RuvA Holliday junction 91.3 2.8 6.1E-05 37.7 10.7 118 155-281 51-183 (201)
41 PRK14600 ruvA Holliday junctio 91.2 1.3 2.9E-05 39.3 8.5 110 158-279 54-170 (186)
42 PF14520 HHH_5: Helix-hairpin- 91.0 0.21 4.5E-06 35.7 2.7 25 186-210 9-34 (60)
43 PRK14667 uvrC excinuclease ABC 91.0 0.17 3.7E-06 52.4 3.1 29 183-211 515-543 (567)
44 TIGR00194 uvrC excinuclease AB 90.9 0.17 3.7E-06 52.5 3.0 30 182-211 541-570 (574)
45 PRK13901 ruvA Holliday junctio 90.8 1 2.2E-05 40.4 7.4 109 159-279 54-169 (196)
46 PF10391 DNA_pol_lambd_f: Fing 90.8 0.22 4.7E-06 34.9 2.5 25 186-210 6-31 (52)
47 PRK14669 uvrC excinuclease ABC 90.7 0.21 4.5E-06 52.4 3.3 28 183-210 553-580 (624)
48 PRK14670 uvrC excinuclease ABC 90.6 0.2 4.3E-06 52.0 3.1 29 183-211 515-543 (574)
49 PRK14604 ruvA Holliday junctio 90.4 1.6 3.4E-05 39.1 8.3 109 160-279 56-174 (195)
50 PF00633 HHH: Helix-hairpin-he 90.4 0.24 5.1E-06 30.6 2.1 15 186-200 15-29 (30)
51 PRK14601 ruvA Holliday junctio 89.7 1.1 2.4E-05 39.7 6.6 105 159-278 55-166 (183)
52 PRK14603 ruvA Holliday junctio 89.3 1.8 4E-05 38.8 7.8 111 160-279 55-177 (197)
53 COG0322 UvrC Nuclease subunit 89.1 0.99 2.1E-05 46.9 6.7 29 183-211 531-559 (581)
54 PRK14602 ruvA Holliday junctio 88.5 0.72 1.6E-05 41.5 4.7 112 159-279 56-180 (203)
55 PRK14672 uvrC excinuclease ABC 88.2 0.38 8.3E-06 50.6 3.1 30 182-211 608-637 (691)
56 PRK14606 ruvA Holliday junctio 86.3 0.92 2E-05 40.4 4.0 108 158-279 54-168 (188)
57 PF02371 Transposase_20: Trans 85.1 0.76 1.7E-05 35.4 2.5 26 182-207 2-27 (87)
58 PRK00558 uvrC excinuclease ABC 84.9 0.68 1.5E-05 48.4 2.9 27 185-211 546-572 (598)
59 PRK14668 uvrC excinuclease ABC 84.6 0.76 1.6E-05 47.8 3.0 29 183-211 526-554 (577)
60 PRK12766 50S ribosomal protein 84.1 0.82 1.8E-05 41.8 2.7 28 184-211 5-33 (232)
61 PRK14666 uvrC excinuclease ABC 83.9 0.85 1.8E-05 48.2 3.0 29 183-211 638-666 (694)
62 smart00278 HhH1 Helix-hairpin- 83.6 0.96 2.1E-05 26.7 2.0 17 185-201 4-20 (26)
63 PRK13766 Hef nuclease; Provisi 83.4 18 0.0004 38.8 13.0 25 186-210 719-743 (773)
64 PF05991 NYN_YacP: YacP-like N 80.9 5.8 0.00013 34.4 6.7 38 97-134 66-109 (166)
65 COG1948 MUS81 ERCC4-type nucle 80.5 1.5 3.2E-05 40.8 2.9 26 186-211 186-211 (254)
66 PRK14601 ruvA Holliday junctio 78.6 1.9 4.2E-05 38.2 3.0 45 155-201 80-127 (183)
67 TIGR01448 recD_rel helicase, p 78.4 7.8 0.00017 41.6 8.0 39 167-213 75-113 (720)
68 PRK14603 ruvA Holliday junctio 75.3 3.9 8.5E-05 36.6 4.0 48 154-203 78-128 (197)
69 PRK14600 ruvA Holliday junctio 74.3 4.2 9.2E-05 36.1 4.0 47 154-202 79-127 (186)
70 PRK02515 psbU photosystem II c 72.9 3.2 6.8E-05 34.7 2.6 24 187-210 66-91 (132)
71 PRK14604 ruvA Holliday junctio 72.8 4.2 9.1E-05 36.4 3.6 46 155-202 80-128 (195)
72 PRK13901 ruvA Holliday junctio 72.5 3 6.4E-05 37.4 2.5 45 155-201 79-126 (196)
73 PRK14606 ruvA Holliday junctio 71.9 4.6 0.0001 35.9 3.6 47 154-202 79-128 (188)
74 TIGR00575 dnlj DNA ligase, NAD 71.5 3.6 7.8E-05 43.6 3.3 25 186-210 502-526 (652)
75 TIGR00596 rad1 DNA repair prot 69.8 3.9 8.4E-05 44.4 3.2 25 186-210 761-785 (814)
76 PF01927 Mut7-C: Mut7-C RNAse 69.8 6.9 0.00015 33.2 4.1 89 85-181 7-99 (147)
77 PRK14351 ligA NAD-dependent DN 68.9 4.6 9.9E-05 43.0 3.4 25 186-210 532-556 (689)
78 PRK14602 ruvA Holliday junctio 68.8 5.7 0.00012 35.7 3.6 46 155-202 81-129 (203)
79 TIGR01259 comE comEA protein. 66.8 5.9 0.00013 32.5 3.0 17 186-202 72-88 (120)
80 PF11798 IMS_HHH: IMS family H 66.1 4.5 9.7E-05 25.2 1.7 13 186-198 15-27 (32)
81 cd00141 NT_POLXc Nucleotidyltr 64.7 6.9 0.00015 37.4 3.5 26 186-212 89-116 (307)
82 smart00483 POLXc DNA polymeras 64.1 6 0.00013 38.3 3.0 25 186-211 93-119 (334)
83 COG0632 RuvA Holliday junction 63.2 8.6 0.00019 34.6 3.6 73 120-202 48-128 (201)
84 PF00875 DNA_photolyase: DNA p 62.0 15 0.00033 31.3 4.8 34 85-118 53-86 (165)
85 PRK07956 ligA NAD-dependent DN 61.7 5.9 0.00013 42.1 2.6 15 88-102 239-253 (665)
86 TIGR00114 lumazine-synth 6,7-d 59.4 17 0.00036 30.7 4.5 44 82-125 14-64 (138)
87 TIGR00305 probable toxin-antit 56.6 7.7 0.00017 31.0 1.9 29 105-133 85-113 (114)
88 TIGR00426 competence protein C 56.6 13 0.00029 27.0 3.0 15 187-201 22-36 (69)
89 PRK08609 hypothetical protein; 56.5 18 0.0004 37.6 5.2 28 186-213 92-121 (570)
90 COG1555 ComEA DNA uptake prote 56.4 13 0.00027 31.9 3.3 25 186-210 101-131 (149)
91 PTZ00134 40S ribosomal protein 55.2 14 0.00031 31.8 3.4 34 170-203 9-51 (154)
92 PRK12419 riboflavin synthase s 52.7 22 0.00047 30.8 4.2 44 82-125 24-74 (158)
93 PF00885 DMRL_synthase: 6,7-di 51.5 29 0.00063 29.4 4.7 43 83-125 18-67 (144)
94 TIGR00084 ruvA Holliday juncti 50.2 21 0.00046 31.7 3.9 45 155-201 79-126 (191)
95 PF04019 DUF359: Protein of un 50.1 32 0.00069 28.4 4.6 19 20-38 2-21 (121)
96 COG0272 Lig NAD-dependent DNA 49.9 10 0.00022 40.0 1.9 27 185-211 514-540 (667)
97 COG1656 Uncharacterized conser 49.4 55 0.0012 28.5 6.0 50 84-134 12-61 (165)
98 PF11731 Cdd1: Pathogenicity l 49.2 35 0.00076 26.9 4.4 31 186-216 16-55 (93)
99 PRK13482 DNA integrity scannin 47.7 18 0.00038 35.4 3.1 54 158-211 243-316 (352)
100 PRK00061 ribH 6,7-dimethyl-8-r 46.9 31 0.00067 29.7 4.2 44 82-125 26-76 (154)
101 PRK04053 rps13p 30S ribosomal 46.8 29 0.00063 29.7 4.0 35 169-203 3-46 (149)
102 PLN02404 6,7-dimethyl-8-ribity 46.5 34 0.00074 29.0 4.3 44 82-125 21-71 (141)
103 COG0258 Exo 5'-3' exonuclease 44.6 11 0.00024 35.9 1.2 30 84-114 103-132 (310)
104 PRK14605 ruvA Holliday junctio 43.7 17 0.00037 32.5 2.2 33 167-201 93-127 (194)
105 KOG2841 Structure-specific end 43.6 17 0.00038 33.4 2.2 29 183-211 196-224 (254)
106 PRK00076 recR recombination pr 42.2 16 0.00035 32.7 1.8 15 186-200 15-29 (196)
107 PF12482 DUF3701: Phage integr 42.2 32 0.00069 27.3 3.3 40 161-200 28-68 (96)
108 TIGR00615 recR recombination p 42.1 16 0.00036 32.6 1.8 15 186-200 15-29 (195)
109 PF14635 HHH_7: Helix-hairpin- 42.1 16 0.00034 29.4 1.5 44 156-202 15-70 (104)
110 COG0353 RecR Recombinational D 41.4 15 0.00032 32.9 1.4 15 185-199 15-29 (198)
111 PF01850 PIN: PIN domain; Int 40.8 25 0.00055 27.3 2.6 50 79-134 69-118 (121)
112 TIGR00591 phr2 photolyase PhrI 40.0 78 0.0017 31.8 6.6 12 191-202 225-236 (454)
113 TIGR03629 arch_S13P archaeal r 39.4 34 0.00074 29.1 3.3 17 187-203 26-42 (144)
114 PF10454 DUF2458: Protein of u 38.7 94 0.002 26.6 5.9 36 71-106 91-126 (150)
115 PF00416 Ribosomal_S13: Riboso 38.4 28 0.00061 27.8 2.5 17 187-203 20-36 (107)
116 PRK13844 recombination protein 38.3 20 0.00044 32.2 1.8 15 186-200 19-33 (200)
117 PRK10702 endonuclease III; Pro 36.3 63 0.0014 29.2 4.7 14 187-200 114-127 (211)
118 TIGR02766 crypt_chrom_pln cryp 35.9 1E+02 0.0022 31.1 6.7 13 190-202 201-213 (475)
119 COG1948 MUS81 ERCC4-type nucle 35.7 1.4E+02 0.003 28.0 6.8 25 186-210 218-242 (254)
120 PRK01229 N-glycosylase/DNA lya 34.0 30 0.00065 31.3 2.2 17 186-202 123-139 (208)
121 TIGR01083 nth endonuclease III 33.8 46 0.001 29.3 3.4 15 186-200 110-124 (191)
122 PF14229 DUF4332: Domain of un 32.5 1.1E+02 0.0025 24.9 5.3 49 157-208 31-80 (122)
123 cd06167 LabA_like LabA_like pr 32.4 1.1E+02 0.0023 25.2 5.3 49 87-135 54-116 (149)
124 PRK00124 hypothetical protein; 32.0 38 0.00082 29.1 2.4 91 107-211 56-146 (151)
125 PF14579 HHH_6: Helix-hairpin- 31.1 61 0.0013 24.8 3.3 27 186-212 31-62 (90)
126 PF04760 IF2_N: Translation in 30.8 43 0.00093 23.0 2.2 48 156-203 4-52 (54)
127 COG0177 Nth Predicted EndoIII- 30.7 53 0.0011 29.8 3.2 17 187-203 114-131 (211)
128 PF11977 RNase_Zc3h12a: Zc3h12 30.0 1.6E+02 0.0035 24.9 6.1 24 14-37 25-48 (155)
129 PRK10674 deoxyribodipyrimidine 30.0 1.1E+02 0.0024 30.9 5.9 31 87-117 59-93 (472)
130 cd08556 GDPD Glycerophosphodie 29.9 94 0.002 26.3 4.6 39 88-127 150-188 (189)
131 PF14716 HHH_8: Helix-hairpin- 29.8 41 0.00088 24.4 2.0 14 185-198 50-63 (68)
132 TIGR03631 bact_S13 30S ribosom 29.4 48 0.0011 26.9 2.5 17 187-203 20-36 (113)
133 PF03979 Sigma70_r1_1: Sigma-7 29.3 1.1E+02 0.0023 23.1 4.3 45 61-106 14-60 (82)
134 PF04919 DUF655: Protein of un 28.6 1E+02 0.0023 27.2 4.6 45 167-212 96-151 (181)
135 TIGR00288 conserved hypothetic 28.6 88 0.0019 27.1 4.1 47 89-135 70-122 (160)
136 PF14490 HHH_4: Helix-hairpin- 28.5 1.2E+02 0.0026 23.4 4.6 31 188-220 18-48 (94)
137 PRK05234 mgsA methylglyoxal sy 28.4 78 0.0017 26.7 3.7 36 90-125 41-80 (142)
138 cd00056 ENDO3c endonuclease II 28.2 39 0.00084 28.4 1.9 15 186-200 87-101 (158)
139 TIGR03252 uncharacterized HhH- 28.2 34 0.00073 30.2 1.5 18 186-203 119-136 (177)
140 PRK11613 folP dihydropteroate 27.5 5.3E+02 0.012 24.4 11.0 33 160-192 156-190 (282)
141 PRK05179 rpsM 30S ribosomal pr 27.0 55 0.0012 27.0 2.5 17 187-203 22-38 (122)
142 PF09550 DUF2376: Conserved hy 27.0 2E+02 0.0043 19.3 4.7 34 166-204 10-43 (43)
143 COG1412 Uncharacterized protei 26.9 74 0.0016 26.8 3.3 44 91-134 69-112 (136)
144 PRK14350 ligA NAD-dependent DN 26.7 57 0.0012 34.8 3.2 25 186-210 506-531 (669)
145 CHL00137 rps13 ribosomal prote 26.4 58 0.0013 26.9 2.5 17 187-203 22-38 (122)
146 PF09040 H-K_ATPase_N: Gastric 26.2 24 0.00053 22.8 0.2 23 309-331 17-39 (41)
147 PF09288 UBA_3: Fungal ubiquit 26.2 80 0.0017 22.4 2.8 31 247-279 4-34 (55)
148 cd01422 MGS Methylglyoxal synt 26.1 1.1E+02 0.0024 24.7 4.1 37 90-126 36-76 (115)
149 TIGR00289 conserved hypothetic 26.0 1.2E+02 0.0025 27.7 4.7 42 88-130 48-95 (222)
150 PRK00116 ruvA Holliday junctio 26.0 48 0.001 29.4 2.1 18 186-203 112-129 (192)
151 PF04900 Fcf1: Fcf1; InterPro 25.8 62 0.0013 25.3 2.5 39 102-140 47-90 (101)
152 TIGR02236 recomb_radA DNA repa 25.8 58 0.0012 30.8 2.8 24 186-209 3-27 (310)
153 cd08568 GDPD_TmGDE_like Glycer 25.7 1.2E+02 0.0025 27.2 4.7 42 88-131 184-225 (226)
154 PF06732 Pescadillo_N: Pescadi 25.3 71 0.0015 30.3 3.2 28 153-180 10-37 (281)
155 PRK13913 3-methyladenine DNA g 25.2 47 0.001 30.3 1.9 15 186-200 125-139 (218)
156 PF06415 iPGM_N: BPG-independe 25.1 3.3E+02 0.0071 24.9 7.4 33 5-38 37-73 (223)
157 smart00478 ENDO3c endonuclease 25.0 49 0.0011 27.5 1.9 15 186-200 76-90 (149)
158 COG2266 GTP:adenosylcobinamide 24.9 1.3E+02 0.0029 26.5 4.5 46 83-128 48-95 (177)
159 PLN03060 inositol phosphatase- 24.9 2.1E+02 0.0045 25.9 5.9 103 159-277 76-180 (206)
160 COG1569 Predicted nucleic acid 24.8 58 0.0012 27.6 2.2 31 107-137 91-121 (142)
161 cd00532 MGS-like MGS-like doma 24.7 1.1E+02 0.0023 24.4 3.8 37 90-126 34-74 (112)
162 PRK09454 ugpQ cytoplasmic glyc 24.6 1.1E+02 0.0024 27.9 4.3 41 89-130 200-240 (249)
163 COG4277 Predicted DNA-binding 24.3 1.1E+02 0.0023 29.6 4.1 47 155-201 277-349 (404)
164 PF01936 NYN: NYN domain; Int 23.8 1.4E+02 0.0031 24.0 4.5 49 87-135 49-112 (146)
165 cd01424 MGS_CPS_II Methylglyox 23.8 1.5E+02 0.0033 23.2 4.5 37 90-126 35-73 (110)
166 PRK13266 Thf1-like protein; Re 23.7 2.1E+02 0.0046 26.2 5.9 107 159-276 78-189 (225)
167 PRK01189 V-type ATP synthase s 23.6 94 0.002 24.8 3.2 36 92-127 15-53 (104)
168 cd00194 UBA Ubiquitin Associat 23.4 1.5E+02 0.0032 18.4 3.6 23 254-278 3-25 (38)
169 cd08575 GDPD_GDE4_like Glycero 23.4 1.2E+02 0.0027 27.9 4.4 44 88-132 221-264 (264)
170 PRK00254 ski2-like helicase; P 23.0 66 0.0014 34.4 2.9 26 186-211 649-675 (720)
171 PF05687 DUF822: Plant protein 23.0 3.3E+02 0.0072 23.3 6.4 68 37-136 5-73 (150)
172 COG1491 Predicted RNA-binding 22.7 96 0.0021 27.6 3.3 46 167-213 110-166 (202)
173 smart00165 UBA Ubiquitin assoc 22.1 1.7E+02 0.0036 18.1 3.6 22 254-277 3-24 (37)
174 TIGR00028 Mtu_PIN_fam Mycobact 21.4 1E+02 0.0022 24.8 3.1 31 107-138 105-135 (142)
175 PF04895 DUF651: Archaeal prot 21.1 2E+02 0.0044 23.3 4.7 54 226-293 57-110 (110)
176 COG0054 RibH Riboflavin syntha 21.1 1.8E+02 0.0038 25.1 4.5 44 82-125 26-76 (152)
177 PF14056 DUF4250: Domain of un 20.9 1.2E+02 0.0027 21.4 2.9 32 155-186 20-51 (55)
178 PRK14487 cbb3-type cytochrome 20.9 93 0.002 28.3 2.9 15 106-120 194-208 (217)
179 cd08567 GDPD_SpGDE_like Glycer 20.6 1.8E+02 0.0038 26.4 4.9 41 89-130 222-262 (263)
180 COG3327 PaaX Phenylacetic acid 20.3 1.2E+02 0.0025 28.5 3.4 30 251-281 26-55 (291)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.5e-77 Score=582.72 Aligned_cols=297 Identities=59% Similarity=1.017 Sum_probs=284.6
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhc
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~ 81 (332)
|+|++|++|+||+||++|+++|+++||+|||||||.+|++|++++++|+++|+++++.+.++.+.|+.+++.++++|+++
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHH
Q 020008 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v 161 (332)
||++|++.++++|+.||||||+||||||||||+|++.|+||+|+|+|+|+|+||++.++++++..+..+.++.+|+.+.+
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 99999999999999999999999999999999999999999999999999999999999998764444556789999999
Q ss_pred HHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhCCCCcCCcc
Q 020008 162 LEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (332)
Q Consensus 162 ~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~f~~p~V~~~~ 241 (332)
++.+|++++||+|+|+|+||||++||||||||||++||++||++|+|+++++..++.+|++|++.+++.+|++|.|+.+.
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 99999999999999999999999999999999999999999999999999999889999999999999999999999766
Q ss_pred chhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHhhccCCCCccccccCcccC
Q 020008 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVAN 299 (332)
Q Consensus 242 ~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff~~~~~ 299 (332)
++ +|.|+.||.++|++||+++++|+++||++.|+||.++....+|+|||+||++.++
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 66 7999999999999999999999999999999999998888899999999997654
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.7e-75 Score=548.58 Aligned_cols=282 Identities=45% Similarity=0.807 Sum_probs=265.3
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhcc
Q 020008 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (332)
Q Consensus 3 ~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~v 82 (332)
+|++|++|||++|||+|+++|+++||+|+|||||.+|++|++++++|+++|+++++.+..+.+.|+.+++.+++++++++
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCC---------cc
Q 020008 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------PV 153 (332)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~---------~~ 153 (332)
|++|++.++++|++|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++|++++...+.++. ..
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 999999999999999999999999999999999999999999999999999999999999876543221 34
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc-hHHHHHHh
Q 020008 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP-YQEARRLF 232 (332)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~-~~~~~~~f 232 (332)
+.|+.+.+++.+|++++||+|+|+|+||||++||||||||||++||++|+++|+|+++++ .+++ +.+++++|
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 579999999999999999999999999999999999999999999999999999999653 2333 58999999
Q ss_pred CCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHhhccCCCCcccccc
Q 020008 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (332)
Q Consensus 233 ~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (332)
++|.|+. +. +++|+.||.++|++||+++++|+++||++.++||.++.+..+|+|||+||
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 9999995 44 79999999999999999999999999999999999998888999999998
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=1e-68 Score=514.64 Aligned_cols=283 Identities=46% Similarity=0.805 Sum_probs=263.9
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhc
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~ 81 (332)
|+|++|++|+|++|+++++++|+++||+|+|||||.+|++|.+++++|+++|+++++.+..+.+.|+.+++.++++|+.+
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 cCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCC---------c
Q 020008 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------P 152 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~---------~ 152 (332)
+|.+|++.++++|++|||||++||||||||||+|++.|.||+|+|+|+|+|+||+++|+++++..++++. .
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 9999999999999999999999999999999999999999999999999999999999999876443211 3
Q ss_pred cEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHh
Q 020008 153 VMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (332)
Q Consensus 153 ~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~f 232 (332)
.+.++.+++++.+|++++||+|+|+|+||||++||||||||||++||++||++|+|+++++.. ++ ++.+++.+|
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---NYDEIREFF 280 (338)
T ss_pred ceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcCC---CC---CHHHHHHHh
Confidence 456999999999999999999999999999999999999999999999999999999997532 32 257999999
Q ss_pred CCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHhhccCCCCcccccc
Q 020008 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (332)
Q Consensus 233 ~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (332)
.+|.|+.. . ++.|..||.++|++||+++++|+++||.+.++||+++. +++|+|||+||
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 99999853 4 78999999999999999999999999999999998887 78999999998
No 4
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-64 Score=486.13 Aligned_cols=298 Identities=61% Similarity=1.016 Sum_probs=284.8
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhcc
Q 020008 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (332)
Q Consensus 3 ~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~v 82 (332)
+|..|++|+||.|+|+|+++|+++||+|||||||.+|.+|.+++.+|..+|.++.+....+.+.|......++..|.+.|
T Consensus 50 ~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkv 129 (449)
T KOG2519|consen 50 RNEAGEPTSHLMGMFYRTIRLIENGIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKV 129 (449)
T ss_pred cccCCCchHHHHHHHHHHHHHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhh
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHHH
Q 020008 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKIL 162 (332)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~ 162 (332)
|.++.++++.||..|||||+.||+||+||||+|+++|.|++++|+|||.|.||++.+++++..+.++..++.+|+.+.++
T Consensus 130 tk~~~dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il 209 (449)
T KOG2519|consen 130 TKQHNDEAKRLLSLMGIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRIL 209 (449)
T ss_pred cchhhHHHHHHHHHcCCeeecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999998766677899999999999
Q ss_pred HHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCchHHHHHHhCCCCcCCcc
Q 020008 163 EELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (332)
Q Consensus 163 ~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~-~~~~~~~~~~~~~~~~~~~~~f~~p~V~~~~ 241 (332)
+.|+++.++|+|+|+|+|||||++|.|||+++|++||++|+++++|++ +.+...+.+|++|++..++.+|..|.++...
T Consensus 210 ~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~~i~~ile~~~~~~~~~ip~~w~~~~~r~~f~~p~~~~~~ 289 (449)
T KOG2519|consen 210 EGLGLSRESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHGDIENILEINSDLKEYPIPEDWSYKLARKLFLEPEFPNPE 289 (449)
T ss_pred HHhcccHHHHHHHHHHhcCcccccccccChHHHHHHHHHhcCHHHHhhhccchhhcCCCCCccHHHHHHHhcCcccCCcc
Confidence 999999999999999999999999999999999999999999999999 7777788999999999999999999999776
Q ss_pred chhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHhhccCCCCccccccCcccCC
Q 020008 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVANT 300 (332)
Q Consensus 242 ~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff~~~~~~ 300 (332)
..-++.|..||.+++.+|++.+.+|+++||.+.+.++.+..+..+|+|+|+||+..++.
T Consensus 290 ~~~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~ 348 (449)
T KOG2519|consen 290 SILDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKG 348 (449)
T ss_pred ceeecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCC
Confidence 62389999999999999999999999999999999999999999999999999987765
No 5
>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=3.2e-59 Score=446.30 Aligned_cols=268 Identities=52% Similarity=0.882 Sum_probs=252.1
Q ss_pred CCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhccCH
Q 020008 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTK 84 (332)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~vt~ 84 (332)
+.|.+|+|++||++++.+|+++||+|||||||.+|++|.++..+|+.+|.+.......+++.|+.+++.++.+++..+++
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 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHHHHH
Q 020008 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 164 (332)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~ 164 (332)
.|++.++++|+.|||||++||+|||||||+|++.|.+++|+|+|+|+|+||++.|+++++..+. ..+..|+.+.+++.
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 9999999999999999999999999999999999999999999999999999999998865321 34688999999999
Q ss_pred cCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhCCCCcCCccchh
Q 020008 165 LNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQL 244 (332)
Q Consensus 165 ~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~f~~p~V~~~~~~~ 244 (332)
+|++++||+|+|+|+||||++||||||||||++||++|++++++++++......+|++|++..++++|.+|.|+.. ..
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 9999999999999999999999999999999999999999999999998877778899999999999999999854 22
Q ss_pred ccccCCCCHHHHHHHHHHhcCCChHHHHHHHH
Q 020008 245 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIE 276 (332)
Q Consensus 245 ~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~ 276 (332)
.+.|..||.++|+.|++.+++|+++||.+.+.
T Consensus 284 ~~~~~~p~~~~l~~~~~~~~~~~~~rv~~~~~ 315 (316)
T cd00128 284 DLRWRDPDEEGIIEFLCKEHGFNEDRVLKPLE 315 (316)
T ss_pred ceeecCCCHHHHHHHccCCCCCCHHHHHhhhc
Confidence 68999999999999999999999999998764
No 6
>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=1e-49 Score=419.88 Aligned_cols=218 Identities=25% Similarity=0.435 Sum_probs=196.4
Q ss_pred hhhhhccCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEE
Q 020008 76 SKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 155 (332)
Q Consensus 76 ~~r~~~vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~ 155 (332)
.+++..||.+|+..|+++|++||||||+||||||||||+|++.|+||+|+|+|+|+|+||+++||+|++.. ...+..
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 56688999999999999999999999999999999999999999999999999999999999999998743 345789
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHH---HHHHh----------------
Q 020008 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG--SIETIL---ENINR---------------- 214 (332)
Q Consensus 156 ~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~--sle~il---~~~~~---------------- 214 (332)
|+..++++.+||+++||+++|+|+||||++|||||||+||++||++|+ ++++++ +|++.
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 477666 44432
Q ss_pred ----hcCCCCCCCchHHHHHHhCCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH-HhhccCCCCc
Q 020008 215 ----ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK-AAKNKSSQGR 289 (332)
Q Consensus 215 ----~~~~~~~~~~~~~~~~~f~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~-~~~~~~~Q~~ 289 (332)
.++.+|++||+..++.+|++|.|+.+. ..|.|+.||.++|++||++++||+++||++.|.++. +...+++|+|
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 124689999999999999999999643 279999999999999999999999999999999984 4566789999
Q ss_pred cccccCccc
Q 020008 290 LESFFKPVA 298 (332)
Q Consensus 290 l~~ff~~~~ 298 (332)
|++||+...
T Consensus 998 ld~FF~~~~ 1006 (1034)
T TIGR00600 998 IDSFFRLAQ 1006 (1034)
T ss_pred HHHhhCccc
Confidence 999998533
No 7
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=2.2e-44 Score=337.68 Aligned_cols=239 Identities=23% Similarity=0.290 Sum_probs=195.8
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~ 79 (332)
|+|++|.+|+|++||+++++++++.. -.+++|||+..++||++.++.||++|.++|+.+
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 67999999999999999999999742 245789999989999999999999999999998
Q ss_pred hccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHHc----CCeEEEecCCCccccccCCceEEEeecCCCCCCccE
Q 020008 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (332)
Q Consensus 80 ~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~ 154 (332)
..|++.++++|+.+|||++.+|| ||||+||+|+++ |....|+|+|+|++|+++++|...... . .....
T Consensus 89 ----~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~--~-~~~~~ 161 (281)
T PRK14976 89 ----ISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKK--K-GTSHF 161 (281)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEec--C-CCCcE
Confidence 67899999999999999999998 999999999874 665679999999999999886432222 1 11246
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHh
Q 020008 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (332)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~f 232 (332)
.++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|++++++.+.++.+++.........
T Consensus 162 ~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~~~ 241 (281)
T PRK14976 162 ILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKALL 241 (281)
T ss_pred EEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHHHH
Confidence 79999999999999999999999999 5566667899999999999999999999999987754444444433333333
Q ss_pred CCCCc------CCccchhccccCCCCHHHHHHHHHHhcCCC
Q 020008 233 KEPEV------VTDEEQLQIKWSAPDEEGLINFLVSENGFN 267 (332)
Q Consensus 233 ~~p~V------~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~ 267 (332)
++.+| ++..+++++.+..||.++|.+++ ++++|.
T Consensus 242 s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~-~~~e~~ 281 (281)
T PRK14976 242 SKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIF-EELELK 281 (281)
T ss_pred hhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHH-HHcCCC
Confidence 33333 33334456788899999999998 788873
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=4.7e-44 Score=331.83 Aligned_cols=216 Identities=26% Similarity=0.381 Sum_probs=180.9
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
|+|++|++|+|++||++++.++++. ..| ++|||+..++||++.+++||++|.++|+++
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 789999889999999999999999999998
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHHc----CCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.++++|++||||++.+|+ ||||+||+|+++ |..++|+|+|+|++|+++++|....... .....
T Consensus 83 -----~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~--~~~~~ 155 (259)
T smart00475 83 -----LEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTK--GIKEF 155 (259)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccC--CCCcc
Confidence 67889999999999999999998 999999999984 7778899999999999998875432221 11224
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHH
Q 020008 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (332)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~ 231 (332)
..++.+.+.+.+|++|+||+|+|+|+| ||+.+||||||||||.+||++|||+|+|++++++.+.++.+.+.......+
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 677777899999999999999999999999998764333333333334444
Q ss_pred hCCCCcCCccch
Q 020008 232 FKEPEVVTDEEQ 243 (332)
Q Consensus 232 f~~p~V~~~~~~ 243 (332)
++..++++.+++
T Consensus 236 ls~~L~~l~~d~ 247 (259)
T smart00475 236 LSRKLATIETDV 247 (259)
T ss_pred HhhhhheeeeCC
Confidence 455566655554
No 9
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2e-43 Score=343.21 Aligned_cols=234 Identities=29% Similarity=0.484 Sum_probs=205.3
Q ss_pred CCCCchhHHHHHHHHHHHH-HHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhccC
Q 020008 5 EAGEVTSHLQGMFTRTIRL-LEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVT 83 (332)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~l-l~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~vt 83 (332)
..|.||.....+|..-++| +.+||+||.||||.+.+.|..+..+|+.+|++..+..+.+|.+|+..+|..+++||+.||
T Consensus 47 ~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT 126 (556)
T KOG2518|consen 47 AKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDIT 126 (556)
T ss_pred hcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCc
Confidence 3588887666666555555 468999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHHHH
Q 020008 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILE 163 (332)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~ 163 (332)
++|+..++++|+..||+||+||||||||+|||.+.|++++|||+|||+++|||..||..|...+. ..+++...+-+
T Consensus 127 ~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~----~le~~~~~l~~ 202 (556)
T KOG2518|consen 127 PEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGN----GLEINRSKLPE 202 (556)
T ss_pred HHHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCC----cccccHhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999998876443 34566666655
Q ss_pred Hc----CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCc--hHHHHHHhCCCC
Q 020008 164 EL----NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWP--YQEARRLFKEPE 236 (332)
Q Consensus 164 ~~----gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~-~~~~~~~~~~~~~~--~~~~~~~f~~p~ 236 (332)
.. +++.++|..+|+|.||||.++|||||.+||.++|++|.+.+.++. ++...+..+|++|. +..|...|.+.-
T Consensus 203 ~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~tF~hQr 282 (556)
T KOG2518|consen 203 CKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLTFLHQR 282 (556)
T ss_pred ccccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHhhhhhh
Confidence 44 367899999999999999999999999999999999999999875 44445668999887 457889999998
Q ss_pred cCCccc
Q 020008 237 VVTDEE 242 (332)
Q Consensus 237 V~~~~~ 242 (332)
|.++..
T Consensus 283 VydP~~ 288 (556)
T KOG2518|consen 283 VYDPIE 288 (556)
T ss_pred eeCchH
Confidence 886653
No 10
>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=4.3e-41 Score=355.98 Aligned_cols=238 Identities=29% Similarity=0.452 Sum_probs=198.1
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
|+|++|++|+|++||++++.++++. .+| ++|||+..++||++.+++||++|.++|+++
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 678 679999999999999999999999999999
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHHc----CCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.++++|++||||++.+|| ||||+||+|+++ |+.++|+|+|+|++|+++++|.. +..... ...
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 67899999999999999999998 999999999973 77778999999999999988632 222111 124
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCchHHHHH
Q 020008 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQEARR 230 (332)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~-~~~~~~~~~~~~~ 230 (332)
..++.+.|.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++.++. ++.+++.......
T Consensus 155 ~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~a 234 (887)
T TIGR00593 155 TEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDA 234 (887)
T ss_pred eEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHHH
Confidence 579999999999999999999999999 2444557899999999999999999999999998753 3555554333333
Q ss_pred HhCCC------CcCCccchhccccCCCCHHHHHHHHHHhcCCC
Q 020008 231 LFKEP------EVVTDEEQLQIKWSAPDEEGLINFLVSENGFN 267 (332)
Q Consensus 231 ~f~~p------~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~ 267 (332)
+++.. +|+++.+++++.+..||.+.|.+|| ++++|.
T Consensus 235 ~ls~~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~-~~lef~ 276 (887)
T TIGR00593 235 FLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL-QELEFK 276 (887)
T ss_pred HHHHHhheeecCCCCCCCHHHhccCCCCHHHHHHHH-HHhCCc
Confidence 33333 3443344456788899999999998 799995
No 11
>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=5.7e-41 Score=308.64 Aligned_cols=185 Identities=26% Similarity=0.396 Sum_probs=165.4
Q ss_pred cCC-CCCchhHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhh
Q 020008 3 TNE-AGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (332)
Q Consensus 3 ~~~-~G~~t~~l~g~~~r~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~ 79 (332)
.++ +|.+|+|++||++++.++++.. ..+++||||.+++||++.++.||++|.++|+.+
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 455 8999999999999999999753 456889999989999999999999999999999
Q ss_pred hccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCCeEEEecCCCccccccCCceEEEeecCCCCCCccE
Q 020008 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (332)
Q Consensus 80 ~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~ 154 (332)
..|++.++++|+.||||++.+|+ ||||+||+|++ .|..++|+|+|+|++|+++++|.. .... ...
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 68899999999999999999998 99999999986 577788999999999999887632 2222 135
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhc
Q 020008 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRER 216 (332)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~ 216 (332)
.++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++..+
T Consensus 154 ~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 217 (240)
T cd00008 154 LVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIK 217 (240)
T ss_pred EEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHh
Confidence 79999999999999999999999999 778888899999999999999999999999998654
No 12
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.2e-40 Score=312.55 Aligned_cols=262 Identities=28% Similarity=0.472 Sum_probs=211.7
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHH--cCCCcEEEEeCCCCchhhhhHHHHhhchhh-chHHHHHHHHcCCHHHHHHHhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLE--AGMKPIYVFDGQPPDLKKQELAKRYSKRAD-ATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~--~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~-~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
+.|+.|.+|++++||...+.++++ ..++|++||||.++++|++++++||++|++ ++.++
T Consensus 33 ~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~~l------------------ 94 (310)
T COG0258 33 LGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMPDEL------------------ 94 (310)
T ss_pred cCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCHHHH------------------
Confidence 478899999998888888888775 248999999999999999999999999999 99998
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.+.+++..+|++++..+| ||||.++++++ .|.+++|+|+|+|+|||+++++...... +..+.
T Consensus 95 -----~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~~---~~~~~ 166 (310)
T COG0258 95 -----APQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGK---KGEPE 166 (310)
T ss_pred -----HHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCcEEEecc---CCCCc
Confidence 67888889999999999999888 99988888876 6899999999999999999985432221 22121
Q ss_pred EEEeHHHHHHHc-CCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHH
Q 020008 154 MEFEVAKILEEL-NLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (332)
Q Consensus 154 ~~~~~~~v~~~~-gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~ 230 (332)
..++...+.+.+ |++|+||+|+++|+| |||++||||||||||++||++||++|.++++++..+....+.+ ......
T Consensus 167 ~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l-~~~~~~ 245 (310)
T COG0258 167 KFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKL-LEDKEK 245 (310)
T ss_pred ccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHH-HHHHHH
Confidence 258999999999 999999999999999 9999999999999999999999999999999985444444433 344555
Q ss_pred HhCC-CCcCCccchhccccCCCCHHHHHHHHHHhcCCC---hHHHHHHHHHHHHhhccCCCCcccccc
Q 020008 231 LFKE-PEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN---SDRVTKAIEKIKAAKNKSSQGRLESFF 294 (332)
Q Consensus 231 ~f~~-p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~---~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (332)
+|++ +.|++.+++ .+.|..++. ..+++.+++++ ..++...++++.+......|.+++.||
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 6665 899987776 677877776 45555566666 666777777776655444788888766
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=1.2e-39 Score=347.93 Aligned_cols=239 Identities=25% Similarity=0.404 Sum_probs=197.8
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
|+|++|.+|++++||++++.++++ ..+| ++|||+..++||++.+++||++|.++|+++
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 5777 779999889999999999999999999999
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.++++|+.+|||++.+|| ||||+||+|++ .|..++|+|+|+|++|+++++|. ++.... ....
T Consensus 85 -----~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~--~~~~~~-~~~~ 156 (880)
T PRK05755 85 -----REQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVT--LLDTMG-VSKN 156 (880)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEE--EeeccC-CCCC
Confidence 78899999999999999999998 99999999985 47788899999999999998763 222210 0124
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHH
Q 020008 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (332)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~~ 231 (332)
..++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++.++.++.+++.......+
T Consensus 157 ~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~ 236 (880)
T PRK05755 157 EELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAF 236 (880)
T ss_pred eEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhchHHHHHHHHhHHHHH
Confidence 679999999999999999999999999 566667789999999999999999999999998765555555543322222
Q ss_pred hCCC------CcCCccchhccccCCCCHHHHHHHHHHhcCCCh
Q 020008 232 FKEP------EVVTDEEQLQIKWSAPDEEGLINFLVSENGFNS 268 (332)
Q Consensus 232 f~~p------~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~ 268 (332)
++.. +++.+.+++++.|..||.++|.+|| ++++|+.
T Consensus 237 ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~ 278 (880)
T PRK05755 237 LSRKLATIKTDVPLEVDLEDLELQPPDREKLIALF-KELEFKS 278 (880)
T ss_pred hhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHH-HHhCcHH
Confidence 2222 2222233446889999999999999 8999953
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=6.5e-38 Score=288.81 Aligned_cols=208 Identities=18% Similarity=0.201 Sum_probs=169.9
Q ss_pred CCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCc--hhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhh
Q 020008 4 NEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPD--LKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 4 ~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~--~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
+++|. |++++||++.+.++++. ..| +++||+..++ ||++.++.||++|.++|+++
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 46888 99999999999999974 556 4579998776 99999999999999999999
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHHc----CCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.++++|+++|||++..|| ||||+||+|+++ |.-..|+|.|+|++|+..++|.. +.... .
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 999999999863 55556899999999999887642 22211 2
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHH
Q 020008 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (332)
Q Consensus 154 ~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~---ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~~~~ 230 (332)
.+++.+.+.+++|++|+|++|+++|+| |.+|| |||||||||.+||++|||+|+|+++++.++.++.+.+.......
T Consensus 152 ~~~~~~~v~~~~Gv~P~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~a 230 (256)
T PRK09482 152 RWLDAPFIEQEFGVEPQQLPDYWGLAG-ISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLEEHKEMA 230 (256)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHhC-CCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHHHhHHHH
Confidence 468999999999999999999999999 76665 57999999999999999999999999876433444433333333
Q ss_pred HhCCCCcCCccch
Q 020008 231 LFKEPEVVTDEEQ 243 (332)
Q Consensus 231 ~f~~p~V~~~~~~ 243 (332)
.++...+++.+++
T Consensus 231 ~lsr~L~~l~~dv 243 (256)
T PRK09482 231 RLCRKLAQLQTDL 243 (256)
T ss_pred HHHHhhheEeeCC
Confidence 3444556655554
No 15
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-37 Score=318.36 Aligned_cols=212 Identities=27% Similarity=0.529 Sum_probs=183.9
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeH
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV 158 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~ 158 (332)
+-.+|..|+.+|+++|+.+|||||+||+|||||||.|+..++||+|||+|||+|+||+.+||+|+|... ..+..|.+
T Consensus 460 ~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~kn---k~ve~y~~ 536 (815)
T KOG2520|consen 460 ADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKN---KYVEKYQL 536 (815)
T ss_pred CchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcC---ccceeeeh
Confidence 346889999999999999999999999999999999999999999999999999999999999998643 34789999
Q ss_pred HHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHHHh---------------------
Q 020008 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG---SIETILENINR--------------------- 214 (332)
Q Consensus 159 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~---sle~il~~~~~--------------------- 214 (332)
.++...||+++..+|-++.|+|+||+.||+||||++|+++|.+|+ ++..+-+++..
T Consensus 537 ~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~~~~~~~s~~~~~lrkkl~ 616 (815)
T KOG2520|consen 537 DDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGPADKEVGSTQQKMLRKKLK 616 (815)
T ss_pred HHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCccccccccHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999 54444444431
Q ss_pred -hcCCCCCCCchHHHHHHhCCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHH----HHHHHhhccCCCCc
Q 020008 215 -ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAI----EKIKAAKNKSSQGR 289 (332)
Q Consensus 215 -~~~~~~~~~~~~~~~~~f~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~----~~l~~~~~~~~Q~~ 289 (332)
.+..+|..||...+..+|++|.|++... .|.|+.||.+.|++||...+||+..+....+ +++.+......|.+
T Consensus 617 n~~~~l~~~fP~~~v~~AYLrP~VD~sk~--~f~WG~pdl~~lRef~~~~fgW~~~kT~~~l~p~~~~~~~~~~~~~~~~ 694 (815)
T KOG2520|consen 617 NPKIILPSDFPNPNVIEAYLRPEVDDSKE--KFRWGKPDLDILREFMKRLFGWPDEKTDEELIPVIKRLEKKKTQLKQDR 694 (815)
T ss_pred CcccccCcCCCchhHHHHhhCCccCCCcc--cccCCCCCHHHHHHHHHHHcCCCccccchhhhhhHHHHHHHhhhhcccc
Confidence 1256899999999999999999997765 5999999999999999999999998877664 44544444556666
Q ss_pred cccccC
Q 020008 290 LESFFK 295 (332)
Q Consensus 290 l~~ff~ 295 (332)
+-.||-
T Consensus 695 ~~~~f~ 700 (815)
T KOG2520|consen 695 ISQFFE 700 (815)
T ss_pred HHHHHH
Confidence 666664
No 16
>PHA00439 exonuclease
Probab=99.94 E-value=1.7e-26 Score=214.81 Aligned_cols=210 Identities=15% Similarity=0.175 Sum_probs=151.1
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHc--CCCc---EEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEA--GMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFS 76 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~--gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~ 76 (332)
|+|++|.+|++++||++.+.++++. ..+| +++|| ..++||++.++.||++|.++++..
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 6799999999999999999999963 1455 34699 568999999999999999987774
Q ss_pred hhhhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCC-eEEEecCCCccccccCCceEEEeecCCCCC
Q 020008 77 KRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ-VYAVASEDMDSLTFGAPRFLRHLMDPSSRK 150 (332)
Q Consensus 77 ~r~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~-v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~ 150 (332)
.+++.+++++..+||+++..|| ||||.||+|++ .|+ -..|+|.|+|++|+....++ +...+
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 2467788999999999999999 99999999986 355 55799999999999765332 11111
Q ss_pred CccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHH---cCCHHHHHHHHHhhcCCCCCCCc
Q 020008 151 IPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQ---HGSIETILENINRERYQIPEDWP 224 (332)
Q Consensus 151 ~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~i---pgiG~ktA~~li~~---~~sle~il~~~~~~~~~~~~~~~ 224 (332)
.+..++.+ .++||+|+.+|+| |.+||| |||| |||.+||++ |-.++.++.+-.. +...+.+|.
T Consensus 164 -~~~~~~~~--------~p~~~~d~~AL~G-DsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~sg~~-~~~~~~~~~ 231 (286)
T PHA00439 164 -NILTQTPE--------TADRWHLFQTIKG-DSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKSGKR-KGQTVTKWK 231 (286)
T ss_pred -ceEEcCcc--------cHHHHHhhhhccc-ccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhcccc-cccchhhhh
Confidence 11113322 2999999999999 999976 6899 999999998 4445555544211 222222221
Q ss_pred hHHHHHHhCCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHH
Q 020008 225 YQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVT 272 (332)
Q Consensus 225 ~~~~~~~f~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~ 272 (332)
- ..|... + .=++.+.... .+-|.+++.+.
T Consensus 232 k-------~~~~~~------~-----~~w~~~v~~~-~k~g~~e~~~~ 260 (286)
T PHA00439 232 K-------RAPEPE------E-----TLWDCIVTLG-AKAGMTEEDAI 260 (286)
T ss_pred c-------cCCCcc------c-----cHHHHHHHHH-HHcCCCHHHHH
Confidence 0 000000 1 1147788877 68899887644
No 17
>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=99.93 E-value=3e-26 Score=181.52 Aligned_cols=88 Identities=53% Similarity=0.847 Sum_probs=75.1
Q ss_pred HHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEee-cC-CC----CCCccEEEeHHHHHHHcCCC
Q 020008 95 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLM-DP-SS----RKIPVMEFEVAKILEELNLT 168 (332)
Q Consensus 95 ~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~-~~-~~----~~~~~~~~~~~~v~~~~gl~ 168 (332)
++|||||++||||||||||||+++|+||+|+|+|||+|+||++.|++++. .. +. ....+..|+..++++.+|++
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 57999999999999999999999999999999999999999999999986 22 11 13457899999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 020008 169 MDQFIDLCILSGCD 182 (332)
Q Consensus 169 ~~q~id~~~L~G~D 182 (332)
++||+++|+|+|||
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 18
>PHA02567 rnh RnaseH; Provisional
Probab=99.90 E-value=4.6e-23 Score=192.70 Aligned_cols=161 Identities=14% Similarity=0.113 Sum_probs=124.4
Q ss_pred CcCCCCCchhHHHH-HHHHHHHHHH-cCCCc---EEEEeCCC-CchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHH
Q 020008 2 LTNEAGEVTSHLQG-MFTRTIRLLE-AGMKP---IYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKF 75 (332)
Q Consensus 2 l~~~~G~~t~~l~g-~~~r~~~ll~-~gi~P---v~VFDG~~-~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~ 75 (332)
|++++|.+|+++++ +++.+.+++. ..-.| +++||+.. ++||++.++.||++|.++|+++...++ .+
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 78999999999966 5555555544 12223 56899974 789999999999999999998732111 00
Q ss_pred hhhhhccCHHHH-HHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCCeEEEecCCCccccccC-CceEEEeecCCC
Q 020008 76 SKRTVKVTKQHN-DDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGA-PRFLRHLMDPSS 148 (332)
Q Consensus 76 ~~r~~~vt~~~~-~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~v~~V~S~DsD~l~fg~-~~vi~~l~~~~~ 148 (332)
.+++ +.+.+++..|||+++..|| ||||.+|+|++ .|....|+|+|+|++|+.. ++|.. +..
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 1223 5678899999999999999 99999999997 4665679999999999984 66532 211
Q ss_pred CCCccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCcc
Q 020008 149 RKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIG 191 (332)
Q Consensus 149 ~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG 191 (332)
++.+.+.+++| .|+|++|+.+|+| |.+||||||-
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 24577888999 5999999999999 9999999984
No 19
>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=99.88 E-value=1.9e-22 Score=176.16 Aligned_cols=138 Identities=28% Similarity=0.449 Sum_probs=111.8
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhh
Q 020008 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (332)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r 78 (332)
|.+++|++|++++||+..+.++++. .+| ++|||+..++||++.+++||++|.++|+++
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 6789999999999999999999874 455 558999988999999999999999999999
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEeccc-chHHHHHHHHH----cCCeEEEecCCCccccccCCceEEEeecCCCCCCcc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~-EADaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~ 153 (332)
..|++.++++|+.+||+++..|| ||||.+|+|++ +|.-..|+|+|+|++|+..+++-..+...+ ....
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 67899999999999999999999 99999999997 466667999999999999983321233332 2335
Q ss_pred EEEeHHHHHHHc
Q 020008 154 MEFEVAKILEEL 165 (332)
Q Consensus 154 ~~~~~~~v~~~~ 165 (332)
..|+.+.|.++|
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 20
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.83 E-value=1.5e-20 Score=141.51 Aligned_cols=72 Identities=49% Similarity=0.750 Sum_probs=66.9
Q ss_pred HcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHHHHHcCC
Q 020008 96 LMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNL 167 (332)
Q Consensus 96 ~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl 167 (332)
.+||||++||+|||||||+|+++|++|+|+|+|+|+|+||+++++++++..++...++..++...+++++|+
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 589999999999999999999999999999999999999999999999877655557899999999999985
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=114.76 Aligned_cols=52 Identities=50% Similarity=0.809 Sum_probs=49.5
Q ss_pred HcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhh
Q 020008 164 ELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRE 215 (332)
Q Consensus 164 ~~gl~~~q~id~~~L~G--~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~ 215 (332)
.+|++|+||+++|+|+| |||.+||||||+|||.+||++|+++++++++++..
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 99999999999999999999999999999998764
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=99.41 E-value=1.7e-15 Score=120.96 Aligned_cols=91 Identities=33% Similarity=0.456 Sum_probs=50.0
Q ss_pred CCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCchH-----HHHHHh-CCCC
Q 020008 167 LTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQ-----EARRLF-KEPE 236 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~i---pgiG~ktA~~li~~~~sle~il~~~~~~~~-~~~~~~~~~-----~~~~~f-~~p~ 236 (332)
++|+|++|+.+|+| |.+||| ||||+|||.+||++|||+|+|+++++..+. ++.+.+... ..+.+- ++.+
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 589999999999999999999999987654 333322110 122222 2455
Q ss_pred cCCccchhccccCCCCHHHHHH
Q 020008 237 VVTDEEQLQIKWSAPDEEGLIN 258 (332)
Q Consensus 237 V~~~~~~~~l~~~~pd~~~l~~ 258 (332)
|+...+++++.|..||.++|.+
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 5655667789999999998864
No 23
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.24 E-value=7.1e-12 Score=81.28 Aligned_cols=33 Identities=55% Similarity=0.945 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCccHHHHHHHHHHc
Q 020008 169 MDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQH 202 (332)
Q Consensus 169 ~~q~id~~~L~G~Dy~~---~ipgiG~ktA~~li~~~ 202 (332)
|+||+++|+|+| ||+| ||||||+|||++||++|
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 67899999999999987
No 24
>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=98.91 E-value=1.3e-09 Score=87.13 Aligned_cols=47 Identities=55% Similarity=1.055 Sum_probs=41.6
Q ss_pred hhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhc
Q 020008 10 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (332)
Q Consensus 10 t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~ 56 (332)
++++.++++++..|+.+||+|||||||.+|+.|.++..+|+.+|+++
T Consensus 55 ~~~~~~~~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~r~~~ 101 (101)
T PF00752_consen 55 DSHLRGLFSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKRREEA 101 (101)
T ss_dssp -HHHHHHHHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHHHhcC
Confidence 69999999999999999999999999999999999999999888764
No 25
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=98.88 E-value=2.8e-09 Score=84.88 Aligned_cols=49 Identities=59% Similarity=0.969 Sum_probs=44.2
Q ss_pred Cchh-HHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhc
Q 020008 8 EVTS-HLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (332)
Q Consensus 8 ~~t~-~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~ 56 (332)
.+++ |+.++++++..|+++||+|||||||.+|+.|.++..+|+.+|+++
T Consensus 50 ~~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~~ 99 (99)
T smart00485 50 LPNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99 (99)
T ss_pred CCchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhcC
Confidence 3344 999999999999999999999999999999999999999988753
No 26
>PF12813 XPG_I_2: XPG domain containing
Probab=98.85 E-value=8.8e-09 Score=95.32 Aligned_cols=89 Identities=28% Similarity=0.271 Sum_probs=67.6
Q ss_pred HHHHHHHHHHHc---CCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccC--CceEEEee---cCC------CCCC
Q 020008 86 HNDDCKRLLKLM---GVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA--PRFLRHLM---DPS------SRKI 151 (332)
Q Consensus 86 ~~~~~~~lL~~~---Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~--~~vi~~l~---~~~------~~~~ 151 (332)
+.+.+.+.|+.+ |++++.+|||||..||.++++.-+ .|+|+|||+++|+. ..-|..+. ... ....
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 456788899998 999999999999999999987556 69999999999987 32222221 111 1123
Q ss_pred ccEEEeHHHHHHHcCCCHHHHHHHHH
Q 020008 152 PVMEFEVAKILEELNLTMDQFIDLCI 177 (332)
Q Consensus 152 ~~~~~~~~~v~~~~gl~~~q~id~~~ 177 (332)
....|+.+.++..+|+. .++.++.
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 6666655
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=98.67 E-value=2.7e-08 Score=106.91 Aligned_cols=68 Identities=38% Similarity=0.536 Sum_probs=55.0
Q ss_pred chhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhhhHHHHhhchhhchHHHH----HHHHcCCHHHHHHHh
Q 020008 9 VTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLA----EAVEAGNKEDIEKFS 76 (332)
Q Consensus 9 ~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~----~~~~~g~~~~~~k~~ 76 (332)
.++||.|||+|+++|+.+||+|||||||.+|++|.+++.+|+.+|+++.+... +++..+-...+.+.+
T Consensus 51 ~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a~~~a~~~~~~ll~~~~~~~a~~~~ 122 (1034)
T TIGR00600 51 KNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTA 122 (1034)
T ss_pred CCHHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999988766543 334444444444443
No 28
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=97.05 E-value=0.00054 Score=67.42 Aligned_cols=102 Identities=30% Similarity=0.438 Sum_probs=82.1
Q ss_pred HHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccC-CceEEEeecCCCCCCccEEEeHHHHHHHcC
Q 020008 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA-PRFLRHLMDPSSRKIPVMEFEVAKILEELN 166 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~-~~vi~~l~~~~~~~~~~~~~~~~~v~~~~g 166 (332)
+.+-+.+..-||.|+++|+-|..|||||....+++++. +-+|.+.|.+ ++++..+... ...-|+..++....++-.-
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 35667889999999999999999999999998998665 5599988875 6666555443 3345677778777777777
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCcc
Q 020008 167 LTMDQFIDLCILSGCDYCDSIRGIG 191 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~ipgiG 191 (332)
.+-.-|..+..|.|||.+..++.+-
T Consensus 210 ~s~~lFya~~ll~~c~~~s~~~~C~ 234 (531)
T COG5366 210 LSSRLFYALGLLLGCDFCSTIPRCA 234 (531)
T ss_pred cccchhhhhcccccccccccccccc
Confidence 7889999999999999999887643
No 29
>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=96.66 E-value=0.0099 Score=54.81 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=26.4
Q ss_pred CCCEEec----ccchHHHHHHHHHc---------CCeEEEecCCCcccccc
Q 020008 98 GVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSLTFG 135 (332)
Q Consensus 98 Gi~~i~a----p~EADaq~A~L~~~---------g~v~~V~S~DsD~l~fg 135 (332)
++.+|.+ |||+|--|..+.+. +...+|+|.|+|+++++
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 5667776 78999877666542 46788999999999987
No 30
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=95.84 E-value=0.12 Score=53.83 Aligned_cols=118 Identities=20% Similarity=0.391 Sum_probs=73.7
Q ss_pred HhhhhhccCHHHHHHHHHHHHH------------cCCCEEec----ccchHHHHHHHHHc---------CCeEEEecCCC
Q 020008 75 FSKRTVKVTKQHNDDCKRLLKL------------MGVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDM 129 (332)
Q Consensus 75 ~~~r~~~vt~~~~~~~~~lL~~------------~Gi~~i~a----p~EADaq~A~L~~~---------g~v~~V~S~Ds 129 (332)
|-..|+..-...++.+-+.|+. -++.+|.+ |||+|.-|-.+.+. +-.+.|.+-|-
T Consensus 141 fDSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDA 220 (953)
T COG5049 141 FDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDA 220 (953)
T ss_pred ccccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCc
Confidence 3344554433455555555544 35666654 89999988888773 35778999999
Q ss_pred ccccccC----Cc--eEE-Eee-cCCCC----------------------CCccEEEeHHHHHHHc-------CC----C
Q 020008 130 DSLTFGA----PR--FLR-HLM-DPSSR----------------------KIPVMEFEVAKILEEL-------NL----T 168 (332)
Q Consensus 130 D~l~fg~----~~--vi~-~l~-~~~~~----------------------~~~~~~~~~~~v~~~~-------gl----~ 168 (332)
|++.+|- |+ ++| ..+ ...++ ..++-+++.+-+.+.+ ++ +
T Consensus 221 DLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfd 300 (953)
T COG5049 221 DLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFD 300 (953)
T ss_pred cceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCcccc
Confidence 9999983 33 333 111 11110 1234556666554432 22 1
Q ss_pred ----HHHHHHHHHHhCCCCCCCCCCccH
Q 020008 169 ----MDQFIDLCILSGCDYCDSIRGIGG 192 (332)
Q Consensus 169 ----~~q~id~~~L~G~Dy~~~ipgiG~ 192 (332)
-+.||-+|-++|+||.+.+|++-.
T Consensus 301 lERilDDwIf~~FfvGNDFLPhLP~Ldi 328 (953)
T COG5049 301 LERILDDWIFLCFFVGNDFLPHLPCLDI 328 (953)
T ss_pred HHHhhhhheeeeeeeccccCCCCCcccc
Confidence 266788999999999999998764
No 31
>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=95.83 E-value=0.12 Score=55.40 Aligned_cols=185 Identities=21% Similarity=0.314 Sum_probs=107.7
Q ss_pred HHHHHHHHHHHHcCCCcEE----EEeCCCCchhhhhHHHHhhc-hhhchHHHHHHHHcCCHHHHHHHhhhhhccCHHHHH
Q 020008 14 QGMFTRTIRLLEAGMKPIY----VFDGQPPDLKKQELAKRYSK-RADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHND 88 (332)
Q Consensus 14 ~g~~~r~~~ll~~gi~Pv~----VFDG~~~~~K~~~~~~rk~~-R~~~~~~l~~~~~~g~~~~~~k~~~r~~~vt~~~~~ 88 (332)
..+|+-+-.|.. -|+|-= .-||.+|-.|......|+-+ -..+...+.+|.+.|+.-.-+.|-+.|+..-.+.+.
T Consensus 62 ~~IfnYIdhLf~-~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~ 140 (1493)
T KOG2045|consen 62 QEIFNYIDHLFY-LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMV 140 (1493)
T ss_pred HHHHHHHHHHHH-hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHH
Confidence 344444445555 488833 36999987776554444332 334566778888999864446666667665555555
Q ss_pred HHHHHHHH------------cCCCEEe----cccchHHHHHHHHHc---------CCeEEEecCCCccccccC----Cc-
Q 020008 89 DCKRLLKL------------MGVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR- 138 (332)
Q Consensus 89 ~~~~lL~~------------~Gi~~i~----ap~EADaq~A~L~~~---------g~v~~V~S~DsD~l~fg~----~~- 138 (332)
.+.+-|+. .++.+|- +|||+|.-|--+.+. +--.++..=|-|++++|- ++
T Consensus 141 rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF 220 (1493)
T KOG2045|consen 141 RLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHF 220 (1493)
T ss_pred HHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcce
Confidence 55555544 4777774 599999866665541 234457788999999982 22
Q ss_pred -eEEEe--ecCCCC--CCc---cEEEeHH-----------HHHHH--cCCC----HHHHHHHHHHhCCCCCCCCCCccH-
Q 020008 139 -FLRHL--MDPSSR--KIP---VMEFEVA-----------KILEE--LNLT----MDQFIDLCILSGCDYCDSIRGIGG- 192 (332)
Q Consensus 139 -vi~~l--~~~~~~--~~~---~~~~~~~-----------~v~~~--~gl~----~~q~id~~~L~G~Dy~~~ipgiG~- 192 (332)
++|-- +...++ ... +-..+++ ++... +..+ -+.||.++.|+|+||.+++|++-+
T Consensus 221 ~lLREEVtFgrrn~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn 300 (1493)
T KOG2045|consen 221 VLLREEVTFGRRNKRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHIN 300 (1493)
T ss_pred eeeeeeeecccccccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccC
Confidence 22211 111111 111 1112222 22211 1222 256778888999999999998865
Q ss_pred HHHHHHH
Q 020008 193 QTALKLI 199 (332)
Q Consensus 193 ktA~~li 199 (332)
..|+-|+
T Consensus 301 ~gAlpll 307 (1493)
T KOG2045|consen 301 SGALPLL 307 (1493)
T ss_pred CChHHHH
Confidence 3555554
No 32
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=95.79 E-value=0.06 Score=48.06 Aligned_cols=112 Identities=20% Similarity=0.271 Sum_probs=65.0
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhh---cC-CCCCCCchHHHHHHhC
Q 020008 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRE---RY-QIPEDWPYQEARRLFK 233 (332)
Q Consensus 159 ~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~---~~-~~~~~~~~~~~~~~f~ 233 (332)
++....||+ +.++--.+..|++ |+|||||+|+.++..+ +++++.+.+... .. .+| .+-...|..+..
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 444556887 5666666666654 8999999999999865 577887776531 11 222 222233333331
Q ss_pred --CCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+..+.....+..-.-..+..+.+.+-| ..+||+...++.++..+.
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 111110000000000123456677777 589999999999998874
No 33
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.67 E-value=0.0081 Score=43.89 Aligned_cols=27 Identities=33% Similarity=0.571 Sum_probs=21.8
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 185 ~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-||||||+++|..|++.|+|++++...
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 489999999999999999999987643
No 34
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=95.63 E-value=0.29 Score=48.45 Aligned_cols=110 Identities=21% Similarity=0.335 Sum_probs=66.7
Q ss_pred HHHHHHHc--CCCEEeccc-chHHHHHHHHH-----cCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHH
Q 020008 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (332)
Q Consensus 90 ~~~lL~~~--Gi~~i~ap~-EADaq~A~L~~-----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v 161 (332)
+.++|..+ +|.++...| .||-.+.+=++ .|.=..++|.|-|.|+|.+..-...+... +
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t--------------~ 213 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKT--------------M 213 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHh--------------H
Confidence 34455554 899999999 99987776665 47666789999999999864321111100 0
Q ss_pred HHHcCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHHh
Q 020008 162 LEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENINR 214 (332)
Q Consensus 162 ~~~~gl~~----~q~-id~~~L~G~Dy~~~ipgiG--~kt--A~~li~~~~sle~il~~~~~ 214 (332)
-+.|-+-| .-+ ...++.=||||-+|+-|+- +++ -.+|...| ++++|++.+--
T Consensus 214 ~~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~~ 274 (425)
T PF04599_consen 214 NQLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLAI 274 (425)
T ss_pred HhHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHhh
Confidence 11111111 111 2345566999999999864 332 13444444 57888877653
No 35
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=94.68 E-value=0.84 Score=48.37 Aligned_cols=187 Identities=19% Similarity=0.329 Sum_probs=102.6
Q ss_pred HHHHHHHHHHHHHHcCCCcEE-EEeCCCCchhhhhHHHH--hhchhhchHHH------HHHHHcCCH----HHHHHHhhh
Q 020008 12 HLQGMFTRTIRLLEAGMKPIY-VFDGQPPDLKKQELAKR--YSKRADATDDL------AEAVEAGNK----EDIEKFSKR 78 (332)
Q Consensus 12 ~l~g~~~r~~~ll~~gi~Pv~-VFDG~~~~~K~~~~~~r--k~~R~~~~~~l------~~~~~~g~~----~~~~k~~~r 78 (332)
++.-++.|++.|.+- =+-.| .-||.+|-.|......| ++.|+.+.++. ++...+|.. +..+.|-..
T Consensus 80 avFeyiDrlf~mvRP-RkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDSN 158 (931)
T KOG2044|consen 80 AVFEYIDRLFSMVRP-RKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDSN 158 (931)
T ss_pred HHHHHHHHHHHhccc-hheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccccC
Confidence 444444544444331 12244 58999987776554444 33333333222 112223321 111222334
Q ss_pred hhccCHHHHHHHHHHHHH------------cCCCEEec----ccchHHHHHHHHHc---------CCeEEEecCCCcccc
Q 020008 79 TVKVTKQHNDDCKRLLKL------------MGVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSLT 133 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~------------~Gi~~i~a----p~EADaq~A~L~~~---------g~v~~V~S~DsD~l~ 133 (332)
|++.-...++.+-..|+. -+|.+|.+ |||+|.-|-...+. +-++.+++-|-|++.
T Consensus 159 cITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLIm 238 (931)
T KOG2044|consen 159 CITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIM 238 (931)
T ss_pred ccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCcccee
Confidence 554433455555555554 36777765 89999877777662 347889999999999
Q ss_pred ccC-C-----ceEEEeecCCCC----------------------------------CCccEEEeHHHHHHHc-------C
Q 020008 134 FGA-P-----RFLRHLMDPSSR----------------------------------KIPVMEFEVAKILEEL-------N 166 (332)
Q Consensus 134 fg~-~-----~vi~~l~~~~~~----------------------------------~~~~~~~~~~~v~~~~-------g 166 (332)
+|- . .|+|-.+.++.. +.++.+++..-+.+.| +
T Consensus 239 LgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~ 318 (931)
T KOG2044|consen 239 LGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMPN 318 (931)
T ss_pred eeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCCC
Confidence 983 2 245543332110 1234455655444432 2
Q ss_pred ----CCH----HHHHHHHHHhCCCCCCCCCCccHH-HHHHHH
Q 020008 167 ----LTM----DQFIDLCILSGCDYCDSIRGIGGQ-TALKLI 199 (332)
Q Consensus 167 ----l~~----~q~id~~~L~G~Dy~~~ipgiG~k-tA~~li 199 (332)
++- +.||-+|-++|+||.+.+|-+-+. .|+++|
T Consensus 319 lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeIRegAId~L 360 (931)
T KOG2044|consen 319 LPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEIREGAIDRL 360 (931)
T ss_pred CCccccHHhhhcceEEEEeeecCccCCCCCchhhhhcHHHHH
Confidence 222 556668999999999999976653 344433
No 36
>PHA03065 Hypothetical protein; Provisional
Probab=94.61 E-value=0.67 Score=45.79 Aligned_cols=110 Identities=19% Similarity=0.332 Sum_probs=67.0
Q ss_pred HHHHHHHc--CCCEEeccc-chHHHHHHHHH-----cCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHH
Q 020008 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (332)
Q Consensus 90 ~~~lL~~~--Gi~~i~ap~-EADaq~A~L~~-----~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v 161 (332)
+-+.|..+ +|.++...| .||-.+..-++ .|.=..++|.|-|.|+|.+-.-.-.+ ...+
T Consensus 150 l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki--------------I~t~ 215 (438)
T PHA03065 150 LESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI--------------IKTA 215 (438)
T ss_pred HHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH--------------HHhH
Confidence 34457777 999999999 99987666554 46666789999999999864211000 0111
Q ss_pred HHHcCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHHh
Q 020008 162 LEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENINR 214 (332)
Q Consensus 162 ~~~~gl~~----~q~-id~~~L~G~Dy~~~ipgiG--~kt--A~~li~~~~sle~il~~~~~ 214 (332)
-+.|.+-| ..+ ...++.=||||-+|+-|+- +++ -++|...| ++++++..|--
T Consensus 216 ~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~ 276 (438)
T PHA03065 216 NQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLAI 276 (438)
T ss_pred HHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHHh
Confidence 11222211 112 2234556999999999864 432 24444454 46777776653
No 37
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.47 E-value=0.14 Score=45.58 Aligned_cols=91 Identities=19% Similarity=0.315 Sum_probs=49.1
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHhh---c-CCCCCCCchHHHHHHhC--CCCcC-CccchhccccCCCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILENINRE---R-YQIPEDWPYQEARRLFK--EPEVV-TDEEQLQIKWSAPDEEGLIN 258 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~~~~~~---~-~~~~~~~~~~~~~~~f~--~p~V~-~~~~~~~l~~~~pd~~~l~~ 258 (332)
.|||||||+|..++..|+. +.+.+.+... . ..+| .+....|..++. +.... .......-.-..+..+.+..
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 4999999999999999987 3333322211 0 0121 222223333221 11110 00000000111223678889
Q ss_pred HHHHhcCCChHHHHHHHHHHH
Q 020008 259 FLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 259 fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+| ..+||+...+.+.+..+.
T Consensus 155 aL-~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 155 AL-VALGYKPKEASKAVAKIL 174 (192)
T ss_pred HH-HHcCCCHHHHHHHHHHHh
Confidence 99 699999998888888775
No 38
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=93.11 E-value=0.67 Score=48.68 Aligned_cols=26 Identities=42% Similarity=0.694 Sum_probs=23.7
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 185 ~~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
++|||||+++|..|++.|||+++|..
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 57999999999999999999988764
No 39
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.97 E-value=0.3 Score=43.71 Aligned_cols=111 Identities=17% Similarity=0.278 Sum_probs=61.4
Q ss_pred HHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhc---C-CCCCCCchHHHHHHh
Q 020008 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER---Y-QIPEDWPYQEARRLF 232 (332)
Q Consensus 158 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~---~-~~~~~~~~~~~~~~f 232 (332)
.++....||+ +.++--.|..|+ +|+|||||+|+.++..|+ .+++++.+.... . .+| ..-...|..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vp-GIGkKtAerIi 125 (194)
T PRK14605 54 REDALSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIP-GIGKKTASRIV 125 (194)
T ss_pred ecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHH
Confidence 3444556887 566666666665 589999999999999886 677766653211 0 121 11122233322
Q ss_pred C--CCCcCC--ccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 233 K--EPEVVT--DEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 233 ~--~p~V~~--~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+ +..+.. .... ... .....+.+...| ..+||+...+.+.++.+.
T Consensus 126 lELk~Ki~~~~~~~~-~~~-~~~~~~e~~~aL-~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 126 LELKDKIAKNWEAGV-LSQ-VTEANSDILATL-TALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHHhhhhccc-ccc-ccchHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 1 000000 0000 000 011235666777 599999999998888764
No 40
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=91.27 E-value=2.8 Score=37.70 Aligned_cols=118 Identities=18% Similarity=0.214 Sum_probs=64.7
Q ss_pred EEeHHHHHHHcCCC-HHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc---hHHHHH
Q 020008 155 EFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARR 230 (332)
Q Consensus 155 ~~~~~~v~~~~gl~-~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~---~~~~~~ 230 (332)
.+-.++....||+. .+.=..|..|. +|.|||||+|+.+|.. -+++++.+.+.......=..+| -.-|..
T Consensus 51 ~~vREd~~~LyGF~~~~ER~lF~~Li------sVnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGIGkKtAer 123 (201)
T COG0632 51 LVVREDAHLLYGFLTEEERELFRLLI------SVNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGIGKKTAER 123 (201)
T ss_pred EeehhhHHHHcCCCCHHHHHHHHHHH------ccCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCCCHHHHHH
Confidence 45567778889985 44444455554 4789999999999985 4678888877643222112222 223444
Q ss_pred HhC--C---CCcCC--ccchhccccCC----CCHHHHHHHHHHhcCCChHHHHHHHHHHHHh
Q 020008 231 LFK--E---PEVVT--DEEQLQIKWSA----PDEEGLINFLVSENGFNSDRVTKAIEKIKAA 281 (332)
Q Consensus 231 ~f~--~---p~V~~--~~~~~~l~~~~----pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~ 281 (332)
+.+ . +.... .... ...+.. |-.+.-.+=| ..+||++..+++++..+...
T Consensus 124 ivleLk~K~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~AL-~~LGy~~~e~~~av~~v~~~ 183 (201)
T COG0632 124 IVLELKGKLAAFLKGDGGSP-AEDLSLDESSPALEEAVEAL-VALGYKEKEIKKAVKKVLKE 183 (201)
T ss_pred HHHHHhhhhhhhcccccccc-cccccccccchhhhHHHHHH-HHcCCCHHHHHHHHHHHHhc
Confidence 332 1 11000 0000 111211 1122213344 48999999999998877643
No 41
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.19 E-value=1.3 Score=39.32 Aligned_cols=110 Identities=15% Similarity=0.211 Sum_probs=60.6
Q ss_pred HHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC---CCCCCCchHHHHHHhC
Q 020008 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY---QIPEDWPYQEARRLFK 233 (332)
Q Consensus 158 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~---~~~~~~~~~~~~~~f~ 233 (332)
.++....||+ +.++--.+-.|+ +|.|||||+|+.+|..+ +++++...+..... ++|- .-...|..+.+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li------sV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~vpG-IGkKtAerIil 125 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLV------KVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAALKVNG-IGEKLINRIIT 125 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhheECCC-CcHHHHHHHHH
Confidence 4455566887 455555555554 58899999999999876 57777777653211 2221 11233333331
Q ss_pred --CCCcC-CccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 --EPEVV-TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 --~p~V~-~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+-.+. ..... . . ..+..+.+..=| ..+||+...+++++.++.
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 11110 00000 0 0 111234445555 599999999999998773
No 42
>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=91.04 E-value=0.21 Score=35.71 Aligned_cols=25 Identities=36% Similarity=0.476 Sum_probs=22.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-~~sle~il~ 210 (332)
+|||||+++|..|+.. |.+++++..
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 6899999999999998 899988875
No 43
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=91.03 E-value=0.17 Score=52.39 Aligned_cols=29 Identities=24% Similarity=0.378 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-.|+|||||+++...||+.|||+++|.++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 45789999999999999999999998753
No 44
>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=90.95 E-value=0.17 Score=52.51 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=26.1
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 182 Dy~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
.-.++||||||++...||+.|||+++|.++
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 345789999999999999999999988653
No 45
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.83 E-value=1 Score=40.37 Aligned_cols=109 Identities=20% Similarity=0.267 Sum_probs=58.5
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC
Q 020008 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (332)
Q Consensus 159 ~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f~ 233 (332)
++-...||+ +.++.-.+..|+ +|.|||||+|+.+|..+ +++++...+..... ++|- .-..-|..+.+
T Consensus 54 ED~~~LYGF~t~~Er~lF~~Li------sVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIIl 125 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELI------GVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKG-IGNKMAGKIFL 125 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 444556786 555555566665 47899999999999876 46777776653211 1221 11222333321
Q ss_pred --CCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+-.+...... .- .....+.+.+=| ..+||+...+.+++..+.
T Consensus 126 ELkdKl~~~~~~-~~--~~~~~~ea~~AL-~~LGy~~~ea~~al~~v~ 169 (196)
T PRK13901 126 KLRGKLVKNDEL-ES--SLFKFKELEQSI-VNMGFDRKLVNSAIKEIM 169 (196)
T ss_pred HHHHhhcccccc-cc--CcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1111100000 00 111234444555 499999999999887654
No 46
>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=90.81 E-value=0.22 Score=34.94 Aligned_cols=25 Identities=28% Similarity=0.413 Sum_probs=17.8
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-~~sle~il~ 210 (332)
+|.||||+||.+++.+ +.|++++..
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hcccccHHHHHHHHHhCCCCHHHHhh
Confidence 6899999999999985 678888843
No 47
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=90.69 E-value=0.21 Score=52.37 Aligned_cols=28 Identities=29% Similarity=0.520 Sum_probs=25.3
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
-.++|||||++++.+|++.|||+++|..
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~ 580 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRA 580 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4468999999999999999999999875
No 48
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=90.62 E-value=0.2 Score=51.98 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=26.0
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-.++||||||++..+||+.|||+++|.++
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 45789999999999999999999998754
No 49
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.41 E-value=1.6 Score=39.14 Aligned_cols=109 Identities=17% Similarity=0.217 Sum_probs=56.4
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC-
Q 020008 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (332)
Q Consensus 160 ~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f~- 233 (332)
+....||+ +.++--.|..|+ +|.|||||+|+.+|..+ +++++...+..... ++|- .-..-|..+..
T Consensus 56 d~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpG-IGkKtAerIilE 127 (195)
T PRK14604 56 DALTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPG-IGKKTAERIVLE 127 (195)
T ss_pred CCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 34455776 455555555554 47888999999988864 56777776653211 1211 11122222221
Q ss_pred -CCCcC---CccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 -EPEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 -~p~V~---~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+-.+. ....... . .....+.+.+=| ..+||+...+.+++.++.
T Consensus 128 Lk~K~~~~~~~~~~~~-~-~~~~~~e~~~aL-~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 128 LKGKIDVRQLSGSTSP-A-VSALDRELSEIL-ISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHHhccccccccccc-c-ccccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 00000 0000000 0 011134455666 499999999999998874
No 50
>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=90.36 E-value=0.24 Score=30.64 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.6
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||++||-.++.
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 479999999988763
No 51
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.66 E-value=1.1 Score=39.71 Aligned_cols=105 Identities=14% Similarity=0.243 Sum_probs=57.8
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC
Q 020008 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (332)
Q Consensus 159 ~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f~ 233 (332)
++....||+ +.++--.|..|. +|.|||||+|+.++..+ +++++...+..... ++|- .-..-|..+.+
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li------~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIil 126 (183)
T PRK14601 55 EDSNKLYGFLDKDEQKMFEMLL------KVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPG-IGPKSAKRIIA 126 (183)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 444556787 555555555554 47899999999999875 56777776653211 1221 11222333321
Q ss_pred --CCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHH
Q 020008 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKI 278 (332)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l 278 (332)
+..+. ..+. .....+.+.+=| ..+||++..++++++.+
T Consensus 127 ELkdK~~---~~~~---~~~~~~ea~~AL-~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 127 ELSDAKT---KLEN---VSDDKSEALAAL-LTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHhh---ccCC---CCccHHHHHHHH-HHcCCCHHHHHHHHHhc
Confidence 11110 0000 011234444555 49999999999998776
No 52
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.32 E-value=1.8 Score=38.77 Aligned_cols=111 Identities=15% Similarity=0.118 Sum_probs=54.6
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC-
Q 020008 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (332)
Q Consensus 160 ~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f~- 233 (332)
+....||+ +.++-..|-.|+ +|.|||||+|+.+|..+ +++++.+.+..... ++|- .-...|..+..
T Consensus 55 d~~~LyGF~~~~Er~lF~~L~------~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpG-IGkKtAerIilE 126 (197)
T PRK14603 55 DALSLYGFPDEDSLELFELLL------GVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASG-VGKKLAERIALE 126 (197)
T ss_pred CCceeeCcCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33455776 344444444443 47888888888888765 46677666642210 1111 11111222210
Q ss_pred -CCCcC---Cccch-hcccc-CCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 -EPEVV---TDEEQ-LQIKW-SAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 -~p~V~---~~~~~-~~l~~-~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+-.+. ..... ..... ..+..+.+.+-| ..+||+...+.+++.++.
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 00000 00000 00001 112234455556 599999999999998874
No 53
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=89.13 E-value=0.99 Score=46.93 Aligned_cols=29 Identities=31% Similarity=0.493 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-.|+|||||+++...||+.|||+++|.+.
T Consensus 531 ~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 531 SLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred ccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 45799999999999999999999988754
No 54
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.48 E-value=0.72 Score=41.53 Aligned_cols=112 Identities=14% Similarity=0.206 Sum_probs=59.2
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC
Q 020008 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (332)
Q Consensus 159 ~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f~ 233 (332)
++-...||+ +.++--.|..|.+ |.|||||+|+.+|..+ +.+++.+.+..... ++|- .-...|..+..
T Consensus 56 Ed~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~~ipG-IGkKtAerIil 127 (203)
T PRK14602 56 EDALELFGFATWDERQTFIVLIS------ISKVGAKTALAILSQF-RPDDLRRLVAEEDVAALTRVSG-IGKKTAQHIFL 127 (203)
T ss_pred cCcceeeCCCCHHHHHHHHHHhC------CCCcCHHHHHHHHhhC-CHHHHHHHHHhCCHHHHhcCCC-cCHHHHHHHHH
Confidence 344556787 5666666666654 8899999999999876 46777776653211 1211 11122222221
Q ss_pred --CCCc-----CCccchhcccc-CCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 234 --EPEV-----VTDEEQLQIKW-SAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 234 --~p~V-----~~~~~~~~l~~-~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+-.+ ........... .....+.+.+=| ..+||++..+.+++.++.
T Consensus 128 ELkdK~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL-~~LGy~~~ea~~av~~~~ 180 (203)
T PRK14602 128 ELKYKLKVEGLPAAAVLAGTGAVPGSVFRDALAGL-ANLGYGEEEARPVLKEVL 180 (203)
T ss_pred HHHHhhccccccccccccccccCCCchHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1000 00000000001 111224444555 599999999999998774
No 55
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=88.24 E-value=0.38 Score=50.59 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=26.3
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 182 Dy~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
.-.++|||||++++..||+.|||+++|.++
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 355789999999999999999999998754
No 56
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.32 E-value=0.92 Score=40.39 Aligned_cols=108 Identities=16% Similarity=0.198 Sum_probs=60.8
Q ss_pred HHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHh
Q 020008 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLF 232 (332)
Q Consensus 158 ~~~v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~----~~~~~~~~~~~~~~f 232 (332)
.++....||+ +.++--.|..|+ +|.|||||+|+.+|..+ +++++.+.+..... ++|- .-..-|..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAerIi 125 (188)
T PRK14606 54 SQDGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPG-ISKKTAERIV 125 (188)
T ss_pred ecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHH
Confidence 3444566887 455555555554 48899999999999875 57777777653211 1221 1122233333
Q ss_pred C--CCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 233 K--EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 233 ~--~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
+ +-.+.. ... ......+.+.+=| ..+||++..+++++..+.
T Consensus 126 lELkdK~~~-~~~----~~~~~~~e~~~AL-~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 126 MELKDEFES-AGI----KDMRIYHESLEAL-VSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHhhcc-ccC----CCcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1 111110 000 0011234455555 499999999999998774
No 57
>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=85.07 E-value=0.76 Score=35.38 Aligned_cols=26 Identities=38% Similarity=0.524 Sum_probs=21.3
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHH
Q 020008 182 DYCDSIRGIGGQTALKLIRQHGSIET 207 (332)
Q Consensus 182 Dy~~~ipgiG~ktA~~li~~~~sle~ 207 (332)
+....|||||+.+|..||.+.++++.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchh
Confidence 34457999999999999999887643
No 58
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=84.94 E-value=0.68 Score=48.41 Aligned_cols=27 Identities=37% Similarity=0.634 Sum_probs=24.6
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 185 ~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
++|||||++++..|++.|||+++|.++
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 59
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=84.57 E-value=0.76 Score=47.83 Aligned_cols=29 Identities=34% Similarity=0.635 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
..+.|||||++++.+|++.|||+++|.++
T Consensus 526 ~L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 34689999999999999999999999864
No 60
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=84.10 E-value=0.82 Score=41.84 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=24.7
Q ss_pred CCCCCCccHHHHHHHHHH-cCCHHHHHHH
Q 020008 184 CDSIRGIGGQTALKLIRQ-HGSIETILEN 211 (332)
Q Consensus 184 ~~~ipgiG~ktA~~li~~-~~sle~il~~ 211 (332)
.+.|||||+++|..|++. |+|+++|...
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 357899999999999999 9999988654
No 61
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=83.87 E-value=0.85 Score=48.20 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=25.7
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-.+.|||||++++..|++.|||+++|.+.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 34579999999999999999999999874
No 62
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.63 E-value=0.96 Score=26.69 Aligned_cols=17 Identities=35% Similarity=0.520 Sum_probs=14.5
Q ss_pred CCCCCccHHHHHHHHHH
Q 020008 185 DSIRGIGGQTALKLIRQ 201 (332)
Q Consensus 185 ~~ipgiG~ktA~~li~~ 201 (332)
..|||||+++|..++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 36899999999998863
No 63
>PRK13766 Hef nuclease; Provisional
Probab=83.36 E-value=18 Score=38.79 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=23.2
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
+|||||+++|..|++.||++++++.
T Consensus 719 ~ipgig~~~a~~Ll~~fgs~~~i~~ 743 (773)
T PRK13766 719 SLPDVGPVLARNLLEHFGSVEAVMT 743 (773)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 5899999999999999999998875
No 64
>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=80.90 E-value=5.8 Score=34.42 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=28.8
Q ss_pred cCCCEEeccc--chHHHHHHHHHc----CCeEEEecCCCccccc
Q 020008 97 MGVPVVEAPS--EAEAQCAALCKS----GQVYAVASEDMDSLTF 134 (332)
Q Consensus 97 ~Gi~~i~ap~--EADaq~A~L~~~----g~v~~V~S~DsD~l~f 134 (332)
-||.++.++. .||+.|-.++.. +.-..|+|+|...-..
T Consensus 66 ~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~ 109 (166)
T PF05991_consen 66 GGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRA 109 (166)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHH
Confidence 4888888874 999999888762 4556789998876544
No 65
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=80.53 E-value=1.5 Score=40.84 Aligned_cols=26 Identities=42% Similarity=0.724 Sum_probs=23.8
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
++||||++.|..|++.|||+++++..
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 57999999999999999999998864
No 66
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.63 E-value=1.9 Score=38.19 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=33.2
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 020008 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (332)
Q Consensus 155 ~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~ 201 (332)
-+....-+.-+ ++++++|.. ++..| |..- .+||||+|||-+++-+
T Consensus 80 GIGpK~Al~ILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 80 GIGANTAMAVCSSLDVNSFYK-ALSLG-DESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 35556666666 578888765 46666 6653 6899999999999976
No 67
>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=78.38 E-value=7.8 Score=41.57 Aligned_cols=39 Identities=21% Similarity=0.480 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 020008 167 LTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~ 213 (332)
-+.+.++.+.. .| .|||||+++|.+++..|| ++.++.+.
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 35677777654 33 689999999999999999 34455543
No 68
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.28 E-value=3.9 Score=36.63 Aligned_cols=48 Identities=21% Similarity=0.187 Sum_probs=35.3
Q ss_pred EEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHcC
Q 020008 154 MEFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQHG 203 (332)
Q Consensus 154 ~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~~~ 203 (332)
.-+....-+.-++ +++++|+. ++..| |..- .+||||+|||-+++-+..
T Consensus 78 ~GIGpK~AL~iLs~~~~~~l~~-aI~~~-D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 78 SGVGPKLALALLSALPPALLAR-ALLEG-DARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CCcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHHH
Confidence 3456666677775 78888875 45566 7663 689999999999997643
No 69
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.30 E-value=4.2 Score=36.10 Aligned_cols=47 Identities=21% Similarity=0.340 Sum_probs=34.2
Q ss_pred EEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC-CCCCccHHHHHHHHHHc
Q 020008 154 MEFEVAKILEELN-LTMDQFIDLCILSGCDYCD-SIRGIGGQTALKLIRQH 202 (332)
Q Consensus 154 ~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~-~ipgiG~ktA~~li~~~ 202 (332)
.-+....-+.-+. +++++|+.. +-.| |..- .+||||+|||-+++-+.
T Consensus 79 ~GIGpK~Al~iLs~~~~~~l~~a-I~~~-D~~~L~vpGIGkKtAerIilEL 127 (186)
T PRK14600 79 SGVNYKTAMSILSKLTPEQLFSA-IVNE-DKAALKVNGIGEKLINRIITEL 127 (186)
T ss_pred CCcCHHHHHHHHccCCHHHHHHH-HHcC-CHhheECCCCcHHHHHHHHHHH
Confidence 3456666677675 788888764 4556 6543 68999999999999763
No 70
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=72.87 E-value=3.2 Score=34.72 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=19.3
Q ss_pred CCCccHHHHHHHHHH--cCCHHHHHH
Q 020008 187 IRGIGGQTALKLIRQ--HGSIETILE 210 (332)
Q Consensus 187 ipgiG~ktA~~li~~--~~sle~il~ 210 (332)
+|||||+.|-++|+. |.++|++++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 699999999999963 567777764
No 71
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.83 E-value=4.2 Score=36.39 Aligned_cols=46 Identities=26% Similarity=0.308 Sum_probs=33.2
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 020008 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (332)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~ipgiG~ktA~~li~~~ 202 (332)
-+....-+.-++ +++++|+. ++..| |.. -.+||||+|||-+++-+.
T Consensus 80 GIGpK~Al~iLs~~~~~el~~-aI~~~-D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 80 GVGPKAALNLLSSGTPDELQL-AIAGG-DVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 355566666665 68888775 45555 665 368999999999999764
No 72
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.50 E-value=3 Score=37.42 Aligned_cols=45 Identities=24% Similarity=0.326 Sum_probs=32.8
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 020008 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (332)
Q Consensus 155 ~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~ 201 (332)
-+.....+.-+ .+++++|+. ++..| |..- .+||||+|||-++|-+
T Consensus 79 GIGPK~ALaILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 79 GIGPRAALRVLSGIKYNEFRD-AIDRE-DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 35555566666 478888775 45666 7663 6999999999999976
No 73
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.92 E-value=4.6 Score=35.91 Aligned_cols=47 Identities=19% Similarity=0.262 Sum_probs=34.5
Q ss_pred EEEeHHHHHHHc-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 020008 154 MEFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (332)
Q Consensus 154 ~~~~~~~v~~~~-gl~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~~ 202 (332)
.-+.+..-+.-+ ++++++|+. ++..| |..- .+||||+|||-+++-+-
T Consensus 79 ~GIGpK~AL~iLs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 79 SRLGPKTALKIISNEDAETLVT-MIASQ-DVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred CCccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 345666667777 578888875 45666 6653 68999999999999763
No 74
>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=71.53 E-value=3.6 Score=43.56 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=16.4
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
||||||+++|..|++.|+|++++..
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~ 526 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKA 526 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4667777777777777776666543
No 75
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=69.83 E-value=3.9 Score=44.39 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
++||||+++|..|+.+|+|++++..
T Consensus 761 ~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred HCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4799999999999999999998875
No 76
>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=69.75 E-value=6.9 Score=33.18 Aligned_cols=89 Identities=16% Similarity=0.223 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccccCCc--eEEEeecCCCCCCccEEEeHHHHH
Q 020008 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPR--FLRHLMDPSSRKIPVMEFEVAKIL 162 (332)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~--vi~~l~~~~~~~~~~~~~~~~~v~ 162 (332)
.|+..+-+.|+.+|+.++..+...|+.+..++...-- +++|-|.+++-..... ++. + .+.. ..-.+.+++
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~~~~~~~~~~~l-i-~~~~-----~~~QL~ev~ 78 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLLKRRRVSGGVIL-I-RSDD-----PEEQLREVL 78 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHHHhhccCCEEE-E-cCCC-----HHHHHHHHH
Confidence 3556788899999999999998889999999876433 3789999987654322 221 1 1110 122455667
Q ss_pred HHcCCCH--HHHHHHHHHhCC
Q 020008 163 EELNLTM--DQFIDLCILSGC 181 (332)
Q Consensus 163 ~~~gl~~--~q~id~~~L~G~ 181 (332)
+.+++.+ +.+..-|..|++
T Consensus 79 ~~~~l~~~~~~~~sRC~~CN~ 99 (147)
T PF01927_consen 79 ERFGLKLRLDPIFSRCPKCNG 99 (147)
T ss_pred HHcCCccccCCCCCccCCCCc
Confidence 7777655 333345666653
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=68.90 E-value=4.6 Score=43.04 Aligned_cols=25 Identities=36% Similarity=0.622 Sum_probs=22.1
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
+|||||+++|..|++.|++++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 5799999999999999999988764
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.77 E-value=5.7 Score=35.74 Aligned_cols=46 Identities=20% Similarity=0.288 Sum_probs=33.4
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 020008 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (332)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~ipgiG~ktA~~li~~~ 202 (332)
-+....-+.-++ +++++|+. ++..| |.. -.+||||+|||-+++-+.
T Consensus 81 GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 81 KVGAKTALAILSQFRPDDLRR-LVAEE-DVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CcCHHHHHHHHhhCCHHHHHH-HHHhC-CHHHHhcCCCcCHHHHHHHHHHH
Confidence 355666666665 68887765 45566 665 369999999999999763
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=66.79 E-value=5.9 Score=32.52 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=14.7
Q ss_pred CCCCccHHHHHHHHHHc
Q 020008 186 SIRGIGGQTALKLIRQH 202 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~ 202 (332)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 47999999999999874
No 80
>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=66.06 E-value=4.5 Score=25.20 Aligned_cols=13 Identities=54% Similarity=0.695 Sum_probs=10.2
Q ss_pred CCCCccHHHHHHH
Q 020008 186 SIRGIGGQTALKL 198 (332)
Q Consensus 186 ~ipgiG~ktA~~l 198 (332)
.++|||++|+.+|
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 5799999998875
No 81
>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=64.66 E-value=6.9 Score=37.43 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=21.3
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQH--GSIETILENI 212 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~--~sle~il~~~ 212 (332)
+||||||++|.+|. +. .|++++....
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 58999999999999 64 4888887753
No 82
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=64.08 E-value=6 Score=38.33 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=20.9
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHG--SIETILEN 211 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~--sle~il~~ 211 (332)
+||||||+||..|.+ .| |++++.++
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 589999999999988 65 78887654
No 83
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=63.18 E-value=8.6 Score=34.60 Aligned_cols=73 Identities=26% Similarity=0.321 Sum_probs=45.1
Q ss_pred CeEEEecCCCccccccCCc-----eEEEeecCCCCCCccEEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCcc
Q 020008 120 QVYAVASEDMDSLTFGAPR-----FLRHLMDPSSRKIPVMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIG 191 (332)
Q Consensus 120 ~v~~V~S~DsD~l~fg~~~-----vi~~l~~~~~~~~~~~~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~--~~ipgiG 191 (332)
+..-++.+|. ..+||-.. +++.+. .+.-+....-+.-+. ++++.|+.. +-.+ |++ -.+||||
T Consensus 48 ~t~~~vREd~-~~LyGF~~~~ER~lF~~Li-------sVnGIGpK~ALaiLs~~~~~~l~~a-I~~~-d~~~L~k~PGIG 117 (201)
T COG0632 48 FTHLVVREDA-HLLYGFLTEEERELFRLLI-------SVNGIGPKLALAILSNLDPEELAQA-IANE-DVKALSKIPGIG 117 (201)
T ss_pred EEEEeehhhH-HHHcCCCCHHHHHHHHHHH-------ccCCccHHHHHHHHcCCCHHHHHHH-HHhc-ChHhhhcCCCCC
Confidence 3566778888 77777431 111111 122345555566553 578887754 4445 665 3689999
Q ss_pred HHHHHHHHHHc
Q 020008 192 GQTALKLIRQH 202 (332)
Q Consensus 192 ~ktA~~li~~~ 202 (332)
.|||-+|+-+-
T Consensus 118 kKtAerivleL 128 (201)
T COG0632 118 KKTAERIVLEL 128 (201)
T ss_pred HHHHHHHHHHH
Confidence 99999999764
No 84
>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=61.99 E-value=15 Score=31.27 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHcCCCEEecccchHHHHHHHHHc
Q 020008 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS 118 (332)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~ 118 (332)
+.+.++.+-|+.+|++.++-.|++...+..|++.
T Consensus 53 ~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~ 86 (165)
T PF00875_consen 53 ESLADLQESLRKLGIPLLVLRGDPEEVLPELAKE 86 (165)
T ss_dssp HHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCcceEEEecchHHHHHHHHHh
Confidence 4567788888999999999999999998888774
No 85
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.74 E-value=5.9 Score=42.05 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=10.1
Q ss_pred HHHHHHHHHcCCCEE
Q 020008 88 DDCKRLLKLMGVPVV 102 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i 102 (332)
.+..+.|+.+|+|+.
T Consensus 239 ~e~l~~L~~~GF~v~ 253 (665)
T PRK07956 239 SEALEFLKAWGFPVN 253 (665)
T ss_pred HHHHHHHHHCCCCcC
Confidence 345666788888764
No 86
>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=59.38 E-value=17 Score=30.73 Aligned_cols=44 Identities=25% Similarity=0.290 Sum_probs=36.1
Q ss_pred cCHHHHHHHHHHHHHcCCC-----EEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 82 VTKQHNDDCKRLLKLMGVP-----VVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~-----~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
|+..+.+-+.+.|+..|+. ++..|| |-=-.+..|++.|..|+|+
T Consensus 14 i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI 64 (138)
T TIGR00114 14 ITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVI 64 (138)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 4567888899999999875 788999 8878888899887777776
No 87
>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=56.62 E-value=7.7 Score=31.00 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=23.8
Q ss_pred ccchHHHHHHHHHcCCeEEEecCCCcccc
Q 020008 105 PSEAEAQCAALCKSGQVYAVASEDMDSLT 133 (332)
Q Consensus 105 p~EADaq~A~L~~~g~v~~V~S~DsD~l~ 133 (332)
|-..|+-+..++..+-+++++|+|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 34667777888888889999999999874
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=56.55 E-value=13 Score=26.96 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=13.2
Q ss_pred CCCccHHHHHHHHHH
Q 020008 187 IRGIGGQTALKLIRQ 201 (332)
Q Consensus 187 ipgiG~ktA~~li~~ 201 (332)
+||||+++|..+|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 688999999999887
No 89
>PRK08609 hypothetical protein; Provisional
Probab=56.54 E-value=18 Score=37.63 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=20.2
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHG--SIETILENIN 213 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~--sle~il~~~~ 213 (332)
.||||||++|.+|-++.| |++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 578899998888887654 6776665543
No 90
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=56.41 E-value=13 Score=31.87 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=18.3
Q ss_pred CCCCccHHHHHHHHHH------cCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ------HGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~------~~sle~il~ 210 (332)
.+||||+++|..++.. |.+++++..
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 4689999999999863 456666543
No 91
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=55.23 E-value=14 Score=31.78 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 020008 170 DQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 170 ~q~id~~~L~G~Dy~~~---------ipgiG~ktA~~li~~~~ 203 (332)
++|-.+.-++|+|..++ |.|||+.+|..++++.|
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 57788888899888765 57999999999999876
No 92
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=52.71 E-value=22 Score=30.79 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=36.1
Q ss_pred cCHHHHHHHHHHHHHcC-----CCEEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~G-----i~~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
||..+++-+.+.|...| |.++..|| |-=..+..|++.|..|+|+
T Consensus 24 It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiI 74 (158)
T PRK12419 24 IVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIV 74 (158)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 45677888899999999 67888999 8888888898887777766
No 93
>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=51.50 E-value=29 Score=29.44 Aligned_cols=43 Identities=30% Similarity=0.340 Sum_probs=36.3
Q ss_pred CHHHHHHHHHHHHHcCC-----CEEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 83 TKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 83 t~~~~~~~~~lL~~~Gi-----~~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
+..+++.+.+.|...|+ .++..|| |-=-.+..|.+.+.+|+|+
T Consensus 18 ~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi 67 (144)
T PF00885_consen 18 TDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVI 67 (144)
T ss_dssp HHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEE
T ss_pred HHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEE
Confidence 35677888999999987 7888999 8888999999998888877
No 94
>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=50.21 E-value=21 Score=31.70 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=30.0
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 020008 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (332)
Q Consensus 155 ~~~~~~v~~~~g-l~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~ 201 (332)
-+.....+.-++ ++++++...+ ..| |..- .|||||+|||-+++-+
T Consensus 79 GIGpK~Al~iL~~~~~~el~~aI-~~~-d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 79 GVGPKLALAILSNMSPEEFVYAI-ETE-EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCHHHHHHHHhcCCHHHHHHHH-HhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 355555556665 4677776543 334 5543 6899999999999844
No 95
>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=50.07 E-value=32 Score=28.38 Aligned_cols=19 Identities=47% Similarity=0.754 Sum_probs=15.5
Q ss_pred HHHHHHcCCCcEE-EEeCCC
Q 020008 20 TIRLLEAGMKPIY-VFDGQP 38 (332)
Q Consensus 20 ~~~ll~~gi~Pv~-VFDG~~ 38 (332)
+.+|+++|+.|.. |+||+.
T Consensus 2 T~~ll~~g~~P~laIvD~kT 21 (121)
T PF04019_consen 2 TYNLLEAGIIPDLAIVDGKT 21 (121)
T ss_pred hHHHHhCCCCCCEEEEeCcc
Confidence 4578999999955 899984
No 96
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=49.88 E-value=10 Score=40.05 Aligned_cols=27 Identities=37% Similarity=0.570 Sum_probs=23.7
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 185 ~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-|||.||.++|..|.+.|+|++++++.
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 578999999999999999999988764
No 97
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=49.37 E-value=55 Score=28.52 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccc
Q 020008 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (332)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~f 134 (332)
..|+-.+-++|+.||.+.+..-.+.|+.+..++.+.-. +++|-|.-++-.
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 56788899999999999998888999999988876333 478999998887
No 98
>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=49.21 E-value=35 Score=26.87 Aligned_cols=31 Identities=26% Similarity=0.174 Sum_probs=21.7
Q ss_pred CCCCccHHHHHHHHHH-cC--------CHHHHHHHHHhhc
Q 020008 186 SIRGIGGQTALKLIRQ-HG--------SIETILENINRER 216 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-~~--------sle~il~~~~~~~ 216 (332)
.|||||+.+|..|+.- +. +.+++++.+....
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~ 55 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALT 55 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHc
Confidence 5899999999999852 23 4455666665543
No 99
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=47.72 E-value=18 Score=35.41 Aligned_cols=54 Identities=30% Similarity=0.459 Sum_probs=37.5
Q ss_pred HHHHHHHc-CCCHHHHHHH---HHHhCCCC----CC------------CCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 158 VAKILEEL-NLTMDQFIDL---CILSGCDY----CD------------SIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 158 ~~~v~~~~-gl~~~q~id~---~~L~G~Dy----~~------------~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
.+++++.+ .++.+++.|+ +-++|-.- .| +||+|++..|..|+.+|||+.+|+..
T Consensus 243 ~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 243 PEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred HHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 45666655 4666666554 34556211 11 15899999999999999999999863
No 100
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=46.85 E-value=31 Score=29.70 Aligned_cols=44 Identities=30% Similarity=0.353 Sum_probs=35.0
Q ss_pred cCHHHHHHHHHHHHHcC-----CCEEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~G-----i~~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
|+..+++-+.+.|...| |.++..|| |-=-.+..|++.+..|+|+
T Consensus 26 i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI 76 (154)
T PRK00061 26 ITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVI 76 (154)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEE
Confidence 34677888999999999 45777899 7777888888887777776
No 101
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=46.82 E-value=29 Score=29.71 Aligned_cols=35 Identities=31% Similarity=0.549 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 020008 169 MDQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 169 ~~q~id~~~L~G~Dy~~~---------ipgiG~ktA~~li~~~~ 203 (332)
.++|-.+.-++|+|-.++ |.|||+.+|..++++.|
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 346667777889888765 46999999999999876
No 102
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=46.48 E-value=34 Score=29.01 Aligned_cols=44 Identities=30% Similarity=0.308 Sum_probs=35.4
Q ss_pred cCHHHHHHHHHHHHHcCC-----CEEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 82 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi-----~~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
|+..+++-+.+.|...|+ .++..|| |-=-.+..|++.+..|+|+
T Consensus 21 I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavI 71 (141)
T PLN02404 21 ITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAIL 71 (141)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEE
Confidence 456778889999999996 5788999 8878888888877677766
No 103
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=44.56 E-value=11 Score=35.93 Aligned_cols=30 Identities=33% Similarity=0.281 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHcCCCEEecccchHHHHHH
Q 020008 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAA 114 (332)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~ 114 (332)
..+....+.+|+.+|+| +.+|.|++||+|+
T Consensus 103 ~~~~~~~~~~l~~~G~e-add~i~t~A~~a~ 132 (310)
T COG0258 103 ELLVALGIPLLELMGIE-ADDPIETLAQKAY 132 (310)
T ss_pred HHHHHhCcHhhhcCCCC-cchhHHHHHHHHH
Confidence 44566778899999999 8999999999999
No 104
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.66 E-value=17 Score=32.46 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 020008 167 LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~--~ipgiG~ktA~~li~~ 201 (332)
+++++|+. ++..+ |..- .|||||+|||-+++-+
T Consensus 93 ~~~~~l~~-aI~~~-D~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 93 MNAEALAS-AIISG-NAELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CCHHHHHH-HHHhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 56776654 34445 6653 6899999999998866
No 105
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=43.57 E-value=17 Score=33.41 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=25.3
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 183 y~~~ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
+.-+||||+...|..|+..|||++.|+.+
T Consensus 196 ~Lt~i~~VnKtda~~LL~~FgsLq~~~~A 224 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLLQKFGSLQQISNA 224 (254)
T ss_pred HHHhCCCCCcccHHHHHHhcccHHHHHhc
Confidence 44579999999999999999999988754
No 106
>PRK00076 recR recombination protein RecR; Reviewed
Probab=42.24 E-value=16 Score=32.72 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.8
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||+|+|.++.-
T Consensus 15 ~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 15 KLPGIGPKSAQRLAF 29 (196)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988764
No 107
>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=42.19 E-value=32 Score=27.26 Aligned_cols=40 Identities=18% Similarity=0.325 Sum_probs=33.1
Q ss_pred HHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHH
Q 020008 161 ILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIR 200 (332)
Q Consensus 161 v~~~~gl-~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~ 200 (332)
-+..-|| |-..+++.+...|.-.--.|||||+..|-.+..
T Consensus 28 ~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~a 68 (96)
T PF12482_consen 28 RLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEA 68 (96)
T ss_pred HHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHH
Confidence 3455687 789999999999977778899999998877654
No 108
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.11 E-value=16 Score=32.65 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.6
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 15 KLPGIGPKSAQRLAF 29 (195)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988753
No 109
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=42.07 E-value=16 Score=29.43 Aligned_cols=44 Identities=27% Similarity=0.456 Sum_probs=28.3
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC------------CCCccHHHHHHHHHHc
Q 020008 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDS------------IRGIGGQTALKLIRQH 202 (332)
Q Consensus 156 ~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~------------ipgiG~ktA~~li~~~ 202 (332)
++.+++++.+ ...|+|.-..+|.|-+.- |.|+||.+|..|++..
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 4445555544 566888888888876532 5799999999999864
No 110
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=41.38 E-value=15 Score=32.88 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.1
Q ss_pred CCCCCccHHHHHHHH
Q 020008 185 DSIRGIGGQTALKLI 199 (332)
Q Consensus 185 ~~ipgiG~ktA~~li 199 (332)
..+||||||+|.++.
T Consensus 15 ~kLPGvG~KsA~R~A 29 (198)
T COG0353 15 KKLPGVGPKSAQRLA 29 (198)
T ss_pred hhCCCCChhHHHHHH
Confidence 357999999987764
No 111
>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=40.79 E-value=25 Score=27.34 Aligned_cols=50 Identities=22% Similarity=0.173 Sum_probs=37.6
Q ss_pred hhccCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccc
Q 020008 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (332)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~f 134 (332)
.++++.+....+.++....+ .+-+|+.++.++...-+..++|.|.|+..+
T Consensus 69 i~~~~~~~~~~~~~~~~~~~------~~~~Da~~~a~A~~~~~~~v~T~D~~f~~~ 118 (121)
T PF01850_consen 69 ILPITSEVFERAAELMRKYG------LDFADALIAATAKENGAPLVVTFDKDFRKV 118 (121)
T ss_dssp EEEBCHHHHHHHHHHHHHHH------SSHHHHHHHHHHHHHT-EEE-ESSHHHHHH
T ss_pred cccchhHHHHHHHHHHHhcc------CChhHHHHHHHHHHcCCEEEEECCcCHHhc
Confidence 34667788888888888777 557899999999876676677999997544
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=40.02 E-value=78 Score=31.77 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=10.6
Q ss_pred cHHHHHHHHHHc
Q 020008 191 GGQTALKLIRQH 202 (332)
Q Consensus 191 G~ktA~~li~~~ 202 (332)
|...|.+.|..|
T Consensus 225 Ge~aA~~~L~~F 236 (454)
T TIGR00591 225 GTTAGLIMLESF 236 (454)
T ss_pred cHHHHHHHHHHH
Confidence 899999998887
No 113
>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=39.39 E-value=34 Score=29.12 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 020008 187 IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~ 203 (332)
|.|||+.+|..++++.|
T Consensus 26 I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 26 IKGIGRRFARAIARKLG 42 (144)
T ss_pred eeccCHHHHHHHHHHcC
Confidence 57899999998888765
No 114
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=38.72 E-value=94 Score=26.59 Aligned_cols=36 Identities=28% Similarity=0.482 Sum_probs=26.0
Q ss_pred HHHHHhhhhhccCHHHHHHHHHHHHHcCCCEEeccc
Q 020008 71 DIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (332)
Q Consensus 71 ~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~ap~ 106 (332)
++.+|-.+...-...|.......|+.+|||++....
T Consensus 91 EL~~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 91 ELDKFDEKVYKASKQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeCCC
Confidence 445555555555577888888999999999986544
No 115
>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=38.35 E-value=28 Score=27.84 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 020008 187 IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~ 203 (332)
|.|||+.+|..++...|
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 68999999999998866
No 116
>PRK13844 recombination protein RecR; Provisional
Probab=38.32 E-value=20 Score=32.18 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=12.7
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||+|+|.+|.-
T Consensus 19 ~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 19 KLPTIGKKSSQRLAL 33 (200)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988764
No 117
>PRK10702 endonuclease III; Provisional
Probab=36.31 E-value=63 Score=29.15 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=11.6
Q ss_pred CCCccHHHHHHHHH
Q 020008 187 IRGIGGQTALKLIR 200 (332)
Q Consensus 187 ipgiG~ktA~~li~ 200 (332)
+||||++||--++-
T Consensus 114 lpGVG~ktA~~ill 127 (211)
T PRK10702 114 LPGVGRKTANVVLN 127 (211)
T ss_pred CCcccHHHHHHHHH
Confidence 69999999977664
No 118
>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=35.94 E-value=1e+02 Score=31.15 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=10.4
Q ss_pred ccHHHHHHHHHHc
Q 020008 190 IGGQTALKLIRQH 202 (332)
Q Consensus 190 iG~ktA~~li~~~ 202 (332)
.|...|.+.|+.|
T Consensus 201 gGe~~A~~~L~~F 213 (475)
T TIGR02766 201 PGWSNADKALTEF 213 (475)
T ss_pred CccHHHHHHHHHH
Confidence 4888888888876
No 119
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=35.67 E-value=1.4e+02 Score=27.98 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=18.5
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~sle~il~ 210 (332)
.+.|||+++|.++=+-|.+.-...+
T Consensus 218 ~v~gig~k~A~~I~~~~~t~~~~~~ 242 (254)
T COG1948 218 KVKGIGEKKAREIYRFLRTEYKLIE 242 (254)
T ss_pred HhcCccHHHHHHHHHHHhchhhhhc
Confidence 3689999999998777777544443
No 120
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=34.04 E-value=30 Score=31.30 Aligned_cols=17 Identities=35% Similarity=0.614 Sum_probs=14.3
Q ss_pred CCCCccHHHHHHHHHHc
Q 020008 186 SIRGIGGQTALKLIRQH 202 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~ 202 (332)
++||||+|||--++.-.
T Consensus 123 ~lpGIG~KTAd~vL~~~ 139 (208)
T PRK01229 123 NIKGIGYKEASHFLRNV 139 (208)
T ss_pred cCCCCcHHHHHHHHHHc
Confidence 78999999998888533
No 121
>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=33.77 E-value=46 Score=29.30 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.0
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||++||--++.
T Consensus 110 ~l~GIG~ktA~~ill 124 (191)
T TIGR01083 110 KLPGVGRKTANVVLN 124 (191)
T ss_pred hCCCCcHHHHHHHHH
Confidence 369999999877664
No 122
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=32.47 E-value=1.1e+02 Score=24.93 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=35.1
Q ss_pred eHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHH-cCCHHHH
Q 020008 157 EVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ-HGSIETI 208 (332)
Q Consensus 157 ~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~-~~sle~i 208 (332)
....+....|++...+..+..++ |.+ -|||||+..|.=|... +.|++++
T Consensus 31 ~r~~La~~~~i~~~~l~~w~~~A--dL~-ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 31 GRKALAKKLGISERNLLKWVNQA--DLM-RIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred HHHHHHHhcCCCHHHHHHHHhHH--Hhh-hcCCCCHHHHHHHHHhCcCcHHHH
Confidence 34457788999999988887764 677 8999999987655543 3354443
No 123
>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=32.37 E-value=1.1e+02 Score=25.22 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=34.1
Q ss_pred HHHHHHHHHHcCCCEEeccc--------chHHHHHHHH-----HcC-CeEEEecCCCcccccc
Q 020008 87 NDDCKRLLKLMGVPVVEAPS--------EAEAQCAALC-----KSG-QVYAVASEDMDSLTFG 135 (332)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~ap~--------EADaq~A~L~-----~~g-~v~~V~S~DsD~l~fg 135 (332)
.....+.|+..|+.++..|. .+|..++.-+ .++ .+.+++|+|+|+....
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 45577789999999998872 4665554322 122 3667899999998764
No 124
>PRK00124 hypothetical protein; Validated
Probab=31.96 E-value=38 Score=29.11 Aligned_cols=91 Identities=13% Similarity=0.139 Sum_probs=49.6
Q ss_pred chHHHHHHHHHcCCeEEEecCCCccccccCCceEEEeecCCCCCCccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC
Q 020008 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (332)
Q Consensus 107 EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ 186 (332)
.||..|+.+++.| |.|||.|.=+=...-.+-..-+...+ ..|+.+.|-..|.. +...-++- -.| -.+.|
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 67899987654443222111232222 45777666554422 11112221 234 24456
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHH
Q 020008 187 IRGIGGQTALKLIRQHGSIETILEN 211 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~sle~il~~ 211 (332)
-+..+.+.-..+.+. ++.++..
T Consensus 125 p~~~~~~Dr~~F~~~---L~~~l~~ 146 (151)
T PRK00124 125 PKPFTQEDRSRFEAE---LDKLIRR 146 (151)
T ss_pred CCCCCHHHHHHHHHH---HHHHHHH
Confidence 666777665555543 5555544
No 125
>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=31.06 E-value=61 Score=24.84 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=20.5
Q ss_pred CCCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ-----HGSIETILENI 212 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-----~~sle~il~~~ 212 (332)
.|+|||...|.+++.+ |.|+++++..+
T Consensus 31 ~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 31 AIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred hcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 3789999999999975 56888888765
No 126
>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=30.84 E-value=43 Score=23.00 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=30.4
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHH-hCCCCCCCCCCccHHHHHHHHHHcC
Q 020008 156 FEVAKILEELNLTMDQFIDLCIL-SGCDYCDSIRGIGGQTALKLIRQHG 203 (332)
Q Consensus 156 ~~~~~v~~~~gl~~~q~id~~~L-~G~Dy~~~ipgiG~ktA~~li~~~~ 203 (332)
++..++.+.+|+++..++..+.- .|-.....--.|....|..+...|+
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 55678889999999999999977 8866222224466666666666554
No 127
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=30.66 E-value=53 Score=29.80 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=13.0
Q ss_pred CCCccHHHHHHHHHH-cC
Q 020008 187 IRGIGGQTALKLIRQ-HG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~-~~ 203 (332)
+||||+|||-=.|.. ||
T Consensus 114 LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 114 LPGVGRKTANVVLSFAFG 131 (211)
T ss_pred CCCcchHHHHHHHHhhcC
Confidence 489999999777765 44
No 128
>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=30.03 E-value=1.6e+02 Score=24.87 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHcCCCcEEEEeCC
Q 020008 14 QGMFTRTIRLLEAGMKPIYVFDGQ 37 (332)
Q Consensus 14 ~g~~~r~~~ll~~gi~Pv~VFDG~ 37 (332)
.|+..-+-.+.+.|.+++.||+..
T Consensus 25 ~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 25 RGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp HHHHHHHHHHHHTT---EEEEEEG
T ss_pred HHHHHHHHHHHHcCCCeEEEEcch
Confidence 344443444667899999999954
No 129
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=30.02 E-value=1.1e+02 Score=30.94 Aligned_cols=31 Identities=13% Similarity=0.204 Sum_probs=17.3
Q ss_pred HHHHHHHHHHcCCCEEeccc----chHHHHHHHHH
Q 020008 87 NDDCKRLLKLMGVPVVEAPS----EAEAQCAALCK 117 (332)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~ap~----EADaq~A~L~~ 117 (332)
+.++.+-|+.+|++.++.-| +..+++..|++
T Consensus 59 L~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~ 93 (472)
T PRK10674 59 LNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQ 93 (472)
T ss_pred HHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHH
Confidence 34455555666666665543 45556666655
No 130
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=29.86 E-value=94 Score=26.34 Aligned_cols=39 Identities=15% Similarity=0.156 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecC
Q 020008 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASE 127 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~ 127 (332)
+.+.+.++..|++++.-.-.-..++.++.+.| ||+|+|+
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 45666677788888776665566666677777 6777765
No 131
>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=29.77 E-value=41 Score=24.41 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=11.8
Q ss_pred CCCCCccHHHHHHH
Q 020008 185 DSIRGIGGQTALKL 198 (332)
Q Consensus 185 ~~ipgiG~ktA~~l 198 (332)
..|||||++.|.++
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 57899999988775
No 132
>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=29.43 E-value=48 Score=26.93 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 020008 187 IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~ 203 (332)
|.|||+.+|..++.+.|
T Consensus 20 i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 20 IYGIGRTRARKILEKAG 36 (113)
T ss_pred eecccHHHHHHHHHHhC
Confidence 57999999999998876
No 133
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=29.34 E-value=1.1e+02 Score=23.13 Aligned_cols=45 Identities=16% Similarity=0.215 Sum_probs=21.2
Q ss_pred HHHHHcCC--HHHHHHHhhhhhccCHHHHHHHHHHHHHcCCCEEeccc
Q 020008 61 AEAVEAGN--KEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (332)
Q Consensus 61 ~~~~~~g~--~~~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~ap~ 106 (332)
......|. ..++..+.. ...+++.+++.+...|..+||.++....
T Consensus 14 ~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~Vvd~~~ 60 (82)
T PF03979_consen 14 EKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEVVDEEE 60 (82)
T ss_dssp HHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----B--S-
T ss_pred HHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 33344443 334444433 2236688999999999999999998554
No 134
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=28.56 E-value=1e+02 Score=27.22 Aligned_cols=45 Identities=24% Similarity=0.371 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhCCCCCCC------CCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 020008 167 LTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENI 212 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~------ipgiG~ktA~~li~~-----~~sle~il~~~ 212 (332)
=+.+.|+++.--+| --+.. +||||.|+..++|.+ |.|.++|-+.+
T Consensus 96 ~~E~~FV~FfN~A~-PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 96 ENEERFVDFFNEAQ-PITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp TTHHHHHHHH------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred hChHHHHHHhhcCC-CChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 46899999999888 22222 599999999999975 77888877665
No 135
>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=28.55 E-value=88 Score=27.14 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=32.9
Q ss_pred HHHHHHHHcCCCEEecccchHHHHHH--HHH--cC--CeEEEecCCCcccccc
Q 020008 89 DCKRLLKLMGVPVVEAPSEAEAQCAA--LCK--SG--QVYAVASEDMDSLTFG 135 (332)
Q Consensus 89 ~~~~lL~~~Gi~~i~ap~EADaq~A~--L~~--~g--~v~~V~S~DsD~l~fg 135 (332)
.+++.|..+|+..+...|..|-.++- |.- .+ .+.+++|+|+|+..+.
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 46789999999988888866644332 211 23 3567899999998775
No 136
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=28.49 E-value=1.2e+02 Score=23.41 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=18.8
Q ss_pred CCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCC
Q 020008 188 RGIGGQTALKLIRQHGSIETILENINRERYQIP 220 (332)
Q Consensus 188 pgiG~ktA~~li~~~~sle~il~~~~~~~~~~~ 220 (332)
-||++..|.+|.+.||+ +.++.+++.++.+-
T Consensus 18 ~gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~ 48 (94)
T PF14490_consen 18 YGLSPKLAMKLYKKYGD--DAIEILKENPYRLI 48 (94)
T ss_dssp TT--HHHHHHHHHHH-T--THHHHHHH-STCCC
T ss_pred cCCCHHHHHHHHHHHhH--HHHHHHHHChHHHH
Confidence 36888899999999986 45566665555443
No 137
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=28.40 E-value=78 Score=26.70 Aligned_cols=36 Identities=22% Similarity=0.284 Sum_probs=25.7
Q ss_pred HHHHHHHc-CCCEEecccc---hHHHHHHHHHcCCeEEEe
Q 020008 90 CKRLLKLM-GVPVVEAPSE---AEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 90 ~~~lL~~~-Gi~~i~ap~E---ADaq~A~L~~~g~v~~V~ 125 (332)
.-++|+.. |+++-....| ++.+++.+.++|.+++|+
T Consensus 41 Ta~~L~~~~Gi~v~~vi~~~~gg~~~i~~~I~~g~i~lVI 80 (142)
T PRK05234 41 TGGLIQEATGLDVTRLLSGPLGGDQQIGALIAEGKIDMLI 80 (142)
T ss_pred HHHHHHhccCCeeEEEEcCCCCCchhHHHHHHcCceeEEE
Confidence 44556677 8876543344 678889999998888776
No 138
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=28.16 E-value=39 Score=28.40 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.3
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.|||||++||--++.
T Consensus 87 ~l~GIG~~tA~~~l~ 101 (158)
T cd00056 87 ALPGVGRKTANVVLL 101 (158)
T ss_pred cCCCCCHHHHHHHHH
Confidence 579999999877665
No 139
>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=28.16 E-value=34 Score=30.21 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=13.9
Q ss_pred CCCCccHHHHHHHHHHcC
Q 020008 186 SIRGIGGQTALKLIRQHG 203 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~ 203 (332)
.+||||+|||-=++...+
T Consensus 119 ~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 119 ALPGFGKQKAKIFLALLG 136 (177)
T ss_pred cCCCCCHHHHHHHHHHHH
Confidence 589999999977666443
No 140
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=27.52 E-value=5.3e+02 Score=24.37 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=16.6
Q ss_pred HHHHHcCCCHHHHHHHHHHhCCCCCCCC--CCccH
Q 020008 160 KILEELNLTMDQFIDLCILSGCDYCDSI--RGIGG 192 (332)
Q Consensus 160 ~v~~~~gl~~~q~id~~~L~G~Dy~~~i--pgiG~ 192 (332)
++.+...-.-++-++.|.-.|-+-.+=| ||+|-
T Consensus 156 dv~~~v~~~l~~~i~~a~~~GI~~~~IilDPGiGF 190 (282)
T PRK11613 156 DVFAEVNRYFIEQIARCEAAGIAKEKLLLDPGFGF 190 (282)
T ss_pred cHHHHHHHHHHHHHHHHHHcCCChhhEEEeCCCCc
Confidence 3444432234455666777774433222 77774
No 141
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=26.96 E-value=55 Score=27.01 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 020008 187 IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~ 203 (332)
|.|||+.+|..++.+.|
T Consensus 22 I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 22 IYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccHHHHHHHHHHhC
Confidence 57999999999998876
No 142
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=26.95 E-value=2e+02 Score=19.27 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCC
Q 020008 166 NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGS 204 (332)
Q Consensus 166 gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~s 204 (332)
.+||.+| .+|+|-+- +-..++-..--+|++.|++
T Consensus 10 ~lTP~El---~a~~g~~~--~~~pl~R~~L~~Lm~~~PD 43 (43)
T PF09550_consen 10 RLTPAEL---RAMLGADA--GAAPLDRAELDALMRRFPD 43 (43)
T ss_pred hcCHHHH---HHhcCccc--CCCCCCHHHHHHHHHHCcC
Confidence 4555555 67788443 3466777777778888764
No 143
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=26.85 E-value=74 Score=26.83 Aligned_cols=44 Identities=14% Similarity=-0.003 Sum_probs=31.1
Q ss_pred HHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccccc
Q 020008 91 KRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (332)
Q Consensus 91 ~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~f 134 (332)
..+....+.+++..-..||+.+-..+.+.-+++|+|+|..+-.-
T Consensus 69 ia~~~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~r 112 (136)
T COG1412 69 IALKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRR 112 (136)
T ss_pred HHHHHhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHH
Confidence 33455778888888558888777666543366799999987543
No 144
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.70 E-value=57 Score=34.77 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=16.3
Q ss_pred CCCCccHHHHHHHH-HHcCCHHHHHH
Q 020008 186 SIRGIGGQTALKLI-RQHGSIETILE 210 (332)
Q Consensus 186 ~ipgiG~ktA~~li-~~~~sle~il~ 210 (332)
|||+||..+|..|. +.|++++++.+
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 46677777766666 66777666543
No 145
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=26.40 E-value=58 Score=26.88 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=14.9
Q ss_pred CCCccHHHHHHHHHHcC
Q 020008 187 IRGIGGQTALKLIRQHG 203 (332)
Q Consensus 187 ipgiG~ktA~~li~~~~ 203 (332)
|.|||+.+|..++...|
T Consensus 22 i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 22 IYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccHHHHHHHHHHcC
Confidence 57999999999998866
No 146
>PF09040 H-K_ATPase_N: Gastric H+/K+-ATPase, N terminal domain; InterPro: IPR015127 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the N-terminal domain found in gastric H+/K+-transporter ATPases. This domain adopts an alpha-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0008900 hydrogen:potassium-exchanging ATPase activity, 0015991 ATP hydrolysis coupled proton transport, 0016020 membrane; PDB: 1IWF_A 1IWC_A.
Probab=26.22 E-value=24 Score=22.77 Aligned_cols=23 Identities=43% Similarity=0.687 Sum_probs=8.1
Q ss_pred CCCCccccccccccCCCCCCCCC
Q 020008 309 PENTPKATTNKKSKAGGGGGRKR 331 (332)
Q Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~ 331 (332)
|...+.++-.|+++.+++++||-
T Consensus 17 PgGDm~AK~~kkk~~~ggg~rke 39 (41)
T PF09040_consen 17 PGGDMAAKMSKKKAGGGGGKRKE 39 (41)
T ss_dssp SSSSSSHCCHHHT-S--------
T ss_pred CCccHHHHHhhhhccCCCCcccc
Confidence 44445566666666666666653
No 147
>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=26.20 E-value=80 Score=22.40 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=20.6
Q ss_pred ccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 020008 247 KWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (332)
Q Consensus 247 ~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (332)
.....|.+-+.+|. .+||..++|-..++++.
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 34467888888885 89999999999998864
No 148
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=26.09 E-value=1.1e+02 Score=24.65 Aligned_cols=37 Identities=24% Similarity=0.254 Sum_probs=27.4
Q ss_pred HHHHHHH-cCCCEEecc---cchHHHHHHHHHcCCeEEEec
Q 020008 90 CKRLLKL-MGVPVVEAP---SEAEAQCAALCKSGQVYAVAS 126 (332)
Q Consensus 90 ~~~lL~~-~Gi~~i~ap---~EADaq~A~L~~~g~v~~V~S 126 (332)
.-++|+. .|+++-..+ .|++.+++.+.+.|.++.|+.
T Consensus 36 Ta~~L~~~~Gi~v~~vk~~~~~g~~~i~~~i~~g~i~~VIn 76 (115)
T cd01422 36 TGLLIQEATGLTVNRMKSGPLGGDQQIGALIAEGEIDAVIF 76 (115)
T ss_pred HHHHHHHhhCCcEEEEecCCCCchhHHHHHHHcCceeEEEE
Confidence 3445666 899874333 688999999999999888863
No 149
>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=26.04 E-value=1.2e+02 Score=27.74 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCCCEEec--ccchHHHH----HHHHHcCCeEEEecCCCc
Q 020008 88 DDCKRLLKLMGVPVVEA--PSEAEAQC----AALCKSGQVYAVASEDMD 130 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i~a--p~EADaq~----A~L~~~g~v~~V~S~DsD 130 (332)
+.+...-+++|||++.. +++-++.. ..|...| +++|+++|-+
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 45667778999997654 44434433 3333345 6678887655
No 150
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=25.96 E-value=48 Score=29.37 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=15.8
Q ss_pred CCCCccHHHHHHHHHHcC
Q 020008 186 SIRGIGGQTALKLIRQHG 203 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~~~ 203 (332)
.+||||+++|.+++.++.
T Consensus 112 ~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 112 KVPGIGKKTAERIVLELK 129 (192)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 589999999999998754
No 151
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=25.84 E-value=62 Score=25.28 Aligned_cols=39 Identities=26% Similarity=0.347 Sum_probs=27.1
Q ss_pred EecccchHHHHHHHHHcCCeEEEecCCCcccc-----ccCCceE
Q 020008 102 VEAPSEAEAQCAALCKSGQVYAVASEDMDSLT-----FGAPRFL 140 (332)
Q Consensus 102 i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l~-----fg~~~vi 140 (332)
+..+..||+.+..++..+-..+|+|+|.++-. -|.|.++
T Consensus 47 ~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~ 90 (101)
T PF04900_consen 47 KETPGSADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIY 90 (101)
T ss_pred CCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEE
Confidence 33366899999999965443679999998753 3555543
No 152
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=25.78 E-value=58 Score=30.78 Aligned_cols=24 Identities=33% Similarity=0.437 Sum_probs=20.4
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-~~sle~il 209 (332)
.+||||+++|.+|.+. |.+++++.
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~ 27 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIA 27 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHH
Confidence 5799999999999998 88877664
No 153
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=25.67 E-value=1.2e+02 Score=27.18 Aligned_cols=42 Identities=21% Similarity=0.243 Sum_probs=28.8
Q ss_pred HHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCcc
Q 020008 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDS 131 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~ 131 (332)
+.+.+.++..|+++..---.-..++..|.. + ||+|+|++.|.
T Consensus 184 ~~~v~~~~~~G~~v~~WTvn~~~~~~~l~~-~-vdgiiTD~p~~ 225 (226)
T cd08568 184 VELLRLLRKLGLKIVLWTVNDPELVPKLKG-L-VDGVITDDVEK 225 (226)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHHHHHh-h-CCEEEccCccc
Confidence 456667888899988776522344455543 5 99999987765
No 154
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
Probab=25.25 E-value=71 Score=30.27 Aligned_cols=28 Identities=32% Similarity=0.572 Sum_probs=26.3
Q ss_pred cEEEeHHHHHHHcCCCHHHHHHHHHHhC
Q 020008 153 VMEFEVAKILEELNLTMDQFIDLCILSG 180 (332)
Q Consensus 153 ~~~~~~~~v~~~~gl~~~q~id~~~L~G 180 (332)
...++....+..|+++...|.-+|||-|
T Consensus 10 ~~yiTR~qAlkkLQlsl~dFRRLCILKG 37 (281)
T PF06732_consen 10 KNYITRNQALKKLQLSLKDFRRLCILKG 37 (281)
T ss_pred cccccHHHHHHHhcCCHHHHhhHHhhcC
Confidence 4678999999999999999999999999
No 155
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=25.15 E-value=47 Score=30.27 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=12.7
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||++||--++-
T Consensus 125 ~l~GIG~kTAd~iLl 139 (218)
T PRK13913 125 DQKGIGKESADAILC 139 (218)
T ss_pred cCCCccHHHHHHHHH
Confidence 479999999988775
No 156
>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5.4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.
Probab=25.07 E-value=3.3e+02 Score=24.94 Aligned_cols=33 Identities=39% Similarity=0.746 Sum_probs=21.1
Q ss_pred CCCCchhHHHHHHHHHHHHH-HcCCCcEEE---EeCCC
Q 020008 5 EAGEVTSHLQGMFTRTIRLL-EAGMKPIYV---FDGQP 38 (332)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~ll-~~gi~Pv~V---FDG~~ 38 (332)
|+|-+=||+.-++. ++.+. ++|+++||| .||..
T Consensus 37 SdGGVHSh~~Hl~a-l~~~a~~~gv~~V~vH~f~DGRD 73 (223)
T PF06415_consen 37 SDGGVHSHIDHLFA-LIKLAKKQGVKKVYVHAFTDGRD 73 (223)
T ss_dssp SS-SSS--HHHHHH-HHHHHHHTT-SEEEEEEEE-SSS
T ss_pred cCCCccccHHHHHH-HHHHHHHcCCCEEEEEEecCCCC
Confidence 67888899998887 55554 689999974 89973
No 157
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=24.99 E-value=49 Score=27.51 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.8
Q ss_pred CCCCccHHHHHHHHH
Q 020008 186 SIRGIGGQTALKLIR 200 (332)
Q Consensus 186 ~ipgiG~ktA~~li~ 200 (332)
.+||||+++|--++.
T Consensus 76 ~l~GIG~~tA~~~l~ 90 (149)
T smart00478 76 KLPGVGRKTANAVLS 90 (149)
T ss_pred cCCCCcHHHHHHHHH
Confidence 589999999866544
No 158
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=24.87 E-value=1.3e+02 Score=26.49 Aligned_cols=46 Identities=35% Similarity=0.415 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHcCCCEEecccc--hHHHHHHHHHcCCeEEEecCC
Q 020008 83 TKQHNDDCKRLLKLMGVPVVEAPSE--AEAQCAALCKSGQVYAVASED 128 (332)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~ap~E--ADaq~A~L~~~g~v~~V~S~D 128 (332)
+...-+.++.++...||++|..||| =+|.-..|..-|.-..|+|.|
T Consensus 48 isp~tp~t~~~~~~~gv~vi~tpG~GYv~Dl~~al~~l~~P~lvvsaD 95 (177)
T COG2266 48 ISPHTPKTKEYLESVGVKVIETPGEGYVEDLRFALESLGTPILVVSAD 95 (177)
T ss_pred eCCCCHhHHHHHHhcCceEEEcCCCChHHHHHHHHHhcCCceEEEecc
Confidence 4456678899999999999999985 234444455556444566643
No 159
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=24.86 E-value=2.1e+02 Score=25.95 Aligned_cols=103 Identities=18% Similarity=0.216 Sum_probs=58.5
Q ss_pred HHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHH--HHHHhCCCC
Q 020008 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQE--ARRLFKEPE 236 (332)
Q Consensus 159 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~~sle~il~~~~~~~~~~~~~~~~~~--~~~~f~~p~ 236 (332)
+.+|+..|.+|+|+..-+.=+. +. ..|.+...-..++..-+..++.+..+-. .....++|.|.. |..+|.--.
T Consensus 76 ~Alc~a~~~dp~~~r~dA~~l~-~~---a~~~s~~~l~~~l~~~~~~~~~l~~~~~-~~~~~~~f~YSRl~AIGL~~LLe 150 (206)
T PLN03060 76 KAYIEALGEDPDQYRKDAKKLE-EW---ASSQSASGIADFNSGDGEVEAVLKDIAE-RAAGKTKFHYSRFFAIGLFRLLE 150 (206)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-HH---HhcCCHHHHHHHHhcccccchHHHHHHH-HhhcCCCcchHHHHHHHHHHHHH
Confidence 4566777888888876655444 22 2456666677777765554444443211 111235566654 555553110
Q ss_pred cCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHH
Q 020008 237 VVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEK 277 (332)
Q Consensus 237 V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~ 277 (332)
.. .-. |.+.+.+++ +.+|++.++|.+-|.-
T Consensus 151 ~a--------~~~--d~~~l~~l~-~~L~ls~~kv~kDL~l 180 (206)
T PLN03060 151 CA--------KAS--DPAVLEKLS-KALNVSKRSVDRDLDV 180 (206)
T ss_pred Hc--------CCC--CHHHHHHHH-HHcCCCHHHHHhhHHH
Confidence 00 001 445676776 8999999999876543
No 160
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=24.85 E-value=58 Score=27.63 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=24.4
Q ss_pred chHHHHHHHHHcCCeEEEecCCCccccccCC
Q 020008 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAP 137 (332)
Q Consensus 107 EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~ 137 (332)
+=|.-.-.++-.|.+++++|+|.|+|.+-..
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~~ 121 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRDE 121 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheeccc
Confidence 4466666677788899999999999977653
No 161
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=24.66 E-value=1.1e+02 Score=24.36 Aligned_cols=37 Identities=27% Similarity=0.351 Sum_probs=25.4
Q ss_pred HHHHHHHcCCCEEe--cccc-hHHHHHHHHHc-CCeEEEec
Q 020008 90 CKRLLKLMGVPVVE--APSE-AEAQCAALCKS-GQVYAVAS 126 (332)
Q Consensus 90 ~~~lL~~~Gi~~i~--ap~E-ADaq~A~L~~~-g~v~~V~S 126 (332)
.-++|+..||++.. .+.| .+.++..+.++ |.+|.|+.
T Consensus 34 Ta~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn 74 (112)
T cd00532 34 TSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVIN 74 (112)
T ss_pred HHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEE
Confidence 34456668888633 3446 67788888888 88887764
No 162
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=24.58 E-value=1.1e+02 Score=27.92 Aligned_cols=41 Identities=20% Similarity=0.285 Sum_probs=17.1
Q ss_pred HHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCc
Q 020008 89 DCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMD 130 (332)
Q Consensus 89 ~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD 130 (332)
.+.+.++..|++++.-----.+++..|...| ||+|+|+..|
T Consensus 200 ~~v~~~~~~g~~v~~WTvn~~~~~~~l~~~G-VdgIiTD~p~ 240 (249)
T PRK09454 200 ARVAALKAAGLRILVYTVNDPARARELLRWG-VDCICTDRID 240 (249)
T ss_pred HHHHHHHHCCCEEEEEeCCCHHHHHHHHHcC-CCEEEeCChH
Confidence 3344444455554433322222333343344 4455554444
No 163
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=24.31 E-value=1.1e+02 Score=29.60 Aligned_cols=47 Identities=17% Similarity=0.299 Sum_probs=31.2
Q ss_pred EEeHHHHHHHcCCCHHHHHHH--------------HHHhCCCCCC------------CCCCccHHHHHHHHHH
Q 020008 155 EFEVAKILEELNLTMDQFIDL--------------CILSGCDYCD------------SIRGIGGQTALKLIRQ 201 (332)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~id~--------------~~L~G~Dy~~------------~ipgiG~ktA~~li~~ 201 (332)
.|..+.++.-||+.++++.+. ++|--.|.-+ .|||||+++|..++..
T Consensus 277 LYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 277 LYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 477888999999998887653 2222222221 1478898888888764
No 164
>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=23.78 E-value=1.4e+02 Score=24.03 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=24.8
Q ss_pred HHHHHHHHHHcCCCEEeccc---------chHHHHHH----HHH--cCCeEEEecCCCcccccc
Q 020008 87 NDDCKRLLKLMGVPVVEAPS---------EAEAQCAA----LCK--SGQVYAVASEDMDSLTFG 135 (332)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~ap~---------EADaq~A~----L~~--~g~v~~V~S~DsD~l~fg 135 (332)
...+...|+..|+++...|. .+|-.++. ++. .-...+++|+|+|+....
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 45566788999998877654 35544432 221 124667899999987654
No 165
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=23.76 E-value=1.5e+02 Score=23.22 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=24.0
Q ss_pred HHHHHHHcCCCE--EecccchHHHHHHHHHcCCeEEEec
Q 020008 90 CKRLLKLMGVPV--VEAPSEAEAQCAALCKSGQVYAVAS 126 (332)
Q Consensus 90 ~~~lL~~~Gi~~--i~ap~EADaq~A~L~~~g~v~~V~S 126 (332)
.-+.|+..|+++ +..+.+++.++..+.++|.++.|+.
T Consensus 35 T~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn 73 (110)
T cd01424 35 TAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVIN 73 (110)
T ss_pred HHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEE
Confidence 344566677775 3334466777777777887777764
No 166
>PRK13266 Thf1-like protein; Reviewed
Probab=23.75 E-value=2.1e+02 Score=26.21 Aligned_cols=107 Identities=12% Similarity=0.132 Sum_probs=53.9
Q ss_pred HHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHc--CCHHHHHHHHHhhcCCCCCCCchHH--HHHHhCC
Q 020008 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQH--GSIETILENINRERYQIPEDWPYQE--ARRLFKE 234 (332)
Q Consensus 159 ~~v~~~~gl~~~q~id~~~L~G~Dy~~~ipgiG~ktA~~li~~~--~sle~il~~~~~~~~~~~~~~~~~~--~~~~f~~ 234 (332)
+.+|...|.+|+|+..-+.=+. +. ..|.+...-..++.+- +..+.+...+..+. -..+|.|.. |..+|.-
T Consensus 78 ~Alc~a~~~dp~~~r~dA~~l~-~~---a~~~s~~~i~~~l~~~~~~~~~~l~~~l~~ia--~~~~f~YSRl~AIGL~~L 151 (225)
T PRK13266 78 NALCQAVGFDPEQLRQDAERLL-EL---AKGKSLKEILSWLTQKALGEPGGLLATLLAIA--NNSKFKYSRLFAIGLYTL 151 (225)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-HH---HhcCCHHHHHHHHhccccccchhHHHHHHHHh--cCCCCchHHHHHHHHHHH
Confidence 4556677888888766554443 22 2345555556666543 23334444443332 225566543 5555531
Q ss_pred CCcCCccchhccccCCC-CHHHHHHHHHHhcCCChHHHHHHHH
Q 020008 235 PEVVTDEEQLQIKWSAP-DEEGLINFLVSENGFNSDRVTKAIE 276 (332)
Q Consensus 235 p~V~~~~~~~~l~~~~p-d~~~l~~fl~~~~~f~~~rv~~~~~ 276 (332)
-... . ...-..| +......-+++.+|++.++|.+-|.
T Consensus 152 Le~a--~---~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~ 189 (225)
T PRK13266 152 LEEA--Q---PDLVKDEEKLNEALKDISEGLGLSKEKVEKDLD 189 (225)
T ss_pred HHhc--C---cccccCHHHHHHHHHHHHHHcCCCHHHHHhhHH
Confidence 0000 0 0001111 2234444455899999999987654
No 167
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=23.57 E-value=94 Score=24.84 Aligned_cols=36 Identities=19% Similarity=0.228 Sum_probs=27.5
Q ss_pred HHHHHcCCC-EEeccc--chHHHHHHHHHcCCeEEEecC
Q 020008 92 RLLKLMGVP-VVEAPS--EAEAQCAALCKSGQVYAVASE 127 (332)
Q Consensus 92 ~lL~~~Gi~-~i~ap~--EADaq~A~L~~~g~v~~V~S~ 127 (332)
--+++.||. ++.+.. ||++....|+..++-..++|+
T Consensus 15 lGFrlaGi~~v~~~~~~e~~~~~~~~l~~~~~gII~iTE 53 (104)
T PRK01189 15 LGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSE 53 (104)
T ss_pred HHHHHcCCceEEEcCCHHHHHHHHHHHhcCCeEEEEEEH
Confidence 357889996 666543 778888889888887777887
No 168
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=23.42 E-value=1.5e+02 Score=18.37 Aligned_cols=23 Identities=35% Similarity=0.537 Sum_probs=16.3
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHHH
Q 020008 254 EGLINFLVSENGFNSDRVTKAIEKI 278 (332)
Q Consensus 254 ~~l~~fl~~~~~f~~~rv~~~~~~l 278 (332)
+.+..++ .+||+++++..++..-
T Consensus 3 ~~v~~L~--~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLL--EMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHH--HcCCCHHHHHHHHHHh
Confidence 4444553 7899999888888653
No 169
>cd08575 GDPD_GDE4_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function is not elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests mammalian GDE4 may play some distinct role from other members of mammalian GDEs family. Also included in this subfamily are uncharacterized mammalian glycerophosphodiester phosphodiesterase domain-containing protein 3 (GDPD3) and similar proteins which display very high sequence homology to mammalian GDE4.
Probab=23.35 E-value=1.2e+02 Score=27.95 Aligned_cols=44 Identities=16% Similarity=0.101 Sum_probs=30.8
Q ss_pred HHHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCccc
Q 020008 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSL 132 (332)
Q Consensus 88 ~~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD~l 132 (332)
+.+.+.++..|+++..---.-.+.+..|...| ||+|+|++.|.+
T Consensus 221 ~~~v~~~~~~G~~v~vWTVNd~~~~~~l~~~G-VdgIiTD~P~~~ 264 (264)
T cd08575 221 PNLFDHLRKRGIQVYLWVLNDEEDFEEAFDLG-ADGVMTDSPTKL 264 (264)
T ss_pred HHHHHHHHhcCCcEEEEEECCHHHHHHHHhcC-CCEEEeCCcccC
Confidence 34556667789998776654455666777777 788999877653
No 170
>PRK00254 ski2-like helicase; Provisional
Probab=22.98 E-value=66 Score=34.39 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=23.1
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHHH
Q 020008 186 SIRGIGGQTALKLIRQ-HGSIETILEN 211 (332)
Q Consensus 186 ~ipgiG~ktA~~li~~-~~sle~il~~ 211 (332)
.|||||+++|.+|++. |+++++|.+.
T Consensus 649 ~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 649 RLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred cCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 3699999999999999 9999988763
No 171
>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=22.97 E-value=3.3e+02 Score=23.27 Aligned_cols=68 Identities=21% Similarity=0.247 Sum_probs=37.5
Q ss_pred CCCchhhhhHHHHhhchhhchHHHHHHHHcCCHHHHHHHhhhhhccCHHHHHHHHHHHHHcCCCEEecccchHHHHHHHH
Q 020008 37 QPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALC 116 (332)
Q Consensus 37 ~~~~~K~~~~~~rk~~R~~~~~~l~~~~~~g~~~~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~ap~EADaq~A~L~ 116 (332)
..|++|..+..+++++|.. .+...|..-|+..|---+-.-..-.++++.||
T Consensus 5 r~pt~kErEnnk~RERrRR-----------------------------AIaakIfaGLR~~Gny~Lp~~aD~NeVLkALc 55 (150)
T PF05687_consen 5 RRPTWKERENNKRRERRRR-----------------------------AIAAKIFAGLRAHGNYKLPKHADNNEVLKALC 55 (150)
T ss_pred ccccHhhhHHHHHHHHHHH-----------------------------HHHHHHHHHHHHhcCCCCCCcCCHHHHHHHHH
Confidence 4577887777776665432 22333445566666533333334456777777
Q ss_pred Hc-CCeEEEecCCCccccccC
Q 020008 117 KS-GQVYAVASEDMDSLTFGA 136 (332)
Q Consensus 117 ~~-g~v~~V~S~DsD~l~fg~ 136 (332)
+. |. ||.+|-..+--++
T Consensus 56 ~eAGw---~Ve~DGTtyr~~~ 73 (150)
T PF05687_consen 56 REAGW---TVEPDGTTYRKGC 73 (150)
T ss_pred HhCCE---EEccCCCeeccCC
Confidence 63 53 3456666555444
No 172
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=22.71 E-value=96 Score=27.61 Aligned_cols=46 Identities=22% Similarity=0.333 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHhCCCCCCC------CCCccHHHHHHHHHH-----cCCHHHHHHHHH
Q 020008 167 LTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENIN 213 (332)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~------ipgiG~ktA~~li~~-----~~sle~il~~~~ 213 (332)
-..+.|+++.-=++ --+.. +||||.|+...+|.+ |.|+++|-+.+.
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 35677888765555 22211 499999999999975 678888777654
No 173
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=22.11 E-value=1.7e+02 Score=18.06 Aligned_cols=22 Identities=32% Similarity=0.519 Sum_probs=15.7
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHH
Q 020008 254 EGLINFLVSENGFNSDRVTKAIEK 277 (332)
Q Consensus 254 ~~l~~fl~~~~~f~~~rv~~~~~~ 277 (332)
+.+..+. .+||+.+.+..++..
T Consensus 3 ~~v~~L~--~mGf~~~~a~~aL~~ 24 (37)
T smart00165 3 EKIDQLL--EMGFSREEALKALRA 24 (37)
T ss_pred HHHHHHH--HcCCCHHHHHHHHHH
Confidence 4455553 889999988888764
No 174
>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=21.42 E-value=1e+02 Score=24.76 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=22.0
Q ss_pred chHHHHHHHHHcCCeEEEecCCCccccccCCc
Q 020008 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (332)
Q Consensus 107 EADaq~A~L~~~g~v~~V~S~DsD~l~fg~~~ 138 (332)
-+|+.++..+...-+ .++|.|.|+-.|+.-.
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 589998888775434 5779999976555433
No 175
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=21.12 E-value=2e+02 Score=23.28 Aligned_cols=54 Identities=15% Similarity=0.211 Sum_probs=31.3
Q ss_pred HHHHHHhCCCCcCCccchhccccCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHhhccCCCCccccc
Q 020008 226 QEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESF 293 (332)
Q Consensus 226 ~~~~~~f~~p~V~~~~~~~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~f 293 (332)
+-++.+|.++... + -+.+...+++...+..+.....+.-.-|+.. ..|++||+|
T Consensus 57 E~vR~A~~~~p~~---------f--~~l~eAl~~~~~~l~~~~~~w~~~s~ll~~~---~~Q~tL~~F 110 (110)
T PF04895_consen 57 ENVRKAMKGKPEK---------F--ETLEEALEYVSSRLKLPIKEWLRKSKLLKRI---RRQKTLDDF 110 (110)
T ss_pred HHHHHHHhCCCcc---------c--CCHHHHHHHHHHHhCCCHHHHHHHhHHHHHH---hcccccccC
Confidence 3577788765432 1 1345666777777777655443332223322 279999998
No 176
>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]
Probab=21.06 E-value=1.8e+02 Score=25.07 Aligned_cols=44 Identities=27% Similarity=0.369 Sum_probs=32.7
Q ss_pred cCHHHHHHHHHHHHHcC-----CCEEeccc--chHHHHHHHHHcCCeEEEe
Q 020008 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (332)
Q Consensus 82 vt~~~~~~~~~lL~~~G-----i~~i~ap~--EADaq~A~L~~~g~v~~V~ 125 (332)
|+..++.-+.+.|...| |.++..|| |-=-..-.|++.+..|+|+
T Consensus 26 I~d~ll~gA~~~l~~~G~~~~~i~vv~VPGa~EiPl~a~~La~~~~yDAvv 76 (152)
T COG0054 26 ITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTGKYDAVV 76 (152)
T ss_pred HHHHHHHHHHHHHHHcCCCcccceEEEeCCcchhHHHHHHHHhcCCcceEE
Confidence 34556667777777777 56788999 7776777888888777776
No 177
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=20.90 E-value=1.2e+02 Score=21.42 Aligned_cols=32 Identities=6% Similarity=0.176 Sum_probs=28.2
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC
Q 020008 155 EFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (332)
Q Consensus 155 ~~~~~~v~~~~gl~~~q~id~~~L~G~Dy~~~ 186 (332)
.-++++++..++++.+.+..-..-.|..|...
T Consensus 20 ~~sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~~ 51 (55)
T PF14056_consen 20 YSSLDELCYDYDIDKEELEEKLASIGYEYDEE 51 (55)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHcCCeEchh
Confidence 45889999999999999999999999888753
No 178
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=20.85 E-value=93 Score=28.34 Aligned_cols=15 Identities=33% Similarity=0.295 Sum_probs=12.0
Q ss_pred cchHHHHHHHHHcCC
Q 020008 106 SEAEAQCAALCKSGQ 120 (332)
Q Consensus 106 ~EADaq~A~L~~~g~ 120 (332)
.|.||.+|||..-|.
T Consensus 194 te~~AliAYLq~LG~ 208 (217)
T PRK14487 194 TEMDALIAYLQSLGT 208 (217)
T ss_pred cHHHHHHHHHHHhcc
Confidence 388889999988774
No 179
>cd08567 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=20.64 E-value=1.8e+02 Score=26.41 Aligned_cols=41 Identities=20% Similarity=0.196 Sum_probs=17.8
Q ss_pred HHHHHHHHcCCCEEecccchHHHHHHHHHcCCeEEEecCCCc
Q 020008 89 DCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMD 130 (332)
Q Consensus 89 ~~~~lL~~~Gi~~i~ap~EADaq~A~L~~~g~v~~V~S~DsD 130 (332)
.+.+.++..|+++++---.-..++.+|...| |++|+|++.|
T Consensus 222 ~~i~~~~~~G~~v~vwtvn~~~~~~~~~~~G-vdgi~TD~P~ 262 (263)
T cd08567 222 ELVDEAHALGLKVVPWTVNDPEDMARLIDLG-VDGIITDYPD 262 (263)
T ss_pred HHHHHHHHCCCEEEEecCCCHHHHHHHHHcC-CCEEEcCCCC
Confidence 3444455555555443332122333444444 4455555443
No 180
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=20.33 E-value=1.2e+02 Score=28.54 Aligned_cols=30 Identities=27% Similarity=0.297 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHhcCCChHHHHHHHHHHHHh
Q 020008 251 PDEEGLINFLVSENGFNSDRVTKAIEKIKAA 281 (332)
Q Consensus 251 pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~ 281 (332)
.-...|+.+| .++||++.-|+.++-|++++
T Consensus 26 Iw~gsLI~il-~~fG~sE~~vRaal~Rm~ka 55 (291)
T COG3327 26 IWIGSLIQIL-AEFGISETTVRAALSRMVKA 55 (291)
T ss_pred eeHHHHHHHH-HHcCccHHHHHHHHHHHHhc
Confidence 3457899998 79999999999999999876
Done!