Query 019386
Match_columns 342
No_of_seqs 297 out of 1709
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 09:02:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019386hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 1.9E-77 4.1E-82 587.8 37.7 297 2-299 55-351 (393)
2 PRK03980 flap endonuclease-1; 100.0 4.8E-75 1E-79 550.9 33.0 282 3-294 1-292 (292)
3 TIGR03674 fen_arch flap struct 100.0 2.2E-68 4.7E-73 515.9 32.3 283 2-294 47-338 (338)
4 KOG2519 5'-3' exonuclease [Rep 100.0 7.3E-66 1.6E-70 498.6 25.4 303 3-305 50-353 (449)
5 cd00128 XPG Xeroderma pigmento 100.0 3.7E-59 8E-64 448.9 30.0 268 5-276 48-315 (316)
6 TIGR00600 rad2 DNA excision re 100.0 1E-49 2.2E-54 423.0 24.4 218 76-298 763-1006(1034)
7 PRK14976 5'-3' exonuclease; Pr 100.0 8.4E-44 1.8E-48 336.2 22.5 239 2-267 28-281 (281)
8 smart00475 53EXOc 5'-3' exonuc 100.0 1.4E-43 3.1E-48 331.0 20.1 216 2-243 22-247 (259)
9 KOG2518 5'-3' exonuclease [Rep 100.0 1.1E-42 2.3E-47 340.7 20.3 234 5-242 47-288 (556)
10 TIGR00593 pola DNA polymerase 100.0 1.8E-40 3.8E-45 353.9 23.2 238 2-267 22-276 (887)
11 cd00008 53EXOc 5'-3' exonuclea 100.0 1.9E-40 4E-45 307.4 19.2 188 3-219 23-220 (240)
12 COG0258 Exo 5'-3' exonuclease 100.0 1.8E-39 3.8E-44 311.6 23.3 262 2-294 33-309 (310)
13 PRK05755 DNA polymerase I; Pro 100.0 3.1E-39 6.7E-44 347.1 22.5 239 2-268 24-278 (880)
14 KOG2520 5'-3' exonuclease [Rep 100.0 2.9E-38 6.3E-43 326.3 16.7 212 79-295 460-700 (815)
15 PRK09482 flap endonuclease-lik 100.0 2.3E-37 5.1E-42 287.2 19.6 208 4-243 23-243 (256)
16 PHA00439 exonuclease 99.9 4.3E-26 9.4E-31 213.7 15.0 218 2-280 34-270 (286)
17 PF00867 XPG_I: XPG I-region; 99.9 5.1E-26 1.1E-30 181.5 6.4 88 95-182 1-94 (94)
18 PHA02567 rnh RnaseH; Provision 99.9 1.2E-22 2.5E-27 191.5 16.3 162 1-191 32-206 (304)
19 PF02739 5_3_exonuc_N: 5'-3' e 99.9 7.8E-22 1.7E-26 173.6 11.7 136 2-165 24-169 (169)
20 smart00484 XPGI Xeroderma pigm 99.8 2E-20 4.2E-25 142.0 7.7 72 96-167 2-73 (73)
21 cd00080 HhH2_motif Helix-hairp 99.6 1.7E-15 3.7E-20 115.8 6.2 52 164-215 2-55 (75)
22 PF01367 5_3_exonuc: 5'-3' exo 99.4 2.4E-15 5.2E-20 121.1 -7.2 91 167-258 1-101 (101)
23 smart00279 HhH2 Helix-hairpin- 99.2 7.8E-12 1.7E-16 81.8 3.8 33 169-202 1-36 (36)
24 PF00752 XPG_N: XPG N-terminal 98.9 1.5E-09 3.4E-14 87.2 5.0 47 10-56 55-101 (101)
25 PF12813 XPG_I_2: XPG domain c 98.9 4.3E-09 9.4E-14 98.1 8.0 89 86-177 5-107 (246)
26 smart00485 XPGN Xeroderma pigm 98.9 3.7E-09 8E-14 84.8 5.9 48 9-56 51-99 (99)
27 TIGR00600 rad2 DNA excision re 98.7 3.4E-08 7.3E-13 107.0 7.0 52 9-60 51-102 (1034)
28 COG5366 Protein involved in pr 96.7 0.0011 2.4E-08 65.8 3.3 100 89-190 133-233 (531)
29 KOG2045 5'-3' exonuclease XRN1 96.1 0.12 2.5E-06 55.8 13.6 183 16-199 64-307 (1493)
30 PF03159 XRN_N: XRN 5'-3' exon 96.0 0.035 7.5E-07 51.6 8.7 38 98-135 172-222 (237)
31 COG5049 XRN1 5'-3' exonuclease 95.7 0.14 3E-06 53.8 12.3 95 98-192 176-328 (953)
32 PF12826 HHH_2: Helix-hairpin- 95.7 0.0077 1.7E-07 44.4 2.4 26 185-210 6-31 (64)
33 TIGR00084 ruvA Holliday juncti 95.5 0.11 2.4E-06 46.7 9.6 112 159-279 54-172 (191)
34 PRK00116 ruvA Holliday junctio 94.5 0.15 3.3E-06 45.8 7.7 91 186-279 77-174 (192)
35 KOG2044 5'-3' exonuclease HKE1 94.0 0.65 1.4E-05 49.5 11.7 181 11-192 79-352 (931)
36 PF04599 Pox_G5: Poxvirus G5 p 93.5 1.4 3.1E-05 44.0 12.8 113 90-217 148-277 (425)
37 PRK14671 uvrC excinuclease ABC 93.1 0.57 1.2E-05 49.5 10.0 26 185-210 572-597 (621)
38 COG0632 RuvA Holliday junction 91.3 3.5 7.6E-05 37.4 11.4 117 155-280 51-182 (201)
39 PRK14600 ruvA Holliday junctio 91.1 1.2 2.7E-05 39.8 8.2 110 158-279 54-170 (186)
40 PF14520 HHH_5: Helix-hairpin- 91.0 0.2 4.4E-06 36.1 2.6 25 186-210 9-34 (60)
41 PF10391 DNA_pol_lambd_f: Fing 91.0 0.2 4.4E-06 35.4 2.4 24 186-209 6-30 (52)
42 PHA03065 Hypothetical protein; 90.8 3.4 7.4E-05 41.3 11.6 113 90-217 150-279 (438)
43 TIGR00194 uvrC excinuclease AB 90.5 0.2 4.2E-06 52.5 3.0 29 182-210 541-569 (574)
44 PRK14667 uvrC excinuclease ABC 90.5 0.23 4.9E-06 51.9 3.4 29 182-210 514-542 (567)
45 PF00633 HHH: Helix-hairpin-he 90.4 0.23 5E-06 31.0 2.1 15 186-200 15-29 (30)
46 PRK14669 uvrC excinuclease ABC 90.4 0.22 4.8E-06 52.5 3.3 28 183-210 553-580 (624)
47 PRK14670 uvrC excinuclease ABC 90.1 0.23 5E-06 51.9 3.1 29 183-211 515-543 (574)
48 PRK14603 ruvA Holliday junctio 89.9 2.7 5.8E-05 38.0 9.4 26 253-279 152-177 (197)
49 PRK13901 ruvA Holliday junctio 89.4 1.8 3.9E-05 39.1 7.8 108 160-279 55-169 (196)
50 PRK14605 ruvA Holliday junctio 87.9 0.74 1.6E-05 41.5 4.3 110 159-279 55-173 (194)
51 PRK14672 uvrC excinuclease ABC 87.7 0.48 1.1E-05 50.2 3.4 30 182-211 608-637 (691)
52 PRK14602 ruvA Holliday junctio 87.6 0.81 1.8E-05 41.5 4.5 47 160-213 57-104 (203)
53 PF02371 Transposase_20: Trans 85.5 0.7 1.5E-05 35.9 2.5 26 182-207 2-27 (87)
54 PRK14606 ruvA Holliday junctio 84.9 1.6 3.4E-05 39.2 4.8 107 159-279 55-168 (188)
55 PRK00558 uvrC excinuclease ABC 84.4 0.83 1.8E-05 48.1 3.2 26 185-210 546-571 (598)
56 PRK14604 ruvA Holliday junctio 84.3 1.7 3.7E-05 39.2 4.8 107 162-279 58-174 (195)
57 PRK14601 ruvA Holliday junctio 84.3 1.8 3.9E-05 38.7 4.9 104 160-278 56-166 (183)
58 PRK14668 uvrC excinuclease ABC 83.9 0.84 1.8E-05 47.9 3.0 29 183-211 526-554 (577)
59 PRK12766 50S ribosomal protein 83.7 0.99 2.1E-05 41.7 3.0 28 184-211 5-33 (232)
60 PRK14666 uvrC excinuclease ABC 83.2 0.98 2.1E-05 48.1 3.2 29 183-211 638-666 (694)
61 smart00278 HhH1 Helix-hairpin- 83.0 1 2.3E-05 26.8 2.0 17 185-201 4-20 (26)
62 PRK13766 Hef nuclease; Provisi 82.8 17 0.00037 39.3 12.6 25 186-210 719-743 (773)
63 TIGR01448 recD_rel helicase, p 82.2 4.6 0.0001 43.6 7.9 39 167-213 75-113 (720)
64 COG0322 UvrC Nuclease subunit 80.1 1.4 3E-05 46.2 3.0 30 182-211 530-559 (581)
65 PRK14601 ruvA Holliday junctio 79.6 1.7 3.7E-05 38.8 3.0 45 155-201 80-127 (183)
66 COG1948 MUS81 ERCC4-type nucle 79.6 1.6 3.5E-05 40.9 2.9 26 186-211 186-211 (254)
67 PRK13901 ruvA Holliday junctio 76.5 2.4 5.1E-05 38.4 3.0 45 155-201 79-126 (196)
68 PRK14603 ruvA Holliday junctio 76.4 3.6 7.8E-05 37.2 4.1 44 156-201 80-126 (197)
69 PRK13482 DNA integrity scannin 75.6 6 0.00013 38.9 5.7 53 158-210 243-315 (352)
70 PRK14606 ruvA Holliday junctio 75.2 4.1 8.9E-05 36.5 4.2 46 155-202 80-128 (188)
71 PRK14600 ruvA Holliday junctio 75.1 4.4 9.4E-05 36.3 4.3 47 154-202 79-127 (186)
72 PRK14604 ruvA Holliday junctio 74.7 3.6 7.9E-05 37.1 3.7 46 155-202 80-128 (195)
73 PRK14602 ruvA Holliday junctio 73.9 4.4 9.5E-05 36.8 4.1 45 155-201 81-128 (203)
74 PRK02515 psbU photosystem II c 73.2 3 6.5E-05 35.1 2.6 24 187-210 66-91 (132)
75 TIGR00575 dnlj DNA ligase, NAD 71.8 3.5 7.6E-05 44.0 3.3 24 186-209 502-525 (652)
76 TIGR00596 rad1 DNA repair prot 69.7 3.9 8.4E-05 44.7 3.1 25 186-210 761-785 (814)
77 PRK14351 ligA NAD-dependent DN 69.1 4.5 9.7E-05 43.4 3.4 25 186-210 532-556 (689)
78 PF05991 NYN_YacP: YacP-like N 68.3 11 0.00025 32.8 5.3 38 97-134 66-109 (166)
79 TIGR01259 comE comEA protein. 68.1 5.3 0.00012 33.1 3.0 17 186-202 72-88 (120)
80 COG0632 RuvA Holliday junction 65.6 7.3 0.00016 35.4 3.6 73 120-202 48-128 (201)
81 PF11798 IMS_HHH: IMS family H 65.5 4.6 9.9E-05 25.4 1.6 13 186-198 15-27 (32)
82 PF01927 Mut7-C: Mut7-C RNAse 63.5 8.6 0.00019 32.9 3.5 89 85-181 7-99 (147)
83 PF00875 DNA_photolyase: DNA p 63.4 13 0.00028 31.9 4.7 34 85-118 53-86 (165)
84 cd00141 NT_POLXc Nucleotidyltr 62.7 7.8 0.00017 37.3 3.5 26 186-212 89-116 (307)
85 smart00483 POLXc DNA polymeras 62.4 6.7 0.00014 38.3 3.0 25 186-211 93-119 (334)
86 PRK07956 ligA NAD-dependent DN 62.2 5.7 0.00012 42.5 2.6 29 88-116 239-273 (665)
87 COG1555 ComEA DNA uptake prote 60.0 9.9 0.00021 32.8 3.3 25 186-210 101-131 (149)
88 PF11731 Cdd1: Pathogenicity l 59.7 8.3 0.00018 30.6 2.5 31 186-216 16-55 (93)
89 TIGR00426 competence protein C 57.9 12 0.00026 27.4 3.0 15 187-201 22-36 (69)
90 PRK08609 hypothetical protein; 56.1 19 0.00041 37.8 5.2 28 186-213 92-121 (570)
91 TIGR00114 lumazine-synth 6,7-d 55.4 23 0.0005 30.2 4.7 44 82-125 14-64 (138)
92 PTZ00134 40S ribosomal protein 55.0 14 0.00031 32.0 3.4 35 169-203 8-51 (154)
93 COG0272 Lig NAD-dependent DNA 54.6 9 0.0002 40.7 2.5 27 185-211 514-540 (667)
94 TIGR00305 probable toxin-antit 54.3 8.7 0.00019 30.9 1.9 29 105-133 85-113 (114)
95 PRK12419 riboflavin synthase s 49.1 28 0.0006 30.4 4.3 44 82-125 24-74 (158)
96 TIGR02765 crypto_DASH cryptoch 49.1 42 0.00091 33.6 6.3 11 27-37 28-38 (429)
97 TIGR00084 ruvA Holliday juncti 48.8 23 0.0005 31.8 3.9 44 156-201 80-126 (191)
98 PF12826 HHH_2: Helix-hairpin- 48.7 14 0.0003 26.9 2.0 21 186-206 39-59 (64)
99 PF00885 DMRL_synthase: 6,7-di 47.9 34 0.00073 29.3 4.6 44 82-125 17-67 (144)
100 PRK04053 rps13p 30S ribosomal 46.2 30 0.00065 29.9 4.0 35 169-203 3-46 (149)
101 PF12482 DUF3701: Phage integr 44.2 28 0.00061 27.8 3.3 40 161-200 28-68 (96)
102 COG1656 Uncharacterized conser 44.2 61 0.0013 28.5 5.6 50 84-134 12-61 (165)
103 PF14635 HHH_7: Helix-hairpin- 43.4 15 0.00032 29.8 1.6 44 156-202 15-70 (104)
104 COG0258 Exo 5'-3' exonuclease 43.3 12 0.00025 36.0 1.2 30 84-114 103-132 (310)
105 PRK00061 ribH 6,7-dimethyl-8-r 43.0 39 0.00084 29.3 4.3 44 82-125 26-76 (154)
106 PRK14605 ruvA Holliday junctio 43.0 17 0.00038 32.6 2.2 33 167-201 93-127 (194)
107 PLN02404 6,7-dimethyl-8-ribity 42.9 42 0.00091 28.7 4.4 44 82-125 21-71 (141)
108 PF01850 PIN: PIN domain; Int 42.4 23 0.0005 27.8 2.7 50 79-134 69-118 (121)
109 TIGR00591 phr2 photolyase PhrI 42.3 65 0.0014 32.6 6.5 12 191-202 225-236 (454)
110 TIGR03629 arch_S13P archaeal r 41.5 30 0.00065 29.7 3.3 17 187-203 26-42 (144)
111 PRK00076 recR recombination pr 41.3 17 0.00037 32.9 1.8 15 186-200 15-29 (196)
112 TIGR00615 recR recombination p 41.3 17 0.00037 32.8 1.8 15 186-200 15-29 (195)
113 PF10454 DUF2458: Protein of u 40.5 84 0.0018 27.1 5.9 36 71-106 91-126 (150)
114 KOG2841 Structure-specific end 40.1 21 0.00046 33.2 2.2 29 183-211 196-224 (254)
115 COG0353 RecR Recombinational D 39.5 16 0.00036 32.9 1.4 15 185-199 15-29 (198)
116 PF05687 DUF822: Plant protein 39.0 1.5E+02 0.0033 25.5 7.0 68 37-136 5-73 (150)
117 COG1948 MUS81 ERCC4-type nucle 38.3 93 0.002 29.3 6.2 25 186-210 218-242 (254)
118 PRK13844 recombination protein 37.4 21 0.00046 32.3 1.8 15 186-200 19-33 (200)
119 PF00416 Ribosomal_S13: Riboso 36.5 31 0.00068 27.8 2.5 18 186-203 19-36 (107)
120 PRK10702 endonuclease III; Pro 36.3 63 0.0014 29.4 4.7 14 187-200 114-127 (211)
121 TIGR02766 crypt_chrom_pln cryp 35.8 89 0.0019 31.8 6.3 13 190-202 201-213 (475)
122 TIGR01083 nth endonuclease III 34.2 45 0.00097 29.6 3.4 15 186-200 110-124 (191)
123 PLN03060 inositol phosphatase- 33.0 1.7E+02 0.0036 26.7 6.8 103 159-277 76-180 (206)
124 PRK01229 N-glycosylase/DNA lya 32.8 32 0.00069 31.4 2.2 17 186-202 123-139 (208)
125 PF14579 HHH_6: Helix-hairpin- 32.7 54 0.0012 25.4 3.2 27 186-212 31-62 (90)
126 PF03979 Sigma70_r1_1: Sigma-7 30.7 95 0.0021 23.6 4.3 45 61-106 14-60 (82)
127 PRK11613 folP dihydropteroate 30.6 4.8E+02 0.01 24.9 11.0 27 89-115 81-107 (282)
128 PF14490 HHH_4: Helix-hairpin- 30.4 1E+02 0.0023 24.0 4.6 30 189-220 19-48 (94)
129 PRK10674 deoxyribodipyrimidine 30.2 96 0.0021 31.7 5.5 32 87-118 59-94 (472)
130 PF04900 Fcf1: Fcf1; InterPro 29.9 53 0.0012 25.9 2.8 46 95-140 40-90 (101)
131 PF04760 IF2_N: Translation in 29.4 50 0.0011 22.9 2.3 48 156-203 4-52 (54)
132 PF14716 HHH_8: Helix-hairpin- 28.9 42 0.00092 24.5 2.0 14 185-198 50-63 (68)
133 PRK14487 cbb3-type cytochrome 28.4 65 0.0014 29.6 3.4 34 87-120 151-208 (217)
134 PRK14350 ligA NAD-dependent DN 28.2 51 0.0011 35.4 3.1 24 186-209 506-530 (669)
135 PF06415 iPGM_N: BPG-independe 27.8 2.7E+02 0.0058 25.7 7.4 34 5-38 37-73 (223)
136 PF14229 DUF4332: Domain of un 27.8 1.3E+02 0.0028 24.8 4.9 49 157-208 31-80 (122)
137 cd06167 LabA_like LabA_like pr 27.7 1.2E+02 0.0025 25.2 4.7 49 87-135 54-116 (149)
138 cd00056 ENDO3c endonuclease II 27.6 40 0.00087 28.5 1.9 15 186-200 87-101 (158)
139 TIGR03631 bact_S13 30S ribosom 27.5 55 0.0012 26.9 2.5 17 187-203 20-36 (113)
140 PLN00047 photosystem II biogen 27.4 2.5E+02 0.0054 26.9 7.2 103 159-277 129-233 (283)
141 PF11977 RNase_Zc3h12a: Zc3h12 27.1 93 0.002 26.6 4.1 33 96-129 69-110 (155)
142 TIGR02236 recomb_radA DNA repa 27.1 52 0.0011 31.3 2.8 25 186-210 3-28 (310)
143 PRK13266 Thf1-like protein; Re 26.9 1.8E+02 0.004 26.9 6.1 108 159-277 78-190 (225)
144 TIGR00028 Mtu_PIN_fam Mycobact 26.9 60 0.0013 26.3 2.8 32 107-139 105-136 (142)
145 COG1778 Low specificity phosph 26.6 67 0.0015 28.2 3.0 42 156-202 86-134 (170)
146 COG1412 Uncharacterized protei 26.3 76 0.0016 27.0 3.3 49 91-139 69-121 (136)
147 PF04019 DUF359: Protein of un 26.3 45 0.00097 27.8 1.8 51 80-138 44-95 (121)
148 PRK00124 hypothetical protein; 26.2 51 0.0011 28.5 2.3 91 107-211 56-146 (151)
149 COG0177 Nth Predicted EndoIII- 26.2 70 0.0015 29.3 3.2 17 187-203 114-131 (211)
150 TIGR00289 conserved hypothetic 25.9 1.1E+02 0.0023 28.3 4.4 42 88-130 48-95 (222)
151 TIGR03252 uncharacterized HhH- 25.7 46 0.00099 29.6 1.9 17 186-202 119-135 (177)
152 PRK05179 rpsM 30S ribosomal pr 25.4 61 0.0013 27.0 2.5 17 187-203 22-38 (122)
153 PRK00116 ruvA Holliday junctio 25.3 50 0.0011 29.5 2.1 18 186-203 112-129 (192)
154 PF09550 DUF2376: Conserved hy 25.1 2.2E+02 0.0049 19.2 4.7 34 166-204 10-43 (43)
155 COG1569 Predicted nucleic acid 24.7 53 0.0011 28.1 2.0 31 107-137 91-121 (142)
156 smart00478 ENDO3c endonuclease 24.5 50 0.0011 27.7 1.9 15 186-200 76-90 (149)
157 CHL00137 rps13 ribosomal prote 24.5 65 0.0014 26.8 2.5 17 187-203 22-38 (122)
158 PRK13913 3-methyladenine DNA g 24.4 49 0.0011 30.4 1.9 15 186-200 125-139 (218)
159 PF04919 DUF655: Protein of un 24.4 1.4E+02 0.003 26.7 4.6 46 167-212 96-151 (181)
160 COG2266 GTP:adenosylcobinamide 24.1 1.5E+02 0.0032 26.5 4.7 46 83-128 48-95 (177)
161 cd08556 GDPD Glycerophosphodie 23.9 1.1E+02 0.0023 26.1 4.0 39 88-127 150-188 (189)
162 PRK00254 ski2-like helicase; P 23.9 62 0.0013 34.9 2.9 26 186-211 649-675 (720)
163 TIGR00288 conserved hypothetic 23.8 96 0.0021 27.1 3.5 47 89-135 70-122 (160)
164 PF06732 Pescadillo_N: Pescadi 23.6 81 0.0018 30.1 3.2 28 153-180 10-37 (281)
165 PRK05234 mgsA methylglyoxal sy 23.3 83 0.0018 26.8 3.0 37 90-126 41-81 (142)
166 cd01422 MGS Methylglyoxal synt 22.3 1.1E+02 0.0024 24.8 3.5 36 91-126 37-76 (115)
167 PF04895 DUF651: Archaeal prot 22.1 1.9E+02 0.004 23.7 4.6 54 226-293 57-110 (110)
168 PF01936 NYN: NYN domain; Int 21.7 1.5E+02 0.0032 24.1 4.3 49 87-135 49-112 (146)
169 COG4277 Predicted DNA-binding 21.3 1.3E+02 0.0029 29.2 4.1 48 154-201 276-349 (404)
170 PF14056 DUF4250: Domain of un 21.2 1.2E+02 0.0027 21.6 3.0 32 155-186 20-51 (55)
171 PF05182 Fip1: Fip1 motif; In 21.1 1.1E+02 0.0023 21.0 2.6 34 245-281 10-43 (45)
172 COG3327 PaaX Phenylacetic acid 21.1 1.1E+02 0.0024 29.0 3.4 43 252-296 27-71 (291)
173 PRK01189 V-type ATP synthase s 21.0 1.1E+02 0.0024 24.6 3.2 37 91-127 14-53 (104)
174 cd00532 MGS-like MGS-like doma 20.5 1.1E+02 0.0023 24.6 3.0 37 90-126 34-74 (112)
175 PF12836 HHH_3: Helix-hairpin- 20.3 80 0.0017 22.8 2.0 15 186-200 18-32 (65)
176 cd01424 MGS_CPS_II Methylglyox 20.2 1.3E+02 0.0027 23.9 3.3 37 90-126 35-73 (110)
177 COG1491 Predicted RNA-binding 20.2 1.2E+02 0.0025 27.3 3.3 46 167-213 110-166 (202)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.9e-77 Score=587.81 Aligned_cols=297 Identities=59% Similarity=1.017 Sum_probs=285.4
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhccc
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~ 81 (342)
|+|++|++|+||+|||+|+++|+++||+|||||||.+|++|++++++|+++|+++++.+.++.+.|+.+++.++++|++.
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 cCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHH
Q 019386 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v 161 (342)
||++|++.++++|+.||||||+||||||||||+|++.|++|+|+|+|+|+|+||++.++++++.++..+.++++|+.+.+
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 99999999999999999999999999999999999999999999999999999999999998764444556889999999
Q ss_pred HHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhCCCCcCCcc
Q 019386 162 LEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (342)
Q Consensus 162 ~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~f~~p~v~~~~ 241 (342)
++.+|++++||+|+|+|+||||++||||||||||++||++|+++|+|+++++..++.+|++|++.+++.+|++|.|+.+.
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 99999999999999999999999999999999999999999999999999999899999999999999999999999776
Q ss_pred ccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCccccccCcccC
Q 019386 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVAN 299 (342)
Q Consensus 242 ~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff~~~~~ 299 (342)
++ +|.|++||.++|++||+++++|+++||++.|+||.++....+|+|||+||+++++
T Consensus 295 ~~-~l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~ 351 (393)
T PTZ00217 295 EI-DLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKK 351 (393)
T ss_pred CC-CCCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhccCccCCHHHhcCCCCC
Confidence 66 7999999999999999999999999999999999999888899999999998765
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=4.8e-75 Score=550.90 Aligned_cols=282 Identities=45% Similarity=0.807 Sum_probs=265.6
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhcccc
Q 019386 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (342)
Q Consensus 3 ~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~v 82 (342)
+|++|++|||++|||+|+++|+++||+|+|||||.+|++|++++++|+++|+++++.+..+.++|+.+++.++++|++++
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 CHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCC---------cc
Q 019386 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------PV 153 (342)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~---------~~ 153 (342)
|++|++.++++|++|||||++||||||||||+|++.|++|+|+|+|+|+|+||+++|+++++..+.++. ..
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 999999999999999999999999999999999999999999999999999999999999876543321 34
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCC-chHHHHHHh
Q 019386 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDW-PYQEARRLF 232 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~-~~~~~~~~f 232 (342)
+.|+.+.+++.+|++++||+|+|+|+||||++||||||||||++||++|+++|+|+++++ .++ ++.+++++|
T Consensus 161 e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~-------~~~~~~~~~r~~f 233 (292)
T PRK03980 161 ELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG-------FEIENYDEIREFF 233 (292)
T ss_pred eeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc-------CCCCCHHHHHHHh
Confidence 579999999999999999999999999999999999999999999999999999999653 233 358999999
Q ss_pred CCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCcccccc
Q 019386 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (342)
Q Consensus 233 ~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (342)
++|.|+. +. +++|+.||.++|++|||++++|+++||+++++||.++..+.+|+|||+||
T Consensus 234 ~~p~v~~--~~-~~~~~~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~~~~~~~~q~~l~~ff 292 (292)
T PRK03980 234 LNPPVTD--DY-ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292 (292)
T ss_pred cCCCCCC--CC-CccCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccCcccchhhcC
Confidence 9999995 44 79999999999999999999999999999999999998888999999998
No 3
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=2.2e-68 Score=515.93 Aligned_cols=283 Identities=46% Similarity=0.803 Sum_probs=264.1
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhccc
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVK 81 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~ 81 (342)
|+|++|++|+||+|||+++++|+++||+|+|||||.+|++|.+++++|+++|+++++.+..+.+.|+.+++.++++|+.+
T Consensus 47 l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~ 126 (338)
T TIGR03674 47 LMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSR 126 (338)
T ss_pred hhhccCCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCC---------c
Q 019386 82 VTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKI---------P 152 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~---------~ 152 (342)
+|.+|++.++++|++|||||++||||||||||+|++.|.||+|+|+|+|+|+||+++|+++++..+.++. .
T Consensus 127 ~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~ 206 (338)
T TIGR03674 127 LTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVK 206 (338)
T ss_pred CCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999876543221 3
Q ss_pred cEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHh
Q 019386 153 VMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (342)
Q Consensus 153 ~~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~f 232 (342)
...|+.+.+++.+|++++||+|+|+|+||||++||||||||||++||++||++|+|+++++. .++ ++.+++.+|
T Consensus 207 ~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~---~~~---~~~~~~~~f 280 (338)
T TIGR03674 207 PELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGE---DIE---NYDEIREFF 280 (338)
T ss_pred ceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcC---CCC---CHHHHHHHh
Confidence 45699999999999999999999999999999999999999999999999999999999753 232 357999999
Q ss_pred CCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCcccccc
Q 019386 233 KEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFF 294 (342)
Q Consensus 233 ~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (342)
.+|.|+.. . ++.|..||.++|++|++++++|+++||++.++||+++. +++|+|||+||
T Consensus 281 ~~~~v~~~--~-~~~~~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~~-~~~q~~l~~ff 338 (338)
T TIGR03674 281 LNPPVTDD--Y-ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAY-KSKQKTLDRWF 338 (338)
T ss_pred CCCCCCCC--C-CccCCCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHhh-cccccchhhcC
Confidence 99999853 4 78999999999999999999999999999999999887 88999999998
No 4
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=7.3e-66 Score=498.65 Aligned_cols=303 Identities=61% Similarity=1.000 Sum_probs=288.1
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhcccc
Q 019386 3 TNEAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKV 82 (342)
Q Consensus 3 ~~~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~v 82 (342)
+|..|++|+||+|||+|+++|+++||+|||||||.+|.+|.+++.+|..+|..+.+....+.+.|+.....+|++|.+.|
T Consensus 50 ~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkv 129 (449)
T KOG2519|consen 50 RNEAGEPTSHLMGMFYRTIRLIENGIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKV 129 (449)
T ss_pred cccCCCchHHHHHHHHHHHHHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhh
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHHH
Q 019386 83 TKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKIL 162 (342)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~ 162 (342)
|.++.++|+.||..|||||+.||+||+||||+|+++|.|++++|+|||.|.||++.+++++..+..++.++.+|+.+.++
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 99999999999999999999999999999999999999999999999999999999999998766678899999999999
Q ss_pred HHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCchHHHHHHhCCCCcCCcc
Q 019386 163 EELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWPYQEARRLFKEPEVVTDE 241 (342)
Q Consensus 163 ~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~-~l~~~k~~i~~~~~~~~~~~~f~~p~v~~~~ 241 (342)
+.|+++.++|+|+|+|+|||||++|.|||+++|++||++|+++++|++ +.+..++.+|++|++..++.+|+.|.++.+.
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 7777789999999999999999999999877
Q ss_pred ccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCccccccCcccCCCcccc
Q 019386 242 EQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESFFKPVANTSAPIK 305 (342)
Q Consensus 242 ~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~ff~~~~~~~~~~~ 305 (342)
..-++.|..||.+++++|++.+.+|+++||+++++++.+..+..+|+|+|+||+.+++.+.+.+
T Consensus 290 ~~~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~~~~~~ 353 (449)
T KOG2519|consen 290 SILDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKGSPVRK 353 (449)
T ss_pred ceeecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCCCCcch
Confidence 6238999999999999999999999999999999999999999999999999998886544333
No 5
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=3.7e-59 Score=448.87 Aligned_cols=268 Identities=52% Similarity=0.882 Sum_probs=252.4
Q ss_pred CCCCcchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhccccCH
Q 019386 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTK 84 (342)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~ 84 (342)
+.|.+|+|++||++|+.+|+++||+|||||||.+|++|.++..+|+.+|.+.......++++|+.+++.++.+++..+|+
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 hHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHHHHH
Q 019386 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEE 164 (342)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~ 164 (342)
+|++.++++|+.|||||++||+|||||||+|++.|.+++|+|+|+|+|+||++.|+++++..+. ..++.|+.+.+++.
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 9999999999999999999999999999999999999999999999999999999998875321 35788999999999
Q ss_pred hCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHhCCCCcCCccccc
Q 019386 165 LNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLFKEPEVVTDEEQL 244 (342)
Q Consensus 165 lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~f~~p~v~~~~~~~ 244 (342)
+|++++||+|+|+|+||||++||||||||||++||++|++++++++++......+|++|++..++++|.+|.|+.. ..
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 9999999999999999999999999999999999999999999999998877788999999999999999999864 22
Q ss_pred cCCCCCCCHHHHHHHHHHhcCCChHHHHHHHH
Q 019386 245 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIE 276 (342)
Q Consensus 245 ~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~ 276 (342)
.+.|..||.++|+.|++.+++|+++||.+.+.
T Consensus 284 ~~~~~~p~~~~l~~~~~~~~~~~~~rv~~~~~ 315 (316)
T cd00128 284 DLRWRDPDEEGIIEFLCKEHGFNEDRVLKPLE 315 (316)
T ss_pred ceeecCCCHHHHHHHccCCCCCCHHHHHhhhc
Confidence 68999999999999999999999999998764
No 6
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1e-49 Score=422.97 Aligned_cols=218 Identities=25% Similarity=0.440 Sum_probs=197.1
Q ss_pred hhhccccCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEE
Q 019386 76 SKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVME 155 (342)
Q Consensus 76 ~~r~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~ 155 (342)
.++++.||.+|+..|++||++||||||+||||||||||+|++.|+||+|+|+|+|+|+||+++|||+++.. ...+..
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 56788999999999999999999999999999999999999999999999999999999999999998753 346789
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHH---HHHHh----------------
Q 019386 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG--SIETIL---ENINR---------------- 214 (342)
Q Consensus 156 ~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~--sle~il---~~l~~---------------- 214 (342)
|+.+++++.+||+++||+++|+|+||||++|||||||+||++||++|+ ++++++ +|++.
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 466666 44432
Q ss_pred ----hcCCCCCCCchHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH-hhhccCCCCc
Q 019386 215 ----ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK-AAKNKSSQGR 289 (342)
Q Consensus 215 ----~k~~i~~~~~~~~~~~~f~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~-~~~~~~~Q~~ 289 (342)
.++.+|++||+..++.+|++|.|+.+.. .|.|+.||.++|+.||++++||+++||++.|.++. +...+++|+|
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 KKKLRLLQLTPGFPNPAVADAYLRPVVDDSKG--SFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLR 997 (1034)
T ss_pred hhcccccccCCCCCcHHHHHHhcCCCCCCCcC--CCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHccCCccC
Confidence 1256899999999999999999996442 79999999999999999999999999999999984 4667889999
Q ss_pred cccccCccc
Q 019386 290 LESFFKPVA 298 (342)
Q Consensus 290 l~~ff~~~~ 298 (342)
|++||+...
T Consensus 998 ld~FF~~~~ 1006 (1034)
T TIGR00600 998 IDSFFRLAQ 1006 (1034)
T ss_pred HHHhhCccc
Confidence 999998643
No 7
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=8.4e-44 Score=336.15 Aligned_cols=239 Identities=23% Similarity=0.293 Sum_probs=195.9
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhc
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~ 79 (342)
|+|++|.+|+|++||+++++++++.. -.+++|||+..+++|++.++.||++|.++|+.+
T Consensus 28 l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p~~l------------------- 88 (281)
T PRK14976 28 LKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKKTPESL------------------- 88 (281)
T ss_pred ccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCCCCHHH-------------------
Confidence 67999999999999999999999742 245789999989999999999999999999998
Q ss_pred cccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHHc----CCeEEEecCCCCcccccCCeeEEEeecCCCCCCccE
Q 019386 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (342)
Q Consensus 80 ~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~ 154 (342)
..|++.++++|+.+|||++.+|| ||||+||+|++. |....|+|+|+|++|+++++|...... . .....
T Consensus 89 ----~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~--~-~~~~~ 161 (281)
T PRK14976 89 ----ISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKK--K-GTSHF 161 (281)
T ss_pred ----HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEec--C-CCCcE
Confidence 67899999999999999999998 999999999874 665679999999999999876433222 1 12246
Q ss_pred EEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHHh
Q 019386 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRLF 232 (342)
Q Consensus 155 ~~~~~~v~~~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~f 232 (342)
.++.+.+.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|++++++.+.++.+.+.........
T Consensus 162 ~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~~~ 241 (281)
T PRK14976 162 ILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKALL 241 (281)
T ss_pred EEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHHHH
Confidence 79999999999999999999999999 5666667899999999999999999999999987754444444433333334
Q ss_pred CCCCcCCcc------ccccCCCCCCCHHHHHHHHHHhcCCC
Q 019386 233 KEPEVVTDE------EQLQIKWSAPDEEGLINFLVSENGFN 267 (342)
Q Consensus 233 ~~p~v~~~~------~~~~~~~~~pd~e~l~~fl~~~~~f~ 267 (342)
++.+|++.+ ++..+.+.+||.+.|.+|| ++++|.
T Consensus 242 s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~-~~~e~~ 281 (281)
T PRK14976 242 SKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIF-EELELK 281 (281)
T ss_pred hhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHH-HHcCCC
Confidence 444444333 3335677789999999999 788873
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.4e-43 Score=331.02 Aligned_cols=216 Identities=26% Similarity=0.383 Sum_probs=182.0
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
|+|++|++|+|++||++++.++++. ..| ++|||+..+++|++.+++||++|.++|+.+
T Consensus 22 l~~~~G~~t~a~~g~~~~l~~l~~~-~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe~L------------------ 82 (259)
T smart00475 22 LKNSKGEPTNAVYGFLRMLLKLIKE-EKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPDEL------------------ 82 (259)
T ss_pred ccCCCCCcccHHHHHHHHHHHHHHH-cCCCeEEEEEeCCCCccccchhHHHHhCCCCCCHHH------------------
Confidence 6789999999999999999999984 567 789999889999999999999999999998
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHHc----CCeEEEecCCCCcccccCCeeEEEeecCCCCCCcc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~ 153 (342)
..|++.++++|+.||||++.+|+ ||||+||+|++. |..++|+|+|+|++|+++++|.......+ ....
T Consensus 83 -----~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~--~~~~ 155 (259)
T smart00475 83 -----LEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKG--IKEF 155 (259)
T ss_pred -----HHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCC--CCcc
Confidence 67889999999999999999998 999999999984 77788999999999999988754332211 1224
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHH
Q 019386 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~ 231 (342)
..++.+.+.+.+|++|+||+|+|+|+| ||+.+||||||||||.+||++|||+|+|++++++.+.++.+.+.......+
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 677777899999999999999999999999998765334443333344444
Q ss_pred hCCCCcCCcccc
Q 019386 232 FKEPEVVTDEEQ 243 (342)
Q Consensus 232 f~~p~v~~~~~~ 243 (342)
++...+++.+++
T Consensus 236 ls~~L~~l~~d~ 247 (259)
T smart00475 236 LSRKLATIETDV 247 (259)
T ss_pred HhhhhheeeeCC
Confidence 555666666655
No 9
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-42 Score=340.74 Aligned_cols=234 Identities=29% Similarity=0.484 Sum_probs=207.0
Q ss_pred CCCCcchHHHHHHHHHHHHH-HcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhccccC
Q 019386 5 EAGEVTSHLQGMFTRTIRLL-EAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVT 83 (342)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~ll-~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt 83 (342)
..|++|.-...||..-++|| ..||+||.||||.+.+.|..+..+|+.+|++..+....+|.+|+..++..+++|++.||
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 35888877767766666655 68999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHHHH
Q 019386 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILE 163 (342)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~ 163 (342)
++|...+++.|+..||+||+||||||||+|||.+.|++++|||+|||+++|||..||..|+..+. ..+++...+-+
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 99999999999999999999999999999999999999999999999999999999998876543 34566666655
Q ss_pred Hh----CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HHHhhcCCCCCCCc--hHHHHHHhCCCC
Q 019386 164 EL----NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILE-NINRERYQIPEDWP--YQEARRLFKEPE 236 (342)
Q Consensus 164 ~l----gl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~-~l~~~k~~i~~~~~--~~~~~~~f~~p~ 236 (342)
.+ +++.++|..+|+|.||||.++|||||.+||.++|++|.+.+.++. ++...+..+|++|. +..|...|+|..
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 367999999999999999999999999999999999999999875 44455668999987 458889999999
Q ss_pred cCCccc
Q 019386 237 VVTDEE 242 (342)
Q Consensus 237 v~~~~~ 242 (342)
|.++.+
T Consensus 283 VydP~~ 288 (556)
T KOG2518|consen 283 VYDPIE 288 (556)
T ss_pred eeCchH
Confidence 987653
No 10
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.8e-40 Score=353.87 Aligned_cols=238 Identities=29% Similarity=0.440 Sum_probs=197.8
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
|+|++|++|+|++||+++++++++. .+| ++|||+..++||++.+++||++|.++|+++
T Consensus 22 l~~~~G~~t~av~Gf~~~l~~ll~~-~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~Pe~l------------------ 82 (887)
T TIGR00593 22 LTNSKGEPTNAVYGFTKMLLKLLKE-EKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPEEL------------------ 82 (887)
T ss_pred CcCCCCCEecHHHHHHHHHHHHHHh-cCCCEEEEEEcCCCCcchHHHHHHHHhCCCCChHHH------------------
Confidence 7899999999999999999999984 578 679999999999999999999999999998
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHHc----CCeEEEecCCCCcccccCCeeEEEeecCCCCCCcc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~ 153 (342)
..|++.++++|++||||++.+|| ||||+||+|++. |+.++|+|+|+|++|+++++|.. ..... ....
T Consensus 83 -----~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~--~~~~~-~~~~ 154 (887)
T TIGR00593 83 -----IEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKV--LIPKG-KTSF 154 (887)
T ss_pred -----HHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEE--EeccC-CCCc
Confidence 67899999999999999999999 999999999973 77778999999999999988632 22211 1134
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCchHHHHH
Q 019386 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQEARR 230 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~-~i~~~~~~~~~~~ 230 (342)
..++.+.|.+++|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|++++++++. ++.+++.......
T Consensus 155 ~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~a 234 (887)
T TIGR00593 155 TEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDA 234 (887)
T ss_pred eEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHHH
Confidence 579999999999999999999999999 3444567899999999999999999999999998753 3555555443333
Q ss_pred HhCCCCc------CCccccccCCCCCCCHHHHHHHHHHhcCCC
Q 019386 231 LFKEPEV------VTDEEQLQIKWSAPDEEGLINFLVSENGFN 267 (342)
Q Consensus 231 ~f~~p~v------~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~ 267 (342)
+++..++ .++.+++++.+..||.+.|.+|| ++++|+
T Consensus 235 ~ls~~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~-~~lef~ 276 (887)
T TIGR00593 235 FLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL-QELEFK 276 (887)
T ss_pred HHHHHhheeecCCCCCCCHHHhccCCCCHHHHHHHH-HHhCCc
Confidence 3333333 33333345778899999999999 799995
No 11
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=100.00 E-value=1.9e-40 Score=307.41 Aligned_cols=188 Identities=26% Similarity=0.390 Sum_probs=166.4
Q ss_pred cCC-CCCcchHHHHHHHHHHHHHHcC--CCcEEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhc
Q 019386 3 TNE-AGEVTSHLQGMFTRTIRLLEAG--MKPIYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRT 79 (342)
Q Consensus 3 ~~~-~G~~t~~l~g~~~r~~~ll~~g--i~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~ 79 (342)
.++ +|++|+|++||++++.++++.. ..+++||||..+++|++.++.||++|.++|+.+
T Consensus 23 ~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p~~l------------------- 83 (240)
T cd00008 23 KNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMPEEL------------------- 83 (240)
T ss_pred CCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCCHHH-------------------
Confidence 455 8999999999999999999753 456889999989999999999999999999998
Q ss_pred cccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccE
Q 019386 80 VKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVM 154 (342)
Q Consensus 80 ~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~ 154 (342)
..|++.++++|+.||||++.+|+ ||||+||+|++ .|...+|+|+|+|++|+++++|.. .... ...
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 67899999999999999999998 99999999986 577788999999999998887632 2221 135
Q ss_pred EEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCC
Q 019386 155 EFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQI 219 (342)
Q Consensus 155 ~~~~~~v~~~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i 219 (342)
.++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++..+.++
T Consensus 154 ~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~ 220 (240)
T cd00008 154 LVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKGKL 220 (240)
T ss_pred EEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhHHH
Confidence 79999999999999999999999999 788888899999999999999999999999998764333
No 12
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.8e-39 Score=311.55 Aligned_cols=262 Identities=28% Similarity=0.472 Sum_probs=211.6
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHH--cCCCcEEEEeCCCCchhhHHHHHHHhhhhh-chHHHHHHHHcCCHHHHHHHhhh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLE--AGMKPIYVFDGQPPDLKKQELAKRYSKRAD-ATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~--~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~-~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
+.|+.|.+|++++||...+.++++ ..++|++||||.++++|++++++||++|++ +++++
T Consensus 33 ~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~~l------------------ 94 (310)
T COG0258 33 LGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMPDEL------------------ 94 (310)
T ss_pred cCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCHHHH------------------
Confidence 578899999888888887777774 248999999999999999999999999999 99888
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCCeEEEecCCCCcccccCCeeEEEeecCCCCCCcc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~ 153 (342)
..++..+.+++..+|++++..+| ||||.++++++ .|.+++|+|+|+|++||+++++...... +..+.
T Consensus 95 -----~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~~---~~~~~ 166 (310)
T COG0258 95 -----APQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGK---KGEPE 166 (310)
T ss_pred -----HHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCcEEEecc---CCCCc
Confidence 67788888888888888888888 88888888876 6899999999999999999986432222 12221
Q ss_pred EEEeHHHHHHHh-CCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHH
Q 019386 154 MEFEVAKILEEL-NLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (342)
Q Consensus 154 ~~~~~~~v~~~l-gl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~ 230 (342)
..++...+.+.+ |++|+||+|+++|+| |||++||||||||||++||++||+++.++++++..+....+.+ ......
T Consensus 167 ~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l-~~~~~~ 245 (310)
T COG0258 167 KFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKL-LEDKEK 245 (310)
T ss_pred ccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHH-HHHHHH
Confidence 258999999999 999999999999999 9999999999999999999999999999999985444444432 345556
Q ss_pred HhCC-CCcCCccccccCCCCCCCHHHHHHHHHHhcCCC---hHHHHHHHHHHHhhhccCCCCcccccc
Q 019386 231 LFKE-PEVVTDEEQLQIKWSAPDEEGLINFLVSENGFN---SDRVTKAIEKIKAAKNKSSQGRLESFF 294 (342)
Q Consensus 231 ~f~~-p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~---~~rv~~~~~~l~~~~~~~~Q~~l~~ff 294 (342)
+|++ +.|++..++ .+.|..++. ..+++.+++|+ ..++...++++.+......|.+++.||
T Consensus 246 afl~~~l~t~~~d~-~l~~~~~~~---~~~~~~~~d~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 309 (310)
T COG0258 246 AFLSKPLATIKTDV-PLEFDLEDI---LELLVPEHDFSKLLEERVELGFKRLLKAIGSVEQATLDEFF 309 (310)
T ss_pred HhcCcccccccccc-cCCcCccch---hhhccCcccHHHHHHHHHHHhHHHHHHHHhhhccccccccc
Confidence 6665 899988777 777887776 45555566666 667777777776655444788887765
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=3.1e-39 Score=347.15 Aligned_cols=239 Identities=24% Similarity=0.383 Sum_probs=197.7
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
|+|++|.+|++++||++++.++++ ..+| ++|||+..+++|++.+++||++|.++|+.+
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 688999999999999999999996 4777 679999889999999999999999999998
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCCeEEEecCCCCcccccCCeeEEEeecCCCCCCcc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~ 153 (342)
..|++.++++|+.+|||++.+|| ||||+||+|++ .|..++|+|+|+|++|+++++|.. ..... ....
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 67899999999999999999998 99999999985 477888999999999999987632 22110 0124
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHHH
Q 019386 154 MEFEVAKILEELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARRL 231 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~~ 231 (342)
..++.+.+.+.+|++|+||+|+++|+| ||+.+||||||||||.+||++|||+|+|+++++..+.++.+++.......+
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 566667899999999999999999999999998766555555554333222
Q ss_pred hCCCCc------CCccccccCCCCCCCHHHHHHHHHHhcCCCh
Q 019386 232 FKEPEV------VTDEEQLQIKWSAPDEEGLINFLVSENGFNS 268 (342)
Q Consensus 232 f~~p~v------~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~ 268 (342)
++...+ ..+.++..+.|..||.++|.+|| ++++|+.
T Consensus 237 ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~ 278 (880)
T PRK05755 237 LSRKLATIKTDVPLEVDLEDLELQPPDREKLIALF-KELEFKS 278 (880)
T ss_pred hhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHH-HHhCcHH
Confidence 222222 22222335788899999999999 8999963
No 14
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.9e-38 Score=326.32 Aligned_cols=212 Identities=27% Similarity=0.529 Sum_probs=185.5
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeH
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEV 158 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~ 158 (342)
+-.+|..|+.+|+++|+.||||||+||+|||||||.|...++||+|||+|||+|+||+.+||+|++..+ ..+..|..
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 446889999999999999999999999999999999999999999999999999999999999998643 34789999
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHHHh---------------------
Q 019386 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHG---SIETILENINR--------------------- 214 (342)
Q Consensus 159 ~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~---sle~il~~l~~--------------------- 214 (342)
.+++..||+++..+|-+|.|+||||+.||+||||++|+++|.+|+ ++..+-+++..
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 55544444431
Q ss_pred -hcCCCCCCCchHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHH----HHHHhhhccCCCCc
Q 019386 215 -ERYQIPEDWPYQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAI----EKIKAAKNKSSQGR 289 (342)
Q Consensus 215 -~k~~i~~~~~~~~~~~~f~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~----~~l~~~~~~~~Q~~ 289 (342)
.+..+|..||...+..+|++|.|+...+ .|.|+.||.+.|++||...+||+..+....+ +++.+......|.+
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 1256899999999999999999997776 6999999999999999999999999877764 44554445566666
Q ss_pred cccccC
Q 019386 290 LESFFK 295 (342)
Q Consensus 290 l~~ff~ 295 (342)
+-+||-
T Consensus 695 ~~~~f~ 700 (815)
T KOG2520|consen 695 ISQFFE 700 (815)
T ss_pred HHHHHH
Confidence 666664
No 15
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=2.3e-37 Score=287.25 Aligned_cols=208 Identities=18% Similarity=0.201 Sum_probs=170.9
Q ss_pred CCCCCcchHHHHHHHHHHHHHHcCCCc---EEEEeCCCCc--hhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhh
Q 019386 4 NEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPD--LKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 4 ~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~--~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
+++|. |++++||++.+.++++. ..| ++|||+..++ +|++.++.||++|.++|+.+
T Consensus 23 ~~~g~-t~av~gf~~~l~~ll~~-~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe~l------------------ 82 (256)
T PRK09482 23 SPNDI-NACVETCQHALDKLIRH-SQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEAL------------------ 82 (256)
T ss_pred CCCCc-chHHHHHHHHHHHHHHH-cCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcHHH------------------
Confidence 46888 99999999999999974 556 3579998776 99999999999999999999
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHHc----CCeEEEecCCCCcccccCCeeEEEeecCCCCCCcc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCKS----GQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPV 153 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~~----g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~ 153 (342)
..|++.++++|..+|||++..|| ||||+||+|+.+ |.-..|+|.|+|++|+..++|.. +.... .
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 67899999999999999999999 999999999863 55556899999999999887643 22111 2
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC---CCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHHHHH
Q 019386 154 MEFEVAKILEELNLTMDQFIDLCILSGCDYCDS---IRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQEARR 230 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~---IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~~~~ 230 (342)
..++.+.+.+++|++|+|++|+++|+| |.+|| |||||||||.+||++|||+|+|++++++.+.++.+.+.......
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 66665 57999999999999999999999999876434444444333333
Q ss_pred HhCCCCcCCcccc
Q 019386 231 LFKEPEVVTDEEQ 243 (342)
Q Consensus 231 ~f~~p~v~~~~~~ 243 (342)
.+++..+++.+++
T Consensus 231 ~lsr~L~~l~~dv 243 (256)
T PRK09482 231 RLCRKLAQLQTDL 243 (256)
T ss_pred HHHHhhheEeeCC
Confidence 4445566666665
No 16
>PHA00439 exonuclease
Probab=99.94 E-value=4.3e-26 Score=213.66 Aligned_cols=218 Identities=16% Similarity=0.173 Sum_probs=155.0
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHc--CCCc--E-EEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEA--GMKP--I-YVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFS 76 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~--gi~P--v-~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~ 76 (342)
|+|++|.+|++++||++.+.++++. ..+| + ++|| ..+++|++.++.||++|.++|+..
T Consensus 34 l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~~tfR~elyp~YKanR~~~p~~~---------------- 96 (286)
T PHA00439 34 IWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DSVNWRKEVVPTYKANRKAKRKPV---------------- 96 (286)
T ss_pred CCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CCCChHhhhhhHhcCCCCCCCCch----------------
Confidence 6799999999999999999999963 1455 3 4699 467999999999999999987664
Q ss_pred hhccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCC-eEEEecCCCCcccccCCeeEEEeecCCCCC
Q 019386 77 KRTVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQ-VYAVASEDMDSLTFGAPRFLRHLMDPSSRK 150 (342)
Q Consensus 77 ~r~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~-v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~ 150 (342)
.+.+.+++++..+||+++..|| ||||.||+|++ .|. -..|+|.|+|++|+.+..++ + ....
T Consensus 97 --------~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~--~-~~~~-- 163 (286)
T PHA00439 97 --------GYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFL--W-CTTG-- 163 (286)
T ss_pred --------hhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEE--E-ccCC--
Confidence 2466788999999999999999 99999999986 355 55689999999999765332 1 1111
Q ss_pred CccEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHH---cCCHHHHHHHHHhhcCCCCCCCc
Q 019386 151 IPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQ---HGSIETILENINRERYQIPEDWP 224 (342)
Q Consensus 151 ~~~~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~I---pGiG~ktA~~Li~~---~~sle~il~~l~~~k~~i~~~~~ 224 (342)
.+..++.+ .|+||+|+.+|+| |.+||| |||| |||.+||++ |-.++.++++-. .+...+.+|.
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 999976 6899 999999998 445555554431 1222333322
Q ss_pred hHHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHH--HHHHHh
Q 019386 225 YQEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKA--IEKIKA 280 (342)
Q Consensus 225 ~~~~~~~f~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~--~~~l~~ 280 (342)
-. .| . -..+=++.++... .+-|.+++.+... +.|+.+
T Consensus 232 k~-------~~------~-----~~~~~w~~~v~~~-~k~g~~e~~~~~q~~~ari~r 270 (286)
T PHA00439 232 KR-------AP------E-----PEETLWDCIVTLG-AKAGMTEEDAIKQAQMARILR 270 (286)
T ss_pred cc-------CC------C-----ccccHHHHHHHHH-HHcCCCHHHHHHHHHHHHHhh
Confidence 00 00 0 0001257888887 6889998765433 344443
No 17
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.92 E-value=5.1e-26 Score=181.53 Aligned_cols=88 Identities=53% Similarity=0.847 Sum_probs=75.2
Q ss_pred HHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEee-cC-CC----CCCccEEEeHHHHHHHhCCC
Q 019386 95 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLM-DP-SS----RKIPVMEFEVAKILEELNLT 168 (342)
Q Consensus 95 ~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~-~~-~~----~~~~~~~~~~~~v~~~lgl~ 168 (342)
++|||||++||||||||||||+++|+||+|+|+|||+|+||+++|++++. .. +. ....+..|+...+++.++++
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 57999999999999999999999999999999999999999999999996 22 21 13467899999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 019386 169 MDQFIDLCILSGCD 182 (342)
Q Consensus 169 ~~q~id~~~L~G~D 182 (342)
++||+++|+|+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 99999999999998
No 18
>PHA02567 rnh RnaseH; Provisional
Probab=99.89 E-value=1.2e-22 Score=191.45 Aligned_cols=162 Identities=14% Similarity=0.108 Sum_probs=124.3
Q ss_pred CCcCCCCCcchHHHH-HHHHHHHHHH-cCCCc---EEEEeCCC-CchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHH
Q 019386 1 MLTNEAGEVTSHLQG-MFTRTIRLLE-AGMKP---IYVFDGQP-PDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEK 74 (342)
Q Consensus 1 ~l~~~~G~~t~~l~g-~~~r~~~ll~-~gi~P---v~VFDG~~-~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k 74 (342)
+|++++|.+|+++++ +++.+.+++. ..-.| +++||+.. +.||++.++.||++|.++|+++..-++ .
T Consensus 32 ~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~~Peel~~q~~--------~ 103 (304)
T PHA02567 32 NFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDREESPWDWE--------G 103 (304)
T ss_pred hCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCCCChHHHHHHH--------H
Confidence 378999999999977 5554444443 12223 56899974 789999999999999999998732111 0
Q ss_pred HhhhccccCHhHH-HHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCCeEEEecCCCCcccccC-CeeEEEeecCC
Q 019386 75 FSKRTVKVTKQHN-DDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGA-PRFLRHLMDPS 147 (342)
Q Consensus 75 ~~~r~~~vt~~~~-~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~v~~V~S~DsD~l~fg~-~~v~~~l~~~~ 147 (342)
+ .+++ +.+++++..|||+++..|| ||||.||+|++ .|.-..|+|.|+|++|+.. ++|.. +..
T Consensus 104 l--------~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~--~~~- 172 (304)
T PHA02567 104 L--------FEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQ--WSP- 172 (304)
T ss_pred h--------hhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEE--eec-
Confidence 0 1223 5678899999999999999 99999999987 4665678999999999974 55532 211
Q ss_pred CCCCccEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCcc
Q 019386 148 SRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIG 191 (342)
Q Consensus 148 ~~~~~~~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG 191 (342)
++.+.+.+++| .|+|++|+.+|+| |.+||||||-
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 23477888999 5999999999999 9999999984
No 19
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.87 E-value=7.8e-22 Score=173.61 Aligned_cols=136 Identities=29% Similarity=0.473 Sum_probs=111.8
Q ss_pred CcCCCCCcchHHHHHHHHHHHHHHcCCCc---EEEEeCCCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhh
Q 019386 2 LTNEAGEVTSHLQGMFTRTIRLLEAGMKP---IYVFDGQPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKR 78 (342)
Q Consensus 2 l~~~~G~~t~~l~g~~~r~~~ll~~gi~P---v~VFDG~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r 78 (342)
|.+++|++|++++||+..+.++++. ..| ++|||+..+++|++.+++||++|.++|+++
T Consensus 24 l~~~~G~~t~ai~g~~~~l~~l~~~-~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~~p~~l------------------ 84 (169)
T PF02739_consen 24 LRNSDGEPTNAIYGFLRMLLKLLKD-FKPDYVVVAFDSKGPTFRKELYPEYKANRKPMPEEL------------------ 84 (169)
T ss_dssp -BETTSEB-HHHHHHHHHHHHHHHH-TTEEEEEEEEEBSSCHHHHHCCTTTTHHHHHHHHHH------------------
T ss_pred CcCCCCCChHHHHHHHHHHHHHHHH-cCCceEEEEecCCCcchHHHHHHHHHhCCCCCCHHH------------------
Confidence 6789999999999999999999974 455 568999988999999999999999999998
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcC-cHHHHHHHHHH----cCCeEEEecCCCCcccccCC--eeEEEeecCCCCCC
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPS-EAEAQCAALCK----SGQVYAVASEDMDSLTFGAP--RFLRHLMDPSSRKI 151 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~-EAdaq~A~L~~----~g~v~~V~S~DsD~l~fg~~--~v~~~l~~~~~~~~ 151 (342)
..|++.++++|+.+||+++..|| ||||.||+|++ +|.-..|+|.|+|++|+..+ +|+ +...+ ..
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 67899999999999999999999 99999999987 46666789999999999998 553 33332 23
Q ss_pred ccEEEeHHHHHHHh
Q 019386 152 PVMEFEVAKILEEL 165 (342)
Q Consensus 152 ~~~~~~~~~v~~~l 165 (342)
....|+.+.|.++|
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 45789999998875
No 20
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.82 E-value=2e-20 Score=141.98 Aligned_cols=72 Identities=49% Similarity=0.750 Sum_probs=67.1
Q ss_pred HcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHHHHHhCC
Q 019386 96 LMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNL 167 (342)
Q Consensus 96 ~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~lgl 167 (342)
.+||||++||+|||||||+|+++|++|+|+|+|+|+|+||+++++++++..+++..+++.++...+++++|+
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 689999999999999999999999999999999999999999999999887655567899999999999985
No 21
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.59 E-value=1.7e-15 Score=115.81 Aligned_cols=52 Identities=50% Similarity=0.809 Sum_probs=49.5
Q ss_pred HhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhh
Q 019386 164 ELNLTMDQFIDLCILSG--CDYCDSIRGIGGQTALKLIRQHGSIETILENINRE 215 (342)
Q Consensus 164 ~lgl~~~q~id~~~L~G--~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~ 215 (342)
.+|++|+||+|+|+|+| |||.+||||||+|+|.+||++|+++++++++++..
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 57999999999999999 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=99.39 E-value=2.4e-15 Score=121.06 Aligned_cols=91 Identities=33% Similarity=0.456 Sum_probs=50.1
Q ss_pred CCHHHHHHHHHHhCCCCCCCC---CCccHHHHHHHHHHcCCHHHHHHHHHhhcC-CCCCCCchH-----HHHHHh-CCCC
Q 019386 167 LTMDQFIDLCILSGCDYCDSI---RGIGGQTALKLIRQHGSIETILENINRERY-QIPEDWPYQ-----EARRLF-KEPE 236 (342)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~I---pGiG~ktA~~Li~~~~sle~il~~l~~~k~-~i~~~~~~~-----~~~~~f-~~p~ 236 (342)
++|+|++||.+|+| |.+||| ||||+|||.+||++|||+|+|+++++..+. ++.+.+... ..+.+- ++.+
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 999976 589999999999999999999999987654 443322110 122222 2455
Q ss_pred cCCccccccCCCCCCCHHHHHH
Q 019386 237 VVTDEEQLQIKWSAPDEEGLIN 258 (342)
Q Consensus 237 v~~~~~~~~~~~~~pd~e~l~~ 258 (342)
|.++.+++++.|..||.++|.+
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 5555666688999999998863
No 23
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.23 E-value=7.8e-12 Score=81.81 Aligned_cols=33 Identities=55% Similarity=0.945 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCccHHHHHHHHHHc
Q 019386 169 MDQFIDLCILSGCDYCD---SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 169 ~~q~id~~~L~G~Dy~~---~IpGiG~ktA~~Li~~~ 202 (342)
|+||+++|+|+| ||+| ||||||+|+|++||++|
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 589999999999 9999 67899999999999987
No 24
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=98.91 E-value=1.5e-09 Score=87.23 Aligned_cols=47 Identities=55% Similarity=1.055 Sum_probs=41.5
Q ss_pred chHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhc
Q 019386 10 TSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (342)
Q Consensus 10 t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~ 56 (342)
++++.++++++..|+.+||+|||||||.+|+.|.++..+|+.+|+++
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 69999999999999999999999999999999999999999888753
No 25
>PF12813 XPG_I_2: XPG domain containing
Probab=98.89 E-value=4.3e-09 Score=98.09 Aligned_cols=89 Identities=28% Similarity=0.271 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHc---CCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccC--CeeEEEee---cCC------CCCC
Q 019386 86 HNDDCKRLLKLM---GVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA--PRFLRHLM---DPS------SRKI 151 (342)
Q Consensus 86 ~~~~~~~lL~~~---Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~--~~v~~~l~---~~~------~~~~ 151 (342)
+.+.+.+.|+.+ |++++++|||||..||.++++.-+ .|+|+|||+++|+. ..-|..+. ... ....
T Consensus 5 ~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i 83 (246)
T PF12813_consen 5 LVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYI 83 (246)
T ss_pred hHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCee
Confidence 456788899998 999999999999999999997666 69999999999986 32222222 111 1123
Q ss_pred ccEEEeHHHHHHHhCCCHHHHHHHHH
Q 019386 152 PVMEFEVAKILEELNLTMDQFIDLCI 177 (342)
Q Consensus 152 ~~~~~~~~~v~~~lgl~~~q~id~~~ 177 (342)
....|+.+.++..+|+. .++.++.
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 6666665
No 26
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=98.87 E-value=3.7e-09 Score=84.80 Aligned_cols=48 Identities=60% Similarity=1.008 Sum_probs=43.8
Q ss_pred cch-HHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhc
Q 019386 9 VTS-HLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADA 56 (342)
Q Consensus 9 ~t~-~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~ 56 (342)
++. |+.++++|+..|+++||+|||||||.+|+.|.++..+|+.+|+++
T Consensus 51 ~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~~ 99 (99)
T smart00485 51 PNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99 (99)
T ss_pred CchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhcC
Confidence 344 999999999999999999999999999999999999999888753
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=98.66 E-value=3.4e-08 Score=107.00 Aligned_cols=52 Identities=46% Similarity=0.722 Sum_probs=48.4
Q ss_pred cchHHHHHHHHHHHHHHcCCCcEEEEeCCCCchhhHHHHHHHhhhhhchHHH
Q 019386 9 VTSHLQGMFTRTIRLLEAGMKPIYVFDGQPPDLKKQELAKRYSKRADATDDL 60 (342)
Q Consensus 9 ~t~~l~g~~~r~~~ll~~gi~Pv~VFDG~~~~~K~~~~~~rk~~R~~~~~~l 60 (342)
+++||.|||+|+++|+.+||+|||||||.+|.+|.+++.+|+.+|+++.+..
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=96.73 E-value=0.0011 Score=65.81 Aligned_cols=100 Identities=30% Similarity=0.428 Sum_probs=81.2
Q ss_pred HHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccC-CeeEEEeecCCCCCCccEEEeHHHHHHHhCC
Q 019386 89 DCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGA-PRFLRHLMDPSSRKIPVMEFEVAKILEELNL 167 (342)
Q Consensus 89 ~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~-~~v~~~l~~~~~~~~~~~~~~~~~v~~~lgl 167 (342)
.+-.++..-||.|+++|+-|..|||||.....|+++ -+-+|.+.|.+ ++++..+... ...-|+..++....++-.-.
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~-~gp~d~l~ld~vdr~il~m~fg-~d~Ppl~~~~vp~~lem~l~ 210 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYA-FGPSDILLLDGVDRIILDMSFG-SDKPPLDVFHVPRFLEMFLL 210 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhc-CCchHhHHHhhhhhheeecccC-CCCCCCcccccchHHHhccc
Confidence 556688899999999999999999999999899865 46699999865 6666655543 34456777887777777777
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCc
Q 019386 168 TMDQFIDLCILSGCDYCDSIRGI 190 (342)
Q Consensus 168 ~~~q~id~~~L~G~Dy~~~IpGi 190 (342)
+-.-|.-+..|.|||.+..++.+
T Consensus 211 s~~lFya~~ll~~c~~~s~~~~C 233 (531)
T COG5366 211 SSRLFYALGLLLGCDFCSTIPRC 233 (531)
T ss_pred ccchhhhhccccccccccccccc
Confidence 88899999999999999988764
No 29
>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=96.07 E-value=0.12 Score=55.79 Aligned_cols=183 Identities=21% Similarity=0.308 Sum_probs=105.4
Q ss_pred HHHHHHHHHHcCCCcEE----EEeCCCCchhhHHHHHHHh-hhhhchHHHHHHHHcCCHHHHHHHhhhccccCHhHHHHH
Q 019386 16 MFTRTIRLLEAGMKPIY----VFDGQPPDLKKQELAKRYS-KRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDC 90 (342)
Q Consensus 16 ~~~r~~~ll~~gi~Pv~----VFDG~~~~~K~~~~~~rk~-~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~~~~~~~ 90 (342)
+|+-+-.|.. -|+|-= .-||..|-.|......|+- .-..+..++.+|.+.|+.-..+.|-+.|+..-.+.+..+
T Consensus 64 IfnYIdhLf~-~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~rl 142 (1493)
T KOG2045|consen 64 IFNYIDHLFY-LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMVRL 142 (1493)
T ss_pred HHHHHHHHHH-hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHHHH
Confidence 3443444444 488842 3699999877766555443 334556778899999986544666656654433445555
Q ss_pred HHHHHH------------cCCCee----cCcCcHHHHHHHHHHc---------CCeEEEecCCCCcccccC----Ce--e
Q 019386 91 KRLLKL------------MGVPVV----EAPSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR--F 139 (342)
Q Consensus 91 ~~lL~~------------~Gi~~i----~Ap~EAdaq~A~L~~~---------g~v~~V~S~DsD~l~fg~----~~--v 139 (342)
.+-|+. -++.+| .+|||+|--|--+.+. +--++++.-|-|++.+|- ++ +
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 555544 366666 4699999766655541 224557788999999982 32 2
Q ss_pred EEEe-ec-CCCC--CCc---cEEEeHH-----------HHHHH--hCCCH----HHHHHHHHHhCCCCCCCCCCccH-HH
Q 019386 140 LRHL-MD-PSSR--KIP---VMEFEVA-----------KILEE--LNLTM----DQFIDLCILSGCDYCDSIRGIGG-QT 194 (342)
Q Consensus 140 ~~~l-~~-~~~~--~~~---~~~~~~~-----------~v~~~--lgl~~----~q~id~~~L~G~Dy~~~IpGiG~-kt 194 (342)
+|-- +. ..++ ... +-..+++ ++... +..+. +.||.++.|+|+||.+++|++-. ..
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 3211 11 1111 111 1112222 22211 12232 56778888999999999998865 34
Q ss_pred HHHHH
Q 019386 195 ALKLI 199 (342)
Q Consensus 195 A~~Li 199 (342)
|+-|+
T Consensus 303 Alpll 307 (1493)
T KOG2045|consen 303 ALPLL 307 (1493)
T ss_pred hHHHH
Confidence 55554
No 30
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=96.03 E-value=0.035 Score=51.62 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=25.6
Q ss_pred CCCeecC----cCcHHHHHHHHHHc---------CCeEEEecCCCCccccc
Q 019386 98 GVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSLTFG 135 (342)
Q Consensus 98 Gi~~i~A----p~EAdaq~A~L~~~---------g~v~~V~S~DsD~l~fg 135 (342)
++.+|.+ |||+|--|..+.+. ...++|+|.|+|+++++
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 4566665 78999877665542 45788999999999987
No 31
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=95.73 E-value=0.14 Score=53.79 Aligned_cols=95 Identities=23% Similarity=0.413 Sum_probs=61.5
Q ss_pred CCCeec----CcCcHHHHHHHHHHc---------CCeEEEecCCCCcccccC----Ce--eEE-Eeec-CCCC-------
Q 019386 98 GVPVVE----APSEAEAQCAALCKS---------GQVYAVASEDMDSLTFGA----PR--FLR-HLMD-PSSR------- 149 (342)
Q Consensus 98 Gi~~i~----Ap~EAdaq~A~L~~~---------g~v~~V~S~DsD~l~fg~----~~--v~~-~l~~-~~~~------- 149 (342)
++.+|. .|||+|--|-.+.++ +-.++|.+-|-|++.+|- |+ ++| ..+. ..++
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 455554 489999988888773 347789999999999983 33 344 1221 1110
Q ss_pred ---------------CCccEEEeHHHHHHHh-------CCC--------HHHHHHHHHHhCCCCCCCCCCccH
Q 019386 150 ---------------KIPVMEFEVAKILEEL-------NLT--------MDQFIDLCILSGCDYCDSIRGIGG 192 (342)
Q Consensus 150 ---------------~~~~~~~~~~~v~~~l-------gl~--------~~q~id~~~L~G~Dy~~~IpGiG~ 192 (342)
..++.+++.+-+.+.+ +++ -+.||.+|-++|+||.+++|++-.
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 1234556665443321 221 267888999999999999998754
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.69 E-value=0.0077 Score=44.37 Aligned_cols=26 Identities=35% Similarity=0.597 Sum_probs=21.8
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
-||||||+++|..|+++|+|++++..
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 48999999999999999999998764
No 33
>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=95.52 E-value=0.11 Score=46.68 Aligned_cols=112 Identities=20% Similarity=0.271 Sum_probs=64.7
Q ss_pred HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhh---cC-CCCCCCchHHHHHHhC
Q 019386 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRE---RY-QIPEDWPYQEARRLFK 233 (342)
Q Consensus 159 ~~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~---k~-~i~~~~~~~~~~~~f~ 233 (342)
++...-||+ +.++--.|..|++ |+|||||+|+.++..+ +++++.+.+... .. ++| .+-...|..+.+
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 6666666777764 8999999999999865 577777776531 11 222 222333333331
Q ss_pred --CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 234 --~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
...+.....+..-.-..+..+.+.+-| ..+||++..++.++..+.
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 111100000000000123456677777 589999999999998774
No 34
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.55 E-value=0.15 Score=45.79 Aligned_cols=91 Identities=19% Similarity=0.315 Sum_probs=49.5
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHhh---c-CCCCCCCchHHHHHHhC--CCCcC-CccccccCCCCCCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILENINRE---R-YQIPEDWPYQEARRLFK--EPEVV-TDEEQLQIKWSAPDEEGLIN 258 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~~l~~~---k-~~i~~~~~~~~~~~~f~--~p~v~-~~~~~~~~~~~~pd~e~l~~ 258 (342)
.||||||++|..++..|++ +.+.+.+... . ..+| .+....|..++. +.... .......-.-..+..+.+..
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 4999999999999999986 3333322211 0 0121 222333333331 11110 00000000111223678889
Q ss_pred HHHHhcCCChHHHHHHHHHHH
Q 019386 259 FLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 259 fl~~~~~f~~~rv~~~~~~l~ 279 (342)
+| ..+||+...+.+.+..+.
T Consensus 155 aL-~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 155 AL-VALGYKPKEASKAVAKIL 174 (192)
T ss_pred HH-HHcCCCHHHHHHHHHHHh
Confidence 99 699999998888888775
No 35
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=93.97 E-value=0.65 Score=49.53 Aligned_cols=181 Identities=20% Similarity=0.335 Sum_probs=98.8
Q ss_pred hHHHHHHHHHHHHHHcCCCcEE-EEeCCCCchhhHHHHHHH--hhhhhchHHH------HHHHHcCCH----HHHHHHhh
Q 019386 11 SHLQGMFTRTIRLLEAGMKPIY-VFDGQPPDLKKQELAKRY--SKRADATDDL------AEAVEAGNK----EDIEKFSK 77 (342)
Q Consensus 11 ~~l~g~~~r~~~ll~~gi~Pv~-VFDG~~~~~K~~~~~~rk--~~R~~~~~~l------~~a~~~g~~----~~~~k~~~ 77 (342)
-+++-++.|++.|.+- =+-.| .-||.+|-.|......|+ +.|+.+.++. ++...+|.. ..-+.|-.
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 4555555666665541 12234 589999877766544442 2333332221 111222321 11112222
Q ss_pred hccccCHhHHHHHHHHHHH------------cCCCeecC----cCcHHHHHHHHHHc---------CCeEEEecCCCCcc
Q 019386 78 RTVKVTKQHNDDCKRLLKL------------MGVPVVEA----PSEAEAQCAALCKS---------GQVYAVASEDMDSL 132 (342)
Q Consensus 78 r~~~vt~~~~~~~~~lL~~------------~Gi~~i~A----p~EAdaq~A~L~~~---------g~v~~V~S~DsD~l 132 (342)
.|++.-...++.+-..|+. -+|.+|.+ |||+|--|-...+. +-++++++-|-|++
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 2333212344555555543 46677754 89999877777662 23788999999999
Q ss_pred cccC-C-----eeEEEeecCCC----------------------------------CCCccEEEeHHHHHH----Hh---
Q 019386 133 TFGA-P-----RFLRHLMDPSS----------------------------------RKIPVMEFEVAKILE----EL--- 165 (342)
Q Consensus 133 ~fg~-~-----~v~~~l~~~~~----------------------------------~~~~~~~~~~~~v~~----~l--- 165 (342)
.+|- . .|+|-.+.++. .+.++..++..-+.+ +|
T Consensus 238 mLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p 317 (931)
T KOG2044|consen 238 MLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMP 317 (931)
T ss_pred eeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCC
Confidence 9983 2 34554433211 012345555543333 22
Q ss_pred C----CC----HHHHHHHHHHhCCCCCCCCCCccH
Q 019386 166 N----LT----MDQFIDLCILSGCDYCDSIRGIGG 192 (342)
Q Consensus 166 g----l~----~~q~id~~~L~G~Dy~~~IpGiG~ 192 (342)
+ ++ -+.||-+|-++|+||.+.+|-+-+
T Consensus 318 ~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeI 352 (931)
T KOG2044|consen 318 NLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEI 352 (931)
T ss_pred CCCccccHHhhhcceEEEEeeecCccCCCCCchhh
Confidence 2 12 256777999999999999997655
No 36
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=93.54 E-value=1.4 Score=43.98 Aligned_cols=113 Identities=21% Similarity=0.353 Sum_probs=67.1
Q ss_pred HHHHHHHc--CCCeecCcC-cHHHHHHHHHH-----cCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHH
Q 019386 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (342)
Q Consensus 90 ~~~lL~~~--Gi~~i~Ap~-EAdaq~A~L~~-----~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v 161 (342)
+.++|..+ +|.++...| .||=.+.+=++ .|.=..++|.|-|.++|.+..-...+... +
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t--------------~ 213 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKT--------------M 213 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHh--------------H
Confidence 44455554 899999999 99987666555 47666789999999999864211111000 0
Q ss_pred HHHhCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHHhhcC
Q 019386 162 LEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENINRERY 217 (342)
Q Consensus 162 ~~~lgl~~----~q~-id~~~L~G~Dy~~~IpGiG--~kt--A~~Li~~~~sle~il~~l~~~k~ 217 (342)
-+.|.+-| .-+ ...++.=||||-+|+-|+- +++ -.+|...| ++++++..|--..+
T Consensus 214 ~~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL~~kny 277 (425)
T PF04599_consen 214 NQLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSLAIKNY 277 (425)
T ss_pred HhHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHHhhhhh
Confidence 11111111 111 2345556999999998864 332 13444443 57888887753333
No 37
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=93.14 E-value=0.57 Score=49.51 Aligned_cols=26 Identities=42% Similarity=0.694 Sum_probs=23.6
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
++|||||+++|..|++.|||+++|..
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 57999999999999999999988754
No 38
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=91.27 E-value=3.5 Score=37.39 Aligned_cols=117 Identities=19% Similarity=0.223 Sum_probs=63.3
Q ss_pred EEeHHHHHHHhCCC-HHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCc---hHHHHH
Q 019386 155 EFEVAKILEELNLT-MDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWP---YQEARR 230 (342)
Q Consensus 155 ~~~~~~v~~~lgl~-~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~---~~~~~~ 230 (342)
.+-.++...-||+. .+.=..|..|. +|.|||||+|+.+|.. -+++++.+.+.......=..+| ..-|..
T Consensus 51 ~~vREd~~~LyGF~~~~ER~lF~~Li------sVnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGIGkKtAer 123 (201)
T COG0632 51 LVVREDAHLLYGFLTEEERELFRLLI------SVNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGIGKKTAER 123 (201)
T ss_pred EeehhhHHHHcCCCCHHHHHHHHHHH------ccCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCCCHHHHHH
Confidence 34566777788974 44444455554 4789999999999985 4678888877643322112222 233444
Q ss_pred HhCC-----CCcC--CccccccCCCCC----CCHHHHHHHHHHhcCCChHHHHHHHHHHHh
Q 019386 231 LFKE-----PEVV--TDEEQLQIKWSA----PDEEGLINFLVSENGFNSDRVTKAIEKIKA 280 (342)
Q Consensus 231 ~f~~-----p~v~--~~~~~~~~~~~~----pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~ 280 (342)
+.+. +... ..... ...+.. |-.+.-++=| ..+||++..+++++..+..
T Consensus 124 ivleLk~K~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~AL-~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 124 IVLELKGKLAAFLKGDGGSP-AEDLSLDESSPALEEAVEAL-VALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred HHHHHhhhhhhhcccccccc-cccccccccchhhhHHHHHH-HHcCCCHHHHHHHHHHHHh
Confidence 3320 1100 00000 111211 1122213333 4899999999988887764
No 39
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.05 E-value=1.2 Score=39.82 Aligned_cols=110 Identities=15% Similarity=0.211 Sum_probs=58.8
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC---CCCCCCchHHHHHHhC
Q 019386 158 VAKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY---QIPEDWPYQEARRLFK 233 (342)
Q Consensus 158 ~~~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~---~i~~~~~~~~~~~~f~ 233 (342)
.++...-||+ +.++--.|-.|+ +|.|||||+|+.++..+ +.++++..+..... ++|- .-..-|..+.+
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 3444556776 555555555554 47889999999998875 56777776653211 2221 11233333331
Q ss_pred --CCCcC-CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 234 --EPEVV-TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 234 --~p~v~-~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
+-.+. ..... . . ..+..+.+..=| ..+||++..+++++.++.
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 111234444555 589999999999988773
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=91.04 E-value=0.2 Score=36.08 Aligned_cols=25 Identities=36% Similarity=0.476 Sum_probs=22.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~-~~sle~il~ 210 (342)
+||||||++|..|+.. |.+++++..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~~~l~~ 34 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTLEDLAN 34 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred cCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence 6899999999999998 899988765
No 41
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=90.95 E-value=0.2 Score=35.40 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=17.5
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ-HGSIETIL 209 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~-~~sle~il 209 (342)
+|.||||+||.+++.+ +.|++++.
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 6899999999999984 77999884
No 42
>PHA03065 Hypothetical protein; Provisional
Probab=90.81 E-value=3.4 Score=41.27 Aligned_cols=113 Identities=19% Similarity=0.350 Sum_probs=67.6
Q ss_pred HHHHHHHc--CCCeecCcC-cHHHHHHHHHH-----cCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHH
Q 019386 90 CKRLLKLM--GVPVVEAPS-EAEAQCAALCK-----SGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKI 161 (342)
Q Consensus 90 ~~~lL~~~--Gi~~i~Ap~-EAdaq~A~L~~-----~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v 161 (342)
+-+.|..+ +|.++...| .||-.+..-++ .|.=..++|.|-|.|+|.+-.-.-.+ ...+
T Consensus 150 l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki--------------I~t~ 215 (438)
T PHA03065 150 LESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI--------------IKTA 215 (438)
T ss_pred HHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH--------------HHhH
Confidence 34457777 999999999 99976655554 47666789999999999863210000 0111
Q ss_pred HHHhCCCH----HHH-HHHHHHhCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHHHhhcC
Q 019386 162 LEELNLTM----DQF-IDLCILSGCDYCDSIRGIG--GQT--ALKLIRQHGSIETILENINRERY 217 (342)
Q Consensus 162 ~~~lgl~~----~q~-id~~~L~G~Dy~~~IpGiG--~kt--A~~Li~~~~sle~il~~l~~~k~ 217 (342)
-+.|.+-| .-+ ...++.=||||-+|+-|+- +++ -.+|...| ++++++..|--..+
T Consensus 216 ~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~kny 279 (438)
T PHA03065 216 NQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLAIKNY 279 (438)
T ss_pred HHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHHhhhh
Confidence 11222211 112 2234455999999998864 432 24445454 47777777653333
No 43
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=90.53 E-value=0.2 Score=52.48 Aligned_cols=29 Identities=28% Similarity=0.416 Sum_probs=25.8
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 182 DYCDSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 182 Dy~~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
.-.++||||||++...||+.|||+++|.+
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~ 569 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYFGSLKGIKK 569 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 35578999999999999999999998865
No 44
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=90.52 E-value=0.23 Score=51.89 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=26.0
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 182 DYCDSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 182 Dy~~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
.-.++||||||++...|++.|||+++|.+
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 45
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=90.44 E-value=0.23 Score=31.01 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.8
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||+++|-.++.
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 579999999988764
No 46
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=90.43 E-value=0.22 Score=52.51 Aligned_cols=28 Identities=29% Similarity=0.520 Sum_probs=25.3
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 183 YCDSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 183 y~~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
-.++|||||++++.+|++.|||+++|..
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~ 580 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRA 580 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4468999999999999999999999875
No 47
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=90.12 E-value=0.23 Score=51.89 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 183 y~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
-.++||||||++..+|++.|||+++|.+.
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 55789999999999999999999998753
No 48
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.90 E-value=2.7 Score=38.01 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 253 EEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 253 ~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
.+.+..=| ..+||+...+.++++++.
T Consensus 152 ~~ea~~AL-~~LGy~~~ea~~al~~i~ 177 (197)
T PRK14603 152 AEDAVLAL-LALGFREAQVRSVVAELL 177 (197)
T ss_pred HHHHHHHH-HHcCCCHHHHHHHHHHHH
Confidence 34455555 589999999999998774
No 49
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.37 E-value=1.8 Score=39.09 Aligned_cols=108 Identities=20% Similarity=0.269 Sum_probs=55.5
Q ss_pred HHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC-
Q 019386 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (342)
Q Consensus 160 ~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~----~i~~~~~~~~~~~~f~- 233 (342)
+-..-||+ +.++--.|..|+ +|.|||||+|+.++..+ +.+++...+..... ++|- .=..-|..+.+
T Consensus 55 D~~~LYGF~t~~Er~lF~~Li------sVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIIlE 126 (196)
T PRK13901 55 DELKLFGFLNSSEREVFEELI------GVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKG-IGNKMAGKIFLK 126 (196)
T ss_pred CCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33445675 555555566665 47888888888888765 46667666542211 1221 11122222221
Q ss_pred -CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 234 -EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 234 -~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
.-.+...... .- .....+....=| ..+||++..+.+++..+.
T Consensus 127 LkdKl~~~~~~-~~--~~~~~~ea~~AL-~~LGy~~~ea~~al~~v~ 169 (196)
T PRK13901 127 LRGKLVKNDEL-ES--SLFKFKELEQSI-VNMGFDRKLVNSAIKEIM 169 (196)
T ss_pred HHHhhcccccc-cc--CcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 1101000000 00 111234444555 489999999998887664
No 50
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.89 E-value=0.74 Score=41.50 Aligned_cols=110 Identities=17% Similarity=0.276 Sum_probs=60.5
Q ss_pred HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhc---C-CCCCCCchHHHHHHhC
Q 019386 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRER---Y-QIPEDWPYQEARRLFK 233 (342)
Q Consensus 159 ~~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k---~-~i~~~~~~~~~~~~f~ 233 (342)
++...-||+ +.++--.|..|+ +|+|||||+|+.++..|+ .+.++..+.... . ++| ..-...|..+.+
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 334455786 566666666665 489999999999999886 677766653211 0 121 112223333211
Q ss_pred --CCCcC--CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 234 --EPEVV--TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 234 --~p~v~--~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
...+. ..... ... .....+.+...| ..+||+...+.+.+..+.
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 011235667777 689999999988887764
No 51
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=87.68 E-value=0.48 Score=50.23 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=26.3
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 182 Dy~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
.-.++|||||++++..||+.|||+++|.+.
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 355799999999999999999999998753
No 52
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.63 E-value=0.81 Score=41.54 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=32.0
Q ss_pred HHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 019386 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (342)
Q Consensus 160 ~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~ 213 (342)
+-..-||+ +.++--.|..|++ |.|||||+|+.++..+ +.++++..+.
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 33445675 5666666666654 7888999998888875 4677776664
No 53
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=85.51 E-value=0.7 Score=35.88 Aligned_cols=26 Identities=38% Similarity=0.524 Sum_probs=21.2
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHH
Q 019386 182 DYCDSIRGIGGQTALKLIRQHGSIET 207 (342)
Q Consensus 182 Dy~~~IpGiG~ktA~~Li~~~~sle~ 207 (342)
+....|||||+.+|..||.+.++++.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchh
Confidence 34457999999999999999887543
No 54
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.91 E-value=1.6 Score=39.21 Aligned_cols=107 Identities=16% Similarity=0.203 Sum_probs=58.6
Q ss_pred HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC
Q 019386 159 AKILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK 233 (342)
Q Consensus 159 ~~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~----~i~~~~~~~~~~~~f~ 233 (342)
++...-||+ +.++--.|..|+ +|.|||||+|+.++..+ +.+++.+.+..... ++|- .-..-|..+.+
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 344456776 555555566664 48889999999999865 57777776653211 1221 11222333321
Q ss_pred --CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 234 --EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 234 --~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
+-.+.. ... ......+.+..=| ..+||++..+++++..+.
T Consensus 127 ELkdK~~~-~~~----~~~~~~~e~~~AL-~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 127 ELKDEFES-AGI----KDMRIYHESLEAL-VSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHhhcc-ccC----CCcccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 111110 000 0011234455555 489999999999988774
No 55
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=84.38 E-value=0.83 Score=48.13 Aligned_cols=26 Identities=38% Similarity=0.662 Sum_probs=24.2
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 185 DSIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
++|||||++++..|++.|||+++|.+
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
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.33 E-value=1.7 Score=39.20 Aligned_cols=107 Identities=17% Similarity=0.222 Sum_probs=52.8
Q ss_pred HHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC--C
Q 019386 162 LEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK--E 234 (342)
Q Consensus 162 ~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~----~i~~~~~~~~~~~~f~--~ 234 (342)
..-||+ +.++--.|..|+ +|.|||||+|+.++..+ +.++++..+..... ++|- .-..-|..+.+ +
T Consensus 58 ~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpG-IGkKtAerIilELk 129 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPG-IGKKTAERIVLELK 129 (195)
T ss_pred ceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHHHH
Confidence 344665 455555555554 37788888888888754 46666666542211 1111 11112222221 0
Q ss_pred CCcC---CccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHH
Q 019386 235 PEVV---TDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIK 279 (342)
Q Consensus 235 p~v~---~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~ 279 (342)
-.+. ....... . .....+.+..=| ..+||++..+++++.++.
T Consensus 130 ~K~~~~~~~~~~~~-~-~~~~~~e~~~aL-~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 130 GKIDVRQLSGSTSP-A-VSALDRELSEIL-ISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHhccccccccccc-c-ccccHHHHHHHH-HHcCCCHHHHHHHHHHHh
Confidence 0000 0000000 0 011124455555 489999999999998774
No 57
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.29 E-value=1.8 Score=38.69 Aligned_cols=104 Identities=14% Similarity=0.245 Sum_probs=54.1
Q ss_pred HHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcC----CCCCCCchHHHHHHhC-
Q 019386 160 KILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERY----QIPEDWPYQEARRLFK- 233 (342)
Q Consensus 160 ~v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~----~i~~~~~~~~~~~~f~- 233 (342)
+-..-||+ +.++--.|..|+ +|.|||||+|+.++..+ +.+++...+..... ++|- .=..-|..+.+
T Consensus 56 d~~~LyGF~~~~Er~lF~~Li------~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpG-IGkKtAeRIilE 127 (183)
T PRK14601 56 DSNKLYGFLDKDEQKMFEMLL------KVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPG-IGPKSAKRIIAE 127 (183)
T ss_pred CCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCC-CCHHHHHHHHHH
Confidence 33445675 555555555554 37888888888888765 46677766643211 1221 11122222221
Q ss_pred -CCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHH
Q 019386 234 -EPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKI 278 (342)
Q Consensus 234 -~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l 278 (342)
+-.+. .... .....+...+=| ..+||++..+++++..+
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 011223444444 48999999999888766
No 58
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=83.90 E-value=0.84 Score=47.88 Aligned_cols=29 Identities=34% Similarity=0.635 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 183 y~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
..+.|||||++++.+|++.|||+++|..+
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 59
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=83.70 E-value=0.99 Score=41.67 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=24.6
Q ss_pred CCCCCCccHHHHHHHHHH-cCCHHHHHHH
Q 019386 184 CDSIRGIGGQTALKLIRQ-HGSIETILEN 211 (342)
Q Consensus 184 ~~~IpGiG~ktA~~Li~~-~~sle~il~~ 211 (342)
.+.|||||+++|..|+.. |+|+++|...
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 357899999999999999 9999988653
No 60
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=83.19 E-value=0.98 Score=48.08 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=25.7
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 183 y~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
-.+.|||||++++..|++.|||+++|.+.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 34579999999999999999999998873
No 61
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.01 E-value=1 Score=26.79 Aligned_cols=17 Identities=35% Similarity=0.520 Sum_probs=14.6
Q ss_pred CCCCCccHHHHHHHHHH
Q 019386 185 DSIRGIGGQTALKLIRQ 201 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li~~ 201 (342)
..|||||+++|..++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 36899999999998863
No 62
>PRK13766 Hef nuclease; Provisional
Probab=82.81 E-value=17 Score=39.27 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=23.3
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
+|||||+++|..|+..|||+++++.
T Consensus 719 ~ipgig~~~a~~Ll~~fgs~~~i~~ 743 (773)
T PRK13766 719 SLPDVGPVLARNLLEHFGSVEAVMT 743 (773)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 5899999999999999999998875
No 63
>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=82.18 E-value=4.6 Score=43.57 Aligned_cols=39 Identities=21% Similarity=0.480 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Q 019386 167 LTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENIN 213 (342)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~ 213 (342)
-+.+.++.|.. .| .||||||++|-+|+..|| ++.++.+.
T Consensus 75 ~~~~~i~~yL~-s~-----~~~GIG~~~A~~iv~~fg--~~~~~~i~ 113 (720)
T TIGR01448 75 TSKEGIVAYLS-SR-----SIKGVGKKLAQRIVKTFG--EAAFDVLD 113 (720)
T ss_pred CCHHHHHHHHh-cC-----CCCCcCHHHHHHHHHHhC--HhHHHHHH
Confidence 35677777654 33 699999999999999999 45555554
No 64
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=80.09 E-value=1.4 Score=46.18 Aligned_cols=30 Identities=30% Similarity=0.482 Sum_probs=26.3
Q ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 182 DYCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 182 Dy~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
.-.|+|||||+++...|++.|||+++|.+.
T Consensus 530 s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 530 SSLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred CccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 355799999999999999999999988754
No 65
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.62 E-value=1.7 Score=38.82 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=33.8
Q ss_pred EEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 155 ~~~~~~v~~~l-gl~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
-+.+..-+.-+ .+++++|.. ++..| |..- .+||||+|||-++|-+
T Consensus 80 GIGpK~Al~ILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 80 GIGANTAMAVCSSLDVNSFYK-ALSLG-DESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CccHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 35566666666 478998875 55666 6663 6899999999999976
No 66
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=79.59 E-value=1.6 Score=40.88 Aligned_cols=26 Identities=42% Similarity=0.724 Sum_probs=23.8
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
++||||++.|..|+..|||+++++..
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 57999999999999999999998764
No 67
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.51 E-value=2.4 Score=38.35 Aligned_cols=45 Identities=24% Similarity=0.326 Sum_probs=33.5
Q ss_pred EEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 155 ~~~~~~v~~~l-gl~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
-+.+..-+.-+ .+++++|.. ++..| |... .+||||+|||-++|-+
T Consensus 79 GIGPK~ALaILs~~~~~el~~-aI~~~-D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 79 GIGPRAALRVLSGIKYNEFRD-AIDRE-DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHH
Confidence 35566666666 478998875 45566 7663 7999999999999965
No 68
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.40 E-value=3.6 Score=37.16 Aligned_cols=44 Identities=23% Similarity=0.243 Sum_probs=22.7
Q ss_pred EeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 156 ~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
+.+..-+.-++ +++++|+. ++..| |..- .+||||+|||-++|-+
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 34444444453 55665553 23344 4442 4566666666666654
No 69
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=75.55 E-value=6 Score=38.91 Aligned_cols=53 Identities=30% Similarity=0.470 Sum_probs=39.0
Q ss_pred HHHHHHHh-CCCHHHHHHH---HHHhCCCC----CC------------CCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 158 VAKILEEL-NLTMDQFIDL---CILSGCDY----CD------------SIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 158 ~~~v~~~l-gl~~~q~id~---~~L~G~Dy----~~------------~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
.+++++.+ .++.+++.|+ +-++|-.- .| +||+|++..|..|+.+|||+.+++.
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 56677766 5777777665 45566211 11 1589999999999999999999986
No 70
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.17 E-value=4.1 Score=36.52 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=34.7
Q ss_pred EEeHHHHHHHh-CCCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 019386 155 EFEVAKILEEL-NLTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 155 ~~~~~~v~~~l-gl~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~~ 202 (342)
-+.+..-+.-+ ++++++|+. ++..| |..- .+||||+|||-+||-+-
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 35666667777 478998885 45566 6653 68999999999999763
No 71
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.14 E-value=4.4 Score=36.31 Aligned_cols=47 Identities=21% Similarity=0.352 Sum_probs=34.5
Q ss_pred EEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC-CCCCccHHHHHHHHHHc
Q 019386 154 MEFEVAKILEELN-LTMDQFIDLCILSGCDYCD-SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 154 ~~~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~-~IpGiG~ktA~~Li~~~ 202 (342)
.-+.+..-+.-+. +++++|+. ++-.| |..- .+||||+|||-++|-+.
T Consensus 79 ~GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~vpGIGkKtAerIilEL 127 (186)
T PRK14600 79 SGVNYKTAMSILSKLTPEQLFS-AIVNE-DKAALKVNGIGEKLINRIITEL 127 (186)
T ss_pred CCcCHHHHHHHHccCCHHHHHH-HHHcC-CHhheECCCCcHHHHHHHHHHH
Confidence 3466666677775 78999886 44456 6543 78999999999999763
No 72
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.70 E-value=3.6 Score=37.08 Aligned_cols=46 Identities=26% Similarity=0.308 Sum_probs=33.9
Q ss_pred EEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHHc
Q 019386 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 155 ~~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~~ 202 (342)
-+.+..-+.-++ +++++|+. ++..| |..- .+||||+|||-+|+-+.
T Consensus 80 GIGpK~Al~iLs~~~~~el~~-aI~~~-D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 80 GVGPKAALNLLSSGTPDELQL-AIAGG-DVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CcCHHHHHHHHcCCCHHHHHH-HHHhC-CHHHHhhCCCCCHHHHHHHHHHH
Confidence 355666666665 78998875 45555 6663 68999999999999764
No 73
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.93 E-value=4.4 Score=36.78 Aligned_cols=45 Identities=20% Similarity=0.306 Sum_probs=33.5
Q ss_pred EEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 155 EFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 155 ~~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
-+.+..-+.-++ +++++|+. ++..| |..- .+||||+|||-+||-+
T Consensus 81 GIGpK~Al~iLs~~~~~~l~~-aI~~~-D~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 81 KVGAKTALAILSQFRPDDLRR-LVAEE-DVAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred CcCHHHHHHHHhhCCHHHHHH-HHHhC-CHHHHhcCCCcCHHHHHHHHHH
Confidence 356666666665 78888875 45566 6663 7999999999999976
No 74
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=73.25 E-value=3 Score=35.13 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=19.6
Q ss_pred CCCccHHHHHHHHHH--cCCHHHHHH
Q 019386 187 IRGIGGQTALKLIRQ--HGSIETILE 210 (342)
Q Consensus 187 IpGiG~ktA~~Li~~--~~sle~il~ 210 (342)
+|||||..|-++|+. |.++|++++
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 689999999999973 668888764
No 75
>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=71.79 E-value=3.5 Score=43.97 Aligned_cols=24 Identities=29% Similarity=0.558 Sum_probs=13.9
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETIL 209 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il 209 (342)
||||||+++|..|.+.|+|++++.
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~ 525 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLK 525 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHH
Confidence 355666666666666666655543
No 76
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=69.73 E-value=3.9 Score=44.72 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.1
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
++||||+++|..|+.+|+|+++++.
T Consensus 761 ~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred HCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 4799999999999999999999875
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=69.13 E-value=4.5 Score=43.44 Aligned_cols=25 Identities=36% Similarity=0.622 Sum_probs=21.7
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
+|||||+++|..|++.|+|++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHh
Confidence 4789999999999999999988764
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=68.34 E-value=11 Score=32.82 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=28.0
Q ss_pred cCCCeecCcC--cHHHHHHHHHHc----CCeEEEecCCCCcccc
Q 019386 97 MGVPVVEAPS--EAEAQCAALCKS----GQVYAVASEDMDSLTF 134 (342)
Q Consensus 97 ~Gi~~i~Ap~--EAdaq~A~L~~~----g~v~~V~S~DsD~l~f 134 (342)
-||.++.++. .||+.|-.|+.. +.-..|+|+|...-..
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 4778887773 999999888762 4555788988776544
No 79
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=68.10 E-value=5.3 Score=33.07 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=14.8
Q ss_pred CCCCccHHHHHHHHHHc
Q 019386 186 SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~ 202 (342)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 57999999999999874
No 80
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=65.59 E-value=7.3 Score=35.36 Aligned_cols=73 Identities=26% Similarity=0.317 Sum_probs=46.6
Q ss_pred CeEEEecCCCCcccccCCe-----eEEEeecCCCCCCccEEEeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCcc
Q 019386 120 QVYAVASEDMDSLTFGAPR-----FLRHLMDPSSRKIPVMEFEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIG 191 (342)
Q Consensus 120 ~v~~V~S~DsD~l~fg~~~-----v~~~l~~~~~~~~~~~~~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~--~IpGiG 191 (342)
++.-++.+|. ..+||-.. +++.+. .+.-+...--+.-+. ++++.|+.. +-.+ |++- .+||||
T Consensus 48 ~t~~~vREd~-~~LyGF~~~~ER~lF~~Li-------sVnGIGpK~ALaiLs~~~~~~l~~a-I~~~-d~~~L~k~PGIG 117 (201)
T COG0632 48 FTHLVVREDA-HLLYGFLTEEERELFRLLI-------SVNGIGPKLALAILSNLDPEELAQA-IANE-DVKALSKIPGIG 117 (201)
T ss_pred EEEEeehhhH-HHHcCCCCHHHHHHHHHHH-------ccCCccHHHHHHHHcCCCHHHHHHH-HHhc-ChHhhhcCCCCC
Confidence 3566778888 77777321 111111 122355566666664 588888864 4455 6663 689999
Q ss_pred HHHHHHHHHHc
Q 019386 192 GQTALKLIRQH 202 (342)
Q Consensus 192 ~ktA~~Li~~~ 202 (342)
.|+|-+|+-+-
T Consensus 118 kKtAerivleL 128 (201)
T COG0632 118 KKTAERIVLEL 128 (201)
T ss_pred HHHHHHHHHHH
Confidence 99999999763
No 81
>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=65.49 E-value=4.6 Score=25.41 Aligned_cols=13 Identities=54% Similarity=0.695 Sum_probs=10.3
Q ss_pred CCCCccHHHHHHH
Q 019386 186 SIRGIGGQTALKL 198 (342)
Q Consensus 186 ~IpGiG~ktA~~L 198 (342)
.++|||++|+.+|
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 82
>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=63.55 E-value=8.6 Score=32.86 Aligned_cols=89 Identities=16% Similarity=0.223 Sum_probs=57.9
Q ss_pred hHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccccCCe--eEEEeecCCCCCCccEEEeHHHHH
Q 019386 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTFGAPR--FLRHLMDPSSRKIPVMEFEVAKIL 162 (342)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~--v~~~l~~~~~~~~~~~~~~~~~v~ 162 (342)
.|+..+-+.|+.+|+..+.++...|+.+..++....- +++|.|.+++-..... ++. + .+.. ..-.+..|+
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~~~~~~~~~~~l-i-~~~~-----~~~QL~ev~ 78 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLLKRRRVSGGVIL-I-RSDD-----PEEQLREVL 78 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHHHhhccCCEEE-E-cCCC-----HHHHHHHHH
Confidence 4566788899999999999998889999999876433 3789999987664321 221 2 1110 112345677
Q ss_pred HHhCCCH--HHHHHHHHHhCC
Q 019386 163 EELNLTM--DQFIDLCILSGC 181 (342)
Q Consensus 163 ~~lgl~~--~q~id~~~L~G~ 181 (342)
+.+++.+ +.+..-|..|++
T Consensus 79 ~~~~l~~~~~~~~sRC~~CN~ 99 (147)
T PF01927_consen 79 ERFGLKLRLDPIFSRCPKCNG 99 (147)
T ss_pred HHcCCccccCCCCCccCCCCc
Confidence 7777654 333345666663
No 83
>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=63.35 E-value=13 Score=31.89 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHc
Q 019386 85 QHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKS 118 (342)
Q Consensus 85 ~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~ 118 (342)
+.+.++.+-|+.+|++.++-.|++...+..|++.
T Consensus 53 ~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~ 86 (165)
T PF00875_consen 53 ESLADLQESLRKLGIPLLVLRGDPEEVLPELAKE 86 (165)
T ss_dssp HHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCcceEEEecchHHHHHHHHHh
Confidence 4567788888999999999999999999888774
No 84
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=62.65 E-value=7.8 Score=37.33 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=21.4
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQH--GSIETILENI 212 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~--~sle~il~~l 212 (342)
+||||||++|.+|. +. .|++++....
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 54 5888887753
No 85
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=62.43 E-value=6.7 Score=38.30 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=20.9
Q ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHG--SIETILEN 211 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~--sle~il~~ 211 (342)
.||||||++|..|.. .| |++++.+.
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 54 78888654
No 86
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=62.25 E-value=5.7 Score=42.49 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=16.8
Q ss_pred HHHHHHHHHcCCCeecC------cCcHHHHHHHHH
Q 019386 88 DDCKRLLKLMGVPVVEA------PSEAEAQCAALC 116 (342)
Q Consensus 88 ~~~~~lL~~~Gi~~i~A------p~EAdaq~A~L~ 116 (342)
.+..+.|+.+|+|+... ..|+.+.+.++.
T Consensus 239 ~e~l~~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~ 273 (665)
T PRK07956 239 SEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIE 273 (665)
T ss_pred HHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHH
Confidence 34666788888887521 114555555554
No 87
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=59.98 E-value=9.9 Score=32.76 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=18.7
Q ss_pred CCCCccHHHHHHHHHH------cCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ------HGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~------~~sle~il~ 210 (342)
.+||||+++|.++|.. |.+++++..
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 4689999999999973 456666543
No 88
>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=59.71 E-value=8.3 Score=30.62 Aligned_cols=31 Identities=29% Similarity=0.199 Sum_probs=21.6
Q ss_pred CCCCccHHHHHHHHH-HcCCH--------HHHHHHHHhhc
Q 019386 186 SIRGIGGQTALKLIR-QHGSI--------ETILENINRER 216 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~-~~~sl--------e~il~~l~~~k 216 (342)
.|||||+.+|..|+. -+.++ +++++.+....
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~ 55 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALT 55 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHc
Confidence 589999999999986 34444 45556665443
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=57.94 E-value=12 Score=27.42 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=13.3
Q ss_pred CCCccHHHHHHHHHH
Q 019386 187 IRGIGGQTALKLIRQ 201 (342)
Q Consensus 187 IpGiG~ktA~~Li~~ 201 (342)
+||||+++|..||..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 688999999999987
No 90
>PRK08609 hypothetical protein; Provisional
Probab=56.07 E-value=19 Score=37.82 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=19.6
Q ss_pred CCCCccHHHHHHHHHHc--CCHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQH--GSIETILENIN 213 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~--~sle~il~~l~ 213 (342)
.||||||++|.+|-.+. .|++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 57888888888887654 36676665543
No 91
>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=55.39 E-value=23 Score=30.17 Aligned_cols=44 Identities=25% Similarity=0.290 Sum_probs=36.0
Q ss_pred cCHhHHHHHHHHHHHcCCC-----eecCcC--cHHHHHHHHHHcCCeEEEe
Q 019386 82 VTKQHNDDCKRLLKLMGVP-----VVEAPS--EAEAQCAALCKSGQVYAVA 125 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi~-----~i~Ap~--EAdaq~A~L~~~g~v~~V~ 125 (342)
|+..+.+-+.+.|+..|+. ++..|| |-=-.+..|++.|..|+|+
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 4567888999999999975 788999 7777888898887777776
No 92
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=55.01 E-value=14 Score=32.03 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 019386 169 MDQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 169 ~~q~id~~~L~G~Dy~~~---------IpGiG~ktA~~Li~~~~ 203 (342)
+++|-.+.-++|+|..++ |.|||+.+|..++...|
T Consensus 8 ~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 8 ADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 357888888999888765 57999999999999876
No 93
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=54.61 E-value=9 Score=40.67 Aligned_cols=27 Identities=37% Similarity=0.570 Sum_probs=24.3
Q ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 185 DSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
-|||.||+++|..|.+.|+|++++++.
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 478999999999999999999998764
No 94
>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=54.29 E-value=8.7 Score=30.94 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=24.1
Q ss_pred cCcHHHHHHHHHHcCCeEEEecCCCCccc
Q 019386 105 PSEAEAQCAALCKSGQVYAVASEDMDSLT 133 (342)
Q Consensus 105 p~EAdaq~A~L~~~g~v~~V~S~DsD~l~ 133 (342)
+-..|+-+..++..+.+++++|+|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 44677877888888889999999999874
No 95
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=49.07 E-value=28 Score=30.41 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=36.1
Q ss_pred cCHhHHHHHHHHHHHcC-----CCeecCcC--cHHHHHHHHHHcCCeEEEe
Q 019386 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~G-----i~~i~Ap~--EAdaq~A~L~~~g~v~~V~ 125 (342)
||..+++-+.+.|...| |.++..|| |-=..+..|++.|..|+|+
T Consensus 24 It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiI 74 (158)
T PRK12419 24 IVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIV 74 (158)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 45678888999999999 67888999 8878888888887777766
No 96
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=49.06 E-value=42 Score=33.63 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=8.8
Q ss_pred CCCcEEEEeCC
Q 019386 27 GMKPIYVFDGQ 37 (342)
Q Consensus 27 gi~Pv~VFDG~ 37 (342)
.+-||||||..
T Consensus 28 ~vl~vfi~dp~ 38 (429)
T TIGR02765 28 TLIPLYCFDPR 38 (429)
T ss_pred eEEEEEEECch
Confidence 37899999964
No 97
>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=48.85 E-value=23 Score=31.76 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=30.5
Q ss_pred EeHHHHHHHhC-CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 156 FEVAKILEELN-LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 156 ~~~~~v~~~lg-l~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
+.....+.-++ ++++++...+. .| |..- .|||||+|||-+++-+
T Consensus 80 IGpK~Al~iL~~~~~~el~~aI~-~~-d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 80 VGPKLALAILSNMSPEEFVYAIE-TE-EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCHHHHHHHHhcCCHHHHHHHHH-hC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 55555566665 47877775433 44 5543 6899999999999844
No 98
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=48.72 E-value=14 Score=26.91 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=14.5
Q ss_pred CCCCccHHHHHHHHHHcCCHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIE 206 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle 206 (342)
.|||||++.|..+..-|...+
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 99
>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=47.86 E-value=34 Score=29.28 Aligned_cols=44 Identities=30% Similarity=0.356 Sum_probs=37.0
Q ss_pred cCHhHHHHHHHHHHHcCC-----CeecCcC--cHHHHHHHHHHcCCeEEEe
Q 019386 82 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi-----~~i~Ap~--EAdaq~A~L~~~g~v~~V~ 125 (342)
++..+++.+.+.|...|+ .++..|| |-=-.+..|.+.+.+|+|+
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 346678889999999987 7888898 8888999999998888887
No 100
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=46.16 E-value=30 Score=29.89 Aligned_cols=35 Identities=31% Similarity=0.549 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCccHHHHHHHHHHcC
Q 019386 169 MDQFIDLCILSGCDYCDS---------IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 169 ~~q~id~~~L~G~Dy~~~---------IpGiG~ktA~~Li~~~~ 203 (342)
.++|-.+.-++|+|-.++ |.|||+.+|..++.+.|
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 346667777899888765 46999999999999875
No 101
>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=44.21 E-value=28 Score=27.81 Aligned_cols=40 Identities=18% Similarity=0.325 Sum_probs=33.3
Q ss_pred HHHHhCC-CHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHH
Q 019386 161 ILEELNL-TMDQFIDLCILSGCDYCDSIRGIGGQTALKLIR 200 (342)
Q Consensus 161 v~~~lgl-~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~ 200 (342)
-+..-|| |-..+++.+...|.-.-..|||||+..|-.+..
T Consensus 28 ~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~a 68 (96)
T PF12482_consen 28 RLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEA 68 (96)
T ss_pred HHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHH
Confidence 3555687 789999999999977778999999999887654
No 102
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=44.20 E-value=61 Score=28.48 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=41.5
Q ss_pred HhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccc
Q 019386 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (342)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~f 134 (342)
..|+-.+-++|+.||.+.+..-.+.|+.+..++...-. +++|-|.-++-.
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 56788899999999999998888899999888875332 478999988887
No 103
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=43.44 E-value=15 Score=29.79 Aligned_cols=44 Identities=27% Similarity=0.456 Sum_probs=28.7
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC------------CCCccHHHHHHHHHHc
Q 019386 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDS------------IRGIGGQTALKLIRQH 202 (342)
Q Consensus 156 ~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~------------IpGiG~ktA~~Li~~~ 202 (342)
+..+++++.+ ...|+|.-..+|.|-+.- |.|+||.+|..|++..
T Consensus 15 l~~d~L~~~l---e~~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l 70 (104)
T PF14635_consen 15 LPKDKLLEAL---ERAFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKAL 70 (104)
T ss_dssp S-HHHHHHHH---HHHHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHH---HHHHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHH
Confidence 4455555555 466888888888876532 5799999999999863
No 104
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=43.29 E-value=12 Score=36.03 Aligned_cols=30 Identities=33% Similarity=0.281 Sum_probs=26.3
Q ss_pred HhHHHHHHHHHHHcCCCeecCcCcHHHHHHH
Q 019386 84 KQHNDDCKRLLKLMGVPVVEAPSEAEAQCAA 114 (342)
Q Consensus 84 ~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~ 114 (342)
..+......+|+.+|+| +.+|.|++||+|+
T Consensus 103 ~~~~~~~~~~l~~~G~e-add~i~t~A~~a~ 132 (310)
T COG0258 103 ELLVALGIPLLELMGIE-ADDPIETLAQKAY 132 (310)
T ss_pred HHHHHhCcHhhhcCCCC-cchhHHHHHHHHH
Confidence 44566778899999999 9999999999999
No 105
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=43.02 E-value=39 Score=29.30 Aligned_cols=44 Identities=30% Similarity=0.353 Sum_probs=34.9
Q ss_pred cCHhHHHHHHHHHHHcC-----CCeecCcC--cHHHHHHHHHHcCCeEEEe
Q 019386 82 VTKQHNDDCKRLLKLMG-----VPVVEAPS--EAEAQCAALCKSGQVYAVA 125 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~G-----i~~i~Ap~--EAdaq~A~L~~~g~v~~V~ 125 (342)
|+..+++-+.+.|...| |.++..|| |-=-.+..|++.+..|+|+
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 44678888999999999 45677899 7777888888887777776
No 106
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.99 E-value=17 Score=32.63 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHhCCCCCC--CCCCccHHHHHHHHHH
Q 019386 167 LTMDQFIDLCILSGCDYCD--SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~--~IpGiG~ktA~~Li~~ 201 (342)
+++++|+. ++..+ |..- .|||||+|||-+++-+
T Consensus 93 ~~~~~l~~-aI~~~-D~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 93 MNAEALAS-AIISG-NAELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CCHHHHHH-HHHhC-CHHHHHhCCCCCHHHHHHHHHH
Confidence 56777664 34455 6663 6899999999998865
No 107
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=42.88 E-value=42 Score=28.70 Aligned_cols=44 Identities=30% Similarity=0.308 Sum_probs=35.4
Q ss_pred cCHhHHHHHHHHHHHcCC-----CeecCcC--cHHHHHHHHHHcCCeEEEe
Q 019386 82 VTKQHNDDCKRLLKLMGV-----PVVEAPS--EAEAQCAALCKSGQVYAVA 125 (342)
Q Consensus 82 vt~~~~~~~~~lL~~~Gi-----~~i~Ap~--EAdaq~A~L~~~g~v~~V~ 125 (342)
|+..+++-+.+.|...|+ .++..|| |-=-.+..|++.+..|+|+
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 456788889999999996 5788898 8777888888877677766
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=42.43 E-value=23 Score=27.75 Aligned_cols=50 Identities=22% Similarity=0.173 Sum_probs=37.8
Q ss_pred ccccCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccc
Q 019386 79 TVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF 134 (342)
Q Consensus 79 ~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~f 134 (342)
.+.++.+....+.++....+ .+-+|+.++.++...-+..++|.|.|+..+
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 557999999999877777777999997544
No 109
>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=42.33 E-value=65 Score=32.56 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=10.5
Q ss_pred cHHHHHHHHHHc
Q 019386 191 GGQTALKLIRQH 202 (342)
Q Consensus 191 G~ktA~~Li~~~ 202 (342)
|...|.+.|..|
T Consensus 225 Ge~aA~~~L~~F 236 (454)
T TIGR00591 225 GTTAGLIMLESF 236 (454)
T ss_pred cHHHHHHHHHHH
Confidence 899999988886
No 110
>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=41.50 E-value=30 Score=29.71 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=13.9
Q ss_pred CCCccHHHHHHHHHHcC
Q 019386 187 IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 187 IpGiG~ktA~~Li~~~~ 203 (342)
|.|||+.+|..+++..+
T Consensus 26 I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 26 IKGIGRRFARAIARKLG 42 (144)
T ss_pred eeccCHHHHHHHHHHcC
Confidence 57899999998888765
No 111
>PRK00076 recR recombination protein RecR; Reviewed
Probab=41.29 E-value=17 Score=32.86 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.9
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 15 KLPGIGPKSAQRLAF 29 (196)
T ss_pred HCCCCCHHHHHHHHH
Confidence 679999999988864
No 112
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.28 E-value=17 Score=32.81 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.8
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||+|+|.+|.-
T Consensus 15 ~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 15 KLPGIGPKSAQRLAF 29 (195)
T ss_pred HCCCCCHHHHHHHHH
Confidence 579999999988854
No 113
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=40.47 E-value=84 Score=27.13 Aligned_cols=36 Identities=28% Similarity=0.482 Sum_probs=25.8
Q ss_pred HHHHHhhhccccCHhHHHHHHHHHHHcCCCeecCcC
Q 019386 71 DIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (342)
Q Consensus 71 ~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~ 106 (342)
++.+|-.+...-...|.......|+.+|||++....
T Consensus 91 EL~~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 91 ELDKFDEKVYKASKQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeeCCC
Confidence 455565554455567788888899999999976654
No 114
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=40.09 E-value=21 Score=33.16 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=25.5
Q ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 183 YCDSIRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 183 y~~~IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
+...||||+...|..|+..|||++.|+..
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 115
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=39.47 E-value=16 Score=32.88 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.3
Q ss_pred CCCCCccHHHHHHHH
Q 019386 185 DSIRGIGGQTALKLI 199 (342)
Q Consensus 185 ~~IpGiG~ktA~~Li 199 (342)
..+||||||+|.++.
T Consensus 15 ~kLPGvG~KsA~R~A 29 (198)
T COG0353 15 KKLPGVGPKSAQRLA 29 (198)
T ss_pred hhCCCCChhHHHHHH
Confidence 368999999988764
No 116
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=38.97 E-value=1.5e+02 Score=25.52 Aligned_cols=68 Identities=22% Similarity=0.260 Sum_probs=40.0
Q ss_pred CCCchhhHHHHHHHhhhhhchHHHHHHHHcCCHHHHHHHhhhccccCHhHHHHHHHHHHHcCCCeecCcCcHHHHHHHHH
Q 019386 37 QPPDLKKQELAKRYSKRADATDDLAEAVEAGNKEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPSEAEAQCAALC 116 (342)
Q Consensus 37 ~~~~~K~~~~~~rk~~R~~~~~~l~~a~~~g~~~~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~ 116 (342)
..|++|..+..+++++|..+ +...|..-|+..|---+-.-..-.++++.||
T Consensus 5 r~pt~kErEnnk~RERrRRA-----------------------------IaakIfaGLR~~Gny~Lp~~aD~NeVLkALc 55 (150)
T PF05687_consen 5 RRPTWKERENNKRRERRRRA-----------------------------IAAKIFAGLRAHGNYKLPKHADNNEVLKALC 55 (150)
T ss_pred ccccHhhhHHHHHHHHHHHH-----------------------------HHHHHHHHHHHhcCCCCCCcCCHHHHHHHHH
Confidence 35778888877776665422 2233455666666644444446667777777
Q ss_pred Hc-CCeEEEecCCCCcccccC
Q 019386 117 KS-GQVYAVASEDMDSLTFGA 136 (342)
Q Consensus 117 ~~-g~v~~V~S~DsD~l~fg~ 136 (342)
+. |. |+.+|-..+--++
T Consensus 56 ~eAGw---~Ve~DGTtyr~~~ 73 (150)
T PF05687_consen 56 REAGW---TVEPDGTTYRKGC 73 (150)
T ss_pred HhCCE---EEccCCCeeccCC
Confidence 74 54 3456666555444
No 117
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=38.29 E-value=93 Score=29.29 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=18.9
Q ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQHGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~sle~il~ 210 (342)
.+.|||+++|.++=.-|.+.-....
T Consensus 218 ~v~gig~k~A~~I~~~~~t~~~~~~ 242 (254)
T COG1948 218 KVKGIGEKKAREIYRFLRTEYKLIE 242 (254)
T ss_pred HhcCccHHHHHHHHHHHhchhhhhc
Confidence 3689999999998877777554443
No 118
>PRK13844 recombination protein RecR; Provisional
Probab=37.38 E-value=21 Score=32.31 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=12.9
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||+|+|.+|.-
T Consensus 19 ~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 19 KLPTIGKKSSQRLAL 33 (200)
T ss_pred HCCCCCHHHHHHHHH
Confidence 679999999988864
No 119
>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=36.48 E-value=31 Score=27.80 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=15.3
Q ss_pred CCCCccHHHHHHHHHHcC
Q 019386 186 SIRGIGGQTALKLIRQHG 203 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~ 203 (342)
.|.|||+.+|..++...+
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 378999999999988765
No 120
>PRK10702 endonuclease III; Provisional
Probab=36.34 E-value=63 Score=29.41 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=11.9
Q ss_pred CCCccHHHHHHHHH
Q 019386 187 IRGIGGQTALKLIR 200 (342)
Q Consensus 187 IpGiG~ktA~~Li~ 200 (342)
+||||++||--++.
T Consensus 114 lpGVG~ktA~~ill 127 (211)
T PRK10702 114 LPGVGRKTANVVLN 127 (211)
T ss_pred CCcccHHHHHHHHH
Confidence 69999999987664
No 121
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=35.75 E-value=89 Score=31.81 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=10.3
Q ss_pred ccHHHHHHHHHHc
Q 019386 190 IGGQTALKLIRQH 202 (342)
Q Consensus 190 iG~ktA~~Li~~~ 202 (342)
.|...|.+.|..|
T Consensus 201 gGe~~A~~~L~~F 213 (475)
T TIGR02766 201 PGWSNADKALTEF 213 (475)
T ss_pred CccHHHHHHHHHH
Confidence 4888888888776
No 122
>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=34.24 E-value=45 Score=29.63 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.2
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||++||--++.
T Consensus 110 ~l~GIG~ktA~~ill 124 (191)
T TIGR01083 110 KLPGVGRKTANVVLN 124 (191)
T ss_pred hCCCCcHHHHHHHHH
Confidence 379999999987764
No 123
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=33.04 E-value=1.7e+02 Score=26.75 Aligned_cols=103 Identities=17% Similarity=0.210 Sum_probs=59.4
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHH--HHHHhCCCC
Q 019386 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQE--ARRLFKEPE 236 (342)
Q Consensus 159 ~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~--~~~~f~~p~ 236 (342)
+.+|+..|.+|+|+..-+.=+. +. ..|.+...-..++..-+..++.+..+-. .....++|.|.+ |.-+|.--.
T Consensus 76 ~Alc~a~~~dp~~~r~dA~~l~-~~---a~~~s~~~l~~~l~~~~~~~~~l~~~~~-~~~~~~~f~YSRl~AIGL~~LLe 150 (206)
T PLN03060 76 KAYIEALGEDPDQYRKDAKKLE-EW---ASSQSASGIADFNSGDGEVEAVLKDIAE-RAAGKTKFHYSRFFAIGLFRLLE 150 (206)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-HH---HhcCCHHHHHHHHhcccccchHHHHHHH-HhhcCCCcchHHHHHHHHHHHHH
Confidence 4567778889988876655444 22 2456666667777655554444443211 112346677754 666664111
Q ss_pred cCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHH
Q 019386 237 VVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEK 277 (342)
Q Consensus 237 v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~ 277 (342)
.. . -. |.+.+.+++ +.+|++.++|.+-|.-
T Consensus 151 ~a--~------~~--d~~~l~~l~-~~L~ls~~kv~kDL~l 180 (206)
T PLN03060 151 CA--K------AS--DPAVLEKLS-KALNVSKRSVDRDLDV 180 (206)
T ss_pred Hc--C------CC--CHHHHHHHH-HHcCCCHHHHHhhHHH
Confidence 11 0 01 445666676 8999999999876543
No 124
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=32.85 E-value=32 Score=31.38 Aligned_cols=17 Identities=35% Similarity=0.614 Sum_probs=14.3
Q ss_pred CCCCccHHHHHHHHHHc
Q 019386 186 SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~ 202 (342)
++||||+|||--++...
T Consensus 123 ~lpGIG~KTAd~vL~~~ 139 (208)
T PRK01229 123 NIKGIGYKEASHFLRNV 139 (208)
T ss_pred cCCCCcHHHHHHHHHHc
Confidence 78999999998888533
No 125
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=32.67 E-value=54 Score=25.35 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=20.8
Q ss_pred CCCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ-----HGSIETILENI 212 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~-----~~sle~il~~l 212 (342)
.|+|||...|.+++.. |.|+++++..+
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 4789999999999975 56888888776
No 126
>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=30.70 E-value=95 Score=23.62 Aligned_cols=45 Identities=16% Similarity=0.215 Sum_probs=21.5
Q ss_pred HHHHHcCC--HHHHHHHhhhccccCHhHHHHHHHHHHHcCCCeecCcC
Q 019386 61 AEAVEAGN--KEDIEKFSKRTVKVTKQHNDDCKRLLKLMGVPVVEAPS 106 (342)
Q Consensus 61 ~~a~~~g~--~~~~~k~~~r~~~vt~~~~~~~~~lL~~~Gi~~i~Ap~ 106 (342)
......|. ..++..+.. ...+++++++.+...|..+||.++....
T Consensus 14 ~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~Vvd~~~ 60 (82)
T PF03979_consen 14 EKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEVVDEEE 60 (82)
T ss_dssp HHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----B--S-
T ss_pred HHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 33344443 344444443 2236688999999999999999998544
No 127
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=30.64 E-value=4.8e+02 Score=24.86 Aligned_cols=27 Identities=11% Similarity=0.015 Sum_probs=14.7
Q ss_pred HHHHHHHHcCCCeecCcCcHHHHHHHH
Q 019386 89 DCKRLLKLMGVPVVEAPSEAEAQCAAL 115 (342)
Q Consensus 89 ~~~~lL~~~Gi~~i~Ap~EAdaq~A~L 115 (342)
.++.+.+.+++|+-+.-+-++-.-+.|
T Consensus 81 vI~~l~~~~~~~ISIDT~~~~va~~AL 107 (282)
T PRK11613 81 VVEAIAQRFEVWISVDTSKPEVIRESA 107 (282)
T ss_pred HHHHHHhcCCCeEEEECCCHHHHHHHH
Confidence 344444445677666666555554545
No 128
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=30.35 E-value=1e+02 Score=23.96 Aligned_cols=30 Identities=23% Similarity=0.506 Sum_probs=19.0
Q ss_pred CccHHHHHHHHHHcCCHHHHHHHHHhhcCCCC
Q 019386 189 GIGGQTALKLIRQHGSIETILENINRERYQIP 220 (342)
Q Consensus 189 GiG~ktA~~Li~~~~sle~il~~l~~~k~~i~ 220 (342)
||++..|.+|.+.||+ +.++.+++.+|.+-
T Consensus 19 gl~~~~a~kl~~~yg~--~ai~~l~~nPY~L~ 48 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD--DAIEILKENPYRLI 48 (94)
T ss_dssp T--HHHHHHHHHHH-T--THHHHHHH-STCCC
T ss_pred CCCHHHHHHHHHHHhH--HHHHHHHHChHHHH
Confidence 5888999999999986 55666666555543
No 129
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=30.17 E-value=96 Score=31.66 Aligned_cols=32 Identities=13% Similarity=0.200 Sum_probs=18.0
Q ss_pred HHHHHHHHHHcCCCeecCcC----cHHHHHHHHHHc
Q 019386 87 NDDCKRLLKLMGVPVVEAPS----EAEAQCAALCKS 118 (342)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~Ap~----EAdaq~A~L~~~ 118 (342)
+.++.+-|+.+|++.++.-| +..+++..|++.
T Consensus 59 L~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~ 94 (472)
T PRK10674 59 LNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQ 94 (472)
T ss_pred HHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHH
Confidence 44455556666666666543 456666666553
No 130
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=29.90 E-value=53 Score=25.87 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=31.0
Q ss_pred HHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcc-----cccCCeeE
Q 019386 95 KLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSL-----TFGAPRFL 140 (342)
Q Consensus 95 ~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l-----~fg~~~v~ 140 (342)
.......+..+..||+.+..++..+...+|+|+|.++- .-|.|.++
T Consensus 40 ~~~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~ 90 (101)
T PF04900_consen 40 ERRKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIY 90 (101)
T ss_pred HhhcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEE
Confidence 33334444446689999999997554477999999874 34566554
No 131
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=29.38 E-value=50 Score=22.88 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=30.1
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHH-hCCCCCCCCCCccHHHHHHHHHHcC
Q 019386 156 FEVAKILEELNLTMDQFIDLCIL-SGCDYCDSIRGIGGQTALKLIRQHG 203 (342)
Q Consensus 156 ~~~~~v~~~lgl~~~q~id~~~L-~G~Dy~~~IpGiG~ktA~~Li~~~~ 203 (342)
++..++.+.+|+++.+++..+.- +|-.....--.|....|..+..+|+
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 55678889999999999999966 8855222224455666666665554
No 132
>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=28.91 E-value=42 Score=24.52 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=11.9
Q ss_pred CCCCCccHHHHHHH
Q 019386 185 DSIRGIGGQTALKL 198 (342)
Q Consensus 185 ~~IpGiG~ktA~~L 198 (342)
..|||||+..|.++
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 57999999988776
No 133
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=28.40 E-value=65 Score=29.58 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=23.2
Q ss_pred HHHHHHHHHHcCCCeecC---------------------c---CcHHHHHHHHHHcCC
Q 019386 87 NDDCKRLLKLMGVPVVEA---------------------P---SEAEAQCAALCKSGQ 120 (342)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~A---------------------p---~EAdaq~A~L~~~g~ 120 (342)
+..-.+.|+.+||||-.+ | -|.||.+|||...|.
T Consensus 151 ~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~ 208 (217)
T PRK14487 151 TAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGT 208 (217)
T ss_pred HHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhcc
Confidence 344455667779998542 1 488889999988764
No 134
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=28.18 E-value=51 Score=35.38 Aligned_cols=24 Identities=33% Similarity=0.494 Sum_probs=15.8
Q ss_pred CCCCccHHHHHHHH-HHcCCHHHHH
Q 019386 186 SIRGIGGQTALKLI-RQHGSIETIL 209 (342)
Q Consensus 186 ~IpGiG~ktA~~Li-~~~~sle~il 209 (342)
|||+||..+|..|. +.|++++++.
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~ 530 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIS 530 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHH
Confidence 46667777666666 6667766654
No 135
>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=27.80 E-value=2.7e+02 Score=25.73 Aligned_cols=34 Identities=32% Similarity=0.543 Sum_probs=21.3
Q ss_pred CCCCcchHHHHHHHHHHHHHHcCCCcEEE---EeCCC
Q 019386 5 EAGEVTSHLQGMFTRTIRLLEAGMKPIYV---FDGQP 38 (342)
Q Consensus 5 ~~G~~t~~l~g~~~r~~~ll~~gi~Pv~V---FDG~~ 38 (342)
|+|-+=||+..++.-+--+.++|+++||| .||..
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 67888899999888444445689999874 89984
No 136
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.78 E-value=1.3e+02 Score=24.80 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=35.6
Q ss_pred eHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHH-cCCHHHH
Q 019386 157 EVAKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQ-HGSIETI 208 (342)
Q Consensus 157 ~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~-~~sle~i 208 (342)
....+.+..|++...+..+..++ |.+ -|||||+..|.=|... +.|++++
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 34457788899999988887664 677 8999999987766653 3455543
No 137
>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=27.71 E-value=1.2e+02 Score=25.17 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=34.2
Q ss_pred HHHHHHHHHHcCCCeecCcC--------cHHHHHHHHH----H-cC-CeEEEecCCCCccccc
Q 019386 87 NDDCKRLLKLMGVPVVEAPS--------EAEAQCAALC----K-SG-QVYAVASEDMDSLTFG 135 (342)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~Ap~--------EAdaq~A~L~----~-~g-~v~~V~S~DsD~l~fg 135 (342)
.....+.|+..|+.++..|. -+|..++.-+ . .+ -+.+++|+|+|+....
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 45677789999999988872 4666555322 1 22 3667889999998764
No 138
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=27.60 E-value=40 Score=28.53 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.4
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.||||||+||--++.
T Consensus 87 ~l~GIG~~tA~~~l~ 101 (158)
T cd00056 87 ALPGVGRKTANVVLL 101 (158)
T ss_pred cCCCCCHHHHHHHHH
Confidence 579999999877665
No 139
>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=27.46 E-value=55 Score=26.85 Aligned_cols=17 Identities=41% Similarity=0.685 Sum_probs=14.9
Q ss_pred CCCccHHHHHHHHHHcC
Q 019386 187 IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 187 IpGiG~ktA~~Li~~~~ 203 (342)
|.|||+.+|..++.+.|
T Consensus 20 i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 20 IYGIGRTRARKILEKAG 36 (113)
T ss_pred eecccHHHHHHHHHHhC
Confidence 57999999999998866
No 140
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=27.42 E-value=2.5e+02 Score=26.86 Aligned_cols=103 Identities=17% Similarity=0.287 Sum_probs=61.7
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhhcCCCCCCCchHH--HHHHhCCCC
Q 019386 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGSIETILENINRERYQIPEDWPYQE--ARRLFKEPE 236 (342)
Q Consensus 159 ~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~sle~il~~l~~~k~~i~~~~~~~~--~~~~f~~p~ 236 (342)
+.+|+.+|.+|+|+..-+.=+. ++ ..|.+......++..-+.++..+..+... ....++|.|.+ |.-+|.--.
T Consensus 129 ~Alc~a~g~Dp~qyr~dA~~l~-~~---A~~~s~~~l~~~l~~~~~l~~~l~~IA~~-a~~~~~f~YSRlfAIGLf~LLe 203 (283)
T PLN00047 129 KAYIKALGEDPEQYRKDAAKLE-EW---ARSQTGSSLVDFSSKEGEIEGILKDIAER-AGSKGKFSYSRFFAIGLFRLLE 203 (283)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-HH---HhcCCHHHHHHHHhcchHHHHHHHHHHHh-hccCCCcchHHHHHHHHHHHHH
Confidence 4567777899999877665444 22 24566677777776656666666665311 11236677764 666664111
Q ss_pred cCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHH
Q 019386 237 VVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEK 277 (342)
Q Consensus 237 v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~ 277 (342)
-. .- . |.+.|.+++ +.+|++.++|.+-|.-
T Consensus 204 ~a------~~--~--d~~~l~~l~-e~Lgls~~kv~KDLdl 233 (283)
T PLN00047 204 LA------NA--T--EPTALEKLC-AALNINKRSVDRDLDV 233 (283)
T ss_pred hc------CC--C--CHHHHHHHH-HHcCCCHHHHHhhHHH
Confidence 00 00 1 335666655 8999999999876543
No 141
>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=27.15 E-value=93 Score=26.59 Aligned_cols=33 Identities=9% Similarity=0.115 Sum_probs=18.9
Q ss_pred HcCCCeecCcC-c--------HHHHHHHHHHcCCeEEEecCCC
Q 019386 96 LMGVPVVEAPS-E--------AEAQCAALCKSGQVYAVASEDM 129 (342)
Q Consensus 96 ~~Gi~~i~Ap~-E--------Adaq~A~L~~~g~v~~V~S~Ds 129 (342)
..|+=++..++ . +|..+.++|...-. .|+|+|.
T Consensus 69 ~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~~~a-~IVSND~ 110 (155)
T PF11977_consen 69 RKGIIYFTPSGSNYGSRSRNYDDRYILYYAEEKDA-VIVSNDR 110 (155)
T ss_dssp HTTSEEEE-EEEETTEEEEB-HHHHHHHHHHHTT--EEE-S--
T ss_pred HCCeEEEcCCCCCCCCcccccchHHHHHHHHHcCC-EEEeCch
Confidence 36765555555 4 88888888876444 3679884
No 142
>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=27.06 E-value=52 Score=31.28 Aligned_cols=25 Identities=32% Similarity=0.395 Sum_probs=21.1
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ-HGSIETILE 210 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~-~~sle~il~ 210 (342)
.+||||+++|.+|.+. |.+++++..
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~~ 28 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIAV 28 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 5799999999999998 888877643
No 143
>PRK13266 Thf1-like protein; Reviewed
Probab=26.88 E-value=1.8e+02 Score=26.86 Aligned_cols=108 Identities=12% Similarity=0.118 Sum_probs=56.8
Q ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHc--CCHHHHHHHHHhhcCCCCCCCchHH--HHHHhCC
Q 019386 159 AKILEELNLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQH--GSIETILENINRERYQIPEDWPYQE--ARRLFKE 234 (342)
Q Consensus 159 ~~v~~~lgl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~--~sle~il~~l~~~k~~i~~~~~~~~--~~~~f~~ 234 (342)
+.+|...|.+|+|+..-+.=+. + -..|.+...-..++.+- +..+.+.+.+..+. -..+|.|.+ |.-+|.-
T Consensus 78 ~Alc~a~~~dp~~~r~dA~~l~-~---~a~~~s~~~i~~~l~~~~~~~~~~l~~~l~~ia--~~~~f~YSRl~AIGL~~L 151 (225)
T PRK13266 78 NALCQAVGFDPEQLRQDAERLL-E---LAKGKSLKEILSWLTQKALGEPGGLLATLLAIA--NNSKFKYSRLFAIGLYTL 151 (225)
T ss_pred HHHHHHcCCCHHHHHHHHHHHH-H---HHhcCCHHHHHHHHhccccccchhHHHHHHHHh--cCCCCchHHHHHHHHHHH
Confidence 4566777888888876654443 1 12345555555666543 22334444443322 236677654 5566631
Q ss_pred CCcCCccccccCCCCCC-CHHHHHHHHHHhcCCChHHHHHHHHH
Q 019386 235 PEVVTDEEQLQIKWSAP-DEEGLINFLVSENGFNSDRVTKAIEK 277 (342)
Q Consensus 235 p~v~~~~~~~~~~~~~p-d~e~l~~fl~~~~~f~~~rv~~~~~~ 277 (342)
-... . ...-..| +...+..-+++.+||+.++|.+-|.-
T Consensus 152 Le~a--~---~~~~~d~~~~~~~l~~l~~~L~ls~~kv~KDL~l 190 (225)
T PRK13266 152 LEEA--Q---PDLVKDEEKLNEALKDISEGLGLSKEKVEKDLDL 190 (225)
T ss_pred HHhc--C---cccccCHHHHHHHHHHHHHHcCCCHHHHHhhHHH
Confidence 1000 0 0011112 23345555668999999999876543
No 144
>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=26.87 E-value=60 Score=26.33 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=23.0
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCCcccccCCee
Q 019386 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRF 139 (342)
Q Consensus 107 EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v 139 (342)
-+|+.++..+...-+ .++|.|.|+-.|+.-.+
T Consensus 105 ~~D~~i~a~A~~~~~-~lvT~D~~f~~~~~~~i 136 (142)
T TIGR00028 105 VTDAHLAALAREHGA-ELVTFDRGFARFAGIRW 136 (142)
T ss_pred chHHHHHHHHHHcCC-EEEecCCCccccCCCee
Confidence 589998888775444 57799999766654443
No 145
>COG1778 Low specificity phosphatase (HAD superfamily) [General function prediction only]
Probab=26.64 E-value=67 Score=28.21 Aligned_cols=42 Identities=24% Similarity=0.371 Sum_probs=28.9
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCC---C----ccHHHHHHHHHHc
Q 019386 156 FEVAKILEELNLTMDQFIDLCILSGCDYCDSIR---G----IGGQTALKLIRQH 202 (342)
Q Consensus 156 ~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~Ip---G----iG~ktA~~Li~~~ 202 (342)
.-..+++++++++++| ++-+|-|+.| +| . +-|..|..+++++
T Consensus 86 ~a~~~L~~~~~l~~e~----~ayiGDD~~D-lpvm~~vGls~a~~dAh~~v~~~ 134 (170)
T COG1778 86 AAFEELLKKLNLDPEE----VAYVGDDLVD-LPVMEKVGLSVAVADAHPLLKQR 134 (170)
T ss_pred HHHHHHHHHhCCCHHH----hhhhcCcccc-HHHHHHcCCcccccccCHHHHHh
Confidence 4567889999999988 6678944444 43 2 3367777777753
No 146
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=26.34 E-value=76 Score=26.99 Aligned_cols=49 Identities=16% Similarity=0.082 Sum_probs=34.3
Q ss_pred HHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecCCCCcccc----cCCee
Q 019386 91 KRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASEDMDSLTF----GAPRF 139 (342)
Q Consensus 91 ~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~DsD~l~f----g~~~v 139 (342)
..+....+.+++..-..||+.+-..+...-+++|+|+|..+-.- |.|.+
T Consensus 69 ia~~~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi 121 (136)
T COG1412 69 IALKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVI 121 (136)
T ss_pred HHHHHhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEE
Confidence 33455678888888448988777777654466799999987543 55544
No 147
>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=26.31 E-value=45 Score=27.76 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=28.6
Q ss_pred cccCHhHHHHHHHHHHHcCCCeecCcCcHH-HHHHHHHHcCCeEEEecCCCCcccccCCe
Q 019386 80 VKVTKQHNDDCKRLLKLMGVPVVEAPSEAE-AQCAALCKSGQVYAVASEDMDSLTFGAPR 138 (342)
Q Consensus 80 ~~vt~~~~~~~~~lL~~~Gi~~i~Ap~EAd-aq~A~L~~~g~v~~V~S~DsD~l~fg~~~ 138 (342)
-.||.+.++.+++.+..-+=-.|...||=| +.+... .+..+-.+.+||.|.
T Consensus 44 G~It~el~~ai~~a~~~~~~~~I~V~GEEDL~~lPai--------l~aP~gs~V~YGQP~ 95 (121)
T PF04019_consen 44 GTITEELIEAIKKALESGKPVVIFVDGEEDLAVLPAI--------LYAPEGSVVLYGQPG 95 (121)
T ss_pred CcccHHHHHHHHHHHhCCCCEEEEEeChHHHHHHHHH--------HhCCCCCEEEECCCC
Confidence 456777788888887553333455566544 222222 233444556777764
No 148
>PRK00124 hypothetical protein; Validated
Probab=26.22 E-value=51 Score=28.52 Aligned_cols=91 Identities=13% Similarity=0.139 Sum_probs=50.2
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCCcccccCCeeEEEeecCCCCCCccEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC
Q 019386 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAPRFLRHLMDPSSRKIPVMEFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (342)
Q Consensus 107 EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~~v~~~l~~~~~~~~~~~~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~ 186 (342)
.||..|+.++..| |.|+|.|.=+-...-.+-..-+...+ ..|+.+.|-..|.. +...-++- -.| -.+.|
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 45777776555432 11111111 224 24456
Q ss_pred CCCccHHHHHHHHHHcCCHHHHHHH
Q 019386 187 IRGIGGQTALKLIRQHGSIETILEN 211 (342)
Q Consensus 187 IpGiG~ktA~~Li~~~~sle~il~~ 211 (342)
-+..+++.-..+.+. ++.++..
T Consensus 125 p~~~~~~Dr~~F~~~---L~~~l~~ 146 (151)
T PRK00124 125 PKPFTQEDRSRFEAE---LDKLIRR 146 (151)
T ss_pred CCCCCHHHHHHHHHH---HHHHHHH
Confidence 666777665555443 4555554
No 149
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=26.19 E-value=70 Score=29.25 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=13.3
Q ss_pred CCCccHHHHHHHHHH-cC
Q 019386 187 IRGIGGQTALKLIRQ-HG 203 (342)
Q Consensus 187 IpGiG~ktA~~Li~~-~~ 203 (342)
+||||+|||-=.+.. ||
T Consensus 114 LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 114 LPGVGRKTANVVLSFAFG 131 (211)
T ss_pred CCCcchHHHHHHHHhhcC
Confidence 489999999877764 44
No 150
>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=25.88 E-value=1.1e+02 Score=28.26 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=25.6
Q ss_pred HHHHHHHHHcCCCeec--CcCcHHH----HHHHHHHcCCeEEEecCCCC
Q 019386 88 DDCKRLLKLMGVPVVE--APSEAEA----QCAALCKSGQVYAVASEDMD 130 (342)
Q Consensus 88 ~~~~~lL~~~Gi~~i~--Ap~EAda----q~A~L~~~g~v~~V~S~DsD 130 (342)
+.+....+.||||++. .+++-++ ....|...| +++|+++|-+
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 4566778899999764 3453343 333343345 6677777654
No 151
>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=25.68 E-value=46 Score=29.62 Aligned_cols=17 Identities=24% Similarity=0.350 Sum_probs=13.3
Q ss_pred CCCCccHHHHHHHHHHc
Q 019386 186 SIRGIGGQTALKLIRQH 202 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~ 202 (342)
.+||||+|||-=++...
T Consensus 119 ~LpGVG~KTAnvVL~~l 135 (177)
T TIGR03252 119 ALPGFGKQKAKIFLALL 135 (177)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 58999999997666543
No 152
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=25.40 E-value=61 Score=26.98 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=15.0
Q ss_pred CCCccHHHHHHHHHHcC
Q 019386 187 IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 187 IpGiG~ktA~~Li~~~~ 203 (342)
|.|||+.+|..++.+.|
T Consensus 22 I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 22 IYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccHHHHHHHHHHhC
Confidence 67999999999998866
No 153
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=25.27 E-value=50 Score=29.49 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=15.8
Q ss_pred CCCCccHHHHHHHHHHcC
Q 019386 186 SIRGIGGQTALKLIRQHG 203 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~~~ 203 (342)
.+||||+++|.+++.++.
T Consensus 112 ~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 112 KVPGIGKKTAERIVLELK 129 (192)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 589999999999998754
No 154
>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=25.14 E-value=2.2e+02 Score=19.22 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCC
Q 019386 166 NLTMDQFIDLCILSGCDYCDSIRGIGGQTALKLIRQHGS 204 (342)
Q Consensus 166 gl~~~q~id~~~L~G~Dy~~~IpGiG~ktA~~Li~~~~s 204 (342)
.+||.+| .+|+|-+- +-..++-..--+|++.|++
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 4566555 67788444 3466777777778887763
No 155
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=24.66 E-value=53 Score=28.10 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=24.7
Q ss_pred cHHHHHHHHHHcCCeEEEecCCCCcccccCC
Q 019386 107 EAEAQCAALCKSGQVYAVASEDMDSLTFGAP 137 (342)
Q Consensus 107 EAdaq~A~L~~~g~v~~V~S~DsD~l~fg~~ 137 (342)
+=|+-.-.++-.|.+++++|+|.|+|.+...
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~~ 121 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRDE 121 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheeccc
Confidence 4566666677889999999999999987643
No 156
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=24.52 E-value=50 Score=27.66 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.9
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||+++|--++.
T Consensus 76 ~l~GIG~~tA~~~l~ 90 (149)
T smart00478 76 KLPGVGRKTANAVLS 90 (149)
T ss_pred cCCCCcHHHHHHHHH
Confidence 589999999866554
No 157
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=24.52 E-value=65 Score=26.80 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=14.8
Q ss_pred CCCccHHHHHHHHHHcC
Q 019386 187 IRGIGGQTALKLIRQHG 203 (342)
Q Consensus 187 IpGiG~ktA~~Li~~~~ 203 (342)
|.|||+.+|..++...|
T Consensus 22 i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 22 IYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccHHHHHHHHHHcC
Confidence 57999999999998765
No 158
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=24.40 E-value=49 Score=30.39 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=12.9
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||++||--++-
T Consensus 125 ~l~GIG~kTAd~iLl 139 (218)
T PRK13913 125 DQKGIGKESADAILC 139 (218)
T ss_pred cCCCccHHHHHHHHH
Confidence 589999999988775
No 159
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=24.37 E-value=1.4e+02 Score=26.73 Aligned_cols=46 Identities=24% Similarity=0.315 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhCCCCCC-----CCCCccHHHHHHHHHH-----cCCHHHHHHHH
Q 019386 167 LTMDQFIDLCILSGCDYCD-----SIRGIGGQTALKLIRQ-----HGSIETILENI 212 (342)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~-----~IpGiG~ktA~~Li~~-----~~sle~il~~l 212 (342)
=+.+.|+++.--+|--..- =+||||.|+..++|.+ |.|.++|-+.+
T Consensus 96 ~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 96 ENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp TTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred hChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 4689999999988822221 1599999999999975 77888877665
No 160
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]
Probab=24.12 E-value=1.5e+02 Score=26.45 Aligned_cols=46 Identities=35% Similarity=0.415 Sum_probs=30.9
Q ss_pred CHhHHHHHHHHHHHcCCCeecCcCc--HHHHHHHHHHcCCeEEEecCC
Q 019386 83 TKQHNDDCKRLLKLMGVPVVEAPSE--AEAQCAALCKSGQVYAVASED 128 (342)
Q Consensus 83 t~~~~~~~~~lL~~~Gi~~i~Ap~E--Adaq~A~L~~~g~v~~V~S~D 128 (342)
+....+.++.++...||++|..||| -+|.-..|...|--..|+|.|
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 3455678888999999999999985 344444455556444566644
No 161
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=23.90 E-value=1.1e+02 Score=26.13 Aligned_cols=39 Identities=15% Similarity=0.156 Sum_probs=24.1
Q ss_pred HHHHHHHHHcCCCeecCcCcHHHHHHHHHHcCCeEEEecC
Q 019386 88 DDCKRLLKLMGVPVVEAPSEAEAQCAALCKSGQVYAVASE 127 (342)
Q Consensus 88 ~~~~~lL~~~Gi~~i~Ap~EAdaq~A~L~~~g~v~~V~S~ 127 (342)
+.+.+.++..|++++.-.-.-..+..++.+.| ||+|+|+
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 45556666677777666554455556666666 6667664
No 162
>PRK00254 ski2-like helicase; Provisional
Probab=23.85 E-value=62 Score=34.87 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=23.0
Q ss_pred CCCCccHHHHHHHHHH-cCCHHHHHHH
Q 019386 186 SIRGIGGQTALKLIRQ-HGSIETILEN 211 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~~-~~sle~il~~ 211 (342)
.|||||+++|.+|++. |+|+++|.+.
T Consensus 649 ~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 649 RLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred cCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 3699999999999999 9999988763
No 163
>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=23.85 E-value=96 Score=27.11 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=33.1
Q ss_pred HHHHHHHHcCCCeecCcCcHHHHHHH--HHH--cC--CeEEEecCCCCccccc
Q 019386 89 DCKRLLKLMGVPVVEAPSEAEAQCAA--LCK--SG--QVYAVASEDMDSLTFG 135 (342)
Q Consensus 89 ~~~~lL~~~Gi~~i~Ap~EAdaq~A~--L~~--~g--~v~~V~S~DsD~l~fg 135 (342)
.+++.|..+|+..+...|..|-.++- |.- .+ -+.+++|+|+|+--+.
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv 122 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVI 122 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHH
Confidence 46789999999988888866654442 211 23 3557889999998775
No 164
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
Probab=23.56 E-value=81 Score=30.12 Aligned_cols=28 Identities=32% Similarity=0.572 Sum_probs=26.4
Q ss_pred cEEEeHHHHHHHhCCCHHHHHHHHHHhC
Q 019386 153 VMEFEVAKILEELNLTMDQFIDLCILSG 180 (342)
Q Consensus 153 ~~~~~~~~v~~~lgl~~~q~id~~~L~G 180 (342)
...++....+..|.|+...|.-+|||-|
T Consensus 10 ~~yiTR~qAlkkLQlsl~dFRRLCILKG 37 (281)
T PF06732_consen 10 KNYITRNQALKKLQLSLKDFRRLCILKG 37 (281)
T ss_pred cccccHHHHHHHhcCCHHHHhhHHhhcC
Confidence 4678999999999999999999999999
No 165
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=23.31 E-value=83 Score=26.76 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=25.6
Q ss_pred HHHHHHHc-CCCeecCcCc---HHHHHHHHHHcCCeEEEec
Q 019386 90 CKRLLKLM-GVPVVEAPSE---AEAQCAALCKSGQVYAVAS 126 (342)
Q Consensus 90 ~~~lL~~~-Gi~~i~Ap~E---Adaq~A~L~~~g~v~~V~S 126 (342)
.-++|+.. ||++-....| ++.+++.+.+.|.+++|+.
T Consensus 41 Ta~~L~~~~Gi~v~~vi~~~~gg~~~i~~~I~~g~i~lVIn 81 (142)
T PRK05234 41 TGGLIQEATGLDVTRLLSGPLGGDQQIGALIAEGKIDMLIF 81 (142)
T ss_pred HHHHHHhccCCeeEEEEcCCCCCchhHHHHHHcCceeEEEE
Confidence 34456667 8876443334 6788888989998888763
No 166
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=22.25 E-value=1.1e+02 Score=24.78 Aligned_cols=36 Identities=28% Similarity=0.341 Sum_probs=26.7
Q ss_pred HHHHHH-cCCCeecC---cCcHHHHHHHHHHcCCeEEEec
Q 019386 91 KRLLKL-MGVPVVEA---PSEAEAQCAALCKSGQVYAVAS 126 (342)
Q Consensus 91 ~~lL~~-~Gi~~i~A---p~EAdaq~A~L~~~g~v~~V~S 126 (342)
-++|+. .||++-.. |.|++.+++.+.+.|.+++|+.
T Consensus 37 a~~L~~~~Gi~v~~vk~~~~~g~~~i~~~i~~g~i~~VIn 76 (115)
T cd01422 37 GLLIQEATGLTVNRMKSGPLGGDQQIGALIAEGEIDAVIF 76 (115)
T ss_pred HHHHHHhhCCcEEEEecCCCCchhHHHHHHHcCceeEEEE
Confidence 445565 88886422 3688899999999999988863
No 167
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=22.07 E-value=1.9e+02 Score=23.72 Aligned_cols=54 Identities=15% Similarity=0.207 Sum_probs=31.8
Q ss_pred HHHHHHhCCCCcCCccccccCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhhhccCCCCccccc
Q 019386 226 QEARRLFKEPEVVTDEEQLQIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAAKNKSSQGRLESF 293 (342)
Q Consensus 226 ~~~~~~f~~p~v~~~~~~~~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~~~Q~~l~~f 293 (342)
.-++.+|.++... +. +.+...+++...+..+.......-.-|+. -.+|.+||+|
T Consensus 57 E~vR~A~~~~p~~---------f~--~l~eAl~~~~~~l~~~~~~w~~~s~ll~~---~~~Q~tL~~F 110 (110)
T PF04895_consen 57 ENVRKAMKGKPEK---------FE--TLEEALEYVSSRLKLPIKEWLRKSKLLKR---IRRQKTLDDF 110 (110)
T ss_pred HHHHHHHhCCCcc---------cC--CHHHHHHHHHHHhCCCHHHHHHHhHHHHH---HhcccccccC
Confidence 3477777765322 22 45666778877877765543333222222 2279999998
No 168
>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=21.67 E-value=1.5e+02 Score=24.10 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=25.0
Q ss_pred HHHHHHHHHHcCCCeecCcC---------cHHHHHHH----HHH--cCCeEEEecCCCCccccc
Q 019386 87 NDDCKRLLKLMGVPVVEAPS---------EAEAQCAA----LCK--SGQVYAVASEDMDSLTFG 135 (342)
Q Consensus 87 ~~~~~~lL~~~Gi~~i~Ap~---------EAdaq~A~----L~~--~g~v~~V~S~DsD~l~fg 135 (342)
...+.+.|+..|+++...|. .+|-.++. ++. .--..+++|+|+|+.-..
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 45666788999998876654 35554442 221 124667899999987664
No 169
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=21.27 E-value=1.3e+02 Score=29.21 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=31.9
Q ss_pred EEEeHHHHHHHhCCCHHHHHHH--------------HHHhCCCCCC------------CCCCccHHHHHHHHHH
Q 019386 154 MEFEVAKILEELNLTMDQFIDL--------------CILSGCDYCD------------SIRGIGGQTALKLIRQ 201 (342)
Q Consensus 154 ~~~~~~~v~~~lgl~~~q~id~--------------~~L~G~Dy~~------------~IpGiG~ktA~~Li~~ 201 (342)
+.|..+.++.-||+.++++.+. ++|--.|.-+ .|||||++.|..+|..
T Consensus 276 RLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 276 RLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 3477788889999999887653 2222222222 1489999999888864
No 170
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=21.19 E-value=1.2e+02 Score=21.63 Aligned_cols=32 Identities=6% Similarity=0.176 Sum_probs=28.1
Q ss_pred EEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCC
Q 019386 155 EFEVAKILEELNLTMDQFIDLCILSGCDYCDS 186 (342)
Q Consensus 155 ~~~~~~v~~~lgl~~~q~id~~~L~G~Dy~~~ 186 (342)
.-++++++..++++.+.+..-..-.|..|.+.
T Consensus 20 ~~sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~~ 51 (55)
T PF14056_consen 20 YSSLDELCYDYDIDKEELEEKLASIGYEYDEE 51 (55)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHcCCeEchh
Confidence 45889999999999999999999999888753
No 171
>PF05182 Fip1: Fip1 motif; InterPro: IPR007854 This short motif is about 40 amino acids in length and is found in the Fip1 protein that is a component of a Saccharomyces cerevisiae pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase []. This region of Fip1 is needed for the interaction with the Yth1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor [].
Probab=21.10 E-value=1.1e+02 Score=21.02 Aligned_cols=34 Identities=18% Similarity=0.509 Sum_probs=26.8
Q ss_pred cCCCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHhh
Q 019386 245 QIKWSAPDEEGLINFLVSENGFNSDRVTKAIEKIKAA 281 (342)
Q Consensus 245 ~~~~~~pd~e~l~~fl~~~~~f~~~rv~~~~~~l~~~ 281 (342)
+=.|..|-.+ |.+|+ .+||++..-+.++.++...
T Consensus 10 ~KPWr~pGaD-isDyF--NYGf~E~tW~~Y~~kq~~~ 43 (45)
T PF05182_consen 10 EKPWRKPGAD-ISDYF--NYGFNEETWREYCKKQRQL 43 (45)
T ss_pred cCCccCCCCC-hhhhc--CCCCCHHHHHHHHHHHHHh
Confidence 4569888754 78898 7999999888888877654
No 172
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=21.08 E-value=1.1e+02 Score=28.96 Aligned_cols=43 Identities=23% Similarity=0.286 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHhcCCChHHHHHHHHHHHhhh--ccCCCCccccccCc
Q 019386 252 DEEGLINFLVSENGFNSDRVTKAIEKIKAAK--NKSSQGRLESFFKP 296 (342)
Q Consensus 252 d~e~l~~fl~~~~~f~~~rv~~~~~~l~~~~--~~~~Q~~l~~ff~~ 296 (342)
-.-.|+.+| +++||++.-|+.++-|++++- .... ..=++|++.
T Consensus 27 w~gsLI~il-~~fG~sE~~vRaal~Rm~kaG~l~~er-~grks~Y~L 71 (291)
T COG3327 27 WIGSLIQIL-AEFGISETTVRAALSRMVKAGWLVGER-EGRKSFYRL 71 (291)
T ss_pred eHHHHHHHH-HHcCccHHHHHHHHHHHHhccchheee-cccccceee
Confidence 356899998 799999999999999998762 1222 233677764
No 173
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=21.04 E-value=1.1e+02 Score=24.60 Aligned_cols=37 Identities=19% Similarity=0.206 Sum_probs=27.5
Q ss_pred HHHHHHcCCC-eecCcC--cHHHHHHHHHHcCCeEEEecC
Q 019386 91 KRLLKLMGVP-VVEAPS--EAEAQCAALCKSGQVYAVASE 127 (342)
Q Consensus 91 ~~lL~~~Gi~-~i~Ap~--EAdaq~A~L~~~g~v~~V~S~ 127 (342)
.--+++.||. ++.+.. ||++....|++.++...++|+
T Consensus 14 ilGFrlaGi~~v~~~~~~e~~~~~~~~l~~~~~gII~iTE 53 (104)
T PRK01189 14 VLGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSE 53 (104)
T ss_pred HHHHHHcCCceEEEcCCHHHHHHHHHHHhcCCeEEEEEEH
Confidence 3457899996 555543 778888889888887777776
No 174
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=20.52 E-value=1.1e+02 Score=24.56 Aligned_cols=37 Identities=27% Similarity=0.353 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCee--cCcCc-HHHHHHHHHHc-CCeEEEec
Q 019386 90 CKRLLKLMGVPVV--EAPSE-AEAQCAALCKS-GQVYAVAS 126 (342)
Q Consensus 90 ~~~lL~~~Gi~~i--~Ap~E-Adaq~A~L~~~-g~v~~V~S 126 (342)
.-++|+..||++. ..+.| .+.++..+.+. |.+|.|+.
T Consensus 34 Ta~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn 74 (112)
T cd00532 34 TSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVIN 74 (112)
T ss_pred HHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEE
Confidence 3445666888863 33445 56788888888 88887764
No 175
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=20.26 E-value=80 Score=22.80 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=11.4
Q ss_pred CCCCccHHHHHHHHH
Q 019386 186 SIRGIGGQTALKLIR 200 (342)
Q Consensus 186 ~IpGiG~ktA~~Li~ 200 (342)
.+||||++.|..+|.
T Consensus 18 ~lpgi~~~~A~~Iv~ 32 (65)
T PF12836_consen 18 ALPGIGPKQAKAIVE 32 (65)
T ss_dssp TSTT--HHHHHHHHH
T ss_pred HcCCCCHHHHHHHHH
Confidence 479999999999997
No 176
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=20.17 E-value=1.3e+02 Score=23.89 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=23.8
Q ss_pred HHHHHHHcCCCe--ecCcCcHHHHHHHHHHcCCeEEEec
Q 019386 90 CKRLLKLMGVPV--VEAPSEAEAQCAALCKSGQVYAVAS 126 (342)
Q Consensus 90 ~~~lL~~~Gi~~--i~Ap~EAdaq~A~L~~~g~v~~V~S 126 (342)
.-+.|+..|+++ +..+.+++.++..+.++|.++.|+.
T Consensus 35 T~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn 73 (110)
T cd01424 35 TAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVIN 73 (110)
T ss_pred HHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEE
Confidence 334566677774 3334466677777777887777765
No 177
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.16 E-value=1.2e+02 Score=27.34 Aligned_cols=46 Identities=22% Similarity=0.320 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHhCCCCCC------CCCCccHHHHHHHHHH-----cCCHHHHHHHHH
Q 019386 167 LTMDQFIDLCILSGCDYCD------SIRGIGGQTALKLIRQ-----HGSIETILENIN 213 (342)
Q Consensus 167 l~~~q~id~~~L~G~Dy~~------~IpGiG~ktA~~Li~~-----~~sle~il~~l~ 213 (342)
-..+.|+++.--++ --+. -+||||.|+...+|.+ |.|.++|-+.+.
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 35677887765555 1111 1499999999999975 678888777653
Done!