Query 017910
Match_columns 364
No_of_seqs 339 out of 1732
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 04:29:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017910hhsearch_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 1E-75 2.2E-80 585.4 37.5 299 2-301 55-353 (393)
2 PRK03980 flap endonuclease-1; 100.0 1.7E-73 3.8E-78 549.5 33.1 282 3-294 1-292 (292)
3 TIGR03674 fen_arch flap struct 100.0 2.6E-67 5.5E-72 516.8 32.3 284 1-294 46-338 (338)
4 KOG2519 5'-3' exonuclease [Rep 100.0 8.1E-63 1.8E-67 486.7 24.2 299 3-301 50-349 (449)
5 cd00128 XPG Xeroderma pigmento 100.0 1.5E-57 3.3E-62 444.1 30.1 268 5-276 48-315 (316)
6 TIGR00600 rad2 DNA excision re 100.0 5.7E-47 1.2E-51 409.2 24.0 218 76-298 763-1006(1034)
7 PRK14976 5'-3' exonuclease; Pr 100.0 3.4E-46 7.4E-51 358.4 21.9 238 2-267 28-281 (281)
8 smart00475 53EXOc 5'-3' exonuc 100.0 1.1E-45 2.3E-50 351.2 20.1 216 2-243 22-247 (259)
9 TIGR00593 pola DNA polymerase 100.0 6.3E-43 1.4E-47 378.7 23.2 237 2-267 22-276 (887)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 2.5E-42 5.4E-47 325.1 19.1 207 3-238 23-239 (240)
11 COG0258 Exo 5'-3' exonuclease 100.0 4.9E-41 1.1E-45 327.3 23.1 263 2-294 33-309 (310)
12 KOG2518 5'-3' exonuclease [Rep 100.0 3.2E-41 6.9E-46 336.9 20.4 233 5-241 47-287 (556)
13 PRK05755 DNA polymerase I; Pro 100.0 4.9E-41 1.1E-45 366.5 22.7 238 2-267 24-277 (880)
14 PRK09482 flap endonuclease-lik 100.0 3.3E-40 7.1E-45 311.9 18.8 208 4-243 23-243 (256)
15 KOG2520 5'-3' exonuclease [Rep 100.0 6.1E-35 1.3E-39 307.3 15.9 213 79-296 460-701 (815)
16 PHA00439 exonuclease 100.0 4E-28 8.7E-33 231.7 15.1 219 2-281 34-271 (286)
17 PHA02567 rnh RnaseH; Provision 99.9 1.6E-24 3.5E-29 207.9 16.3 161 2-191 33-206 (304)
18 PF00867 XPG_I: XPG I-region; 99.9 7.6E-25 1.6E-29 177.9 6.6 88 95-182 1-94 (94)
19 PF02739 5_3_exonuc_N: 5'-3' e 99.9 6.4E-24 1.4E-28 190.1 11.9 136 2-165 24-169 (169)
20 smart00484 XPGI Xeroderma pigm 99.8 2.8E-19 6E-24 138.6 8.0 72 96-167 2-73 (73)
21 cd00080 HhH2_motif Helix-hairp 99.6 2.7E-15 5.9E-20 117.0 6.3 52 164-215 2-55 (75)
22 PF01367 5_3_exonuc: 5'-3' exo 99.5 9.6E-18 2.1E-22 137.8 -12.3 91 167-258 1-101 (101)
23 smart00279 HhH2 Helix-hairpin- 99.2 1.2E-11 2.7E-16 82.9 3.9 33 169-202 1-36 (36)
24 PF00752 XPG_N: XPG N-terminal 98.8 7.1E-09 1.5E-13 84.8 5.0 47 10-56 55-101 (101)
25 smart00485 XPGN Xeroderma pigm 98.7 1.5E-08 3.3E-13 82.7 5.8 49 8-56 50-99 (99)
26 PF12813 XPG_I_2: XPG domain c 98.7 2.9E-08 6.3E-13 94.2 8.2 89 86-177 5-107 (246)
27 TIGR00600 rad2 DNA excision re 98.5 1.2E-07 2.7E-12 104.6 7.1 52 9-60 51-102 (1034)
28 COG5366 Protein involved in pr 96.3 0.0035 7.6E-08 63.6 3.5 102 87-190 131-233 (531)
29 TIGR00084 ruvA Holliday juncti 95.8 0.071 1.5E-06 48.9 9.6 112 159-279 54-172 (191)
30 PF12826 HHH_2: Helix-hairpin- 95.7 0.0078 1.7E-07 45.3 2.4 26 185-210 6-31 (64)
31 KOG2045 5'-3' exonuclease XRN1 95.6 0.24 5.2E-06 54.5 13.7 183 16-199 64-307 (1493)
32 PRK00116 ruvA Holliday junctio 95.3 0.071 1.5E-06 48.8 7.6 91 186-279 77-174 (192)
33 PF03159 XRN_N: XRN 5'-3' exon 95.1 0.14 2.9E-06 48.6 9.3 38 98-135 172-222 (237)
34 COG5049 XRN1 5'-3' exonuclease 94.3 0.54 1.2E-05 50.6 12.1 95 98-192 176-328 (953)
35 PRK14671 uvrC excinuclease ABC 92.9 0.6 1.3E-05 50.2 9.8 26 185-210 572-597 (621)
36 PRK14600 ruvA Holliday junctio 92.8 0.6 1.3E-05 42.7 8.4 110 158-279 54-170 (186)
37 PRK14605 ruvA Holliday junctio 92.5 0.37 8.1E-06 44.2 6.6 110 159-279 55-173 (194)
38 TIGR00194 uvrC excinuclease AB 91.6 0.13 2.9E-06 54.6 3.0 30 182-211 541-570 (574)
39 PRK14667 uvrC excinuclease ABC 91.5 0.16 3.4E-06 54.0 3.4 29 182-210 514-542 (567)
40 PF14520 HHH_5: Helix-hairpin- 91.2 0.19 4.1E-06 37.0 2.7 25 186-210 9-34 (60)
41 PRK14670 uvrC excinuclease ABC 91.1 0.16 3.5E-06 54.0 3.1 29 183-211 515-543 (574)
42 PRK14669 uvrC excinuclease ABC 91.1 0.18 3.8E-06 54.2 3.3 28 183-210 553-580 (624)
43 KOG2044 5'-3' exonuclease HKE1 91.0 3 6.6E-05 45.6 12.3 181 11-192 79-352 (931)
44 COG0632 RuvA Holliday junction 90.9 3.2 6.9E-05 38.4 11.0 117 156-281 52-183 (201)
45 PRK14606 ruvA Holliday junctio 90.8 0.86 1.9E-05 41.7 7.1 107 159-279 55-168 (188)
46 PRK14604 ruvA Holliday junctio 90.2 1.9 4.2E-05 39.6 8.9 108 161-279 57-174 (195)
47 PRK13901 ruvA Holliday junctio 90.1 1.4 3.1E-05 40.6 7.9 109 159-279 54-169 (196)
48 PRK14601 ruvA Holliday junctio 90.0 1.2 2.7E-05 40.5 7.4 104 160-278 56-166 (183)
49 PRK14603 ruvA Holliday junctio 90.0 1.9 4.2E-05 39.7 8.7 26 253-279 152-177 (197)
50 PF00633 HHH: Helix-hairpin-he 89.8 0.27 5.8E-06 31.5 2.1 15 186-200 15-29 (30)
51 PF10391 DNA_pol_lambd_f: Fing 89.3 0.33 7.1E-06 35.2 2.5 24 186-209 6-30 (52)
52 PRK14672 uvrC excinuclease ABC 89.0 0.35 7.6E-06 52.2 3.4 30 182-211 608-637 (691)
53 PRK14602 ruvA Holliday junctio 87.4 0.9 1.9E-05 42.1 4.7 47 160-213 57-104 (203)
54 PF04599 Pox_G5: Poxvirus G5 p 86.2 9.7 0.00021 39.0 11.6 109 90-213 148-273 (425)
55 PRK00558 uvrC excinuclease ABC 85.3 0.7 1.5E-05 49.5 3.2 26 185-210 546-571 (598)
56 PRK14668 uvrC excinuclease ABC 85.2 0.67 1.4E-05 49.5 3.0 29 183-211 526-554 (577)
57 PRK14666 uvrC excinuclease ABC 84.7 0.77 1.7E-05 49.8 3.2 29 183-211 638-666 (694)
58 PRK12766 50S ribosomal protein 84.4 0.86 1.9E-05 43.0 3.0 28 184-211 5-33 (232)
59 PF02371 Transposase_20: Trans 83.8 0.91 2E-05 36.0 2.5 25 183-207 3-27 (87)
60 smart00278 HhH1 Helix-hairpin- 83.2 0.99 2.1E-05 27.6 2.0 17 185-201 4-20 (26)
61 TIGR01448 recD_rel helicase, p 82.8 3.6 7.7E-05 45.2 7.4 39 167-213 75-113 (720)
62 COG0322 UvrC Nuclease subunit 81.8 1.1 2.4E-05 47.8 3.0 47 164-211 513-559 (581)
63 PHA03065 Hypothetical protein; 81.1 13 0.00028 38.1 10.0 109 90-213 150-275 (438)
64 PRK14601 ruvA Holliday junctio 79.3 1.7 3.8E-05 39.6 3.0 46 155-202 80-128 (183)
65 COG1948 MUS81 ERCC4-type nucle 78.9 1.7 3.8E-05 41.5 2.9 26 186-211 186-211 (254)
66 PRK14603 ruvA Holliday junctio 77.4 3.1 6.6E-05 38.4 4.0 44 156-201 80-126 (197)
67 PRK14600 ruvA Holliday junctio 75.6 3.9 8.5E-05 37.3 4.2 48 154-203 79-128 (186)
68 PRK14604 ruvA Holliday junctio 75.1 3.3 7.2E-05 38.1 3.6 47 155-203 80-129 (195)
69 PRK14602 ruvA Holliday junctio 75.0 3.8 8.1E-05 37.9 4.0 46 155-202 81-129 (203)
70 PRK14606 ruvA Holliday junctio 74.3 3.7 7.9E-05 37.6 3.7 46 155-202 80-128 (188)
71 TIGR00575 dnlj DNA ligase, NAD 71.8 3.4 7.4E-05 44.8 3.3 15 186-200 470-484 (652)
72 PRK02515 psbU photosystem II c 71.8 3.3 7.3E-05 35.7 2.6 24 187-210 66-91 (132)
73 PF01927 Mut7-C: Mut7-C RNAse 70.5 6.2 0.00013 34.4 4.1 88 85-180 7-98 (147)
74 PRK14351 ligA NAD-dependent DN 69.3 4.3 9.4E-05 44.3 3.4 25 186-210 532-556 (689)
75 TIGR00596 rad1 DNA repair prot 69.0 4 8.7E-05 45.4 3.2 25 186-210 761-785 (814)
76 TIGR01259 comE comEA protein. 67.5 5.5 0.00012 33.7 3.0 17 186-202 72-88 (120)
77 PF11798 IMS_HHH: IMS family H 65.9 4.4 9.5E-05 26.2 1.6 13 186-198 15-27 (32)
78 PF05991 NYN_YacP: YacP-like N 65.9 14 0.0003 32.9 5.4 38 97-134 66-109 (166)
79 cd00141 NT_POLXc Nucleotidyltr 65.8 6.2 0.00013 38.7 3.5 26 186-212 89-116 (307)
80 smart00483 POLXc DNA polymeras 65.6 5.3 0.00011 39.7 3.0 25 186-211 93-119 (334)
81 PRK13766 Hef nuclease; Provisi 63.4 6.4 0.00014 43.2 3.4 25 186-210 719-743 (773)
82 PF00875 DNA_photolyase: DNA p 63.4 14 0.0003 32.3 4.9 35 84-118 52-86 (165)
83 COG0632 RuvA Holliday junction 62.7 8.6 0.00019 35.6 3.6 74 120-203 48-129 (201)
84 TIGR00305 probable toxin-antit 62.4 13 0.00027 30.6 4.2 29 105-133 85-113 (114)
85 PRK07956 ligA NAD-dependent DN 62.1 5.6 0.00012 43.3 2.6 27 186-212 483-514 (665)
86 PRK13901 ruvA Holliday junctio 61.7 9.9 0.00021 35.1 3.8 46 155-202 79-127 (196)
87 PRK08609 hypothetical protein; 58.3 16 0.00036 39.0 5.3 28 186-213 92-121 (570)
88 COG1555 ComEA DNA uptake prote 56.9 12 0.00025 33.0 3.3 25 186-210 101-131 (149)
89 TIGR00426 competence protein C 56.3 13 0.00028 27.8 3.0 15 187-201 22-36 (69)
90 PTZ00134 40S ribosomal protein 53.5 15 0.00033 32.6 3.4 34 170-203 9-51 (154)
91 COG0272 Lig NAD-dependent DNA 53.2 9.6 0.00021 41.2 2.5 27 185-211 514-540 (667)
92 TIGR00084 ruvA Holliday juncti 52.8 18 0.00039 33.1 3.9 44 156-201 80-126 (191)
93 PF11731 Cdd1: Pathogenicity l 52.5 27 0.00058 28.4 4.4 32 186-217 16-56 (93)
94 PF14520 HHH_5: Helix-hairpin- 51.8 13 0.00029 27.1 2.4 17 186-202 42-58 (60)
95 TIGR00114 lumazine-synth 6,7-d 46.8 38 0.00083 29.4 4.8 44 82-125 14-64 (138)
96 PF12826 HHH_2: Helix-hairpin- 46.7 16 0.00034 27.3 2.1 21 186-206 39-59 (64)
97 TIGR02765 crypto_DASH cryptoch 46.4 60 0.0013 33.0 7.0 31 87-117 63-93 (429)
98 PRK13482 DNA integrity scannin 46.4 18 0.0004 36.3 3.1 53 158-210 243-315 (352)
99 PRK04053 rps13p 30S ribosomal 45.3 31 0.00066 30.5 4.0 35 169-203 3-46 (149)
100 PF10454 DUF2458: Protein of u 43.0 66 0.0014 28.4 5.8 36 71-106 91-126 (150)
101 PRK14605 ruvA Holliday junctio 42.8 17 0.00038 33.3 2.2 45 156-202 81-128 (194)
102 TIGR00591 phr2 photolyase PhrI 41.5 71 0.0015 32.9 6.7 12 191-202 225-236 (454)
103 KOG2841 Structure-specific end 40.1 21 0.00045 33.9 2.2 29 183-211 196-224 (254)
104 TIGR00615 recR recombination p 39.5 19 0.00041 33.3 1.8 15 186-200 15-29 (195)
105 PRK12419 riboflavin synthase s 39.5 49 0.0011 29.5 4.4 45 81-125 23-74 (158)
106 PRK00076 recR recombination pr 39.4 19 0.00041 33.3 1.8 15 186-200 15-29 (196)
107 COG0353 RecR Recombinational D 39.4 16 0.00036 33.6 1.4 15 185-199 15-29 (198)
108 PF01850 PIN: PIN domain; Int 39.3 27 0.00059 27.8 2.6 50 79-134 69-118 (121)
109 PF00885 DMRL_synthase: 6,7-di 37.8 65 0.0014 28.1 4.9 44 82-125 17-67 (144)
110 PF03979 Sigma70_r1_1: Sigma-7 36.9 67 0.0014 25.0 4.4 47 59-106 12-60 (82)
111 COG1656 Uncharacterized conser 36.6 55 0.0012 29.4 4.3 50 84-134 12-61 (165)
112 PF00416 Ribosomal_S13: Riboso 36.1 32 0.00069 28.4 2.6 18 186-203 19-36 (107)
113 PRK13844 recombination protein 35.9 23 0.0005 32.8 1.8 15 186-200 19-33 (200)
114 COG0258 Exo 5'-3' exonuclease 35.8 16 0.00036 35.6 0.9 30 84-114 103-132 (310)
115 PRK00061 ribH 6,7-dimethyl-8-r 35.0 63 0.0014 28.6 4.4 44 82-125 26-76 (154)
116 PLN02404 6,7-dimethyl-8-ribity 34.7 69 0.0015 28.0 4.5 44 82-125 21-71 (141)
117 PF14490 HHH_4: Helix-hairpin- 34.5 78 0.0017 25.2 4.5 31 189-221 19-49 (94)
118 TIGR03629 arch_S13P archaeal r 33.9 54 0.0012 28.7 3.8 17 187-203 26-42 (144)
119 TIGR02766 crypt_chrom_pln cryp 33.5 1.2E+02 0.0025 31.5 6.8 13 190-202 201-213 (475)
120 PRK01229 N-glycosylase/DNA lya 32.7 32 0.00069 32.0 2.2 18 186-203 123-140 (208)
121 PF14579 HHH_6: Helix-hairpin- 32.3 54 0.0012 25.9 3.3 27 186-212 31-62 (90)
122 PF04919 DUF655: Protein of un 32.0 46 0.001 30.3 3.1 47 166-212 95-151 (181)
123 COG1412 Uncharacterized protei 31.4 79 0.0017 27.5 4.3 43 92-134 70-112 (136)
124 PF12482 DUF3701: Phage integr 31.3 75 0.0016 26.0 3.9 41 160-200 27-68 (96)
125 PF04019 DUF359: Protein of un 29.3 37 0.00079 28.9 1.9 88 20-138 2-95 (121)
126 PRK10674 deoxyribodipyrimidine 28.8 1.6E+02 0.0035 30.5 6.9 13 190-202 203-215 (472)
127 PF14716 HHH_8: Helix-hairpin- 28.6 43 0.00093 25.1 2.0 14 185-198 50-63 (68)
128 TIGR02236 recomb_radA DNA repa 28.5 47 0.001 32.1 2.8 24 186-209 3-27 (310)
129 cd00056 ENDO3c endonuclease II 28.4 38 0.00082 29.2 1.9 15 186-200 87-101 (158)
130 cd06167 LabA_like LabA_like pr 28.2 1.2E+02 0.0027 25.5 5.0 49 87-135 54-116 (149)
131 TIGR03252 uncharacterized HhH- 28.1 39 0.00083 30.7 1.9 18 186-203 119-136 (177)
132 PRK14350 ligA NAD-dependent DN 27.8 52 0.0011 36.0 3.2 23 187-209 507-530 (669)
133 PF11977 RNase_Zc3h12a: Zc3h12 27.6 1.1E+02 0.0025 26.6 4.8 25 13-37 24-48 (155)
134 PRK10702 endonuclease III; Pro 27.3 39 0.00084 31.4 1.8 14 187-200 114-127 (211)
135 PF01936 NYN: NYN domain; Int 27.1 1.4E+02 0.0031 24.7 5.2 49 87-135 49-112 (146)
136 TIGR00289 conserved hypothetic 26.8 1.1E+02 0.0023 28.8 4.7 42 88-130 48-95 (222)
137 PF04900 Fcf1: Fcf1; InterPro 26.3 60 0.0013 26.1 2.6 40 100-139 45-89 (101)
138 TIGR03631 bact_S13 30S ribosom 25.8 60 0.0013 27.2 2.5 17 187-203 20-36 (113)
139 PRK00116 ruvA Holliday junctio 25.7 48 0.001 30.2 2.1 18 186-203 112-129 (192)
140 COG1948 MUS81 ERCC4-type nucle 25.6 2E+02 0.0044 27.7 6.3 24 187-210 219-242 (254)
141 PF09550 DUF2376: Conserved hy 25.1 2.2E+02 0.0047 19.8 4.7 34 166-204 10-43 (43)
142 COG1569 Predicted nucleic acid 24.9 55 0.0012 28.6 2.2 31 107-137 91-121 (142)
143 PRK00254 ski2-like helicase; P 24.9 58 0.0013 35.7 2.9 26 186-211 649-675 (720)
144 PRK03739 2-isopropylmalate syn 24.8 5.6E+02 0.012 27.4 10.2 40 80-119 47-91 (552)
145 COG1491 Predicted RNA-binding 24.8 80 0.0017 29.0 3.3 46 167-213 110-166 (202)
146 smart00478 ENDO3c endonuclease 24.6 50 0.0011 28.2 1.9 15 186-200 76-90 (149)
147 COG2266 GTP:adenosylcobinamide 24.5 1.7E+02 0.0038 26.6 5.4 46 83-128 48-95 (177)
148 PRK06524 biotin carboxylase-li 24.3 94 0.002 32.8 4.2 25 88-112 116-140 (493)
149 PRK13913 3-methyladenine DNA g 24.1 50 0.0011 31.0 1.9 15 186-200 125-139 (218)
150 PRK00124 hypothetical protein; 24.0 62 0.0014 28.6 2.4 91 107-211 56-146 (151)
151 PF04760 IF2_N: Translation in 24.0 65 0.0014 22.8 2.1 48 156-203 4-52 (54)
152 PRK05179 rpsM 30S ribosomal pr 23.8 67 0.0015 27.3 2.5 17 187-203 22-38 (122)
153 PF14229 DUF4332: Domain of un 23.3 2E+02 0.0042 24.2 5.3 49 157-208 31-80 (122)
154 CHL00137 rps13 ribosomal prote 23.1 71 0.0015 27.2 2.5 17 187-203 22-38 (122)
155 COG4021 Uncharacterized conser 22.7 3.2E+02 0.007 25.8 6.8 99 10-122 97-207 (249)
156 COG3327 PaaX Phenylacetic acid 22.5 94 0.002 30.0 3.4 45 251-297 26-72 (291)
157 PF00627 UBA: UBA/TS-N domain; 22.4 1E+02 0.0022 20.0 2.7 24 252-277 2-25 (37)
158 PF06415 iPGM_N: BPG-independe 22.4 3.6E+02 0.0077 25.4 7.2 34 5-38 37-73 (223)
159 TIGR01083 nth endonuclease III 22.3 56 0.0012 29.6 1.8 15 186-200 110-124 (191)
160 TIGR00028 Mtu_PIN_fam Mycobact 22.1 99 0.0022 25.4 3.3 31 107-138 105-135 (142)
161 cd04246 AAK_AK-DapG-like AAK_A 21.7 6.4E+02 0.014 23.2 11.0 30 12-41 16-45 (239)
162 TIGR00288 conserved hypothetic 21.3 1.4E+02 0.0031 26.7 4.1 49 88-136 69-123 (160)
163 PRK01189 V-type ATP synthase s 20.9 1.2E+02 0.0026 25.0 3.3 36 92-127 15-53 (104)
164 smart00165 UBA Ubiquitin assoc 20.8 1.7E+02 0.0038 18.6 3.6 22 254-277 3-24 (37)
165 cd00194 UBA Ubiquitin Associat 20.7 1.7E+02 0.0038 18.7 3.6 22 254-277 3-24 (38)
166 TIGR02660 nifV_homocitr homoci 20.6 5.2E+02 0.011 25.8 8.5 38 81-118 19-61 (365)
167 PF09288 UBA_3: Fungal ubiquit 20.3 1.3E+02 0.0028 22.1 3.0 31 247-279 4-34 (55)
168 TIGR00290 MJ0570_dom MJ0570-re 20.2 1.9E+02 0.0042 27.1 5.0 43 88-131 48-96 (223)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1e-75 Score=585.36 Aligned_cols=299 Identities=59% Similarity=1.008 Sum_probs=286.3
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhccccc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~ 81 (364)
|+|++|++|+||+||++|+++|+++||+|+|||||.+|++|++++++|+++|+++++.+.++.+.|+.+++.++++|+++
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 cchhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHH
Q 017910 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (364)
Q Consensus 82 vt~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v 161 (364)
||++|++.++++|+.||||||+||||||||||+|++.|++++|+|+|+|+|+||++.++++++..+..+.++++|+.+.+
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 99999999999999999999999999999999999999999999999999999999999988754444556889999999
Q ss_pred HHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHHhCCCCcCCcc
Q 017910 162 LEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (364)
Q Consensus 162 ~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~lf~~p~V~~~~ 241 (364)
++.+|++++||+|+|+|+||||++||||||||||++||++||++|+|+++++..++.+|++|++.+++.+|++|.|+.+.
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 99999999999999999999999999999999999999999999999999999899999999999999999999999766
Q ss_pred ccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCCcccccCcccCCC
Q 017910 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVANTS 301 (364)
Q Consensus 242 ~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~~~~~~Q~rld~ff~~~~~~~ 301 (364)
++ +|+|++||.++|++||+++++|+++||++.++||.++..+.+|+|||+||++.+++.
T Consensus 295 ~~-~l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~~~ 353 (393)
T PTZ00217 295 EI-DLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPI 353 (393)
T ss_pred CC-CCCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhccCccCCHHHhcCCCCCcc
Confidence 66 799999999999999999999999999999999999988889999999999987753
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.7e-73 Score=549.53 Aligned_cols=282 Identities=45% Similarity=0.807 Sum_probs=265.4
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcccccc
Q 017910 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (364)
Q Consensus 3 ~~~~G~~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~v 82 (364)
+|++|++|||++|||+|+++|+++||+|+|||||.+|++|++++++|+++|+++++.+..+.+.|+.+++.++++|+++|
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 chhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCC---------cc
Q 017910 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------PV 153 (364)
Q Consensus 83 t~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~---------~v 153 (364)
|++|++.++++|++|||||++||||||||||+|++.|++++|+|+|+|+||||++++++++...+.++. ..
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 EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCc-chHHHHHHh
Q 017910 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDW-PYQEARRLF 232 (364)
Q Consensus 154 ~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~-~~~~~~~lf 232 (364)
+.|+.+.+++.+|++++||+|+|+|+||||++||||||||||++||++|+|+|+|+++++ .++ ++.+++++|
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 579999999999999999999999999999999999999999999999999999998653 233 368999999
Q ss_pred CCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCCccccc
Q 017910 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (364)
Q Consensus 233 ~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~~~~~~Q~rld~ff 294 (364)
++|.|+. +. +++|+.||.++|++||+++++|+++||++.++||.++.++.+|+|||+||
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 45 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=2.6e-67 Score=516.83 Aligned_cols=284 Identities=45% Similarity=0.802 Sum_probs=264.3
Q ss_pred CCcCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcccc
Q 017910 1 MLTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTV 80 (364)
Q Consensus 1 ~L~~~~G~~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~ 80 (364)
+|+|++|++|+|++||++|+++|+++||+|+|||||.+|++|++++++|++.|+++++.+..+.+.|+.+++.++++|+.
T Consensus 46 ~l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~ 125 (338)
T TIGR03674 46 PLMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSS 125 (338)
T ss_pred hhhhccCCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcC
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCC---------
Q 017910 81 KVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI--------- 151 (364)
Q Consensus 81 ~vt~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~--------- 151 (364)
++|.+|++.++++|++|||||++||||||||||+|++.|.|++|+|+|+|+||||+++|++++...+.++.
T Consensus 126 ~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~ 205 (338)
T TIGR03674 126 RLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEV 205 (338)
T ss_pred CCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999998875443211
Q ss_pred ccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHH
Q 017910 152 PVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (364)
Q Consensus 152 ~v~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~l 231 (364)
..+.|+.+.+++.+|++|+||+|+|+|+||||++||||||||||++||++||++|+|+++++.. + + ++.+++.+
T Consensus 206 ~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~~---~-~--~~~~~~~~ 279 (338)
T TIGR03674 206 KPELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGED---I-E--NYDEIREF 279 (338)
T ss_pred cceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcCC---C-C--CHHHHHHH
Confidence 3456999999999999999999999999999999999999999999999999999999997632 2 2 25789999
Q ss_pred hCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCCccccc
Q 017910 232 FKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (364)
Q Consensus 232 f~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~~~~~~Q~rld~ff 294 (364)
|.+|.|+. +. ++.|..||.++|++||+++++|+++||++.++||+++. +.+|+|||+||
T Consensus 280 f~~~~v~~--~~-~~~~~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~~-~~~q~~l~~ff 338 (338)
T TIGR03674 280 FLNPPVTD--DY-ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAY-KSKQKTLDRWF 338 (338)
T ss_pred hCCCCCCC--CC-CccCCCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHhh-cccccchhhcC
Confidence 99999985 34 78999999999999999999999999999999999887 78999999998
No 4
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=8.1e-63 Score=486.73 Aligned_cols=299 Identities=61% Similarity=1.015 Sum_probs=286.5
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcccccc
Q 017910 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (364)
Q Consensus 3 ~~~~G~~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~v 82 (364)
+|..|++|+||+|||+|+++|+++|++|||||||.+|.+|.+++.+|...|..+.+....+.+.|......+|..|.+.|
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 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHHH
Q 017910 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKIL 162 (364)
Q Consensus 83 t~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v~ 162 (364)
|.+++++|++||..|||||+.||+||+||||+|+++|.|++++|+|+|.+.||++.+++++..+..+..++.+|+++.++
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 99999999999999999999999999999999999999999999999999999999999988766667899999999999
Q ss_pred HHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhccCCCCCCcchHHHHHHhCCCCcCCcc
Q 017910 163 EELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (364)
Q Consensus 163 e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~-~l~~~k~~i~e~~~~~~~~~lf~~p~V~~~~ 241 (364)
+.|+++.++|+|+|+|+|||||++|.|||+++|++||++|++++++++ +.+..++.+|++|++..++.+|..|.++...
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 7777788999999999999999999998776
Q ss_pred ccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCCcccccCcccCCC
Q 017910 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVANTS 301 (364)
Q Consensus 242 ~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~~~~~~Q~rld~ff~~~~~~~ 301 (364)
..-++.|..||.+++++|++.+.+|+++||++++.++.+..+..+|+|+|+||+..++.+
T Consensus 290 ~~~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~~ 349 (449)
T KOG2519|consen 290 SILDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKGS 349 (449)
T ss_pred ceeecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCCC
Confidence 623899999999999999999999999999999999999999999999999999988765
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=1.5e-57 Score=444.11 Aligned_cols=268 Identities=52% Similarity=0.882 Sum_probs=251.9
Q ss_pred CCCCchhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhccccccch
Q 017910 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTK 84 (364)
Q Consensus 5 ~~G~~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~ 84 (364)
+.|.+|+|++||++|+.+|+++||+|+|||||.+|++|.++..+|+..|++.......++++|+.+++.++.+++..+|.
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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHHHHH
Q 017910 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 164 (364)
Q Consensus 85 ~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v~e~ 164 (364)
+|++.++++|+.|||||++||+|||||||+|++.|.+++|+|+|+|+|+||++.|++++...+. ..++.|+.+.+++.
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 9999999999999999999999999999999999999999999999999999999988764321 35788999999999
Q ss_pred cCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHHhCCCCcCCccccc
Q 017910 165 LNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQL 244 (364)
Q Consensus 165 lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~lf~~p~V~~~~~~~ 244 (364)
+|++++||+|+|+|+||||++||||||+|||++||++|++++++++++.+....+|++|++.+++++|.+|.|... ..
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 9999999999999999999999999999999999999999999999998877788899999999999999998854 22
Q ss_pred cCCCCCCCHHHHHHHHHHhcCCChHHHHHHHH
Q 017910 245 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIE 276 (364)
Q Consensus 245 ~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~ 276 (364)
.+.|..||.++|+.|++.+++|+++||.+.+.
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=5.7e-47 Score=409.17 Aligned_cols=218 Identities=25% Similarity=0.434 Sum_probs=196.9
Q ss_pred hccccccchhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEE
Q 017910 76 SKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 155 (364)
Q Consensus 76 ~~r~~~vt~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~ 155 (364)
.++++.||.+|+..|+++|++||||||+||+|||||||+|++.|+||+|+|+|+|+|+||+++|++|++.. ...+..
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 56789999999999999999999999999999999999999999999999999999999999999998742 346788
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHH---HHHHhc---------------
Q 017910 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG--SIETIL---ENINRE--------------- 215 (364)
Q Consensus 156 ~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~g--sle~il---~~l~~~--------------- 215 (364)
|+.+++++.+||+++|||++|+|+||||++|||||||+||++||++|+ ++++++ +|++..
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 477776 344321
Q ss_pred -----cCCCCCCcchHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH-hhhccCCCCC
Q 017910 216 -----RYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK-AAKNKSSQGR 289 (364)
Q Consensus 216 -----k~~i~e~~~~~~~~~lf~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~-~~~~~~~Q~r 289 (364)
++.+|++||+..++.+|++|.|+... ..|.|+.||.++|++||+++++|+++||++.|.++. +...+.+|+|
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 24689999999999999999998543 379999999999999999999999999999999874 4666789999
Q ss_pred cccccCccc
Q 017910 290 LESFFKPVA 298 (364)
Q Consensus 290 ld~ff~~~~ 298 (364)
|++||+...
T Consensus 998 ld~FF~~~~ 1006 (1034)
T TIGR00600 998 IDSFFRLAQ 1006 (1034)
T ss_pred HHHhhCccc
Confidence 999998654
No 7
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=3.4e-46 Score=358.43 Aligned_cols=238 Identities=24% Similarity=0.303 Sum_probs=201.5
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhccc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~g--i~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~ 79 (364)
|+|++|.+|+|++||+++++++++.. -.+++|||+..++||++.+++||++|.++|+.+
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 67899999999999999999999852 234678999989999999999999999999999
Q ss_pred cccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHHc----CCeEEEecCCCcccccccCeeEEEeecCCCCCCccE
Q 017910 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (364)
Q Consensus 80 ~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~~----g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~ 154 (364)
..|++.++++|+++|||++.+|| ||||+||+|++. |..+.|+|+|+|++||+++++..... ... .+..
T Consensus 89 ----~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~--~~~-~~~~ 161 (281)
T PRK14976 89 ----ISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLK--KKG-TSHF 161 (281)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEe--cCC-CCcE
Confidence 78999999999999999999998 999999999873 66667999999999999988643222 221 1246
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHH
Q 017910 155 EFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (364)
Q Consensus 155 ~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~---IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~l 231 (364)
.++.+.+.+++|++|+||+|+++|+| |.+|| |||||||||.+||++|||+|+|++++++++.++.+.+...+....
T Consensus 162 ~~~~~~v~~~~gv~p~q~~d~~aL~G-D~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~~ 240 (281)
T PRK14976 162 ILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKAL 240 (281)
T ss_pred EEcHHHHHHHhCcCHHHHHHHHHHhC-CccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHHH
Confidence 79999999999999999999999999 66655 579999999999999999999999999876556666665566666
Q ss_pred hCCCCcCCcccc------ccCCCCCCCHHHHHHHHHHhcCCC
Q 017910 232 FKEPEVVTDEEQ------LQIKWSAPDEEGLINFLVSENGFN 267 (364)
Q Consensus 232 f~~p~V~~~~~~------~~l~~~~pd~e~L~~fl~~e~~f~ 267 (364)
+++.+|++.+++ .++.+.+||.++|.++| ++++|+
T Consensus 241 ~s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~-~~~e~~ 281 (281)
T PRK14976 241 LSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIF-EELELK 281 (281)
T ss_pred HhhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHH-HHcCCC
Confidence 777777665543 35677789999999999 788884
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.1e-45 Score=351.19 Aligned_cols=216 Identities=26% Similarity=0.382 Sum_probs=186.6
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~gi~P---v~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
|+|++|++|+|++||++++.++++. .+| ++|||+.+++||++.+++||++|+++|+++
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 6789999999999999999999985 577 779999989999999999999999999999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHHc----CCeEEEecCCCcccccccCeeEEEeecCCCCCCcc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~~----g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v 153 (364)
.+|++.++++|++||||++.+|+ ||||+||+|++. |..++|+|+|+|++||+++++.+.... +.....
T Consensus 83 -----~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~--~~~~~~ 155 (259)
T smart00475 83 -----LEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPT--KGIKEF 155 (259)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEecc--CCCCcc
Confidence 78899999999999999999998 999999999984 677889999999999999987543222 211224
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHH
Q 017910 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (364)
Q Consensus 154 ~~~~~~~v~e~lgl~~~qfidl~iL~G--~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~l 231 (364)
..++.+.+.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|++++++++.++.+.+...+...+
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 455555689999999999999999999999999876555555555666777
Q ss_pred hCCCCcCCcccc
Q 017910 232 FKEPEVVTDEEQ 243 (364)
Q Consensus 232 f~~p~V~~~~~~ 243 (364)
+++.++++.+++
T Consensus 236 ls~~L~~l~~d~ 247 (259)
T smart00475 236 LSRKLATIETDV 247 (259)
T ss_pred HhhhhheeeeCC
Confidence 788888887766
No 9
>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=6.3e-43 Score=378.70 Aligned_cols=237 Identities=29% Similarity=0.449 Sum_probs=204.6
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~gi~P---v~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
|+|++|+||+|++||++++.++++. .+| ++|||++.++||++.|++||++|.++|+++
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 7899999999999999999999985 678 568999999999999999999999999999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCcc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v 153 (364)
..|++.++++|++||||++.+|| ||||+||+|++ .|..++|+|+|+|++|+++++|.. +..... ...
T Consensus 83 -----~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~--~~~~~~-~~~ 154 (887)
T TIGR00593 83 -----IEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKV--LIPKGK-TSF 154 (887)
T ss_pred -----HHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEE--EeccCC-CCc
Confidence 78999999999999999999999 99999999997 377778999999999999998632 222111 134
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhccC-CCCCCcchHHHH
Q 017910 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQEAR 229 (364)
Q Consensus 154 ~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~---IpGIG~ktA~kLik~~gsle~il~~l~~~k~-~i~e~~~~~~~~ 229 (364)
..++.+.|.+++|++|+||+|+++|+| |.+|| |||||||||.+||++|||+|+|++++++++. ++.+++...+..
T Consensus 155 ~~~~~~~v~~~~Gv~p~q~~D~~aL~G-D~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~ 233 (887)
T TIGR00593 155 TEITPEYVVEKYGVTPDQLVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKED 233 (887)
T ss_pred eEEcHHHHHHHhCCCHHHHHHHHHHcC-CcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHH
Confidence 579999999999999999999999999 77776 5789999999999999999999999998864 466777666666
Q ss_pred HHhCCCCcCCcccc------ccCCCCCCCHHHHHHHHHHhcCCC
Q 017910 230 RLFKEPEVVTDEEQ------LQIKWSAPDEEGLINFLVSENGFN 267 (364)
Q Consensus 230 ~lf~~p~V~~~~~~------~~l~~~~pd~e~L~~fl~~e~~f~ 267 (364)
.++++.++++.+++ +++.+..||.+.|.+|| ++++|+
T Consensus 234 a~ls~~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~-~~lef~ 276 (887)
T TIGR00593 234 AFLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL-QELEFK 276 (887)
T ss_pred HHHHHHhheeecCCCCCCCHHHhccCCCCHHHHHHHH-HHhCCc
Confidence 67777777665443 35678899999999999 799995
No 10
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=100.00 E-value=2.5e-42 Score=325.13 Aligned_cols=207 Identities=24% Similarity=0.353 Sum_probs=174.8
Q ss_pred cCC-CCCchhHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhccc
Q 017910 3 TNE-AGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (364)
Q Consensus 3 ~~~-~G~~Tsal~G~~~r~~~ll~~g--i~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~ 79 (364)
.++ +|++|+|++||++++.++++.. ..+++|||+.+++||++.+++||++|.++|+.+
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 345 8999999999999999999853 456789999999999999999999999999999
Q ss_pred cccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCccE
Q 017910 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (364)
Q Consensus 80 ~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~ 154 (364)
..|++.++++|+.||||++.+|+ ||||+||+|++ .|..++|+|+|+|++|+++++|.. .... ...
T Consensus 84 ----~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~--~~~~----~~~ 153 (240)
T cd00008 84 ----REQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKV--VSPM----KKK 153 (240)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEE--EeCC----Cce
Confidence 78999999999999999999998 99999999996 577788999999999999887632 2222 135
Q ss_pred EEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHHh
Q 017910 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (364)
Q Consensus 155 ~~~~~~v~e~lgl~~~qfidl~iL~G--~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~lf 232 (364)
+++.+.+.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++..+.++.+.+...+....+
T Consensus 154 ~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~~ 233 (240)
T cd00008 154 LVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKGKLREKLEEGKEMAFL 233 (240)
T ss_pred EEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhHHHHHHHHHhHHHHHH
Confidence 79999999999999999999999999 5666667899999999999999999999999987654455544444444444
Q ss_pred CCCCcC
Q 017910 233 KEPEVV 238 (364)
Q Consensus 233 ~~p~V~ 238 (364)
+..+|+
T Consensus 234 s~~L~~ 239 (240)
T cd00008 234 SKRLAT 239 (240)
T ss_pred HHHhhc
Confidence 444443
No 11
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.9e-41 Score=327.27 Aligned_cols=263 Identities=27% Similarity=0.462 Sum_probs=214.5
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHH--cCCCcEEEEeCCCCchhhHHHHHHHhhhhh-chHHHHHHHHcCCHHHHHHHhcc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLE--AGMKPIYVFDGQPPDLKKQELAKRYSKRAD-ATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~--~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~-~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
+.|+.|.+|++++||..++.++++ ..++|++||||++++||++++++||++|++ +|+++
T Consensus 33 ~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~~l------------------ 94 (310)
T COG0258 33 LGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMPDEL------------------ 94 (310)
T ss_pred cCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCHHHH------------------
Confidence 468899999999999998888875 238899999999999999999999999999 99999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCcc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v 153 (364)
..|++.+.+++..+|++++..+| ||||.++++++ .|.+++|+|+|+|++||+++++..... . +..+.
T Consensus 95 -----~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~--~-~~~~~ 166 (310)
T COG0258 95 -----APQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVING--K-KGEPE 166 (310)
T ss_pred -----HHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCcEEEec--c-CCCCc
Confidence 78999999999999999999999 99999999886 688999999999999999999543222 1 12121
Q ss_pred EEEeHHHHHHHc-CCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHH
Q 017910 154 MEFEVAKILEEL-NLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (364)
Q Consensus 154 ~~~~~~~v~e~l-gl~~~qfidl~iL~G--~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~ 230 (364)
..++...+.+.+ |++|+||+|+++|+| |||.+||||||||||++||++||++|.++++++.++...++.+.......
T Consensus 167 ~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l~~~~~~a 246 (310)
T COG0258 167 KFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKA 246 (310)
T ss_pred ccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHHHHHHHHH
Confidence 258999999999 999999999999999 99999999999999999999999999999999865555555544444444
Q ss_pred HhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCC---hHHHHHHHHHHHhhhccCCCCCccccc
Q 017910 231 LFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN---SDRVTKAIEKIKAAKNKSSQGRLESFF 294 (364)
Q Consensus 231 lf~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~---~~rv~~~l~~l~~~~~~~~Q~rld~ff 294 (364)
++.+++|++..++ .+.|..++. ..+++.++.|+ ..++...++.+.+......|.+++.||
T Consensus 247 fl~~~l~t~~~d~-~l~~~~~~~---~~~~~~~~d~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 309 (310)
T COG0258 247 FLSKPLATIKTDV-PLEFDLEDI---LELLVPEHDFSKLLEERVELGFKRLLKAIGSVEQATLDEFF 309 (310)
T ss_pred hcCcccccccccc-cCCcCccch---hhhccCcccHHHHHHHHHHHhHHHHHHHHhhhccccccccc
Confidence 5555999987777 677777775 44444555565 566666777776655434677777765
No 12
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.2e-41 Score=336.90 Aligned_cols=233 Identities=29% Similarity=0.481 Sum_probs=205.6
Q ss_pred CCCCchhHHHHHHHHHHHHH-HcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhccccccc
Q 017910 5 EAGEVTSHLQGMFTRTIRLL-EAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVT 83 (364)
Q Consensus 5 ~~G~~Tsal~G~~~r~~~ll-~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt 83 (364)
..|+||.-...||..-++|| ..||+|+.||||.+.+.|.++..+|+..|++..+..+++|.+|+..++..+++|++.||
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 35889977766666555555 68999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHHHH
Q 017910 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILE 163 (364)
Q Consensus 84 ~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v~e 163 (364)
++|...++++|+..||+||+||||||||+|||.+.|++++|||+|+|+++||+..||..|...+. ..+++...+-+
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 99999999999999999999999999999999999999999999999999999999988876443 34566666655
Q ss_pred Hc----CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhccCCCCCCcc--hHHHHHHhCCCC
Q 017910 164 EL----NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWP--YQEARRLFKEPE 236 (364)
Q Consensus 164 ~l----gl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~-~l~~~k~~i~e~~~--~~~~~~lf~~p~ 236 (364)
.. +++.++|..+|+|.||||.++|||||.+||.++|++|.+.|.++. ++...+..+|++|. +.+|...|.|+.
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 357899999999999999999999999999999999999999875 34444567899887 568889999999
Q ss_pred cCCcc
Q 017910 237 VVTDE 241 (364)
Q Consensus 237 V~~~~ 241 (364)
|..+.
T Consensus 283 VydP~ 287 (556)
T KOG2518|consen 283 VYDPI 287 (556)
T ss_pred eeCch
Confidence 98654
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=4.9e-41 Score=366.54 Aligned_cols=238 Identities=24% Similarity=0.384 Sum_probs=202.1
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~gi~P---v~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
|+|++|.+|+|++||++++.++++ ..+| ++|||+++++||++.+++||++|.++|+++
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 4778 668999889999999999999999999999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCcc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v 153 (364)
..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..++|+|+|+|++|++++++.. +.... ....
T Consensus 85 -----~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~--~~~~~-~~~~ 156 (880)
T PRK05755 85 -----REQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTL--LDTMG-VSKN 156 (880)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEE--eeccC-CCCC
Confidence 78999999999999999999998 99999999995 477888999999999999987632 22211 1134
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHHH
Q 017910 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (364)
Q Consensus 154 ~~~~~~~v~e~lgl~~~qfidl~iL~G--~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~l 231 (364)
..++.+.|.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++.++.++.+++.......+
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 344445689999999999999999999999999877666777766655566
Q ss_pred hCCCCcCCcccc------ccCCCCCCCHHHHHHHHHHhcCCC
Q 017910 232 FKEPEVVTDEEQ------LQIKWSAPDEEGLINFLVSENGFN 267 (364)
Q Consensus 232 f~~p~V~~~~~~------~~l~~~~pd~e~L~~fl~~e~~f~ 267 (364)
+++.++++.+++ .++.|..||.++|.+|| ++++|+
T Consensus 237 ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~ 277 (880)
T PRK05755 237 LSRKLATIKTDVPLEVDLEDLELQPPDREKLIALF-KELEFK 277 (880)
T ss_pred hhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHH-HHhCcH
Confidence 666665544332 35778899999999999 899995
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=3.3e-40 Score=311.92 Aligned_cols=208 Identities=19% Similarity=0.198 Sum_probs=178.5
Q ss_pred CCCCCchhHHHHHHHHHHHHHHcCCCcE---EEEeCCCCc--hhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcc
Q 017910 4 NEAGEVTSHLQGMFTRTIRLLEAGMKPI---YVFDGQPPD--LKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 4 ~~~G~~Tsal~G~~~r~~~ll~~gi~Pv---~VFDG~~p~--~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
+++|. |++++||++++.++++. .+|. ++||+..++ ||++.|++||++|.++|+++
T Consensus 23 ~~~g~-t~av~gf~~~l~~ll~~-~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe~l------------------ 82 (256)
T PRK09482 23 SPNDI-NACVETCQHALDKLIRH-SQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEAL------------------ 82 (256)
T ss_pred CCCCc-chHHHHHHHHHHHHHHH-cCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcHHH------------------
Confidence 36788 99999999999999985 6674 479998777 99999999999999999999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCcc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v 153 (364)
..|++.++++|+++|||++..|+ ||||+||+|++ .|.-+.|+|.|+|++|+..++|.. +.... .
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 99999999986 355556899999999999988642 22211 2
Q ss_pred EEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhccCCCCCCcchHHHHH
Q 017910 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (364)
Q Consensus 154 ~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~I---pGIG~ktA~kLik~~gsle~il~~l~~~k~~i~e~~~~~~~~~ 230 (364)
.+++.+.+.+++|++|+|++|+++|+| |.+||| ||||||||.+||++|||+|+|++++++++.++.+.+...+...
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 888875 6899999999999999999999999887555556666566666
Q ss_pred HhCCCCcCCcccc
Q 017910 231 LFKEPEVVTDEEQ 243 (364)
Q Consensus 231 lf~~p~V~~~~~~ 243 (364)
.+++.++++.+++
T Consensus 231 ~lsr~L~~l~~dv 243 (256)
T PRK09482 231 RLCRKLAQLQTDL 243 (256)
T ss_pred HHHHhhheEeeCC
Confidence 6777888887776
No 15
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=6.1e-35 Score=307.27 Aligned_cols=213 Identities=27% Similarity=0.526 Sum_probs=185.0
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeH
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV 158 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~ 158 (364)
.-.+|..|+.+|+++|+.||||||+||+|||||||.|...++|++|||+|+|+|+||+.+||+|++..+ ..++.|.+
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 345889999999999999999999999999999999999999999999999999999999999998643 34789999
Q ss_pred HHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHHHh---------------------
Q 017910 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG---SIETILENINR--------------------- 214 (364)
Q Consensus 159 ~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~g---sle~il~~l~~--------------------- 214 (364)
..+...||+++..+|-+|.|+|+||+.||+||||++|+++|.+|+ ++..+-+++..
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 44444344331
Q ss_pred -ccCCCCCCcchHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHH----HHHHhhhccCCCCC
Q 017910 215 -ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAI----EKIKAAKNKSSQGR 289 (364)
Q Consensus 215 -~k~~i~e~~~~~~~~~lf~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l----~~l~~~~~~~~Q~r 289 (364)
.+..+|..||...+...|++|.|....+ .|.|+.||.+-|++||.+.+||+.++.+..+ +++.+.....+|.+
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 1246889999999999999999986665 5999999999999999999999999987753 55555555566777
Q ss_pred cccccCc
Q 017910 290 LESFFKP 296 (364)
Q Consensus 290 ld~ff~~ 296 (364)
+-.||-.
T Consensus 695 ~~~~f~~ 701 (815)
T KOG2520|consen 695 ISQFFED 701 (815)
T ss_pred HHHHHHh
Confidence 7777765
No 16
>PHA00439 exonuclease
Probab=99.95 E-value=4e-28 Score=231.71 Aligned_cols=219 Identities=16% Similarity=0.174 Sum_probs=157.2
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHc--CCCc--E-EEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHh
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEA--GMKP--I-YVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFS 76 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~--gi~P--v-~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~ 76 (364)
|+|++|.+|++++||++++.++++. ..+| + ++|| ..++||++.|+.||+||.++|+..
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 6789999999999999999999964 1566 3 3699 568999999999999999988664
Q ss_pred ccccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCC-eEEEecCCCcccccccCeeEEEeecCCCCC
Q 017910 77 KRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ-VYAVASEDMDSLTFGAPRFLRHLMDPSSRK 150 (364)
Q Consensus 77 ~r~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~-v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~ 150 (364)
.|++.++++++.+|||++..|| ||||.||+|++ .|. -.+|+|.|+|++|+....++ +....
T Consensus 97 --------~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~---~~~~~-- 163 (286)
T PHA00439 97 --------GYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFL---WCTTG-- 163 (286)
T ss_pred --------hhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEE---EccCC--
Confidence 3567889999999999999999 99999999986 355 55799999999999865332 21111
Q ss_pred CccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHH---cCCHHHHHHHHHhccCCCCCCcc
Q 017910 151 IPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQ---HGSIETILENINRERYQIPEDWP 224 (364)
Q Consensus 151 ~~v~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~I---pGIG~ktA~kLik~---~gsle~il~~l~~~k~~i~e~~~ 224 (364)
.+..++.+ .|+||+|+.+|+| |.+||| |||| |||.+||++ |-.++.+++.-. .+...+.+|.
T Consensus 164 -~~~~~~~~--------~p~~~~d~~AL~G-DsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~sg~-~~~~~~~~~~ 231 (286)
T PHA00439 164 -NILTQTPE--------TADRWHLFQTIKG-DSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKSGK-RKGQTVTKWK 231 (286)
T ss_pred -ceEEcCcc--------cHHHHHhhhhccc-ccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhccc-ccccchhhhh
Confidence 11113322 3999999999999 999987 5899 999999999 445555554421 1222323222
Q ss_pred hHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHH--HHHHHhh
Q 017910 225 YQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKA--IEKIKAA 281 (364)
Q Consensus 225 ~~~~~~lf~~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~--l~~l~~~ 281 (364)
.. . ....+ .=.+.++... .+-|.+++.+... +.|+..+
T Consensus 232 --------k~---~--~~~~~-----~~w~~~v~~~-~k~g~~e~~~~~q~~~ari~r~ 271 (286)
T PHA00439 232 --------KR---A--PEPEE-----TLWDCIVTLG-AKAGMTEEDAIKQAQMARILRA 271 (286)
T ss_pred --------cc---C--CCccc-----cHHHHHHHHH-HHcCCCHHHHHHHHHHHHHhhc
Confidence 00 0 00001 1246788887 6889998875443 4455443
No 17
>PHA02567 rnh RnaseH; Provisional
Probab=99.92 E-value=1.6e-24 Score=207.95 Aligned_cols=161 Identities=14% Similarity=0.117 Sum_probs=125.7
Q ss_pred CcCCCCCchhHHHH-HHHHHHHHHHc-CCCc---EEEEeCCC-CchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHH
Q 017910 2 LTNEAGEVTSHLQG-MFTRTIRLLEA-GMKP---IYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKF 75 (364)
Q Consensus 2 L~~~~G~~Tsal~G-~~~r~~~ll~~-gi~P---v~VFDG~~-p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~ 75 (364)
|++++|.+|++|++ +++.+.+++.. .-.| +++||+.. ++||++.++.||++|.++|+++..-++ .+
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 67899999999966 66666666542 1223 45799974 789999999999999999998722111 00
Q ss_pred hccccccchhhH-HHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCccccccc-CeeEEEeecCCC
Q 017910 76 SKRTVKVTKQHN-DDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGA-PRFLRHLMDPSS 148 (364)
Q Consensus 76 ~~r~~~vt~~~~-~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~-~~vi~~l~~~~~ 148 (364)
.+++ +.+++++..|||+++..|| ||||.||+|++ .|..+.|+|+|+|++|+.. ++|.. +..
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 4666679999999999984 66532 221
Q ss_pred CCCccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCcc
Q 017910 149 RKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIG 191 (364)
Q Consensus 149 ~~~~v~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG 191 (364)
++.+.|.+++| .|+|++|+.+|+| |.+||||||-
T Consensus 173 -------~~~~~V~~k~G-~P~q~iD~kaL~G-DsSDNIPGVp 206 (304)
T PHA02567 173 -------MQKKWVKPKYG-SPEKDLMTKIIKG-DKKDGVASIK 206 (304)
T ss_pred -------CCHHHHHHHhC-CHHHHHHHHHhCC-cccCCcCCCC
Confidence 34577889999 5999999999999 9999999985
No 18
>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=99.91 E-value=7.6e-25 Score=177.93 Aligned_cols=88 Identities=53% Similarity=0.847 Sum_probs=75.1
Q ss_pred HhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEee-cC-CC----CCCccEEEeHHHHHHHcCCC
Q 017910 95 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLM-DP-SS----RKIPVMEFEVAKILEELNLT 168 (364)
Q Consensus 95 ~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~-~~-~~----~~~~v~~~~~~~v~e~lgl~ 168 (364)
++|||||++||||||||||+|+++|+|++|+|+|+|+|+||+++|++++. .. +. ....+..|+.+.+++.+|++
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 13468899999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 017910 169 MDQFIDLCILSGCD 182 (364)
Q Consensus 169 ~~qfidl~iL~G~D 182 (364)
++||+++|+|+|||
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 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=99.91 E-value=6.4e-24 Score=190.14 Aligned_cols=136 Identities=29% Similarity=0.473 Sum_probs=113.1
Q ss_pred CcCCCCCchhHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhcc
Q 017910 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (364)
Q Consensus 2 L~~~~G~~Tsal~G~~~r~~~ll~~gi~P---v~VFDG~~p~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (364)
|.+++|++|++++||+.++.++++. .+| ++|||+..++||++.+++||++|.++|+++
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 6789999999999999999999985 566 447999988999999999999999999999
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccC-cHHHHHHHHHH----cCCeEEEecCCCcccccccC--eeEEEeecCCCCCC
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAP--RFLRHLMDPSSRKI 151 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APg-EADaq~A~L~~----~g~v~~ViS~DsD~l~fg~~--~vi~~l~~~~~~~~ 151 (364)
..|++.++++|+.+||+++..|| ||||.||+|++ +|.-..|+|+|+|++|+..+ +|. ++..+ ..
T Consensus 85 -----~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~--~~~~~--~~ 155 (169)
T PF02739_consen 85 -----IPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVY--LLDPG--KK 155 (169)
T ss_dssp -----HHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEE--EEETT--TT
T ss_pred -----HHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEE--EeecC--CC
Confidence 78899999999999999999999 99999999997 46666799999999999999 543 33332 23
Q ss_pred ccEEEeHHHHHHHc
Q 017910 152 PVMEFEVAKILEEL 165 (364)
Q Consensus 152 ~v~~~~~~~v~e~l 165 (364)
....|+.+.|.|+|
T Consensus 156 ~~~~~~~~~v~eky 169 (169)
T PF02739_consen 156 KFKVYDPEEVEEKY 169 (169)
T ss_dssp CS-EB-HHHHHHHT
T ss_pred CCEEEcHHHHhhcC
Confidence 46789999998875
No 20
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.79 E-value=2.8e-19 Score=138.59 Aligned_cols=72 Identities=49% Similarity=0.750 Sum_probs=66.7
Q ss_pred hcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHHHHHcCC
Q 017910 96 LMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNL 167 (364)
Q Consensus 96 ~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v~e~lgl 167 (364)
.+||||++||+|||||||+|+++|++++|+|+|+|+|+||++++++++...+++..+++.++...+++++|+
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 689999999999999999999999999999999999999999999999876554557899999999999985
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=99.58 E-value=2.7e-15 Score=117.01 Aligned_cols=52 Identities=50% Similarity=0.809 Sum_probs=49.6
Q ss_pred HcCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhc
Q 017910 164 ELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRE 215 (364)
Q Consensus 164 ~lgl~~~qfidl~iL~G--~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~ 215 (364)
.+|++|+||+|+|+|+| |||.+||||||+|||.+||++|+++++++++++..
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=99.53 E-value=9.6e-18 Score=137.77 Aligned_cols=91 Identities=33% Similarity=0.471 Sum_probs=51.8
Q ss_pred CCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhccC-CCCCCcchHH-----HHHHh-CCCC
Q 017910 167 LTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQE-----ARRLF-KEPE 236 (364)
Q Consensus 167 l~~~qfidl~iL~G~Dy~d~I---pGIG~ktA~kLik~~gsle~il~~l~~~k~-~i~e~~~~~~-----~~~lf-~~p~ 236 (364)
++|+|++||.+|+| |.+||| ||||+|||.+||++|||+|+|+++++.++. ++.+.+...+ .+.+- .+.+
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 999987 589999999999999999999999987765 5554433221 22222 2444
Q ss_pred cCCccccccCCCCCCCHHHHHH
Q 017910 237 VVTDEEQLQIKWSAPDEEGLIN 258 (364)
Q Consensus 237 V~~~~~~~~l~~~~pd~e~L~~ 258 (364)
+.+..++++++|..||.++|.+
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 5555566788999999998864
No 23
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.21 E-value=1.2e-11 Score=82.87 Aligned_cols=33 Identities=55% Similarity=0.945 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCccHHHHHHHHHHc
Q 017910 169 MDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQH 202 (364)
Q Consensus 169 ~~qfidl~iL~G~Dy~d---~IpGIG~ktA~kLik~~ 202 (364)
|+||+|+|+|+| ||+| +|||||+|||++||++|
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 56899999999999987
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=98.78 E-value=7.1e-09 Score=84.79 Aligned_cols=47 Identities=55% Similarity=1.055 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhc
Q 017910 10 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (364)
Q Consensus 10 Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~ 56 (364)
++++.++++++..|+++||+|||||||.+|+.|.++..+|+..|+++
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=98.75 E-value=1.5e-08 Score=82.68 Aligned_cols=49 Identities=59% Similarity=0.969 Sum_probs=44.2
Q ss_pred Cchh-HHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhc
Q 017910 8 EVTS-HLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (364)
Q Consensus 8 ~~Ts-al~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~ 56 (364)
.+++ ++.++++|+..|+++||.|||||||.+|+.|.++..+|+..|+++
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 999999999999999999999999999999999999999888753
No 26
>PF12813 XPG_I_2: XPG domain containing
Probab=98.74 E-value=2.9e-08 Score=94.22 Aligned_cols=89 Identities=28% Similarity=0.271 Sum_probs=67.8
Q ss_pred hHHHHHHHHHhc---CCCEEeccCcHHHHHHHHHHcCCeEEEecCCCccccccc--CeeEEEee---cCC------CCCC
Q 017910 86 HNDDCKRLLKLM---GVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA--PRFLRHLM---DPS------SRKI 151 (364)
Q Consensus 86 ~~~~ik~lL~~~---GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~--~~vi~~l~---~~~------~~~~ 151 (364)
+++.+.+.|+.+ |++++..|+|||..||.++++.-+ .|+|+|||+++|.. ..-+..+. ... ....
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 467788999998 999999999999999999987666 69999999999976 22122221 111 0123
Q ss_pred ccEEEeHHHHHHHcCCCHHHHHHHHH
Q 017910 152 PVMEFEVAKILEELNLTMDQFIDLCI 177 (364)
Q Consensus 152 ~v~~~~~~~v~e~lgl~~~qfidl~i 177 (364)
....|+.+.++..+|+. .++.++.
T Consensus 84 ~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 84 SAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 45679999999999999 6666666
No 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=98.54 E-value=1.2e-07 Score=104.56 Aligned_cols=52 Identities=46% Similarity=0.722 Sum_probs=48.5
Q ss_pred chhHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHH
Q 017910 9 VTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60 (364)
Q Consensus 9 ~Tsal~G~~~r~~~ll~~gi~Pv~VFDG~~p~~K~~~~~~rk~~R~~~~~~l 60 (364)
.++||.|||+|+++|+.+||+|||||||.+|++|.+++.+|+.+|+++.+..
T Consensus 51 ~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a~~~a 102 (1034)
T TIGR00600 51 KNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDA 102 (1034)
T ss_pred CCHHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999999999999999998876654
No 28
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=96.26 E-value=0.0035 Score=63.63 Aligned_cols=102 Identities=30% Similarity=0.428 Sum_probs=82.3
Q ss_pred HHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccc-cCeeEEEeecCCCCCCccEEEeHHHHHHHc
Q 017910 87 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFG-APRFLRHLMDPSSRKIPVMEFEVAKILEEL 165 (364)
Q Consensus 87 ~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg-~~~vi~~l~~~~~~~~~v~~~~~~~v~e~l 165 (364)
++.+-.++...||.|+++|+-|..|||||+....++++. +-+|.+.|. .++++..+... +..-|+..++....++-.
T Consensus 131 ~d~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~-gp~d~l~ld~vdr~il~m~fg-~d~Ppl~~~~vp~~lem~ 208 (531)
T COG5366 131 MDVASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAF-GPSDILLLDGVDRIILDMSFG-SDKPPLDVFHVPRFLEMF 208 (531)
T ss_pred cccccccccccceEEEehhhHHHHHHHHHHHHHHHHhcC-CchHhHHHhhhhhheeecccC-CCCCCCcccccchHHHhc
Confidence 346677889999999999999999999999988888654 558888884 45666555543 445677888888888877
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCc
Q 017910 166 NLTMDQFIDLCILSGCDYCDSIRGI 190 (364)
Q Consensus 166 gl~~~qfidl~iL~G~Dy~d~IpGI 190 (364)
-.+-.-|..+..|.|||.+..++.+
T Consensus 209 l~s~~lFya~~ll~~c~~~s~~~~C 233 (531)
T COG5366 209 LLSSRLFYALGLLLGCDFCSTIPRC 233 (531)
T ss_pred ccccchhhhhccccccccccccccc
Confidence 7788999999999999999988763
No 29
>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=95.80 E-value=0.071 Score=48.87 Aligned_cols=112 Identities=20% Similarity=0.268 Sum_probs=64.9
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhcc-C---CCCCCcchHHHHHHhC
Q 017910 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER-Y---QIPEDWPYQEARRLFK 233 (364)
Q Consensus 159 ~~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k-~---~i~e~~~~~~~~~lf~ 233 (364)
++...-||+ +.++--.|..|++ |||||||+|+.++..+ +++++.+.+.... . ++| .+-.+.|..++.
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 334456786 5666666777765 8999999999999875 5778877765311 0 222 122233333321
Q ss_pred --CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+..+.....+..-.-..+..+.+.+-| ..+||++..+++++.++.
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 111100000000000123456777777 589999999999998774
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.68 E-value=0.0078 Score=45.32 Aligned_cols=26 Identities=35% Similarity=0.597 Sum_probs=21.7
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 185 d~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
-||||||+++|..|+++|+|++++.+
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~ 31 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMN 31 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Confidence 48999999999999999999998763
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=95.57 E-value=0.24 Score=54.54 Aligned_cols=183 Identities=22% Similarity=0.329 Sum_probs=102.1
Q ss_pred HHHHHHHHHHcCCCcEE----EEeCCCCchhhHHHHHHH-hhhhhchHHHHHHHHcCCHHHHHHHhccccccchhhHHHH
Q 017910 16 MFTRTIRLLEAGMKPIY----VFDGQPPDLKKQELAKRY-SKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDC 90 (364)
Q Consensus 16 ~~~r~~~ll~~gi~Pv~----VFDG~~p~~K~~~~~~rk-~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~~~~~~i 90 (364)
+|+-+-.|... |+|-= .-||..|-.|...-..|+ ..-..+.+.+.+|.+.|+.-..+.|-+.|+..-.+.+..+
T Consensus 64 IfnYIdhLf~~-IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~rl 142 (1493)
T KOG2045|consen 64 IFNYIDHLFYL-IKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMVRL 142 (1493)
T ss_pred HHHHHHHHHHh-hCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHHHH
Confidence 33333344443 88843 469998865544333332 2223445678888999986555677666664433444445
Q ss_pred HHHHHh------------cCCCEE----eccCcHHHHHHHHHHc---------CCeEEEecCCCccccccc----Ce--e
Q 017910 91 KRLLKL------------MGVPVV----EAPSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR--F 139 (364)
Q Consensus 91 k~lL~~------------~GIp~i----~APgEADaq~A~L~~~---------g~v~~ViS~DsD~l~fg~----~~--v 139 (364)
.+-|+. -++.+| ++|||+|--|--..+. +--.+++.=|-|++.+|- ++ +
T Consensus 143 ~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~l 222 (1493)
T KOG2045|consen 143 QEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVL 222 (1493)
T ss_pred HHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceee
Confidence 444443 366666 4699999766555441 334567888999999982 32 2
Q ss_pred EEEeecCCCCC----Cc---cEEEeHH-----------HHHHH--cCCCH----HHHHHHHHHhCCCCCCCCCCccH-HH
Q 017910 140 LRHLMDPSSRK----IP---VMEFEVA-----------KILEE--LNLTM----DQFIDLCILSGCDYCDSIRGIGG-QT 194 (364)
Q Consensus 140 i~~l~~~~~~~----~~---v~~~~~~-----------~v~e~--lgl~~----~qfidl~iL~G~Dy~d~IpGIG~-kt 194 (364)
+|--..-+++. .. +-..++. ++... +.++. +.||.++.|+|+|+.+++|++-. ..
T Consensus 223 LREEVtFgrrn~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~g 302 (1493)
T KOG2045|consen 223 LREEVTFGRRNKRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSG 302 (1493)
T ss_pred eeeeeecccccccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCC
Confidence 22111111111 11 1112222 22211 12222 56788899999999999998764 34
Q ss_pred HHHHH
Q 017910 195 ALKLI 199 (364)
Q Consensus 195 A~kLi 199 (364)
|+-|+
T Consensus 303 Alpll 307 (1493)
T KOG2045|consen 303 ALPLL 307 (1493)
T ss_pred hHHHH
Confidence 55554
No 32
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.26 E-value=0.071 Score=48.80 Aligned_cols=91 Identities=19% Similarity=0.315 Sum_probs=49.2
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHhc---c-CCCCCCcchHHHHHHhC--CCCcC-CccccccCCCCCCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIETILENINRE---R-YQIPEDWPYQEARRLFK--EPEVV-TDEEQLQIKWSAPDEEGLIN 258 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle~il~~l~~~---k-~~i~e~~~~~~~~~lf~--~p~V~-~~~~~~~l~~~~pd~e~L~~ 258 (364)
+|||||||+|.+++..|++ +.+.+.+... . ..+| .+....|..++. +.... .......-.-..+..+.+..
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 122223332221 11110 00000000111223678999
Q ss_pred HHHHhcCCChHHHHHHHHHHH
Q 017910 259 FLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 259 fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+| ..+||++..+.+.++.+.
T Consensus 155 aL-~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 155 AL-VALGYKPKEASKAVAKIL 174 (192)
T ss_pred HH-HHcCCCHHHHHHHHHHHh
Confidence 99 699999999998888775
No 33
>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=95.12 E-value=0.14 Score=48.64 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=25.4
Q ss_pred CCCEEec----cCcHHHHHHHHHHc---------CCeEEEecCCCcccccc
Q 017910 98 GVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSLTFG 135 (364)
Q Consensus 98 GIp~i~A----PgEADaq~A~L~~~---------g~v~~ViS~DsD~l~fg 135 (364)
++.+|.+ |||+|--|....+. +...+|++.|+|+++++
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 5567665 78999766665542 46788999999999986
No 34
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=94.35 E-value=0.54 Score=50.55 Aligned_cols=95 Identities=23% Similarity=0.413 Sum_probs=62.0
Q ss_pred CCCEEe----ccCcHHHHHHHHHHc---------CCeEEEecCCCccccccc----Ce--eEE-Eeec-CCC-C------
Q 017910 98 GVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR--FLR-HLMD-PSS-R------ 149 (364)
Q Consensus 98 GIp~i~----APgEADaq~A~L~~~---------g~v~~ViS~DsD~l~fg~----~~--vi~-~l~~-~~~-~------ 149 (364)
++.+|. .|||+|--|-.+.+. +-..+|.+-|-|++.+|- |+ ++| ..+. ..+ +
T Consensus 176 nl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~ 255 (953)
T COG5049 176 NLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTK 255 (953)
T ss_pred eEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCccccccccccc
Confidence 455654 489999988888763 357789999999999982 43 333 1111 111 0
Q ss_pred ---------------CCccEEEeHHHHHHHc-------CCC--------HHHHHHHHHHhCCCCCCCCCCccH
Q 017910 150 ---------------KIPVMEFEVAKILEEL-------NLT--------MDQFIDLCILSGCDYCDSIRGIGG 192 (364)
Q Consensus 150 ---------------~~~v~~~~~~~v~e~l-------gl~--------~~qfidl~iL~G~Dy~d~IpGIG~ 192 (364)
..++-+++.+-+.+.+ +++ -+.||.+|-++|+|+.+++|++-.
T Consensus 256 ~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldi 328 (953)
T COG5049 256 CGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDI 328 (953)
T ss_pred ccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCcccc
Confidence 1245566766554432 222 267788999999999999998653
No 35
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=92.89 E-value=0.6 Score=50.24 Aligned_cols=26 Identities=42% Similarity=0.694 Sum_probs=23.7
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 185 d~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
++|||||+++|..|++.|||+++|..
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 57999999999999999999988854
No 36
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.82 E-value=0.6 Score=42.67 Aligned_cols=110 Identities=15% Similarity=0.211 Sum_probs=60.1
Q ss_pred HHHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC---CCCCCcchHHHHHHhC
Q 017910 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY---QIPEDWPYQEARRLFK 233 (364)
Q Consensus 158 ~~~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~---~i~e~~~~~~~~~lf~ 233 (364)
.++...-||+ ++++--.|-.|+ +|.|||||+|+.++..+ +.+++...+..... ++|- .=.+-|..++.
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 3444556786 455555555554 47889999999999875 57777776653211 2221 11222333321
Q ss_pred --CCCcC-CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 --EPEVV-TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 --~p~V~-~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+-.+. ..... . . ..+..+.+..-| ..+||++..+++++.++.
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 111234455666 599999999999998773
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.45 E-value=0.37 Score=44.24 Aligned_cols=110 Identities=17% Similarity=0.270 Sum_probs=61.2
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhcc----CCCCCCcchHHHHHHhC
Q 017910 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER----YQIPEDWPYQEARRLFK 233 (364)
Q Consensus 159 ~~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k----~~i~e~~~~~~~~~lf~ 233 (364)
++...-||+ +.++--.|..|+ +|+|||||+|+.++..|+ .+.+++.+.... .++| .+-.+.|..+..
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vp-GIGkKtAerIil 126 (194)
T PRK14605 55 EDALSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIP-GIGKKTASRIVL 126 (194)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCC-CCCHHHHHHHHH
Confidence 344456887 566666666665 489999999999999886 677766663210 0122 111222322110
Q ss_pred --CCCcC--CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 --EPEVV--TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 --~p~V~--~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+..+. +.... ... .....+.+...| ..+||+...+.+.++++.
T Consensus 127 ELk~Ki~~~~~~~~-~~~-~~~~~~e~~~aL-~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 127 ELKDKIAKNWEAGV-LSQ-VTEANSDILATL-TALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHhhhhccc-ccc-ccchHHHHHHHH-HHcCCCHHHHHHHHHHhh
Confidence 00000 00000 000 011235677777 699999999998888764
No 38
>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=91.55 E-value=0.13 Score=54.62 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=26.4
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 182 Dy~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
.-.|+||||||++..+||+.|||+++|.+.
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 455799999999999999999999998653
No 39
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=91.50 E-value=0.16 Score=53.99 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=26.1
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 182 DYCDSIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 182 Dy~d~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
.-.|+|||||+++..+||+.|||+++|.+
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~ 542 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFKTLYDFLK 542 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhCCHHHHHh
Confidence 35579999999999999999999999875
No 40
>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=91.25 E-value=0.19 Score=37.03 Aligned_cols=25 Identities=36% Similarity=0.476 Sum_probs=22.6
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-~gsle~il~ 210 (364)
+|||||+++|..|... |.+++++..
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 6899999999999999 899988864
No 41
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=91.14 E-value=0.16 Score=53.97 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=26.1
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
-.++||||||++..+||+.|||+++|.+.
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 55799999999999999999999998753
No 42
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=91.08 E-value=0.18 Score=54.22 Aligned_cols=28 Identities=29% Similarity=0.520 Sum_probs=25.4
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
-.++|||||++++.+|++.|||+++|.+
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~ 580 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRA 580 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4468999999999999999999999875
No 43
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=91.02 E-value=3 Score=45.55 Aligned_cols=181 Identities=20% Similarity=0.344 Sum_probs=97.8
Q ss_pred hHHHHHHHHHHHHHHcCCCcEE-EEeCCCCchhhHHHHHH--HhhhhhchHHH--H----HHHHcCC----HHHHHHHhc
Q 017910 11 SHLQGMFTRTIRLLEAGMKPIY-VFDGQPPDLKKQELAKR--YSKRADATDDL--A----EAVEAGN----KEDIEKFSK 77 (364)
Q Consensus 11 sal~G~~~r~~~ll~~gi~Pv~-VFDG~~p~~K~~~~~~r--k~~R~~~~~~l--~----~a~~~g~----~~~~~k~~~ 77 (364)
-+++-++.|++.|.+- -+-.| .-||-.|-.|...-..| ++.|+.+.++. + +...+|. ...-+.|-+
T Consensus 79 ~avFeyiDrlf~mvRP-RkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDS 157 (931)
T KOG2044|consen 79 VAVFEYIDRLFSMVRP-RKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDS 157 (931)
T ss_pred HHHHHHHHHHHHhccc-hheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhcccccc
Confidence 4555566666655542 22234 68999886554432222 23333332221 1 1122232 111122323
Q ss_pred cccccchhhHHHHHHHHHh------------cCCCEEec----cCcHHHHHHHHHHc---------CCeEEEecCCCccc
Q 017910 78 RTVKVTKQHNDDCKRLLKL------------MGVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSL 132 (364)
Q Consensus 78 r~~~vt~~~~~~ik~lL~~------------~GIp~i~A----PgEADaq~A~L~~~---------g~v~~ViS~DsD~l 132 (364)
-|+..-.+.++.+-..|+. -+|.+|-+ |||+|--|-...+. +-+.+++.-|-|++
T Consensus 158 NcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLI 237 (931)
T KOG2044|consen 158 NCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLI 237 (931)
T ss_pred CccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccce
Confidence 3333322445555555543 36777754 89999877777662 34778999999999
Q ss_pred cccc----C--eeEEEeecCCC----------------------------------CCCccEEEeHHHHHHH----cCC-
Q 017910 133 TFGA----P--RFLRHLMDPSS----------------------------------RKIPVMEFEVAKILEE----LNL- 167 (364)
Q Consensus 133 ~fg~----~--~vi~~l~~~~~----------------------------------~~~~v~~~~~~~v~e~----lgl- 167 (364)
.+|= + .|+|-.+.++. .+.++.+++..-+.|. +-+
T Consensus 238 mLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p 317 (931)
T KOG2044|consen 238 MLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMP 317 (931)
T ss_pred eeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCC
Confidence 9982 1 24444333211 0124555666544443 222
Q ss_pred ------C----HHHHHHHHHHhCCCCCCCCCCccH
Q 017910 168 ------T----MDQFIDLCILSGCDYCDSIRGIGG 192 (364)
Q Consensus 168 ------~----~~qfidl~iL~G~Dy~d~IpGIG~ 192 (364)
+ -+.||-+|-++|+|+.+.+|-+-+
T Consensus 318 ~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeI 352 (931)
T KOG2044|consen 318 NLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEI 352 (931)
T ss_pred CCCccccHHhhhcceEEEEeeecCccCCCCCchhh
Confidence 2 256677899999999999996544
No 44
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=90.93 E-value=3.2 Score=38.45 Aligned_cols=117 Identities=19% Similarity=0.195 Sum_probs=62.9
Q ss_pred EeHHHHHHHcCCC-HHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC----CCCCCcchHHHHH
Q 017910 156 FEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARR 230 (364)
Q Consensus 156 ~~~~~v~e~lgl~-~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~----~i~e~~~~~~~~~ 230 (364)
+-.++...-||+. .+.=..|..|. +|.|||||+|+.+|.. .+++++.+.+..... ++|-- --+-|+.
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~Li------sVnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGI-GkKtAer 123 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLLI------SVNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGI-GKKTAER 123 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHHH------ccCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCC-CHHHHHH
Confidence 4556677889984 44444455554 4788999999999986 467888877764321 22211 1222333
Q ss_pred HhC---CCCcCCc-ccc--ccCCCC----CCCHHHHHHHHHHhcCCChHHHHHHHHHHHhh
Q 017910 231 LFK---EPEVVTD-EEQ--LQIKWS----APDEEGLINFLVSENGFNSDRVTKAIEKIKAA 281 (364)
Q Consensus 231 lf~---~p~V~~~-~~~--~~l~~~----~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~ 281 (364)
+.. ....... .+. ....+. .+-.+.-.+-| ..+||++..+++++..+...
T Consensus 124 ivleLk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~AL-~~LGy~~~e~~~av~~v~~~ 183 (201)
T COG0632 124 IVLELKGKLAAFLKGDGGSPAEDLSLDESSPALEEAVEAL-VALGYKEKEIKKAVKKVLKE 183 (201)
T ss_pred HHHHHhhhhhhhcccccccccccccccccchhhhHHHHHH-HHcCCCHHHHHHHHHHHHhc
Confidence 331 1111000 000 011111 11122223444 48999999999988877644
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.79 E-value=0.86 Score=41.70 Aligned_cols=107 Identities=16% Similarity=0.207 Sum_probs=59.6
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC----CCCCCcchHHHHHHhC
Q 017910 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (364)
Q Consensus 159 ~~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~----~i~e~~~~~~~~~lf~ 233 (364)
++...-||+ +.++--.|..|+ +|.|||||+|+.+|..+ +.+++.+.+..... ++|- .-.+-|..+..
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAerIil 126 (188)
T PRK14606 55 QDGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPG-ISKKTAERIVM 126 (188)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 344456787 455555566665 48899999999999875 57777777653211 2221 11122322221
Q ss_pred --CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+..+.. .... .....+.+.+-| ..+||++..+++++.++.
T Consensus 127 ELkdK~~~-~~~~----~~~~~~e~~~AL-~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 127 ELKDEFES-AGIK----DMRIYHESLEAL-VSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHhhcc-ccCC----CcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 111110 0000 011344555666 499999999999988764
No 46
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.23 E-value=1.9 Score=39.63 Aligned_cols=108 Identities=17% Similarity=0.218 Sum_probs=55.4
Q ss_pred HHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC----CCCCCcchHHHHHHhC--
Q 017910 161 ILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK-- 233 (364)
Q Consensus 161 v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~----~i~e~~~~~~~~~lf~-- 233 (364)
...-||+ +.++--.|..|+ +|.|||||+|+.+|..+ +.+++.+.+..... ++|- .=.+-|..+..
T Consensus 57 ~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpG-IGkKtAerIilEL 128 (195)
T PRK14604 57 ALTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPG-IGKKTAERIVLEL 128 (195)
T ss_pred CceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHHH
Confidence 3445676 455555555554 37888888888888864 56777766652210 1211 11111222211
Q ss_pred CCCcC---CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 EPEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 ~p~V~---~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+..+. ....... . .....+.+.+-| ..+||++..+++++.++.
T Consensus 129 k~K~~~~~~~~~~~~-~-~~~~~~e~~~aL-~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 129 KGKIDVRQLSGSTSP-A-VSALDRELSEIL-ISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHhccccccccccc-c-ccccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 00000 0000000 0 011134555666 499999999999998774
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.11 E-value=1.4 Score=40.58 Aligned_cols=109 Identities=21% Similarity=0.286 Sum_probs=57.7
Q ss_pred HHHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC----CCCCCcchHHHHHHhC
Q 017910 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (364)
Q Consensus 159 ~~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~----~i~e~~~~~~~~~lf~ 233 (364)
++-..-||+ +.++--.|..|++ |.|||||+|+.+|..+ +.+++.+.+..... ++|- .=.+-|..+..
T Consensus 54 ED~~~LYGF~t~~Er~lF~~Lis------VsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIIl 125 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELIG------VDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKG-IGNKMAGKIFL 125 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC------cCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHH
Confidence 334456776 5566656666654 7889999999988876 46777766642210 1221 11122222221
Q ss_pred --CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 234 --~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
+..+...... .- .....+...+-| ..+||++..+.+++..+.
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 1101000000 00 112234455555 489999999999887654
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.04 E-value=1.2 Score=40.54 Aligned_cols=104 Identities=14% Similarity=0.241 Sum_probs=56.0
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhccC----CCCCCcchHHHHHHhC-
Q 017910 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (364)
Q Consensus 160 ~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~~~k~----~i~e~~~~~~~~~lf~- 233 (364)
+...-||+ +.++--.|..|++ |.|||||+|+.++..+ +.+++.+.+..... ++|- .=.+-|..+..
T Consensus 56 d~~~LyGF~~~~Er~lF~~Li~------VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIilE 127 (183)
T PRK14601 56 DSNKLYGFLDKDEQKMFEMLLK------VNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPG-IGPKSAKRIIAE 127 (183)
T ss_pred CCceeeCCCCHHHHHHHHHHhc------cCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 34455776 5555555666654 7888888888888775 46777776653210 2221 11122222221
Q ss_pred -CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHH
Q 017910 234 -EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKI 278 (364)
Q Consensus 234 -~p~V~~~~~~~~l~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l 278 (364)
+..+. .... .....+...+-| ..+||++..+++++..+
T Consensus 128 LkdK~~---~~~~---~~~~~~ea~~AL-~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 128 LSDAKT---KLEN---VSDDKSEALAAL-LTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHhh---ccCC---CCccHHHHHHHH-HHcCCCHHHHHHHHHhc
Confidence 11110 0000 011234455555 48999999999988766
No 49
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.98 E-value=1.9 Score=39.70 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 253 EEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 253 ~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
.+.+.+-| ..+||++..+.++++++.
T Consensus 152 ~~ea~~AL-~~LGy~~~ea~~al~~i~ 177 (197)
T PRK14603 152 AEDAVLAL-LALGFREAQVRSVVAELL 177 (197)
T ss_pred HHHHHHHH-HHcCCCHHHHHHHHHHHH
Confidence 34555666 599999999999998774
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=89.84 E-value=0.27 Score=31.52 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.6
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||++||-.++.
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
>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=89.32 E-value=0.33 Score=35.18 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=17.4
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-~gsle~il 209 (364)
+|.||||+||.++..+ +.|++++.
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl~Dl~ 30 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTLEDLR 30 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SHHHHH
T ss_pred hcccccHHHHHHHHHhCCCCHHHHh
Confidence 6899999999999985 56888884
No 52
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=88.96 E-value=0.35 Score=52.21 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=26.6
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 182 Dy~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
.-.++|||||++++..||+.|||+++|.+.
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 456799999999999999999999998753
No 53
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.36 E-value=0.9 Score=42.06 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=33.5
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 017910 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (364)
Q Consensus 160 ~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~ 213 (364)
+...-||+ +.++--.|..|++ |.|||||+|+.+|..+ +.+++++.+.
T Consensus 57 d~~~LyGF~~~~Er~lF~~Li~------V~GIGpK~Al~iLs~~-~~~~l~~aI~ 104 (203)
T PRK14602 57 DALELFGFATWDERQTFIVLIS------ISKVGAKTALAILSQF-RPDDLRRLVA 104 (203)
T ss_pred CcceeeCCCCHHHHHHHHHHhC------CCCcCHHHHHHHHhhC-CHHHHHHHHH
Confidence 34456786 5666666666654 7899999999999886 4677777665
No 54
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=86.22 E-value=9.7 Score=39.02 Aligned_cols=109 Identities=21% Similarity=0.340 Sum_probs=65.5
Q ss_pred HHHHHHhc--CCCEEeccC-cHHHHHHHHHH-----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHH
Q 017910 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (364)
Q Consensus 90 ik~lL~~~--GIp~i~APg-EADaq~A~L~~-----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v 161 (364)
+.++|..+ +|.++...| .||-.+.+=++ .|.=..++|.|.|.|+|.+-.....+. ..+
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI--------------~t~ 213 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKII--------------KTM 213 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHH--------------HhH
Confidence 44455554 899999999 99977666555 465567899999999998643211110 001
Q ss_pred HHHcCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHHH--HHHHHHcCCHHHHHHHHH
Q 017910 162 LEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQTA--LKLIRQHGSIETILENIN 213 (364)
Q Consensus 162 ~e~lgl~~----~qf-idl~iL~G~Dy~d~IpGIG--~ktA--~kLik~~gsle~il~~l~ 213 (364)
-+.|-+-| .-+ ...++.=||||-+|+-|+- +++- .+|...| ++++|+..+-
T Consensus 214 ~~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~ 273 (425)
T PF04599_consen 214 NQLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLA 273 (425)
T ss_pred HhHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHh
Confidence 11122211 111 2344556999999998854 4431 3444443 5788887765
No 55
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=85.32 E-value=0.7 Score=49.54 Aligned_cols=26 Identities=38% Similarity=0.662 Sum_probs=24.3
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 185 d~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
++|||||++++.+|++.|||+++|.+
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~ 571 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIKE 571 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 57999999999999999999999875
No 56
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=85.21 E-value=0.67 Score=49.47 Aligned_cols=29 Identities=34% Similarity=0.635 Sum_probs=26.0
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
..+.|||||++++.+|++.|||+++|.++
T Consensus 526 ~L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 44689999999999999999999999864
No 57
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=84.65 E-value=0.77 Score=49.76 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=25.8
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
-.+.|||||++++.+|++.|||+++|.+.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 44679999999999999999999999863
No 58
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=84.44 E-value=0.86 Score=42.95 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=24.7
Q ss_pred CCCCCCccHHHHHHHHHH-cCCHHHHHHH
Q 017910 184 CDSIRGIGGQTALKLIRQ-HGSIETILEN 211 (364)
Q Consensus 184 ~d~IpGIG~ktA~kLik~-~gsle~il~~ 211 (364)
.+.|||||+++|.+|++. |+|+++|...
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 457899999999999999 9999998643
No 59
>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=83.83 E-value=0.91 Score=35.95 Aligned_cols=25 Identities=40% Similarity=0.509 Sum_probs=21.1
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIET 207 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~ 207 (364)
....|||||+.+|..||.+.++++.
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchh
Confidence 3457999999999999999887654
No 60
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.22 E-value=0.99 Score=27.61 Aligned_cols=17 Identities=35% Similarity=0.520 Sum_probs=14.6
Q ss_pred CCCCCccHHHHHHHHHH
Q 017910 185 DSIRGIGGQTALKLIRQ 201 (364)
Q Consensus 185 d~IpGIG~ktA~kLik~ 201 (364)
..|||||+++|..++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 36899999999998863
No 61
>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=82.84 E-value=3.6 Score=45.18 Aligned_cols=39 Identities=21% Similarity=0.480 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 017910 167 LTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (364)
Q Consensus 167 l~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~l~ 213 (364)
-+.+.++.|.. .| .|||||+++|.+++..|| ++.++.++
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 35677877755 33 699999999999999999 44555554
No 62
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=81.80 E-value=1.1 Score=47.77 Aligned_cols=47 Identities=21% Similarity=0.290 Sum_probs=32.9
Q ss_pred HcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 164 ELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 164 ~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
.|.++...=.--....= .-.|+|||||+++...||+.|||+++|.+.
T Consensus 513 rfAi~~hR~~R~k~~~~-s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 513 RFAITYHRKKRSKAMLQ-SSLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred HHHHHHHHHHhhhhhhc-CccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 44554332222333333 356899999999999999999999988754
No 63
>PHA03065 Hypothetical protein; Provisional
Probab=81.06 E-value=13 Score=38.09 Aligned_cols=109 Identities=19% Similarity=0.333 Sum_probs=65.6
Q ss_pred HHHHHHhc--CCCEEeccC-cHHHHHHHHHH-----cCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHH
Q 017910 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (364)
Q Consensus 90 ik~lL~~~--GIp~i~APg-EADaq~A~L~~-----~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v 161 (364)
+-+.|..+ +|.++...| .||-.+..-++ .|.=..++|.|.|.|+|.+-.-.-.+ ...+
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 34456667 999999999 99976665554 46556789999999999764311000 1111
Q ss_pred HHHcCCCHH----HH-HHHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHH
Q 017910 162 LEELNLTMD----QF-IDLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENIN 213 (364)
Q Consensus 162 ~e~lgl~~~----qf-idl~iL~G~Dy~d~IpGIG--~kt--A~kLik~~gsle~il~~l~ 213 (364)
-+.|.+-|. -+ ...+..=||||-+|+-|+- +++ -.+|...| +++|++..+-
T Consensus 216 ~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~ 275 (438)
T PHA03065 216 NQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLA 275 (438)
T ss_pred HHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHH
Confidence 122222221 11 2234445999999998854 443 23444444 4677777664
No 64
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.29 E-value=1.7 Score=39.57 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=34.5
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 017910 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (364)
Q Consensus 155 ~~~~~~v~e~l-gl~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~~ 202 (364)
-+.+...+.-+ .++|++|.. ++..| |.. ..+||||+|||-++|-+-
T Consensus 80 GIGpK~Al~ILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 80 GIGANTAMAVCSSLDVNSFYK-ALSLG-DESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 36666667777 578888865 45566 765 378999999999999763
No 65
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=78.87 E-value=1.7 Score=41.54 Aligned_cols=26 Identities=42% Similarity=0.724 Sum_probs=23.8
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
+|||||++.|..|++.|||+++++..
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 57999999999999999999998754
No 66
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.42 E-value=3.1 Score=38.37 Aligned_cols=44 Identities=23% Similarity=0.273 Sum_probs=23.9
Q ss_pred EeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHH
Q 017910 156 FEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQ 201 (364)
Q Consensus 156 ~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~ 201 (364)
+.+...+.-++ +++++|+. ++..| |.. ..+||||+|||-++|-+
T Consensus 80 IGpK~AL~iLs~~~~~~l~~-aI~~~-D~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 80 VGPKLALALLSALPPALLAR-ALLEG-DARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred cCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 44455555554 56666543 23334 544 24666666666666655
No 67
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.61 E-value=3.9 Score=37.33 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=35.4
Q ss_pred EEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC-CCCCccHHHHHHHHHHcC
Q 017910 154 MEFEVAKILEELN-LTMDQFIDLCILSGCDYCD-SIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 154 ~~~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~d-~IpGIG~ktA~kLik~~g 203 (364)
.-+.+...+.-+. ++++++++. +-.| |..- .+||||+|||-+++-+..
T Consensus 79 ~GIGpK~Al~iLs~~~~~~l~~a-I~~~-D~~~L~vpGIGkKtAerIilELk 128 (186)
T PRK14600 79 SGVNYKTAMSILSKLTPEQLFSA-IVNE-DKAALKVNGIGEKLINRIITELQ 128 (186)
T ss_pred CCcCHHHHHHHHccCCHHHHHHH-HHcC-CHhheECCCCcHHHHHHHHHHHH
Confidence 3466777777775 789988764 4456 6632 789999999999997643
No 68
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.07 E-value=3.3 Score=38.07 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=34.7
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHcC
Q 017910 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 155 ~~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~~g 203 (364)
-+.+...+.-++ +++++|+. ++..| |.. ..+||||+|||-+++-+..
T Consensus 80 GIGpK~Al~iLs~~~~~el~~-aI~~~-D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 80 GVGPKAALNLLSSGTPDELQL-AIAGG-DVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHHH
Confidence 366666677775 68888865 34455 665 3789999999999997743
No 69
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.96 E-value=3.8 Score=37.94 Aligned_cols=46 Identities=20% Similarity=0.288 Sum_probs=34.3
Q ss_pred EEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 017910 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (364)
Q Consensus 155 ~~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~~ 202 (364)
-+.+...+.-++ +++++|+. ++..| |.. ..+||||+|||-++|-+.
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 366666677776 68888765 45555 665 379999999999999763
No 70
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.26 E-value=3.7 Score=37.58 Aligned_cols=46 Identities=20% Similarity=0.281 Sum_probs=35.0
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 017910 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (364)
Q Consensus 155 ~~~~~~v~e~l-gl~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~~ 202 (364)
-+.+...+.-+ ++++++|+. ++..| |.. -.+||||+|||-+++-+.
T Consensus 80 GIGpK~AL~iLs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 80 RLGPKTALKIISNEDAETLVT-MIASQ-DVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 36677777777 578998875 45566 665 368999999999999764
No 71
>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=71.83 E-value=3.4 Score=44.81 Aligned_cols=15 Identities=27% Similarity=0.634 Sum_probs=7.6
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||+|.|+|.+|+.
T Consensus 470 ~L~GfG~Ksa~nIl~ 484 (652)
T TIGR00575 470 ELEGFGEKSAQNLLN 484 (652)
T ss_pred hccCccHHHHHHHHH
Confidence 345555555555544
No 72
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=71.82 E-value=3.3 Score=35.69 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=19.5
Q ss_pred CCCccHHHHHHHHHH--cCCHHHHHH
Q 017910 187 IRGIGGQTALKLIRQ--HGSIETILE 210 (364)
Q Consensus 187 IpGIG~ktA~kLik~--~gsle~il~ 210 (364)
+|||||+.|.++++. |.++|++++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 689999999999963 668888764
No 73
>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=70.46 E-value=6.2 Score=34.40 Aligned_cols=88 Identities=16% Similarity=0.228 Sum_probs=57.1
Q ss_pred hhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCcccccccCe--eEEEeecCCCCCCccEEEeHHHHH
Q 017910 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPR--FLRHLMDPSSRKIPVMEFEVAKIL 162 (364)
Q Consensus 85 ~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~--vi~~l~~~~~~~~~v~~~~~~~v~ 162 (364)
.|+..+-+.|+.+|+..+..+...|+.+..+|++..- +|+|.|.+++...... ++. +. +.. ..-.+..|+
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-IR-SDD-----PEEQLREVL 78 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHHHhhccCCEEE-Ec-CCC-----HHHHHHHHH
Confidence 4567788999999999999998889999999876544 4789999988764322 221 21 110 112345666
Q ss_pred HHcCCCH--HHHHHHHHHhC
Q 017910 163 EELNLTM--DQFIDLCILSG 180 (364)
Q Consensus 163 e~lgl~~--~qfidl~iL~G 180 (364)
+.+++.+ +.+..-|..|+
T Consensus 79 ~~~~l~~~~~~~~sRC~~CN 98 (147)
T PF01927_consen 79 ERFGLKLRLDPIFSRCPKCN 98 (147)
T ss_pred HHcCCccccCCCCCccCCCC
Confidence 7777654 22234455555
No 74
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=69.33 E-value=4.3 Score=44.32 Aligned_cols=25 Identities=36% Similarity=0.622 Sum_probs=20.8
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
+|||||+++|..|++.|+|++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4789999999999999999887754
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=69.04 E-value=4 Score=45.38 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.1
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
+|||||+++|..|+.+|||++++..
T Consensus 761 ~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred HCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4799999999999999999999875
No 76
>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=67.51 E-value=5.5 Score=33.69 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=14.9
Q ss_pred CCCCccHHHHHHHHHHc
Q 017910 186 SIRGIGGQTALKLIRQH 202 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~ 202 (364)
.|||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 57999999999999874
No 77
>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=65.95 E-value=4.4 Score=26.17 Aligned_cols=13 Identities=54% Similarity=0.695 Sum_probs=10.3
Q ss_pred CCCCccHHHHHHH
Q 017910 186 SIRGIGGQTALKL 198 (364)
Q Consensus 186 ~IpGIG~ktA~kL 198 (364)
.++|||.+|+.+|
T Consensus 15 ~~~GIG~kt~~kL 27 (32)
T PF11798_consen 15 KFWGIGKKTAKKL 27 (32)
T ss_dssp GSTTS-HHHHHHH
T ss_pred hhCCccHHHHHHH
Confidence 5799999999885
No 78
>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=65.87 E-value=14 Score=32.94 Aligned_cols=38 Identities=18% Similarity=0.178 Sum_probs=28.2
Q ss_pred cCCCEEecc-C-cHHHHHHHHHHc----CCeEEEecCCCccccc
Q 017910 97 MGVPVVEAP-S-EAEAQCAALCKS----GQVYAVASEDMDSLTF 134 (364)
Q Consensus 97 ~GIp~i~AP-g-EADaq~A~L~~~----g~v~~ViS~DsD~l~f 134 (364)
-||.++-++ + .||+.|-.++.. +.-..|+|+|...-..
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 467777777 3 999999888762 4556789998876554
No 79
>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=65.78 E-value=6.2 Score=38.71 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=21.3
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQH--GSIETILENI 212 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~--gsle~il~~l 212 (364)
+||||||+||.+|. +. .|++++.+..
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 80
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=65.60 E-value=5.3 Score=39.71 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=21.1
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHG--SIETILEN 211 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g--sle~il~~ 211 (364)
+||||||+||..|.+ .| |++++.+.
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 589999999999998 65 78888654
No 81
>PRK13766 Hef nuclease; Provisional
Probab=63.41 E-value=6.4 Score=43.22 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=23.3
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
+|||||+++|.+|++.|||+++++.
T Consensus 719 ~ipgig~~~a~~Ll~~fgs~~~i~~ 743 (773)
T PRK13766 719 SLPDVGPVLARNLLEHFGSVEAVMT 743 (773)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 6899999999999999999999875
No 82
>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=63.40 E-value=14 Score=32.28 Aligned_cols=35 Identities=20% Similarity=0.340 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHc
Q 017910 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS 118 (364)
Q Consensus 84 ~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~ 118 (364)
.+.+.++++-|+.+|++.+.-.|++...+..|+++
T Consensus 52 ~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~ 86 (165)
T PF00875_consen 52 LESLADLQESLRKLGIPLLVLRGDPEEVLPELAKE 86 (165)
T ss_dssp HHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHh
Confidence 34567788888999999999999999899888874
No 83
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=62.71 E-value=8.6 Score=35.61 Aligned_cols=74 Identities=26% Similarity=0.311 Sum_probs=47.1
Q ss_pred CeEEEecCCCcccccccCe-----eEEEeecCCCCCCccEEEeHHHHHHHcC-CCHHHHHHHHHHhCCCCC--CCCCCcc
Q 017910 120 QVYAVASEDMDSLTFGAPR-----FLRHLMDPSSRKIPVMEFEVAKILEELN-LTMDQFIDLCILSGCDYC--DSIRGIG 191 (364)
Q Consensus 120 ~v~~ViS~DsD~l~fg~~~-----vi~~l~~~~~~~~~v~~~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~--d~IpGIG 191 (364)
++.-++.+|. ..+||-.. +++.+. .+.-+.+...+.-+. +++++|+.. +-.+ |+. -.+||||
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 3556778887 77777431 111111 123356666677664 588888764 4445 665 4789999
Q ss_pred HHHHHHHHHHcC
Q 017910 192 GQTALKLIRQHG 203 (364)
Q Consensus 192 ~ktA~kLik~~g 203 (364)
.|||-+++-+-.
T Consensus 118 kKtAerivleLk 129 (201)
T COG0632 118 KKTAERIVLELK 129 (201)
T ss_pred HHHHHHHHHHHh
Confidence 999999997643
No 84
>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=62.36 E-value=13 Score=30.55 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=23.8
Q ss_pred cCcHHHHHHHHHHcCCeEEEecCCCcccc
Q 017910 105 PSEAEAQCAALCKSGQVYAVASEDMDSLT 133 (364)
Q Consensus 105 PgEADaq~A~L~~~g~v~~ViS~DsD~l~ 133 (364)
+-..|+-+..++..+.+++++|+|+|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 34667777778888889999999999874
No 85
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=62.14 E-value=5.6 Score=43.26 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=17.5
Q ss_pred CCCCccHHHHHHHHHHc-----CCHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQH-----GSIETILENI 212 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~-----gsle~il~~l 212 (364)
.+||+|+|+|.+|++.. .+++.++-.+
T Consensus 483 ~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~al 514 (665)
T PRK07956 483 GLEGFGEKSAQNLLDAIEKSKETSLARFLYAL 514 (665)
T ss_pred cCcCcchHHHHHHHHHHHHhhcCCHHHhhHhh
Confidence 56777777777776643 2456666655
No 86
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.70 E-value=9.9 Score=35.09 Aligned_cols=46 Identities=24% Similarity=0.338 Sum_probs=34.2
Q ss_pred EEeHHHHHHHc-CCCHHHHHHHHHHhCCCCC--CCCCCccHHHHHHHHHHc
Q 017910 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYC--DSIRGIGGQTALKLIRQH 202 (364)
Q Consensus 155 ~~~~~~v~e~l-gl~~~qfidl~iL~G~Dy~--d~IpGIG~ktA~kLik~~ 202 (364)
-+.+...+.-+ .+++++|+. ++..| |.. ..+||||+|||-++|-+-
T Consensus 79 GIGPK~ALaILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 79 GIGPRAALRVLSGIKYNEFRD-AIDRE-DIELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 35666667777 478888865 34566 765 379999999999999763
No 87
>PRK08609 hypothetical protein; Provisional
Probab=58.26 E-value=16 Score=38.95 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=19.4
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQHG--SIETILENIN 213 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g--sle~il~~l~ 213 (364)
.|||||||||.+|-++.| |++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 578888888888876644 6666665443
No 88
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=56.89 E-value=12 Score=32.98 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=18.7
Q ss_pred CCCCccHHHHHHHHHH------cCCHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ------HGSIETILE 210 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~------~gsle~il~ 210 (364)
.+||||+++|.++|.. |.++|++..
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 4689999999999963 457776543
No 89
>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=56.31 E-value=13 Score=27.83 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=13.4
Q ss_pred CCCccHHHHHHHHHH
Q 017910 187 IRGIGGQTALKLIRQ 201 (364)
Q Consensus 187 IpGIG~ktA~kLik~ 201 (364)
+||||+++|.++|..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 688999999999987
No 90
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=53.49 E-value=15 Score=32.56 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 017910 170 DQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 170 ~qfidl~iL~G~Dy~d~---------IpGIG~ktA~kLik~~g 203 (364)
++|-.+.-++|+|..++ |.|||+.+|..++++.|
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 57888888899888765 57999999999999876
No 91
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=53.23 E-value=9.6 Score=41.23 Aligned_cols=27 Identities=37% Similarity=0.570 Sum_probs=23.9
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 185 d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
-|||.||+++|..|.+.|+|++++++.
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 468999999999999999999988764
No 92
>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=52.82 E-value=18 Score=33.13 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=30.4
Q ss_pred EeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 017910 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (364)
Q Consensus 156 ~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~d--~IpGIG~ktA~kLik~ 201 (364)
+.+...+.-++ +++++++..+ ..+ |..- .|||||+|||.+++-+
T Consensus 80 IGpK~Al~iL~~~~~~el~~aI-~~~-d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 80 VGPKLALAILSNMSPEEFVYAI-ETE-EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCHHHHHHHHhcCCHHHHHHHH-HhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 55666666676 4777776543 334 5543 6899999999999844
No 93
>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=52.46 E-value=27 Score=28.44 Aligned_cols=32 Identities=25% Similarity=0.127 Sum_probs=22.2
Q ss_pred CCCCccHHHHHHHHHH-cC--------CHHHHHHHHHhccC
Q 017910 186 SIRGIGGQTALKLIRQ-HG--------SIETILENINRERY 217 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-~g--------sle~il~~l~~~k~ 217 (364)
.|||||+.+|..|+.- +. +.+++++.+....+
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~G 56 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALTG 56 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHcC
Confidence 5899999999999852 33 34556666665443
No 94
>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=51.83 E-value=13 Score=27.05 Aligned_cols=17 Identities=47% Similarity=0.642 Sum_probs=14.7
Q ss_pred CCCCccHHHHHHHHHHc
Q 017910 186 SIRGIGGQTALKLIRQH 202 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~ 202 (364)
.|||||+++|-+|+.+.
T Consensus 42 ~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 42 EIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp TSTTSSHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 58999999999998763
No 95
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=46.85 E-value=38 Score=29.44 Aligned_cols=44 Identities=25% Similarity=0.290 Sum_probs=34.8
Q ss_pred cchhhHHHHHHHHHhcCCC-----EEeccC--cHHHHHHHHHHcCCeEEEe
Q 017910 82 VTKQHNDDCKRLLKLMGVP-----VVEAPS--EAEAQCAALCKSGQVYAVA 125 (364)
Q Consensus 82 vt~~~~~~ik~lL~~~GIp-----~i~APg--EADaq~A~L~~~g~v~~Vi 125 (364)
|+..+.+-+.+.|+..|+. ++..|| |-=-.+..|++.+..|+|+
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 4577888999999999875 788999 7777888888877666554
No 96
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=46.65 E-value=16 Score=27.27 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=14.5
Q ss_pred CCCCccHHHHHHHHHHcCCHH
Q 017910 186 SIRGIGGQTALKLIRQHGSIE 206 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~gsle 206 (364)
.|||||+++|..+..-|.+-+
T Consensus 39 ~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 39 AIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp TSTT--HHHHHHHHHHHH-HH
T ss_pred ccCCcCHHHHHHHHHHHCCHH
Confidence 689999999999887665543
No 97
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=46.42 E-value=60 Score=33.04 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=15.8
Q ss_pred HHHHHHHHHhcCCCEEeccCcHHHHHHHHHH
Q 017910 87 NDDCKRLLKLMGVPVVEAPSEAEAQCAALCK 117 (364)
Q Consensus 87 ~~~ik~lL~~~GIp~i~APgEADaq~A~L~~ 117 (364)
+.++.+-|+.+|++.++.-|++...+..|++
T Consensus 63 L~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~ 93 (429)
T TIGR02765 63 LKDLRTSLRKLGSDLLVRSGKPEDVLPELIK 93 (429)
T ss_pred HHHHHHHHHHcCCCeEEEeCCHHHHHHHHHH
Confidence 3444444555555555555555555555544
No 98
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=46.40 E-value=18 Score=36.26 Aligned_cols=53 Identities=30% Similarity=0.470 Sum_probs=38.2
Q ss_pred HHHHHHHc-CCCHHHHHHH---HHHhCCCC----CC------------CCCCccHHHHHHHHHHcCCHHHHHH
Q 017910 158 VAKILEEL-NLTMDQFIDL---CILSGCDY----CD------------SIRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 158 ~~~v~e~l-gl~~~qfidl---~iL~G~Dy----~d------------~IpGIG~ktA~kLik~~gsle~il~ 210 (364)
.+++++.+ .++.+++.|+ +-++|-.- .| +||+|++..|..|+.+|||+.+|+.
T Consensus 243 ~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~ 315 (352)
T PRK13482 243 PEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLA 315 (352)
T ss_pred HHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHc
Confidence 55666666 5777777665 44566211 12 1589999999999999999999985
No 99
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=45.26 E-value=31 Score=30.49 Aligned_cols=35 Identities=31% Similarity=0.549 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 017910 169 MDQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 169 ~~qfidl~iL~G~Dy~d~---------IpGIG~ktA~kLik~~g 203 (364)
.++|-.+.-++|+|-.++ |.|||+.+|..++++.|
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 356667777889888775 46999999999999876
No 100
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=43.02 E-value=66 Score=28.39 Aligned_cols=36 Identities=28% Similarity=0.482 Sum_probs=25.8
Q ss_pred HHHHHhccccccchhhHHHHHHHHHhcCCCEEeccC
Q 017910 71 DIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (364)
Q Consensus 71 ~~~k~~~r~~~vt~~~~~~ik~lL~~~GIp~i~APg 106 (364)
++.+|-.+...-...|.......|+.+|||++....
T Consensus 91 EL~~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 91 ELDKFDEKVYKASKQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeCCC
Confidence 455565444444467788888899999999987654
No 101
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.75 E-value=17 Score=33.27 Aligned_cols=45 Identities=24% Similarity=0.325 Sum_probs=29.0
Q ss_pred EeHHHHHHHcC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 017910 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (364)
Q Consensus 156 ~~~~~v~e~lg-l~~~qfidl~iL~G~Dy~d--~IpGIG~ktA~kLik~~ 202 (364)
+.+...+.-+. +++++|+.. +..+ |..- .|||||+|||-+++-+-
T Consensus 81 IGpK~Al~ILs~~~~~~l~~a-I~~~-D~~~L~~vpGIGkKtAerIilEL 128 (194)
T PRK14605 81 IGPKLGLAMLSAMNAEALASA-IISG-NAELLSTIPGIGKKTASRIVLEL 128 (194)
T ss_pred CCHHHHHHHHHhCCHHHHHHH-HHhC-CHHHHHhCCCCCHHHHHHHHHHH
Confidence 44444444443 567776543 3345 6653 68999999999988763
No 102
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.50 E-value=71 Score=32.86 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=10.7
Q ss_pred cHHHHHHHHHHc
Q 017910 191 GGQTALKLIRQH 202 (364)
Q Consensus 191 G~ktA~kLik~~ 202 (364)
|...|.+.|+.|
T Consensus 225 Ge~aA~~~L~~F 236 (454)
T TIGR00591 225 GTTAGLIMLESF 236 (454)
T ss_pred cHHHHHHHHHHH
Confidence 899999998887
No 103
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=40.06 E-value=21 Score=33.94 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=25.6
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 183 y~d~IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
+..+||||+...|..|+..|||++.|+..
T Consensus 196 ~Lt~i~~VnKtda~~LL~~FgsLq~~~~A 224 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLLQKFGSLQQISNA 224 (254)
T ss_pred HHHhCCCCCcccHHHHHHhcccHHHHHhc
Confidence 44579999999999999999999998754
No 104
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.51 E-value=19 Score=33.25 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.7
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 15 KLPGIGPKSAQRLAF 29 (195)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988853
No 105
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=39.50 E-value=49 Score=29.53 Aligned_cols=45 Identities=20% Similarity=0.347 Sum_probs=35.0
Q ss_pred ccchhhHHHHHHHHHhcC-----CCEEeccC--cHHHHHHHHHHcCCeEEEe
Q 017910 81 KVTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (364)
Q Consensus 81 ~vt~~~~~~ik~lL~~~G-----Ip~i~APg--EADaq~A~L~~~g~v~~Vi 125 (364)
.||..+++-+.+.|+..| |.++..|| |-=-.+..|++.+..|+|+
T Consensus 23 ~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiI 74 (158)
T PRK12419 23 DIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIV 74 (158)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 355778888899999999 67888999 8778888888877555544
No 106
>PRK00076 recR recombination protein RecR; Reviewed
Probab=39.41 E-value=19 Score=33.28 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.8
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 15 KLPGIGPKSAQRLAF 29 (196)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988864
No 107
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=39.36 E-value=16 Score=33.62 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.4
Q ss_pred CCCCCccHHHHHHHH
Q 017910 185 DSIRGIGGQTALKLI 199 (364)
Q Consensus 185 d~IpGIG~ktA~kLi 199 (364)
..+||||||+|.++.
T Consensus 15 ~kLPGvG~KsA~R~A 29 (198)
T COG0353 15 KKLPGVGPKSAQRLA 29 (198)
T ss_pred hhCCCCChhHHHHHH
Confidence 357999999988874
No 108
>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=39.29 E-value=27 Score=27.79 Aligned_cols=50 Identities=22% Similarity=0.173 Sum_probs=37.6
Q ss_pred ccccchhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCccccc
Q 017910 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~f 134 (364)
.+.++.+....+.++....+ .+-+|+.++.++...-+..++|.|.|+..+
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 34567788888888888777 457899999999977676677999997544
No 109
>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=37.79 E-value=65 Score=28.11 Aligned_cols=44 Identities=30% Similarity=0.356 Sum_probs=35.5
Q ss_pred cchhhHHHHHHHHHhcCC-----CEEeccC--cHHHHHHHHHHcCCeEEEe
Q 017910 82 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (364)
Q Consensus 82 vt~~~~~~ik~lL~~~GI-----p~i~APg--EADaq~A~L~~~g~v~~Vi 125 (364)
++..+++.+.+.|...|+ .++..|| |-=-.+..|.+.+..|+|+
T Consensus 17 i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi 67 (144)
T PF00885_consen 17 ITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVI 67 (144)
T ss_dssp HHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEE
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEE
Confidence 346677888999999987 7888999 8888888999988766665
No 110
>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=36.92 E-value=67 Score=25.03 Aligned_cols=47 Identities=15% Similarity=0.197 Sum_probs=23.4
Q ss_pred HHHHHHHcCC--HHHHHHHhccccccchhhHHHHHHHHHhcCCCEEeccC
Q 017910 59 DLAEAVEAGN--KEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (364)
Q Consensus 59 ~l~~a~~~g~--~~~~~k~~~r~~~vt~~~~~~ik~lL~~~GIp~i~APg 106 (364)
-+..++..|. .+++..+.. ...+++.+++.+...|...||.++....
T Consensus 12 Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~Vvd~~~ 60 (82)
T PF03979_consen 12 LIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEVVDEEE 60 (82)
T ss_dssp HHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----B--S-
T ss_pred HHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 3444455553 345555444 2236688999999999999999998544
No 111
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=36.64 E-value=55 Score=29.39 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=42.2
Q ss_pred hhhHHHHHHHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCccccc
Q 017910 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (364)
Q Consensus 84 ~~~~~~ik~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~f 134 (364)
..|+-.+-++|+.||.+.+..-.+.|+.+..++.+... +++|.|.-++..
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 478999999887
No 112
>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=36.09 E-value=32 Score=28.37 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=15.6
Q ss_pred CCCCccHHHHHHHHHHcC
Q 017910 186 SIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g 203 (364)
.|.|||+.+|..++.+.|
T Consensus 19 ~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 19 KIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp TSTTBCHHHHHHHHHHTT
T ss_pred hhhccCHHHHHHHHHHcC
Confidence 368999999999998876
No 113
>PRK13844 recombination protein RecR; Provisional
Probab=35.89 E-value=23 Score=32.79 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=12.8
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||+|+|.+|.-
T Consensus 19 ~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 19 KLPTIGKKSSQRLAL 33 (200)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988864
No 114
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=35.81 E-value=16 Score=35.63 Aligned_cols=30 Identities=33% Similarity=0.281 Sum_probs=26.3
Q ss_pred hhhHHHHHHHHHhcCCCEEeccCcHHHHHHH
Q 017910 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAA 114 (364)
Q Consensus 84 ~~~~~~ik~lL~~~GIp~i~APgEADaq~A~ 114 (364)
..+......+|+.+|+| +.+|.|++||+|+
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 44567788999999999 8899999999998
No 115
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=34.99 E-value=63 Score=28.61 Aligned_cols=44 Identities=30% Similarity=0.353 Sum_probs=33.5
Q ss_pred cchhhHHHHHHHHHhcC-----CCEEeccC--cHHHHHHHHHHcCCeEEEe
Q 017910 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (364)
Q Consensus 82 vt~~~~~~ik~lL~~~G-----Ip~i~APg--EADaq~A~L~~~g~v~~Vi 125 (364)
|+..+.+-+.+.|+..| |.++..|| |-=-.+..|++.+..|+|+
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 44678888999999998 45777899 7777778888876555554
No 116
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=34.66 E-value=69 Score=28.00 Aligned_cols=44 Identities=30% Similarity=0.308 Sum_probs=34.0
Q ss_pred cchhhHHHHHHHHHhcCC-----CEEeccC--cHHHHHHHHHHcCCeEEEe
Q 017910 82 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (364)
Q Consensus 82 vt~~~~~~ik~lL~~~GI-----p~i~APg--EADaq~A~L~~~g~v~~Vi 125 (364)
|+..+++-+.+.|...|+ .++..|| |-=-.+..|++.+..|+|+
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 457788889999999996 5788998 8777888888876555544
No 117
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=34.46 E-value=78 Score=25.22 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=19.6
Q ss_pred CccHHHHHHHHHHcCCHHHHHHHHHhccCCCCC
Q 017910 189 GIGGQTALKLIRQHGSIETILENINRERYQIPE 221 (364)
Q Consensus 189 GIG~ktA~kLik~~gsle~il~~l~~~k~~i~e 221 (364)
||+++.|.+|.+.||+ +.++.+++.++.+-.
T Consensus 19 gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD--DAIEILKENPYRLIE 49 (94)
T ss_dssp T--HHHHHHHHHHH-T--THHHHHHH-STCCCB
T ss_pred CCCHHHHHHHHHHHhH--HHHHHHHHChHHHHH
Confidence 5889999999999996 556666666655433
No 118
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=33.91 E-value=54 Score=28.73 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.2
Q ss_pred CCCccHHHHHHHHHHcC
Q 017910 187 IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 187 IpGIG~ktA~kLik~~g 203 (364)
|.|||+.+|..++++.|
T Consensus 26 I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 26 IKGIGRRFARAIARKLG 42 (144)
T ss_pred eeccCHHHHHHHHHHcC
Confidence 57899999999888865
No 119
>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=33.54 E-value=1.2e+02 Score=31.50 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=10.8
Q ss_pred ccHHHHHHHHHHc
Q 017910 190 IGGQTALKLIRQH 202 (364)
Q Consensus 190 IG~ktA~kLik~~ 202 (364)
.|...|.+.|+.|
T Consensus 201 gGe~~A~~~L~~F 213 (475)
T TIGR02766 201 PGWSNADKALTEF 213 (475)
T ss_pred CccHHHHHHHHHH
Confidence 4888899988877
No 120
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=32.68 E-value=32 Score=32.02 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=14.6
Q ss_pred CCCCccHHHHHHHHHHcC
Q 017910 186 SIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g 203 (364)
++||||+|||--++.-.+
T Consensus 123 ~lpGIG~KTAd~vL~~~~ 140 (208)
T PRK01229 123 NIKGIGYKEASHFLRNVG 140 (208)
T ss_pred cCCCCcHHHHHHHHHHcc
Confidence 789999999988885333
No 121
>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=32.35 E-value=54 Score=25.89 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=20.8
Q ss_pred CCCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ-----HGSIETILENI 212 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-----~gsle~il~~l 212 (364)
.|+|||...|.+++.+ |.|++++++.+
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 56888887775
No 122
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=32.00 E-value=46 Score=30.33 Aligned_cols=47 Identities=23% Similarity=0.328 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHhCCCCCC-C----CCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 017910 166 NLTMDQFIDLCILSGCDYCD-S----IRGIGGQTALKLIRQ-----HGSIETILENI 212 (364)
Q Consensus 166 gl~~~qfidl~iL~G~Dy~d-~----IpGIG~ktA~kLik~-----~gsle~il~~l 212 (364)
.=..+.|++|---+|--..- . +||||-|+..++|.+ |.|.|+|-+.+
T Consensus 95 ~~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 95 KENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp HTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred HhChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 34678999999888822221 1 499999999999975 77888887665
No 123
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=31.43 E-value=79 Score=27.50 Aligned_cols=43 Identities=14% Similarity=0.013 Sum_probs=31.7
Q ss_pred HHHHhcCCCEEeccCcHHHHHHHHHHcCCeEEEecCCCccccc
Q 017910 92 RLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (364)
Q Consensus 92 ~lL~~~GIp~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~f 134 (364)
.+....+.+++.--..||+.+-..+.+.-+++|+|+|..+=.-
T Consensus 70 a~~~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~r 112 (136)
T COG1412 70 ALKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRR 112 (136)
T ss_pred HHHHhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHH
Confidence 3445678888888449998777777654466799999987654
No 124
>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=31.30 E-value=75 Score=25.99 Aligned_cols=41 Identities=17% Similarity=0.339 Sum_probs=33.4
Q ss_pred HHHHHcCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHH
Q 017910 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIR 200 (364)
Q Consensus 160 ~v~e~lgl-~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik 200 (364)
.-+..-|| |-..+++.+...|.----.|||||+..|-.+..
T Consensus 27 ~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~a 68 (96)
T PF12482_consen 27 RRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEA 68 (96)
T ss_pred HHHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHH
Confidence 34556687 689999999999966677899999999987654
No 125
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=29.33 E-value=37 Score=28.92 Aligned_cols=88 Identities=20% Similarity=0.282 Sum_probs=46.3
Q ss_pred HHHHHHcCCCcEE-EEeCCCCchhhHHHHH----HHhhhhhchHHHHHHHHcCCHHHHHHHhccccccchhhHHHHHHHH
Q 017910 20 TIRLLEAGMKPIY-VFDGQPPDLKKQELAK----RYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLL 94 (364)
Q Consensus 20 ~~~ll~~gi~Pv~-VFDG~~p~~K~~~~~~----rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~~~~~~ik~lL 94 (364)
+.+|+++|+.|.. |+||+.. |...... ++.-+-. .-.-.||.+.++.+++++
T Consensus 2 T~~ll~~g~~P~laIvD~kTk--R~~~~~~~~~~~~~i~v~---------------------NPpG~It~el~~ai~~a~ 58 (121)
T PF04019_consen 2 TYNLLEAGIIPDLAIVDGKTK--REPVVEEVRKFYRVIEVK---------------------NPPGTITEELIEAIKKAL 58 (121)
T ss_pred hHHHHhCCCCCCEEEEeCccc--ccCCcccccCCceEEEEE---------------------CCCCcccHHHHHHHHHHH
Confidence 4578999999966 8999841 2111100 0000000 112346777788888887
Q ss_pred HhcCCCEEeccCcHH-HHHHHHHHcCCeEEEecCCCcccccccCe
Q 017910 95 KLMGVPVVEAPSEAE-AQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (364)
Q Consensus 95 ~~~GIp~i~APgEAD-aq~A~L~~~g~v~~ViS~DsD~l~fg~~~ 138 (364)
..-+=-.|...||=| +.+... .+..+-.+.+||.|.
T Consensus 59 ~~~~~~~I~V~GEEDL~~lPai--------l~aP~gs~V~YGQP~ 95 (121)
T PF04019_consen 59 ESGKPVVIFVDGEEDLAVLPAI--------LYAPEGSVVLYGQPG 95 (121)
T ss_pred hCCCCEEEEEeChHHHHHHHHH--------HhCCCCCEEEECCCC
Confidence 663334456677655 222221 223334445677664
No 126
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=28.79 E-value=1.6e+02 Score=30.54 Aligned_cols=13 Identities=31% Similarity=0.623 Sum_probs=10.4
Q ss_pred ccHHHHHHHHHHc
Q 017910 190 IGGQTALKLIRQH 202 (364)
Q Consensus 190 IG~ktA~kLik~~ 202 (364)
.|...|++-|+.|
T Consensus 203 gGe~~A~~~L~~f 215 (472)
T PRK10674 203 VGEKAAIAQLRQF 215 (472)
T ss_pred CCHHHHHHHHHHH
Confidence 3888888888776
No 127
>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=28.59 E-value=43 Score=25.06 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=11.9
Q ss_pred CCCCCccHHHHHHH
Q 017910 185 DSIRGIGGQTALKL 198 (364)
Q Consensus 185 d~IpGIG~ktA~kL 198 (364)
..|||||+++|.++
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 57899999998876
No 128
>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=28.50 E-value=47 Score=32.14 Aligned_cols=24 Identities=33% Similarity=0.437 Sum_probs=20.7
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-~gsle~il 209 (364)
.|||||+++|.+|.+. |.+++++.
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~ 27 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIA 27 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHH
Confidence 5799999999999998 88887764
No 129
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=28.41 E-value=38 Score=29.21 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.4
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.|||||++||--++.
T Consensus 87 ~l~GIG~~tA~~~l~ 101 (158)
T cd00056 87 ALPGVGRKTANVVLL 101 (158)
T ss_pred cCCCCCHHHHHHHHH
Confidence 579999999877665
No 130
>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=28.19 E-value=1.2e+02 Score=25.47 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=34.7
Q ss_pred HHHHHHHHHhcCCCEEeccC--------cHHHHHHHHH----Hc-C-CeEEEecCCCcccccc
Q 017910 87 NDDCKRLLKLMGVPVVEAPS--------EAEAQCAALC----KS-G-QVYAVASEDMDSLTFG 135 (364)
Q Consensus 87 ~~~ik~lL~~~GIp~i~APg--------EADaq~A~L~----~~-g-~v~~ViS~DsD~l~fg 135 (364)
.....+.|+..|+.++..|. -+|..++.-+ .. + .+.+++|+|+|+....
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 45677889999999988872 4676555322 22 2 4667899999998875
No 131
>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=28.10 E-value=39 Score=30.75 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=14.0
Q ss_pred CCCCccHHHHHHHHHHcC
Q 017910 186 SIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g 203 (364)
.+||||+|||-=++...+
T Consensus 119 ~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 119 ALPGFGKQKAKIFLALLG 136 (177)
T ss_pred cCCCCCHHHHHHHHHHHH
Confidence 589999999987766443
No 132
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.81 E-value=52 Score=35.98 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=12.1
Q ss_pred CCCccHHHHHHHH-HHcCCHHHHH
Q 017910 187 IRGIGGQTALKLI-RQHGSIETIL 209 (364)
Q Consensus 187 IpGIG~ktA~kLi-k~~gsle~il 209 (364)
||+||.++|..|. +.|++++++.
T Consensus 507 I~~vG~~~ak~La~~~f~~~~~l~ 530 (669)
T PRK14350 507 IKDLGENTILLLINNNLNSFDKIS 530 (669)
T ss_pred CCchhHHHHHHHHHHhhCCHHHHH
Confidence 4555555555555 4555555443
No 133
>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=27.59 E-value=1.1e+02 Score=26.56 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHcCCCcEEEEeCC
Q 017910 13 LQGMFTRTIRLLEAGMKPIYVFDGQ 37 (364)
Q Consensus 13 l~G~~~r~~~ll~~gi~Pv~VFDG~ 37 (364)
+.|+...+-.+.+.|.+++.||+..
T Consensus 24 ~~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 24 VRGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp HHHHHHHHHHHHHTT---EEEEEEG
T ss_pred HHHHHHHHHHHHHcCCCeEEEEcch
Confidence 3455554555677899999999954
No 134
>PRK10702 endonuclease III; Provisional
Probab=27.27 E-value=39 Score=31.40 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=11.7
Q ss_pred CCCccHHHHHHHHH
Q 017910 187 IRGIGGQTALKLIR 200 (364)
Q Consensus 187 IpGIG~ktA~kLik 200 (364)
+||||+|||--++-
T Consensus 114 lpGVG~ktA~~ill 127 (211)
T PRK10702 114 LPGVGRKTANVVLN 127 (211)
T ss_pred CCcccHHHHHHHHH
Confidence 69999999987653
No 135
>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=27.05 E-value=1.4e+02 Score=24.66 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=25.6
Q ss_pred HHHHHHHHHhcCCCEEeccC---------cHHHHHHH----HHH--cCCeEEEecCCCcccccc
Q 017910 87 NDDCKRLLKLMGVPVVEAPS---------EAEAQCAA----LCK--SGQVYAVASEDMDSLTFG 135 (364)
Q Consensus 87 ~~~ik~lL~~~GIp~i~APg---------EADaq~A~----L~~--~g~v~~ViS~DsD~l~fg 135 (364)
...+.+.|+..|+++...|. .+|-.++. ++. .-...+++|+|+|+....
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 45566788999998876653 35644442 221 125667999999988765
No 136
>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=26.76 E-value=1.1e+02 Score=28.82 Aligned_cols=42 Identities=17% Similarity=0.300 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCCEEec--cCcHHHH----HHHHHHcCCeEEEecCCCc
Q 017910 88 DDCKRLLKLMGVPVVEA--PSEAEAQ----CAALCKSGQVYAVASEDMD 130 (364)
Q Consensus 88 ~~ik~lL~~~GIp~i~A--PgEADaq----~A~L~~~g~v~~ViS~DsD 130 (364)
+.++...++||||++.. +++-++. ...|...| +.+|+++|-+
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 55677889999997654 4443433 33333345 6678888655
No 137
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=26.33 E-value=60 Score=26.13 Aligned_cols=40 Identities=25% Similarity=0.314 Sum_probs=28.0
Q ss_pred CEEeccCcHHHHHHHHHHcCCeEEEecCCCcccc-----cccCee
Q 017910 100 PVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLT-----FGAPRF 139 (364)
Q Consensus 100 p~i~APgEADaq~A~L~~~g~v~~ViS~DsD~l~-----fg~~~v 139 (364)
..+..+.-||+.+..++..+..++|+|+|.++-. -|.|-+
T Consensus 45 ~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi 89 (101)
T PF04900_consen 45 NHKETPGSADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVI 89 (101)
T ss_pred CCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEE
Confidence 3333356899999999975544789999998753 355544
No 138
>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=25.85 E-value=60 Score=27.22 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=15.2
Q ss_pred CCCccHHHHHHHHHHcC
Q 017910 187 IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 187 IpGIG~ktA~kLik~~g 203 (364)
|.|||+.+|..++.+.|
T Consensus 20 i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 20 IYGIGRTRARKILEKAG 36 (113)
T ss_pred eecccHHHHHHHHHHhC
Confidence 57999999999999876
No 139
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=25.73 E-value=48 Score=30.19 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=16.0
Q ss_pred CCCCccHHHHHHHHHHcC
Q 017910 186 SIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~~g 203 (364)
.+||||+|+|.+++.++.
T Consensus 112 ~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 112 KVPGIGKKTAERIVLELK 129 (192)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 589999999999998764
No 140
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=25.63 E-value=2e+02 Score=27.66 Aligned_cols=24 Identities=25% Similarity=0.444 Sum_probs=18.0
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHH
Q 017910 187 IRGIGGQTALKLIRQHGSIETILE 210 (364)
Q Consensus 187 IpGIG~ktA~kLik~~gsle~il~ 210 (364)
+.|||+++|.++=+-|.+.-...+
T Consensus 219 v~gig~k~A~~I~~~~~t~~~~~~ 242 (254)
T COG1948 219 VKGIGEKKAREIYRFLRTEYKLIE 242 (254)
T ss_pred hcCccHHHHHHHHHHHhchhhhhc
Confidence 689999999998777776544433
No 141
>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=25.06 E-value=2.2e+02 Score=19.85 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCC
Q 017910 166 NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGS 204 (364)
Q Consensus 166 gl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~~gs 204 (364)
.+||.+| .+|.|-+- +-..++-..=-+|+++|++
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 77788444 3466777777788888764
No 142
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=24.87 E-value=55 Score=28.63 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=24.8
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCcccccccC
Q 017910 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAP 137 (364)
Q Consensus 107 EADaq~A~L~~~g~v~~ViS~DsD~l~fg~~ 137 (364)
+=|.-.-.+|-.+.+++++|+|+|+|.+-..
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~~ 121 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRDE 121 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheeccc
Confidence 4566666677889999999999999987554
No 143
>PRK00254 ski2-like helicase; Provisional
Probab=24.87 E-value=58 Score=35.68 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHHH
Q 017910 186 SIRGIGGQTALKLIRQ-HGSIETILEN 211 (364)
Q Consensus 186 ~IpGIG~ktA~kLik~-~gsle~il~~ 211 (364)
.|||||+++|.+|++. |+|+++|.+.
T Consensus 649 ~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 649 RLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred cCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 4699999999999999 9999988753
No 144
>PRK03739 2-isopropylmalate synthase; Validated
Probab=24.80 E-value=5.6e+02 Score=27.35 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=30.3
Q ss_pred cccchhhHHHHHHHHHhcCCCEEec--cC--cHH-HHHHHHHHcC
Q 017910 80 VKVTKQHNDDCKRLLKLMGVPVVEA--PS--EAE-AQCAALCKSG 119 (364)
Q Consensus 80 ~~vt~~~~~~ik~lL~~~GIp~i~A--Pg--EAD-aq~A~L~~~g 119 (364)
+.++.++--.+-+.|..+||++|++ |. ++| ..+..++..+
T Consensus 47 v~~s~~~Ki~ia~~L~~~GV~~IE~GfP~~s~~e~e~v~~i~~~~ 91 (552)
T PRK03739 47 EPMSPERKLRMFDLLVKIGFKEIEVGFPSASQTDFDFVRELIEEG 91 (552)
T ss_pred CCCCHHHHHHHHHHHHHcCCCEEEEECCCcChHHHHHHHHHHHhc
Confidence 4455666677888999999999999 75 777 5666665554
No 145
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=24.76 E-value=80 Score=29.00 Aligned_cols=46 Identities=22% Similarity=0.333 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhCCCCCCC------CCCccHHHHHHHHHH-----cCCHHHHHHHHH
Q 017910 167 LTMDQFIDLCILSGCDYCDS------IRGIGGQTALKLIRQ-----HGSIETILENIN 213 (364)
Q Consensus 167 l~~~qfidl~iL~G~Dy~d~------IpGIG~ktA~kLik~-----~gsle~il~~l~ 213 (364)
-..+.|++|.-=++ =-+.. +||||.|+...+|.+ |.|.++|-+.+.
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 35577777765444 11111 499999999999976 778888877664
No 146
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=24.62 E-value=50 Score=28.20 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.7
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||++||--++.
T Consensus 76 ~l~GIG~~tA~~~l~ 90 (149)
T smart00478 76 KLPGVGRKTANAVLS 90 (149)
T ss_pred cCCCCcHHHHHHHHH
Confidence 589999999865543
No 147
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=24.54 E-value=1.7e+02 Score=26.58 Aligned_cols=46 Identities=35% Similarity=0.415 Sum_probs=31.5
Q ss_pred chhhHHHHHHHHHhcCCCEEeccCc--HHHHHHHHHHcCCeEEEecCC
Q 017910 83 TKQHNDDCKRLLKLMGVPVVEAPSE--AEAQCAALCKSGQVYAVASED 128 (364)
Q Consensus 83 t~~~~~~ik~lL~~~GIp~i~APgE--ADaq~A~L~~~g~v~~ViS~D 128 (364)
+...-+.+++++...||++|..||| -+|.-..|..-|.-..|+|.|
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 3456678899999999999999975 234444455556444566654
No 148
>PRK06524 biotin carboxylase-like protein; Validated
Probab=24.34 E-value=94 Score=32.78 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=19.8
Q ss_pred HHHHHHHHhcCCCEEeccCcHHHHH
Q 017910 88 DDCKRLLKLMGVPVVEAPSEAEAQC 112 (364)
Q Consensus 88 ~~ik~lL~~~GIp~i~APgEADaq~ 112 (364)
..++.+|+.+||||+....+|-+.|
T Consensus 116 G~iQ~lLE~lGIpy~gP~a~asai~ 140 (493)
T PRK06524 116 EETEALARQAGLEVMHPPAELRHRL 140 (493)
T ss_pred HHHHHHHHHCCCeEECcCHHHHHHh
Confidence 5788999999999988776775433
No 149
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=24.11 E-value=50 Score=30.97 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=12.7
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||++||--++-
T Consensus 125 ~l~GIG~kTAd~iLl 139 (218)
T PRK13913 125 DQKGIGKESADAILC 139 (218)
T ss_pred cCCCccHHHHHHHHH
Confidence 489999999988765
No 150
>PRK00124 hypothetical protein; Validated
Probab=24.03 E-value=62 Score=28.63 Aligned_cols=91 Identities=13% Similarity=0.139 Sum_probs=48.3
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCcccccccCeeEEEeecCCCCCCccEEEeHHHHHHHcCCCHHHHHHHHHHhCCCCCCC
Q 017910 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (364)
Q Consensus 107 EADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~vi~~l~~~~~~~~~v~~~~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~ 186 (364)
.||..|+.+++.| |+|+|.|.=+--..-.+-...+...+ ..|+.+.+-..|-. +...-++- =.| -.+.|
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 8999999999988 67899987655443222111233222 35777766554431 11111111 224 24445
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHH
Q 017910 187 IRGIGGQTALKLIRQHGSIETILEN 211 (364)
Q Consensus 187 IpGIG~ktA~kLik~~gsle~il~~ 211 (364)
=+..+.+.-..+.+. ++.++..
T Consensus 125 p~~~~~~Dr~~F~~~---L~~~l~~ 146 (151)
T PRK00124 125 PKPFTQEDRSRFEAE---LDKLIRR 146 (151)
T ss_pred CCCCCHHHHHHHHHH---HHHHHHH
Confidence 556666655555443 4555544
No 151
>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=24.02 E-value=65 Score=22.80 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=30.5
Q ss_pred EeHHHHHHHcCCCHHHHHHHHHH-hCCCCCCCCCCccHHHHHHHHHHcC
Q 017910 156 FEVAKILEELNLTMDQFIDLCIL-SGCDYCDSIRGIGGQTALKLIRQHG 203 (364)
Q Consensus 156 ~~~~~v~e~lgl~~~qfidl~iL-~G~Dy~d~IpGIG~ktA~kLik~~g 203 (364)
++..++.+.+|+++.+++..+.- .|-.....--.|....|..+..+|+
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 55677889999999999999977 8865222224466666666666654
No 152
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=23.76 E-value=67 Score=27.33 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=15.2
Q ss_pred CCCccHHHHHHHHHHcC
Q 017910 187 IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 187 IpGIG~ktA~kLik~~g 203 (364)
|.|||+.+|..++.+.|
T Consensus 22 I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 22 IYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccHHHHHHHHHHhC
Confidence 67999999999998876
No 153
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=23.32 E-value=2e+02 Score=24.23 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=35.0
Q ss_pred eHHHHHHHcCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHH-cCCHHHH
Q 017910 157 EVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ-HGSIETI 208 (364)
Q Consensus 157 ~~~~v~e~lgl~~~qfidl~iL~G~Dy~d~IpGIG~ktA~kLik~-~gsle~i 208 (364)
....+.+..|++...+..+..++ |.. -|||||+..|.=|... +.|++++
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 34457778899999888887664 677 8999999987666543 3354443
No 154
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=23.10 E-value=71 Score=27.18 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=15.1
Q ss_pred CCCccHHHHHHHHHHcC
Q 017910 187 IRGIGGQTALKLIRQHG 203 (364)
Q Consensus 187 IpGIG~ktA~kLik~~g 203 (364)
|.|||+.+|..++++.|
T Consensus 22 i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 22 IYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccHHHHHHHHHHcC
Confidence 67999999999998876
No 155
>COG4021 Uncharacterized conserved protein [Function unknown]
Probab=22.68 E-value=3.2e+02 Score=25.77 Aligned_cols=99 Identities=17% Similarity=0.203 Sum_probs=62.4
Q ss_pred hhHHHHHHHHHHHHHHcCCCcE---EEEeCCCCchhhHHHHHHHhhhhhch-------HHHHHHHHcC-CHHHHHHHhcc
Q 017910 10 TSHLQGMFTRTIRLLEAGMKPI---YVFDGQPPDLKKQELAKRYSKRADAT-------DDLAEAVEAG-NKEDIEKFSKR 78 (364)
Q Consensus 10 Tsal~G~~~r~~~ll~~gi~Pv---~VFDG~~p~~K~~~~~~rk~~R~~~~-------~~l~~a~~~g-~~~~~~k~~~r 78 (364)
+|+..+|+..-.-.+.+++.|+ .-||+..-..-.+++++|-..|+--. -.+|.+...| ++.++++.-+.
T Consensus 97 ~Sv~~Sf~tS~f~r~~~~~~p~~~~~sFDsR~V~~~~~~i~dYf~wRQ~eawrN~L~s~tfW~L~~rgl~~~ea~erLrG 176 (249)
T COG4021 97 DSVFASFFTSAFTRLWAKFFPEKHLPSFDSRCVAYPLDTIPDYFHWRQVEAWRNNLYSTTFWQLIIRGLTPQEAEERLRG 176 (249)
T ss_pred HHHHHHHHHHHHHHHhhccCCCCCCCcccceEEecchhHHHHHHHHHHHHHHHHhhhhHHHHHHHHcCCChHHHHHHhcc
Confidence 5788888887666688899998 67999854444788999988776321 1345555444 23344333322
Q ss_pred ccccchhhHHHHHHHH-HhcCCCEEeccCcHHHHHHHHHHcCCeE
Q 017910 79 TVKVTKQHNDDCKRLL-KLMGVPVVEAPSEAEAQCAALCKSGQVY 122 (364)
Q Consensus 79 ~~~vt~~~~~~ik~lL-~~~GIp~i~APgEADaq~A~L~~~g~v~ 122 (364)
+. .++..++| ..+||-|=..|. +.++|..+
T Consensus 177 ~k------s~e~heiLfsefGIN~~r~P~--------wqkkG~~~ 207 (249)
T COG4021 177 TK------SNEKHEILFSEFGINYNREPE--------WQKKGVGV 207 (249)
T ss_pred cc------cchHHHHHHHHhCCCcCCChH--------HHhcCceE
Confidence 21 24455655 589998876552 56777543
No 156
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=22.53 E-value=94 Score=30.03 Aligned_cols=45 Identities=22% Similarity=0.237 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhc--cCCCCCcccccCcc
Q 017910 251 PDEEGLINFLVSENGFNSDRVTKAIEKIKAAKN--KSSQGRLESFFKPV 297 (364)
Q Consensus 251 pd~e~L~~fl~~e~~f~~~rv~~~l~~l~~~~~--~~~Q~rld~ff~~~ 297 (364)
+-...|+++| .++||++.-|+.++-|++++-. ... ..=++|++..
T Consensus 26 Iw~gsLI~il-~~fG~sE~~vRaal~Rm~kaG~l~~er-~grks~Y~LS 72 (291)
T COG3327 26 IWIGSLIQIL-AEFGISETTVRAALSRMVKAGWLVGER-EGRKSFYRLS 72 (291)
T ss_pred eeHHHHHHHH-HHcCccHHHHHHHHHHHHhccchheee-cccccceeec
Confidence 3456899999 7999999999999999987632 122 2235666543
No 157
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=22.37 E-value=1e+02 Score=20.03 Aligned_cols=24 Identities=29% Similarity=0.589 Sum_probs=15.5
Q ss_pred CHHHHHHHHHHhcCCChHHHHHHHHH
Q 017910 252 DEEGLINFLVSENGFNSDRVTKAIEK 277 (364)
Q Consensus 252 d~e~L~~fl~~e~~f~~~rv~~~l~~ 277 (364)
|.+.+..++ ++||+++....+|..
T Consensus 2 ~~~~v~~L~--~mGf~~~~~~~AL~~ 25 (37)
T PF00627_consen 2 DEEKVQQLM--EMGFSREQAREALRA 25 (37)
T ss_dssp HHHHHHHHH--HHTS-HHHHHHHHHH
T ss_pred CHHHHHHHH--HcCCCHHHHHHHHHH
Confidence 344555554 669999988887754
No 158
>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=22.35 E-value=3.6e+02 Score=25.44 Aligned_cols=34 Identities=32% Similarity=0.543 Sum_probs=21.4
Q ss_pred CCCCchhHHHHHHHHHHHHHHcCCCcEEE---EeCCC
Q 017910 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYV---FDGQP 38 (364)
Q Consensus 5 ~~G~~Tsal~G~~~r~~~ll~~gi~Pv~V---FDG~~ 38 (364)
|+|-+=||+.-++..+--..++|+++||| .||..
T Consensus 37 SdGGVHSh~~Hl~al~~~a~~~gv~~V~vH~f~DGRD 73 (223)
T PF06415_consen 37 SDGGVHSHIDHLFALIKLAKKQGVKKVYVHAFTDGRD 73 (223)
T ss_dssp SS-SSS--HHHHHHHHHHHHHTT-SEEEEEEEE-SSS
T ss_pred cCCCccccHHHHHHHHHHHHHcCCCEEEEEEecCCCC
Confidence 67778899999888444445689999874 89983
No 159
>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=22.30 E-value=56 Score=29.56 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.3
Q ss_pred CCCCccHHHHHHHHH
Q 017910 186 SIRGIGGQTALKLIR 200 (364)
Q Consensus 186 ~IpGIG~ktA~kLik 200 (364)
.+||||++||--++.
T Consensus 110 ~l~GIG~ktA~~ill 124 (191)
T TIGR01083 110 KLPGVGRKTANVVLN 124 (191)
T ss_pred hCCCCcHHHHHHHHH
Confidence 479999999987664
No 160
>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=22.09 E-value=99 Score=25.44 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=22.2
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCcccccccCe
Q 017910 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (364)
Q Consensus 107 EADaq~A~L~~~g~v~~ViS~DsD~l~fg~~~ 138 (364)
-+|+.++..+...-+ .++|.|.|+-.|+.-.
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 589998888775444 5779999976555433
No 161
>cd04246 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulati
Probab=21.68 E-value=6.4e+02 Score=23.24 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHcCCCcEEEEeCCCCch
Q 017910 12 HLQGMFTRTIRLLEAGMKPIYVFDGQPPDL 41 (364)
Q Consensus 12 al~G~~~r~~~ll~~gi~Pv~VFDG~~p~~ 41 (364)
.+..++.-+..+.+.|.+|+.|--|..+..
T Consensus 16 ~~~~~~~~i~~l~~~g~~~viV~sg~g~~~ 45 (239)
T cd04246 16 RIKRVAERIKKAVKKGYQVVVVVSAMGGTT 45 (239)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEECCCCchH
Confidence 355566655566667899999999754433
No 162
>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=21.34 E-value=1.4e+02 Score=26.66 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCEEeccCcHHHHHHH--H--HHcC--CeEEEecCCCccccccc
Q 017910 88 DDCKRLLKLMGVPVVEAPSEAEAQCAA--L--CKSG--QVYAVASEDMDSLTFGA 136 (364)
Q Consensus 88 ~~ik~lL~~~GIp~i~APgEADaq~A~--L--~~~g--~v~~ViS~DsD~l~fg~ 136 (364)
+.+++.|..+|+..+...|-.|-.++- | +..+ -+.+++|+|+|+..+..
T Consensus 69 ~~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~ 123 (160)
T TIGR00288 69 DKLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVIN 123 (160)
T ss_pred HHHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHH
Confidence 356789999999988888866654442 2 1123 35678999999988763
No 163
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=20.85 E-value=1.2e+02 Score=25.03 Aligned_cols=36 Identities=19% Similarity=0.228 Sum_probs=27.3
Q ss_pred HHHHhcCCC-EEeccC--cHHHHHHHHHHcCCeEEEecC
Q 017910 92 RLLKLMGVP-VVEAPS--EAEAQCAALCKSGQVYAVASE 127 (364)
Q Consensus 92 ~lL~~~GIp-~i~APg--EADaq~A~L~~~g~v~~ViS~ 127 (364)
--+++.||. ++.+.. ||++....|++.++..+++|+
T Consensus 15 lGFrlaGi~~v~~~~~~e~~~~~~~~l~~~~~gII~iTE 53 (104)
T PRK01189 15 LGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSE 53 (104)
T ss_pred HHHHHcCCceEEEcCCHHHHHHHHHHHhcCCeEEEEEEH
Confidence 356889996 666544 778888888888887777787
No 164
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=20.81 E-value=1.7e+02 Score=18.61 Aligned_cols=22 Identities=32% Similarity=0.519 Sum_probs=15.7
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHH
Q 017910 254 EGLINFLVSENGFNSDRVTKAIEK 277 (364)
Q Consensus 254 e~L~~fl~~e~~f~~~rv~~~l~~ 277 (364)
+.+..+. ++||+++.+..++..
T Consensus 3 ~~v~~L~--~mGf~~~~a~~aL~~ 24 (37)
T smart00165 3 EKIDQLL--EMGFSREEALKALRA 24 (37)
T ss_pred HHHHHHH--HcCCCHHHHHHHHHH
Confidence 4454553 889999988887754
No 165
>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=20.67 E-value=1.7e+02 Score=18.69 Aligned_cols=22 Identities=36% Similarity=0.570 Sum_probs=15.8
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHH
Q 017910 254 EGLINFLVSENGFNSDRVTKAIEK 277 (364)
Q Consensus 254 e~L~~fl~~e~~f~~~rv~~~l~~ 277 (364)
+.+..++ ++||+++++..++..
T Consensus 3 ~~v~~L~--~mGf~~~~~~~AL~~ 24 (38)
T cd00194 3 EKLEQLL--EMGFSREEARKALRA 24 (38)
T ss_pred HHHHHHH--HcCCCHHHHHHHHHH
Confidence 3444443 789999998888765
No 166
>TIGR02660 nifV_homocitr homocitrate synthase NifV. This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase.
Probab=20.56 E-value=5.2e+02 Score=25.82 Aligned_cols=38 Identities=29% Similarity=0.284 Sum_probs=28.5
Q ss_pred ccchhhHHHHHHHHHhcCCCEEec--cC--cHH-HHHHHHHHc
Q 017910 81 KVTKQHNDDCKRLLKLMGVPVVEA--PS--EAE-AQCAALCKS 118 (364)
Q Consensus 81 ~vt~~~~~~ik~lL~~~GIp~i~A--Pg--EAD-aq~A~L~~~ 118 (364)
.++.++.-.+-+.|..+||++|++ |. |.| ..+..+.+.
T Consensus 19 ~~s~~~k~~ia~~L~~~Gv~~IEvG~p~~~~~~~e~i~~i~~~ 61 (365)
T TIGR02660 19 AFTAAEKLAIARALDEAGVDELEVGIPAMGEEERAVIRAIVAL 61 (365)
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHc
Confidence 455677777888999999999998 75 655 556666654
No 167
>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=20.28 E-value=1.3e+02 Score=22.12 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=19.7
Q ss_pred CCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 017910 247 KWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (364)
Q Consensus 247 ~~~~pd~e~L~~fl~~e~~f~~~rv~~~l~~l~ 279 (364)
.+...|.+-+.+|. .+||..++|-..++++.
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 34567777777885 88999999999988764
No 168
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=20.20 E-value=1.9e+02 Score=27.11 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCCEEe--ccCcHHHHHHHH----HHcCCeEEEecCCCcc
Q 017910 88 DDCKRLLKLMGVPVVE--APSEAEAQCAAL----CKSGQVYAVASEDMDS 131 (364)
Q Consensus 88 ~~ik~lL~~~GIp~i~--APgEADaq~A~L----~~~g~v~~ViS~DsD~ 131 (364)
+.++..-++||||.+. .+++-++....| ...| +++|+++|-+.
T Consensus 48 ~~~~~qA~algipl~~~~~~~~~e~~~e~l~~~l~~~g-v~~vv~GdI~s 96 (223)
T TIGR00290 48 HLTDLQAESIGIPLIKLYTEGTEEDEVEELKGILHTLD-VEAVVFGAIYS 96 (223)
T ss_pred HHHHHHHHHcCCCeEEeecCCCccHHHHHHHHHHHHcC-CCEEEECCccc
Confidence 4566677899999876 344444444444 3334 66787887643
Done!