Query psy8564
Match_columns 341
No_of_seqs 345 out of 2213
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 22:03:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10880 adenine DNA glycosyla 100.0 2E-81 4.3E-86 590.6 34.6 323 1-339 21-345 (350)
2 COG1194 MutY A/G-specific DNA 100.0 4.8E-76 1E-80 541.3 26.0 315 1-339 25-341 (342)
3 TIGR01084 mutY A/G-specific ad 100.0 3.5E-70 7.6E-75 500.8 28.1 247 1-247 17-265 (275)
4 PRK13910 DNA glycosylase MutY; 100.0 5.5E-69 1.2E-73 494.0 29.9 282 19-340 1-283 (289)
5 KOG2457|consensus 100.0 2.1E-59 4.6E-64 427.9 15.1 317 1-324 107-490 (555)
6 COG0177 Nth Predicted EndoIII- 100.0 3.5E-51 7.5E-56 356.6 19.3 182 7-193 26-208 (211)
7 PRK10702 endonuclease III; Pro 100.0 2.5E-49 5.3E-54 350.3 20.8 185 3-192 22-207 (211)
8 TIGR01083 nth endonuclease III 100.0 6.8E-42 1.5E-46 300.2 19.9 170 5-179 21-191 (191)
9 KOG1921|consensus 100.0 4.1E-37 8.9E-42 266.9 14.0 182 9-194 77-263 (286)
10 PRK13913 3-methyladenine DNA g 100.0 3.4E-36 7.4E-41 266.0 18.6 171 2-174 22-216 (218)
11 COG2231 Uncharacterized protei 100.0 5E-33 1.1E-37 237.0 16.4 185 2-192 22-214 (215)
12 smart00478 ENDO3c endonuclease 100.0 4.1E-31 8.9E-36 223.1 15.6 148 19-170 1-149 (149)
13 cd00056 ENDO3c endonuclease II 100.0 1.2E-30 2.6E-35 222.4 17.0 154 11-168 1-158 (158)
14 PRK01229 N-glycosylase/DNA lya 100.0 1.7E-27 3.8E-32 208.7 17.6 156 4-167 31-201 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 99.9 4.4E-26 9.5E-31 213.6 17.2 158 8-169 117-305 (310)
16 TIGR03252 uncharacterized HhH- 99.9 3E-23 6.5E-28 176.1 12.8 105 7-111 15-137 (177)
17 PF14815 NUDIX_4: NUDIX domain 99.9 1.7E-23 3.6E-28 168.6 9.3 112 213-336 1-114 (114)
18 cd03431 DNA_Glycosylase_C DNA 99.9 7.6E-22 1.6E-26 159.0 11.4 114 210-338 3-118 (118)
19 PRK10546 pyrimidine (deoxy)nuc 99.9 7E-22 1.5E-26 163.6 11.4 120 210-340 4-127 (135)
20 TIGR00586 mutt mutator mutT pr 99.9 6.9E-22 1.5E-26 161.8 11.1 119 210-339 4-127 (128)
21 COG0122 AlkA 3-methyladenine D 99.9 1.7E-21 3.7E-26 180.0 14.2 149 8-165 103-272 (285)
22 PRK10776 nucleoside triphospha 99.9 1.8E-21 3.9E-26 159.2 11.6 119 211-340 5-128 (129)
23 PRK10308 3-methyl-adenine DNA 99.9 1.1E-20 2.3E-25 174.9 14.6 142 7-163 110-272 (283)
24 KOG2875|consensus 99.8 2.2E-20 4.9E-25 165.7 10.8 117 7-126 114-256 (323)
25 cd03425 MutT_pyrophosphohydrol 99.8 9.6E-19 2.1E-23 141.5 10.8 117 212-339 3-124 (124)
26 PRK08999 hypothetical protein; 99.8 1.4E-18 3.1E-23 163.9 11.8 119 210-339 5-128 (312)
27 PF00730 HhH-GPD: HhH-GPD supe 99.8 4.2E-18 9E-23 135.8 11.8 101 15-146 1-104 (108)
28 KOG1918|consensus 99.7 5.8E-18 1.3E-22 145.5 9.4 144 6-160 71-234 (254)
29 PRK15472 nucleoside triphospha 99.7 3.7E-16 8E-21 130.4 11.3 118 209-337 3-137 (141)
30 cd03427 MTH1 MutT homolog-1 (M 99.6 4.6E-15 9.9E-20 122.9 10.9 117 212-340 3-126 (137)
31 PRK15434 GDP-mannose mannosyl 99.6 5E-15 1.1E-19 125.9 9.8 114 212-337 19-150 (159)
32 cd04676 Nudix_Hydrolase_17 Mem 99.6 1.7E-14 3.7E-19 117.5 10.5 109 212-336 4-128 (129)
33 cd04696 Nudix_Hydrolase_37 Mem 99.6 1.1E-14 2.5E-19 118.8 9.4 110 213-336 6-125 (125)
34 cd04673 Nudix_Hydrolase_15 Mem 99.5 1.5E-14 3.3E-19 117.1 8.5 108 213-332 3-121 (122)
35 cd04684 Nudix_Hydrolase_25 Con 99.5 3.2E-14 6.9E-19 116.1 10.4 112 212-335 2-127 (128)
36 cd04669 Nudix_Hydrolase_11 Mem 99.5 2.2E-14 4.8E-19 116.6 8.7 102 212-330 3-119 (121)
37 cd03430 GDPMH GDP-mannose glyc 99.5 8.7E-14 1.9E-18 116.6 10.1 102 212-325 15-132 (144)
38 cd04691 Nudix_Hydrolase_32 Mem 99.5 8.3E-14 1.8E-18 112.5 8.9 101 212-324 2-107 (117)
39 cd04682 Nudix_Hydrolase_23 Mem 99.5 4.3E-14 9.3E-19 114.9 7.1 107 212-329 3-118 (122)
40 cd04683 Nudix_Hydrolase_24 Mem 99.5 1.2E-13 2.5E-18 111.8 9.5 102 212-324 2-113 (120)
41 cd04699 Nudix_Hydrolase_39 Mem 99.5 7.9E-14 1.7E-18 113.9 8.3 106 212-328 3-117 (129)
42 cd04679 Nudix_Hydrolase_20 Mem 99.5 1.6E-13 3.5E-18 111.9 10.0 110 213-335 6-124 (125)
43 PRK09438 nudB dihydroneopterin 99.5 8.2E-14 1.8E-18 117.2 7.8 115 212-340 10-144 (148)
44 cd03673 Ap6A_hydrolase Diadeno 99.5 1.6E-13 3.6E-18 112.3 8.5 104 221-339 16-130 (131)
45 cd04681 Nudix_Hydrolase_22 Mem 99.5 1.9E-13 4.2E-18 112.1 8.8 112 214-338 6-129 (130)
46 cd04664 Nudix_Hydrolase_7 Memb 99.5 1.6E-13 3.5E-18 112.5 8.2 112 211-335 3-128 (129)
47 cd04680 Nudix_Hydrolase_21 Mem 99.5 2E-13 4.3E-18 110.2 8.4 109 213-337 4-119 (120)
48 cd04695 Nudix_Hydrolase_36 Mem 99.5 3.3E-13 7.1E-18 111.2 9.2 110 218-340 11-129 (131)
49 cd04688 Nudix_Hydrolase_29 Mem 99.4 4.2E-13 9E-18 109.6 9.1 105 212-331 3-124 (126)
50 cd04687 Nudix_Hydrolase_28 Mem 99.4 4.3E-13 9.4E-18 109.9 9.1 106 212-330 3-126 (128)
51 PLN02325 nudix hydrolase 99.4 8.9E-13 1.9E-17 110.5 11.1 116 210-338 9-137 (144)
52 cd02883 Nudix_Hydrolase Nudix 99.4 3.2E-13 6.9E-18 108.2 7.1 110 213-335 3-122 (123)
53 cd03675 Nudix_Hydrolase_2 Cont 99.4 1.1E-12 2.4E-17 108.2 10.3 115 212-339 2-128 (134)
54 cd04511 Nudix_Hydrolase_4 Memb 99.4 1.1E-12 2.4E-17 107.9 9.8 105 211-329 14-125 (130)
55 cd04670 Nudix_Hydrolase_12 Mem 99.4 7.8E-13 1.7E-17 108.2 8.4 110 212-335 5-123 (127)
56 cd04667 Nudix_Hydrolase_10 Mem 99.4 8E-13 1.7E-17 105.7 8.2 103 213-335 3-111 (112)
57 cd04697 Nudix_Hydrolase_38 Mem 99.4 6.3E-13 1.4E-17 108.8 7.3 102 212-324 3-111 (126)
58 PRK15393 NUDIX hydrolase YfcD; 99.4 1.1E-12 2.3E-17 114.2 9.0 116 212-338 40-164 (180)
59 cd04690 Nudix_Hydrolase_31 Mem 99.4 1E-12 2.3E-17 105.8 8.1 105 212-331 3-116 (118)
60 cd03674 Nudix_Hydrolase_1 Memb 99.4 4.2E-12 9.1E-17 105.6 11.9 112 212-339 5-137 (138)
61 cd04678 Nudix_Hydrolase_19 Mem 99.4 3.6E-12 7.9E-17 104.4 11.1 101 213-325 6-117 (129)
62 cd03426 CoAse Coenzyme A pyrop 99.4 8.7E-13 1.9E-17 112.2 6.1 96 221-327 16-120 (157)
63 cd04672 Nudix_Hydrolase_14 Mem 99.4 3.6E-12 7.9E-17 103.7 9.2 106 212-332 4-119 (123)
64 cd04700 DR1025_like DR1025 fro 99.3 2.8E-12 6E-17 107.2 8.2 100 214-325 18-125 (142)
65 cd04671 Nudix_Hydrolase_13 Mem 99.3 3.7E-12 8E-17 103.9 8.7 104 213-332 4-116 (123)
66 cd04689 Nudix_Hydrolase_30 Mem 99.3 8.9E-12 1.9E-16 101.6 9.8 108 212-336 3-123 (125)
67 COG1059 Thermostable 8-oxoguan 99.3 2.2E-11 4.8E-16 102.9 11.8 150 8-165 37-201 (210)
68 TIGR02150 IPP_isom_1 isopenten 99.3 4.7E-12 1E-16 107.8 7.9 100 212-324 30-141 (158)
69 cd04661 MRP_L46 Mitochondrial 99.3 6E-12 1.3E-16 103.9 7.7 98 219-330 11-124 (132)
70 cd02885 IPP_Isomerase Isopente 99.3 7.4E-12 1.6E-16 107.4 8.1 102 213-325 34-148 (165)
71 cd03429 NADH_pyrophosphatase N 99.3 5.9E-12 1.3E-16 103.8 6.8 109 215-338 6-124 (131)
72 cd03428 Ap4A_hydrolase_human_l 99.3 1.8E-11 3.9E-16 100.3 9.3 101 222-338 18-128 (130)
73 PF00293 NUDIX: NUDIX domain; 99.3 7.2E-12 1.6E-16 102.5 6.2 116 213-339 6-133 (134)
74 cd03671 Ap4A_hydrolase_plant_l 99.3 2.6E-11 5.5E-16 101.9 9.0 112 213-339 7-144 (147)
75 cd04677 Nudix_Hydrolase_18 Mem 99.3 2.4E-11 5.3E-16 99.7 8.6 101 213-328 11-125 (132)
76 cd04694 Nudix_Hydrolase_35 Mem 99.3 1.2E-11 2.6E-16 103.5 6.9 101 213-324 5-130 (143)
77 cd03424 ADPRase_NUDT5 ADP-ribo 99.2 1.2E-11 2.6E-16 102.4 6.4 102 212-324 5-114 (137)
78 cd04692 Nudix_Hydrolase_33 Mem 99.2 3.2E-11 6.9E-16 101.0 8.3 103 211-324 4-126 (144)
79 cd04693 Nudix_Hydrolase_34 Mem 99.2 3.7E-11 8E-16 98.2 7.8 101 212-324 3-112 (127)
80 PRK03759 isopentenyl-diphospha 99.2 1.9E-10 4.2E-15 100.3 11.0 113 213-336 38-169 (184)
81 PRK00241 nudC NADH pyrophospha 99.2 9.7E-11 2.1E-15 107.2 9.3 102 213-329 135-242 (256)
82 cd04666 Nudix_Hydrolase_9 Memb 99.2 1.2E-10 2.6E-15 94.8 8.7 89 221-324 15-114 (122)
83 PRK05379 bifunctional nicotina 99.2 2E-10 4.3E-15 109.6 11.1 118 211-340 204-339 (340)
84 COG1051 ADP-ribose pyrophospha 99.1 2.7E-10 5.9E-15 95.5 10.1 108 210-329 10-126 (145)
85 cd04686 Nudix_Hydrolase_27 Mem 99.1 1.7E-10 3.6E-15 95.1 8.5 98 212-324 2-118 (131)
86 cd03672 Dcp2p mRNA decapping e 99.1 1.8E-10 3.8E-15 96.7 7.5 97 212-325 4-111 (145)
87 cd04685 Nudix_Hydrolase_26 Mem 99.1 3.1E-10 6.7E-15 93.8 8.4 103 212-325 3-123 (133)
88 PRK00714 RNA pyrophosphohydrol 99.1 3.7E-10 8E-15 95.9 7.5 112 212-338 11-147 (156)
89 cd04674 Nudix_Hydrolase_16 Mem 99.0 3.5E-09 7.6E-14 85.5 11.3 78 211-301 6-86 (118)
90 PRK11762 nudE adenosine nucleo 99.0 1E-09 2.2E-14 95.9 6.8 96 217-323 55-157 (185)
91 PRK10707 putative NUDIX hydrol 98.9 6.7E-09 1.4E-13 91.0 8.4 94 220-324 43-145 (190)
92 cd04665 Nudix_Hydrolase_8 Memb 98.9 1.7E-08 3.8E-13 81.5 9.9 96 212-323 2-103 (118)
93 cd03676 Nudix_hydrolase_3 Memb 98.9 8.7E-09 1.9E-13 89.5 8.7 93 221-324 48-157 (180)
94 cd04663 Nudix_Hydrolase_6 Memb 98.8 2.2E-08 4.7E-13 81.7 9.9 88 222-325 15-116 (126)
95 PLN02552 isopentenyl-diphospha 98.8 3.4E-08 7.4E-13 89.6 9.3 130 210-339 57-224 (247)
96 PF00633 HHH: Helix-hairpin-he 98.7 2.7E-09 5.9E-14 64.2 1.1 29 80-108 2-30 (30)
97 TIGR02705 nudix_YtkD nucleosid 98.7 9.4E-08 2E-12 80.8 8.5 77 212-304 26-105 (156)
98 cd04662 Nudix_Hydrolase_5 Memb 98.7 1.7E-07 3.8E-12 76.2 9.2 69 221-302 15-89 (126)
99 PLN02709 nudix hydrolase 98.6 1.3E-07 2.7E-12 84.2 7.2 92 222-324 52-154 (222)
100 TIGR00052 nudix-type nucleosid 98.5 1.4E-07 3.1E-12 82.3 5.9 94 220-324 56-164 (185)
101 COG0494 MutT NTP pyrophosphohy 98.4 2.4E-06 5.3E-11 69.9 9.2 96 221-330 24-139 (161)
102 PLN02791 Nudix hydrolase homol 98.3 2E-06 4.4E-11 89.0 8.9 101 212-323 35-156 (770)
103 cd03670 ADPRase_NUDT9 ADP-ribo 98.2 8E-06 1.7E-10 71.0 9.8 102 222-340 50-184 (186)
104 PRK10729 nudF ADP-ribose pyrop 98.2 4.7E-06 1E-10 73.8 7.0 93 220-323 61-169 (202)
105 PF10576 EndIII_4Fe-2S: Iron-s 98.1 9.2E-07 2E-11 45.8 0.4 17 172-188 1-17 (17)
106 COG2816 NPY1 NTP pyrophosphohy 98.0 2.7E-06 5.8E-11 77.6 2.6 99 212-327 146-253 (279)
107 PRK15009 GDP-mannose pyrophosp 97.7 0.00013 2.8E-09 64.0 7.1 93 220-324 57-165 (191)
108 smart00525 FES FES domain. iro 97.6 2.7E-05 5.9E-10 45.3 1.2 22 171-192 1-22 (26)
109 KOG2839|consensus 97.4 0.00029 6.3E-09 57.8 5.2 87 222-322 25-122 (145)
110 KOG3084|consensus 97.3 0.00035 7.7E-09 64.3 5.8 59 210-280 188-249 (345)
111 PLN03143 nudix hydrolase; Prov 97.3 0.00055 1.2E-08 63.6 7.1 47 218-275 138-189 (291)
112 COG1443 Idi Isopentenyldiphosp 97.2 0.00032 6.9E-09 59.3 3.9 102 210-324 34-152 (185)
113 KOG3069|consensus 97.2 0.00091 2E-08 59.2 6.1 101 221-331 58-169 (246)
114 smart00278 HhH1 Helix-hairpin- 96.0 0.0058 1.3E-07 35.3 2.1 20 90-109 2-21 (26)
115 KOG0648|consensus 95.9 0.0038 8.1E-08 57.6 1.8 104 212-327 118-233 (295)
116 COG4119 Predicted NTP pyrophos 95.3 0.063 1.4E-06 43.1 6.3 42 222-275 19-66 (161)
117 PF03352 Adenine_glyco: Methyl 95.3 0.13 2.9E-06 44.4 8.9 71 8-78 24-99 (179)
118 KOG3041|consensus 95.2 0.073 1.6E-06 46.1 7.0 75 215-302 80-163 (225)
119 PF12826 HHH_2: Helix-hairpin- 95.1 0.031 6.8E-07 39.8 3.8 38 72-109 15-55 (64)
120 PF14716 HHH_8: Helix-hairpin- 94.8 0.14 2.9E-06 36.9 6.5 55 52-108 10-66 (68)
121 PLN02839 nudix hydrolase 94.5 0.11 2.5E-06 49.5 7.0 92 221-323 218-325 (372)
122 TIGR00426 competence protein C 93.0 0.34 7.4E-06 34.8 5.8 58 44-108 9-66 (69)
123 PF14520 HHH_5: Helix-hairpin- 93.0 0.3 6.6E-06 34.1 5.3 22 87-108 36-57 (60)
124 TIGR00624 tag DNA-3-methyladen 92.6 0.77 1.7E-05 39.7 8.3 73 6-78 26-103 (179)
125 PRK10353 3-methyl-adenine DNA 92.4 0.72 1.6E-05 40.1 7.9 72 7-78 28-104 (187)
126 KOG4195|consensus 91.9 0.2 4.2E-06 44.2 3.8 35 222-271 140-176 (275)
127 COG2818 Tag 3-methyladenine DN 91.9 1.1 2.3E-05 38.8 8.2 71 8-78 30-105 (188)
128 PF09674 DUF2400: Protein of u 91.6 0.17 3.7E-06 45.6 3.3 154 14-169 20-230 (232)
129 KOG0142|consensus 91.0 0.41 9E-06 41.6 4.8 124 209-336 52-200 (225)
130 PRK14601 ruvA Holliday junctio 90.6 0.3 6.4E-06 42.5 3.7 27 86-112 105-131 (183)
131 PRK13901 ruvA Holliday junctio 90.5 0.3 6.5E-06 42.9 3.7 35 71-112 96-130 (196)
132 PRK00116 ruvA Holliday junctio 90.3 0.62 1.3E-05 40.8 5.5 24 86-109 105-128 (192)
133 PRK14606 ruvA Holliday junctio 90.1 0.34 7.3E-06 42.3 3.7 27 86-112 105-131 (188)
134 TIGR02757 conserved hypothetic 90.0 0.32 7E-06 43.7 3.5 55 114-169 173-227 (229)
135 PRK14605 ruvA Holliday junctio 89.7 0.41 8.9E-06 42.0 3.9 20 88-107 72-91 (194)
136 PRK14602 ruvA Holliday junctio 89.5 0.4 8.6E-06 42.4 3.7 26 86-111 106-131 (203)
137 PRK14603 ruvA Holliday junctio 89.5 0.41 8.8E-06 42.2 3.7 26 86-111 104-129 (197)
138 COG0632 RuvA Holliday junction 89.4 0.4 8.8E-06 42.2 3.6 26 86-111 105-130 (201)
139 PRK02515 psbU photosystem II c 89.3 0.68 1.5E-05 37.7 4.5 19 87-105 85-103 (132)
140 TIGR00608 radc DNA repair prot 89.3 0.55 1.2E-05 42.0 4.5 59 47-107 13-78 (218)
141 PRK14604 ruvA Holliday junctio 89.3 0.42 9.2E-06 42.0 3.7 27 86-112 105-131 (195)
142 COG4112 Predicted phosphoester 89.0 3.6 7.8E-05 34.7 8.6 111 212-327 63-190 (203)
143 PRK00024 hypothetical protein; 88.8 0.61 1.3E-05 41.9 4.4 59 47-107 23-84 (224)
144 COG0353 RecR Recombinational D 88.5 0.24 5.3E-06 43.0 1.5 29 85-113 8-36 (198)
145 TIGR00615 recR recombination p 87.8 0.5 1.1E-05 41.4 3.1 28 86-113 8-35 (195)
146 PRK00076 recR recombination pr 87.7 0.5 1.1E-05 41.4 3.0 28 86-113 8-35 (196)
147 PRK14605 ruvA Holliday junctio 87.7 0.48 1E-05 41.6 2.9 23 86-108 105-127 (194)
148 PRK13844 recombination protein 87.6 0.28 6.1E-06 43.0 1.4 28 86-113 12-39 (200)
149 PF12836 HHH_3: Helix-hairpin- 87.4 0.57 1.2E-05 33.3 2.7 24 86-109 11-34 (65)
150 PRK14600 ruvA Holliday junctio 87.3 0.55 1.2E-05 41.0 3.0 25 86-111 105-129 (186)
151 PRK00116 ruvA Holliday junctio 87.0 0.62 1.3E-05 40.8 3.2 43 88-132 72-117 (192)
152 PF02371 Transposase_20: Trans 86.9 0.57 1.2E-05 35.4 2.6 41 89-133 2-42 (87)
153 PF14520 HHH_5: Helix-hairpin- 86.7 0.43 9.4E-06 33.3 1.7 43 88-131 4-46 (60)
154 PF05559 DUF763: Protein of un 86.5 3.9 8.4E-05 38.4 8.3 61 67-133 251-314 (319)
155 TIGR01259 comE comEA protein. 86.0 1 2.2E-05 36.3 3.8 59 42-108 59-117 (120)
156 PRK14601 ruvA Holliday junctio 86.0 1 2.2E-05 39.1 4.0 76 88-168 72-153 (183)
157 PF11731 Cdd1: Pathogenicity l 85.9 0.82 1.8E-05 35.1 3.0 28 87-114 10-37 (93)
158 COG1555 ComEA DNA uptake prote 85.3 0.76 1.7E-05 38.6 2.8 23 87-109 95-117 (149)
159 TIGR00084 ruvA Holliday juncti 85.2 1 2.2E-05 39.5 3.6 25 86-110 104-128 (191)
160 PRK14606 ruvA Holliday junctio 84.6 1.2 2.5E-05 39.0 3.7 76 88-168 72-154 (188)
161 COG2003 RadC DNA repair protei 84.5 1.7 3.7E-05 38.8 4.7 57 48-106 24-83 (224)
162 PF12836 HHH_3: Helix-hairpin- 84.5 2.5 5.4E-05 30.0 4.8 52 45-105 8-60 (65)
163 TIGR01259 comE comEA protein. 84.5 0.94 2E-05 36.5 2.9 23 87-109 66-88 (120)
164 PRK13901 ruvA Holliday junctio 83.9 1.5 3.3E-05 38.5 4.1 59 88-151 71-131 (196)
165 PRK14603 ruvA Holliday junctio 83.7 1.5 3.2E-05 38.6 4.0 44 88-132 71-116 (197)
166 PF11798 IMS_HHH: IMS family H 83.5 0.79 1.7E-05 27.8 1.6 16 90-105 12-27 (32)
167 PRK07945 hypothetical protein; 83.3 2.6 5.7E-05 40.2 5.9 58 51-109 8-69 (335)
168 PRK14600 ruvA Holliday junctio 82.9 1 2.2E-05 39.2 2.7 57 88-150 72-130 (186)
169 PRK14602 ruvA Holliday junctio 82.1 1.8 4E-05 38.2 4.1 58 88-150 73-132 (203)
170 PRK14604 ruvA Holliday junctio 81.8 1.8 3.9E-05 38.0 3.9 58 88-150 72-131 (195)
171 PRK02515 psbU photosystem II c 80.4 1.4 3.1E-05 35.8 2.5 29 79-107 48-79 (132)
172 smart00483 POLXc DNA polymeras 79.8 5.1 0.00011 38.2 6.5 55 53-109 13-68 (334)
173 smart00279 HhH2 Helix-hairpin- 79.5 1.5 3.3E-05 27.3 1.9 17 91-107 18-34 (36)
174 TIGR00084 ruvA Holliday juncti 79.3 1.5 3.3E-05 38.4 2.5 21 88-108 71-91 (191)
175 TIGR00575 dnlj DNA ligase, NAD 78.8 7.5 0.00016 40.6 7.8 70 31-108 444-517 (652)
176 PF10391 DNA_pol_lambd_f: Fing 78.5 1.7 3.6E-05 29.6 2.0 23 89-111 2-24 (52)
177 cd00141 NT_POLXc Nucleotidyltr 78.5 4.9 0.00011 37.9 5.9 43 65-109 23-65 (307)
178 PRK13482 DNA integrity scannin 78.2 5.7 0.00012 38.0 6.1 47 30-78 298-344 (352)
179 KOG4548|consensus 78.2 3.9 8.6E-05 36.9 4.8 96 220-328 138-250 (263)
180 PRK00024 hypothetical protein; 78.1 10 0.00022 34.1 7.5 63 13-77 28-93 (224)
181 PRK07956 ligA NAD-dependent DN 76.7 8.2 0.00018 40.4 7.4 42 31-75 457-501 (665)
182 COG1555 ComEA DNA uptake prote 75.9 4.2 9.1E-05 34.1 4.1 55 45-107 91-145 (149)
183 PF03118 RNA_pol_A_CTD: Bacter 73.5 1 2.2E-05 32.3 -0.2 48 57-106 14-61 (66)
184 TIGR00426 competence protein C 73.5 3.6 7.9E-05 29.4 2.8 23 87-109 14-37 (69)
185 TIGR00608 radc DNA repair prot 73.2 17 0.00036 32.5 7.5 55 13-69 18-76 (218)
186 PF14229 DUF4332: Domain of un 72.3 8.9 0.00019 30.9 5.1 75 40-129 17-93 (122)
187 PRK14350 ligA NAD-dependent DN 72.2 16 0.00034 38.3 8.1 39 31-72 448-489 (669)
188 PRK13482 DNA integrity scannin 71.2 4.6 0.0001 38.6 3.6 35 71-105 298-335 (352)
189 COG2003 RadC DNA repair protei 70.9 21 0.00045 32.0 7.4 66 12-78 27-94 (224)
190 cd00080 HhH2_motif Helix-hairp 70.8 2.7 5.9E-05 30.8 1.6 21 88-108 21-41 (75)
191 COG1415 Uncharacterized conser 70.3 11 0.00023 35.9 5.7 29 85-113 274-305 (373)
192 PF14443 DBC1: DBC1 70.2 21 0.00045 29.0 6.6 51 222-278 9-61 (126)
193 smart00483 POLXc DNA polymeras 70.0 3.5 7.6E-05 39.4 2.6 33 79-113 79-111 (334)
194 KOG2534|consensus 70.0 11 0.00023 35.5 5.5 66 65-133 34-107 (353)
195 cd00141 NT_POLXc Nucleotidyltr 69.0 3.8 8.2E-05 38.6 2.6 30 82-113 78-107 (307)
196 KOG2841|consensus 68.9 14 0.00029 33.3 5.8 42 33-76 209-250 (254)
197 COG1796 POL4 DNA polymerase IV 66.8 9.8 0.00021 35.8 4.7 44 65-109 28-73 (326)
198 PF04904 NCD1: NAB conserved r 66.7 21 0.00045 26.3 5.3 51 26-76 19-73 (82)
199 PF00416 Ribosomal_S13: Riboso 66.4 6.3 0.00014 31.0 3.0 41 88-128 14-58 (107)
200 PF14490 HHH_4: Helix-hairpin- 63.9 15 0.00033 27.9 4.7 53 49-108 7-65 (94)
201 PRK14973 DNA topoisomerase I; 60.8 28 0.0006 38.1 7.5 91 37-132 821-919 (936)
202 PRK08609 hypothetical protein; 59.4 7 0.00015 40.2 2.6 25 82-106 81-105 (570)
203 COG0632 RuvA Holliday junction 59.2 5.6 0.00012 35.1 1.6 45 88-132 72-117 (201)
204 PRK08609 hypothetical protein; 58.6 17 0.00036 37.5 5.1 56 52-109 12-68 (570)
205 PRK12766 50S ribosomal protein 57.9 5.8 0.00012 35.6 1.5 20 89-108 36-55 (232)
206 PLN03060 inositol phosphatase- 55.3 44 0.00095 29.6 6.5 92 8-105 21-125 (206)
207 PF12826 HHH_2: Helix-hairpin- 53.1 19 0.00041 25.3 3.3 41 30-72 14-54 (64)
208 COG0272 Lig NAD-dependent DNA 52.4 17 0.00038 37.6 4.0 78 29-108 455-562 (667)
209 PF10343 DUF2419: Protein of u 52.3 44 0.00094 31.2 6.3 51 35-85 59-117 (287)
210 COG0864 NikR Predicted transcr 51.2 22 0.00048 29.3 3.8 32 51-82 17-48 (136)
211 PRK14351 ligA NAD-dependent DN 51.2 12 0.00027 39.3 2.9 67 31-107 474-546 (689)
212 COG4277 Predicted DNA-binding 49.4 13 0.00028 34.8 2.3 22 87-108 328-349 (404)
213 PF01367 5_3_exonuc: 5'-3' exo 49.2 3.9 8.4E-05 31.9 -0.9 28 86-113 15-42 (101)
214 PF00570 HRDC: HRDC domain Blo 49.1 26 0.00057 24.5 3.6 20 84-103 39-58 (68)
215 PF13174 TPR_6: Tetratricopept 46.6 30 0.00065 19.7 3.0 27 15-41 6-32 (33)
216 PRK12766 50S ribosomal protein 45.0 41 0.00088 30.3 4.7 40 32-74 16-57 (232)
217 PRK07758 hypothetical protein; 44.0 18 0.0004 27.7 2.1 21 86-106 64-84 (95)
218 PTZ00134 40S ribosomal protein 42.9 15 0.00033 30.9 1.6 29 81-109 19-50 (154)
219 PRK14976 5'-3' exonuclease; Pr 42.8 15 0.00032 34.2 1.7 21 89-109 191-211 (281)
220 PRK09482 flap endonuclease-lik 41.9 16 0.00035 33.5 1.8 23 89-111 182-204 (256)
221 COG1796 POL4 DNA polymerase IV 41.4 54 0.0012 31.0 5.1 65 31-109 80-148 (326)
222 COG1948 MUS81 ERCC4-type nucle 41.3 35 0.00075 31.2 3.8 23 89-111 182-204 (254)
223 PF13869 NUDIX_2: Nucleotide h 41.2 73 0.0016 27.8 5.6 38 222-275 59-98 (188)
224 CHL00137 rps13 ribosomal prote 40.0 18 0.00038 29.3 1.6 22 88-109 16-37 (122)
225 PRK08097 ligB NAD-dependent DN 39.7 25 0.00053 36.1 2.9 76 30-109 436-540 (562)
226 PRK14667 uvrC excinuclease ABC 39.7 47 0.001 34.2 4.9 24 85-109 542-565 (567)
227 COG1491 Predicted RNA-binding 39.6 19 0.00042 31.1 1.8 42 87-132 128-169 (202)
228 PF13297 Telomere_Sde2_2: Telo 39.6 71 0.0015 22.4 4.2 36 37-72 4-45 (60)
229 cd00008 53EXOc 5'-3' exonuclea 38.6 20 0.00043 32.5 1.8 20 89-108 183-202 (240)
230 COG1948 MUS81 ERCC4-type nucle 38.1 68 0.0015 29.4 5.2 24 86-109 211-234 (254)
231 smart00475 53EXOc 5'-3' exonuc 38.1 22 0.00047 32.7 2.0 21 89-109 186-206 (259)
232 PRK04053 rps13p 30S ribosomal 37.5 28 0.0006 29.2 2.4 29 81-109 14-45 (149)
233 PRK00254 ski2-like helicase; P 37.2 38 0.00082 35.9 3.9 42 68-113 628-669 (720)
234 PRK14670 uvrC excinuclease ABC 36.7 59 0.0013 33.5 5.1 73 18-109 488-566 (574)
235 PF13543 KSR1-SAM: SAM like do 36.7 1.2E+02 0.0025 24.8 5.8 28 37-64 88-115 (129)
236 PRK05179 rpsM 30S ribosomal pr 36.7 22 0.00048 28.7 1.6 22 88-109 16-37 (122)
237 COG1379 PHP family phosphoeste 36.4 64 0.0014 30.7 4.7 47 10-56 305-352 (403)
238 PRK00558 uvrC excinuclease ABC 36.0 40 0.00088 34.9 3.8 20 88-107 542-561 (598)
239 smart00611 SEC63 Domain of unk 35.5 85 0.0019 29.2 5.7 45 58-106 124-168 (312)
240 TIGR00375 conserved hypothetic 35.1 60 0.0013 31.6 4.6 48 9-56 297-345 (374)
241 TIGR01448 recD_rel helicase, p 34.6 40 0.00087 35.8 3.6 56 49-107 76-135 (720)
242 KOG2937|consensus 34.4 24 0.00053 33.3 1.7 146 156-322 34-189 (348)
243 TIGR03631 bact_S13 30S ribosom 33.8 24 0.00052 28.1 1.4 22 88-109 14-35 (113)
244 COG3547 Transposase and inacti 33.5 1.9E+02 0.0041 26.5 7.7 37 68-106 169-205 (303)
245 PF14056 DUF4250: Domain of un 33.4 73 0.0016 21.9 3.5 30 34-63 15-47 (55)
246 TIGR03629 arch_S13P archaeal r 32.7 25 0.00055 29.2 1.4 28 82-109 11-41 (144)
247 PRK14351 ligA NAD-dependent DN 32.6 1.6E+02 0.0034 31.2 7.5 18 89-106 496-513 (689)
248 COG0099 RpsM Ribosomal protein 32.3 34 0.00073 27.5 2.0 28 83-110 8-38 (121)
249 TIGR01448 recD_rel helicase, p 31.6 45 0.00097 35.4 3.4 32 89-121 82-116 (720)
250 PF04919 DUF655: Protein of un 30.9 36 0.00077 29.4 2.0 27 87-113 114-140 (181)
251 PRK04460 nickel responsive reg 30.6 62 0.0013 26.7 3.4 29 51-79 15-43 (137)
252 TIGR01954 nusA_Cterm_rpt trans 29.6 91 0.002 20.1 3.5 39 34-75 8-48 (50)
253 PF11264 ThylakoidFormat: Thyl 29.6 4.1E+02 0.0089 23.7 9.3 98 8-111 18-130 (216)
254 PF13751 DDE_Tnp_1_6: Transpos 29.5 27 0.00058 27.8 1.0 23 175-197 29-51 (125)
255 PRK13266 Thf1-like protein; Re 29.4 4.2E+02 0.0092 23.8 9.6 97 8-111 23-135 (225)
256 TIGR00596 rad1 DNA repair prot 28.8 1.1E+02 0.0023 33.1 5.6 40 31-73 769-808 (814)
257 PRK00630 nickel responsive reg 28.8 70 0.0015 26.8 3.4 29 51-79 23-51 (148)
258 PRK02967 nickel responsive reg 28.8 70 0.0015 26.4 3.4 30 51-80 14-43 (139)
259 KOG2841|consensus 28.7 63 0.0014 29.2 3.3 24 85-108 223-246 (254)
260 PF11480 ImmE5: Colicin-E5 Imm 28.5 20 0.00042 26.6 0.1 15 233-247 25-39 (83)
261 PF02467 Whib: Transcription f 28.3 13 0.00028 26.5 -0.9 17 178-194 31-47 (66)
262 TIGR02793 nikR nickel-responsi 28.2 72 0.0016 26.0 3.3 29 51-79 13-41 (129)
263 COG1468 CRISPR-associated prot 28.2 32 0.00068 30.1 1.3 16 175-190 173-188 (190)
264 PRK01002 nickel responsive reg 27.5 75 0.0016 26.3 3.4 30 51-80 17-46 (141)
265 PF14579 HHH_6: Helix-hairpin- 26.7 51 0.0011 24.8 2.1 26 88-113 26-51 (90)
266 PF01706 FliG_C: FliG C-termin 26.7 91 0.002 24.3 3.6 49 31-79 11-59 (110)
267 COG1623 Predicted nucleic-acid 26.1 94 0.002 29.1 4.0 38 33-72 307-344 (349)
268 PRK01151 rps17E 30S ribosomal 25.4 55 0.0012 22.8 1.8 23 65-87 4-26 (58)
269 PRK04301 radA DNA repair and r 24.9 1E+02 0.0023 28.9 4.3 57 91-153 8-64 (317)
270 PF05166 YcgL: YcgL domain; I 24.3 44 0.00095 24.5 1.2 21 43-63 48-68 (74)
271 PRK14668 uvrC excinuclease ABC 24.2 83 0.0018 32.5 3.7 17 90-106 526-542 (577)
272 PF01930 Cas_Cas4: Domain of u 24.1 42 0.00091 28.0 1.3 15 175-189 147-161 (162)
273 PHA00439 exonuclease 24.0 47 0.001 31.0 1.7 19 89-108 188-206 (286)
274 PRK00254 ski2-like helicase; P 23.9 1.2E+02 0.0026 32.1 5.0 23 86-108 675-697 (720)
275 TIGR03060 PS_II_psb29 photosys 23.8 1.6E+02 0.0035 26.2 5.0 80 8-93 23-115 (214)
276 cd00128 XPG Xeroderma pigmento 23.5 1.3E+02 0.0028 28.3 4.6 18 91-108 225-242 (316)
277 PF08823 PG_binding_2: Putativ 23.4 65 0.0014 23.5 2.0 25 40-64 5-32 (74)
278 PRK14666 uvrC excinuclease ABC 23.2 1.6E+02 0.0034 31.1 5.5 23 86-108 666-688 (694)
279 PF02889 Sec63: Sec63 Brl doma 23.2 1.6E+02 0.0034 27.3 5.2 43 61-107 124-166 (314)
280 PRK01172 ski2-like helicase; P 23.1 5.5E+02 0.012 26.8 9.7 119 28-152 540-669 (674)
281 PRK14670 uvrC excinuclease ABC 23.1 82 0.0018 32.5 3.4 22 88-109 513-534 (574)
282 PRK14666 uvrC excinuclease ABC 23.1 98 0.0021 32.6 4.0 23 88-111 636-658 (694)
283 smart00540 LEM in nuclear memb 22.8 1.8E+02 0.0038 19.0 3.7 33 44-76 2-41 (44)
284 PF14475 Mso1_Sec1_bdg: Sec1-b 22.4 63 0.0014 20.8 1.5 17 114-130 15-31 (41)
285 PF11116 DUF2624: Protein of u 22.1 2.9E+02 0.0062 20.9 5.2 17 152-168 67-83 (85)
286 TIGR00372 cas4 CRISPR-associat 21.5 50 0.0011 27.8 1.3 14 176-189 164-177 (178)
287 PF14964 DUF4507: Domain of un 21.4 3.5E+02 0.0075 26.2 7.0 42 66-107 143-184 (362)
288 PF03755 YicC_N: YicC-like fam 21.4 1.4E+02 0.0031 25.0 4.0 34 65-98 83-116 (159)
289 PLN00047 photosystem II biogen 21.0 2.4E+02 0.0051 26.3 5.5 88 8-101 74-174 (283)
290 PF11372 DUF3173: Domain of un 20.9 1.1E+02 0.0024 21.4 2.6 22 87-109 5-26 (59)
291 PRK14669 uvrC excinuclease ABC 20.8 69 0.0015 33.4 2.3 18 89-106 552-569 (624)
292 PRK02362 ski2-like helicase; P 20.7 1.3E+02 0.0028 32.0 4.4 40 66-109 633-672 (737)
293 PF11842 DUF3362: Domain of un 20.3 1.8E+02 0.0038 24.4 4.2 47 140-186 42-88 (150)
294 PRK13766 Hef nuclease; Provisi 20.2 1.1E+02 0.0024 32.5 3.9 17 91-107 717-733 (773)
295 PRK14671 uvrC excinuclease ABC 20.0 75 0.0016 33.1 2.4 21 89-109 569-589 (621)
No 1
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=2e-81 Score=590.61 Aligned_cols=323 Identities=38% Similarity=0.739 Sum_probs=290.1
Q ss_pred CCCCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHh
Q psy8564 1 MLPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKY 80 (341)
Q Consensus 1 ~~pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~ 80 (341)
+||||.+.|||++||++||+|||++++|.+++.+|+++|||+++|+++++++|.++|+++|||+||++|+++|+.|.++|
T Consensus 21 ~lpWr~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~A~~i~~~~ 100 (350)
T PRK10880 21 TLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLH 100 (350)
T ss_pred CCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHh
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHH
Q psy8564 81 NGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIY 160 (341)
Q Consensus 81 ~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~ 160 (341)
+|.+|+++++|++|||||+|||++||+|+||++.++||+||.||++|+++++..++...+++.++++++.++|.+.+++|
T Consensus 101 ~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~~l~p~~~~~~~ 180 (350)
T PRK10880 101 GGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSEQVTPAVGVERF 180 (350)
T ss_pred CCCchhhHHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCChhHHHHH
Confidence 99999999999999999999999999999999999999999999999999987777778888999999999999999999
Q ss_pred HHHHHHHhhhhcccCCCCCCCCCccccccccccCccccccccc-cCcccceeEEEEEEEeCCEEEEEEeCCCCccccccc
Q psy8564 161 TQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKINNFLIKN-KKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLS 239 (341)
Q Consensus 161 ~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~-kk~~~~~~~~~~ii~~~g~vLl~kR~~~g~~~GlWE 239 (341)
|++||+||+++|+|++|+|+.|||++.|.+++.+.+..+|+|+ |++.+.+..+++++.++|++||.||+++|+|+||||
T Consensus 181 nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~~~~P~k~~k~~~~~~~~~~~~~~~~~~~~l~~r~~~gl~~gl~~ 260 (350)
T PRK10880 181 NQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQTLPERTGYFLLLQHGDEVWLEQRPPSGLWGGLFC 260 (350)
T ss_pred HHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCHhhCCCCCCCCCCCeEEEEEEEEEECCEEEEEECCccChhhcccc
Confidence 9999999999999999999999999999999999999999998 555666666777777889999999999999999999
Q ss_pred ccccccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEEEEEEEEEecccccccCCCCceeee
Q psy8564 240 FPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNNFIWYP 318 (341)
Q Consensus 240 FPgvE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~l~~~~~~~~~~~~~~~~~~~~W~~ 318 (341)
||+++..+ ..+++.+++|+. .....+++++|+|||++|+|++|.+...+........+..|++
T Consensus 261 fP~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~H~fTH~~~~~~~~~~~~~~~~~~~~~~~~~w~~ 324 (350)
T PRK10880 261 FPQFADEE----------------ELRQWLAQRGIAADNLTQLTAFRHTFSHFHLDIVPMWLPVSSFTGCMDEGNGLWYN 324 (350)
T ss_pred CCCCcchh----------------hHHHHHHhcCCchhhhcccCceEEEEeeEEEEEEEEEEEccccccccCCcCCeEec
Confidence 99975222 234555777775 3334478999999999999999988765311101114567999
Q ss_pred CCCCCCCCCCHHHHHHHHHhh
Q psy8564 319 IKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 319 ~~el~~~~~~~a~~~il~~l~ 339 (341)
++++.+++||++++|+++.++
T Consensus 325 ~~~~~~~~~p~~~~k~l~~~~ 345 (350)
T PRK10880 325 LAQPPSVGLAAPVERLLQQLR 345 (350)
T ss_pred hHHhcccCCcHHHHHHHHHhc
Confidence 999999999999999999875
No 2
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.8e-76 Score=541.33 Aligned_cols=315 Identities=39% Similarity=0.711 Sum_probs=280.7
Q ss_pred CCCCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHh
Q psy8564 1 MLPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKY 80 (341)
Q Consensus 1 ~~pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~ 80 (341)
+||||.+.|||.+|||+||+|||++++|.++|.+|+++|||+++||+|+++|+.++|.|+|||+||++|+++|+.|+++|
T Consensus 25 ~LPWR~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A~~v~~~~ 104 (342)
T COG1194 25 DLPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERH 104 (342)
T ss_pred cCCCCCCCCcceehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCC-HHH
Q psy8564 81 NGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKN-IEI 159 (341)
Q Consensus 81 ~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~-~~~ 159 (341)
+|.+|++.+.|.+|||||+|||++||+|+||++.++||+||.||++|+++++.++....+++.++++++.+++++. +++
T Consensus 105 ~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~p~~~~~~ 184 (342)
T COG1194 105 GGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPGD 184 (342)
T ss_pred CCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHHhcCCCCChHH
Confidence 9999999999999999999999999999999999999999999999999999887766788999999999665555 999
Q ss_pred HHHHHHHHhhhhcccCCCCCCCCCccccccccccCccccccccc-cCcccceeEEEEEEEeCCEEEEEEeCCCCcccccc
Q psy8564 160 YTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKINNFLIKN-KKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLL 238 (341)
Q Consensus 160 ~~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~-kk~~~~~~~~~~ii~~~g~vLl~kR~~~g~~~GlW 238 (341)
|||+|||+|+.||++++|+|+.|||++.|.++..|.+..||+|+ |+.++....+.+++..+|++++.||+++|+|+|||
T Consensus 185 fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~~~~~~~~~~~~~~~~~~l~kr~~~gl~~gl~ 264 (342)
T COG1194 185 FNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKLPRRFAAFLILNRDGEVLLEKRPEKGLLGGLW 264 (342)
T ss_pred HHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCcccCCCcCcccccchheeeEEEEccCcchhhhhCcccCceeccc
Confidence 99999999999999999999999999999999999999999999 66666444455666678999999999999999999
Q ss_pred cccccccccchhhhccchhhhhHHHHHHHHHHhcCCcccccccCcEEEEeeceEEEEEEEEEEecccccccCCCCceeee
Q psy8564 239 SFPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNNFIWYP 318 (341)
Q Consensus 239 EFPgvE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~~~~~~~~~~~h~~~h~~~~l~~~~~~~~~~~~~~~~~~~~W~~ 318 (341)
+||.+|.++.. .+...+.++.. +.+++++|+|||++++++ +...... .. .+..|++
T Consensus 265 ~fP~~e~~~~~----------------~~~~~~~~~~~--~~~~~~~H~fth~~l~i~-~~a~~~~----~~-~~~~w~~ 320 (342)
T COG1194 265 CFPQFEDEADL----------------LDWLAADGLAA--EPLGAFRHTFTHFRLTIE-LRASASL----VL-SDGRWYN 320 (342)
T ss_pred ccccccccchh----------------hhHhhhccccc--ccccceeeeeeEEEEEEE-EEeeccc----CC-CCceecc
Confidence 99998866522 11122222211 568899999999999999 5554332 22 3789999
Q ss_pred CCCCCCCCCCHHHHHHHHHhh
Q psy8564 319 IKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 319 ~~el~~~~~~~a~~~il~~l~ 339 (341)
++++..+++|.+.+++++.+.
T Consensus 321 ~~~~~~~~l~~p~~k~l~~~~ 341 (342)
T COG1194 321 LSDLESIGLPAPVKKLLQQLK 341 (342)
T ss_pred ccccccccccHHHHHHHHHhc
Confidence 999999999999999998875
No 3
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=100.00 E-value=3.5e-70 Score=500.77 Aligned_cols=247 Identities=46% Similarity=0.885 Sum_probs=232.8
Q ss_pred CCCCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHh
Q psy8564 1 MLPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKY 80 (341)
Q Consensus 1 ~~pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~ 80 (341)
++|||.+.|||++||++||+|||++++|.+++.+|+++|||+++|+++++++|.++|+++|||+||++|+++|+.|.++|
T Consensus 17 ~lpWr~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~A~~i~~~~ 96 (275)
T TIGR01084 17 TLPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQEVVEEF 96 (275)
T ss_pred CCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHH
Q psy8564 81 NGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIY 160 (341)
Q Consensus 81 ~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~ 160 (341)
+|.+|+++++|++|||||+|||++|++|+||++.++||+||.||++|+++++..++...+++.++..++.++|.+.+++|
T Consensus 97 ~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~~~ 176 (275)
T TIGR01084 97 GGEFPQDFEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLPKADPEAF 176 (275)
T ss_pred CCCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHCChhhHHHH
Confidence 99999999999999999999999999999999999999999999999999987777778888999999999999999999
Q ss_pred HHHHHHHhhhhcccCCCCCCCCCccccccccccCccccccccc-cCcccceeEEEEEEEe-CCEEEEEEeCCCCcccccc
Q psy8564 161 TQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNKINNFLIKN-KKNIKNCSIIMFIVID-DDYVLFQKRSNKGIWGGLL 238 (341)
Q Consensus 161 ~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~-kk~~~~~~~~~~ii~~-~g~vLl~kR~~~g~~~GlW 238 (341)
|++||+||+++|+|++|+|+.|||++.|.++..+.+..||+|+ ||.++....+++++.+ +|++|+.||+++|+|+|||
T Consensus 177 n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~gl~ 256 (275)
T TIGR01084 177 NQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAAPPERTTYFLVLQNYDGEVLLEQRPEKGLWGGLY 256 (275)
T ss_pred HHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCHhhcCCCCCCCCCCeEEEEEEEEEeCCCeEEEEeCCCCchhhccc
Confidence 9999999999999999999999999999999999999999998 5555555556666554 7899999999999999999
Q ss_pred ccccccccc
Q psy8564 239 SFPEWILKD 247 (341)
Q Consensus 239 EFPgvE~~E 247 (341)
|||++|..+
T Consensus 257 ~~p~~~~~~ 265 (275)
T TIGR01084 257 CFPQFEDED 265 (275)
T ss_pred cCCCCCchh
Confidence 999976544
No 4
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=5.5e-69 Score=494.02 Aligned_cols=282 Identities=34% Similarity=0.592 Sum_probs=245.1
Q ss_pred HhhhcChhhHHH-HHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCC
Q psy8564 19 MLQQTQVNTVIP-YYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGI 97 (341)
Q Consensus 19 l~qqt~~~~~~~-~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GI 97 (341)
|+|||++++|.+ +|++|+++|||+++||+++++||+++|+++|||+||++|+++|+.|.++|+|.+|.++++|++||||
T Consensus 1 mlQQT~v~~v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGI 80 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGI 80 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCC
Confidence 799999999986 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhhhhcccCCC
Q psy8564 98 GQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKP 177 (341)
Q Consensus 98 G~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~~~C~~~~P 177 (341)
|+|||++||+|+||++.++||+||+||++|++|+..+.+. +.++..++.++|.+.++++|++||+||+++|+| +|
T Consensus 81 G~kTA~aIl~~af~~~~~~VD~nV~RVl~Rl~g~~~~~~~----~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~iC~~-~P 155 (289)
T PRK13910 81 GAYTANAILCFGFREKSACVDANIKRVLLRLFGLDPNIHA----KDLQIKANDFLNLNESFNHNQALIDLGALICSP-KP 155 (289)
T ss_pred CHHHHHHHHHHHCCCCcCcccHHHHHHHHHHhcCCCCccH----HHHHHHHHHhCCccchHHHHHHHHHHhHHHcCC-CC
Confidence 9999999999999999999999999999999998765433 457777888999999999999999999999999 79
Q ss_pred CCCCCCccccccccccCccccccccccCcccceeEEEEEEEeCCEEEEEEeCCCCcccccccccccccccchhhhccchh
Q psy8564 178 KCKVCPLQLCCISYKTNKINNFLIKNKKNIKNCSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFVDNNL 257 (341)
Q Consensus 178 ~C~~Cpl~~~C~~~~~~~~~~~p~~~kk~~~~~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPgvE~~E~~~~~~~~~~ 257 (341)
+|+.|||++.|.++..+.+..+ |+||.++......+++.++|++||.||+ +|+|+||||||+++...
T Consensus 156 ~C~~CPl~~~C~~~~~~~~~~~--~~kk~~~~~~~~~~~~~~~~~~ll~kr~-~~l~~gl~~fP~~~~~~---------- 222 (289)
T PRK13910 156 KCAICPLNPYCLGKNNPEKHTL--KKKQEIVQEERYLGVVIQNNQIALEKIE-QKLYLGMHHFPNLKENL---------- 222 (289)
T ss_pred CCCCCcChhhhhhhhcCCcccc--CCCCCCCceEEEEEEEEECCEEEEEECC-CchhcccccCCCChhhh----------
Confidence 9999999999999999988865 4433333344444445578899999995 78999999999864210
Q ss_pred hhhHHHHHHHHHHhcCCcccccccCcEEEEeeceEEEEEEEEEEecccccccCCCCceeeeCCCCCCCCCCHHHHHHHHH
Q psy8564 258 KNLIELEIKKFISSFGFIKNYLILPIISHKLTHLQFKIVPCHIFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQ 337 (341)
Q Consensus 258 ~~~~~a~~rE~~ee~g~~~~~~~~~~~~h~~~h~~~~l~~~~~~~~~~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~ 337 (341)
+.. ...+++++|+|||++|++++|.+..... . .+.+|++++++.+++||++.+++++.
T Consensus 223 ---------------~~~--~~~~~~~~H~fTH~~~~~~~~~~~~~~~---~--~~~~w~~~~~~~~~~~p~~~~k~~~~ 280 (289)
T PRK13910 223 ---------------EYK--LPFLGAIKHSHTKFKLNLNLYLAAIKDL---K--NPIRFYSLKDLETLPISSMTLKILNF 280 (289)
T ss_pred ---------------ccc--ccccCceEEEEEeEEEEEEEEEEEeccC---C--ccceEecHHHhhhcCCcHHHHHHHHH
Confidence 011 1136789999999999999998875421 1 46699999999999999999999998
Q ss_pred hhc
Q psy8564 338 IIQ 340 (341)
Q Consensus 338 l~~ 340 (341)
+++
T Consensus 281 l~~ 283 (289)
T PRK13910 281 LKQ 283 (289)
T ss_pred Hhh
Confidence 875
No 5
>KOG2457|consensus
Probab=100.00 E-value=2.1e-59 Score=427.89 Aligned_cols=317 Identities=30% Similarity=0.517 Sum_probs=261.7
Q ss_pred CCCCCCC---------CChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCH-HHHHHHHhhcCcHHHHHHHH
Q psy8564 1 MLPWQNT---------KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKL-ENVMELWSGLGYYSRARNLH 70 (341)
Q Consensus 1 ~~pwr~~---------~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~-~~l~~~l~~~G~~~rA~~i~ 70 (341)
|||||+. +..|++|||+||+|||++.+|..||.+|++++||..+|+.|+. .++..+|.|+|||+|+|+|+
T Consensus 107 dLPWR~r~sEde~DwerRaYeVwVSEiMLQQTrV~TV~~YYt~WMqkwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ 186 (555)
T KOG2457|consen 107 DLPWRNRRSEDEKDWERRAYEVWVSEIMLQQTRVQTVMKYYTRWMQKWPTLYDLAQASLEKEVNELWAGLGYYRRARRLL 186 (555)
T ss_pred cCccccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 6999975 3579999999999999999999999999999999999999999 79999999999999999999
Q ss_pred HHHHHhHHHhCCCCccchHHHhc-CCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHH
Q psy8564 71 ICAKLVFFKYNGIFPKNFISLIN-LPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAI 149 (341)
Q Consensus 71 ~~a~~i~~~~~g~~p~~~~~L~~-l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~ 149 (341)
+.|+.+++..+|.+|.+-+.|++ +||||+|||++|+++|||++.-+||+||.||++|...|..+.+.......+|.++.
T Consensus 187 ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~~wkLA~ 266 (555)
T KOG2457|consen 187 EGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQSSWKLAA 266 (555)
T ss_pred HHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHHHHHHHH
Confidence 99999999999999999999997 99999999999999999999999999999999999999888888888899999999
Q ss_pred hhCCCCCHHHHHHHHHHHhhhhcccCCCCCCCCCccccccccccCc----------------------------------
Q psy8564 150 DLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNK---------------------------------- 195 (341)
Q Consensus 150 ~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~---------------------------------- 195 (341)
.++++..+|+|||++|++|++.|||.+|.|+.||+.+.|++|+...
T Consensus 267 qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~~Eqn~~i~~g~t~~~dve~~~P~~~~C~vCv~~ips 346 (555)
T KOG2457|consen 267 QLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQLSEQNRTISVGDTYPTDVEKAKPRHDFCCVCVLEIPS 346 (555)
T ss_pred HhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhHhhhcceeecCCcCCccHhhcCCCCCceeEeecCCCC
Confidence 9999999999999999999999999999999999999999998211
Q ss_pred --------cccccccccCcccceeEEEEEEEe-------CCEEEEEEeCCCCcccccccccccccccchhhhccchhhhh
Q psy8564 196 --------INNFLIKNKKNIKNCSIIMFIVID-------DDYVLFQKRSNKGIWGGLLSFPEWILKDKIINFVDNNLKNL 260 (341)
Q Consensus 196 --------~~~~p~~~kk~~~~~~~~~~ii~~-------~g~vLl~kR~~~g~~~GlWEFPgvE~~E~~~~~~~~~~~~~ 260 (341)
+..||++..+.++......+|+.. .+.||+.+||+.|+++|||+||.|+.+|.. .+..
T Consensus 347 ~e~~Qs~gv~~~p~~p~~~~~reE~~~v~~~e~~dp~t~~~~ilv~~rp~~gllagLw~fpti~~~e~s------e~~~- 419 (555)
T KOG2457|consen 347 LERNQSGGVFVLPKRPEQLAGREEFPSVILNEEADPATRRNAILVYLRPAFGLLAGLWKFPTIVSRELS------EFVH- 419 (555)
T ss_pred chhhccCcEEEeccChhhcCcccccceeeeeccCCchhhcceeEEEeccchhHHHHhhhcCceeccCcc------hHHH-
Confidence 344555552222333333333332 468999999999999999999998776532 1111
Q ss_pred HHHHH-HHHHHhcCCc--cccccc---CcEEEEeeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCC
Q psy8564 261 IELEI-KKFISSFGFI--KNYLIL---PIISHKLTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 261 ~~a~~-rE~~ee~g~~--~~~~~~---~~~~h~~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~ 324 (341)
..|.+ |.+...++.. ..+... +.+.|+|||+.++-++|.....+ .+.......++|++..+|+.
T Consensus 420 ~~a~~q~~v~~w~~~~~~t~~~~~~~~G~~~htfshi~~ts~V~~~a~~~~~~vt~~p~~~~wi~q~~l~h 490 (555)
T KOG2457|consen 420 IFAHIQRKVYVWLLVVQLTGGTEDLFKGQAKHTFSHICVTSDVLSTAGLTSAVVTVPPFRLQWIKQLSLDH 490 (555)
T ss_pred HHHHHHHHHHHHhcccccccchhhhcccchhhhhhhhhhHHHHHHHhhcCCCccccCCcccchhhhhhhHH
Confidence 23333 3366666654 333444 89999999999988887433222 22222236789999888854
No 6
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.5e-51 Score=356.56 Aligned_cols=182 Identities=29% Similarity=0.472 Sum_probs=172.9
Q ss_pred CCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCc
Q psy8564 7 TKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFP 85 (341)
Q Consensus 7 ~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p 85 (341)
..|||++||+.||||||+++.+.++..+|+++||||++|+++++++|.++|+..||| +||++|+++|+.|+++|+|.+|
T Consensus 26 ~~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP 105 (211)
T COG0177 26 FKDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVP 105 (211)
T ss_pred cCCcHHHHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCC
Confidence 479999999999999999999999999999999999999999999999999999999 5999999999999999999999
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLM 165 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~ 165 (341)
+++++|++|||||+|||++||+++||.|.++|||||.||.+|++..+ ..++.++++.|.+ ++|.+.|..+|.+|+
T Consensus 106 ~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~----~iP~~~~~~~h~~lI 180 (211)
T COG0177 106 DTREELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMK----LIPKELWTDLHHWLI 180 (211)
T ss_pred chHHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHH----HCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999996665 5667777776654 799999999999999
Q ss_pred HHhhhhcccCCCCCCCCCcccccccccc
Q psy8564 166 DFGSIICKKIKPKCKVCPLQLCCISYKT 193 (341)
Q Consensus 166 ~~G~~~C~~~~P~C~~Cpl~~~C~~~~~ 193 (341)
.|||.+|++++|+|+.||++++|+++..
T Consensus 181 ~~GR~iC~ar~P~C~~C~l~~~C~~~~~ 208 (211)
T COG0177 181 LHGRYICKARKPRCEECPLADLCPSAGK 208 (211)
T ss_pred HhhhhhccCCCCCcCcccchhhCchhcc
Confidence 9999999999999999999999999875
No 7
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=2.5e-49 Score=350.34 Aligned_cols=185 Identities=19% Similarity=0.297 Sum_probs=171.5
Q ss_pred CCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHH-HHHHHHHHHHHhHHHhC
Q psy8564 3 PWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYS-RARNLHICAKLVFFKYN 81 (341)
Q Consensus 3 pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~-rA~~i~~~a~~i~~~~~ 81 (341)
+|+..+|||++||++||||||++.++.+++.+|+.+||||++|+++++++|.++|+++|||+ ||++|+++|+.+.++|+
T Consensus 22 ~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~ 101 (211)
T PRK10702 22 TELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHN 101 (211)
T ss_pred CCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcC
Confidence 68889999999999999999999999999999999999999999999999999999999995 99999999999999999
Q ss_pred CCCccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHH
Q psy8564 82 GIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYT 161 (341)
Q Consensus 82 g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~ 161 (341)
|.+|+++++|++|||||+|||++||+|+||++.++||+||.||++|+++.. ..++..+++. .+..+|.+.+.++|
T Consensus 102 ~~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~-~~~~~~~~~~----l~~~lp~~~~~~~~ 176 (211)
T PRK10702 102 GEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAP-GKNVEQVEEK----LLKVVPAEFKVDCH 176 (211)
T ss_pred CCCCchHHHHhcCCcccHHHHHHHHHHHcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHH----HHHhCCchHHHHHH
Confidence 999999999999999999999999999999999999999999999996654 3344444443 45578998899999
Q ss_pred HHHHHHhhhhcccCCCCCCCCCccccccccc
Q psy8564 162 QGLMDFGSIICKKIKPKCKVCPLQLCCISYK 192 (341)
Q Consensus 162 ~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~ 192 (341)
.+||+||+.+|++++|+|+.|||++.|.++.
T Consensus 177 ~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~ 207 (211)
T PRK10702 177 HWLILHGRYTCIARKPRCGSCIIEDLCEYKE 207 (211)
T ss_pred HHHHHHhHHHcCCCCCCCCCCcChhhcCccc
Confidence 9999999999999999999999999999764
No 8
>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=100.00 E-value=6.8e-42 Score=300.15 Aligned_cols=170 Identities=25% Similarity=0.410 Sum_probs=156.9
Q ss_pred CCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHH-HHHHHHHHHHHhHHHhCCC
Q psy8564 5 QNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYS-RARNLHICAKLVFFKYNGI 83 (341)
Q Consensus 5 r~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~-rA~~i~~~a~~i~~~~~g~ 83 (341)
...+|||++||++||+|||+++++.+++.+|+++||||++|+++++++|.++|+++||++ ||++|+++|+.+.++|+|.
T Consensus 21 ~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~ 100 (191)
T TIGR01083 21 LDYNNPFELLVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGE 100 (191)
T ss_pred cCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCC
Confidence 345899999999999999999999999999999999999999999999999999999995 9999999999999999999
Q ss_pred CccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHH
Q psy8564 84 FPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQG 163 (341)
Q Consensus 84 ~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~ 163 (341)
+|+++++|++|||||+|||++||+|++|++.++||+||.|+++|++... ..+++ .+++.++.++|.+.+.+||++
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~-~~~~~----~~~~~l~~~~p~~~~~~~h~~ 175 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSK-GKDPD----KVEEELLKLIPREFWTKLHHW 175 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC-CCCHH----HHHHHHHHHCCchhHHHHHHH
Confidence 9999999999999999999999999999999999999999999986543 33443 344566778999999999999
Q ss_pred HHHHhhhhcccCCCCC
Q psy8564 164 LMDFGSIICKKIKPKC 179 (341)
Q Consensus 164 l~~~G~~~C~~~~P~C 179 (341)
||+||+.+|++++|+|
T Consensus 176 li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 176 LILHGRYTCKARKPLC 191 (191)
T ss_pred HHHHhHHhcCCCCCCC
Confidence 9999999999999999
No 9
>KOG1921|consensus
Probab=100.00 E-value=4.1e-37 Score=266.88 Aligned_cols=182 Identities=23% Similarity=0.348 Sum_probs=168.4
Q ss_pred ChHHHHHHHHHhhhcChhhHHHHHHHHHHhC-CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCcc
Q psy8564 9 NTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF-PNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPK 86 (341)
Q Consensus 9 ~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~-pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~ 86 (341)
-.|++||+.+||.||.++....+..||.+.. .|++++.++++..|.++|..+||| +||.||++.|+.+.++|+|++|+
T Consensus 77 ~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~ 156 (286)
T KOG1921|consen 77 RRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPD 156 (286)
T ss_pred HhHHHHHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCch
Confidence 3599999999999999999999999999988 899999999999999999999999 59999999999999999999999
Q ss_pred chHHHhcCCCCCHHHHHHHHHHHhCC-eeeccChhHHHHHHHHhcccCCc-chHHHHHHHHHHHHhhCCCCCHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVFAYGK-RNAILDGNVKRILIRVLGINCSL-NIKFIEKKLWRYAIDLLPKKNIEIYTQGL 164 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~~~~-~~~~vD~~v~Rvl~Rl~~~~~~~-~~~~~~~~l~~~~~~~~p~~~~~~~~~~l 164 (341)
+.++|++|||||||+|..+|..|+|. ..+.||+||.|+.+|+++++... +++.++..| +.|+|.+.|.++|..|
T Consensus 157 ~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aL----q~wLPk~lW~eIN~lL 232 (286)
T KOG1921|consen 157 TVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVAL----QQWLPKSLWVEINHLL 232 (286)
T ss_pred hHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHH----HHhCcHHHHhhhhcee
Confidence 99999999999999999999999997 68889999999999999998533 355666555 5599999999999999
Q ss_pred HHHhhhhcccCCCCCCCCCc-cccccccccC
Q psy8564 165 MDFGSIICKKIKPKCKVCPL-QLCCISYKTN 194 (341)
Q Consensus 165 ~~~G~~~C~~~~P~C~~Cpl-~~~C~~~~~~ 194 (341)
+.||+++|+|++|+|+.|-+ ++.|++....
T Consensus 233 VGFGQ~iC~p~~prC~~C~~~~~~Cpss~~~ 263 (286)
T KOG1921|consen 233 VGFGQTICTPRRPRCGLCLLSRDLCPSSFKE 263 (286)
T ss_pred ecccceeeecCCCCccccccCcccCchhhhh
Confidence 99999999999999999999 6999996533
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=3.4e-36 Score=265.99 Aligned_cols=171 Identities=15% Similarity=0.201 Sum_probs=146.1
Q ss_pred CCCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHh-------CCCHHHHHhCCHHHHHHHHhhcCcHH-HHHHHHHHH
Q psy8564 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKK-------FPNIMSLAQAKLENVMELWSGLGYYS-RARNLHICA 73 (341)
Q Consensus 2 ~pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~-------~pt~~~la~~~~~~l~~~l~~~G~~~-rA~~i~~~a 73 (341)
.+||...+||++||++||+|||+++++..++.+|.++ +|||++|+++++++|+++|+++|||+ ||++|+++|
T Consensus 22 ~~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la 101 (218)
T PRK13913 22 AWWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLS 101 (218)
T ss_pred CCCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 4799999999999999999999999999999999884 67999999999999999999999995 999999999
Q ss_pred HHhHHHhCC----CCccchHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHH
Q psy8564 74 KLVFFKYNG----IFPKNFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAI 149 (341)
Q Consensus 74 ~~i~~~~~g----~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~ 149 (341)
+.+.++|++ ..++++++|+++||||+|||++||+|++|+|.++||+|+.||++|+ |+.. .++.+.++.+.....
T Consensus 102 ~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~Rl-G~~~-~~y~~~~~~~~~~l~ 179 (218)
T PRK13913 102 ENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKL-GIEI-EDYDELQHFFEKGVQ 179 (218)
T ss_pred HHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHc-CCCC-CCHHHHHHHHHHhhh
Confidence 999999877 2467899999999999999999999999999999999999999998 5532 345444444433221
Q ss_pred hhC-------CC-----CCHHHHHHHHHHHhhhhccc
Q psy8564 150 DLL-------PK-----KNIEIYTQGLMDFGSIICKK 174 (341)
Q Consensus 150 ~~~-------p~-----~~~~~~~~~l~~~G~~~C~~ 174 (341)
.-+ |. ..+.+||..+++||+..|..
T Consensus 180 ~~~~~~~~~~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 180 ENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred hhhhhhhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 100 21 24899999999999999964
No 11
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=5e-33 Score=236.98 Aligned_cols=185 Identities=24% Similarity=0.381 Sum_probs=161.5
Q ss_pred CCCCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhC-CCHHHHHhCCHHHHHHHHhhcCcHH-HHHHHHHHHHHhHHH
Q psy8564 2 LPWQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF-PNIMSLAQAKLENVMELWSGLGYYS-RARNLHICAKLVFFK 79 (341)
Q Consensus 2 ~pwr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~-pt~~~la~~~~~~l~~~l~~~G~~~-rA~~i~~~a~~i~~~ 79 (341)
.-||...+-+|+++++||.|+|++++|..+.+++.... .++.+|..++.++|.+++++.|||+ ||++|+.+++.++..
T Consensus 22 q~WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~ 101 (215)
T COG2231 22 QGWWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKF 101 (215)
T ss_pred ccCCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999999999999999999765 5899999999999999999999996 999998888888876
Q ss_pred hCC---CCcc-chHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCC
Q psy8564 80 YNG---IFPK-NFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKK 155 (341)
Q Consensus 80 ~~g---~~p~-~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~ 155 (341)
|.+ .-+. .|++|++++|||+.|||+||++++++|.|+||.+.+|++.|++++.++ +.++++ +..+.-+|.+
T Consensus 102 ~~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k-~ydeik----~~fe~~l~~~ 176 (215)
T COG2231 102 FINLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEK-KYDEIK----ELFEENLPEN 176 (215)
T ss_pred hhhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHH----HHHHhcchhH
Confidence 543 2222 499999999999999999999999999999999999999999888765 554444 4444445544
Q ss_pred --CHHHHHHHHHHHhhhhcccCCCCCCCCCccccccccc
Q psy8564 156 --NIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYK 192 (341)
Q Consensus 156 --~~~~~~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~ 192 (341)
.+.+||..++.||+.+|+. .|.|+.|||...|..++
T Consensus 177 ~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 177 LRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred HHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 4789999999999999986 69999999999998874
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.97 E-value=4.1e-31 Score=223.14 Aligned_cols=148 Identities=32% Similarity=0.445 Sum_probs=137.6
Q ss_pred HhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCC
Q psy8564 19 MLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFISLINLPGI 97 (341)
Q Consensus 19 l~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GI 97 (341)
|+|||+++++..++.+|.+.||||++|+++++++|.++|+++||+ +||++|+++|+.+.+.++|.+|+++++|++||||
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GI 80 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGV 80 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCC
Confidence 689999999999999999999999999999999999999999998 5999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhhh
Q psy8564 98 GQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGSI 170 (341)
Q Consensus 98 G~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~~ 170 (341)
|+|||++|++|+++++.+++|+|+.|+++|+++++..+++ +.++++++.++|.+.+..+|++++.+|+.
T Consensus 81 G~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~----~~~~~~~~~~~p~~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 81 GRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTP----EEVEKLLEKLLPKEDWRELNLLLIDFGRT 149 (149)
T ss_pred cHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCH----HHHHHHHHHHCCHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999888654444 45677788899988899999999999973
No 13
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.97 E-value=1.2e-30 Score=222.40 Aligned_cols=154 Identities=32% Similarity=0.475 Sum_probs=141.3
Q ss_pred HHHHHHHHHhhhcChhhHHHHHHHHHHhC-CCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCC---cc
Q psy8564 11 YYIWLSEIMLQQTQVNTVIPYYQRFLKKF-PNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIF---PK 86 (341)
Q Consensus 11 ~~~lv~~il~qqt~~~~~~~~~~~l~~~~-pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~---p~ 86 (341)
|++|+++||+|||+++++..++.+|.++| |||++|+++++++|.+++.++||.+||++|+++|+.+.+++++.. ++
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~~~~~ 80 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDPD 80 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccCCCcc
Confidence 78999999999999999999999999999 999999999999999999999955799999999999999988866 78
Q ss_pred chHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMD 166 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~ 166 (341)
.+++|++|||||+|||+++++|+++.+.+|+|+|+.|+++|+++++..++. +.+++.++.+.|......+|+.|++
T Consensus 81 ~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~l~~ 156 (158)
T cd00056 81 AREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTP----EELEELLEELLPKPYWGEANQALMD 156 (158)
T ss_pred cHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCH----HHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 899999999999999999999999988999999999999999887544444 4577778889987789999999999
Q ss_pred Hh
Q psy8564 167 FG 168 (341)
Q Consensus 167 ~G 168 (341)
+|
T Consensus 157 ~g 158 (158)
T cd00056 157 LG 158 (158)
T ss_pred cC
Confidence 87
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.95 E-value=1.7e-27 Score=208.70 Aligned_cols=156 Identities=20% Similarity=0.046 Sum_probs=131.3
Q ss_pred CCCCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcC--cHH-HHHHHHHHHHH---hH
Q psy8564 4 WQNTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLG--YYS-RARNLHICAKL---VF 77 (341)
Q Consensus 4 wr~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G--~~~-rA~~i~~~a~~---i~ 77 (341)
|....|||+.||++||||||++.++..++.+|. ++.+ +++.++|+++|+++| ||+ ||++|+++++. +.
T Consensus 31 ~~~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~ 104 (208)
T PRK01229 31 KGDEEDLFSELSFCILTANSSAEGGIKAQKEIG-----DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLK 104 (208)
T ss_pred ccccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-----HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHH
Confidence 446799999999999999999999999999993 4566 899999999999995 885 99999999987 55
Q ss_pred HHh--CCCCccchHHHh-cCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCC------cchHHHHHHHHHHH
Q psy8564 78 FKY--NGIFPKNFISLI-NLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCS------LNIKFIEKKLWRYA 148 (341)
Q Consensus 78 ~~~--~g~~p~~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~------~~~~~~~~~l~~~~ 148 (341)
+.+ +++.|+++++|+ ++||||+|||++||++.+.++.++||+|+.|++.|++.++.. .++.++++.+.+++
T Consensus 105 ~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~ 184 (208)
T PRK01229 105 EIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIA 184 (208)
T ss_pred HHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHH
Confidence 565 788999999999 999999999999997665589999999999999999777652 45678888888887
Q ss_pred HhhCCCCCHHHHHHHHHHH
Q psy8564 149 IDLLPKKNIEIYTQGLMDF 167 (341)
Q Consensus 149 ~~~~p~~~~~~~~~~l~~~ 167 (341)
..+- -..+.+...|+..
T Consensus 185 ~~~~--~~~~~Ldl~~w~~ 201 (208)
T PRK01229 185 EELG--ISLGELDLYIWYK 201 (208)
T ss_pred HHcC--CCHHHHHHHHHHH
Confidence 7542 2356666666543
No 15
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=99.94 E-value=4.4e-26 Score=213.62 Aligned_cols=158 Identities=20% Similarity=0.232 Sum_probs=128.8
Q ss_pred CChHHHHHHHHHhhhcChhhHHHHHHHHHH---------------hCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQTQVNTVIPYYQRFLK---------------KFPNIMSLAQAKLENVMELWSGLGYYSRARNLHIC 72 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt~~~~~~~~~~~l~~---------------~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~ 72 (341)
.||||++|++|++||+++.++.+++.+|.+ .||||++|++++.++ .|+.+|+..||++|+++
T Consensus 117 ~d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g~Ra~~I~~~ 193 (310)
T TIGR00588 117 QDPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLGYRARYIRET 193 (310)
T ss_pred CCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCHHHHHHHHHH
Confidence 399999999999999999999999999975 389999999876543 45678886699999999
Q ss_pred HHHhHHHhCCC----------CccchHHHhcCCCCCHHHHHHHHHHHhCCe-eeccChhHHHHHHHHhcccCCc-----c
Q psy8564 73 AKLVFFKYNGI----------FPKNFISLINLPGIGQSTASAIRVFAYGKR-NAILDGNVKRILIRVLGINCSL-----N 136 (341)
Q Consensus 73 a~~i~~~~~g~----------~p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~vD~~v~Rvl~Rl~~~~~~~-----~ 136 (341)
|+.+.+++++. .++.+++|++|||||+|||+||++|+++++ ++|+|+||+|+++|+|+..... .
T Consensus 194 A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~ 273 (310)
T TIGR00588 194 ARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGP 273 (310)
T ss_pred HHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccC
Confidence 99999977654 356789999999999999999999999996 7889999999999999875432 1
Q ss_pred hHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhh
Q psy8564 137 IKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGS 169 (341)
Q Consensus 137 ~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~ 169 (341)
....++.+++++.+.+++ ..+..++.|+.+.+
T Consensus 274 ~~~~~~~i~~~~~~~~g~-~ag~aq~~lf~~~~ 305 (310)
T TIGR00588 274 SPFARKELGNFFRSLWGP-YAGWAQAVLFSADL 305 (310)
T ss_pred ChhHHHHHHHHHHHHhcC-cchHHHHHHHHHHh
Confidence 245667788888887764 45555555555443
No 16
>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=99.90 E-value=3e-23 Score=176.12 Aligned_cols=105 Identities=16% Similarity=0.265 Sum_probs=96.5
Q ss_pred CCChHHHHHHHHHhhhcChhhHHHHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhc----CcHH-HHHHHHHHHHHhHHH
Q psy8564 7 TKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF--PNIMSLAQAKLENVMELWSGL----GYYS-RARNLHICAKLVFFK 79 (341)
Q Consensus 7 ~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~----G~~~-rA~~i~~~a~~i~~~ 79 (341)
.++||++||++||||||++++|..++.++++++ +||++|++++.++|+++|+.. |||+ ||++|+++++.|.++
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~ 94 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDT 94 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999998765 699999999999999999866 9995 999999999999999
Q ss_pred hCCCC--------ccc---hHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 80 YNGIF--------PKN---FISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 80 ~~g~~--------p~~---~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
|+|++ |++ +++|++|||||+|||++||.+...
T Consensus 95 y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 95 YDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred hCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 99986 766 789999999999999999996543
No 17
>PF14815 NUDIX_4: NUDIX domain; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A.
Probab=99.89 E-value=1.7e-23 Score=168.64 Aligned_cols=112 Identities=22% Similarity=0.372 Sum_probs=79.5
Q ss_pred EEEEEEeCCEEEEEEeCCCCccccccccccccccc-chhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeec
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWILKD-KIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTH 290 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPgvE~~E-~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h 290 (341)
++++++++|++||.|||++|+|+||||||.+|..+ +. .+++.+.+.+.+|++ .....+++++|+|||
T Consensus 1 ~~~i~~~~~~~Ll~kRp~~gll~GLwefP~~e~~~~~~-----------~~~l~~~~~~~~~~~~~~~~~~~~v~H~fSH 69 (114)
T PF14815_consen 1 VLLIIRSQGRVLLEKRPEKGLLAGLWEFPLIESDEEDD-----------EEELEEWLEEQLGLSIRSVEPLGTVKHVFSH 69 (114)
T ss_dssp EEEEEETTSEEEEEE--SSSTTTT-EE--EEE-SSS-C-----------HHHHHHHTCCSSS-EEEE-S-SEEEEEE-SS
T ss_pred CEEEEEeCCEEEEEECCCCChhhcCcccCEeCccCCCC-----------HHHHHHHHHHHcCCChhhheecCcEEEEccc
Confidence 56788899999999999999999999999988543 11 344555666888887 666789999999999
Q ss_pred eEEEEEEEEEEecccccccCCCCceeeeCCCCCCCCCCHHHHHHHH
Q psy8564 291 LQFKIVPCHIFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILF 336 (341)
Q Consensus 291 ~~~~l~~~~~~~~~~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~ 336 (341)
++|++++|.+++...... ...+.+|++.+++.++|+|++++|+++
T Consensus 70 ~~~~~~~~~~~~~~~~~~-~~~~~~W~~~~~l~~~~~p~~~~kil~ 114 (114)
T PF14815_consen 70 RRWTIHVYEVEVSADPPA-EPEEGQWVSLEELDQYPLPTPMRKILE 114 (114)
T ss_dssp EEEEEEEEEEEEE-SS-----TTEEEEEGGGGGGS---HHHHHHH-
T ss_pred eEEEEEEEEEEecCCCCC-CCCCcEEEEHHHHhhCCCCHHHHHHhC
Confidence 999999999998764322 127899999999999999999999985
No 18
>cd03431 DNA_Glycosylase_C DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to
Probab=99.87 E-value=7.6e-22 Score=158.95 Aligned_cols=114 Identities=23% Similarity=0.385 Sum_probs=91.1
Q ss_pred eeEEEEEEEeCCEEEEEEeCCCCcccccccccccc--cccchhhhccchhhhhHHHHHHHHHHhcCCcccccccCcEEEE
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPEWI--LKDKIINFVDNNLKNLIELEIKKFISSFGFIKNYLILPIISHK 287 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPgvE--~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~~~~~~~~~~~h~ 287 (341)
+..+++++.++|++||+||+++|+|+||||||+++ .+++. ++++.+++.++.++ ....+++++|+
T Consensus 3 ~~~~~~ii~~~~~~ll~kR~~~gl~~glwefP~~~~~~~~~~-----------~~~~~~~~~~~~~~--~~~~~~~~~H~ 69 (118)
T cd03431 3 RGIAVVVIRNDGRVLLEKRPEKGLLAGLWEFPSVEWEEEADG-----------EEALLSALKKALRL--SLEPLGTVKHT 69 (118)
T ss_pred EEEEEEEEecCCeEEEEECCCCCCCCcceeCCCccccCCcCH-----------HHHHHHHHHHHhCc--ccccceeEEEe
Confidence 45666777778999999999999999999999944 44444 66777888777653 22346889999
Q ss_pred eeceEEEEEEEEEEecccccccCCCCceeeeCCCCCCCCCCHHHHHHHHHh
Q psy8564 288 LTHLQFKIVPCHIFLKKCFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQI 338 (341)
Q Consensus 288 ~~h~~~~l~~~~~~~~~~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l 338 (341)
|||++|+|++|.|...+... +..+++|++++++.++++|++++++++.+
T Consensus 70 fth~~~~~~~~~~~~~~~~~--~~~~~~W~~~eel~~~~~p~~~~kil~~~ 118 (118)
T cd03431 70 FTHFRLTLHVYLARLEGDLL--APDEGRWVPLEELDEYALPTVMRKILELL 118 (118)
T ss_pred cCCeEEEEEEEEEEEeCCCc--CccccEEccHHHHhhCCCCHHHHHHHHhC
Confidence 99999999999998754211 22678999999999999999999999764
No 19
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.87 E-value=7e-22 Score=163.56 Aligned_cols=120 Identities=11% Similarity=0.155 Sum_probs=102.9
Q ss_pred eeEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
..++++|+.++|+|||.||+.++.++|+|+||| +|.||++ .+|+.||+.||+|++ .....+..+.|
T Consensus 4 ~~~~~~ii~~~~~vLL~~R~~~~~~~g~w~~PgG~ve~gE~~-----------~~a~~RE~~EE~Gl~~~~~~~~~~~~~ 72 (135)
T PRK10546 4 IDVVAAIIERDGKILLAQRPAHSDQAGLWEFAGGKVEPGESQ-----------PQALIRELREELGIEATVGEYVASHQR 72 (135)
T ss_pred EEEEEEEEecCCEEEEEEccCCCCCCCcEECCcccCCCCCCH-----------HHHHHHHHHHHHCCccccceeEEEEEE
Confidence 456667777889999999999999999999999 8999988 889999999999999 66666788999
Q ss_pred EeeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 287 KLTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
.|+|.++++++|.+...+ .....++.+++|++++++.+++++++++++++.+.+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~l~~~~~ 127 (135)
T PRK10546 73 EVSGRRIHLHAWHVPDFHGELQAHEHQALVWCTPEEALRYPLAPADIPLLEAFMA 127 (135)
T ss_pred ecCCcEEEEEEEEEEEecCcccccccceeEEcCHHHcccCCCCcCcHHHHHHHHH
Confidence 999999999999887543 222223478899999999999999999999998865
No 20
>TIGR00586 mutt mutator mutT protein. All proteins in this family for which functions are known are involved in repairing oxidative damage to dGTP (they are 8-oxo-dGTPases). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.87 E-value=6.9e-22 Score=161.82 Aligned_cols=119 Identities=12% Similarity=0.050 Sum_probs=99.6
Q ss_pred eeEEEEEE-EeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEE
Q psy8564 210 CSIIMFIV-IDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIIS 285 (341)
Q Consensus 210 ~~~~~~ii-~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~ 285 (341)
+.++++|+ .++|++|+.||+.+|+++|+|+||| +|.+|++ .+++.||+.||+|++ .....+..+.
T Consensus 4 ~~~~~~ii~~~~~~vLl~~R~~~~~~~g~w~~Pgg~ve~ge~~-----------~~~~~RE~~EE~g~~~~~~~~~~~~~ 72 (128)
T TIGR00586 4 QQIAVGIIRNENGEIIITRRADGHMFAKLLEFPGGKEEGGETP-----------EQAVVRELEEEIGIPQHFSEFEKLEY 72 (128)
T ss_pred EEEEEEEEECCCCEEEEEEEeCCCCCCCeEECCCcccCCCCCH-----------HHHHHHHHHHHHCCcceeeeEEEEEE
Confidence 34445554 5567999999999999999999999 8889987 888999999999998 6666688999
Q ss_pred EEeeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 286 HKLTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 286 h~~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
|.|+|.++.+++|.+...+ .....+..++.|++++++.+++||++++++++.++
T Consensus 73 h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~l~~~~~p~~~~~~~~~~~ 127 (128)
T TIGR00586 73 EFYPRHITLWFWLLERWEGGPPGKEGQPEEWWVLVGLLADDFFPAANPVIIKLLR 127 (128)
T ss_pred EECCCcEEEEEEEEEEEcCCCcCcccccccEEeCHHHCCccCCCCCCHHHHHHHh
Confidence 9999999999999998754 22112236789999999999999999999998775
No 21
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.87 E-value=1.7e-21 Score=179.98 Aligned_cols=149 Identities=19% Similarity=0.185 Sum_probs=121.1
Q ss_pred CChHHHHHHHHHhhhcChhhHHHHHHHHHHh----------CCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHh
Q psy8564 8 KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKK----------FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLV 76 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~----------~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i 76 (341)
.|||+.+|++|++||.+++.+.++++||.+. ||||++|++++++.+ +.+|+. +||+||+++|+.+
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l----~~~g~s~~Ka~yi~~~A~~~ 178 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEAL----RRCGLSGRKAEYIISLARAA 178 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHH----HHhCCcHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999864 689999999999766 578887 5999999999999
Q ss_pred HHHhCCCC--------ccchHHHhcCCCCCHHHHHHHHHHHhCCe-eec-cChhHHHHHHHHhcccCCcchHHHHHHHHH
Q psy8564 77 FFKYNGIF--------PKNFISLINLPGIGQSTASAIRVFAYGKR-NAI-LDGNVKRILIRVLGINCSLNIKFIEKKLWR 146 (341)
Q Consensus 77 ~~~~~g~~--------p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~-vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~ 146 (341)
.++. -+. .+.+++|++|+|||+|||+++|+|++|++ ++| .|.++++.++++++.+..++ ++.+.+
T Consensus 179 ~~g~-~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~----~~~~~~ 253 (285)
T COG0122 179 AEGE-LDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPT----EKEVRE 253 (285)
T ss_pred HcCC-ccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCch----HHHHHH
Confidence 8731 011 13489999999999999999999999975 554 99999999999984443332 245677
Q ss_pred HHHhhCCCCCHHHHHHHHH
Q psy8564 147 YAIDLLPKKNIEIYTQGLM 165 (341)
Q Consensus 147 ~~~~~~p~~~~~~~~~~l~ 165 (341)
+++.|-|...+..++.+-.
T Consensus 254 ~~e~w~p~rs~A~~yLw~~ 272 (285)
T COG0122 254 LAERWGPYRSYAALYLWRY 272 (285)
T ss_pred HHhcccCHHHHHHHHHHHh
Confidence 8888888765555554443
No 22
>PRK10776 nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=99.86 E-value=1.8e-21 Score=159.24 Aligned_cols=119 Identities=9% Similarity=0.126 Sum_probs=98.8
Q ss_pred eEEEEEE-EeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 211 SIIMFIV-IDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 211 ~~~~~ii-~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
.++++|+ ..+|++||.||+.++.|+|+|+||| ++.+|+. .+++.||+.||+|++ .....++.++|
T Consensus 5 ~~~~~ii~~~~~~vll~rR~~~~~~~g~w~~PgG~~~~gE~~-----------~~a~~Re~~EE~gl~~~~~~~~~~~~~ 73 (129)
T PRK10776 5 QIAVGIIRNPNNEIFITRRAADAHMAGKWEFPGGKIEAGETP-----------EQALIRELQEEVGITVQHATLFEKLEY 73 (129)
T ss_pred EEEEEEEECCCCEEEEEEecCCCCCCCeEECCceecCCCCCH-----------HHHHHHHHHHHHCCceecceEEEEEEe
Confidence 3444444 4568999999999999999999999 8889987 788999999999998 55566788999
Q ss_pred EeeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 287 KLTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
.|+|+.+++++|.+...+ .....+..+.+|++++++..++||++++++++.+.+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~p~~~~~~~~~~~~ 128 (129)
T PRK10776 74 EFPDRHITLWFWLVESWEGEPWGKEGQPGRWVSQVALNADEFPPANEPIIAKLKA 128 (129)
T ss_pred eCCCcEEEEEEEEEEEECCccCCccCCccEEecHHHCccCCCCcccHHHHHHHHh
Confidence 999999999999887543 222223367899999999999999999999998865
No 23
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.85 E-value=1.1e-20 Score=174.93 Aligned_cols=142 Identities=20% Similarity=0.197 Sum_probs=115.6
Q ss_pred CCChHHHHHHHHHhhhcChhhHHHHHHHHHHh-------------CCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHH
Q psy8564 7 TKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKK-------------FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHIC 72 (341)
Q Consensus 7 ~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~-------------~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~ 72 (341)
..||||.+|++|++||.++..+.....++.++ ||||++|+++++++| +.+|++ +||++|+++
T Consensus 110 ~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL----~~~Gl~~~Ra~~L~~l 185 (283)
T PRK10308 110 SVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQAL----KALGMPLKRAEALIHL 185 (283)
T ss_pred CCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHH----HHCCCCHHHHHHHHHH
Confidence 58999999999999999999999999988754 689999999999887 468998 599999999
Q ss_pred HHHhHHH-hCCC----CccchHHHhcCCCCCHHHHHHHHHHHhCCe-ee-ccChhHHHHHHHHhcccCCcchHHHHHHHH
Q psy8564 73 AKLVFFK-YNGI----FPKNFISLINLPGIGQSTASAIRVFAYGKR-NA-ILDGNVKRILIRVLGINCSLNIKFIEKKLW 145 (341)
Q Consensus 73 a~~i~~~-~~g~----~p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~-~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~ 145 (341)
|+.+.++ .... ..+.+++|++|||||+|||++|++|++|++ ++ +.|.+++|.+ .+ .+. +.+.
T Consensus 186 A~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~~----~~~----~~~~ 254 (283)
T PRK10308 186 ANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---PG----MTP----AQIR 254 (283)
T ss_pred HHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---cc----CCH----HHHH
Confidence 9999872 1111 122478999999999999999999999985 44 8999998754 22 222 4566
Q ss_pred HHHHhhCCCCCHHHHHHH
Q psy8564 146 RYAIDLLPKKNIEIYTQG 163 (341)
Q Consensus 146 ~~~~~~~p~~~~~~~~~~ 163 (341)
++++.|.|...+..+|.|
T Consensus 255 ~~a~~w~P~rsya~~~LW 272 (283)
T PRK10308 255 RYAERWKPWRSYALLHIW 272 (283)
T ss_pred HHHHhcCCHHHHHHHHHH
Confidence 778888888777777766
No 24
>KOG2875|consensus
Probab=99.83 E-value=2.2e-20 Score=165.70 Aligned_cols=117 Identities=23% Similarity=0.337 Sum_probs=104.4
Q ss_pred CCChHHHHHHHHHhhhcChhhHHHHHHHHHHh---------------CCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHH
Q psy8564 7 TKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKK---------------FPNIMSLAQAKLENVMELWSGLGYYSRARNLHI 71 (341)
Q Consensus 7 ~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~---------------~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~ 71 (341)
..||+|.+++.|+|+|++++++..+.++|... |||.++|+. .++++.+|.+||..|||||..
T Consensus 114 rQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGYRAkYI~~ 190 (323)
T KOG2875|consen 114 RQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGYRAKYISA 190 (323)
T ss_pred hcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcchhHHHHHH
Confidence 37999999999999999999999999999764 599999985 566677788888779999999
Q ss_pred HHHHhHHHhCCC----------CccchHHHhcCCCCCHHHHHHHHHHHhCCe-eeccChhHHHHHH
Q psy8564 72 CAKLVFFKYNGI----------FPKNFISLINLPGIGQSTASAIRVFAYGKR-NAILDGNVKRILI 126 (341)
Q Consensus 72 ~a~~i~~~~~g~----------~p~~~~~L~~l~GIG~~tA~~il~~~~~~~-~~~vD~~v~Rvl~ 126 (341)
.|++|.++++|. +.+.++.|+.|||||+|+||||++++++.. .+|||+|+.|+.+
T Consensus 191 ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~ 256 (323)
T KOG2875|consen 191 TARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQ 256 (323)
T ss_pred HHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhh
Confidence 999999998871 235689999999999999999999999974 8899999999998
No 25
>cd03425 MutT_pyrophosphohydrolase The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi). This enzyme requires two divalent cations for activity; one coordinates the phosphoryl groups of the NTP/dNTP substrate, and the other coordinates to the enzyme. It also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as metal binding and catalytic site. MutT pyrophosphohydrolase is important in preventing errors in DNA replication by hydrolyzing mutagenic nucleotides such as 8-oxo-dGTP (a product of oxidative damage), which can mispair with template adenine during DNA replication, to guanine nucleotides.
Probab=99.78 E-value=9.6e-19 Score=141.53 Aligned_cols=117 Identities=16% Similarity=0.250 Sum_probs=98.0
Q ss_pred EEEEEEEe-CCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEE
Q psy8564 212 IIMFIVID-DDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHK 287 (341)
Q Consensus 212 ~~~~ii~~-~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~ 287 (341)
++++++.+ +|++|+.||+.+++++|+|+||| ++.+|++ .+++.||+.||+|++ .....++.++|.
T Consensus 3 ~~~~~i~~~~~~~Ll~~r~~~~~~~g~w~~p~G~~~~~e~~-----------~~~a~Re~~EE~g~~~~~~~~~~~~~~~ 71 (124)
T cd03425 3 VVAAIIIDDDGRILIAQRPAGKHLGGLWEFPGGKVEPGETP-----------EQALVRELREELGIEVEVGELLATVEHD 71 (124)
T ss_pred EEEEEEECCCCEEEEEEeCCCCCCCCeEeCCCcccCCCCCH-----------HHHHHHHHHHhhCcEEeccceEEEEEee
Confidence 44445544 49999999998889999999999 8888887 888999999999998 666778899999
Q ss_pred eeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 288 LTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 288 ~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
|+|.++.+++|.+...+ .....+..+..|++++++.+++||++++++++.|+
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~l~~~~ 124 (124)
T cd03425 72 YPDKRVTLHVFLVELWSGEPQLLEHQELRWVPPEELDDLDFPPADVPIVAALQ 124 (124)
T ss_pred CCCCeEEEEEEEEeeeCCCcccccCceEEEeeHHHcccCCCCcccHHHHHhhC
Confidence 99999999999998654 21122337899999999999999999999998764
No 26
>PRK08999 hypothetical protein; Provisional
Probab=99.77 E-value=1.4e-18 Score=163.88 Aligned_cols=119 Identities=13% Similarity=0.170 Sum_probs=99.4
Q ss_pred eeEEEE-EEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEE
Q psy8564 210 CSIIMF-IVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIIS 285 (341)
Q Consensus 210 ~~~~~~-ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~ 285 (341)
+.++++ |+..+|++||.||+.+++|+|+|+||| +|.+|++ .+++.||+.||+|+. .....+..+.
T Consensus 5 ~~~~~~vi~~~~~~vLL~kR~~~~~~~g~w~~PgG~ve~gE~~-----------~~aa~RE~~EE~Gl~~~~~~~l~~~~ 73 (312)
T PRK08999 5 IHVAAGVIRDADGRILLARRPEGKHQGGLWEFPGGKVEPGETV-----------EQALARELQEELGIEVTAARPLITVR 73 (312)
T ss_pred eEEEEEEEECCCCeEEEEEecCCCCCCCeEECCccCCCCCCCH-----------HHHHHHHHHHHhCCceecceeEEEEE
Confidence 344444 444569999999999999999999999 8899987 888999999999998 6666678899
Q ss_pred EEeeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 286 HKLTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 286 h~~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
|.|+|.++++++|.+...+ .....++.+++|++++++.+++||++++++++.+.
T Consensus 74 h~~~~~~~~i~~y~~~~~~~~~~~~e~~~~~Wv~~~el~~~~~~~~~~~i~~~l~ 128 (312)
T PRK08999 74 HDYPDKRVRLDVRRVTAWQGEPHGREGQPLAWVAPDELAVYPFPPANQPIVRALR 128 (312)
T ss_pred EEcCCCeEEEEEEEEEEecCcccCccCCccEEecHHHcccCCCCcchHHHHHHhc
Confidence 9999999999999887543 22222347889999999999999999999999873
No 27
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.77 E-value=4.2e-18 Score=135.77 Aligned_cols=101 Identities=29% Similarity=0.386 Sum_probs=87.8
Q ss_pred HHHHHhhhcChhhHHHHHHHHHHh--CCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHHH
Q psy8564 15 LSEIMLQQTQVNTVIPYYQRFLKK--FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFISL 91 (341)
Q Consensus 15 v~~il~qqt~~~~~~~~~~~l~~~--~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~L 91 (341)
|++||+|||+++++.+++.+|+++ ||||++|+++++++|.++|+++||+ +||++|+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~-------------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL-------------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH--------------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh--------------
Confidence 789999999999999999999999 5999999999999999999999999 69999999999997
Q ss_pred hcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHH
Q psy8564 92 INLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWR 146 (341)
Q Consensus 92 ~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~ 146 (341)
+.....+++|+|+.|++.|+++++...+.+.+++.+++
T Consensus 67 -----------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e 104 (108)
T PF00730_consen 67 -----------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEE 104 (108)
T ss_dssp -----------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHH
T ss_pred -----------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHh
Confidence 22235899999999999999999877777666665544
No 28
>KOG1918|consensus
Probab=99.74 E-value=5.8e-18 Score=145.52 Aligned_cols=144 Identities=19% Similarity=0.270 Sum_probs=120.5
Q ss_pred CCCChHHHHHHHHHhhhcChhhHHHHHHHHHHh------CCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHH
Q psy8564 6 NTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKK------FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFF 78 (341)
Q Consensus 6 ~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~------~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~ 78 (341)
.++.||+.|+++|++||.+..++..++.||... ||+|+.+..++.+++ +.|||+ +||.||+.+|.+..+
T Consensus 71 ~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~n 146 (254)
T KOG1918|consen 71 ETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEEL----RKCGFSKRKASYLHSLAEAYTN 146 (254)
T ss_pred cccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHHH----HHhCcchhhHHHHHHHHHHHhc
Confidence 467899999999999999999999999999864 689999999999776 778999 699999999999987
Q ss_pred HhCCCCccc-----------hHHHhcCCCCCHHHHHHHHHHHhCCe--eeccChhHHHHHHHHhcccCCcchHHHHHHHH
Q psy8564 79 KYNGIFPKN-----------FISLINLPGIGQSTASAIRVFAYGKR--NAILDGNVKRILIRVLGINCSLNIKFIEKKLW 145 (341)
Q Consensus 79 ~~~g~~p~~-----------~~~L~~l~GIG~~tA~~il~~~~~~~--~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~ 145 (341)
+ .+|.. ++.|..++|||+||+.++|.|+++++ .++-|..+++-.+.++|+...+.+. ++.
T Consensus 147 g---~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~~p~~~----eve 219 (254)
T KOG1918|consen 147 G---YIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKPLPLPK----EVE 219 (254)
T ss_pred C---CCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCCCCchH----HHH
Confidence 4 35532 56788999999999999999999997 4568999999999999998766664 444
Q ss_pred HHHHhhCCCCCHHHH
Q psy8564 146 RYAIDLLPKKNIEIY 160 (341)
Q Consensus 146 ~~~~~~~p~~~~~~~ 160 (341)
++.+.+-|....+.+
T Consensus 220 kl~e~~kpyRtvaaw 234 (254)
T KOG1918|consen 220 KLCEKCKPYRTVAAW 234 (254)
T ss_pred HHhhhccchHHHHHH
Confidence 556667776554433
No 29
>PRK15472 nucleoside triphosphatase NudI; Provisional
Probab=99.67 E-value=3.7e-16 Score=130.41 Aligned_cols=118 Identities=14% Similarity=0.167 Sum_probs=85.1
Q ss_pred ceeEEEEEEEeCCEEEEEEeCC-CCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccc----
Q psy8564 209 NCSIIMFIVIDDDYVLFQKRSN-KGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLI---- 280 (341)
Q Consensus 209 ~~~~~~~ii~~~g~vLl~kR~~-~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~---- 280 (341)
.+.++++|+.++|+|||.||+. ++.++|.|+||| +|.||++ .+|+.||+.||+|++ .....
T Consensus 3 ~r~~~~~ii~~~~~vLl~~R~~~~~~~~g~W~lPgG~ve~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~ 71 (141)
T PRK15472 3 QRTIVCPLIQNDGAYLLCKMADDRGVFPGQWALSGGGVEPGERI-----------EEALRREIREELGEQLLLTEITPWT 71 (141)
T ss_pred ceeEEEEEEecCCEEEEEEecccCCCCCCceeCCcccCCCCCCH-----------HHHHHHHHHHHHCCceeeeeecccc
Confidence 3567788888899999999976 468999999999 9999998 999999999999987 32211
Q ss_pred cC--cEEEEeeceE---E-E-EEEEEEEecc-c-ccccCCCCceeeeCCCCCCCCCCHHHHHHHHH
Q psy8564 281 LP--IISHKLTHLQ---F-K-IVPCHIFLKK-C-FLKENKNNFIWYPIKKIKNSPIPAPVRKILFQ 337 (341)
Q Consensus 281 ~~--~~~h~~~h~~---~-~-l~~~~~~~~~-~-~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~ 337 (341)
+. ...|.|++.. + . ..+|.|...+ . ....++.+++|++++||.+++++++++.++..
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~l~~~~~~~~~~~~ 137 (141)
T PRK15472 72 FRDDIRTKTYADGRKEEIYMIYLIFDCVSANRDVKINEEFQDYAWVKPEDLVHYDLNVATRKTLRL 137 (141)
T ss_pred ccccceeEEecCCCceeEEEEEEEEEeecCCCcccCChhhheEEEccHHHhccccccHHHHHHHHH
Confidence 10 1123443221 1 1 1234454332 1 12234578999999999999999999999875
No 30
>cd03427 MTH1 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved nudix motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a m
Probab=99.61 E-value=4.6e-15 Score=122.92 Aligned_cols=117 Identities=16% Similarity=0.163 Sum_probs=93.4
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
++.+++.++|++||.+|..++ ..|.|+||| +|.+|++ .+|++||+.||+|+. .....++.+.+.+
T Consensus 3 ~~~~~i~~~~~vLL~~r~~~~-~~~~w~~PgG~ve~gEs~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~ 70 (137)
T cd03427 3 TTLCFIKDPDKVLLLNRKKGP-GWGGWNGPGGKVEPGETP-----------EECAIRELKEETGLTIDNLKLVGIIKFPF 70 (137)
T ss_pred EEEEEEEECCEEEEEEecCCC-CCCeEeCCceeCCCCCCH-----------HHHHHHHHHHhhCeEeecceEEEEEEEEc
Confidence 455666777999999998765 889999999 9999988 999999999999998 6666677776665
Q ss_pred ec--eEEEEEEEEEEecc-ccc-ccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 289 TH--LQFKIVPCHIFLKK-CFL-KENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 289 ~h--~~~~l~~~~~~~~~-~~~-~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
+. .+..+++|.+...+ ... ..+..+..|++++++.++++++.++.+++.+.+
T Consensus 71 ~~~~~~~~~~~f~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~l~~~~~ 126 (137)
T cd03427 71 PGEEERYGVFVFLATEFEGEPLKESEEGILDWFDIDDLPLLPMWPGDREWLPLMLE 126 (137)
T ss_pred CCCCcEEEEEEEEECCcccccCCCCccccceEEcHhhcccccCCCCcHHHHHHHhC
Confidence 54 56777888887544 222 223367899999999999999999999988754
No 31
>PRK15434 GDP-mannose mannosyl hydrolase NudD; Provisional
Probab=99.59 E-value=5e-15 Score=125.92 Aligned_cols=114 Identities=14% Similarity=0.191 Sum_probs=84.5
Q ss_pred EEEEEEE-eCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c--cccccCcEE
Q psy8564 212 IIMFIVI-DDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K--NYLILPIIS 285 (341)
Q Consensus 212 ~~~~ii~-~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~--~~~~~~~~~ 285 (341)
++.+|+. .+|+|||.||.. +..+|+|+||| +|.|||+ ++|++||++||+|+. . ....++...
T Consensus 19 ~v~~vI~~~~g~VLL~kR~~-~~~~g~W~lPGG~VE~GEt~-----------~~Aa~REl~EEtGl~v~~~~~~~~~~~~ 86 (159)
T PRK15434 19 SLDFIVENSRGEFLLGKRTN-RPAQGYWFVPGGRVQKDETL-----------EAAFERLTMAELGLRLPITAGQFYGVWQ 86 (159)
T ss_pred EEEEEEECCCCEEEEEEccC-CCCCCcEECCceecCCCCCH-----------HHHHHHHHHHHHCCccccccceEEEEEE
Confidence 4444444 469999999975 46789999999 9999998 999999999999997 3 234455445
Q ss_pred EEee--------ceEEEEEEEEEEecc-cc--cccCCCCceeeeCCCCCCC-CCCHHHHHHHHH
Q psy8564 286 HKLT--------HLQFKIVPCHIFLKK-CF--LKENKNNFIWYPIKKIKNS-PIPAPVRKILFQ 337 (341)
Q Consensus 286 h~~~--------h~~~~l~~~~~~~~~-~~--~~~~~~~~~W~~~~el~~~-~~~~a~~~il~~ 337 (341)
|.|+ +.++.+.+|.|...+ .. ...++.+++|++++++..+ .+.+.++.++..
T Consensus 87 ~~~~~~~~~~~~~~~~i~~~f~~~~~~g~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~~~~~~ 150 (159)
T PRK15434 87 HFYDDNFSGTDFTTHYVVLGFRLRVAEEDLLLPDEQHDDYRWLTPDALLASDNVHANSRAYFLA 150 (159)
T ss_pred eecccccCCCccceEEEEEEEEEEecCCcccCChHHeeEEEEEeHHHhhhccccCHHHHHHhcc
Confidence 5554 235677788888654 22 2223589999999999886 777777777653
No 32
>cd04676 Nudix_Hydrolase_17 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.57 E-value=1.7e-14 Score=117.50 Aligned_cols=109 Identities=13% Similarity=0.147 Sum_probs=79.0
Q ss_pred EEEEEE-EeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccc---cCcE
Q psy8564 212 IIMFIV-IDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLI---LPII 284 (341)
Q Consensus 212 ~~~~ii-~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~---~~~~ 284 (341)
.+.+|+ +++|++||.||+.. |+|+||| ++.+|++ ++|+.||+.||+|++ ..... +...
T Consensus 4 ~v~~ii~~~~~~vLl~~r~~~----~~w~lPgG~v~~~E~~-----------~~aa~REl~EE~Gl~~~~~~~~~~~~~~ 68 (129)
T cd04676 4 GVTAVVRDDEGRVLLIRRSDN----GLWALPGGAVEPGESP-----------ADTAVREVREETGLDVEVTGLVGIYTGP 68 (129)
T ss_pred eEEEEEECCCCeEEEEEecCC----CcEECCeeccCCCCCH-----------HHHHHHHHHHHhCceeEeeEEEEEeecc
Confidence 444454 45599999999765 8999999 9999988 899999999999998 44443 2234
Q ss_pred EEEee------ceEEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCCCCCCHHHHHHHH
Q psy8564 285 SHKLT------HLQFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKNSPIPAPVRKILF 336 (341)
Q Consensus 285 ~h~~~------h~~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~~~~~~a~~~il~ 336 (341)
.|.++ |..+. .+|.+...+ . ....+..+++|++++++.+++++++++++++
T Consensus 69 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~~~~~~~~~~~~ 128 (129)
T cd04676 69 VHVVTYPNGDVRQYLD-ITFRCRVVGGELRVGDDESLDVAWFDPDGLPPLLMHPSMRLRID 128 (129)
T ss_pred cceeecCCCCcEEEEE-EEEEEEeeCCeecCCCCceeEEEEEChhhCccccCCHhHHHHhc
Confidence 45554 33333 344455433 1 1222336789999999999999999999986
No 33
>cd04696 Nudix_Hydrolase_37 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.57 E-value=1.1e-14 Score=118.76 Aligned_cols=110 Identities=15% Similarity=0.213 Sum_probs=80.5
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
.++|.+.+|++||.||.. ++|.|+||| ++.||++ .+|+.||++||+|++ .....+....+.|+
T Consensus 6 ~~~i~~~~~~iLL~r~~~---~~~~w~lPGG~ve~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~~ 71 (125)
T cd04696 6 GALIYAPDGRILLVRTTK---WRGLWGVPGGKVEWGETL-----------EEALKREFREETGLKLRDIKFAMVQEAIFS 71 (125)
T ss_pred EEEEECCCCCEEEEEccC---CCCcEeCCceeccCCCCH-----------HHHHHHHHHHHhCCcccccceEEEEEEecc
Confidence 344444489999999853 579999999 9999988 999999999999998 54444444344442
Q ss_pred -----ceEEEEEEEEEEecc-c-ccccCCCCceeeeCCCCCCCCCCHHHHHHHH
Q psy8564 290 -----HLQFKIVPCHIFLKK-C-FLKENKNNFIWYPIKKIKNSPIPAPVRKILF 336 (341)
Q Consensus 290 -----h~~~~l~~~~~~~~~-~-~~~~~~~~~~W~~~~el~~~~~~~a~~~il~ 336 (341)
+.++.+..|.+...+ . ....++.+++|++++++.++++++++..+++
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~~~ 125 (125)
T cd04696 72 EEFHKPAHFVLFDFFARTDGTEVTPNEEIVEWEWVTPEEALDYPLNSFTRLLLE 125 (125)
T ss_pred CCCCCccEEEEEEEEEEecCCcccCCcccceeEEECHHHHhcCCCCHHHHHHhC
Confidence 234445667776543 1 1223347899999999999999999998763
No 34
>cd04673 Nudix_Hydrolase_15 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.55 E-value=1.5e-14 Score=117.06 Aligned_cols=108 Identities=15% Similarity=0.253 Sum_probs=83.6
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
+++++.++|++||.||.. +.+.|.|+||| ++.+|++ ++|+.||+.||+|++ .....++...+.++
T Consensus 3 v~~ii~~~~~vLl~~r~~-~~~~~~w~~PgG~ie~gE~~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~ 70 (122)
T cd04673 3 VGAVVFRGGRVLLVRRAN-PPDAGLWSFPGGKVELGETL-----------EQAALRELLEETGLEAEVGRLLTVVDVIER 70 (122)
T ss_pred EEEEEEECCEEEEEEEcC-CCCCCeEECCCcccCCCCCH-----------HHHHHHHHHHhhCcEeeeceeEEEEEEeec
Confidence 455566779999999964 45789999999 9999988 999999999999998 66667776666552
Q ss_pred ------ceEEEEEEEEEEecc-cc-cccCCCCceeeeCCCCCCCCCCHHHH
Q psy8564 290 ------HLQFKIVPCHIFLKK-CF-LKENKNNFIWYPIKKIKNSPIPAPVR 332 (341)
Q Consensus 290 ------h~~~~l~~~~~~~~~-~~-~~~~~~~~~W~~~~el~~~~~~~a~~ 332 (341)
..++.+++|.+...+ .. ...+..++.|++++++.++++++.++
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~ 121 (122)
T cd04673 71 DAAGRVEFHYVLIDFLCRYLGGEPVAGDDALDARWVPLDELAALSLTESTR 121 (122)
T ss_pred cCCCccceEEEEEEEEEEeCCCcccCCcccceeEEECHHHHhhCcCCcccc
Confidence 345667778887644 11 12334678999999999999998765
No 35
>cd04684 Nudix_Hydrolase_25 Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability
Probab=99.55 E-value=3.2e-14 Score=116.05 Aligned_cols=112 Identities=12% Similarity=0.071 Sum_probs=87.7
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+++|+.++|++||.||...+ .+|.|+||| +|.||++ .+|+.||+.||+|++ .....++...+.|
T Consensus 2 ~~~~ii~~~~~vLl~~~~~~~-~~~~w~lPgG~ve~gE~~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~ 69 (128)
T cd04684 2 GAYAVIPRDGKLLLIQKNGGP-YEGRWDLPGGGIEPGESP-----------EEALHREVLEETGLTVEIGRRLGSASRYF 69 (128)
T ss_pred eeEEEEEeCCEEEEEEccCCC-CCCeEECCCcccCCCCCH-----------HHHHHHHHHHHhCcEeecceeeeEEEEEE
Confidence 355667778999999997765 889999999 9999988 999999999999998 6666777776665
Q ss_pred ec------eEEEEEEEEEEecccc-----cccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 289 TH------LQFKIVPCHIFLKKCF-----LKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 289 ~h------~~~~l~~~~~~~~~~~-----~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
.. .+...++|.|...... ...+..+.+|++++++....+.+...+.+
T Consensus 70 ~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~~~~~~~a~ 127 (128)
T cd04684 70 YSPDGDYDAHHLCVFYDARVVGGALPVQEPGEDSHGAAWLPLDEAIERLLSPLVLWAV 127 (128)
T ss_pred ECCCCCeeccEEEEEEEEEEecCccccCCCCCCceeeEEECHHHhhccCCCHHHHHhh
Confidence 42 2456678888865521 12234678999999999999988887654
No 36
>cd04669 Nudix_Hydrolase_11 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.54 E-value=2.2e-14 Score=116.62 Aligned_cols=102 Identities=14% Similarity=0.196 Sum_probs=73.9
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
++++|++++|+|||.||..++ .++|+||| +|.||++ .+|+.||+.||+|++ .....+..+.+
T Consensus 3 ~~~ii~~~~~~vLL~~r~~~~--~~~w~lPGG~ve~gEs~-----------~~a~~REl~EEtGl~~~~~~~~~~~~~-- 67 (121)
T cd04669 3 ASIVIINDQGEILLIRRIKPG--KTYYVFPGGGIEEGETP-----------EEAAKREALEELGLDVRVEEIFLIVNQ-- 67 (121)
T ss_pred eEEEEEeCCCEEEEEEEecCC--CCcEECCceeccCCCCH-----------HHHHHHHHHHhhCeeEeeeeEEEEEee--
Confidence 445555555999999997655 68999999 9999998 999999999999998 55444433332
Q ss_pred eceEEEEEEEEEEecc-ccc-----------ccCCCCceeeeCCCCCCCCCCHH
Q psy8564 289 THLQFKIVPCHIFLKK-CFL-----------KENKNNFIWYPIKKIKNSPIPAP 330 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~-~~~-----------~~~~~~~~W~~~~el~~~~~~~a 330 (341)
.+ ...++|.|...+ ... ...+.+++|+++++|..+++.|.
T Consensus 68 ~~--~~~~~f~~~~~~g~~~~~~~~e~~~~~~~~~~~~~Wv~~~el~~l~~~p~ 119 (121)
T cd04669 68 NG--RTEHYFLARVISGKLGLGVGEEFERQSDDNQYHPVWVDLDQLETIPLRPE 119 (121)
T ss_pred CC--cEEEEEEEEEECCeecCCCchhhcccCCCCceEEEEEEHHHcccCCCCCC
Confidence 23 346788887543 110 11123579999999999998773
No 37
>cd03430 GDPMH GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix signature sequence. The slight changes to the conserved sequence motif, GX5EX7REUXEEXGU, where U = I, L or V), are believed to contribute to the removal of all magnesium binding sites but one, retaining only the metal site that coordinates the pyrophosphate of the substrate. Secondly, it is not a pyrophosphatase that substitutes at a phosphorus; instead, it hydrolyzes nucleotide sugars such as GDP-mannose to GDP and mannose, cleaving the phosphoglycosyl bond by substituting at a carbon position. GDP-mannose provides mannosyl components for cell wall synthesis and is required for the synthesis of other glycosyl donors (such as GDP-fucose and colitose) for the cell wall. The importance of GDP-sugar hydrolase activities is thus close
Probab=99.51 E-value=8.7e-14 Score=116.64 Aligned_cols=102 Identities=15% Similarity=0.199 Sum_probs=76.0
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc--cccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY--LILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~--~~~~~~~h 286 (341)
+.++|++.+|++|+.||.. ....|+|+||| +|.||++ .+|++||++||+|++ ... +.++.+.|
T Consensus 15 v~~vI~~~~g~vLl~~R~~-~p~~g~w~lPGG~ve~gEs~-----------~~aa~RE~~EE~Gl~v~~~~~~~l~~~~~ 82 (144)
T cd03430 15 IDLIVENEDGQYLLGKRTN-RPAQGYWFVPGGRIRKNETL-----------TEAFERIAKDELGLEFLISDAELLGVFEH 82 (144)
T ss_pred EEEEEEeCCCeEEEEEccC-CCCCCcEECCCceecCCCCH-----------HHHHHHHHHHHHCCCcccccceEEEEEEE
Confidence 3444445569999999975 35789999999 9999998 999999999999998 555 56666666
Q ss_pred Eeec--------eEEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCCC
Q psy8564 287 KLTH--------LQFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 287 ~~~h--------~~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~~ 325 (341)
.|++ .++...+|.|...+ . ....+..+++|++++++.+.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~ 132 (144)
T cd03430 83 FYDDNFFGDDFSTHYVVLGYVLKLSSNELLLPDEQHSEYQWLTSDELLAD 132 (144)
T ss_pred EeccccccCCCccEEEEEEEEEEEcCCcccCCchhccEeEEecHHHHhcC
Confidence 6542 24556677777644 2 12233478999999999875
No 38
>cd04691 Nudix_Hydrolase_32 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.50 E-value=8.3e-14 Score=112.52 Aligned_cols=101 Identities=16% Similarity=0.145 Sum_probs=75.7
Q ss_pred EEEEEEEeCCEEEEEEeCCCC-cccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG-IWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHK 287 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g-~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~ 287 (341)
++++++.++|+|||.||...+ ...|.|+||| +|.||++ ++|+.||+.||+|++ .....+..+.+.
T Consensus 2 ~v~~vi~~~~~vLL~rR~~~~~~~~g~w~lPgG~ve~gE~~-----------~~aa~REl~EEtGl~~~~~~~l~~~~~~ 70 (117)
T cd04691 2 GVVGVLFSDDKVLLERRSLTKNADPGKLNIPGGHIEAGESQ-----------EEALLREVQEELGVDPLSYTYLCSLYHP 70 (117)
T ss_pred eEEEEEEECCEEEEEEeCCCCCCCCCeEECcceeecCCCCH-----------HHHHHHHHHHHHCCCcccceEEEEEecc
Confidence 345556667999999997665 4899999999 9999988 999999999999998 555555555544
Q ss_pred eeceEEEEEEEEEEecc-cccccCCCCceeeeCCCCCC
Q psy8564 288 LTHLQFKIVPCHIFLKK-CFLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 288 ~~h~~~~l~~~~~~~~~-~~~~~~~~~~~W~~~~el~~ 324 (341)
.+ ....+++|.+...+ .....+..++.|++++++..
T Consensus 71 ~~-~~~~~~~~~~~~~~~~~~~~E~~~~~W~~~~~l~~ 107 (117)
T cd04691 71 TS-ELQLLHYYVVTFWQGEIPAQEAAEVHWMTANDIVL 107 (117)
T ss_pred CC-CeEEEEEEEEEEecCCCCcccccccEEcCHHHcch
Confidence 43 34567888887543 22223447899999988864
No 39
>cd04682 Nudix_Hydrolase_23 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.50 E-value=4.3e-14 Score=114.92 Aligned_cols=107 Identities=11% Similarity=0.096 Sum_probs=77.3
Q ss_pred EEEEEEEeCCEEEEEEeCCC--Ccccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNK--GIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~--g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
++++++.++|++|+.+|... ..+.|+|+||| +|.+|++ ++|+.||+.||+|++ ..........+
T Consensus 3 v~~~~~~~~g~vLl~~r~~~~~~~~~g~w~~PgG~ve~gE~~-----------~~aa~RE~~EE~Gl~~~~~~~~~~~~~ 71 (122)
T cd04682 3 VALALLIGDGRLLLQLRDDKPGIPYPGHWDLPGGHREGGETP-----------LECVLRELLEEIGLTLPESRIPWFRVY 71 (122)
T ss_pred eEEEEEEcCCEEEEEEccCCCCCCCCCcEeCCCccccCCCCH-----------HHHHHHHHHHHhCCcccccccceeEec
Confidence 45566667799999999764 57899999999 9999988 999999999999998 43222222333
Q ss_pred EeeceEEEEEEEEEEeccc----ccccCCCCceeeeCCCCCCCCCCH
Q psy8564 287 KLTHLQFKIVPCHIFLKKC----FLKENKNNFIWYPIKKIKNSPIPA 329 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~~----~~~~~~~~~~W~~~~el~~~~~~~ 329 (341)
.+......+++|.+...+. ....++.++.|++++|+.+...+.
T Consensus 72 ~~~~~~~~~~~f~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~~ 118 (122)
T cd04682 72 PSASPPGTEHVFVVPLTAREDAILFGDEGQALRLMTVEEFLAHEDAI 118 (122)
T ss_pred ccCCCCceEEEEEEEEecCCCccccCchhheeecccHHHHhhccccC
Confidence 3333456677787775431 223345789999999997765543
No 40
>cd04683 Nudix_Hydrolase_24 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.50 E-value=1.2e-13 Score=111.81 Aligned_cols=102 Identities=13% Similarity=0.235 Sum_probs=74.1
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c--cccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K--NYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~--~~~~~~~~~h 286 (341)
.+.+++.++|+|||.||...+..+|+|+||| +|.||++ .+|+.||+.||+|+. . ....+..+.+
T Consensus 2 ~v~~vi~~~~~vLL~~r~~~~~~~~~w~lPgG~ve~gE~~-----------~~aa~REl~EEtGl~v~~~~~~~~~~~~~ 70 (120)
T cd04683 2 AVYVLLRRDDEVLLQRRANTGYMDGQWALPAGHLEKGEDA-----------VTAAVREAREEIGVTLDPEDLRLAHTMHR 70 (120)
T ss_pred cEEEEEEECCEEEEEEccCCCCCCCeEeCCccccCCCCCH-----------HHHHHHHHHHHHCCccChhheEEEEEEEe
Confidence 3566677889999999988888899999999 9999988 899999999999998 4 3334544444
Q ss_pred Eeec-eEEEEEEEEEEecc-cc---cccCCCCceeeeCCCCCC
Q psy8564 287 KLTH-LQFKIVPCHIFLKK-CF---LKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 287 ~~~h-~~~~l~~~~~~~~~-~~---~~~~~~~~~W~~~~el~~ 324 (341)
.+.. .+....+|.|.... .+ ...+..+++|+++++|..
T Consensus 71 ~~~~~~~~~~~~f~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~ 113 (120)
T cd04683 71 RTEDIESRIGLFFTVRRWSGEPRNCEPDKCAELRWFPLDALPD 113 (120)
T ss_pred cCCCCceEEEEEEEEEeecCccccCCCCcEeeEEEEchHHCcc
Confidence 4432 33444566676432 11 112236799999999976
No 41
>cd04699 Nudix_Hydrolase_39 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.49 E-value=7.9e-14 Score=113.88 Aligned_cols=106 Identities=12% Similarity=0.172 Sum_probs=75.0
Q ss_pred EEEEEEEeC-CEEEEEEeCCCCc-ccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccc-cCcEE
Q psy8564 212 IIMFIVIDD-DYVLFQKRSNKGI-WGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLI-LPIIS 285 (341)
Q Consensus 212 ~~~~ii~~~-g~vLl~kR~~~g~-~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~-~~~~~ 285 (341)
++++++.++ |++||.||+.++. ++|+|+||| +|.||++ .+|+.||+.||+|++ ..... ...+.
T Consensus 3 ~v~~vv~~~~~~iLl~kr~~~~~~~~g~w~~PgG~ve~gEs~-----------~~aa~RE~~EE~Gl~~~~~~~~~~~~~ 71 (129)
T cd04699 3 AVAALIVKDVGRILILKRSKDERTAPGKWELPGGKVEEGETF-----------EEALKREVYEETGLTVTPFLRYPSTVT 71 (129)
T ss_pred eEEEEEECCCCcEEEEEecCCCCCCCCcCcCCccCccCCCCH-----------HHHHHHHHHHhhCcEEEeeeeeeEEEE
Confidence 344555454 8999999988775 599999999 8999988 899999999999998 44443 23556
Q ss_pred EEeec-eEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCCCCCC
Q psy8564 286 HKLTH-LQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKNSPIP 328 (341)
Q Consensus 286 h~~~h-~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~~~~~ 328 (341)
|..+. .+....+|.+..... ....+..+++|++++++..++++
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~~~~ 117 (129)
T cd04699 72 HEDSGVYNVIYLVFVCEALSGAVKLSDEHEEYAWVTLEELAILKAD 117 (129)
T ss_pred EcCCCEEEEEEEEEEeeecCCcccCChhheEEEEecHHHhhhhhcc
Confidence 66552 334445566654331 11223367899999998776665
No 42
>cd04679 Nudix_Hydrolase_20 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.49 E-value=1.6e-13 Score=111.92 Aligned_cols=110 Identities=13% Similarity=0.156 Sum_probs=82.1
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
.++|++.+|++||.+|... ...|.|+||| +|.||++ .+|++||+.||+|++ .....+..+.|.++
T Consensus 6 ~~~i~~~~~~vLL~~r~~~-~~~~~w~lPgG~ve~gEt~-----------~eaa~RE~~EEtGl~~~~~~~~~~~~~~~~ 73 (125)
T cd04679 6 GAAILRDDGKLLLVKRLRA-PEAGHWGIPGGKVDWMEAV-----------EDAVVREIEEETGLSIHSTRLLCVVDHIIE 73 (125)
T ss_pred EEEEECCCCEEEEEEecCC-CCCCeEeCCeeeccCCCCH-----------HHHHHHHHHHHHCCCcccceEEEEEeeccc
Confidence 3445555699999999643 4579999999 9999988 999999999999999 66666666666553
Q ss_pred --ceEEEEEEEEEEecc-cc---cccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 290 --HLQFKIVPCHIFLKK-CF---LKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 290 --h~~~~l~~~~~~~~~-~~---~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
..++...+|.+...+ .. ...+..+++|++++++.+ ++.++.+.++
T Consensus 74 ~~~~~~~~~~f~~~~~~~~~~~~~~~E~~~~~W~~~~~l~~-~l~~~~~~~~ 124 (125)
T cd04679 74 EPPQHWVAPVYLAENFSGEPRLMEPDKLLELGWFALDALPQ-PLTRATRDAV 124 (125)
T ss_pred CCCCeEEEEEEEEeecCCccccCCCccccEEEEeCHHHCCc-hhHHHHHHHh
Confidence 345666778887644 11 122346799999999987 7777776654
No 43
>PRK09438 nudB dihydroneopterin triphosphate pyrophosphatase; Provisional
Probab=99.48 E-value=8.2e-14 Score=117.17 Aligned_cols=115 Identities=10% Similarity=0.059 Sum_probs=82.7
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccc--ccC----
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYL--ILP---- 282 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~--~~~---- 282 (341)
+++++++.+|+|||.||..+ .|.|+||| +|.|||+ .+|++||+.||+|++ .... .+.
T Consensus 10 v~~vi~~~~~~vLl~~r~~~---~~~W~lPgG~ve~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~ 75 (148)
T PRK09438 10 VLVVIYTPDLGVLMLQRADD---PDFWQSVTGSLEEGETP-----------AQTAIREVKEETGIDVLAEQLTLIDCQRS 75 (148)
T ss_pred EEEEEEeCCCeEEEEEecCC---CCcEeCCcccCCCCCCH-----------HHHHHHHHHHHhCcCccccceeecccccc
Confidence 34445556889999998643 48999999 9999998 999999999999997 3221 111
Q ss_pred -------cEEEEee--ceEEEEEEEEEEecc--cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 283 -------IISHKLT--HLQFKIVPCHIFLKK--CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 283 -------~~~h~~~--h~~~~l~~~~~~~~~--~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
...|.++ ..+...++|.|...+ .....++.+++|++++++.++.+.+.++.+++.+.+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~e~~~~~~~~~~~~~l~~~~~ 144 (148)
T PRK09438 76 IEYEIFPHWRHRYAPGVTRNTEHWFCLALPHERPVVLTEHLAYQWLDAREAAALTKSWSNAEAIEQLVI 144 (148)
T ss_pred cccccchhhhhccccccCCceeEEEEEecCCCCccccCcccceeeCCHHHHHHHhcChhHHHHHHHHHH
Confidence 0111222 124556888887543 222234588999999999999999999999988764
No 44
>cd03673 Ap6A_hydrolase Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most preferred substrate, hydrolyzes to produce two ATP molecules, which is a novel hydrolysis mode for Ap6A. These results indicate that Ap6A hydrolase is a diadenosine polyphosphate hydrolase. It requires the presence of a divalent cation, such as Mn2+, Mg2+, Zn2+, and Co2+, for activity. Members of the Nudix superfamily are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site.
Probab=99.47 E-value=1.6e-13 Score=112.28 Aligned_cols=104 Identities=14% Similarity=0.088 Sum_probs=82.9
Q ss_pred CEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee----ceEE
Q psy8564 221 DYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT----HLQF 293 (341)
Q Consensus 221 g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~----h~~~ 293 (341)
++|||.||..+ |.|+||| ++.||++ .+|+.||+.||+|++ .....+..+.+.++ ....
T Consensus 16 ~~vLl~~~~~~----~~w~~PgG~v~~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~ 80 (131)
T cd03673 16 IEVLLIHRPRG----DDWSLPKGKLEPGETP-----------PEAAVREVEEETGIRAEVGDPLGTIRYWFSSSGKRVHK 80 (131)
T ss_pred eEEEEEEcCCC----CcccCCCCccCCCCCH-----------HHHHHHHHhhhhCCceEecceEEEEEEeccCCCCCcce
Confidence 89999999654 8999999 9999988 999999999999998 66667777777665 4556
Q ss_pred EEEEEEEEecc-cc---cccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 294 KIVPCHIFLKK-CF---LKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 294 ~l~~~~~~~~~-~~---~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
.+++|.+...+ .. ...+..++.|++++++.++-..+.++.++++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~~l~~~~ 130 (131)
T cd03673 81 TVHWWLMRALGGEFTPQPDEEVDEVRWLPPDEARDRLSYPNDRELLRAAL 130 (131)
T ss_pred EEEEEEEEEcCCCcccCCCCcEEEEEEcCHHHHHHHcCCHhHHHHHHHhh
Confidence 77778877544 11 223335789999999999888899999988764
No 45
>cd04681 Nudix_Hydrolase_22 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.47 E-value=1.9e-13 Score=112.10 Aligned_cols=112 Identities=14% Similarity=0.147 Sum_probs=77.1
Q ss_pred EEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeec
Q psy8564 214 MFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTH 290 (341)
Q Consensus 214 ~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h 290 (341)
++|+.++|++||.||...+ ..|.|+||| +|.||++ .+++.||+.||+|++ .....++.+.+.|+.
T Consensus 6 ~~i~~~~~~vLL~~r~~~~-~~~~w~~PgG~ve~gEs~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~ 73 (130)
T cd04681 6 VLILNEDGELLVVRRAREP-GKGTLDLPGGFVDPGESA-----------EEALIREIREETGLKVTELSYLFSLPNTYPY 73 (130)
T ss_pred EEEEcCCCcEEEEEecCCC-CCCcEeCCceeecCCCCH-----------HHHHHHHHHHHhCCcccceeEEEeecceeee
Confidence 4444567999999997654 689999999 9999988 999999999999998 666666655544432
Q ss_pred e--E--EEEEEEEEEeccc---ccccCCCCceeeeCCCCC--CCCCCHHHHHHHHHh
Q psy8564 291 L--Q--FKIVPCHIFLKKC---FLKENKNNFIWYPIKKIK--NSPIPAPVRKILFQI 338 (341)
Q Consensus 291 ~--~--~~l~~~~~~~~~~---~~~~~~~~~~W~~~~el~--~~~~~~a~~~il~~l 338 (341)
. . ....+|.|.+.+. ....+..+++|+++++|. +++++ ..+.+++.+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~-~~~~~~~~~ 129 (130)
T cd04681 74 GGMEYDTLDLFFVCQVDDKPIVKAPDDVAELKWVVPQDIELENFAFP-SIRQAVERW 129 (130)
T ss_pred CCceeEEEEEEEEEEeCCCCCcCChHHhheeEEecHHHCCcccCCcH-HHHHHHHhh
Confidence 2 2 2223566776542 111233678999999994 45553 555565543
No 46
>cd04664 Nudix_Hydrolase_7 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.47 E-value=1.6e-13 Score=112.55 Aligned_cols=112 Identities=16% Similarity=0.171 Sum_probs=84.0
Q ss_pred eEEEEEEEe--CCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEE
Q psy8564 211 SIIMFIVID--DDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIIS 285 (341)
Q Consensus 211 ~~~~~ii~~--~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~ 285 (341)
.+++++... +|+|||.||..+ .+|.|+||| +|.+|++ .+|+.||+.||+|++ .....+....
T Consensus 3 ~~~v~~~~~~~~~~vLL~~r~~~--~~~~w~~PgG~ve~~Es~-----------~~aa~RE~~EE~Gl~~~~~~~~~~~~ 69 (129)
T cd04664 3 SVLVVPYRLTGEGRVLLLRRSDK--YAGFWQSVTGGIEDGESP-----------AEAARREVAEETGLDPERLTLLDRGA 69 (129)
T ss_pred EEEEEEEEeCCCCEEEEEEeCCC--CCCcccccCcccCCCCCH-----------HHHHHHHHHHHHCCChhheEEEeecc
Confidence 345555555 799999999765 899999999 9999988 999999999999998 4444433322
Q ss_pred ----EEeec--eEEEEEEEEEEeccc---ccccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 286 ----HKLTH--LQFKIVPCHIFLKKC---FLKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 286 ----h~~~h--~~~~l~~~~~~~~~~---~~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
+.+++ .++.+++|.+...+. ....++.++.|++++++.++...+.+++++
T Consensus 70 ~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~E~~~~~W~~~~e~~~~~~~~~~~~~~ 128 (129)
T cd04664 70 SIAFVEFTDNGRVWTEHPFAFHLPSDAVVTLDWEHDAFEWVPPEEAAALLLWESNRRAW 128 (129)
T ss_pred cccccccCCCceEEEEeEEEEEcCCCCcccCCccccccEecCHHHHHHHHcChhhhhhh
Confidence 22322 456778898886542 122344789999999999999988888875
No 47
>cd04680 Nudix_Hydrolase_21 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.46 E-value=2e-13 Score=110.22 Aligned_cols=109 Identities=10% Similarity=0.111 Sum_probs=81.7
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c-cccccCcEEEEe
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K-NYLILPIISHKL 288 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~-~~~~~~~~~h~~ 288 (341)
.++|++.+|++||.||...+ .|+||| ++.||++ ++|+.||+.||+|+. . ....++.+.+.+
T Consensus 4 ~~~i~~~~~~vLL~~r~~~~----~w~~PgG~ve~gEt~-----------~~aa~REl~EEtG~~~~~~~~~~~~~~~~~ 68 (120)
T cd04680 4 RAVVTDADGRVLLVRHTYGP----GWYLPGGGLERGETF-----------AEAARRELLEELGIRLAVVAELLGVYYHSA 68 (120)
T ss_pred EEEEECCCCeEEEEEECCCC----cEeCCCCcCCCCCCH-----------HHHHHHHHHHHHCCccccccceEEEEecCC
Confidence 34455567999999997544 999999 9999998 999999999999998 6 666666666666
Q ss_pred eceEEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCCCCCCHHHHHHHHH
Q psy8564 289 THLQFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKNSPIPAPVRKILFQ 337 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~ 337 (341)
+.....+++|.|...+ . ....+..+.+|++++++.+ .+.++.+..+++
T Consensus 69 ~~~~~~~~~f~~~~~~~~~~~~~~E~~~~~w~~~~~l~~-~~~~~~~~~~~~ 119 (120)
T cd04680 69 SGSWDHVIVFRARADTQPVIRPSHEISEARFFPPDALPE-PTTPATRRRIAE 119 (120)
T ss_pred CCCceEEEEEEecccCCCccCCcccEEEEEEECHHHCcc-cCChHHHHHhhc
Confidence 5445567888888654 2 1222335789999999998 666666666543
No 48
>cd04695 Nudix_Hydrolase_36 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.45 E-value=3.3e-13 Score=111.17 Aligned_cols=110 Identities=10% Similarity=0.110 Sum_probs=82.7
Q ss_pred EeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeece---
Q psy8564 218 IDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHL--- 291 (341)
Q Consensus 218 ~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~--- 291 (341)
..++++||.||+.+ +.|.|.||| +|.||++ .+|++||+.||+|++ ........+.+.|++.
T Consensus 11 ~~~~~vLl~~r~~~--~~g~w~~PgG~ve~gEs~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~ 77 (131)
T cd04695 11 DKETKVLLLKRVKT--LGGFWCHVAGGVEAGETA-----------WQAALRELKEETGISLPELYNADYLEQFYEANDNR 77 (131)
T ss_pred CCCCEEEEEEecCC--CCCcEECCcccccCCCCH-----------HHHHHHHHHHHhCCCccccccccceeeEeecCCce
Confidence 35689999999865 789999999 9999998 999999999999998 4333333344545432
Q ss_pred EEEEEEEEEEecc---cccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 292 QFKIVPCHIFLKK---CFLKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 292 ~~~l~~~~~~~~~---~~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
...+.+|.+...+ .....++.+.+|++++++.++...+.++.+++.+..
T Consensus 78 ~~~~~~f~~~~~~~~~~~~~~E~~~~~W~~~~e~~~~~~~~~~~~~~~~~~~ 129 (131)
T cd04695 78 ILMAPVFVGFVPPHQEVVLNHEHTEYRWCSFAEALELAPFPGQRALYDHVWR 129 (131)
T ss_pred EEEEEEEEEEecCCCccccCchhcccEecCHHHHHHhcCChhHHHHHHHHHh
Confidence 2345567666533 112234588999999999999999999999987653
No 49
>cd04688 Nudix_Hydrolase_29 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.44 E-value=4.2e-13 Score=109.61 Aligned_cols=105 Identities=18% Similarity=0.191 Sum_probs=79.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+.+|+.++|+|||.||.. .+.|+||| +|.||++ .+|+.||+.||+|++ .....++...|.|
T Consensus 3 ~v~~vi~~~~~vLl~~~~~----~~~w~lPgG~ve~gEs~-----------~~aa~RE~~EEtGl~~~~~~~~~~~~~~~ 67 (126)
T cd04688 3 RAAAIIIHNGKLLVQKNPD----ETFYRPPGGGIEFGESS-----------EEALIREFKEELGLKIEITRLLGVVENIF 67 (126)
T ss_pred EEEEEEEECCEEEEEEeCC----CCeEECCCccccCCCCH-----------HHHHHHHHHHHhCCceecceeeEEEEEee
Confidence 3455555678999999865 68999999 9999988 999999999999998 6666666666544
Q ss_pred e--c--eEEEEEEEEEEecccc----------cccCCCCceeeeCCCCCCCCCCHHH
Q psy8564 289 T--H--LQFKIVPCHIFLKKCF----------LKENKNNFIWYPIKKIKNSPIPAPV 331 (341)
Q Consensus 289 ~--h--~~~~l~~~~~~~~~~~----------~~~~~~~~~W~~~~el~~~~~~~a~ 331 (341)
+ . .+...++|.|...+.. ...++.++.|++++++..+++.|++
T Consensus 68 ~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~~~~p~~ 124 (126)
T cd04688 68 TYNGKPGHEIEFYYLVTLLDESLYQQDIEILEEEGEKIVFRWIPIDELKEIKLYPEF 124 (126)
T ss_pred ccCCcccEEEEEEEEEEeCCCcccccccceeccCCCEEEEEEeeHHHcccCccCCcc
Confidence 3 2 2455778888875521 1123357899999999999988754
No 50
>cd04687 Nudix_Hydrolase_28 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.44 E-value=4.3e-13 Score=109.88 Aligned_cols=106 Identities=14% Similarity=0.166 Sum_probs=76.4
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+.+|+.++|+||+.||...+ ++.|+||| +|.||++ ++|+.||+.||+|++ ...+.+....+.+
T Consensus 3 ~a~~iv~~~~~vLl~~r~~~~--~~~~~lPGG~ve~gEt~-----------~~aa~RE~~EEtGl~v~~~~~~~~~~~~~ 69 (128)
T cd04687 3 SAKAVIIKNDKILLIKHHDDG--GVWYILPGGGQEPGETL-----------EDAAHRECKEEIGIDVEIGPLLFVREYIG 69 (128)
T ss_pred EEEEEEEECCEEEEEEEEcCC--CCeEECCCcccCCCCCH-----------HHHHHHHHHHHHCCccccCcEEEEEEEec
Confidence 466676788999999996543 58999998 9999988 999999999999998 5444333333321
Q ss_pred --------eceEEEEEEEEEEecccc-------cccCCCCceeeeCCCCCCCCCCHH
Q psy8564 289 --------THLQFKIVPCHIFLKKCF-------LKENKNNFIWYPIKKIKNSPIPAP 330 (341)
Q Consensus 289 --------~h~~~~l~~~~~~~~~~~-------~~~~~~~~~W~~~~el~~~~~~~a 330 (341)
...+...++|.|...+.. ...+..+++|++++++.++++.++
T Consensus 70 ~~~~~~~~~~~~~i~~~f~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~l~~~~~~p~ 126 (128)
T cd04687 70 HNPTSELPGHFHQVELMFECKIKSGTPAKTPSKPDPNQIGVEWLKLKELGDIPLYPS 126 (128)
T ss_pred cCccccCCCceeEEEEEEEEEECCCCcccccCCCCCCEEeeEEEcHHHhCcccccCC
Confidence 224555677888865411 111124789999999999988764
No 51
>PLN02325 nudix hydrolase
Probab=99.44 E-value=8.9e-13 Score=110.52 Aligned_cols=116 Identities=14% Similarity=0.232 Sum_probs=81.5
Q ss_pred eeEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
+..+.+++.++|++||.||... ...|.|.+|| +|.||+. .+|+.||++||+|++ .....+..+.+
T Consensus 9 ~~~v~~vi~~~~~vLL~rr~~~-~~~g~W~lPGG~ve~gEs~-----------~~aa~REv~EEtGl~v~~~~~l~~~~~ 76 (144)
T PLN02325 9 RVAVVVFLLKGNSVLLGRRRSS-IGDSTFALPGGHLEFGESF-----------EECAAREVKEETGLEIEKIELLTVTNN 76 (144)
T ss_pred eEEEEEEEEcCCEEEEEEecCC-CCCCeEECCceeCCCCCCH-----------HHHHHHHHHHHHCCCCcceEEEEEecc
Confidence 3455566667889999999753 4579999999 9999988 999999999999998 66666665555
Q ss_pred Eeec----eEEEEEEEEEEeccc---c---cccCCCCceeeeCCCCCCCCCCHHHHHHHHHh
Q psy8564 287 KLTH----LQFKIVPCHIFLKKC---F---LKENKNNFIWYPIKKIKNSPIPAPVRKILFQI 338 (341)
Q Consensus 287 ~~~h----~~~~l~~~~~~~~~~---~---~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l 338 (341)
.|.+ .++...+|.+...+. . ...+..+++|+++++|.. .+..+.+.+++.+
T Consensus 77 ~~~~~~~~~~~i~~~f~~~~~~~~~~~~~~e~~e~~~~~W~~~d~Lp~-~~~~p~~~~~~~~ 137 (144)
T PLN02325 77 VFLEEPKPSHYVTVFMRAVLADPSQVPQNLEPEKCYGWDWYEWDNLPE-PLFWPLEKLVGSG 137 (144)
T ss_pred eeecCCCCcEEEEEEEEEEECCCCCCCCcCCchhcCceEEEChHHCCh-hhhHHHHHHHHcC
Confidence 4422 344445566665431 1 111236689999999987 4555666666543
No 52
>cd02883 Nudix_Hydrolase Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzy
Probab=99.42 E-value=3.2e-13 Score=108.24 Aligned_cols=110 Identities=15% Similarity=0.241 Sum_probs=83.8
Q ss_pred EEEEEEe-CCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCc--EEE
Q psy8564 213 IMFIVID-DDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPI--ISH 286 (341)
Q Consensus 213 ~~~ii~~-~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~--~~h 286 (341)
+++++.+ ++++||.||+.+ ++|+|+||| ++.+|++ .+++.||+.||+|+. ........ ..|
T Consensus 3 ~~~i~~~~~~~ill~kr~~~--~~~~~~~p~G~~~~~e~~-----------~~~a~RE~~EE~Gl~~~~~~~~~~~~~~~ 69 (123)
T cd02883 3 VGAVILDEDGRVLLVRRADS--PGGLWELPGGGVEPGETL-----------EEAAIREVREETGLDVDVLRLLGVYEVES 69 (123)
T ss_pred eEEEEECCCCCEEEEEEcCC--CCCeEeCCcccccCCCCH-----------HHHHHHHHHHhhCccceeeeEEEEEEeec
Confidence 3444444 489999999876 999999999 8899987 889999999999998 43333333 344
Q ss_pred EeeceEEEEEEEEEEeccc----ccccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 287 KLTHLQFKIVPCHIFLKKC----FLKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~~----~~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
.++|....+.+|.+..... ....+..+..|++++++.+++.+++.++++
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~w~~~~~l~~~~~~~~~~~~~ 122 (123)
T cd02883 70 PDEGEHAVVFVFLARLVGGEPTLLPPDEISEVRWVTLDELPALALSPALRPAL 122 (123)
T ss_pred cCCCceEEEEEEEEEeCCCCcCCCCCCccceEEEEcHHHCccccccccccccc
Confidence 4457889999999886542 122333578999999999999999887765
No 53
>cd03675 Nudix_Hydrolase_2 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability,
Probab=99.42 E-value=1.1e-12 Score=108.16 Aligned_cols=115 Identities=13% Similarity=0.155 Sum_probs=83.0
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+++++.++|++||.||... -+|.|+||| +|.||++ .+|+.||+.||+|++ .....+....+.+
T Consensus 2 ~v~~ii~~~~~vLlv~r~~~--~~~~w~~PgG~ve~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~ 68 (134)
T cd03675 2 TVAAVVERDGRFLLVEEETD--GGLVFNQPAGHLEPGESL-----------IEAAVRETLEETGWHVEPTALLGIYQWTA 68 (134)
T ss_pred eEEEEEEECCEEEEEEEccC--CCceEECCCccCCCCCCH-----------HHHHHHHHHHHHCcccccceEEEEEEeec
Confidence 45667778899999999654 578999999 9999998 999999999999998 5544444433333
Q ss_pred e--ceEEEEEEEEEEeccc----ccccCCCCceeeeCCCCCCCC---CCHHHHHHHHHhh
Q psy8564 289 T--HLQFKIVPCHIFLKKC----FLKENKNNFIWYPIKKIKNSP---IPAPVRKILFQII 339 (341)
Q Consensus 289 ~--h~~~~l~~~~~~~~~~----~~~~~~~~~~W~~~~el~~~~---~~~a~~~il~~l~ 339 (341)
+ ...+...+|.+...+. ....+..+..|++++++..+. .++..++.++.+.
T Consensus 69 ~~~~~~~~~~~f~~~~~~~~~~~~~~~e~~~~~w~~~~el~~~~~~~~~~~~~~~i~~~l 128 (134)
T cd03675 69 PDSDTTYLRFAFAAELLEHLPDQPLDSGIVRAHWLTLEEILALAARLRSPLVLRCIEDYL 128 (134)
T ss_pred CCCCeeEEEEEEEEEECCCCCCCCCCCCceeeEEEeHHHHHhhhhhhcCchHHHHHHHHH
Confidence 3 2344556777776541 122234678999999999886 3666777776553
No 54
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=99.41 E-value=1.1e-12 Score=107.89 Aligned_cols=105 Identities=10% Similarity=0.054 Sum_probs=76.7
Q ss_pred eEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEE
Q psy8564 211 SIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHK 287 (341)
Q Consensus 211 ~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~ 287 (341)
.++.+|+.++|++||.||..+ ...|.|+||| +|.||++ ++++.||+.||+|++ .....+.. +.
T Consensus 14 ~~v~~ii~~~~~vLL~kr~~~-~~~g~w~lPgG~ve~gE~~-----------~~a~~REl~EEtGl~~~~~~~~~~--~~ 79 (130)
T cd04511 14 IIVGCVPEWEGKVLLCRRAIE-PRHGFWTLPAGFMENGETT-----------EQGALRETWEEAGARVEIDGLYAV--YS 79 (130)
T ss_pred EEEEEEEecCCEEEEEEecCC-CCCCeEECCcccccCCCCH-----------HHHHHHHHHHHhCCEEEeeeEEEE--Ee
Confidence 445556667899999999764 4789999999 9999988 999999999999998 54433332 23
Q ss_pred eeceEEEEEEEEEEeccc--ccccCCCCceeeeCCCCC--CCCCCH
Q psy8564 288 LTHLQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIK--NSPIPA 329 (341)
Q Consensus 288 ~~h~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~--~~~~~~ 329 (341)
+++.+..+++|.+.+.+. ....++.+.+|+++++|. ++.++.
T Consensus 80 ~~~~~~~~~~f~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~l~~~~ 125 (130)
T cd04511 80 VPHISQVYMFYRARLLDLDFAPGPESLEVRLFTEEEIPWDELAFPT 125 (130)
T ss_pred cCCceEEEEEEEEEEcCCcccCCcchhceEEECHHHCCchhccccc
Confidence 445555677888887552 112234778999999996 566643
No 55
>cd04670 Nudix_Hydrolase_12 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.41 E-value=7.8e-13 Score=108.15 Aligned_cols=110 Identities=15% Similarity=0.184 Sum_probs=74.1
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCc-EEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPI-ISHK 287 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~-~~h~ 287 (341)
+.++|++.+|+||+.||..+ +.|+|+||| +|.|||+ .+|+.||+.||+|+. .....+.. ..|.
T Consensus 5 ~~~~v~~~~~~vLl~~r~~~--~~~~w~~PGG~ve~gEt~-----------~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~ 71 (127)
T cd04670 5 VGGLVLNEKNEVLVVQERNK--TPNGWKLPGGLVDPGEDI-----------FDGAVREVLEETGIDTEFVSVVGFRHAHP 71 (127)
T ss_pred EEEEEEcCCCeEEEEEccCC--CCCcEECCCccCCCCCCH-----------HHHHHHHHHHHHCCCcceeEEEEEEecCC
Confidence 34455556799999998664 789999999 9999988 999999999999998 54443321 1222
Q ss_pred eeceEEEEEEEEEEecc---c--ccccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 288 LTHLQFKIVPCHIFLKK---C--FLKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 288 ~~h~~~~l~~~~~~~~~---~--~~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
++..... .+|.+.+.. . ....+..+.+|++++++.+.+++......+
T Consensus 72 ~~~~~~~-~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~~~~ 123 (127)
T cd04670 72 GAFGKSD-LYFICRLKPLSFDINFDTSEIAAAKWMPLEEYISQPITSEVNRLI 123 (127)
T ss_pred CCcCcee-EEEEEEEccCcCcCCCChhhhheeEEEcHHHHhcchhHHHHHHHH
Confidence 2211111 224444432 1 112233678999999999999998855544
No 56
>cd04667 Nudix_Hydrolase_10 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.41 E-value=8e-13 Score=105.75 Aligned_cols=103 Identities=12% Similarity=0.105 Sum_probs=76.4
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
+++|+.++|++||.||.. |.|+||| ++.||++ .+|+.||+.||+|++ .....+.. |.
T Consensus 3 a~~i~~~~~~vLlv~r~~-----~~w~~PgG~ve~gE~~-----------~~aa~REl~EEtGl~~~~~~~~~~----~~ 62 (112)
T cd04667 3 ATVICRRGGRVLLVRKSG-----SRWALPGGKIEPGETP-----------LQAARRELQEETGLQGLDLLYLFH----VD 62 (112)
T ss_pred eEEEEecCCEEEEEEcCC-----CcEeCCCCcCCCCCCH-----------HHHHHHHHHHHhCCcccceEEEEE----Ee
Confidence 455666789999999963 8999999 9999988 999999999999998 44333322 22
Q ss_pred ceEEEEEEEEEEeccc--c-cccCCCCceeeeCCCCCCCCCCHHHHHHH
Q psy8564 290 HLQFKIVPCHIFLKKC--F-LKENKNNFIWYPIKKIKNSPIPAPVRKIL 335 (341)
Q Consensus 290 h~~~~l~~~~~~~~~~--~-~~~~~~~~~W~~~~el~~~~~~~a~~~il 335 (341)
+.+...++|.+.+.+. . ...+..++.|++++++.++++++++++|.
T Consensus 63 ~~~~~~~~f~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~~ 111 (112)
T cd04667 63 GGSTRHHVFVASVPPSAQPKPSNEIADCRWLSLDALGDLNASAATRLIV 111 (112)
T ss_pred CCCEEEEEEEEEcCCcCCCCCchheeEEEEecHHHhhhcccchhhhhhc
Confidence 3333456777765431 1 12233678999999999999999998874
No 57
>cd04697 Nudix_Hydrolase_38 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.40 E-value=6.3e-13 Score=108.76 Aligned_cols=102 Identities=10% Similarity=0.086 Sum_probs=74.7
Q ss_pred EEEEEEEeCCEEEEEEeCCCC-cccccccc-cc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG-IWGGLLSF-PE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g-~~~GlWEF-Pg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
+.+++++.+|+||++||...+ .+.|+|+| || ++.||++ .++++||+.||+|++ .....+..+.+
T Consensus 3 ~~v~i~~~~~~iLl~~R~~~~~~~~g~w~~~~GG~ve~gE~~-----------~~aa~REl~EEtGl~~~~l~~~~~~~~ 71 (126)
T cd04697 3 TYIFVFNSEGKLCVHKRTLTKDWCPGYWDIAFGGVVQAGESY-----------LQNAQRELEEELGIDGVQLTPLGLFYY 71 (126)
T ss_pred EEEEEEcCCCeEEEEECCCCCCCCCCcccCcCCcccCCCCCH-----------HHHHHHHHHHHHCCCccccEEeeEEEe
Confidence 345666778999999998765 57999999 55 9999988 899999999999998 54555555544
Q ss_pred EeeceEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCC
Q psy8564 287 KLTHLQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~ 324 (341)
......+..++|.+..... ....+..+++|++++++.+
T Consensus 72 ~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~w~~~~el~~ 111 (126)
T cd04697 72 DTDGNRVWGKVFSCVYDGPLKLQEEEVEEITWLSINEILQ 111 (126)
T ss_pred cCCCceEEEEEEEEEECCCCCCCHhHhhheEEcCHHHHHH
Confidence 4333355567787775432 2223347899999988865
No 58
>PRK15393 NUDIX hydrolase YfcD; Provisional
Probab=99.40 E-value=1.1e-12 Score=114.18 Aligned_cols=116 Identities=10% Similarity=0.076 Sum_probs=81.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCC-ccccccc-ccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG-IWGGLLS-FPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g-~~~GlWE-FPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
+.++|++.+|++||++|...+ .++|.|+ ||| +++||++ .+|+.||+.||+|+. .....++.+.+
T Consensus 40 ~~v~v~~~~g~iLL~~R~~~~~~~pg~~~~~pGG~ve~GEs~-----------~eAA~REL~EEtGl~~~~~~~~~~~~~ 108 (180)
T PRK15393 40 TYIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQAGEQL-----------LESARREAEEELGIAGVPFAEHGQFYF 108 (180)
T ss_pred EEEEEECCCCeEEEEEeCCCCCCCCCcccccCCCcCCCCCCH-----------HHHHHHHHHHHHCCCCccceeceeEEe
Confidence 344444556999999997654 5688885 788 9999988 999999999999998 55455555544
Q ss_pred EeeceEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCCC--CCCHHHHHHHHHh
Q psy8564 287 KLTHLQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKNS--PIPAPVRKILFQI 338 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~~--~~~~a~~~il~~l 338 (341)
.....+...++|.+...+. ....+..++.|++++++.++ .|++.....+..+
T Consensus 109 ~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~~~~l~~~ 164 (180)
T PRK15393 109 EDENCRVWGALFSCVSHGPFALQEEEVSEVCWMTPEEITARCDEFTPDSLKALALW 164 (180)
T ss_pred cCCCceEEEEEEEEEeCCCCCCChHHeeEEEECCHHHHhhhhhhcCccHHHHHHHH
Confidence 4444455556777765432 12223478999999999986 6866666655433
No 59
>cd04690 Nudix_Hydrolase_31 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.39 E-value=1e-12 Score=105.80 Aligned_cols=105 Identities=10% Similarity=0.128 Sum_probs=78.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cc--ccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KN--YLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~--~~~~~~~~h 286 (341)
++++++.++|++|+.||.. .|.|+||| ++.+|++ ++|+.||+.||+|+. .. ...+..+.+
T Consensus 3 ~~~~v~~~~~~vLl~~r~~----~~~w~~PgG~ve~~Es~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~ 67 (118)
T cd04690 3 AAALILVRDGRVLLVRKRG----TDVFYLPGGKIEAGETP-----------LQALIRELSEELGLDLDPDSLEYLGTFRA 67 (118)
T ss_pred EEEEEEecCCeEEEEEECC----CCcEECCCCccCCCCCH-----------HHHHHHHHHHHHCCccChhheEEEEEEec
Confidence 4566677889999999864 36899999 9999988 999999999999998 55 555555544
Q ss_pred E---eeceEEEEEEEEEEecccc-cccCCCCceeeeCCCCCCCCCCHHH
Q psy8564 287 K---LTHLQFKIVPCHIFLKKCF-LKENKNNFIWYPIKKIKNSPIPAPV 331 (341)
Q Consensus 287 ~---~~h~~~~l~~~~~~~~~~~-~~~~~~~~~W~~~~el~~~~~~~a~ 331 (341)
. .++.+..+++|.+...... ...+..++.|++++++...++++.+
T Consensus 68 ~~~~~~~~~~~~~~f~~~~~~~~~~~~e~~~~~W~~~~e~~~~~~~~~~ 116 (118)
T cd04690 68 PAANEPGVDVRATVYVAELTGEPVPAAEIEEIRWVDYDDPADDRLAPLL 116 (118)
T ss_pred ccccCCCcEEEEEEEEEcccCCcCCCchhhccEEecHHHccccccCccc
Confidence 2 2234577888888865421 1223477899999999888888754
No 60
>cd03674 Nudix_Hydrolase_1 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamil
Probab=99.39 E-value=4.2e-12 Score=105.57 Aligned_cols=112 Identities=16% Similarity=0.273 Sum_probs=79.7
Q ss_pred EEEEEEEeC-CEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCc----
Q psy8564 212 IIMFIVIDD-DYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPI---- 283 (341)
Q Consensus 212 ~~~~ii~~~-g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~---- 283 (341)
+.++|++.+ ++|||.||.. .|.|.+|| +|.||++ .+|+.||++||+|++ ........
T Consensus 5 ~~~~v~~~~~~~vLLv~r~~----~~~w~lPgG~ve~gE~~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~ 69 (138)
T cd03674 5 ASAFVVNPDRGKVLLTHHRK----LGSWLQPGGHIDPDESL-----------LEAALRELREETGIELLGLRPLSVLVDL 69 (138)
T ss_pred EEEEEEeCCCCeEEEEEEcC----CCcEECCceecCCCCCH-----------HHHHHHHHHHHHCCCcccceeccccccc
Confidence 445555555 8999999865 48999999 9999998 999999999999997 44333221
Q ss_pred EEEE-ee--------ceEEEEEEEEEEecc-cc---cccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 284 ISHK-LT--------HLQFKIVPCHIFLKK-CF---LKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 284 ~~h~-~~--------h~~~~l~~~~~~~~~-~~---~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
..|. +. +.++ ..+|.|.... .. ...+..+++|++++++..+++++..+.+++...
T Consensus 70 ~~~~~~~~~~~~~~~~~~~-~~~y~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~~~~~~~~i~~~~ 137 (138)
T cd03674 70 DVHPIDGHPKRGVPGHLHL-DLRFLAVAPADDVAPPKSDESDAVRWFPLDELASLELPEDVRRLVEKAL 137 (138)
T ss_pred eeEeecCCCCCCCCCcEEE-EEEEEEEccCccccCCCCCcccccEEEcHHHhhhccCCHHHHHHHHHHh
Confidence 1222 11 2222 3457777533 21 233447899999999999999999999998754
No 61
>cd04678 Nudix_Hydrolase_19 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.39 E-value=3.6e-12 Score=104.41 Aligned_cols=101 Identities=13% Similarity=0.223 Sum_probs=74.5
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe-
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL- 288 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~- 288 (341)
.++|++.+|++||.||.. +..+|.|.||| ++.||+. .+|+.||+.||+|++ .....+..+.+.+
T Consensus 6 ~~ii~~~~~~iLl~~r~~-~~~~~~w~~PGG~ve~gEt~-----------~~Aa~REl~EE~Gl~~~~~~~~~~~~~~~~ 73 (129)
T cd04678 6 GVFVLNPKGKVLLGKRKG-SHGAGTWALPGGHLEFGESF-----------EECAAREVLEETGLHIENVQFLTVTNDVFE 73 (129)
T ss_pred EEEEECCCCeEEEEeccC-CCCCCeEECCcccccCCCCH-----------HHHHHHHHHHHhCCcccceEEEEEEeEEeC
Confidence 344444569999999975 46889999999 9999988 999999999999998 6655665555543
Q ss_pred -eceEEEEEEEEEEeccc---cc---ccCCCCceeeeCCCCCCC
Q psy8564 289 -THLQFKIVPCHIFLKKC---FL---KENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 289 -~h~~~~l~~~~~~~~~~---~~---~~~~~~~~W~~~~el~~~ 325 (341)
.+.+....+|.|...+. .. ..+..+++|+++++|.++
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~~l~~~ 117 (129)
T cd04678 74 EEGKHYVTIFVKAEVDDGEAEPNKMEPEKCEGWEWFDWEELPSV 117 (129)
T ss_pred CCCcEEEEEEEEEEeCCCCcccCCCCCceeCceEEeCHHHCCCc
Confidence 34455566777776541 11 122367899999999985
No 62
>cd03426 CoAse Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative stress. CoAse has a conserved Nudix fold and requires a single divalent cation for catalysis. In addition to a signature Nudix motif G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val, CoAse contains an additional motif upstream called the NuCoA motif (LLTXT(SA)X3RX3GX3FPGG) which is postulated to be involved in CoA recognition. CoA plays a central role in lipid metabolism. It is involved in the initial steps of fatty acid sythesis in the cytosol, in the oxidation of fatty acids and the citric acid cycle in the mitochondria, and in the oxidation of long-chain fatty acids in peroxisomes. CoA has the important role of activating fatty acids for further modification into key biological signalling molecules.
Probab=99.36 E-value=8.7e-13 Score=112.20 Aligned_cols=96 Identities=14% Similarity=0.162 Sum_probs=70.3
Q ss_pred CEEEEEEeCCCC-cccccccccc--cccc-cchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEEE
Q psy8564 221 DYVLFQKRSNKG-IWGGLLSFPE--WILK-DKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFKI 295 (341)
Q Consensus 221 g~vLl~kR~~~g-~~~GlWEFPg--vE~~-E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~l 295 (341)
++|||.||...+ .++|+|+||| +|.| |++ .+|+.||+.||+|++ .....+..+.+.++.....+
T Consensus 16 ~~vLL~~R~~~~~~~~g~w~lPGG~ve~gdEs~-----------~eaa~REl~EEtGl~~~~~~~l~~~~~~~~~~~~~v 84 (157)
T cd03426 16 LRVLLTKRASHLRSHPGQVAFPGGKVDPGDEDP-----------VATALREAEEEIGLPPDSVEVLGRLPPYYTRSGFVV 84 (157)
T ss_pred eEEEEEEcccccccCCCcEECCCCCcCCCcCCH-----------HHHHHHHHHHHhCCCccceEEEEECCCccccCCCEE
Confidence 699999998765 5899999999 9999 988 999999999999998 65555554443333334455
Q ss_pred EEEEEEecc----cccccCCCCceeeeCCCCCCCCC
Q psy8564 296 VPCHIFLKK----CFLKENKNNFIWYPIKKIKNSPI 327 (341)
Q Consensus 296 ~~~~~~~~~----~~~~~~~~~~~W~~~~el~~~~~ 327 (341)
++|.+.... .+...+..++.|++++++.+..+
T Consensus 85 ~~~~~~~~~~~~~~~~~~E~~~~~W~~~~el~~~~~ 120 (157)
T cd03426 85 TPVVGLVPPPLPLVLNPDEVAEVFEVPLSFLLDPAN 120 (157)
T ss_pred EEEEEEECCCCCCCCCHHHhheeEEEcHHHHhCcCC
Confidence 666665433 11222347899999999988654
No 63
>cd04672 Nudix_Hydrolase_14 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.36 E-value=3.6e-12 Score=103.68 Aligned_cols=106 Identities=11% Similarity=0.065 Sum_probs=75.0
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE--
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH-- 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h-- 286 (341)
.+++++.++|++||.||.. .|.|+||| ++.+|++ .+|+.||+.||+|++ .....++...+
T Consensus 4 ~v~~~i~~~~~vLL~~~~~----~~~w~~PGG~ve~gEs~-----------~~aa~REl~EEtG~~~~~~~~~~~~~~~~ 68 (123)
T cd04672 4 DVRAAIFKDGKILLVREKS----DGLWSLPGGWADVGLSP-----------AENVVKEVKEETGLDVKVRKLAAVDDRNK 68 (123)
T ss_pred eEEEEEEECCEEEEEEEcC----CCcEeCCccccCCCCCH-----------HHHHHHHHHHHhCCeeeEeEEEEEecccc
Confidence 4555556679999999864 58999999 9999988 999999999999998 44443333222
Q ss_pred -Ee--eceEEEEEEEEEEeccc-c-cccCCCCceeeeCCCCCCCCCCHHHH
Q psy8564 287 -KL--THLQFKIVPCHIFLKKC-F-LKENKNNFIWYPIKKIKNSPIPAPVR 332 (341)
Q Consensus 287 -~~--~h~~~~l~~~~~~~~~~-~-~~~~~~~~~W~~~~el~~~~~~~a~~ 332 (341)
.+ ...++...+|.|...+. . ...+..++.|+++++|.++.+|..+.
T Consensus 69 ~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~~~~W~~~~el~~l~~~~~~~ 119 (123)
T cd04672 69 HHPPPQPYQVYKLFFLCEILGGEFKPNIETSEVGFFALDDLPPLSEKRNTE 119 (123)
T ss_pred ccCCCCceEEEEEEEEEEecCCcccCCCceeeeEEECHHHCcccccCCcch
Confidence 22 22344456777776441 1 11233678999999999998886554
No 64
>cd04700 DR1025_like DR1025 from Deinococcus radiodurans, a member of the Nudix hydrolase superfamily, show nucleoside triphosphatase and dinucleoside polyphosphate pyrophosphatase activities. Like other enzymes belonging to this superfamily, it requires a divalent cation, in this case Mg2+, for its activity. It also contains a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. In general, substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is us
Probab=99.35 E-value=2.8e-12 Score=107.23 Aligned_cols=100 Identities=9% Similarity=0.030 Sum_probs=72.4
Q ss_pred EEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeec
Q psy8564 214 MFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTH 290 (341)
Q Consensus 214 ~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h 290 (341)
++|++.++++||.||.. +...|+|+||| +++||++ ++|+.||+.||+|++ .....+..+.+.+++
T Consensus 18 ~vv~~~~~~vLL~~r~~-~~~~~~w~lPgG~ve~gEt~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~ 85 (142)
T cd04700 18 AVILNERNDVLLVQEKG-GPKKGLWHIPSGAVEDGEFP-----------QDAAVREACEETGLRVRPVKFLGTYLGRFDD 85 (142)
T ss_pred EEEEeCCCcEEEEEEcC-CCCCCeEECCceecCCCCCH-----------HHHHHHHHHHhhCceeeccEEEEEEEEEcCC
Confidence 34445578999988853 45689999999 9999998 999999999999998 666666655555554
Q ss_pred eE-EEEEEEEEEeccc---c-cccCCCCceeeeCCCCCCC
Q psy8564 291 LQ-FKIVPCHIFLKKC---F-LKENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 291 ~~-~~l~~~~~~~~~~---~-~~~~~~~~~W~~~~el~~~ 325 (341)
.. ...++|.+...+. + ...+..+++|++++++.++
T Consensus 86 ~~~~~~~~f~~~~~~~~~~~~~~~E~~~~~w~~~~el~~~ 125 (142)
T cd04700 86 GVLVLRHVWLAEPEGQTLAPKFTDEIAEASFFSREDVAQL 125 (142)
T ss_pred CcEEEEEEEEEEecCCccccCCCCCEEEEEEECHHHhhhc
Confidence 33 3346787876431 1 1123467999999998764
No 65
>cd04671 Nudix_Hydrolase_13 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.35 E-value=3.7e-12 Score=103.88 Aligned_cols=104 Identities=13% Similarity=0.112 Sum_probs=73.5
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
.+++++.+|++|+.||..+ ...|.|+||| +|.+|++ ++|+.||+.||+|++ .....+. +.+..
T Consensus 4 ~~vv~~~~~~vLl~~r~~~-~~~~~w~lPgG~ve~gEt~-----------~~aa~REl~EEtG~~~~~~~~~~-~~~~~- 69 (123)
T cd04671 4 AAVILNNQGEVLLIQEAKR-SCRGKWYLPAGRMEPGETI-----------EEAVKREVKEETGLDCEPTTLLS-VEEQG- 69 (123)
T ss_pred EEEEEcCCCEEEEEEecCC-CCCCeEECceeecCCCCCH-----------HHHHHHHHHHHHCCeeecceEEE-EEccC-
Confidence 3444556799999999754 4689999999 9999998 999999999999998 6555443 22222
Q ss_pred ceEEEEEEEEEEecc-ccc-----ccCCCCceeeeCCCCCCCCCCHHHH
Q psy8564 290 HLQFKIVPCHIFLKK-CFL-----KENKNNFIWYPIKKIKNSPIPAPVR 332 (341)
Q Consensus 290 h~~~~l~~~~~~~~~-~~~-----~~~~~~~~W~~~~el~~~~~~~a~~ 332 (341)
.++..++|.|...+ ... ..+..+.+|++.++| ..++.+++.
T Consensus 70 -~~~~~~~f~a~~~~g~~~~~~~~~~e~~~~~W~~~~el-~~~~~~~~~ 116 (123)
T cd04671 70 -GSWFRFVFTGNITGGDLKTEKEADSESLQARWYSNKDL-PLPLRAHDI 116 (123)
T ss_pred -CeEEEEEEEEEEeCCeEccCCCCCcceEEEEEECHHHC-CCccchhee
Confidence 33456677787654 111 111136899999999 567776654
No 66
>cd04689 Nudix_Hydrolase_30 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate sp
Probab=99.32 E-value=8.9e-12 Score=101.57 Aligned_cols=108 Identities=14% Similarity=0.097 Sum_probs=76.5
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+.+++.++|++|+.||.. .|.|+||| +|.+|++ .+|+.||+.||+|++ .....++.+.+.|
T Consensus 3 ~~~~vi~~~~~vLlv~~~~----~~~~~lPGG~ve~gEt~-----------~~aa~REl~EEtGl~~~~~~~l~~~~~~~ 67 (125)
T cd04689 3 RARAIVRAGNKVLLARVIG----QPHYFLPGGHVEPGETA-----------ENALRRELQEELGVAVSDGRFLGAIENQW 67 (125)
T ss_pred EEEEEEEeCCEEEEEEecC----CCCEECCCCcCCCCCCH-----------HHHHHHHHHHHhCceeeccEEEEEEeeee
Confidence 4556667899999999964 36899999 9999988 999999999999998 6666666666544
Q ss_pred ec----eEEEEEEEEEEeccc-----c-cccCCCCceeeeCCCCCCCCCCHHHHHHHH
Q psy8564 289 TH----LQFKIVPCHIFLKKC-----F-LKENKNNFIWYPIKKIKNSPIPAPVRKILF 336 (341)
Q Consensus 289 ~h----~~~~l~~~~~~~~~~-----~-~~~~~~~~~W~~~~el~~~~~~~a~~~il~ 336 (341)
.. .+...++|.+..... . ..++..+.+|++.+++..+ |....+++.
T Consensus 68 ~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~--p~~l~~~~~ 123 (125)
T cd04689 68 HEKGVRTHEINHIFAVESSWLASDGPPQADEDHLSFSWVPVSDLSLY--PALLRDLVK 123 (125)
T ss_pred ccCCceEEEEEEEEEEEcccccccCCccCccceEEEEEccHHHcccC--cHHHHHHhh
Confidence 21 233456777775421 1 1122357899999999865 455555544
No 67
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.32 E-value=2.2e-11 Score=102.92 Aligned_cols=150 Identities=19% Similarity=0.082 Sum_probs=116.0
Q ss_pred CChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCc--HH-HHHHHHHHHHHhHHHh----
Q psy8564 8 KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGY--YS-RARNLHICAKLVFFKY---- 80 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~--~~-rA~~i~~~a~~i~~~~---- 80 (341)
.+.|..|..+|+..|++...+..+..++-+.|.. ++.+||.+.++.+|| |+ ||+||+.+-+.+-+--
T Consensus 37 e~lf~ELsFCILTANsSA~~~~~~q~~lG~gfly------~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v~ 110 (210)
T COG1059 37 EDLFKELSFCILTANSSATMGLRAQNELGDGFLY------LSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIVK 110 (210)
T ss_pred HHHHHHHHHHhccccchHHHHHHHHHHhcccccc------CCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHHh
Confidence 5779999999999999999999999988766654 478999999999986 45 9999999887663200
Q ss_pred CCCCcc-chHHHh-cCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcch------HHHHHHHHHHHHhhC
Q psy8564 81 NGIFPK-NFISLI-NLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNI------KFIEKKLWRYAIDLL 152 (341)
Q Consensus 81 ~g~~p~-~~~~L~-~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~------~~~~~~l~~~~~~~~ 152 (341)
....+. .|+.|. +++|||.|-|+.+|....-...+++|.|+.|-|.|.+.+++.+.+ -.+++.++.+++.+-
T Consensus 111 ~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g 190 (210)
T COG1059 111 ADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVG 190 (210)
T ss_pred cCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhC
Confidence 111222 688888 999999999999999886678899999999999999888876421 356677777777652
Q ss_pred CCCCHHHHHHHHH
Q psy8564 153 PKKNIEIYTQGLM 165 (341)
Q Consensus 153 p~~~~~~~~~~l~ 165 (341)
-.++.+...++
T Consensus 191 --~s~gelDL~IW 201 (210)
T COG1059 191 --ISLGELDLYIW 201 (210)
T ss_pred --CCcchhHHHHH
Confidence 23455554443
No 68
>TIGR02150 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate.
Probab=99.32 E-value=4.7e-12 Score=107.83 Aligned_cols=100 Identities=15% Similarity=0.259 Sum_probs=71.4
Q ss_pred EEEEEEEeCCEEEEEEeCCCC-ccccccccc--c-cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccc--ccCcE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG-IWGGLLSFP--E-WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYL--ILPII 284 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g-~~~GlWEFP--g-vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~--~~~~~ 284 (341)
+.++|++.+|++||+||+.++ .+.|+|++| | ++.|| .+|++||+.||+|++ .... .+..+
T Consensus 30 v~v~v~~~~g~vLl~kR~~~k~~~PG~W~~~~gG~v~~GE-------------~eaa~REl~EE~Gl~~~~~~l~~~~~~ 96 (158)
T TIGR02150 30 FSVFLFNEEGQLLLQRRALSKITWPGVWTNSCCSHPLPGE-------------LEAAIRRLREELGIPADDVPLTVLPRF 96 (158)
T ss_pred EEEEEEcCCCeEEEEeccCCCcCCCCCccccccCCCCccc-------------HHHHHHHHHHHHCCCccccceEEcceE
Confidence 344555567999999998764 789999998 4 89998 578999999999998 4432 34555
Q ss_pred EEEee---ceEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCC
Q psy8564 285 SHKLT---HLQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 285 ~h~~~---h~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~ 324 (341)
.|.++ ..+..+++|.+..... +...+..++.|++++|+.+
T Consensus 97 ~~~~~~~~g~~~~~~~f~~~~~~~~~~~~~Ev~~~~W~~~~el~~ 141 (158)
T TIGR02150 97 SYRARDAWGEHELCPVFFARAPVPLNPNPEEVAEYRWVSLEELKE 141 (158)
T ss_pred EEEEecCCCcEEEEEEEEEecCCcccCChhHeeeEEEeCHHHHHH
Confidence 55443 2345567887775442 2222447899999998865
No 69
>cd04661 MRP_L46 Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the Nudix hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. MRP L46 appears to contain a modified nudix motif.
Probab=99.30 E-value=6e-12 Score=103.89 Aligned_cols=98 Identities=15% Similarity=0.208 Sum_probs=69.9
Q ss_pred eCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc----cccCcEEEEeec-
Q psy8564 219 DDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY----LILPIISHKLTH- 290 (341)
Q Consensus 219 ~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~----~~~~~~~h~~~h- 290 (341)
++++|||.||..++ +|.|+||| +|.|||+ .+|+.||+.||+|+. ... ..++.+.+.++.
T Consensus 11 ~~~~~Llvk~~~~~--~g~W~fPgG~ve~gEt~-----------~eaa~REl~EEtGl~v~~~~i~~~~~~~~~~~~~~~ 77 (132)
T cd04661 11 DDTLVLLVQQKVGS--QNHWILPQGKREEGETL-----------RQTAERTLKELCGNNLKAKFYGNAPVGFYKYKYPKA 77 (132)
T ss_pred cCcEEEEEEeecCC--CCeeECCcccccCCCCH-----------HHHHHHHHHHhhCCCceEEEEEecCcEEEEEecCcc
Confidence 46799999996543 79999999 9999998 999999999999997 431 112233333321
Q ss_pred ------eEEEEEEEEEEecc-cc-cccCCCCceeeeCCCCCCCCCCHH
Q psy8564 291 ------LQFKIVPCHIFLKK-CF-LKENKNNFIWYPIKKIKNSPIPAP 330 (341)
Q Consensus 291 ------~~~~l~~~~~~~~~-~~-~~~~~~~~~W~~~~el~~~~~~~a 330 (341)
....+++|.|.+.+ .. ...++.+++|++++||.++ +++.
T Consensus 78 ~~~~~~~~~~~~~f~~~~~~g~~~~~~e~~~~~W~~~~el~~~-l~~~ 124 (132)
T cd04661 78 VRNEGIVGAKVFFFKARYMSGQFELSQNQVDFKWLAKEELQKY-LNPP 124 (132)
T ss_pred cccccCcccEEEEEEEEEecCccccCCCcceeEecCHHHHHhh-cCHH
Confidence 22467888888755 22 2234588999999999874 4443
No 70
>cd02885 IPP_Isomerase Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mamm
Probab=99.29 E-value=7.4e-12 Score=107.36 Aligned_cols=102 Identities=10% Similarity=0.153 Sum_probs=71.9
Q ss_pred EEEEEEeCCEEEEEEeCCCC-ccccccccc--c-cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccccc-CcEEE
Q psy8564 213 IMFIVIDDDYVLFQKRSNKG-IWGGLLSFP--E-WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLIL-PIISH 286 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g-~~~GlWEFP--g-vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~-~~~~h 286 (341)
+++|++.+|+|||.||+.++ .++|+|++| | +|.||++ ++|+.||+.||+|++ .....+ ..+.+
T Consensus 34 ~v~i~~~~~~iLl~kR~~~~~~~Pg~w~~~~gG~ie~GEt~-----------~eaa~REl~EEtGl~~~~~~~~~~~~~~ 102 (165)
T cd02885 34 SVFLFNSKGRLLLQRRALSKYTFPGLWTNTCCSHPLPGEGV-----------KDAAQRRLREELGITGDLLELVLPRFRY 102 (165)
T ss_pred EEEEEcCCCcEEEEeccCCCccCCCcccccccCCCCCCCCH-----------HHHHHHHHHHHhCCCccchhhccceEEE
Confidence 34455667899999998765 789999998 5 9999998 999999999999998 554443 44444
Q ss_pred Eeec-----eEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCCC
Q psy8564 287 KLTH-----LQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 287 ~~~h-----~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~~ 325 (341)
..++ .+...++|.+..... ....+..+++|++++++.++
T Consensus 103 ~~~~~~~~~~~~i~~~f~~~~~~~~~~~~~Ev~~~~w~~~~el~~~ 148 (165)
T cd02885 103 RAPDDGGLVEHEIDHVFFARADVTLIPNPDEVSEYRWVSLEDLKEL 148 (165)
T ss_pred EEEcCCCceeeEEEEEEEEEeCCCCCCCccceeEEEEECHHHHHHH
Confidence 3221 122345676765431 22233467999999998763
No 71
>cd03429 NADH_pyrophosphatase NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity. Members of this family are also recognized by the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. A block of 8 conserved amino acids downstream of the nudix motif is thought to give NADH pyrophosphatase its specificity for NADH. NADH pyrophosphatase forms a dimer.
Probab=99.29 E-value=5.9e-12 Score=103.76 Aligned_cols=109 Identities=12% Similarity=0.137 Sum_probs=76.0
Q ss_pred EEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeece
Q psy8564 215 FIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHL 291 (341)
Q Consensus 215 ~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~ 291 (341)
++...++++||.||... -.|.|+||| +|.||++ .+|+.||+.||+|++ .....+....+.++
T Consensus 6 ~l~~~~~~vLL~~r~~~--~~~~w~lPgG~ie~gEt~-----------~~aA~REl~EEtGl~~~~~~~l~~~~~~~~-- 70 (131)
T cd03429 6 LVIDGGDRILLARQPRF--PPGMYSLLAGFVEPGESL-----------EEAVRREVKEEVGIRVKNIRYVGSQPWPFP-- 70 (131)
T ss_pred EEEeCCCEEEEEEecCC--CCCcCcCCcccccCCCCH-----------HHHHhhhhhhccCceeeeeEEEeecCCCCC--
Confidence 33444489999999643 379999999 9999988 999999999999998 55555544333333
Q ss_pred EEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCC----CCCCHHHHHHHHHh
Q psy8564 292 QFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKN----SPIPAPVRKILFQI 338 (341)
Q Consensus 292 ~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~----~~~~~a~~~il~~l 338 (341)
+..+.+|.+...+ . ....+..++.|++++++.+ ++..+++.++.+.+
T Consensus 71 ~~~~~~f~~~~~~~~~~~~~~E~~~~~w~~~~el~~~~~~~~~~~~~~~~~~~~ 124 (131)
T cd03429 71 SSLMLGFTAEADSGEIVVDDDELEDARWFSRDEVRAAGEGLPELPPPGSIARQL 124 (131)
T ss_pred ceEEEEEEEEEcCCcccCCchhhhccEeecHHHHhhcccCCccCCCcchHHHHH
Confidence 2334667777654 1 1223346799999999877 56666666655554
No 72
>cd03428 Ap4A_hydrolase_human_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and
Probab=99.28 E-value=1.8e-11 Score=100.25 Aligned_cols=101 Identities=15% Similarity=0.187 Sum_probs=75.2
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe----eceEEE
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL----THLQFK 294 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~----~h~~~~ 294 (341)
++||.||+. |.|+||| +|.+|++ .+++.||+.||+|++ .....+..+...+ ......
T Consensus 18 ~vLl~~~~~-----~~w~~PgG~ve~gEs~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (130)
T cd03428 18 EYLLLQASY-----GHWDFPKGHVEPGEDD-----------LEAALRETEEETGITAEQLFIVLGFKETLNYQVRGKLKT 81 (130)
T ss_pred eEEEEEccC-----CcCcCCcCCCCCCCCH-----------HHHHHHHHHHHHCCChhhhhhhccceeEEEccccCcceE
Confidence 799999975 8999999 9999998 999999999999998 5555442232222 223455
Q ss_pred EEEEEEEecc--cc-cccCCCCceeeeCCCCCCCCCCHHHHHHHHHh
Q psy8564 295 IVPCHIFLKK--CF-LKENKNNFIWYPIKKIKNSPIPAPVRKILFQI 338 (341)
Q Consensus 295 l~~~~~~~~~--~~-~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l 338 (341)
+++|.+.+.. .. ...+..++.|++++++.++..++.++.++++.
T Consensus 82 ~~~f~~~~~~~~~~~~~~E~~~~~W~~~~e~~~~~~~~~~~~~~~~~ 128 (130)
T cd03428 82 VTYFLAELRPDVEVKLSEEHQDYRWLPYEEALKLLTYEDLKAVLDKA 128 (130)
T ss_pred EEEEEEEeCCCCccccccceeeEEeecHHHHHHHcCchhHHHHHHHh
Confidence 6778887652 11 11334779999999999988888888888764
No 73
>PF00293 NUDIX: NUDIX domain; InterPro: IPR000086 The generic name 'NUDIX hydrolases' (NUcleoside DIphosphate linked to some other moiety X) has been coined for this domain family []. The family can be divided into a number of subgroups, of which MutT anti- mutagenic activity represents only one type; most of the rest hydrolyse diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP- mannose, TDP-glucose, NADH, UDP-sugars, dNTP and NTP).; GO: 0016787 hydrolase activity; PDB: 3FJY_A 3MGM_A 2XSQ_A 3COU_A 2O5F_A 1Q27_A 3F6A_A 3E57_B 3SON_B 2GT4_C ....
Probab=99.27 E-value=7.2e-12 Score=102.53 Aligned_cols=116 Identities=17% Similarity=0.144 Sum_probs=87.1
Q ss_pred EEEEEEeCCEEEEEEeCCCC-cccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 213 IMFIVIDDDYVLFQKRSNKG-IWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g-~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.++|+..+|+|||.||...+ ..+|.|+||| ++.+|++ .+|++||+.||+|++ ..........+..
T Consensus 6 ~~ii~~~~~~vLl~~r~~~~~~~~~~~~~pgG~i~~~E~~-----------~~aa~REl~EE~g~~~~~~~~~~~~~~~~ 74 (134)
T PF00293_consen 6 GVIIFNEDGKVLLIKRSRSPITFPGYWELPGGGIEPGESP-----------EEAARRELKEETGLDVSPLELLGLFSYPS 74 (134)
T ss_dssp EEEEEETTTEEEEEEESTTSSSSTTEEESSEEEECTTSHH-----------HHHHHHHHHHHHSEEEEEEEEEEEEEEEE
T ss_pred EEEEEeCCcEEEEEEecCCCCCCCCeEecceeeEEcCCch-----------hhhHHhhhhhcccceecccccceeeeecc
Confidence 34555556799999998765 4899999999 9999988 999999999999998 5555555555555
Q ss_pred ece---EEEEEEEEEEeccc-----ccccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 289 THL---QFKIVPCHIFLKKC-----FLKENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 289 ~h~---~~~l~~~~~~~~~~-----~~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
... ....++|.+.+... ....+..++.|++++|+.++.....+..++..+.
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~el~~~~~~~~~~~~i~~~~ 133 (134)
T PF00293_consen 75 PSGDPEGEIVIFFIAELPSEQSEIQPQDEEISEVKWVPPDELLELLLNGRIRKIIPWLY 133 (134)
T ss_dssp TTTESSEEEEEEEEEEEEEEESECHTTTTTEEEEEEEEHHHHHHHHHTTHHHHHHHHHH
T ss_pred cCCCcccEEEEEEEEEEeCCccccCCCCccEEEEEEEEHHHhhhchhCcchhhhhcccc
Confidence 433 25666777665431 1111336789999999999999999988887764
No 74
>cd03671 Ap4A_hydrolase_plant_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally
Probab=99.25 E-value=2.6e-11 Score=101.93 Aligned_cols=112 Identities=13% Similarity=0.181 Sum_probs=75.7
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcE----E
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPII----S 285 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~----~ 285 (341)
.++|++.+|++||.||...+ |.|+||| +|.||+. .+++.||+.||+|+. .....+... .
T Consensus 7 ~~ii~~~~~~vLL~~r~~~~---~~W~~PgG~~e~gE~~-----------~~aA~REv~EEtGl~~~~~~~l~~~~~~~~ 72 (147)
T cd03671 7 GVVLFNEDGKVFVGRRIDTP---GAWQFPQGGIDEGEDP-----------EQAALRELEEETGLDPDSVEIIAEIPDWLR 72 (147)
T ss_pred EEEEEeCCCEEEEEEEcCCC---CCEECCcCCCCCCcCH-----------HHHHHHHHHHHHCCCcCceEEEEEcCCeeE
Confidence 44555668999999997766 9999999 9999988 999999999999998 444444332 2
Q ss_pred EEeec-----------eEEEEEEEEEEecc---c--cc---ccCCCCceeeeCCCCCCCCCCHHHHHHHHHhh
Q psy8564 286 HKLTH-----------LQFKIVPCHIFLKK---C--FL---KENKNNFIWYPIKKIKNSPIPAPVRKILFQII 339 (341)
Q Consensus 286 h~~~h-----------~~~~l~~~~~~~~~---~--~~---~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~ 339 (341)
+.++. .....++|.+.+.. . .. ..+..+++|++++++.++..| -.+.|++++.
T Consensus 73 y~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~E~~~~~W~~~~el~~~~~~-~~~~~~~~~~ 144 (147)
T cd03671 73 YDLPPELKLKIWGGRYRGQEQKWFLFRFTGDDSEIDLNAPEHPEFDEWRWVPLEELPDLIVP-FKRPVYEAVL 144 (147)
T ss_pred eeChhhhhccccCCcCCCEEEEEEEEEecCCCccccCCCCCCCCEeeEEeCCHHHHHHhchh-hhHHHHHHHH
Confidence 22220 01234555555432 1 11 123477899999999987665 5555666654
No 75
>cd04677 Nudix_Hydrolase_18 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.25 E-value=2.4e-11 Score=99.70 Aligned_cols=101 Identities=14% Similarity=0.150 Sum_probs=65.8
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEE--EE
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIIS--HK 287 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~--h~ 287 (341)
.++++..+|++||.+|... |.|+||| ++.||++ .+|+.||+.||+|++ .....+.... +.
T Consensus 11 ~~~v~~~~~~vLL~~r~~~----~~w~~PgG~v~~gEt~-----------~~aa~REl~EE~Gi~~~~~~~~~~~~~~~~ 75 (132)
T cd04677 11 GVILLNEQGEVLLQKRSDT----GDWGLPGGAMELGESL-----------EETARRELKEETGLEVEELELLGVYSGKEF 75 (132)
T ss_pred EEEEEeCCCCEEEEEecCC----CcEECCeeecCCCCCH-----------HHHHHHHHHHHhCCeeeeeEEEEEecCCce
Confidence 3444555699999999654 7899999 9999988 999999999999998 5544443221 11
Q ss_pred ee-----c-eEEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCCCCCC
Q psy8564 288 LT-----H-LQFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKNSPIP 328 (341)
Q Consensus 288 ~~-----h-~~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~~~~~ 328 (341)
|. . ..+.+.+|.+...+ . ....+..+.+|++++++.+...+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~W~~~~e~~~~~~~ 125 (132)
T cd04677 76 YVKPNGDDEQYIVTLYYVTKVFGGKLVPDGDETLELKFFSLDELPELINP 125 (132)
T ss_pred eecCCCCcEEEEEEEEEEEeccCCcccCCCCceeeEEEEChhHCccchhH
Confidence 21 1 12333334443322 1 11223357899999999876554
No 76
>cd04694 Nudix_Hydrolase_35 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.25 E-value=1.2e-11 Score=103.50 Aligned_cols=101 Identities=11% Similarity=0.126 Sum_probs=68.0
Q ss_pred EEEEEEeCCEEEEEEeCCCC-cccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc----cccCcE
Q psy8564 213 IMFIVIDDDYVLFQKRSNKG-IWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY----LILPII 284 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g-~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~----~~~~~~ 284 (341)
+++++..+|++||.||...+ .++|+|+||| ++.+|++ .+++.||+.||+|+. ... ..++..
T Consensus 5 ~viv~~~~~~vLl~rr~~~~~~~~g~w~~PgG~v~~~E~~-----------~~aa~RE~~EE~gi~~~~~~~~~~~l~~~ 73 (143)
T cd04694 5 AVLLQSSDQKLLLTRRASSLRIFPNVWVPPGGHVELGENL-----------LEAGLRELNEETGLTLDPIDKSWQVLGLW 73 (143)
T ss_pred EEEEEcCCCEEEEEEECCCCCCCCCeEECcccccCCCCCH-----------HHHHHHHHHHHHCCCccccccceeEEeee
Confidence 33445678999999998754 7999999999 9999987 899999999999998 432 445555
Q ss_pred EEEeec---------eEEEEEEEEEEecc------c--ccccCCCCceeeeCCCCCC
Q psy8564 285 SHKLTH---------LQFKIVPCHIFLKK------C--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 285 ~h~~~h---------~~~~l~~~~~~~~~------~--~~~~~~~~~~W~~~~el~~ 324 (341)
.|.|++ .++.+.++.+.... . +...+.++.+|++++++..
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~Ev~~~~Wv~~~~a~~ 130 (143)
T cd04694 74 ESVYPPLLSRGLPKRHHIVVYILVKSSETHQQLQARLQPDPNEVSAAAWLDKSLAKA 130 (143)
T ss_pred ccccccccCCCcccceeEEEEEEEEeccccccccccccCChhhccceEeeCHHHHHH
Confidence 555542 23333333322211 1 1113447889999887643
No 77
>cd03424 ADPRase_NUDT5 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirem
Probab=99.24 E-value=1.2e-11 Score=102.41 Aligned_cols=102 Identities=12% Similarity=0.043 Sum_probs=72.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
+.++++..+|++||.+|...+..+++|+||| +|.+|++ .+|+.||+.||+|++ .....+..+.+..
T Consensus 5 v~v~~~~~~~~iLl~~~~~~~~~~~~w~~PgG~ve~gEs~-----------~~aa~RE~~EE~Gl~~~~~~~~~~~~~~~ 73 (137)
T cd03424 5 VAVLPYDDDGKVVLVRQYRPPVGGWLLELPAGLIDPGEDP-----------EEAARRELEEETGYEAGDLEKLGSFYPSP 73 (137)
T ss_pred EEEEEEcCCCeEEEEEeeecCCCCEEEEeCCccCCCCCCH-----------HHHHHHHHHHHHCCCccceEEEeeEecCC
Confidence 3445556669999988766666789999999 9999988 999999999999998 5555555544322
Q ss_pred eceEEEEEEEEEEeccc-----ccccCCCCceeeeCCCCCC
Q psy8564 289 THLQFKIVPCHIFLKKC-----FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~~-----~~~~~~~~~~W~~~~el~~ 324 (341)
......+++|.+...+. ....+..+.+|++++|+..
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~ 114 (137)
T cd03424 74 GFSDERIHLFLAEDLSPGEEGLLDEGEDIEVVLVPLDEALE 114 (137)
T ss_pred cccCccEEEEEEEcccccccCCCCCCCeeEEEEecHHHHHH
Confidence 22234567787776541 1122346789999998864
No 78
>cd04692 Nudix_Hydrolase_33 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.23 E-value=3.2e-11 Score=100.96 Aligned_cols=103 Identities=20% Similarity=0.276 Sum_probs=72.5
Q ss_pred eEEEEEEEeC---CEEEEEEeCCC-Cccccccccc-c--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c--cccc
Q psy8564 211 SIIMFIVIDD---DYVLFQKRSNK-GIWGGLLSFP-E--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K--NYLI 280 (341)
Q Consensus 211 ~~~~~ii~~~---g~vLl~kR~~~-g~~~GlWEFP-g--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~--~~~~ 280 (341)
.+.+.|++++ +++|+++|... ..+.|.|+|| | +|.||++ .+|++||+.||+|+. . ....
T Consensus 4 ~v~~~v~~~~~~~~~vLl~~R~~~~~~~pg~W~~~~gG~ve~gEt~-----------~~aa~REl~EEtGl~~~~~~l~~ 72 (144)
T cd04692 4 TFHCWIITKDEGKGYVLLQKRSANKKTYPGLWDISSAGHILAGETP-----------LEDGIRELEEELGLDVSADDLIP 72 (144)
T ss_pred EEEEEEEEccCCCCEEEEEecCCCCCCCCCccccccCcccCCCCCH-----------HHHHHHHHHHHhCCCCChHHeEE
Confidence 3456666666 89999999875 4789999995 4 9999988 999999999999997 3 3345
Q ss_pred cCcEEEEeec-----eEEEEEEEEEEecc---c--ccccCCCCceeeeCCCCCC
Q psy8564 281 LPIISHKLTH-----LQFKIVPCHIFLKK---C--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 281 ~~~~~h~~~h-----~~~~l~~~~~~~~~---~--~~~~~~~~~~W~~~~el~~ 324 (341)
++.+.+.+.+ .....++|.+.... . +...+..+++|++++++.+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~E~~~~~W~~~~el~~ 126 (144)
T cd04692 73 LGTFKIEYDHIGKLIDREFHHVYLYELKVPLEEFTLQKEEVAGVVLIPLDEFAE 126 (144)
T ss_pred eeEEEEeccccCCCccceEEEEEEEeccCChhhcCCChhHhheEEEECHHHHHH
Confidence 6667666641 11234566665432 1 2223347899999888753
No 79
>cd04693 Nudix_Hydrolase_34 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.21 E-value=3.7e-11 Score=98.23 Aligned_cols=101 Identities=13% Similarity=0.105 Sum_probs=64.2
Q ss_pred EEEEEEEeCCEEEEEEeCCCC-ccccccccc-c--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG-IWGGLLSFP-E--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g-~~~GlWEFP-g--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
+.+++++.+|+|||+||...+ .+.|.|+|| | +|.||+ . +|+.||+.||+|++ ..........+
T Consensus 3 v~v~~~~~~g~vLl~~R~~~~~~~pg~w~~p~GG~ve~gE~-----------~-~aa~REl~EEtGl~~~~~~~~~~~~~ 70 (127)
T cd04693 3 VHVCIFNSKGELLLQKRSPNKDGWPGMWDLSVGGHVQAGET-----------S-TAAEREVKEELGLELDFSELRPLFRY 70 (127)
T ss_pred EEEEEEeCCCeEEEEEccCCCCCCCCcccccCCCcCCCCCC-----------H-HHHHHHHHHHhCCCcChhhcEEEEEE
Confidence 445566678999999998754 578999998 5 999995 3 78999999999998 43222111222
Q ss_pred Eeec-eEEEEEEEEEEecc---cccccCCCCceeeeCCCCCC
Q psy8564 287 KLTH-LQFKIVPCHIFLKK---CFLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 287 ~~~h-~~~~l~~~~~~~~~---~~~~~~~~~~~W~~~~el~~ 324 (341)
.+.+ .+..+.+|.+.... .....+..+++|++++|+..
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~w~~~~el~~ 112 (127)
T cd04693 71 FFEAEGFDDYYLFYADVEIGKLILQKEEVDEVKFVSKDEIDG 112 (127)
T ss_pred EeecCCeEEEEEEEecCcccccccCHHHhhhEEEeCHHHHHH
Confidence 2222 22233344443222 11222347899999888754
No 80
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=99.18 E-value=1.9e-10 Score=100.34 Aligned_cols=113 Identities=10% Similarity=0.091 Sum_probs=75.0
Q ss_pred EEEEEEeCCEEEEEEeCCCC-ccccccccc--c-cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccc-ccCcEEE
Q psy8564 213 IMFIVIDDDYVLFQKRSNKG-IWGGLLSFP--E-WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYL-ILPIISH 286 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g-~~~GlWEFP--g-vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~-~~~~~~h 286 (341)
.++|++.+|+|||.||+.++ .+.|.|.+| | ++.||++ ++|+.||+.||+|++ .... .++.+.+
T Consensus 38 ~v~i~~~~g~vLL~rR~~~~~~~PG~w~~~~gG~ve~GEt~-----------~~aa~REl~EEtGl~~~~~~~~~~~~~~ 106 (184)
T PRK03759 38 SCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQPGESL-----------EDAVIRRCREELGVEITDLELVLPDFRY 106 (184)
T ss_pred EEEEEcCCCeEEEEEccCCCCCCCCcccccccCCCCCCCCH-----------HHHHHHHHHHHhCCCccccccccceEEE
Confidence 34445557999999997654 678999998 5 9999998 999999999999998 4322 2333333
Q ss_pred Eee--c---eEEEEEEEEEEeccc--ccccCCCCceeeeCCCCCC------CCCCHHHHHHHH
Q psy8564 287 KLT--H---LQFKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKN------SPIPAPVRKILF 336 (341)
Q Consensus 287 ~~~--h---~~~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~------~~~~~a~~~il~ 336 (341)
.+. . .+-..++|.+...+. +...+..++.|++++++.+ ..+.+..+.++.
T Consensus 107 ~~~~~~~~~~~~~~~vf~~~~~~~~~~~~~Ev~~~~W~~~~el~~~i~~~~~~~~~~l~~~~~ 169 (184)
T PRK03759 107 RATDPNGIVENEVCPVFAARVTSALQPNPDEVMDYQWVDPADLLRAVDATPWAFSPWMVLQAA 169 (184)
T ss_pred EEecCCCceeeEEEEEEEEEECCCCCCChhHeeeEEEECHHHHHHHHHhCCcccChHHHHHHH
Confidence 221 1 122346777775442 2222336899999999843 355565555554
No 81
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=99.17 E-value=9.7e-11 Score=107.17 Aligned_cols=102 Identities=13% Similarity=0.201 Sum_probs=76.8
Q ss_pred EEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEee
Q psy8564 213 IMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLT 289 (341)
Q Consensus 213 ~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~ 289 (341)
+++++.+++++||.||.... .|+|++|| +|.|||+ ++|+.||+.||+|++ .....++...+.|+
T Consensus 135 Viv~V~~~~~iLL~rr~~~~--~g~wslPgG~vE~GEs~-----------eeAa~REv~EEtGl~v~~~~~~~s~~~~~p 201 (256)
T PRK00241 135 IIVAVRRGDEILLARHPRHR--NGVYTVLAGFVEVGETL-----------EQCVAREVMEESGIKVKNLRYVGSQPWPFP 201 (256)
T ss_pred EEEEEEeCCEEEEEEccCCC--CCcEeCcccCCCCCCCH-----------HHHhhhhhhhccCceeeeeEEEEeEeecCC
Confidence 44556678999999986543 79999999 9999998 999999999999998 66677766666666
Q ss_pred ceEEEEEEEEEEecc-c--ccccCCCCceeeeCCCCCCCCCCH
Q psy8564 290 HLQFKIVPCHIFLKK-C--FLKENKNNFIWYPIKKIKNSPIPA 329 (341)
Q Consensus 290 h~~~~l~~~~~~~~~-~--~~~~~~~~~~W~~~~el~~~~~~~ 329 (341)
+. .++.|.+...+ . ....+..+.+|++++|+..++-..
T Consensus 202 ~~--lm~~f~a~~~~~~~~~~~~Ei~~a~W~~~del~~lp~~~ 242 (256)
T PRK00241 202 HS--LMLGFHADYDSGEIVFDPKEIADAQWFRYDELPLLPPSG 242 (256)
T ss_pred Ce--EEEEEEEEecCCcccCCcccEEEEEEECHHHCcccCCch
Confidence 54 45678777654 2 111223578999999998766543
No 82
>cd04666 Nudix_Hydrolase_9 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=99.17 E-value=1.2e-10 Score=94.82 Aligned_cols=89 Identities=10% Similarity=0.035 Sum_probs=68.6
Q ss_pred CEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc-cccCcEEEEeec----eE
Q psy8564 221 DYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY-LILPIISHKLTH----LQ 292 (341)
Q Consensus 221 g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~-~~~~~~~h~~~h----~~ 292 (341)
+++||.+|... |.|.||| +|.+|++ .+|+.||+.||+|++ ... ..++.+.|.+++ .+
T Consensus 15 ~~vLLv~~~~~----~~w~~PgG~ve~~E~~-----------~~aa~RE~~EEtG~~~~~~~~~l~~~~~~~~~~~~~~~ 79 (122)
T cd04666 15 VEVLLVTSRRT----GRWIVPKGGPEKDESP-----------AEAAAREAWEEAGVRGKIGKRPLGRFEYRKRSKNRPPR 79 (122)
T ss_pred eEEEEEEecCC----CeEECCCCCcCCCCCH-----------HHHHHHHHHHHhCCcccccceEEEEEEeeecCCCCCce
Confidence 68999998643 8999999 9999988 999999999999999 666 788888887764 36
Q ss_pred EEEEEEEEEecccc---cccCCCCceeeeCCCCCC
Q psy8564 293 FKIVPCHIFLKKCF---LKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 293 ~~l~~~~~~~~~~~---~~~~~~~~~W~~~~el~~ 324 (341)
...++|.+...+.. ...+..+.+|++++++..
T Consensus 80 ~~~~~f~~~~~~~~~~~~~~e~~~~~W~~~~ea~~ 114 (122)
T cd04666 80 CEVAVFPLEVTEELDEWPEMHQRKRKWFSPEEAAL 114 (122)
T ss_pred EEEEEEEEEEeccccCCcccCceEEEEecHHHHHH
Confidence 67778877764411 112235789999888743
No 83
>PRK05379 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional
Probab=99.16 E-value=2e-10 Score=109.60 Aligned_cols=118 Identities=10% Similarity=0.141 Sum_probs=84.3
Q ss_pred eEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCc--EE
Q psy8564 211 SIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPI--IS 285 (341)
Q Consensus 211 ~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~--~~ 285 (341)
..+.+|+.++|+|||.+|.. +...|+|.||| +|.||+. ++|+.||+.||+|++ ......+. ..
T Consensus 204 vtv~avv~~~g~VLLvrR~~-~p~~g~W~lPGG~ve~gEt~-----------~~Aa~REl~EETGl~v~~~~l~~~~~~~ 271 (340)
T PRK05379 204 VTVDAVVVQSGHVLLVRRRA-EPGKGLWALPGGFLEQDETL-----------LDACLRELREETGLKLPEPVLRGSIRDQ 271 (340)
T ss_pred eEEEEEEEECCEEEEEEecC-CCCCCeEECCcccCCCCCCH-----------HHHHHHHHHHHHCCcccccccceeeeee
Confidence 45556667889999999965 34589999999 9999988 999999999999997 43322222 22
Q ss_pred EEeec--e----EEEEEEEEEEecc-c----ccccCCCCceeeeCCCCCCC--CCCHHHHHHHHHhhc
Q psy8564 286 HKLTH--L----QFKIVPCHIFLKK-C----FLKENKNNFIWYPIKKIKNS--PIPAPVRKILFQIIQ 340 (341)
Q Consensus 286 h~~~h--~----~~~l~~~~~~~~~-~----~~~~~~~~~~W~~~~el~~~--~~~~a~~~il~~l~~ 340 (341)
+.|++ + +...++|.+.... . ....+..+++|++++++..+ .+...+..||+.+..
T Consensus 272 ~~f~~p~r~~~~~~i~~~f~~~~~~~~~~~~~~~de~~~~~W~~~~el~~~~~~~~~dh~~ii~~~~~ 339 (340)
T PRK05379 272 QVFDHPGRSLRGRTITHAFLFEFPAGELPRVKGGDDADKARWVPLAELLAMRDRMFEDHFQIITHFLG 339 (340)
T ss_pred EEEcCCCCCCCCcEEEEEEEEEecCCccCccCCCCceeeEEEEEHHHhhhhhhhhhhHHHHHHHHHhc
Confidence 34432 1 3445677776542 1 11223478999999999886 688899999987653
No 84
>COG1051 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]
Probab=99.15 E-value=2.7e-10 Score=95.49 Aligned_cols=108 Identities=10% Similarity=0.219 Sum_probs=74.4
Q ss_pred eeEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEE
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISH 286 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h 286 (341)
...+.+++..+|+|||.||. +...+|+|.+|| +|.|||. ++|+.||++||.|++ ...+.+..+.-
T Consensus 10 ~~~v~~~i~~~~~iLLvrR~-~~p~~g~WalPGG~ve~GEt~-----------eeaa~REl~EETgL~~~~~~~~~v~~~ 77 (145)
T COG1051 10 LVAVGALIVRNGRILLVRRA-NEPGAGYWALPGGFVEIGETL-----------EEAARRELKEETGLRVRVLELLAVFDD 77 (145)
T ss_pred ceeeeEEEEeCCEEEEEEec-CCCCCCcEeCCCccCCCCCCH-----------HHHHHHHHHHHhCCcccceeEEEEecC
Confidence 34566677778899999996 457889999999 9999998 999999999999998 55444433222
Q ss_pred Ee---eceEEEEEEEEEEeccc--ccc-cCCCCceeeeCCCCCCCCCCH
Q psy8564 287 KL---THLQFKIVPCHIFLKKC--FLK-ENKNNFIWYPIKKIKNSPIPA 329 (341)
Q Consensus 287 ~~---~h~~~~l~~~~~~~~~~--~~~-~~~~~~~W~~~~el~~~~~~~ 329 (341)
.- ..+++.+.+|.+...+. ..+ .......|++.++|...+.+.
T Consensus 78 ~~rd~r~~~v~~~~~~~~~~g~~~~~~~~d~~~~~~~~~~~l~~~~~~~ 126 (145)
T COG1051 78 PGRDPRGHHVSFLFFAAEPEGELLAGDGDDAAEVGWFPLDELPELPLPL 126 (145)
T ss_pred CCCCCceeEEEEEEEEEecCCCcccCChhhHhhcceecHhHcccccccc
Confidence 21 12445555555554332 111 122578999999999854443
No 85
>cd04686 Nudix_Hydrolase_27 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.14 E-value=1.7e-10 Score=95.07 Aligned_cols=98 Identities=14% Similarity=0.113 Sum_probs=68.2
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c-cccccCcEEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K-NYLILPIISHK 287 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~-~~~~~~~~~h~ 287 (341)
.+.+|+.++|+|||.||... |.|+||| +|.||++ .+|+.||++||+|+. . ....++.+.+.
T Consensus 2 ~~~~ii~~~~~vLLv~~~~~----~~w~lPgG~ve~gEt~-----------~~aa~REl~EEtGl~~~~~~~~l~~~~~~ 66 (131)
T cd04686 2 AVRAIILQGDKILLLYTKRY----GDYKFPGGGVEKGEDH-----------IEGLIRELQEETGATNIRVIEKFGTYTER 66 (131)
T ss_pred cEEEEEEECCEEEEEEEcCC----CcEECccccCCCCCCH-----------HHHHHHHHHHHHCCcccccceEEEEEEee
Confidence 45677778899999998642 5899999 9999998 999999999999997 3 34455555432
Q ss_pred e----e---ceEEEEEEEEEEeccc---c-ccc-C---CCCceeeeCCCCCC
Q psy8564 288 L----T---HLQFKIVPCHIFLKKC---F-LKE-N---KNNFIWYPIKKIKN 324 (341)
Q Consensus 288 ~----~---h~~~~l~~~~~~~~~~---~-~~~-~---~~~~~W~~~~el~~ 324 (341)
+ + ..+...++|.|..... . ..+ + .....|++++++..
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~W~~~~ea~~ 118 (131)
T cd04686 67 RPWRKPDADIFHMISYYYLCEVDAELGAQQLEDYEAELGMKPIWINIHEAIE 118 (131)
T ss_pred ccccCCCCceeEEEEEEEEEEEcCCcCCcccchhhHhcCCCcEEecHHHHHH
Confidence 2 2 2344567888886531 1 111 0 12479999988754
No 86
>cd03672 Dcp2p mRNA decapping enzyme 2 (Dcp2p), the catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'-3' mRNA-decay pathways. Dcp2p contains an all-alpha helical N-terminal domain and a C-terminal domain which has the Nudix fold. While decapping is not dependent on the N-terminus of Dcp2p, it does affect its efficiency. Dcp1p binds the N-terminal domain of Dcp2p stimulating the decapping activity of Dcp2p. Decapping permits the degradation of the transcript and is a site of numerous control inputs. It is responsible for nonsense-mediated decay as well as AU-rich element (ARE)-mediated decay. In addition, it may also play a role in the levels of mRNA. Enzymes belonging to the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V).
Probab=99.11 E-value=1.8e-10 Score=96.71 Aligned_cols=97 Identities=18% Similarity=0.197 Sum_probs=62.4
Q ss_pred EEEEEEEeC-CEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccC-cEEE
Q psy8564 212 IIMFIVIDD-DYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILP-IISH 286 (341)
Q Consensus 212 ~~~~ii~~~-g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~-~~~h 286 (341)
+.++|++.+ |+|||.||... +.|+||| +|.||++ .+|+.||+.||+|+. ....... ...+
T Consensus 4 ~gaii~~~~~~~vLLvr~~~~----~~W~lPGG~ve~gEs~-----------~~AA~REl~EETGl~v~~~~~~~~~~~~ 68 (145)
T cd03672 4 YGAIILNEDLDKVLLVKGWKS----KSWSFPKGKINKDEDD-----------HDCAIREVYEETGFDISKYIDKDDYIEL 68 (145)
T ss_pred eEEEEEeCCCCEEEEEEecCC----CCEECCCccCCCCcCH-----------HHHHHHHHHHhhCccceeccccceeeec
Confidence 344555544 79999998543 4899999 9999988 999999999999997 4321111 1112
Q ss_pred EeeceEEEEEEEEEEec-c----cc-cccCCCCceeeeCCCCCCC
Q psy8564 287 KLTHLQFKIVPCHIFLK-K----CF-LKENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 287 ~~~h~~~~l~~~~~~~~-~----~~-~~~~~~~~~W~~~~el~~~ 325 (341)
.+++. .+++|.+... + .+ ...+..+++|++++++.+.
T Consensus 69 ~~~~~--~~~~f~~~~~~~~~~~~~~~~~E~~~~~Wv~~~el~~~ 111 (145)
T cd03672 69 IIRGQ--NVKLYIVPGVPEDTPFEPKTRKEISKIEWFDIKDLPTK 111 (145)
T ss_pred ccCCc--EEEEEEEecCCCCcccCcCChhhhheEEEeeHHHhhhh
Confidence 22232 3455555422 1 11 1223478999999998764
No 87
>cd04685 Nudix_Hydrolase_26 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.10 E-value=3.1e-10 Score=93.81 Aligned_cols=103 Identities=10% Similarity=-0.003 Sum_probs=70.4
Q ss_pred EEEEEEEeCCEEEEEEeCCC-Ccccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc--ccccccCcEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSNK-GIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI--KNYLILPIISH 286 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~-g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~--~~~~~~~~~~h 286 (341)
+-+++++.+|+||+.+|..+ +..++.|++|| +|.+|++ .+|+.||+.||+|++ .....+....+
T Consensus 3 ~~~~i~~~~g~vLl~r~~~~~~~~~~~w~~PgG~ve~gE~~-----------~~a~~Re~~EE~G~~~~~~~~~~~~~~~ 71 (133)
T cd04685 3 ARVVLLDPDDRVLLLRGDDPDSPGPDWWFTPGGGVEPGESP-----------EQAARRELREETGITVADLGPPVWRRDA 71 (133)
T ss_pred EEEEEEcCCCeEEEEEEeCCCCCCCCEEECCcCCCCCCCCH-----------HHHHHHHHHHHHCCccccccceEEEEEE
Confidence 34566677899999998764 35889999999 9999988 999999999999987 33333333344
Q ss_pred Eeece----EEEEEEEEEEecc-c---c----cc-cCCCCceeeeCCCCCCC
Q psy8564 287 KLTHL----QFKIVPCHIFLKK-C---F----LK-ENKNNFIWYPIKKIKNS 325 (341)
Q Consensus 287 ~~~h~----~~~l~~~~~~~~~-~---~----~~-~~~~~~~W~~~~el~~~ 325 (341)
.|++. +-..++|.+...+ . . .+ .....++|+++++|.++
T Consensus 72 ~f~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~E~~~~~~~~W~~~~el~~~ 123 (133)
T cd04685 72 AFTFLGVDGRQEERFFLARTPRTEPSPAGWTALERRSILGWRWWTRAELAAT 123 (133)
T ss_pred EEEecCccceeeEEEEEEEcCCccccCCCCChhhhhhcccccCCCHHHHhhC
Confidence 34322 2234567776543 1 0 11 11246899999999886
No 88
>PRK00714 RNA pyrophosphohydrolase; Reviewed
Probab=99.06 E-value=3.7e-10 Score=95.93 Aligned_cols=112 Identities=13% Similarity=0.147 Sum_probs=72.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcE----
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPII---- 284 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~---- 284 (341)
+.++|++.+|++||.||... +|.|+||| ++.+|++ .+|+.||+.||+|+. .....++..
T Consensus 11 v~~~i~~~~g~vLL~~r~~~---~~~w~~P~G~~~~gE~~-----------~~aa~REl~EEtG~~~~~~~~~~~~~~~~ 76 (156)
T PRK00714 11 VGIILLNRQGQVFWGRRIGQ---GHSWQFPQGGIDPGETP-----------EQAMYRELYEEVGLRPEDVEILAETRDWL 76 (156)
T ss_pred EEEEEEecCCEEEEEEEcCC---CCeEECCcccCCCCcCH-----------HHHHHHHHHHHhCCCccceEEEEEcCCeE
Confidence 34455566899999999643 48999999 9999988 999999999999998 544444432
Q ss_pred EEEeece----------EEEEEEEEEEecc---c--c---cccCCCCceeeeCCCCCCCCCCHHHHHHHHHh
Q psy8564 285 SHKLTHL----------QFKIVPCHIFLKK---C--F---LKENKNNFIWYPIKKIKNSPIPAPVRKILFQI 338 (341)
Q Consensus 285 ~h~~~h~----------~~~l~~~~~~~~~---~--~---~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l 338 (341)
.+.|+.. .-..++|.+.... . . ...+..+++|++++|+.+.-++. .+.++.++
T Consensus 77 ~y~~~~~~~~~~~~~~~~~~~~~fl~~~~~~~~~~~l~~~~~~E~~~~~W~~~del~~~~~~~-~r~~~~~~ 147 (156)
T PRK00714 77 RYDLPKRLVRRSKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPLDQVVPF-KRDVYRRV 147 (156)
T ss_pred EecCcHHHhhccCCcccCcEEEEEEEEecCCCccccCCCCCCCCeeeeEeCCHHHHHHhchhh-hHHHHHHH
Confidence 2222110 0134566666532 1 1 11234678999999998854443 25555444
No 89
>cd04674 Nudix_Hydrolase_16 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=99.03 E-value=3.5e-09 Score=85.50 Aligned_cols=78 Identities=13% Similarity=0.089 Sum_probs=50.6
Q ss_pred eEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEE
Q psy8564 211 SIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHK 287 (341)
Q Consensus 211 ~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~ 287 (341)
.+++++...+ ++|+.+|.. ....|.|+||| +|.+|++ .+|+.||+.||+|++ ..........|.
T Consensus 6 ~av~vl~~~~-~~lL~~r~~-~~~~~~w~lPgG~ve~~E~~-----------~~aa~REl~EE~g~~~~~~~l~~~~~~~ 72 (118)
T cd04674 6 VVVALLPVDD-GLLVIRRGI-EPGRGKLALPGGFIELGETW-----------QDAVARELLEETGVAVDPADIRLFDVRS 72 (118)
T ss_pred EEEEEEEECC-CEEEEEeec-CCCCCeEECCceecCCCCCH-----------HHHHHHHHHHHHCCcccccEEEEEEEEe
Confidence 3444444555 466666654 34689999999 9999988 999999999999998 432211122344
Q ss_pred eeceEEEEEEEEEE
Q psy8564 288 LTHLQFKIVPCHIF 301 (341)
Q Consensus 288 ~~h~~~~l~~~~~~ 301 (341)
.+...+.+..|.+.
T Consensus 73 ~~~~~~~~~~~~~~ 86 (118)
T cd04674 73 APDGTLLVFGLLPE 86 (118)
T ss_pred cCCCeEEEEEEEec
Confidence 44455555555544
No 90
>PRK11762 nudE adenosine nucleotide hydrolase NudE; Provisional
Probab=98.97 E-value=1e-09 Score=95.87 Aligned_cols=96 Identities=16% Similarity=0.143 Sum_probs=71.5
Q ss_pred EEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEE
Q psy8564 217 VIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQF 293 (341)
Q Consensus 217 i~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~ 293 (341)
+.++|++||.++...+...+.||||+ +|.||++ ++++.||+.||.|+. .....++.+.+..+....
T Consensus 55 ~~~~~~vlLvrq~r~~~~~~~~elPaG~ve~gE~~-----------~~aA~REl~EEtG~~~~~l~~l~~~~~~~~~~~~ 123 (185)
T PRK11762 55 ILDDDTLLLIREYAAGTERYELGFPKGLIDPGETP-----------LEAANRELKEEVGFGARQLTFLKELSLAPSYFSS 123 (185)
T ss_pred EeCCCEEEEEEeecCCCCCcEEEccceeCCCCCCH-----------HHHHHHHHHHHHCCCCcceEEEEEEecCCCccCc
Confidence 44678899998877777889999999 9999988 999999999999999 777777776666665666
Q ss_pred EEEEEEEEeccc----ccccCCCCceeeeCCCCC
Q psy8564 294 KIVPCHIFLKKC----FLKENKNNFIWYPIKKIK 323 (341)
Q Consensus 294 ~l~~~~~~~~~~----~~~~~~~~~~W~~~~el~ 323 (341)
.+++|.+..... ..+.+..+..|++.+++.
T Consensus 124 ~~~~f~a~~~~~~~~~~~e~E~i~~~~~~~~e~~ 157 (185)
T PRK11762 124 KMNIVLAEDLYPERLEGDEPEPLEVVRWPLADLD 157 (185)
T ss_pred EEEEEEEEccccccCCCCCCceeEEEEEcHHHHH
Confidence 778888764321 111212356788877663
No 91
>PRK10707 putative NUDIX hydrolase; Provisional
Probab=98.88 E-value=6.7e-09 Score=90.98 Aligned_cols=94 Identities=10% Similarity=0.152 Sum_probs=68.5
Q ss_pred CCEEEEEEeCCC-Ccccccccccc--cccc-cchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEE
Q psy8564 220 DDYVLFQKRSNK-GIWGGLLSFPE--WILK-DKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFK 294 (341)
Q Consensus 220 ~g~vLl~kR~~~-g~~~GlWEFPg--vE~~-E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~ 294 (341)
++.+|+.||... ..+.|.|+||| +|++ |++ ++++.||+.||+|++ .....++.+...++...+.
T Consensus 43 ~~~vLl~~R~~~~r~~~G~~~~PGG~~e~~de~~-----------~~tA~REl~EEtGl~~~~~~~lg~l~~~~~~~~~~ 111 (190)
T PRK10707 43 QPTLLLTQRSIHLRKHAGQVAFPGGAVDPTDASL-----------IATALREAQEEVAIPPSAVEVIGVLPPVDSSTGYQ 111 (190)
T ss_pred CCEEEEEEeCCcccCCCCcEEcCCcccCCCcccH-----------HHHHHHHHHHHHCCCccceEEEEEeeeeeccCCcE
Confidence 469999999765 36889999999 8875 556 889999999999999 7777777777655555566
Q ss_pred EEEEEEEecc----cccccCCCCceeeeCCCCCC
Q psy8564 295 IVPCHIFLKK----CFLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 295 l~~~~~~~~~----~~~~~~~~~~~W~~~~el~~ 324 (341)
++++.+.+.. .+...+-.+..|++++++.+
T Consensus 112 ~~~~v~~~~~~~~~~~d~~Ev~~v~~vpl~e~~~ 145 (190)
T PRK10707 112 VTPVVGIIPPDLPYRANEDEVAAVFEMPLAEALH 145 (190)
T ss_pred EEEEEEEECCCCCCCCChhhhheEEEEeHHHHhC
Confidence 6777665432 11112235678999888755
No 92
>cd04665 Nudix_Hydrolase_8 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=98.87 E-value=1.7e-08 Score=81.52 Aligned_cols=96 Identities=11% Similarity=0.065 Sum_probs=66.0
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+.+|+..+|++|+.++. .+.|+||| +|.+|++ ++|+.||+.||.|+. .....++.+.-..
T Consensus 2 ~v~vi~~~~~~vLl~~~~-----~~~w~lPgG~ve~gE~~-----------~~aa~REl~EE~G~~~~~~~~l~~~~~~~ 65 (118)
T cd04665 2 SVLVICFYDDGLLLVRHK-----DRGWEFPGGHVEPGETI-----------EEAARREVWEETGAELGSLTLVGYYQVDL 65 (118)
T ss_pred EEEEEEEECCEEEEEEeC-----CCEEECCccccCCCCCH-----------HHHHHHHHHHHHCCccCceEEEEEEEecC
Confidence 355666778999999885 35799999 9999988 999999999999998 5556665443222
Q ss_pred eceEEEEEEEEEEecc-cc--cccCCCCceeeeCCCCC
Q psy8564 289 THLQFKIVPCHIFLKK-CF--LKENKNNFIWYPIKKIK 323 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~-~~--~~~~~~~~~W~~~~el~ 323 (341)
........+|.+...+ .. ...+.....|++.+...
T Consensus 66 ~~~~~~~~~y~a~~~~~~~~~~~~E~~~~~~~~~~~~~ 103 (118)
T cd04665 66 FESGFETLVYPAVSAQLEEKASYLETDGPVLFKNEPEE 103 (118)
T ss_pred CCCcEEEEEEEEEEEecccccccccccCcEEeccCCcc
Confidence 2124455667766543 11 12233778999866553
No 93
>cd03676 Nudix_hydrolase_3 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate spe
Probab=98.87 E-value=8.7e-09 Score=89.54 Aligned_cols=93 Identities=13% Similarity=0.049 Sum_probs=66.4
Q ss_pred CEEEEEEeCCCC-cccccc-cccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc---cccCcEEEEee--c
Q psy8564 221 DYVLFQKRSNKG-IWGGLL-SFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY---LILPIISHKLT--H 290 (341)
Q Consensus 221 g~vLl~kR~~~g-~~~GlW-EFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~---~~~~~~~h~~~--h 290 (341)
+++|++||+..+ .+.|+| ++|+ ++.||++ .+|++||+.||+|++ ... ..++.+.+.|. .
T Consensus 48 ~~l~lqrRs~~K~~~Pg~wd~~~~G~v~~gE~~-----------~~aA~REl~EE~Gl~~~~~~~l~~~g~~~~~~~~~~ 116 (180)
T cd03676 48 LRIWIPRRSPTKATWPGMLDNLVAGGLGHGEGP-----------EETLVKECDEEAGLPEDLVRQLKPVGVVSYLREGEA 116 (180)
T ss_pred eEEEEEeccCCCCCCCCceeeecccCCCCCCCH-----------HHHHHHHHHHHhCCCHHHHhhceeccEEEEEEEcCC
Confidence 899999998865 589999 6987 9999988 999999999999998 432 23444454443 1
Q ss_pred ---eEEEEEEEEEEecc--c--ccccCCCCceeeeCCCCCC
Q psy8564 291 ---LQFKIVPCHIFLKK--C--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 291 ---~~~~l~~~~~~~~~--~--~~~~~~~~~~W~~~~el~~ 324 (341)
.+..+++|.+.+.. . +...+..++.|++++|+.+
T Consensus 117 ~~~~~e~~~~f~~~~~~~~~~~~~~~Ev~~~~~~~~~el~~ 157 (180)
T cd03676 117 GGLQPEVEYVYDLELPPDFIPAPQDGEVESFRLLTIDEVLR 157 (180)
T ss_pred CcEeeeEEEEEEEEcCCCCeeCCCCCcEeEEEEECHHHHHH
Confidence 12446777776532 1 1222336789999998863
No 94
>cd04663 Nudix_Hydrolase_6 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V) which functions as metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are
Probab=98.85 E-value=2.2e-08 Score=81.65 Aligned_cols=88 Identities=8% Similarity=0.088 Sum_probs=58.2
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc-cccCcEE--EEeeceEEEE
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY-LILPIIS--HKLTHLQFKI 295 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~-~~~~~~~--h~~~h~~~~l 295 (341)
++|+.|.+. +.|+||| +|.+|++ .+|+.||+.||+|++ ... ....... +.+++..+++
T Consensus 15 ~ll~~r~~~-----~~~~lPgG~ve~~E~~-----------~~aa~Rel~EEtGl~~~~~~~~~~~~~~~~~~~~~~~~l 78 (126)
T cd04663 15 ELLVFEHPL-----AGFQIVKGTVEPGETP-----------EAAALRELQEESGLPSFLSDYILHVWERRFYQKRHFWHL 78 (126)
T ss_pred EEEEEEcCC-----CcEECCCccCCCCCCH-----------HHHHHHHHHHHHCCeeeeeeecceeeeCCEeeccEEEEE
Confidence 777776654 3499999 9999988 999999999999998 332 1122111 2246667777
Q ss_pred EEEEEEe------cccccccCCCCce--eeeCCCCCCC
Q psy8564 296 VPCHIFL------KKCFLKENKNNFI--WYPIKKIKNS 325 (341)
Q Consensus 296 ~~~~~~~------~~~~~~~~~~~~~--W~~~~el~~~ 325 (341)
+.+.+.. ...+...+++.+. |++++++..-
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~E~~~i~~~Wv~l~~~~~~ 116 (126)
T cd04663 79 TLCEVDQDLPDSWVHFVQDDGGHEFRFFWVDLASCLDE 116 (126)
T ss_pred EEEEecCCCcccccCcccCCCCceEEEEEEcccccccc
Confidence 7776632 1112222345566 9999998653
No 95
>PLN02552 isopentenyl-diphosphate delta-isomerase
Probab=98.77 E-value=3.4e-08 Score=89.55 Aligned_cols=130 Identities=10% Similarity=0.141 Sum_probs=76.5
Q ss_pred eeEEEEEEEeCCEEEEEEeCCC-Cccccccccc--c-cccccch------hhhccchhhhhHHHHHHHHHHhcCCc-cc-
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNK-GIWGGLLSFP--E-WILKDKI------INFVDNNLKNLIELEIKKFISSFGFI-KN- 277 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~-g~~~GlWEFP--g-vE~~E~~------~~~~~~~~~~~~~a~~rE~~ee~g~~-~~- 277 (341)
+.+.++|++++|++||+||... ..+.|+|+.. | +..||++ ....+.+..++.+|+.||+.||+||. ..
T Consensus 57 ra~~v~i~n~~g~lLLQkRs~~K~~~Pg~Wd~s~~GHp~~ge~~~e~~~e~~~~~~~~~~~~eAA~REL~EElGI~~~~~ 136 (247)
T PLN02552 57 RAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLYGQDPNEVDRESELIDGNVLGVKNAAQRKLLHELGIPAEDV 136 (247)
T ss_pred EEEEEEEEcCCCeEEEEEecCCCCCCCcceecccCCccccccccccccccccccccchhhHHHHHHhHHHHHhCCCcccc
Confidence 4445666677899999999875 4699999655 2 3333221 01112233335789999999999998 32
Q ss_pred ----ccccCcEEEEeec------------eEEEEEEEEEEecc---cccccCCCCceeeeCCCCCCC-------CCCHHH
Q psy8564 278 ----YLILPIISHKLTH------------LQFKIVPCHIFLKK---CFLKENKNNFIWYPIKKIKNS-------PIPAPV 331 (341)
Q Consensus 278 ----~~~~~~~~h~~~h------------~~~~l~~~~~~~~~---~~~~~~~~~~~W~~~~el~~~-------~~~~a~ 331 (341)
...+..+.+.... ..+...+|...... .+...+-.+++|++++||..+ .|.+..
T Consensus 137 ~~~~l~~~~~~~y~~~~~~~~~~~~~~~E~e~~~v~~~~~~~~~~l~lq~eEV~~~~wvs~~el~~~~~~~~~~~~tpw~ 216 (247)
T PLN02552 137 PVDQFTFLTRLHYKAADDVTHGPDGKWGEHELDYLLFIRPVRDVKVNPNPDEVADVKYVNREELKEMMRKESGLKLSPWF 216 (247)
T ss_pred ccccceeeeEEEEecccccccccCCCccceEEEEEEEEEecCCCcccCCHHHhheEEEEeHHHHHHHHhhcCCcccCHHH
Confidence 2233434443321 12221222211211 112223368999999999864 288888
Q ss_pred HHHHHHhh
Q psy8564 332 RKILFQII 339 (341)
Q Consensus 332 ~~il~~l~ 339 (341)
+.+++.+.
T Consensus 217 ~~~~~~~l 224 (247)
T PLN02552 217 RLIVDNFL 224 (247)
T ss_pred HHHHHHHH
Confidence 88887654
No 96
>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=98.75 E-value=2.7e-09 Score=64.18 Aligned_cols=29 Identities=45% Similarity=0.818 Sum_probs=25.6
Q ss_pred hCCCCccchHHHhcCCCCCHHHHHHHHHH
Q psy8564 80 YNGIFPKNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 80 ~~g~~p~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
|+|.+|.++++|+++||||+|||++|+.|
T Consensus 2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 2 LDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 55778999999999999999999999986
No 97
>TIGR02705 nudix_YtkD nucleoside triphosphatase YtkD. The functional assignment to the proteins of this family is contentious. Reference challenges the findings of reference, both in interpretation and in enzyme assay results. This protein belongs to the nudix family and shares some sequence identity with E. coli MutT but appears not to be functionally interchangeable with it.
Probab=98.67 E-value=9.4e-08 Score=80.78 Aligned_cols=77 Identities=16% Similarity=0.094 Sum_probs=58.8
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
.+++|...++++|+.++.. ..||||| +|.||++ ++|+.||+.||.|+. .....++.+....
T Consensus 26 ~V~ii~~~~~~~LL~~~~~-----~~~elPgG~vE~gEt~-----------~eaA~REl~EETG~~~~~~~~lg~~~~~~ 89 (156)
T TIGR02705 26 HVLVIPRYKDQWLLTEHKR-----RGLEFPGGKVEPGETS-----------KEAAIREVMEETGAIVKELHYIGQYEVEG 89 (156)
T ss_pred EEEEEEEECCEEEEEEEcC-----CcEECCceecCCCCCH-----------HHHHHHHHHHHhCcEeeeeEEEEEEEecC
Confidence 4556656778999988753 3499999 8999998 999999999999998 6666776554444
Q ss_pred eceEEEEEEEEEEecc
Q psy8564 289 THLQFKIVPCHIFLKK 304 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~ 304 (341)
.......++|.+....
T Consensus 90 ~~~~~~~~vf~A~~~~ 105 (156)
T TIGR02705 90 ESTDFVKDVYFAEVSA 105 (156)
T ss_pred CCcEEEEEEEEEEEec
Confidence 4456677888888653
No 98
>cd04662 Nudix_Hydrolase_5 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate s
Probab=98.65 E-value=1.7e-07 Score=76.16 Aligned_cols=69 Identities=14% Similarity=0.047 Sum_probs=46.4
Q ss_pred CEEEEEEeCCC---Ccccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEE
Q psy8564 221 DYVLFQKRSNK---GIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFK 294 (341)
Q Consensus 221 g~vLl~kR~~~---g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~ 294 (341)
.+|||.+|... ..-.|.|+||| ++.+|++ .++++||+.||+|++ . ...+....+.++.. ..
T Consensus 15 ~~vlL~~~~~~~~~~~~~~~W~lPgG~ie~~E~~-----------~~aA~REl~EEtGl~~~-~~~~~l~~~~~~~~-~~ 81 (126)
T cd04662 15 IEVLLVHPGGPFWANKDLGAWSIPKGEYTEGEDP-----------LLAAKREFSEETGFCVD-GPFIDLGSLKQSGG-KV 81 (126)
T ss_pred EEEEEEEccCccccCCCCCEEECCcccCCCCcCH-----------HHHHHHHHHHHhCCcce-eeEEeEEEEECCCC-eE
Confidence 46999987432 24468999999 9999988 999999999999997 4 22222222222222 24
Q ss_pred EEEEEEEe
Q psy8564 295 IVPCHIFL 302 (341)
Q Consensus 295 l~~~~~~~ 302 (341)
+++|.+..
T Consensus 82 v~~fl~~~ 89 (126)
T cd04662 82 VHAWAVEA 89 (126)
T ss_pred EEEEEEEe
Confidence 56666553
No 99
>PLN02709 nudix hydrolase
Probab=98.58 E-value=1.3e-07 Score=84.18 Aligned_cols=92 Identities=15% Similarity=0.191 Sum_probs=66.2
Q ss_pred EEEEEEeCCC-Ccccccccccc--ccccc-chhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEEEE
Q psy8564 222 YVLFQKRSNK-GIWGGLLSFPE--WILKD-KIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFKIV 296 (341)
Q Consensus 222 ~vLl~kR~~~-g~~~GlWEFPg--vE~~E-~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~l~ 296 (341)
++|+.+|+.. +.++|.|.||| +|.++ +. .++++||..||+|++ ...+.++.....++...+.++
T Consensus 52 ~vLl~~Rs~~l~~h~GqiafPGG~~e~~D~~~-----------~~tAlRE~~EEiGl~~~~v~vlg~L~~~~t~sg~~V~ 120 (222)
T PLN02709 52 RVILTKRSSTLSSHPGEVALPGGKRDEEDKDD-----------IATALREAREEIGLDPSLVTIISVLEPFVNKKGMSVA 120 (222)
T ss_pred EEEEEEcCCCCCCCCCCccCCCcccCCCCCCH-----------HHHHHHHHHHHHCCCchheEEeeecCCeECCCCCEEE
Confidence 8999999875 35899999999 88875 34 789999999999998 655666666655555566788
Q ss_pred EEEEEecc----c--ccccCCCCceeeeCCCCCC
Q psy8564 297 PCHIFLKK----C--FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 297 ~~~~~~~~----~--~~~~~~~~~~W~~~~el~~ 324 (341)
+|.+.+.. . +...|-.++.|+++++|.+
T Consensus 121 P~V~~~~~~~~~~~~~np~EV~~vf~vPL~~ll~ 154 (222)
T PLN02709 121 PVIGFLHDKKAFKPLPNPAEVEEIFDVPLEMFLK 154 (222)
T ss_pred EEEEEecCCCCccccCChhhhheeEEecHHHHhC
Confidence 88776532 1 1112235677777776654
No 100
>TIGR00052 nudix-type nucleoside diphosphatase, YffH/AdpP family.
Probab=98.53 E-value=1.4e-07 Score=82.28 Aligned_cols=94 Identities=12% Similarity=-0.012 Sum_probs=61.8
Q ss_pred CCEEEEEEeCCCCc-----ccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeece
Q psy8564 220 DDYVLFQKRSNKGI-----WGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHL 291 (341)
Q Consensus 220 ~g~vLl~kR~~~g~-----~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~ 291 (341)
+++|||.+.-..+. -.++||||+ +|.||++ ++|+.||+.||+|+. .....+..+.-.....
T Consensus 56 ~~~vlLvrq~R~~~~~~~~~~~~lelPaG~ve~gE~~-----------~~aA~REl~EEtG~~~~~~~~~~~~~~~~g~~ 124 (185)
T TIGR00052 56 KDTVVLIEQFRIAAYVNGEEPWLLELSAGMVEKGESP-----------EDVARREAIEEAGYQVKNLRKLLSFYSSPGGV 124 (185)
T ss_pred CCEEEEEECceeeeeecCCcceEEEECcEecCCCCCH-----------HHHHHHHccccccceecceEEEEEEEcCCCCC
Confidence 47899987643333 368999999 9999998 999999999999998 5555544332222223
Q ss_pred EEEEEEEEEEeccc-------ccccCCCCceeeeCCCCCC
Q psy8564 292 QFKIVPCHIFLKKC-------FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 292 ~~~l~~~~~~~~~~-------~~~~~~~~~~W~~~~el~~ 324 (341)
...+++|.+...+. ....+..+..|++++++.+
T Consensus 125 ~~~~~~f~a~~~~~~~~~~~~~~~~E~ie~~~~~~~e~~~ 164 (185)
T TIGR00052 125 TELIHLFIAEVDDNQAAGIGGGADEEEIEVLHLVFSQALQ 164 (185)
T ss_pred cEEEEEEEEEEchhhcCCCCCCCCccceEEEEeCHHHHHH
Confidence 45678888875431 0112223457777766643
No 101
>COG0494 MutT NTP pyrophosphohydrolases including oxidative damage repair enzymes [DNA replication, recombination, and repair / General function prediction only]
Probab=98.36 E-value=2.4e-06 Score=69.91 Aligned_cols=96 Identities=17% Similarity=0.209 Sum_probs=61.3
Q ss_pred CEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHH-HHHHHHHHhcCCc-c--cccccCcEEEEeece---
Q psy8564 221 DYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIE-LEIKKFISSFGFI-K--NYLILPIISHKLTHL--- 291 (341)
Q Consensus 221 g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~-a~~rE~~ee~g~~-~--~~~~~~~~~h~~~h~--- 291 (341)
+++|+.+|...+ |.|+||| +|.+|++ .+ |++||+.||+|+. . ....++.+.......
T Consensus 24 ~~vl~~~~~~~~---~~~~~PgG~ve~~e~~-----------~~~aa~RE~~EEtGl~~~~~~~~~~~~~~~~~~~~~~~ 89 (161)
T COG0494 24 GEVLLAQRRDDG---GLWELPGGKVEPGEEL-----------PEEAAARELEEETGLRVKDERLELLGEFPPSPGDGSSV 89 (161)
T ss_pred CEEeEEEccccC---CceecCCcccCCCCch-----------HHHHHHHHHHHHhCCeeeeecceeeeeccCcccCcccc
Confidence 899999998876 9999999 9999965 45 9999999999998 5 333333332222211
Q ss_pred --EEEEEEEEEEec--c--c--cc---ccCCCCceeeeCCCCCCCCCCHH
Q psy8564 292 --QFKIVPCHIFLK--K--C--FL---KENKNNFIWYPIKKIKNSPIPAP 330 (341)
Q Consensus 292 --~~~l~~~~~~~~--~--~--~~---~~~~~~~~W~~~~el~~~~~~~a 330 (341)
......+..... . . .. ..+..++.|+..+++........
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~ 139 (161)
T COG0494 90 GGREHRVFFVAEVDDSLAVAIEGLSAPSEELEDLEWVPLDELAALVLAED 139 (161)
T ss_pred cceEEEEEEeeeccccccccccccCCCcchhhceeeeeHHHcccccccch
Confidence 222222222211 1 1 11 12236789999998888766653
No 102
>PLN02791 Nudix hydrolase homolog
Probab=98.31 E-value=2e-06 Score=89.03 Aligned_cols=101 Identities=13% Similarity=0.204 Sum_probs=66.7
Q ss_pred EEEEEEEe-CCEEEEEEeCC-CCcccccccc-cc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cc--ccccCc
Q psy8564 212 IIMFIVID-DDYVLFQKRSN-KGIWGGLLSF-PE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KN--YLILPI 283 (341)
Q Consensus 212 ~~~~ii~~-~g~vLl~kR~~-~g~~~GlWEF-Pg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~--~~~~~~ 283 (341)
+.+.|++. +|++||+||+. +..+.|+|.+ || ++.||++ .++++||+.||+||. .. ...++.
T Consensus 35 vhVwIfn~~~gelLLQkRS~~K~~~PG~WDiS~gGHv~aGEs~-----------~eAA~REL~EELGI~l~~~~l~~l~~ 103 (770)
T PLN02791 35 VHVWIYSESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTS-----------LLSAQRELEEELGIILPKDAFELLFV 103 (770)
T ss_pred EEEEEEECCCCeEEEEEecCCCCCCCCcccCcCCCCCCCCCCH-----------HHHHHHHHHHHhCCCCChhheeeeee
Confidence 34444454 58999999976 4579999999 56 9999987 889999999999997 22 233333
Q ss_pred EEEEe--ec----eEEEEEEEEEEecc-------cccccCCCCceeeeCCCCC
Q psy8564 284 ISHKL--TH----LQFKIVPCHIFLKK-------CFLKENKNNFIWYPIKKIK 323 (341)
Q Consensus 284 ~~h~~--~h----~~~~l~~~~~~~~~-------~~~~~~~~~~~W~~~~el~ 323 (341)
+.+.+ .+ -+...++|.+.... .+...|..+++|++.+|+.
T Consensus 104 ~~~~~~~~~g~~~e~E~~~VYlv~~~~~~p~~~~~lq~eEV~~v~wvsl~El~ 156 (770)
T PLN02791 104 FLQECVINDGKFINNEYNDVYLVTTLDPIPLEAFTLQESEVSAVKYMSIEEYK 156 (770)
T ss_pred EEEEeeccCCCcceeeEEEEEEEEECCCCCcccCCCChhhhheeEEEcHHHHH
Confidence 22211 11 11234567665322 1122344789999999985
No 103
>cd03670 ADPRase_NUDT9 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the Nudix hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer.
Probab=98.24 E-value=8e-06 Score=71.03 Aligned_cols=102 Identities=13% Similarity=0.056 Sum_probs=63.3
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc---ccccc----------cCcEEE
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI---KNYLI----------LPIISH 286 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~---~~~~~----------~~~~~h 286 (341)
++|+.||+.. |.|.||| ++.+|+. .+|+.||+.||+++. ...+. ...-..
T Consensus 50 ~vLl~~r~~~----g~walPGG~v~~~E~~-----------~~aa~Rel~EEt~l~l~~~~~~~~~l~~l~~~~~~~~~~ 114 (186)
T cd03670 50 QFVAIKRPDS----GEWAIPGGMVDPGEKI-----------SATLKREFGEEALNSLQKSDEEKEEIKKLVELFSKDGVE 114 (186)
T ss_pred EEEEEEeCCC----CcCcCCeeeccCCCCH-----------HHHHHHHHHHHHcccccccchhhhhhcchhhhhcccccE
Confidence 7899999763 8999999 9999988 899999999999653 11100 000111
Q ss_pred Ee------ece----EEEEEEEEEEec-----c--cc-cccCCCCceeeeCCCCCCCCCCHHHHHHHHHhhc
Q psy8564 287 KL------THL----QFKIVPCHIFLK-----K--CF-LKENKNNFIWYPIKKIKNSPIPAPVRKILFQIIQ 340 (341)
Q Consensus 287 ~~------~h~----~~~l~~~~~~~~-----~--~~-~~~~~~~~~W~~~~el~~~~~~~a~~~il~~l~~ 340 (341)
+| +.. .+....|.+... . .+ ...+..+.+|++++++. +|+.-+..||+...+
T Consensus 115 vy~~~~~dpr~td~~w~~Tva~~f~~~~~~~~~~~~~~a~dda~~a~W~~v~~l~--~L~~dH~~Il~~a~~ 184 (186)
T cd03670 115 VYKGYVDDPRNTDNAWMETVAVNFHDEDGNDVENLPLEAGDDAGSVRWQDIDSKL--PLYANHSQFLKKVAE 184 (186)
T ss_pred EEeccccCCCCCCcceEEEEEEEEEecCcccccccccCCCCchheeEEEEccccc--ccccCHHHHHHHHHH
Confidence 23 111 112233333221 0 11 11123678999999987 677788888887654
No 104
>PRK10729 nudF ADP-ribose pyrophosphatase NudF; Provisional
Probab=98.17 E-value=4.7e-06 Score=73.76 Aligned_cols=93 Identities=8% Similarity=-0.114 Sum_probs=60.9
Q ss_pred CCEEEEEEeCCCCc-----ccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeece
Q psy8564 220 DDYVLFQKRSNKGI-----WGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHL 291 (341)
Q Consensus 220 ~g~vLl~kR~~~g~-----~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~ 291 (341)
+|+|+|.+---.+. -+-+||||+ +|.||++ ++|+.||+.||.|+. .....+..+.......
T Consensus 61 ~~~vlLvrQyR~~~~~~~~~~~~lE~PAG~vd~gE~p-----------~~aA~REL~EETGy~a~~~~~l~~~~~spg~~ 129 (202)
T PRK10729 61 RDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESV-----------EDVARREAIEEAGLIVGRTKPVLSYLASPGGT 129 (202)
T ss_pred CCEEEEEEeeecccccCCCCCeEEEccceEcCCCCCH-----------HHHHHHHHHHHhCceeeEEEEEEEEEcCCCcC
Confidence 46877754322222 236899999 8999988 999999999999998 6555555444443344
Q ss_pred EEEEEEEEEEecc----c----ccccCCCCceeeeCCCCC
Q psy8564 292 QFKIVPCHIFLKK----C----FLKENKNNFIWYPIKKIK 323 (341)
Q Consensus 292 ~~~l~~~~~~~~~----~----~~~~~~~~~~W~~~~el~ 323 (341)
.-.+++|.+.... . ..+.+.-+..|++.+++.
T Consensus 130 ~e~~~~fla~~~~~~~~~~~~~~de~E~i~v~~~~~~e~~ 169 (202)
T PRK10729 130 SERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAY 169 (202)
T ss_pred ceEEEEEEEEEcchhcccCCCCCCCCCceEEEEEcHHHHH
Confidence 5677888877411 1 111222346788887764
No 105
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=98.08 E-value=9.2e-07 Score=45.75 Aligned_cols=17 Identities=53% Similarity=1.243 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCccccc
Q psy8564 172 CKKIKPKCKVCPLQLCC 188 (341)
Q Consensus 172 C~~~~P~C~~Cpl~~~C 188 (341)
|++++|+|+.|||++.|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999988
No 106
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=98.03 E-value=2.7e-06 Score=77.56 Aligned_cols=99 Identities=12% Similarity=0.152 Sum_probs=73.4
Q ss_pred EEEEEEEeCCEEEEEEeCCCCcccccccc-cc-cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKGIWGGLLSF-PE-WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL 288 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g~~~GlWEF-Pg-vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~ 288 (341)
++.+++.+++++||.+++..- .|++.- -| ||+|||. ++|..||+.||.|+. ...++++.-.+-|
T Consensus 146 ~vIv~v~~~~~ilLa~~~~h~--~g~yS~LAGFVE~GETl-----------E~AV~REv~EE~Gi~V~~vrY~~SQPWPf 212 (279)
T COG2816 146 CVIVAVIRGDEILLARHPRHF--PGMYSLLAGFVEPGETL-----------EQAVAREVFEEVGIKVKNVRYVGSQPWPF 212 (279)
T ss_pred eEEEEEecCCceeecCCCCCC--CcceeeeeecccCCccH-----------HHHHHHHHHHhhCeEEeeeeEEeccCCCC
Confidence 445555677779999997653 788864 34 9999998 999999999999999 7778888888888
Q ss_pred eceEEEEEEEEEEecc-c----ccccCCCCceeeeCCC-CCCCCC
Q psy8564 289 THLQFKIVPCHIFLKK-C----FLKENKNNFIWYPIKK-IKNSPI 327 (341)
Q Consensus 289 ~h~~~~l~~~~~~~~~-~----~~~~~~~~~~W~~~~e-l~~~~~ 327 (341)
+|-- |.-|.+.+.+ + ..+. .+.+|++.+| |..++-
T Consensus 213 P~SL--Migf~aey~sgeI~~d~~El--eda~WFs~~evl~~L~~ 253 (279)
T COG2816 213 PHSL--MLGFMAEYDSGEITPDEGEL--EDARWFSRDEVLPALPP 253 (279)
T ss_pred chhh--hhhheeeeccccccCCcchh--hhccccCHhHHhhhcCC
Confidence 8853 3444555443 1 1222 5789999999 777664
No 107
>PRK15009 GDP-mannose pyrophosphatase NudK; Provisional
Probab=97.66 E-value=0.00013 Score=63.96 Aligned_cols=93 Identities=10% Similarity=-0.066 Sum_probs=56.5
Q ss_pred CCEEEEEEeCCCCc------ccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeec
Q psy8564 220 DDYVLFQKRSNKGI------WGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTH 290 (341)
Q Consensus 220 ~g~vLl~kR~~~g~------~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h 290 (341)
+++++|.+---.+. -+=.||||+ ++.+ ++ +++++||+.||.|.. .....++.+.=.-..
T Consensus 57 ~~~vvLvrQyR~~v~~~~~~~~~~lElPAG~vd~~-~p-----------~~aA~REL~EETGy~a~~~~~l~~~~~spG~ 124 (191)
T PRK15009 57 KKTVVLIRQFRVATWVNGNESGQLIETCAGLLDND-EP-----------EVCIRKEAIEETGYEVGEVRKLFELYMSPGG 124 (191)
T ss_pred CCEEEEEEcccccccccCCCCceEEEEeccccCCC-CH-----------HHHHHHHHHHhhCCccceEEEeeEEEcCCcc
Confidence 56888866433343 345799999 7754 46 899999999999998 555555433211112
Q ss_pred eEEEEEEEEEEecc----c---ccccCCCCceeeeCCCCCC
Q psy8564 291 LQFKIVPCHIFLKK----C---FLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 291 ~~~~l~~~~~~~~~----~---~~~~~~~~~~W~~~~el~~ 324 (341)
..-.+|+|.++... . ..+.+.-+..|++.+|+.+
T Consensus 125 s~e~~~lf~a~~~~~~~~~~~~~de~E~iev~~~~~~e~~~ 165 (191)
T PRK15009 125 VTELIHFFIAEYSDSQRANAGGGVEDEDIEVLELPFSQALE 165 (191)
T ss_pred cCcEEEEEEEEECchhcccCCCCCCCceEEEEEEcHHHHHH
Confidence 23456777777431 1 1112223468888877643
No 108
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=97.59 E-value=2.7e-05 Score=45.26 Aligned_cols=22 Identities=45% Similarity=1.099 Sum_probs=20.1
Q ss_pred hcccCCCCCCCCCccccccccc
Q psy8564 171 ICKKIKPKCKVCPLQLCCISYK 192 (341)
Q Consensus 171 ~C~~~~P~C~~Cpl~~~C~~~~ 192 (341)
+|++++|+|+.||++++|.++.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999999854
No 109
>KOG2839|consensus
Probab=97.40 E-value=0.00029 Score=57.79 Aligned_cols=87 Identities=17% Similarity=0.133 Sum_probs=56.5
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEe--eceEE-EE
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKL--THLQF-KI 295 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~--~h~~~-~l 295 (341)
+|||..=+.+ +-.|-||+ +|++|+. .+|+.||..||-|+. .....++.+.-.- +|... .=
T Consensus 25 eVLlvsSs~~---~~~wi~PKGGwE~dE~~-----------~eAA~REt~EEAGv~G~l~~~~~g~~~~~~~~~~~~~k~ 90 (145)
T KOG2839|consen 25 EVLLVSSSKK---PHRWIVPKGGWEPDESV-----------EEAALRETWEEAGVKGKLGRLLGGFEDFLSKKHRTKPKG 90 (145)
T ss_pred EEEEEecCCC---CCCccCCCCCCCCCCCH-----------HHHHHHHHHHHhCceeeeeccccchhhccChhhcccccc
Confidence 7999986554 36899999 9999988 899999999999998 5555444443222 33322 11
Q ss_pred EEEEEEecc-----cccccCCCCceeeeCCCC
Q psy8564 296 VPCHIFLKK-----CFLKENKNNFIWYPIKKI 322 (341)
Q Consensus 296 ~~~~~~~~~-----~~~~~~~~~~~W~~~~el 322 (341)
..|...+.. .-..+++.+.+|++++|-
T Consensus 91 ~~~~l~v~e~le~wp~~~~~~r~r~W~~ledA 122 (145)
T KOG2839|consen 91 VMYVLAVTEELEDWPESEHEFREREWLKLEDA 122 (145)
T ss_pred eeehhhhhhhcccChhhhcccceeEEeeHHHH
Confidence 123222222 113344688999998774
No 110
>KOG3084|consensus
Probab=97.35 E-value=0.00035 Score=64.29 Aligned_cols=59 Identities=17% Similarity=0.076 Sum_probs=47.6
Q ss_pred eeEEEEEEEeCCEEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccc
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLI 280 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~ 280 (341)
..+..+|+.++|+.+|-.| ..+.-.|||.-+- +|+||+. ++|.+||..||.|++ ....+
T Consensus 188 PvVIm~li~~d~~~~LL~R-~~r~~~gl~t~lAGFlEpGES~-----------eeav~REtwEEtGi~V~~I~~ 249 (345)
T KOG3084|consen 188 PVVIMLLIDHDGKHALLGR-QKRYPPGLWTCLAGFLEPGESI-----------EEAVRRETWEETGIEVEVISY 249 (345)
T ss_pred CeEEEEEEcCCCCEeeeec-ccCCCCchhhhhhccCCccccH-----------HHHHHHHHHHHhCceeeeEee
Confidence 3566778888887777667 5678889999887 9999988 999999999999997 54433
No 111
>PLN03143 nudix hydrolase; Provisional
Probab=97.35 E-value=0.00055 Score=63.64 Aligned_cols=47 Identities=6% Similarity=0.085 Sum_probs=35.8
Q ss_pred EeCCE--EEEEEeCCCCcccccccccc--cccc-cchhhhccchhhhhHHHHHHHHHHhcCCc
Q psy8564 218 IDDDY--VLFQKRSNKGIWGGLLSFPE--WILK-DKIINFVDNNLKNLIELEIKKFISSFGFI 275 (341)
Q Consensus 218 ~~~g~--vLl~kR~~~g~~~GlWEFPg--vE~~-E~~~~~~~~~~~~~~~a~~rE~~ee~g~~ 275 (341)
..+|+ ++|.++..-+.-.-.||||+ +|.+ |++ .+++.||+.||+|+.
T Consensus 138 ~~~ge~~VlLVrQ~R~pvg~~~lE~PAG~lD~~~edp-----------~~aA~REL~EETG~~ 189 (291)
T PLN03143 138 ESEGETYAVLTEQVRVPVGKFVLELPAGMLDDDKGDF-----------VGTAVREVEEETGIK 189 (291)
T ss_pred eCCCCEEEEEEEeEecCCCcEEEEecccccCCCCCCH-----------HHHHHHHHHHHHCCc
Confidence 33454 78877755444455899999 8864 676 899999999999996
No 112
>COG1443 Idi Isopentenyldiphosphate isomerase [Lipid metabolism]
Probab=97.24 E-value=0.00032 Score=59.29 Aligned_cols=102 Identities=16% Similarity=0.285 Sum_probs=62.2
Q ss_pred eeEEEEEEEeCCEEEEEEeCC-CCccccccc-----ccccccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc---c
Q psy8564 210 CSIIMFIVIDDDYVLFQKRSN-KGIWGGLLS-----FPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY---L 279 (341)
Q Consensus 210 ~~~~~~ii~~~g~vLl~kR~~-~g~~~GlWE-----FPgvE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~---~ 279 (341)
+-+.+.|.+.+|++||+||.. +..|.|.|. -|+ ++|+. ..|.+|-+..||||+ ... +
T Consensus 34 rAFS~~lFne~g~LLltrRA~~K~twP~vWTNSvCsHP~--~~es~-----------~~A~~rRl~~ELGie~~~~d~~~ 100 (185)
T COG1443 34 RAFSSFLFNERGQLLLTRRALSKKTWPGVWTNSVCSHPL--PGESN-----------EDAARRRLAYELGIEPDQYDKLE 100 (185)
T ss_pred hhhheeEECCCCceeeehhhhhcccCcccccccccCCCc--CCCch-----------HHHHHHHHHHHhCCCCcccCccc
Confidence 345678888899999999976 467999995 233 34544 788999999999998 421 2
Q ss_pred ccCcEEEEee--c--eEEEEE-EEEEEecc--cccccCCCCceeeeCCCCCC
Q psy8564 280 ILPIISHKLT--H--LQFKIV-PCHIFLKK--CFLKENKNNFIWYPIKKIKN 324 (341)
Q Consensus 280 ~~~~~~h~~~--h--~~~~l~-~~~~~~~~--~~~~~~~~~~~W~~~~el~~ 324 (341)
.+..+.+.-+ . ..+.|- ++.++..+ .+...+-.+++|++++++..
T Consensus 101 il~rf~YrA~~~~~~~E~Eic~V~~~~~~~~~~~npdEV~~~~wv~~e~l~~ 152 (185)
T COG1443 101 ILPRFRYRAADPDGIVENEICPVLAARLDSALDPNPDEVMDYRWVSPEDLKE 152 (185)
T ss_pred cccceEEeccCCCCcceeeeeeEEEEeecCCCCCChHHhhheeccCHHHHHH
Confidence 2333332211 1 122322 22333332 12222337899999999865
No 113
>KOG3069|consensus
Probab=97.16 E-value=0.00091 Score=59.24 Aligned_cols=101 Identities=18% Similarity=0.224 Sum_probs=68.7
Q ss_pred CEEEEEEeCCC-Ccccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEEeeceEEEEE
Q psy8564 221 DYVLFQKRSNK-GIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHKLTHLQFKIV 296 (341)
Q Consensus 221 g~vLl~kR~~~-g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~~~h~~~~l~ 296 (341)
-++|++||... ..+.|--.||| .+..++. .+.++.||-.||.|+. .....++...-.+.-..+.+.
T Consensus 58 l~vLltkRSr~LrshsGev~fPGG~~d~~D~s----------~~~tAlREt~EEIGl~~~~~~~~g~l~~~~~r~~~~v~ 127 (246)
T KOG3069|consen 58 LSVLLTKRSRTLRSHSGEVCFPGGRRDPHDKS----------DIQTALRETEEEIGLDPELVDVLGALPPFVLRSGWSVF 127 (246)
T ss_pred eEEEEEeccccccccCCceeCCCCcCCccccc----------hHHHHHHHHHHHhCCCHHHhhhhhhccceeeccCcccc
Confidence 38999999765 67999999999 5544422 1678999999999999 666666666655555666777
Q ss_pred EEEEEeccc-------ccccCCCCceeeeCCCCCCCCCCHHH
Q psy8564 297 PCHIFLKKC-------FLKENKNNFIWYPIKKIKNSPIPAPV 331 (341)
Q Consensus 297 ~~~~~~~~~-------~~~~~~~~~~W~~~~el~~~~~~~a~ 331 (341)
++.+-+... +...+-..+.||++++|-.-.-..++
T Consensus 128 p~v~~l~~~~~l~~~~ln~gEv~~~F~VPL~~ll~~~~~~~~ 169 (246)
T KOG3069|consen 128 PVVGFLSDKKILPSLRLNSGEVESAFWVPLTDLLLPKHQTAF 169 (246)
T ss_pred eeEEEEecccccccccCCchheeeeeeeeHHHHhhhhcchHH
Confidence 766554321 11223367899998888664444433
No 114
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=95.97 E-value=0.0058 Score=35.33 Aligned_cols=20 Identities=40% Similarity=0.601 Sum_probs=17.7
Q ss_pred HHhcCCCCCHHHHHHHHHHH
Q psy8564 90 SLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 90 ~L~~l~GIG~~tA~~il~~~ 109 (341)
.|+++||||+++|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999999754
No 115
>KOG0648|consensus
Probab=95.92 E-value=0.0038 Score=57.57 Aligned_cols=104 Identities=14% Similarity=0.151 Sum_probs=61.8
Q ss_pred EEEEEEEeCCEEEEEEeCC-CCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccccccCcEEEE
Q psy8564 212 IIMFIVIDDDYVLFQKRSN-KGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYLILPIISHK 287 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~-~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~~~~~~~h~ 287 (341)
+.++|++.+++||+.+-.. .-...|.|-||+ ++.+|.. .+.++||++||+|++ .-.+.+ .+.|.
T Consensus 118 vg~~V~n~~~eVlVv~e~d~~~~~~~~wK~ptG~v~~~e~i-----------~~gavrEvkeetgid~ef~eVl-a~r~~ 185 (295)
T KOG0648|consen 118 VGAFVLNKKKEVLVVQEKDGAVKIRGGWKLPTGRVEEGEDI-----------WHGAVREVKEETGIDTEFVEVL-AFRRA 185 (295)
T ss_pred eeeeEecCCceeEEEEecccceeecccccccceEecccccc-----------hhhhhhhhHHHhCcchhhhhHH-HHHhh
Confidence 3456666667999987422 235789999999 8888876 888999999999987 322211 12221
Q ss_pred eece-E-EEE-EEEEEEecc-----cccccCCCCceeeeCCCCCCCCC
Q psy8564 288 LTHL-Q-FKI-VPCHIFLKK-----CFLKENKNNFIWYPIKKIKNSPI 327 (341)
Q Consensus 288 ~~h~-~-~~l-~~~~~~~~~-----~~~~~~~~~~~W~~~~el~~~~~ 327 (341)
.+.. . ..- .++.|.+.. .....+-..+.|++.+|..+.|+
T Consensus 186 H~~~~~~~ksd~f~~c~L~p~s~~i~~~~~ei~~~~Wmp~~e~v~qp~ 233 (295)
T KOG0648|consen 186 HNATFGLIKSDMFFTCELRPRSLDITKCKREIEAAAWMPIEEYVSQPL 233 (295)
T ss_pred hcchhhcccccceeEEEeeccccccchhHHHHHHHhcccHHHhhcccc
Confidence 1111 0 011 223344322 11011113459999999888777
No 116
>COG4119 Predicted NTP pyrophosphohydrolase [DNA replication, recombination, and repair / General function prediction only]
Probab=95.30 E-value=0.063 Score=43.12 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=33.6
Q ss_pred EEEEEEeCCCCccc----ccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc
Q psy8564 222 YVLFQKRSNKGIWG----GLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI 275 (341)
Q Consensus 222 ~vLl~kR~~~g~~~----GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~ 275 (341)
.|||.- |.+.+|+ |-|..|- +..+|.+ ..|+.||+.||+||.
T Consensus 19 ~VLLvH-PGGPFWa~kD~GAWSIPKGey~~gEdp-----------~~AArREf~EE~Gi~ 66 (161)
T COG4119 19 DVLLVH-PGGPFWAGKDDGAWSIPKGEYTGGEDP-----------WLAARREFSEEIGIC 66 (161)
T ss_pred EEEEec-CCCCccccCCCCcccccccccCCCcCH-----------HHHHHHHhhhhhcee
Confidence 566664 5667776 5799998 6777877 888999999999987
No 117
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=95.30 E-value=0.13 Score=44.39 Aligned_cols=71 Identities=14% Similarity=0.155 Sum_probs=58.2
Q ss_pred CChHHHHHHHHHhhhcChhhHHHHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH---HHHHHHHHHHHHhHH
Q psy8564 8 KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY---SRARNLHICAKLVFF 78 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~---~rA~~i~~~a~~i~~ 78 (341)
+.-|+.|+-+++-.--++.++..-.+.|.+.| .+|+.+|..++++|.++++.-|.- .|.+.++.-|+.+.+
T Consensus 24 ~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~ 99 (179)
T PF03352_consen 24 RKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILK 99 (179)
T ss_dssp HHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHH
Confidence 34689999999999999999999999999998 589999999999999999888863 377788888877765
No 118
>KOG3041|consensus
Probab=95.24 E-value=0.073 Score=46.09 Aligned_cols=75 Identities=19% Similarity=0.168 Sum_probs=48.6
Q ss_pred EEEEeCCE--EEEEE--eCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccc--ccCcEE
Q psy8564 215 FIVIDDDY--VLFQK--RSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYL--ILPIIS 285 (341)
Q Consensus 215 ~ii~~~g~--vLl~k--R~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~--~~~~~~ 285 (341)
+++..+|+ ++|+| ||+-| +=--|||- ++.||+. +.|++||++||.|.. .... ......
T Consensus 80 ~il~~dG~~~ivL~kQfRpP~G--k~ciElPAGLiD~ge~~-----------~~aAiREl~EEtGy~gkv~~~s~~~f~D 146 (225)
T KOG3041|consen 80 AILESDGKPYIVLVKQFRPPTG--KICIELPAGLIDDGEDF-----------EGAAIRELEEETGYKGKVDMVSPTVFLD 146 (225)
T ss_pred EEEecCCcEEEEEEEeecCCCC--cEEEEcccccccCCCch-----------HHHHHHHHHHHhCccceeeeccccEEcC
Confidence 34556774 55554 44432 12369998 9999988 999999999999987 3321 111222
Q ss_pred EEeeceEEEEEEEEEEe
Q psy8564 286 HKLTHLQFKIVPCHIFL 302 (341)
Q Consensus 286 h~~~h~~~~l~~~~~~~ 302 (341)
--|++-.+.|.++.++.
T Consensus 147 PGltn~~~~iv~v~idg 163 (225)
T KOG3041|consen 147 PGLTNCNLCIVVVDIDG 163 (225)
T ss_pred CCCCCCceEEEEEEecC
Confidence 24677777777776653
No 119
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.11 E-value=0.031 Score=39.82 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=24.6
Q ss_pred HHHHhHHHhCC---CCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 72 CAKLVFFKYNG---IFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 72 ~a~~i~~~~~g---~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.|+.+.+.|+. -.-.+.++|.++||||+.+|..|..|-
T Consensus 15 ~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 15 TAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp HHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHH
Confidence 34555555553 123578999999999999999998764
No 120
>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=94.79 E-value=0.14 Score=36.95 Aligned_cols=55 Identities=27% Similarity=0.242 Sum_probs=36.8
Q ss_pred HHHHHHhhc-CcHHHHHHHHHHHHHhHHHhCCCCccchHH-HhcCCCCCHHHHHHHHHH
Q psy8564 52 NVMELWSGL-GYYSRARNLHICAKLVFFKYNGIFPKNFIS-LINLPGIGQSTASAIRVF 108 (341)
Q Consensus 52 ~l~~~l~~~-G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~-L~~l~GIG~~tA~~il~~ 108 (341)
++.+..+-. |-..|++.-.+++..|.. +...+. +.++ +.+|||||+++|.-|--|
T Consensus 10 ~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~~i~-~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 10 ELADLYELQGGDPFRARAYRRAAAAIKA-LPYPIT-SGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS-HH-SHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCHhHh-hHHHHHhhCCCCCHHHHHHHHHH
Confidence 444444444 333488888899988876 333332 3465 999999999999988544
No 121
>PLN02839 nudix hydrolase
Probab=94.50 E-value=0.11 Score=49.54 Aligned_cols=92 Identities=13% Similarity=0.080 Sum_probs=61.4
Q ss_pred CEEEEEEeCCC-Cccccccccc--c-cccccchhhhccchhhhhHHHHHHHHHHhcCCc-c---cccccCcEEEEeece-
Q psy8564 221 DYVLFQKRSNK-GIWGGLLSFP--E-WILKDKIINFVDNNLKNLIELEIKKFISSFGFI-K---NYLILPIISHKLTHL- 291 (341)
Q Consensus 221 g~vLl~kR~~~-g~~~GlWEFP--g-vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~---~~~~~~~~~h~~~h~- 291 (341)
+++++.||... ..+.|+|.== | +..||++ .++++||..||.|+. . .....+.++|.+...
T Consensus 218 ~~lWV~RRS~tK~t~PGmLDn~VAGGi~aGesp-----------~etliREa~EEAgLp~~l~~~~~~~G~VsY~~~~~~ 286 (372)
T PLN02839 218 KFLWIGKRSLSKSTYPGMLDHLVAGGLPHGISC-----------GENLVKECEEEAGISKAIADRAIAVGAVSYMDIDQY 286 (372)
T ss_pred eEEEeeccCCCCCCCCChhhhccccCccCCCCH-----------HHHHHHHHHHHcCCCHHHHhcceEeEEEEEEEEcCC
Confidence 57999999875 4577777632 2 7788887 999999999999997 3 345567777664221
Q ss_pred ---EEEEEEEEEEeccc----ccccCCCCceeeeCCCCC
Q psy8564 292 ---QFKIVPCHIFLKKC----FLKENKNNFIWYPIKKIK 323 (341)
Q Consensus 292 ---~~~l~~~~~~~~~~----~~~~~~~~~~W~~~~el~ 323 (341)
.=.+++|.+.+..+ +...|-+++.+++++|+.
T Consensus 287 g~~~evly~YDLeLP~df~P~~qDGEVe~F~Lm~v~EV~ 325 (372)
T PLN02839 287 CFKRDVLFCYDLELPQDFVPKNQDGEVESFKLIPVAQVA 325 (372)
T ss_pred ccccCEEEEeeeecCCccccCCCccceeEEEEecHHHHH
Confidence 11245677675542 222333568888887774
No 122
>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=93.04 E-value=0.34 Score=34.82 Aligned_cols=58 Identities=24% Similarity=0.402 Sum_probs=38.1
Q ss_pred HHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHH
Q psy8564 44 SLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 44 ~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
+|-.++.++|..++.++|. .+|+.|.+--. .++ .+ .+.++|.+++|||.++++-|..+
T Consensus 9 nvNta~~~~L~~~ipgig~-~~a~~Il~~R~----~~g-~~-~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL-KKAEAIVSYRE----EYG-PF-KTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH-HHHHHHHHHHH----HcC-Cc-CCHHHHHcCCCCCHHHHHHHHhh
Confidence 3445777888776777775 23333333221 122 22 37899999999999999988765
No 123
>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=93.00 E-value=0.3 Score=34.08 Aligned_cols=22 Identities=36% Similarity=0.478 Sum_probs=17.8
Q ss_pred chHHHhcCCCCCHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~ 108 (341)
+.++|.++||||+++|+.+...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4678889999999999887654
No 124
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.60 E-value=0.77 Score=39.69 Aligned_cols=73 Identities=14% Similarity=0.089 Sum_probs=63.1
Q ss_pred CCCChHHHHHHHHHhhhcChhhHHHHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-H--HHHHHHHHHHHhHH
Q psy8564 6 NTKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-S--RARNLHICAKLVFF 78 (341)
Q Consensus 6 ~~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~--rA~~i~~~a~~i~~ 78 (341)
..+.-|+.|+-+++-.-.++.++..-.+.|.+.| .+|+.+|..+++++++++..-|.- + |.+.+++-|+.+.+
T Consensus 26 dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 26 DSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred CCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 3456799999999999999999999999999988 599999999999999999988875 3 56668888888775
No 125
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=92.43 E-value=0.72 Score=40.13 Aligned_cols=72 Identities=15% Similarity=0.084 Sum_probs=62.4
Q ss_pred CCChHHHHHHHHHhhhcChhhHHHHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-H--HHHHHHHHHHHhHH
Q psy8564 7 TKNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-S--RARNLHICAKLVFF 78 (341)
Q Consensus 7 ~~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~--rA~~i~~~a~~i~~ 78 (341)
.+.-||.|+-+.+-.-.++.++..-.+.|.+.| .+|+.+|..+++++++++..-|.- + |.+.+++-|+.+.+
T Consensus 28 d~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 28 SKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred cHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999988 599999999999999999988874 2 66678887777764
No 126
>KOG4195|consensus
Probab=91.90 E-value=0.2 Score=44.20 Aligned_cols=35 Identities=17% Similarity=0.161 Sum_probs=28.6
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHh
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISS 271 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee 271 (341)
+++..||+.. |.|-.|| +++||.. ...++||+.||
T Consensus 140 e~vavkr~d~----~~WAiPGGmvdpGE~v-----------s~tLkRef~eE 176 (275)
T KOG4195|consen 140 EFVAVKRPDN----GEWAIPGGMVDPGEKV-----------SATLKREFGEE 176 (275)
T ss_pred EEEEEecCCC----CcccCCCCcCCchhhh-----------hHHHHHHHHHH
Confidence 5677899775 6888999 9999965 67788999877
No 127
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=91.86 E-value=1.1 Score=38.75 Aligned_cols=71 Identities=17% Similarity=0.113 Sum_probs=58.9
Q ss_pred CChHHHHHHHHHhhhcChhhHHHHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-H--HHHHHHHHHHHhHH
Q psy8564 8 KNTYYIWLSEIMLQQTQVNTVIPYYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-S--RARNLHICAKLVFF 78 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~--rA~~i~~~a~~i~~ 78 (341)
+.-|+.++-++.-.-.++.++..-.+.|.+.| .+|+.+|..+++++++++...|.- + |.+.++.-|+.+.+
T Consensus 30 ~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~ 105 (188)
T COG2818 30 QRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLE 105 (188)
T ss_pred HHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHH
Confidence 34688888888777779999999999999988 699999999999999999999975 3 56667776766654
No 128
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=91.63 E-value=0.17 Score=45.60 Aligned_cols=154 Identities=14% Similarity=0.183 Sum_probs=86.4
Q ss_pred HHHHHHhhhcChhhHHHHHHHHHHhC-CCHHH-HHhCCHHHHHHHHhhcCcH--H--HHHHHHHHHHHhHHHhCCC---C
Q psy8564 14 WLSEIMLQQTQVNTVIPYYQRFLKKF-PNIMS-LAQAKLENVMELWSGLGYY--S--RARNLHICAKLVFFKYNGI---F 84 (341)
Q Consensus 14 lv~~il~qqt~~~~~~~~~~~l~~~~-pt~~~-la~~~~~~l~~~l~~~G~~--~--rA~~i~~~a~~i~~~~~g~---~ 84 (341)
+|+++++=- +++++.+..+++++.. ++|.+ +.+.++.++.+.+++.-|. + -...+....+.+..+||+- +
T Consensus 20 fiaA~lAyG-~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsLe~~f 98 (232)
T PF09674_consen 20 FIAALLAYG-NRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSLEEAF 98 (232)
T ss_pred HHHHHHHcc-CHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCHHHHH
Confidence 344443333 6677777777777665 45655 5666666676766665442 2 3556666666666666541 0
Q ss_pred ----c--cc--------hHHHhcC-------CCC----CH-------HHHHHHHHHHhCCe----------------eec
Q psy8564 85 ----P--KN--------FISLINL-------PGI----GQ-------STASAIRVFAYGKR----------------NAI 116 (341)
Q Consensus 85 ----p--~~--------~~~L~~l-------~GI----G~-------~tA~~il~~~~~~~----------------~~~ 116 (341)
. .+ .+.+.++ .++ .+ |--.++|.---.+. .+|
T Consensus 99 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~p~~~SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~LiiP 178 (232)
T PF09674_consen 99 AKGYNKSEDVLEAICAFIEEFFELPHSSRGYKHLFGLLPPPEKGSACKRLNMFLRWMVRKDSPVDFGLWSSIDPSDLIIP 178 (232)
T ss_pred HhhccCCCCHHHHHHHHHHHHHHhhcccccccccccccCCCCCCcHHHHHHHHHHhhccCCCCCCCcCCCCCCHHHcccc
Confidence 0 00 2223331 111 11 22334443322111 378
Q ss_pred cChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhh
Q psy8564 117 LDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGS 169 (341)
Q Consensus 117 vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~ 169 (341)
+|+||.|+.++|+.+......-++..++.+...++.|. +|-.+..||..+|.
T Consensus 179 LDtHv~~var~LGL~~rk~~d~k~A~elT~~lr~~~p~-DPvKYDFAL~~~Gi 230 (232)
T PF09674_consen 179 LDTHVFRVARKLGLLKRKSADWKAARELTEALREFDPD-DPVKYDFALFRLGI 230 (232)
T ss_pred chHhHHHHHHHcCCccCCCccHHHHHHHHHHHHhcCCC-CCcchhhhcccCCc
Confidence 99999999999966654333334455666666665554 78888888888775
No 129
>KOG0142|consensus
Probab=90.99 E-value=0.41 Score=41.65 Aligned_cols=124 Identities=14% Similarity=0.172 Sum_probs=68.0
Q ss_pred ceeEEEEEEEeCCEEEEEEeCCCCc-cccccc-----ccccccccchhhhccchhhhhHHHHHHHHHHhcCCc-cccc--
Q psy8564 209 NCSIIMFIVIDDDYVLFQKRSNKGI-WGGLLS-----FPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNYL-- 279 (341)
Q Consensus 209 ~~~~~~~ii~~~g~vLl~kR~~~g~-~~GlWE-----FPgvE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~~-- 279 (341)
.+-+.+++...+|+.||+||+..++ +.|+|. -|.-.++|-. .+.......|++|.+.-|+||. ....
T Consensus 52 HRaFSVFlFns~~~lLlQqRS~~KitFP~~~TNtccSHPL~~~~el~----~~d~lGVr~AAqRkL~~ELGIp~e~v~pe 127 (225)
T KOG0142|consen 52 HRAFSVFLFNSKNELLLQQRSDEKITFPGLWTNTCCSHPLYNPGELE----ENDALGVRRAAQRKLKAELGIPLEEVPPE 127 (225)
T ss_pred hheeeEEEecCcchHHHhhhccccccccchhhhhhhcCcCCChhhhc----cCchHHHHHHHHHHHHHhhCCCccccCHH
Confidence 3445667777889999999987653 566663 2332233211 1223445778999999999998 3322
Q ss_pred ---ccCcEEEEe-ece-----EEEEEEEEEE-ecccccccCCCCceeeeCCCCCC------CCCCHHHHHHHH
Q psy8564 280 ---ILPIISHKL-THL-----QFKIVPCHIF-LKKCFLKENKNNFIWYPIKKIKN------SPIPAPVRKILF 336 (341)
Q Consensus 280 ---~~~~~~h~~-~h~-----~~~l~~~~~~-~~~~~~~~~~~~~~W~~~~el~~------~~~~~a~~~il~ 336 (341)
+++.+.|.- |+. .+....|... +.-.+-..+-++++|++.+||.. ++|.|=.+-|.+
T Consensus 128 e~~~ltrihYkA~sdg~wGEhEiDYiL~~~~~~~~nPnpnEv~e~ryvs~eelkel~~~~~~~~TPWfkli~~ 200 (225)
T KOG0142|consen 128 EFNFLTRIHYKAPSDGIWGEHEIDYILFLVKDVTLNPNPNEVSEIRYVSREELKELVAKASAGFTPWFKLISE 200 (225)
T ss_pred HcccceeeeeecCCCCCcccceeeEEEEEeccCCCCCChhhhhHhheecHHHHHHHHhccccCCChHHHHHHH
Confidence 344443332 221 2221122111 11112112237899999999864 555555554443
No 130
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.59 E-value=0.3 Score=42.49 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=23.0
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGK 112 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~ 112 (341)
.+.+.|.++||||+|||+-+.+---++
T Consensus 105 ~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 105 GDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 478999999999999999998765554
No 131
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.55 E-value=0.3 Score=42.86 Aligned_cols=35 Identities=20% Similarity=0.184 Sum_probs=26.9
Q ss_pred HHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHHhCC
Q psy8564 71 ICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGK 112 (341)
Q Consensus 71 ~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~ 112 (341)
+++++|.+ .+.+.|.++||||+|||+-|.+---++
T Consensus 96 el~~aI~~-------~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 96 EFRDAIDR-------EDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred HHHHHHHh-------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 44555554 478999999999999999998765443
No 132
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=90.30 E-value=0.62 Score=40.82 Aligned_cols=24 Identities=33% Similarity=0.498 Sum_probs=17.4
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.+.+.|.++||||+++|+.|+..-
T Consensus 105 ~d~~~L~~v~Gig~k~A~~I~~~l 128 (192)
T PRK00116 105 GDVKALTKVPGIGKKTAERIVLEL 128 (192)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHH
Confidence 456777788888888888777543
No 133
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.13 E-value=0.34 Score=42.34 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=22.7
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGK 112 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~ 112 (341)
.+.+.|.++||||+|||+-|..---++
T Consensus 105 ~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 105 QDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 478999999999999999998665443
No 134
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=90.00 E-value=0.32 Score=43.67 Aligned_cols=55 Identities=16% Similarity=0.036 Sum_probs=36.8
Q ss_pred eeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhh
Q psy8564 114 NAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLPKKNIEIYTQGLMDFGS 169 (341)
Q Consensus 114 ~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~ 169 (341)
.+|+|+||.||.++|+.+......-++..++.+...++- +++|-.+..||..+|.
T Consensus 173 iiPLDtH~~rvar~LgL~~Rk~~d~kaa~ElT~~Lr~~d-p~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLLKRKSYDLKAAIEITEALRELN-PEDPIKYDFALFRLGQ 227 (229)
T ss_pred eeechHhHHHHHHHhCCcccCchhHHHHHHHHHHHHhcC-CCCCcchhhhcccCCc
Confidence 478999999999998544432222233445555555544 5578888888888885
No 135
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.69 E-value=0.41 Score=42.04 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=14.5
Q ss_pred hHHHhcCCCCCHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~ 107 (341)
...|.+++||||++|-.||+
T Consensus 72 F~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 72 FETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHhCCCCCCHHHHHHHHH
Confidence 45577777777777777776
No 136
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.54 E-value=0.4 Score=42.44 Aligned_cols=26 Identities=27% Similarity=0.312 Sum_probs=22.1
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
.+.+.|.++||||+|||+-|..---+
T Consensus 106 ~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 106 EDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred CCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 47899999999999999999865444
No 137
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.45 E-value=0.41 Score=42.15 Aligned_cols=26 Identities=23% Similarity=0.271 Sum_probs=22.0
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
.+...|.++||||+|||+-|..---+
T Consensus 104 ~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 104 GDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 47899999999999999999865444
No 138
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=89.44 E-value=0.4 Score=42.22 Aligned_cols=26 Identities=35% Similarity=0.544 Sum_probs=22.4
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
.+...|.++||||.|||.-+++---|
T Consensus 105 ~d~~~L~k~PGIGkKtAerivleLk~ 130 (201)
T COG0632 105 EDVKALSKIPGIGKKTAERIVLELKG 130 (201)
T ss_pred cChHhhhcCCCCCHHHHHHHHHHHhh
Confidence 47889999999999999999876544
No 139
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=89.34 E-value=0.68 Score=37.66 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=9.2
Q ss_pred chHHHhcCCCCCHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAI 105 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~i 105 (341)
+.++|.++||||+++.+.+
T Consensus 85 sveDL~~V~GIgekqk~~l 103 (132)
T PRK02515 85 SVEDVLNLPGLSERQKELL 103 (132)
T ss_pred CHHHHHcCCCCCHHHHHHH
Confidence 3455555555555444433
No 140
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.33 E-value=0.55 Score=42.00 Aligned_cols=59 Identities=14% Similarity=0.222 Sum_probs=42.3
Q ss_pred hCCHHHHHHHHhhcCcHHHHH-HHHHHHHHhHHHh---CC---CCccchHHHhcCCCCCHHHHHHHHH
Q psy8564 47 QAKLENVMELWSGLGYYSRAR-NLHICAKLVFFKY---NG---IFPKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 47 ~~~~~~l~~~l~~~G~~~rA~-~i~~~a~~i~~~~---~g---~~p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
..+..||.+++=+.|. +-+ ....+|+.+.+.| |+ -...+.++|++++|||+..|..++.
T Consensus 13 ~Lsd~ELLailL~~g~--~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a 78 (218)
T TIGR00608 13 ALSDYELLAIILRTGT--PKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKA 78 (218)
T ss_pred cCCHHHHHHHHHhCCC--CCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHH
Confidence 3466778777644554 444 7889999999988 44 1235689999999999977666653
No 141
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.31 E-value=0.42 Score=41.97 Aligned_cols=27 Identities=37% Similarity=0.529 Sum_probs=22.8
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGK 112 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~ 112 (341)
.+...|.++||||+|||+-+..---++
T Consensus 105 ~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 105 GDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 478999999999999999998765443
No 142
>COG4112 Predicted phosphoesterase (MutT family) [General function prediction only]
Probab=89.02 E-value=3.6 Score=34.68 Aligned_cols=111 Identities=14% Similarity=0.130 Sum_probs=57.2
Q ss_pred EEEEEEEeCCEEEEEEeCCCC---ccccccccc--c-cccccchhhhccchhhh-hHHHHHHHHHHhcCCc-cccc---c
Q psy8564 212 IIMFIVIDDDYVLFQKRSNKG---IWGGLLSFP--E-WILKDKIINFVDNNLKN-LIELEIKKFISSFGFI-KNYL---I 280 (341)
Q Consensus 212 ~~~~ii~~~g~vLl~kR~~~g---~~~GlWEFP--g-vE~~E~~~~~~~~~~~~-~~~a~~rE~~ee~g~~-~~~~---~ 280 (341)
.-+++|.+.++||+.+|..+| -+.|++..= | .-.++.. .+... +.--+.||+.||++++ ...+ .
T Consensus 63 IpYvvi~~edevliyeRltgggE~RLHn~~SlG~GGHmn~~~GA-----~s~~evLk~n~~REleEEv~vseqd~q~~e~ 137 (203)
T COG4112 63 IPYVVIMDEDEVLIYERLTGGGEKRLHNLYSLGIGGHMNEGDGA-----TSREEVLKGNLERELEEEVDVSEQDLQELEF 137 (203)
T ss_pred ccEEEEecCCEEEEEEeccCcchhhhccccccccccccccCCCc-----ccHHHHHccchHHHHHHHhCcCHHHhhhhee
Confidence 345567777899999998876 356666542 1 2222211 01111 1122579999999998 4333 3
Q ss_pred cCcEEEEe-eceEEEEEE-EEEEecc---cccccCCCCceeeeCCCCCC-CCC
Q psy8564 281 LPIISHKL-THLQFKIVP-CHIFLKK---CFLKENKNNFIWYPIKKIKN-SPI 327 (341)
Q Consensus 281 ~~~~~h~~-~h~~~~l~~-~~~~~~~---~~~~~~~~~~~W~~~~el~~-~~~ 327 (341)
++-+.-.- +-.+++|-+ |..+..- ...+.+--++.|+..++|.+ |+-
T Consensus 138 lGlINdd~neVgkVHiG~lf~~~~k~ndvevKEkd~~~~kwik~~ele~~y~~ 190 (203)
T COG4112 138 LGLINDDTNEVGKVHIGALFLGRGKFNDVEVKEKDLFEWKWIKLEELEKFYGV 190 (203)
T ss_pred eeeecCCCcccceEEEEEEEEeeccccceeeeecceeeeeeeeHHHHHHHhhh
Confidence 33332211 112344332 2233221 11111114679999999988 443
No 143
>PRK00024 hypothetical protein; Reviewed
Probab=88.81 E-value=0.61 Score=41.94 Aligned_cols=59 Identities=12% Similarity=0.298 Sum_probs=42.3
Q ss_pred hCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCC---CccchHHHhcCCCCCHHHHHHHHH
Q psy8564 47 QAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGI---FPKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 47 ~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~---~p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
..+..||.+++=+.|. +-+....+|+.+.++||+- ...+.++|.+++|||+..|..++.
T Consensus 23 ~Lsd~ELLa~lL~~g~--~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a 84 (224)
T PRK00024 23 ALSDAELLAILLRTGT--KGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKA 84 (224)
T ss_pred cCCHHHHHHHHHcCCC--CCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHH
Confidence 3466778777644444 4456788999999888652 235689999999999988866644
No 144
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=88.49 E-value=0.24 Score=43.01 Aligned_cols=29 Identities=24% Similarity=0.397 Sum_probs=23.4
Q ss_pred ccchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 85 PKNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 85 p~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
...++.|.+|||||+|+|.-+..+-++++
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 34578899999999999998877766654
No 145
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.85 E-value=0.5 Score=41.36 Aligned_cols=28 Identities=32% Similarity=0.452 Sum_probs=22.8
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
...+.|.+|||||+|+|.-+..+-+..+
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 3567899999999999998877776654
No 146
>PRK00076 recR recombination protein RecR; Reviewed
Probab=87.74 E-value=0.5 Score=41.43 Aligned_cols=28 Identities=29% Similarity=0.437 Sum_probs=23.1
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
...+.|.+|||||+|+|.-+..+-+..+
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~~ll~~~ 35 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAFHLLQRD 35 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 4567899999999999998888776654
No 147
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.67 E-value=0.48 Score=41.61 Aligned_cols=23 Identities=43% Similarity=0.492 Sum_probs=19.9
Q ss_pred cchHHHhcCCCCCHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
.+.+.|.++||||+|||+-|..-
T Consensus 105 ~D~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 105 GNAELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHH
Confidence 47889999999999999996643
No 148
>PRK13844 recombination protein RecR; Provisional
Probab=87.63 E-value=0.28 Score=43.03 Aligned_cols=28 Identities=25% Similarity=0.432 Sum_probs=22.9
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
...+.|.+|||||+|+|.-+..+-+..+
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 39 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLALYLLDKS 39 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 4567899999999999998887776654
No 149
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=87.40 E-value=0.57 Score=33.32 Aligned_cols=24 Identities=38% Similarity=0.497 Sum_probs=18.6
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.+.++|.++||||++.|..|+.+=
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHH
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHH
Confidence 357899999999999999999774
No 150
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.27 E-value=0.55 Score=40.96 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=20.8
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
.+.+.| ++||||+|||+-|+.---+
T Consensus 105 ~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 105 EDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred CCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 367889 9999999999999865544
No 151
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=86.97 E-value=0.62 Score=40.81 Aligned_cols=43 Identities=40% Similarity=0.500 Sum_probs=26.3
Q ss_pred hHHHhcCCCCCHHHHHHHHHHHhCCe-e--eccChhHHHHHHHHhccc
Q psy8564 88 FISLINLPGIGQSTASAIRVFAYGKR-N--AILDGNVKRILIRVLGIN 132 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~~~~~-~--~~vD~~v~Rvl~Rl~~~~ 132 (341)
...|.++|||||++|..++.. |+.. . .+.+....+ +.++-|+.
T Consensus 72 f~~L~~i~GIGpk~A~~il~~-fg~~~l~~~i~~~d~~~-L~~v~Gig 117 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSG-LSPEELVQAIANGDVKA-LTKVPGIG 117 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHh-CCHHHHHHHHHhCCHHH-HHhCCCCC
Confidence 457889999999999998653 3422 1 144444444 34444544
No 152
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=86.86 E-value=0.57 Score=35.39 Aligned_cols=41 Identities=22% Similarity=0.175 Sum_probs=29.2
Q ss_pred HHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccC
Q psy8564 89 ISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINC 133 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~ 133 (341)
+.|+++||||+-||..++....+...|.-..+ +..+.|+..
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~----l~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQ----LASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchh----hhhcccccc
Confidence 45889999999999999998855445554444 344456654
No 153
>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=86.70 E-value=0.43 Score=33.29 Aligned_cols=43 Identities=23% Similarity=0.437 Sum_probs=28.2
Q ss_pred hHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcc
Q psy8564 88 FISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGI 131 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~ 131 (341)
.++|.++||||+++|..+...+++-..-+.+..... +..+-|+
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~-L~~i~Gi 46 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEE-LAEIPGI 46 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHH-HHTSTTS
T ss_pred HHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHH-HhcCCCC
Confidence 568999999999999999888766432233333332 3334444
No 154
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=86.53 E-value=3.9 Score=38.41 Aligned_cols=61 Identities=25% Similarity=0.345 Sum_probs=39.4
Q ss_pred HHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHH---hCCeeeccChhHHHHHHHHhcccC
Q psy8564 67 RNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFA---YGKRNAILDGNVKRILIRVLGINC 133 (341)
Q Consensus 67 ~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~---~~~~~~~vD~~v~Rvl~Rl~~~~~ 133 (341)
+.+.++...+.+ .-|.+.++|+.++||||+|.-++.+.+ +|.+.---|-- |..--++|-++
T Consensus 251 ~~~~~~l~~~~e----~~p~~feeLL~~~GvGp~TlRALaLvaelIyg~p~s~~DPa--kfsfA~GGKDG 314 (319)
T PF05559_consen 251 RRLWKVLEKAYE----RQPSDFEELLLIKGVGPSTLRALALVAELIYGVPPSFRDPA--KFSFAHGGKDG 314 (319)
T ss_pred HHHHHHHHHHhh----CCccCHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCccChh--HHHHhhcCCCC
Confidence 334444444433 358899999999999999999988877 66542222221 55555555443
No 155
>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=86.03 E-value=1 Score=36.30 Aligned_cols=59 Identities=24% Similarity=0.469 Sum_probs=34.0
Q ss_pred HHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHH
Q psy8564 42 IMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 42 ~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
+-+|-.|+.++|.. +.++|- .+|+.|.+--+. .|.+ .+.++|.+++|||+++++-+.-+
T Consensus 59 ~iniNtA~~~eL~~-lpGIG~-~~A~~Ii~~R~~-----~g~f-~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 59 AVNINAASLEELQA-LPGIGP-AKAKAIIEYREE-----NGAF-KSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhc-CCCCCH-HHHHHHHHHHHh-----cCCc-CCHHHHHcCCCCCHHHHHHHHhc
Confidence 34455666767644 345553 345555444332 1222 46788888888888887766543
No 156
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.02 E-value=1 Score=39.13 Aligned_cols=76 Identities=22% Similarity=0.255 Sum_probs=43.5
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCC-eeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCC----CCCHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGK-RNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLP----KKNIEIYT 161 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~-~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p----~~~~~~~~ 161 (341)
.+.|.++.|||||+|=+||+- ..+. ...+...++ ..+.++-|+. ++..++.+-++-+++.. .+...+.-
T Consensus 72 F~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~-~~L~~vpGIG----kKtAeRIilELkdK~~~~~~~~~~~~ea~ 146 (183)
T PRK14601 72 FEMLLKVNGIGANTAMAVCSSLDVNSFYKALSLGDE-SVLKKVPGIG----PKSAKRIIAELSDAKTKLENVSDDKSEAL 146 (183)
T ss_pred HHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCH-HHHhhCCCCC----HHHHHHHHHHHHHHhhccCCCCccHHHHH
Confidence 567999999999999999974 2222 122333333 3456765654 34444555555555411 11234555
Q ss_pred HHHHHHh
Q psy8564 162 QGLMDFG 168 (341)
Q Consensus 162 ~~l~~~G 168 (341)
.+|+.+|
T Consensus 147 ~AL~~LG 153 (183)
T PRK14601 147 AALLTLG 153 (183)
T ss_pred HHHHHcC
Confidence 6666666
No 157
>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=85.94 E-value=0.82 Score=35.06 Aligned_cols=28 Identities=25% Similarity=0.531 Sum_probs=23.4
Q ss_pred chHHHhcCCCCCHHHHHHHHHHHhCCee
Q psy8564 87 NFISLINLPGIGQSTASAIRVFAYGKRN 114 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~~~~~~ 114 (341)
...+|..|||||+.+|.-+...++..+.
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~~ 37 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSPA 37 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCHH
Confidence 4678999999999999999888876553
No 158
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=85.26 E-value=0.76 Score=38.56 Aligned_cols=23 Identities=39% Similarity=0.507 Sum_probs=21.0
Q ss_pred chHHHhcCCCCCHHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+.++|..|||||++.|.+|..+-
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHH
Confidence 47899999999999999999876
No 159
>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=85.20 E-value=1 Score=39.48 Aligned_cols=25 Identities=24% Similarity=0.495 Sum_probs=20.9
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHh
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAY 110 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~ 110 (341)
.+...|.++||||+|||+-|+.---
T Consensus 104 ~d~~~L~~ipGiGkKtAerIileLk 128 (191)
T TIGR00084 104 EEVKALVKIPGVGKKTAERLLLELK 128 (191)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4678899999999999999985433
No 160
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.55 E-value=1.2 Score=39.01 Aligned_cols=76 Identities=21% Similarity=0.228 Sum_probs=42.8
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCCe-eeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCC-----CCCHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGKR-NAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLP-----KKNIEIY 160 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~~-~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p-----~~~~~~~ 160 (341)
.+.|.++.|||||+|=+||+. ....- ..+....+ ..+.++-|+. .+..++.+-++-.++.. .....+.
T Consensus 72 F~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~-~~L~~vpGIG----kKtAerIilELkdK~~~~~~~~~~~~~e~ 146 (188)
T PRK14606 72 FLSLTKVSRLGPKTALKIISNEDAETLVTMIASQDV-EGLSKLPGIS----KKTAERIVMELKDEFESAGIKDMRIYHES 146 (188)
T ss_pred HHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCH-HHHhhCCCCC----HHHHHHHHHHHHHhhccccCCCcccHHHH
Confidence 567899999999999999964 33321 22222222 4456765654 33444555555454421 1123455
Q ss_pred HHHHHHHh
Q psy8564 161 TQGLMDFG 168 (341)
Q Consensus 161 ~~~l~~~G 168 (341)
-.+|+.+|
T Consensus 147 ~~AL~~LG 154 (188)
T PRK14606 147 LEALVSLG 154 (188)
T ss_pred HHHHHHcC
Confidence 56666665
No 161
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=84.54 E-value=1.7 Score=38.79 Aligned_cols=57 Identities=16% Similarity=0.256 Sum_probs=41.9
Q ss_pred CCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCC---CCccchHHHhcCCCCCHHHHHHHH
Q psy8564 48 AKLENVMELWSGLGYYSRARNLHICAKLVFFKYNG---IFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 48 ~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g---~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
.+..||.+++=.-|- |-+..+.+|+.+..+||+ -...+.++|+++||||+..|--+.
T Consensus 24 Lsd~ELLailLrtG~--~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~ 83 (224)
T COG2003 24 LSDAELLAILLRTGT--KGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIK 83 (224)
T ss_pred cchHHHHHHHHhcCC--CCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHH
Confidence 456777777655554 455789999999999876 235679999999999986554443
No 162
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=84.49 E-value=2.5 Score=29.95 Aligned_cols=52 Identities=27% Similarity=0.386 Sum_probs=30.1
Q ss_pred HHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHH
Q psy8564 45 LAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAI 105 (341)
Q Consensus 45 la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~i 105 (341)
|-.|+.+||..+ -|+. ..|+.|.+.-+.. |.+ .+.++|.+++|||+++.+-+
T Consensus 8 iN~as~~eL~~l---pgi~~~~A~~Iv~~R~~~-----G~f-~s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQAL---PGIGPKQAKAIVEYREKN-----GPF-KSLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTS---TT--HHHHHHHHHHHHHH------S--SSGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHc---CCCCHHHHHHHHHHHHhC-----cCC-CCHHHHhhCCCCCHHHHHHH
Confidence 345677776432 2555 4677777655443 333 46899999999999998765
No 163
>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=84.46 E-value=0.94 Score=36.53 Aligned_cols=23 Identities=39% Similarity=0.596 Sum_probs=20.8
Q ss_pred chHHHhcCCCCCHHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+.++|.++||||+++|..|+.+-
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 47899999999999999999875
No 164
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.88 E-value=1.5 Score=38.46 Aligned_cols=59 Identities=27% Similarity=0.336 Sum_probs=35.1
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCCe-eeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhh
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGKR-NAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDL 151 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~~-~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~ 151 (341)
.+.|.++.|||||+|=+||+- ....- ..+.... ...+.++-|+. .+..++.+-++-.++
T Consensus 71 F~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~D-~~~L~~vpGIG----kKtAeRIIlELkdKl 131 (196)
T PRK13901 71 FEELIGVDGIGPRAALRVLSGIKYNEFRDAIDRED-IELISKVKGIG----NKMAGKIFLKLRGKL 131 (196)
T ss_pred HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCC-HHHHhhCCCCC----HHHHHHHHHHHHHhh
Confidence 567999999999999999974 22221 2222222 24456665554 344455555555554
No 165
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.67 E-value=1.5 Score=38.65 Aligned_cols=44 Identities=27% Similarity=0.454 Sum_probs=28.8
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCCe-eeccChhHHHHHHHHhccc
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGKR-NAILDGNVKRILIRVLGIN 132 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~~-~~~vD~~v~Rvl~Rl~~~~ 132 (341)
.+.|.++.|||||+|=+||+. ..+.- ..+...++ ..++++-|+.
T Consensus 71 F~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~-~~L~kvpGIG 116 (197)
T PRK14603 71 FELLLGVSGVGPKLALALLSALPPALLARALLEGDA-RLLTSASGVG 116 (197)
T ss_pred HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCH-HHHhhCCCCC
Confidence 567899999999999999984 44332 23333333 3456665654
No 166
>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=83.51 E-value=0.79 Score=27.77 Aligned_cols=16 Identities=31% Similarity=0.517 Sum_probs=12.3
Q ss_pred HHhcCCCCCHHHHHHH
Q psy8564 90 SLINLPGIGQSTASAI 105 (341)
Q Consensus 90 ~L~~l~GIG~~tA~~i 105 (341)
.+.+++|||++|+.-+
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 3668999999999864
No 167
>PRK07945 hypothetical protein; Provisional
Probab=83.29 E-value=2.6 Score=40.23 Aligned_cols=58 Identities=26% Similarity=0.257 Sum_probs=37.8
Q ss_pred HHHHHHHhhcCcHH-HHHHHHHHHHHhHHHhCCC-Cccc-hH-HHhcCCCCCHHHHHHHHHHH
Q psy8564 51 ENVMELWSGLGYYS-RARNLHICAKLVFFKYNGI-FPKN-FI-SLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 51 ~~l~~~l~~~G~~~-rA~~i~~~a~~i~~~~~g~-~p~~-~~-~L~~l~GIG~~tA~~il~~~ 109 (341)
+++..++.-.|=.. |++.-+++|+.|.. .+.+ +... .+ .|.+|||||.-+|+.|.-+.
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~ 69 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA-LDAAERARRARAGSLTSLPGIGPKTAKVIAQAL 69 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cChhHHHHHHhcCCcccCCCcCHHHHHHHHHHH
Confidence 34555555566332 78888888888754 2222 1111 11 68899999999999988775
No 168
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.92 E-value=1 Score=39.23 Aligned_cols=57 Identities=23% Similarity=0.287 Sum_probs=33.2
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCC-eeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHh
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGK-RNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAID 150 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~-~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~ 150 (341)
.+.|.++.|||||+|=.+|+. .... -..+.-..+ ..+ ++-|+. .+..++.+-++-.+
T Consensus 72 F~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~-~~L-~vpGIG----kKtAerIilELk~K 130 (186)
T PRK14600 72 LRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVNEDK-AAL-KVNGIG----EKLINRIITELQYK 130 (186)
T ss_pred HHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHcCCH-hhe-ECCCCc----HHHHHHHHHHHHHH
Confidence 467899999999999999984 3332 123333333 233 555554 33444444444444
No 169
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.15 E-value=1.8 Score=38.21 Aligned_cols=58 Identities=28% Similarity=0.321 Sum_probs=34.4
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCCe-eeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHh
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGKR-NAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAID 150 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~~-~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~ 150 (341)
...|.++.|||||+|=.||+. ....- ..+...++ ..+.++-|+. .+..++.+-++-.+
T Consensus 73 F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~-~~L~~ipGIG----kKtAerIilELkdK 132 (203)
T PRK14602 73 FIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDV-AALTRVSGIG----KKTAQHIFLELKYK 132 (203)
T ss_pred HHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCH-HHHhcCCCcC----HHHHHHHHHHHHHh
Confidence 467899999999999999985 33321 23333333 3456665654 33344444444333
No 170
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.82 E-value=1.8 Score=38.00 Aligned_cols=58 Identities=29% Similarity=0.311 Sum_probs=34.5
Q ss_pred hHHHhcCCCCCHHHHHHHHHHH-hCCe-eeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHh
Q psy8564 88 FISLINLPGIGQSTASAIRVFA-YGKR-NAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAID 150 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~-~~~~-~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~ 150 (341)
...|.++.|||||+|=.||+.. .+.- ..+...++ ..++++-|+. ++..++.+-++-.+
T Consensus 72 F~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~-~~L~kvpGIG----kKtAerIilELk~K 131 (195)
T PRK14604 72 FELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDV-ARLARVPGIG----KKTAERIVLELKGK 131 (195)
T ss_pred HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCH-HHHhhCCCCC----HHHHHHHHHHHHHH
Confidence 5679999999999999999842 3321 22333333 4456766665 33344444444443
No 171
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=80.39 E-value=1.4 Score=35.79 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=22.9
Q ss_pred HhCCCCc---cchHHHhcCCCCCHHHHHHHHH
Q psy8564 79 KYNGIFP---KNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 79 ~~~g~~p---~~~~~L~~l~GIG~~tA~~il~ 107 (341)
.+++.+. .+.++|.++|||||..|..|..
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHH
Confidence 3455443 4578899999999999999994
No 172
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=79.79 E-value=5.1 Score=38.24 Aligned_cols=55 Identities=18% Similarity=0.227 Sum_probs=36.7
Q ss_pred HHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 53 VMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 53 l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+.++++-.|=. .|+++..++|..|.. +...+ .+.++|.+|||||+.+|+-|--+.
T Consensus 13 la~l~el~gen~~k~~ay~~Aa~~i~~-l~~~i-~~~~~l~~lpgIG~~ia~kI~Eil 68 (334)
T smart00483 13 LAENYEVFGENKRKCSYFRKAASVLKS-LPFPI-NSMKDLKGLPGIGDKIKKKIEEII 68 (334)
T ss_pred HHHHHHHhcccHHHHHHHHHHHHHHHh-CCCCC-CCHHHHhcCCCccHHHHHHHHHHH
Confidence 33444434422 367777788877754 22223 346789999999999999998664
No 173
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=79.50 E-value=1.5 Score=27.32 Aligned_cols=17 Identities=29% Similarity=0.391 Sum_probs=13.7
Q ss_pred HhcCCCCCHHHHHHHHH
Q psy8564 91 LINLPGIGQSTASAIRV 107 (341)
Q Consensus 91 L~~l~GIG~~tA~~il~ 107 (341)
+-.+||||++||--++.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 34689999999987764
No 174
>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=79.33 E-value=1.5 Score=38.35 Aligned_cols=21 Identities=38% Similarity=0.479 Sum_probs=18.2
Q ss_pred hHHHhcCCCCCHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~ 108 (341)
...|++++|||||+|-.+|+.
T Consensus 71 F~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 71 FKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred HHHHhCCCCCCHHHHHHHHhc
Confidence 567999999999999999664
No 175
>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=78.76 E-value=7.5 Score=40.63 Aligned_cols=70 Identities=20% Similarity=0.280 Sum_probs=42.0
Q ss_pred HHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCc-cchHHHhcCCCCCHHHHHHHH
Q psy8564 31 YYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFP-KNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 31 ~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p-~~~~~L~~l~GIG~~tA~~il 106 (341)
.++.|++.. -++++|..+..++|.++ . ||. ..|.+|.+..+.-.. .| ...-..+.|||||+++|..++
T Consensus 444 ~i~~L~~~g~I~~~~Dl~~L~~~~L~~L-~--GfG~Ksa~nIl~~Ie~sk~-----~~l~r~L~aLgIpgVG~~~ak~L~ 515 (652)
T TIGR00575 444 VIEQLFEKKLVRSVADLYALKKEDLLEL-E--GFGEKSAQNLLNAIEKSKE-----KPLARLLFALGIRHVGEVTAKNLA 515 (652)
T ss_pred HHHHHHHcCCcCCHHHHHhcCHHHHhhc-c--CccHHHHHHHHHHHHHhcc-----CcHHHHHhhccCCCcCHHHHHHHH
Confidence 445566543 48999998888777543 3 554 356666666554322 12 123334478888888887666
Q ss_pred HH
Q psy8564 107 VF 108 (341)
Q Consensus 107 ~~ 108 (341)
..
T Consensus 516 ~~ 517 (652)
T TIGR00575 516 KH 517 (652)
T ss_pred HH
Confidence 43
No 176
>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=78.53 E-value=1.7 Score=29.57 Aligned_cols=23 Identities=17% Similarity=0.117 Sum_probs=16.1
Q ss_pred HHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 89 ISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
..+.++.|||+.||.-....++.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--
T ss_pred cchhhcccccHHHHHHHHHhCCC
Confidence 56889999999999998775543
No 177
>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=78.52 E-value=4.9 Score=37.89 Aligned_cols=43 Identities=23% Similarity=0.291 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 65 RARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 65 rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
|++.-.++|..|.. +.-.+ .+.+++.+|||||+++|+.|--+.
T Consensus 23 r~~aY~~Aa~~l~~-l~~~i-~~~~~~~~ipgiG~~ia~kI~E~~ 65 (307)
T cd00141 23 RVRAYRKAARALES-LPEPI-ESLEEAKKLPGIGKKIAEKIEEIL 65 (307)
T ss_pred hHHHHHHHHHHHHh-CCccc-CCHHHhcCCCCccHHHHHHHHHHH
Confidence 66666666666654 22222 345566777777777777776654
No 178
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=78.22 E-value=5.7 Score=38.02 Aligned_cols=47 Identities=21% Similarity=0.338 Sum_probs=33.3
Q ss_pred HHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHH
Q psy8564 30 PYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFF 78 (341)
Q Consensus 30 ~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~ 78 (341)
+..+++.++|.|.+.+.+|+.++|.+. +|+| ..||+.|++.++.+.+
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~V-eGIG-e~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEV-EGIG-EVRARAIREGLSRLAE 344 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhC-CCcC-HHHHHHHHHHHHHHHH
Confidence 455677788888888888888887544 5555 3477777777777665
No 179
>KOG4548|consensus
Probab=78.20 E-value=3.9 Score=36.95 Aligned_cols=96 Identities=13% Similarity=0.098 Sum_probs=51.4
Q ss_pred CCEEEEEEeCCCCcccccccccc--c-ccccchhhhccchhhhhHHHHHHHHHHhcCC---c--ccccccCcEEEEeece
Q psy8564 220 DDYVLFQKRSNKGIWGGLLSFPE--W-ILKDKIINFVDNNLKNLIELEIKKFISSFGF---I--KNYLILPIISHKLTHL 291 (341)
Q Consensus 220 ~g~vLl~kR~~~g~~~GlWEFPg--v-E~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~---~--~~~~~~~~~~h~~~h~ 291 (341)
..=|||.+|+-|. .+.|-||. + +.+++. .....|++..-.|= + ....+++...|.++.-
T Consensus 138 r~LyLLV~~k~g~--~s~w~fP~~~~s~~~~~l-----------r~~ae~~Lk~~~ge~~~t~fvgnaP~g~~~~q~pr~ 204 (263)
T KOG4548|consen 138 RKLYLLVKRKFGK--SSVWIFPNRQFSSSEKTL-----------RGHAERDLKVLSGENKSTWFVGNAPFGHTPLQSPRE 204 (263)
T ss_pred ceEEEEEeeccCc--cceeeCCCcccCCccchH-----------HHHHHHHHHHHhcchhhhheeccCccccccccCccc
Confidence 3457777775333 35999999 4 445543 33334444433332 2 2234566556666432
Q ss_pred E-------EEEEEEEEEeccc--ccccCCCCceeeeCCCCCCCCCC
Q psy8564 292 Q-------FKIVPCHIFLKKC--FLKENKNNFIWYPIKKIKNSPIP 328 (341)
Q Consensus 292 ~-------~~l~~~~~~~~~~--~~~~~~~~~~W~~~~el~~~~~~ 328 (341)
. -++.+|.+.+... .......++.|++-++|.++-=+
T Consensus 205 ~~~e~~~~sk~ff~k~~lv~~~~~kn~n~edfvWvTkdel~e~l~~ 250 (263)
T KOG4548|consen 205 MTTEEPVSSKVFFFKASLVANSNQKNQNKEDFVWVTKDELGEKLPK 250 (263)
T ss_pred ccccccccceeEEeeeeeccccchhcccccceEEechHHHhhhcch
Confidence 2 2345566665431 11111246999999999886433
No 180
>PRK00024 hypothetical protein; Reviewed
Probab=78.11 E-value=10 Score=34.11 Aligned_cols=63 Identities=21% Similarity=0.327 Sum_probs=48.0
Q ss_pred HHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHH---HHHHHHHhH
Q psy8564 13 IWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARN---LHICAKLVF 77 (341)
Q Consensus 13 ~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~---i~~~a~~i~ 77 (341)
.|+..+|..-++-..+.+...++.++|.+..++.+++.+++.+ ++|+|- .||.. +.++++.+.
T Consensus 28 ELLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~-i~GIG~-akA~~L~a~~El~~R~~ 93 (224)
T PRK00024 28 ELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQS-IKGIGP-AKAAQLKAALELARRIL 93 (224)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhh-ccCccH-HHHHHHHHHHHHHHHHH
Confidence 4677788888888889999999999999999999999999976 467774 34443 444444443
No 181
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=76.70 E-value=8.2 Score=40.42 Aligned_cols=42 Identities=19% Similarity=0.243 Sum_probs=25.3
Q ss_pred HHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHH
Q psy8564 31 YYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKL 75 (341)
Q Consensus 31 ~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~ 75 (341)
.++.|.+.. -++++|..+..++|..+ . ||. .+|.+|.+..+.
T Consensus 457 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~ll~~Ie~ 501 (665)
T PRK07956 457 IIEQLFEKGLIHDPADLFKLTAEDLLGL-E--GFGEKSAQNLLDAIEK 501 (665)
T ss_pred HHHHHHHcCCCCCHHHHHhcCHHHHhcC-c--CcchHHHHHHHHHHHH
Confidence 344555542 58899988887776433 2 565 356666655543
No 182
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=75.94 E-value=4.2 Score=34.11 Aligned_cols=55 Identities=24% Similarity=0.390 Sum_probs=36.6
Q ss_pred HHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHH
Q psy8564 45 LAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 45 la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
|-.|+.+|| +.+.|+|- .+|+.|++--+ ++ |.+ .+.++|...+|||+++.+-...
T Consensus 91 iNtAs~eeL-~~lpgIG~-~kA~aIi~yRe----~~-G~f-~sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEEL-QALPGIGP-KKAQAIIDYRE----EN-GPF-KSVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHH-HHCCCCCH-HHHHHHHHHHH----Hc-CCC-CcHHHHHhccCCCHHHHHHHHh
Confidence 446778888 66777773 35555544332 22 333 5789999999999999775543
No 183
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=73.52 E-value=1 Score=32.29 Aligned_cols=48 Identities=19% Similarity=0.208 Sum_probs=28.9
Q ss_pred HhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHH
Q psy8564 57 WSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 57 l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
+..+|++.||.+...-+..-.= +.-+--+.++|++++|+|+++.+-|.
T Consensus 14 I~~L~LS~Ra~n~L~~~~I~tv--~dL~~~s~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 14 IEDLGLSVRAYNCLKRAGIHTV--GDLVKYSEEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGGSTSBHHHHHHHHCTT--BH--HHHHCS-HHHHHTSTTSHHHHHHHHH
T ss_pred HHHhCCCHHHHHHHHHhCCcCH--HHHHhCCHHHHHhCCCCCHhHHHHHH
Confidence 3557888787765544321100 00112356899999999999988764
No 184
>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=73.47 E-value=3.6 Score=29.38 Aligned_cols=23 Identities=26% Similarity=0.369 Sum_probs=20.0
Q ss_pred chHHHhc-CCCCCHHHHHHHHHHH
Q psy8564 87 NFISLIN-LPGIGQSTASAIRVFA 109 (341)
Q Consensus 87 ~~~~L~~-l~GIG~~tA~~il~~~ 109 (341)
..++|.. +||||+++|..|+.+=
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHHH
Confidence 4678888 9999999999999873
No 185
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.18 E-value=17 Score=32.54 Aligned_cols=55 Identities=25% Similarity=0.301 Sum_probs=43.5
Q ss_pred HHHHHHHhhhcChh-hHHHHHHHHHHhC---CCHHHHHhCCHHHHHHHHhhcCcHHHHHHH
Q psy8564 13 IWLSEIMLQQTQVN-TVIPYYQRFLKKF---PNIMSLAQAKLENVMELWSGLGYYSRARNL 69 (341)
Q Consensus 13 ~lv~~il~qqt~~~-~~~~~~~~l~~~~---pt~~~la~~~~~~l~~~l~~~G~~~rA~~i 69 (341)
.|++.+|..-++.. .+.+...++.++| ++...|.+++.+||.+ ++|+|-. ||-.|
T Consensus 18 ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~-i~GiG~a-ka~~l 76 (218)
T TIGR00608 18 ELLAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSS-VPGIGEA-KAIQL 76 (218)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHh-CcCCcHH-HHHHH
Confidence 46777777777777 8999999999999 8999999999999976 4777742 44444
No 186
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=72.25 E-value=8.9 Score=30.91 Aligned_cols=75 Identities=21% Similarity=0.212 Sum_probs=45.3
Q ss_pred CCHHHHHhCCHHHHHH--HHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHHhCCeeecc
Q psy8564 40 PNIMSLAQAKLENVME--LWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKRNAIL 117 (341)
Q Consensus 40 pt~~~la~~~~~~l~~--~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~~~~v 117 (341)
-|+++|.+.+.+...+ +....|.. +++|.+.. .+..|..+||||+..|..++--++.-..-..
T Consensus 17 ~t~~~Ll~~~~~~~~r~~La~~~~i~--~~~l~~w~-------------~~AdL~ri~gi~~~~a~LL~~AGv~Tv~~LA 81 (122)
T PF14229_consen 17 KTTGDLLEAGDTPLGRKALAKKLGIS--ERNLLKWV-------------NQADLMRIPGIGPQYAELLEHAGVDTVEELA 81 (122)
T ss_pred CcHHHHHHcCCCHHHHHHHHHhcCCC--HHHHHHHH-------------hHHHhhhcCCCCHHHHHHHHHhCcCcHHHHH
Confidence 5777777777766555 44445542 22333222 3566788999999999888777765432234
Q ss_pred ChhHHHHHHHHh
Q psy8564 118 DGNVKRILIRVL 129 (341)
Q Consensus 118 D~~v~Rvl~Rl~ 129 (341)
..+..++..++.
T Consensus 82 ~~~p~~L~~~l~ 93 (122)
T PF14229_consen 82 QRNPQNLHQKLG 93 (122)
T ss_pred hCCHHHHHHHHH
Confidence 455555555553
No 187
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=72.24 E-value=16 Score=38.32 Aligned_cols=39 Identities=18% Similarity=0.301 Sum_probs=22.0
Q ss_pred HHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHH
Q psy8564 31 YYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-SRARNLHIC 72 (341)
Q Consensus 31 ~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~ 72 (341)
.++.|++.- -++.+|..++.++|.++ =||. .+|.+|.+.
T Consensus 448 ~i~~L~~~G~i~~~~Dly~L~~~~l~~l---~g~geksa~nl~~~ 489 (669)
T PRK14350 448 TIEFLFEKKFISSEIDLYTFNFDRLINL---KGFKDKRINNLKRS 489 (669)
T ss_pred HHHHHHHcCCcCCHHHHhhCCHHHHhhc---cCccHHHHHHHHHH
Confidence 455566542 47777777777666443 2554 345555543
No 188
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=71.22 E-value=4.6 Score=38.63 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=25.0
Q ss_pred HHHHHhHHHhCC---CCccchHHHhcCCCCCHHHHHHH
Q psy8564 71 ICAKLVFFKYNG---IFPKNFISLINLPGIGQSTASAI 105 (341)
Q Consensus 71 ~~a~~i~~~~~g---~~p~~~~~L~~l~GIG~~tA~~i 105 (341)
.+|+.++++||+ -+..+.++|.+++|||++.|..|
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHH
Confidence 457777777764 23456788888888888888763
No 189
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=70.87 E-value=21 Score=31.99 Aligned_cols=66 Identities=17% Similarity=0.275 Sum_probs=53.5
Q ss_pred HHHHHHHHhhhcChhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHH--HHHHHHHHHHHhHH
Q psy8564 12 YIWLSEIMLQQTQVNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYS--RARNLHICAKLVFF 78 (341)
Q Consensus 12 ~~lv~~il~qqt~~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~--rA~~i~~~a~~i~~ 78 (341)
..|++.+|.--|.-..+.+..+++...|.+...|..++.+++... +|+|-.. -.+.+.++++.+..
T Consensus 27 ~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v-~GiG~aka~~l~a~~El~~R~~~ 94 (224)
T COG2003 27 AELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSV-KGIGLAKAIQIKAAIELGKRILA 94 (224)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhC-CCccHHHHHHHHHHHHHHHHHHH
Confidence 457888888888999999999999999999999999999999654 7888542 44556666766665
No 190
>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=70.82 E-value=2.7 Score=30.77 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=16.7
Q ss_pred hHHHhcCCCCCHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~ 108 (341)
-+.+-.+||||++||.-++.-
T Consensus 21 ~D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 21 SDNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cccCCCCCcccHHHHHHHHHH
Confidence 344557999999999998865
No 191
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=70.30 E-value=11 Score=35.92 Aligned_cols=29 Identities=45% Similarity=0.841 Sum_probs=25.0
Q ss_pred ccchHHHhcCCCCCHHHHHHHHHHH---hCCe
Q psy8564 85 PKNFISLINLPGIGQSTASAIRVFA---YGKR 113 (341)
Q Consensus 85 p~~~~~L~~l~GIG~~tA~~il~~~---~~~~ 113 (341)
|.+.++|+-+||||++|+-+..+.| +|.+
T Consensus 274 p~Df~elLl~~GiGpstvRALalVAEvIyg~~ 305 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVAEVIYGEP 305 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHHHHHhCCC
Confidence 6789999999999999999888876 6654
No 192
>PF14443 DBC1: DBC1
Probab=70.23 E-value=21 Score=28.98 Aligned_cols=51 Identities=24% Similarity=0.174 Sum_probs=33.3
Q ss_pred EEEEEEeCC-CCcccccccccccccccchhhhccchhhhhHHHHHHHHHHhcCCc-ccc
Q psy8564 222 YVLFQKRSN-KGIWGGLLSFPEWILKDKIINFVDNNLKNLIELEIKKFISSFGFI-KNY 278 (341)
Q Consensus 222 ~vLl~kR~~-~g~~~GlWEFPgvE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~-~~~ 278 (341)
+||+.+|.. -.-.||-|. |.++.+... .+...+..+++|-.++-+||+ ...
T Consensus 9 kFlv~~k~ke~~aiGG~Ws-psLDG~DP~-----~dp~~LI~TAiR~~K~~tgiDLS~C 61 (126)
T PF14443_consen 9 KFLVGKKDKEIMAIGGPWS-PSLDGGDPS-----SDPSVLIRTAIRTCKALTGIDLSNC 61 (126)
T ss_pred eeEEeecCceEEecCCcCC-cccCCCCCC-----CCcHHHHHHHHHHHHHHhccchhhc
Confidence 566666533 245789999 887655422 123335778899999999998 443
No 193
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=70.05 E-value=3.5 Score=39.38 Aligned_cols=33 Identities=27% Similarity=0.249 Sum_probs=26.1
Q ss_pred HhCCCCccchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 79 KYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 79 ~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
......|....+|+++|||||+||..+-. +|..
T Consensus 79 ~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi~ 111 (334)
T smart00483 79 ILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGIR 111 (334)
T ss_pred HhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCCC
Confidence 34456788899999999999999988765 5543
No 194
>KOG2534|consensus
Probab=69.97 E-value=11 Score=35.54 Aligned_cols=66 Identities=26% Similarity=0.338 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhHHHhCCCCc-cchHHHhcCCCCCHHHHHHHHHHHh-CC-e---eeccC--hhHHHHHHHHhcccC
Q psy8564 65 RARNLHICAKLVFFKYNGIFP-KNFISLINLPGIGQSTASAIRVFAY-GK-R---NAILD--GNVKRILIRVLGINC 133 (341)
Q Consensus 65 rA~~i~~~a~~i~~~~~g~~p-~~~~~L~~l~GIG~~tA~~il~~~~-~~-~---~~~vD--~~v~Rvl~Rl~~~~~ 133 (341)
||+.-..++..+.. -.+| .+.+++.+|||||+++|..|--|.- |. + .+.-| .-+...+.+.+|+..
T Consensus 34 r~~~y~~Aasvlk~---~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ 107 (353)
T KOG2534|consen 34 RARAYRRAASVLKS---LPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGL 107 (353)
T ss_pred HHHHHHHHHHHHHh---CCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCH
Confidence 77777777777765 2233 4689999999999999999987752 32 1 22222 234566788888864
No 195
>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=69.00 E-value=3.8 Score=38.64 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=24.5
Q ss_pred CCCccchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 82 GIFPKNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 82 g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
.+.|....+|+++|||||+||..+- .+|..
T Consensus 78 ~~~~~~l~~l~~i~GiGpk~a~~l~--~lGi~ 107 (307)
T cd00141 78 EDVPPGLLLLLRVPGVGPKTARKLY--ELGIR 107 (307)
T ss_pred ccchHHHHHHHcCCCCCHHHHHHHH--HcCCC
Confidence 3468888999999999999998887 55543
No 196
>KOG2841|consensus
Probab=68.86 E-value=14 Score=33.33 Aligned_cols=42 Identities=26% Similarity=0.403 Sum_probs=32.2
Q ss_pred HHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHh
Q psy8564 33 QRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLV 76 (341)
Q Consensus 33 ~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i 76 (341)
..|...|+|.+.+..|+++||+.+ -|+| .+||++|++...+.
T Consensus 209 ~~LL~~FgsLq~~~~AS~~ele~~-~G~G-~~kak~l~~~l~~p 250 (254)
T KOG2841|consen 209 QLLLQKFGSLQQISNASEGELEQC-PGLG-PAKAKRLHKFLHQP 250 (254)
T ss_pred HHHHHhcccHHHHHhcCHhHHHhC-cCcC-HHHHHHHHHHHhcc
Confidence 357788999999999999999654 3444 26999999876543
No 197
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=66.79 E-value=9.8 Score=35.83 Aligned_cols=44 Identities=23% Similarity=0.254 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhHHHhCCCCccchHH--HhcCCCCCHHHHHHHHHHH
Q psy8564 65 RARNLHICAKLVFFKYNGIFPKNFIS--LINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 65 rA~~i~~~a~~i~~~~~g~~p~~~~~--L~~l~GIG~~tA~~il~~~ 109 (341)
|++.-+++|+.+-. -+-+++...+. +.+|||||+.+|+.|.-+.
T Consensus 28 k~~aYr~Aa~sle~-~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 28 KIRAYRKAAQSLEN-LTEDLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred chHHHHHHHHhhhh-cccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 67777778877754 23455555555 8899999999999998776
No 198
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=66.65 E-value=21 Score=26.28 Aligned_cols=51 Identities=22% Similarity=0.387 Sum_probs=38.8
Q ss_pred hhHHHHHHHHHHhC-CCHHHHHhCCHHHHHHHHhhcCcHHH---HHHHHHHHHHh
Q psy8564 26 NTVIPYYQRFLKKF-PNIMSLAQAKLENVMELWSGLGYYSR---ARNLHICAKLV 76 (341)
Q Consensus 26 ~~~~~~~~~l~~~~-pt~~~la~~~~~~l~~~l~~~G~~~r---A~~i~~~a~~i 76 (341)
++-..||..|++.- .+.+.|..+.++|+.+++.-+|..+| .++++++.+..
T Consensus 19 AnLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~sKPLHVrRlqKAL~ew 73 (82)
T PF04904_consen 19 ANLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEW 73 (82)
T ss_pred hhHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccCccHHHHHHHHHHHHH
Confidence 45567888888765 58999999999999999999998765 44555544443
No 199
>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=66.38 E-value=6.3 Score=31.01 Aligned_cols=41 Identities=20% Similarity=0.269 Sum_probs=27.8
Q ss_pred hHHHhcCCCCCHHHHHHHHHHHhCCe----eeccChhHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVFAYGKR----NAILDGNVKRILIRV 128 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~~~~~----~~~vD~~v~Rvl~Rl 128 (341)
.-.|.++.|||+++|..|+....=.+ .-.-|..+.++-.-+
T Consensus 14 ~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i 58 (107)
T PF00416_consen 14 YIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKII 58 (107)
T ss_dssp HHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHH
T ss_pred HhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHH
Confidence 67899999999999999987753222 223455555554444
No 200
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=63.88 E-value=15 Score=27.94 Aligned_cols=53 Identities=30% Similarity=0.313 Sum_probs=31.7
Q ss_pred CHHHHHHHHhhcCcHH-HHHHHHHHHHHhHHHhCCCCc----cchHHHhc-CCCCCHHHHHHHHHH
Q psy8564 49 KLENVMELWSGLGYYS-RARNLHICAKLVFFKYNGIFP----KNFISLIN-LPGIGQSTASAIRVF 108 (341)
Q Consensus 49 ~~~~l~~~l~~~G~~~-rA~~i~~~a~~i~~~~~g~~p----~~~~~L~~-l~GIG~~tA~~il~~ 108 (341)
+..++...|...|++. .|..|. +.|+.+.- ++.-.|+. ++|||-++||.|...
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~-------~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLY-------KKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHH-------HHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-------HHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH
Confidence 3456777888899863 444443 44444322 23345665 999999999999875
No 201
>PRK14973 DNA topoisomerase I; Provisional
Probab=60.78 E-value=28 Score=38.06 Aligned_cols=91 Identities=12% Similarity=0.100 Sum_probs=54.9
Q ss_pred HhCCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHH-HhHHH-hC----CCCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 37 KKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAK-LVFFK-YN----GIFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 37 ~~~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~-~i~~~-~~----g~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
..|-++++++.+++++|... -|+. ..+..+...|. .+... .. ..+...+.+|++++|||++|++..-.-+
T Consensus 821 ~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag 897 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAG 897 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcC
Confidence 34789999999999998543 5776 46655655544 33321 00 1122345669999999999997665555
Q ss_pred hCCe-eeccChhHHHHHHHHhccc
Q psy8564 110 YGKR-NAILDGNVKRILIRVLGIN 132 (341)
Q Consensus 110 ~~~~-~~~vD~~v~Rvl~Rl~~~~ 132 (341)
.-.. .+..+ .+.++..+ .|++
T Consensus 898 ~~~~e~l~~~-d~~~la~~-~~i~ 919 (936)
T PRK14973 898 VYDGDLLVSA-DPKKLAKV-TGID 919 (936)
T ss_pred CCCHHHhccC-CHHHHhhh-cCCC
Confidence 4433 22222 44555444 3555
No 202
>PRK08609 hypothetical protein; Provisional
Probab=59.45 E-value=7 Score=40.17 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=21.2
Q ss_pred CCCccchHHHhcCCCCCHHHHHHHH
Q psy8564 82 GIFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 82 g~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
.++|....+|+++|||||+||..+-
T Consensus 81 ~~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 81 KEVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred hhCcHHHHHHhcCCCCCHHHHHHHH
Confidence 4578888899999999999997654
No 203
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=59.24 E-value=5.6 Score=35.10 Aligned_cols=45 Identities=27% Similarity=0.296 Sum_probs=29.4
Q ss_pred hHHHhcCCCCCHHHHHHHHHH-HhCCeeeccChhHHHHHHHHhccc
Q psy8564 88 FISLINLPGIGQSTASAIRVF-AYGKRNAILDGNVKRILIRVLGIN 132 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~-~~~~~~~~vD~~v~Rvl~Rl~~~~ 132 (341)
...|.++.||||++|=+||+. ..+.-.-+++..=...+.|+=|+.
T Consensus 72 F~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIG 117 (201)
T COG0632 72 FRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIG 117 (201)
T ss_pred HHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCC
Confidence 567999999999999999986 333222233333334567765554
No 204
>PRK08609 hypothetical protein; Provisional
Probab=58.57 E-value=17 Score=37.49 Aligned_cols=56 Identities=16% Similarity=0.225 Sum_probs=36.4
Q ss_pred HHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 52 NVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 52 ~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
++..++.-.|=. -|++.-+++|+.|... ..++ .+..+|.+|||||..+|+.|--+.
T Consensus 12 ~~A~~le~~g~n~fr~~aYr~Aa~~i~~l-~~~i-~~~~~l~~ipgIG~~ia~kI~Eil 68 (570)
T PRK08609 12 TIATYMELKGENPFKISAFRKAAQALELD-ERSL-SEIDDFTKLKGIGKGTAEVIQEYR 68 (570)
T ss_pred HHHHHHHhcCCCcHHHHHHHHHHHHHHhC-chhh-hhhhhhccCCCcCHHHHHHHHHHH
Confidence 344444444411 2777778888877652 2222 234678999999999999988765
No 205
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=57.91 E-value=5.8 Score=35.64 Aligned_cols=20 Identities=30% Similarity=0.443 Sum_probs=12.2
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~ 108 (341)
++|.+++|||.++|..|..+
T Consensus 36 eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 36 SELAEVDGIGNALAARIKAD 55 (232)
T ss_pred HHHHHccCCCHHHHHHHHHH
Confidence 35666666666666666555
No 206
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=55.27 E-value=44 Score=29.58 Aligned_cols=92 Identities=14% Similarity=0.126 Sum_probs=57.5
Q ss_pred CChHHHHHHHHHhhhc------C-------hhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQT------Q-------VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAK 74 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt------~-------~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~ 74 (341)
..-|..+|-++|.++- + .--+..++.+|++.||..++... -+..+++.+|+ -+..+++-|+
T Consensus 21 ~siYrrvv~ELLVE~HLl~~n~~f~yD~lfAlGlvt~fd~fm~GY~Pee~~~~----IF~Alc~a~~~--dp~~~r~dA~ 94 (206)
T PLN03060 21 PSIYSNVIQELLVQQHLMRYNATYKYDPIFALGFVTVYDQLMDGYPNATDRDA----IFKAYIEALGE--DPDQYRKDAK 94 (206)
T ss_pred chHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHH----HHHHHHHHcCC--CHHHHHHHHH
Confidence 4456777777776654 1 11246789999999988775432 34466778898 4455666666
Q ss_pred HhHHHhCCCCccchHHHhcCCCCCHHHHHHH
Q psy8564 75 LVFFKYNGIFPKNFISLINLPGIGQSTASAI 105 (341)
Q Consensus 75 ~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~i 105 (341)
.+.+...|.-.+++..+++-.|-|+-....+
T Consensus 95 ~l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~ 125 (206)
T PLN03060 95 KLEEWASSQSASGIADFNSGDGEVEAVLKDI 125 (206)
T ss_pred HHHHHHhcCCHHHHHHHHhcccccchHHHHH
Confidence 6666555655666666666666554433333
No 207
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=53.06 E-value=19 Score=25.33 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHH
Q psy8564 30 PYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHIC 72 (341)
Q Consensus 30 ~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~ 72 (341)
...+.|.+.|+|.+.|.+++.++|.. +.++|- ..|+.|.+.
T Consensus 14 ~~ak~L~~~f~sl~~l~~a~~e~L~~-i~gIG~-~~A~si~~f 54 (64)
T PF12826_consen 14 KTAKLLAKHFGSLEALMNASVEELSA-IPGIGP-KIAQSIYEF 54 (64)
T ss_dssp HHHHHHHHCCSCHHHHCC--HHHHCT-STT--H-HHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHcCHHHHhc-cCCcCH-HHHHHHHHH
Confidence 34467889999999999999999854 355562 345555544
No 208
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=52.40 E-value=17 Score=37.65 Aligned_cols=78 Identities=23% Similarity=0.369 Sum_probs=41.0
Q ss_pred HHHHHHHHHh--CCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHH-------------------------hHHHhC
Q psy8564 29 IPYYQRFLKK--FPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKL-------------------------VFFKYN 81 (341)
Q Consensus 29 ~~~~~~l~~~--~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~-------------------------i~~~~~ 81 (341)
...++.|++. .-++.+|..++.+++..+ .+.| ...|++|.+.-+. +...|+
T Consensus 455 ~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l-~~~~-~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~ 532 (667)
T COG0272 455 EKIIEQLFEKGLIKDIADLYTLTEEDLLSL-EGFG-EKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFG 532 (667)
T ss_pred HHHHHHHHHcCccCCHHHHHhCCHHHHhhc-cchh-hhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHHHhh
Confidence 3455566654 357777777777776443 2222 1245555444322 222221
Q ss_pred C---CCccchHHHhcCCCCCHHHHHHHHHH
Q psy8564 82 G---IFPKNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 82 g---~~p~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
. -.-.+.++|.+++|||...|..|..|
T Consensus 533 sl~~l~~a~~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 533 TLEALLAASEEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred hHHHHHhcCHHHHhhccchhHHHHHHHHHH
Confidence 1 01234566777777777777776655
No 209
>PF10343 DUF2419: Protein of unknown function (DUF2419); InterPro: IPR019438 This entry contains proteins that have no known function.
Probab=52.31 E-value=44 Score=31.21 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=42.1
Q ss_pred HHHhCC--CHHHHHhCCHHHHHHHHhhcC---cH---HHHHHHHHHHHHhHHHhCCCCc
Q psy8564 35 FLKKFP--NIMSLAQAKLENVMELWSGLG---YY---SRARNLHICAKLVFFKYNGIFP 85 (341)
Q Consensus 35 l~~~~p--t~~~la~~~~~~l~~~l~~~G---~~---~rA~~i~~~a~~i~~~~~g~~p 85 (341)
+.+..| +|+-++.++.++|..++++-. .+ .|++.|+++.+.+.++|+|.+-
T Consensus 59 l~~~~pi~~~~~~~~~t~~~l~~if~s~~~~~iPll~eR~~~L~E~G~vL~~~f~gs~~ 117 (287)
T PF10343_consen 59 LDEGIPITDPKYYAKMTDEELRHIFRSDTEEEIPLLEERARLLREVGRVLLEKFDGSFA 117 (287)
T ss_pred HhcCCCCcCHHHHHhCCHHHHHHHhcCCCCCcCCCHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 344555 899999999999999999762 33 5999999999999999999753
No 210
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=51.22 E-value=22 Score=29.28 Aligned_cols=32 Identities=25% Similarity=0.265 Sum_probs=27.8
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCC
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFKYNG 82 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g 82 (341)
+++.++++.-||.+|.+.|.++.+..+.+|..
T Consensus 17 ~elD~~i~~rg~~sRSE~IrdAir~yl~e~~~ 48 (136)
T COG0864 17 EELDELIEERGYSSRSELIRDALREYLEEYRW 48 (136)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHHHHHHHHhhh
Confidence 57777888899999999999999999987654
No 211
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=51.21 E-value=12 Score=39.26 Aligned_cols=67 Identities=21% Similarity=0.301 Sum_probs=38.2
Q ss_pred HHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHHHhCCCCccchHH-H--hcCCCCCHHHHHH
Q psy8564 31 YYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFFKYNGIFPKNFIS-L--INLPGIGQSTASA 104 (341)
Q Consensus 31 ~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~~~~g~~p~~~~~-L--~~l~GIG~~tA~~ 104 (341)
.++.|++.. -++.+|..+..++|..+ . ||. ..|.+|.+.-+.-. ..| ... | +.|||||+++|..
T Consensus 474 ~i~~L~~~g~V~~~~Dl~~L~~~~L~~l-~--g~g~Ksa~~Ll~~Ie~sk-----~~~--l~r~l~ALgIpgIG~~~ak~ 543 (689)
T PRK14351 474 RVQQLVDAGLVESLADLYDLTVADLAEL-E--GWGETSAENLLAELEASR-----EPP--LADFLVALGIPEVGPTTARN 543 (689)
T ss_pred HHHHHHHcCCCCCHHHHHHcCHHHHhcC-c--CcchhHHHHHHHHHHHHc-----cCC--HHHHHHHcCCCCcCHHHHHH
Confidence 344555543 48899999888775433 2 555 35666555544221 111 222 2 2678888888776
Q ss_pred HHH
Q psy8564 105 IRV 107 (341)
Q Consensus 105 il~ 107 (341)
++.
T Consensus 544 L~~ 546 (689)
T PRK14351 544 LAR 546 (689)
T ss_pred HHH
Confidence 654
No 212
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=49.42 E-value=13 Score=34.80 Aligned_cols=22 Identities=32% Similarity=0.593 Sum_probs=19.2
Q ss_pred chHHHhcCCCCCHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~ 108 (341)
..++|+.+||||.++|.-|++.
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred CHHHhcccCCCChHHHHHHHHH
Confidence 3789999999999999988764
No 213
>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=49.19 E-value=3.9 Score=31.94 Aligned_cols=28 Identities=21% Similarity=0.194 Sum_probs=17.6
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
++-+-+--+||||+|||.-++.--....
T Consensus 15 D~sDNIPGV~GIG~KtA~~LL~~ygsle 42 (101)
T PF01367_consen 15 DSSDNIPGVPGIGPKTAAKLLQEYGSLE 42 (101)
T ss_dssp CCCCTB---TTSTCHCCCCCHHHHTSCH
T ss_pred CcccCCCCCCCCCHHHHHHHHHHcCCHH
Confidence 3344556789999999988776655443
No 214
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=49.12 E-value=26 Score=24.45 Aligned_cols=20 Identities=25% Similarity=0.733 Sum_probs=16.2
Q ss_pred CccchHHHhcCCCCCHHHHH
Q psy8564 84 FPKNFISLINLPGIGQSTAS 103 (341)
Q Consensus 84 ~p~~~~~L~~l~GIG~~tA~ 103 (341)
.|.+.++|.+++|+|++-+.
T Consensus 39 ~P~s~~~L~~i~g~~~~~~~ 58 (68)
T PF00570_consen 39 LPTSIEELLQIPGMGKRKVR 58 (68)
T ss_dssp --SSHHHHHTSTTCGHHHHH
T ss_pred CCCCHHHHHHccCCCHHHHH
Confidence 48899999999999997655
No 215
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=46.59 E-value=30 Score=19.73 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=21.9
Q ss_pred HHHHHhhhcChhhHHHHHHHHHHhCCC
Q psy8564 15 LSEIMLQQTQVNTVIPYYQRFLKKFPN 41 (341)
Q Consensus 15 v~~il~qqt~~~~~~~~~~~l~~~~pt 41 (341)
++.+..++...+.+...++++.+.||+
T Consensus 6 ~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 6 LARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 455566667889999999999999995
No 216
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=44.95 E-value=41 Score=30.31 Aligned_cols=40 Identities=13% Similarity=0.133 Sum_probs=29.5
Q ss_pred HHHHHHh-CCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHH
Q psy8564 32 YQRFLKK-FPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAK 74 (341)
Q Consensus 32 ~~~l~~~-~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~ 74 (341)
...|.+. |.|.++|..++.++|.++ -|+. .+|..|++...
T Consensus 16 akkLl~~GF~Sve~Ik~AS~eEL~~V---~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 16 AEALREAGFESVEDVRAADQSELAEV---DGIGNALAARIKADVG 57 (232)
T ss_pred HHHHHHcCCCCHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHhc
Confidence 4567777 999999999999998554 3555 46777766644
No 217
>PRK07758 hypothetical protein; Provisional
Probab=44.04 E-value=18 Score=27.73 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=17.9
Q ss_pred cchHHHhcCCCCCHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il 106 (341)
-+.++|++|+|+|+++.+-|-
T Consensus 64 ~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 64 YSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCHHHHHHccCCCHHHHHHHH
Confidence 468999999999999987764
No 218
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=42.94 E-value=15 Score=30.94 Aligned_cols=29 Identities=24% Similarity=0.172 Sum_probs=22.6
Q ss_pred CCCCccc---hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 81 NGIFPKN---FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 81 ~g~~p~~---~~~L~~l~GIG~~tA~~il~~~ 109 (341)
|-++|.+ .-.|..|.|||+.+|..|+.-+
T Consensus 19 ~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~l 50 (154)
T PTZ00134 19 NTNVDGKRKVPYALTAIKGIGRRFAYLVCKKA 50 (154)
T ss_pred CccCCCCCEEEEeecccccccHHHHHHHHHHc
Confidence 3455544 5678999999999999988765
No 219
>PRK14976 5'-3' exonuclease; Provisional
Probab=42.77 E-value=15 Score=34.20 Aligned_cols=21 Identities=24% Similarity=0.194 Sum_probs=16.2
Q ss_pred HHHhcCCCCCHHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~ 109 (341)
+-+-.+||||+|||..++.--
T Consensus 191 DnipGVpGIG~KtA~~LL~~~ 211 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLNKY 211 (281)
T ss_pred CCCCCCCcccHHHHHHHHHHc
Confidence 345568999999999888543
No 220
>PRK09482 flap endonuclease-like protein; Provisional
Probab=41.87 E-value=16 Score=33.47 Aligned_cols=23 Identities=17% Similarity=0.222 Sum_probs=17.1
Q ss_pred HHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 89 ISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
+-+-.+||||+|||.-++.--..
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~gs 204 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFRS 204 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhCC
Confidence 34567899999999888765433
No 221
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=41.42 E-value=54 Score=31.02 Aligned_cols=65 Identities=17% Similarity=0.302 Sum_probs=39.7
Q ss_pred HHHHHHHhCC----CHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHH
Q psy8564 31 YYQRFLKKFP----NIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 31 ~~~~l~~~~p----t~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
.+..|...+| +...+...++..+..+|+.+|..+. ..++++++. + .+..|+|+|.+.+.-||
T Consensus 80 ~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~-e~l~~a~~~------~-------~~~~l~GfG~kse~~il 145 (326)
T COG1796 80 KLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDL-EELQEALEN------G-------KIRGLRGFGKKSEAKIL 145 (326)
T ss_pred HHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCcccH-HHHHHHHHh------C-------CccccCCccchhHHHHH
Confidence 4556666676 2333444566777777777775332 223333331 1 23469999999999999
Q ss_pred HHH
Q psy8564 107 VFA 109 (341)
Q Consensus 107 ~~~ 109 (341)
-+.
T Consensus 146 ~~i 148 (326)
T COG1796 146 ENI 148 (326)
T ss_pred HHH
Confidence 776
No 222
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=41.34 E-value=35 Score=31.24 Aligned_cols=23 Identities=26% Similarity=0.257 Sum_probs=14.9
Q ss_pred HHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 89 ISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
.-|.++||||+..|.-++..-..
T Consensus 182 ~il~s~pgig~~~a~~ll~~fgS 204 (254)
T COG1948 182 YILESIPGIGPKLAERLLKKFGS 204 (254)
T ss_pred HHHHcCCCccHHHHHHHHHHhcC
Confidence 44667777777777776654433
No 223
>PF13869 NUDIX_2: Nucleotide hydrolase; PDB: 3MDG_B 2J8Q_B 3Q2S_A 3P5T_D 3BAP_A 2CL3_A 3P6Y_A 3Q2T_B 3BHO_A 3N9U_A ....
Probab=41.18 E-value=73 Score=27.79 Aligned_cols=38 Identities=18% Similarity=0.157 Sum_probs=25.8
Q ss_pred EEEEEEeCCCCcccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc
Q psy8564 222 YVLFQKRSNKGIWGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI 275 (341)
Q Consensus 222 ~vLl~kR~~~g~~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~ 275 (341)
.|||-|.... .|-+|| +.+||++ .+.++|.+.+.++..
T Consensus 59 HvLLLq~~~~-----~fkLPGg~l~~gE~e-----------~~gLkrkL~~~l~~~ 98 (188)
T PF13869_consen 59 HVLLLQIGNT-----FFKLPGGRLRPGEDE-----------IEGLKRKLTEKLSPE 98 (188)
T ss_dssp EEEEEEETTT-----EEE-SEEE--TT--H-----------HHHHHHHHHHHHB-S
T ss_pred EEEEEeccCc-----cccCCccEeCCCCCh-----------hHHHHHHHHHHcCCC
Confidence 6888887543 788999 8889977 788999999988865
No 224
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=39.96 E-value=18 Score=29.27 Aligned_cols=22 Identities=32% Similarity=0.279 Sum_probs=19.4
Q ss_pred hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.-.|..+.|||+.+|..|+..+
T Consensus 16 ~~aLt~i~GIG~~~A~~ic~~l 37 (122)
T CHL00137 16 EYALTYIYGIGLTSAKEILEKA 37 (122)
T ss_pred eeeecccccccHHHHHHHHHHc
Confidence 5678999999999999999875
No 225
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=39.69 E-value=25 Score=36.10 Aligned_cols=76 Identities=18% Similarity=0.191 Sum_probs=46.3
Q ss_pred HHHHHHHHhC--CCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHHhHH----------------------HhCCCC
Q psy8564 30 PYYQRFLKKF--PNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKLVFF----------------------KYNGIF 84 (341)
Q Consensus 30 ~~~~~l~~~~--pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~i~~----------------------~~~g~~ 84 (341)
..++.|++.- -++.+|..++.++|..+ -||. ..|.+|.+.-+.-.+ .| +.+
T Consensus 436 ~~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~-~~i 511 (562)
T PRK08097 436 GTWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDD-RSW 511 (562)
T ss_pred HHHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhc-CCH
Confidence 3455666542 58888888887766443 2555 356666555321111 11 111
Q ss_pred ----ccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 85 ----PKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 85 ----p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
..+.++|.+++|||+.+|..|..|-
T Consensus 512 ~~l~~a~~e~l~~i~gIG~~~a~si~~~f 540 (562)
T PRK08097 512 QQLLSRSEQQWQQLPGIGEGRARQLIAFL 540 (562)
T ss_pred HHHHcCCHHHHhcCCCchHHHHHHHHHHH
Confidence 2346788899999999999988774
No 226
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=39.68 E-value=47 Score=34.18 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=19.9
Q ss_pred ccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 85 PKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 85 p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
..+.++|.++ |||.++|..|..+-
T Consensus 542 ~As~eeL~~v-gi~~~~A~~I~~~l 565 (567)
T PRK14667 542 KADDEELKKL-GIPPSVKQEVKKYL 565 (567)
T ss_pred hCCHHHHHHc-CCCHHHHHHHHHHh
Confidence 3578999999 99999999987653
No 227
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.63 E-value=19 Score=31.10 Aligned_cols=42 Identities=33% Similarity=0.305 Sum_probs=28.9
Q ss_pred chHHHhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhccc
Q psy8564 87 NFISLINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGIN 132 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~ 132 (341)
-.-.|.-|||||.|+...||----.+|+-.. .-+-.|+.++.
T Consensus 128 RLH~LELLpGiGkK~m~~ILeERkkkpFeSF----eDi~~Rv~~~~ 169 (202)
T COG1491 128 RLHQLELLPGIGKKTMWAILEERKKKPFESF----EDIKERVKGLH 169 (202)
T ss_pred HHHHHHhcccccHHHHHHHHHHHhcCCCcCH----HHHHHHhcCCC
Confidence 3678999999999999999987655553221 23445665543
No 228
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=39.61 E-value=71 Score=22.36 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=27.9
Q ss_pred HhCCCHHHHHhCCHHHHHHHHhhcCc------HHHHHHHHHH
Q psy8564 37 KKFPNIMSLAQAKLENVMELWSGLGY------YSRARNLHIC 72 (341)
Q Consensus 37 ~~~pt~~~la~~~~~~l~~~l~~~G~------~~rA~~i~~~ 72 (341)
..|-++++|...+.|.|...+...|+ ..||.+|..+
T Consensus 4 ~~f~sa~eLe~lGldrLK~~L~a~GLKcGGTl~ERA~RLfs~ 45 (60)
T PF13297_consen 4 DAFSSAEELEALGLDRLKSALMALGLKCGGTLQERAARLFSV 45 (60)
T ss_pred hhcCCHHHHHHhCHHHHHHHHHHcCCccCCCHHHHHHHHHHh
Confidence 35789999999999999999988886 2366666543
No 229
>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=38.57 E-value=20 Score=32.48 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=15.7
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~ 108 (341)
+-+-.+||||+|||.-++.-
T Consensus 183 DnipGv~GiG~ktA~~Ll~~ 202 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLKE 202 (240)
T ss_pred cCCCCCCccCHHHHHHHHHH
Confidence 44667899999999777654
No 230
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=38.14 E-value=68 Score=29.36 Aligned_cols=24 Identities=29% Similarity=0.416 Sum_probs=15.7
Q ss_pred cchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.+.++|++++|||.+.|..|-.|-
T Consensus 211 as~~eL~~v~gig~k~A~~I~~~~ 234 (254)
T COG1948 211 ASEEELMKVKGIGEKKAREIYRFL 234 (254)
T ss_pred cCHHHHHHhcCccHHHHHHHHHHH
Confidence 345777777777777777666553
No 231
>smart00475 53EXOc 5'-3' exonuclease.
Probab=38.07 E-value=22 Score=32.69 Aligned_cols=21 Identities=29% Similarity=0.389 Sum_probs=16.3
Q ss_pred HHHhcCCCCCHHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~ 109 (341)
+-+-.+||||+|||.-++.--
T Consensus 186 DnipGV~GIG~KtA~~Ll~~y 206 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLKEF 206 (259)
T ss_pred cCCCCCCCCCHHHHHHHHHHh
Confidence 346678999999999887543
No 232
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=37.52 E-value=28 Score=29.19 Aligned_cols=29 Identities=28% Similarity=0.245 Sum_probs=22.5
Q ss_pred CCCCccc---hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 81 NGIFPKN---FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 81 ~g~~p~~---~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+-++|.. .-.|.+|.|||+.+|..|+..+
T Consensus 14 ~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~l 45 (149)
T PRK04053 14 GTDLDGTKPVEYALTGIKGIGRRTARAIARKL 45 (149)
T ss_pred CccCCCCCEEeeeccccccccHHHHHHHHHHc
Confidence 3455544 5679999999999999987655
No 233
>PRK00254 ski2-like helicase; Provisional
Probab=37.19 E-value=38 Score=35.89 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=31.4
Q ss_pred HHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 68 NLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 68 ~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
.|..+++.+.. | +++..-.|.++||||+++|...+..+|+-.
T Consensus 628 ~l~~l~~rl~~---g-~~~~~~~L~~ipgig~~~~~~l~~~g~~s~ 669 (720)
T PRK00254 628 YLETLHLRVKH---G-VREELLELMRLPMIGRKRARALYNAGFRSI 669 (720)
T ss_pred HHHHHHHHHHc---C-CCHHHhhhhcCCCCCHHHHHHHHHccCCCH
Confidence 45577777764 3 455566788999999999999888877754
No 234
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=36.71 E-value=59 Score=33.53 Aligned_cols=73 Identities=15% Similarity=0.149 Sum_probs=44.0
Q ss_pred HHhhhcChhh---HHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCC---CCccchHHH
Q psy8564 18 IMLQQTQVNT---VIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFKYNG---IFPKNFISL 91 (341)
Q Consensus 18 il~qqt~~~~---~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g---~~p~~~~~L 91 (341)
-++|+.++++ |..+.+++..+.- ... .-+.|+|--+|. .+.+.||+ .--.+.++|
T Consensus 488 ~lLq~iRDEaHRFAit~hRk~R~k~~-------s~L----~~I~GiG~kr~~--------~LL~~Fgs~~~I~~As~eeL 548 (574)
T PRK14670 488 RILQNVRDEAHRKANGFNKKLRENIK-------LNY----TKIKGIGEKKAK--------KILKSLGTYKDILLLNEDEI 548 (574)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccc-------ccc----ccCCCCCHHHHH--------HHHHHhCCHHHHHhCCHHHH
Confidence 3566776554 4555555555511 112 334788854332 23333433 113578999
Q ss_pred hcCCCCCHHHHHHHHHHH
Q psy8564 92 INLPGIGQSTASAIRVFA 109 (341)
Q Consensus 92 ~~l~GIG~~tA~~il~~~ 109 (341)
.++||||.++|..|..+-
T Consensus 549 ~~v~gi~~~~A~~I~~~l 566 (574)
T PRK14670 549 AEKMKINIKMAKKIKKFA 566 (574)
T ss_pred HhCCCCCHHHHHHHHHHH
Confidence 999999999999998764
No 235
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=36.70 E-value=1.2e+02 Score=24.83 Aligned_cols=28 Identities=18% Similarity=0.183 Sum_probs=24.5
Q ss_pred HhCCCHHHHHhCCHHHHHHHHhhcCcHH
Q psy8564 37 KKFPNIMSLAQAKLENVMELWSGLGYYS 64 (341)
Q Consensus 37 ~~~pt~~~la~~~~~~l~~~l~~~G~~~ 64 (341)
.+.-|.++|.++++++|..++..+|++.
T Consensus 88 ~~~~tLe~Llemsd~el~~~l~~~g~~~ 115 (129)
T PF13543_consen 88 SKVLTLEALLEMSDEELKEILNRCGARE 115 (129)
T ss_pred HhhcCHHHHHhCCHHHHHHHHHHhCCCH
Confidence 3456999999999999999999999873
No 236
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=36.69 E-value=22 Score=28.72 Aligned_cols=22 Identities=36% Similarity=0.477 Sum_probs=19.3
Q ss_pred hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.-.|..|.|||+.+|..|+..+
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~l 37 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAA 37 (122)
T ss_pred EeeecccccccHHHHHHHHHHh
Confidence 4678999999999999998775
No 237
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=36.44 E-value=64 Score=30.65 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=37.9
Q ss_pred hHHHHHHHHHhhhcChhhHHHHHHHHHHhCCC-HHHHHhCCHHHHHHH
Q psy8564 10 TYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPN-IMSLAQAKLENVMEL 56 (341)
Q Consensus 10 p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt-~~~la~~~~~~l~~~ 56 (341)
|.+.+++..+.--.+.+.|...|++|.+.|.| .+.|.+++.|+|.++
T Consensus 305 PLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi~vLi~a~~e~La~V 352 (403)
T COG1379 305 PLAEIISMALGKGITTKAVKRTWERLVRAFGTEIDVLIDAPIEELARV 352 (403)
T ss_pred cHHHHHHHHhccceechhHHHHHHHHHHHhcchhhhHhcCCHHHHhhh
Confidence 56666766667777889999999999999984 677888999888554
No 238
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=35.96 E-value=40 Score=34.90 Aligned_cols=20 Identities=30% Similarity=0.461 Sum_probs=12.1
Q ss_pred hHHHhcCCCCCHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~ 107 (341)
...|..|||||++++..++.
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~ 561 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLK 561 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHH
Confidence 34566666666666665544
No 239
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=35.50 E-value=85 Score=29.17 Aligned_cols=45 Identities=18% Similarity=0.309 Sum_probs=33.5
Q ss_pred hhcCcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHH
Q psy8564 58 SGLGYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 58 ~~~G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
...|+.+-|.++.++++.|.. |.+++ ...|.+|||||+..+..+-
T Consensus 124 ~~~~~~~~~~~~l~L~q~i~q---~~w~~-~~~L~Qlp~i~~~~~~~l~ 168 (312)
T smart00611 124 LERGWLSTALNALNLSQMIIQ---ALWPT-DSPLLQLPHLPEEILKRLE 168 (312)
T ss_pred HhcchHHHHHHHHHHHHHHHH---hhCCC-CCccccCCCCCHHHHHHHH
Confidence 345666678889999999986 44443 3469999999998877664
No 240
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=35.12 E-value=60 Score=31.55 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=39.7
Q ss_pred ChHHHHHHHHHhhhcChhhHHHHHHHHHHhCCC-HHHHHhCCHHHHHHH
Q psy8564 9 NTYYIWLSEIMLQQTQVNTVIPYYQRFLKKFPN-IMSLAQAKLENVMEL 56 (341)
Q Consensus 9 ~p~~~lv~~il~qqt~~~~~~~~~~~l~~~~pt-~~~la~~~~~~l~~~ 56 (341)
=|.+.++++++.--...+.|...|++|.++|.| .+-|.+++.+||.+.
T Consensus 297 iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E~~iL~~~~~eel~~~ 345 (374)
T TIGR00375 297 IPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTEIAVLHEAAEEDLARV 345 (374)
T ss_pred CCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccHHHHHhcCCHHHHHHH
Confidence 377888898888777889999999999999964 677888899888554
No 241
>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=34.63 E-value=40 Score=35.76 Aligned_cols=56 Identities=13% Similarity=0.130 Sum_probs=34.2
Q ss_pred CHHHHHHHHhhcCcHHHHHHHHHHHHHhHHHhCCCC----ccchHHHhcCCCCCHHHHHHHHH
Q psy8564 49 KLENVMELWSGLGYYSRARNLHICAKLVFFKYNGIF----PKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 49 ~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~~g~~----p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
+.+.+...|..--+.. -=...|+.|++.||.+. .++.+.|.++||||++.++.|..
T Consensus 76 ~~~~i~~yL~s~~~~G---IG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKG---VGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred CHHHHHHHHhcCCCCC---cCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 4566666665322220 00234555556666542 34577899999999999887765
No 242
>KOG2937|consensus
Probab=34.42 E-value=24 Score=33.30 Aligned_cols=146 Identities=14% Similarity=0.100 Sum_probs=75.4
Q ss_pred CHHHHHHHHHHHhhhhcccCCCCCCCCCccccccccccCc-cccccccccCcccceeEEEEEEEe-CCEEEEEEeCCCCc
Q psy8564 156 NIEIYTQGLMDFGSIICKKIKPKCKVCPLQLCCISYKTNK-INNFLIKNKKNIKNCSIIMFIVID-DDYVLFQKRSNKGI 233 (341)
Q Consensus 156 ~~~~~~~~l~~~G~~~C~~~~P~C~~Cpl~~~C~~~~~~~-~~~~p~~~kk~~~~~~~~~~ii~~-~g~vLl~kR~~~g~ 233 (341)
.+..+.+|++.+-.-+ ..++.-..||+.---....... +.-.|- |+.+|. ..+.|++. --++|+.+=..
T Consensus 34 ~~f~ve~a~w~y~d~~--~~ndpsl~c~~~~~~~~~~~e~~~~f~~y--k~~iPv--~ga~ild~~~sr~llv~g~q--- 104 (348)
T KOG2937|consen 34 PLFSVEKALWFYEDFI--NKNDPSLQCPLLWPWKNEKDEAFVDFAPY--KARIPV--RGAIILDEKRSRCLLVKGWQ--- 104 (348)
T ss_pred chHHHHHHHHHHHHHH--hcCCcccCCccccchhhHHHHHHHhhccc--cCCCCC--chHhhhhhhhhhhheeecee---
Confidence 3456667776666666 3466556777754322221111 111111 333332 22334433 25788887433
Q ss_pred ccccccccc--cccccchhhhccchhhhhHHHHHHHHHHhcCCc--ccccccCcEEEEeeceEEEEEEE---EEEecccc
Q psy8564 234 WGGLLSFPE--WILKDKIINFVDNNLKNLIELEIKKFISSFGFI--KNYLILPIISHKLTHLQFKIVPC---HIFLKKCF 306 (341)
Q Consensus 234 ~~GlWEFPg--vE~~E~~~~~~~~~~~~~~~a~~rE~~ee~g~~--~~~~~~~~~~h~~~h~~~~l~~~---~~~~~~~~ 306 (341)
+.=|.||. +..+|+. ..+.+||..||.|.+ .....-.-|.-.+-+..+.+.+. .+...-.+
T Consensus 105 -a~sw~fprgK~~kdesd-----------~~caiReV~eetgfD~skql~~~e~Ie~nI~dq~~~~fIi~gvs~d~~f~~ 172 (348)
T KOG2937|consen 105 -ASSWSFPRGKISKDESD-----------SDCAIREVTEETGFDYSKQLQDNEGIETNIRDQLVRLFIINGVSEDTNFNP 172 (348)
T ss_pred -cccccccCccccccchh-----------hhcchhcccchhhcCHHHHhccccCcccchhhceeeeeeeccceeeeecch
Confidence 34499999 4444433 677899999999987 22222222444444444443332 22222111
Q ss_pred -cccCCCCceeeeCCCC
Q psy8564 307 -LKENKNNFIWYPIKKI 322 (341)
Q Consensus 307 -~~~~~~~~~W~~~~el 322 (341)
.-.+-+...|...+++
T Consensus 173 ~v~~eis~ihW~~l~~l 189 (348)
T KOG2937|consen 173 RVRKEISKIHWHYLDHL 189 (348)
T ss_pred hhhccccceeeeehhhh
Confidence 1111267889999988
No 243
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=33.83 E-value=24 Score=28.08 Aligned_cols=22 Identities=36% Similarity=0.360 Sum_probs=19.2
Q ss_pred hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~ 109 (341)
.-.|.++.|||+.+|..|+..+
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~l 35 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKA 35 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHh
Confidence 5678999999999999998764
No 244
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.46 E-value=1.9e+02 Score=26.47 Aligned_cols=37 Identities=24% Similarity=0.287 Sum_probs=24.2
Q ss_pred HHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHH
Q psy8564 68 NLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIR 106 (341)
Q Consensus 68 ~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il 106 (341)
.|..+.+.+........+... |.++||||+-+|..|.
T Consensus 169 ~i~~l~~~~~~~~~~~~~~~~--l~~~pgig~~~a~~i~ 205 (303)
T COG3547 169 EIAALDREIEARLGIGVVTDR--LASIPGIGELTAAAIA 205 (303)
T ss_pred HHHHHHHHHHHhhcccchHHH--HHhCCCccHHHHHHHH
Confidence 344444444443333334344 8899999999999998
No 245
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=33.38 E-value=73 Score=21.92 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=26.0
Q ss_pred HHHHhCCCHHHHH---hCCHHHHHHHHhhcCcH
Q psy8564 34 RFLKKFPNIMSLA---QAKLENVMELWSGLGYY 63 (341)
Q Consensus 34 ~l~~~~pt~~~la---~~~~~~l~~~l~~~G~~ 63 (341)
+|+..|+|.++|. .++.++|.+-++..||.
T Consensus 15 kLRD~~~sLd~Lc~~~~id~~~l~~kL~~~Gy~ 47 (55)
T PF14056_consen 15 KLRDEYSSLDELCYDYDIDKEELEEKLASIGYE 47 (55)
T ss_pred HHHhccCCHHHHHHHhCCCHHHHHHHHHHcCCe
Confidence 6778899999986 57889999999999985
No 246
>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=32.74 E-value=25 Score=29.25 Aligned_cols=28 Identities=29% Similarity=0.233 Sum_probs=21.6
Q ss_pred CCCccc---hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 82 GIFPKN---FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 82 g~~p~~---~~~L~~l~GIG~~tA~~il~~~ 109 (341)
-++|.+ .-.|.+|.|||+.+|..|+..+
T Consensus 11 ~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~l 41 (144)
T TIGR03629 11 TDLDGNKPVEYALTGIKGIGRRFARAIARKL 41 (144)
T ss_pred ccCCCCCEEEEeecceeccCHHHHHHHHHHc
Confidence 345543 5679999999999999987655
No 247
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=32.56 E-value=1.6e+02 Score=31.25 Aligned_cols=18 Identities=28% Similarity=0.488 Sum_probs=9.8
Q ss_pred HHHhcCCCCCHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIR 106 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il 106 (341)
+.|.+++|+|.|+|..++
T Consensus 496 ~~L~~l~g~g~Ksa~~Ll 513 (689)
T PRK14351 496 ADLAELEGWGETSAENLL 513 (689)
T ss_pred HHHhcCcCcchhHHHHHH
Confidence 345555666666555443
No 248
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=32.34 E-value=34 Score=27.50 Aligned_cols=28 Identities=36% Similarity=0.363 Sum_probs=22.3
Q ss_pred CCccc---hHHHhcCCCCCHHHHHHHHHHHh
Q psy8564 83 IFPKN---FISLINLPGIGQSTASAIRVFAY 110 (341)
Q Consensus 83 ~~p~~---~~~L~~l~GIG~~tA~~il~~~~ 110 (341)
++|.+ .-.|..|.|||..+|..|+.-+.
T Consensus 8 dip~~K~v~iALt~IyGIG~~~a~~I~~~~g 38 (121)
T COG0099 8 DIPGNKRVVIALTYIYGIGRRRAKEICKKAG 38 (121)
T ss_pred CCCCCceEeehhhhhccccHHHHHHHHHHcC
Confidence 45644 45799999999999999997663
No 249
>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=31.58 E-value=45 Score=35.40 Aligned_cols=32 Identities=25% Similarity=0.444 Sum_probs=21.0
Q ss_pred HHHhc--CCCCCHHHHHHHHHHHhCCeee-ccChhH
Q psy8564 89 ISLIN--LPGIGQSTASAIRVFAYGKRNA-ILDGNV 121 (341)
Q Consensus 89 ~~L~~--l~GIG~~tA~~il~~~~~~~~~-~vD~~v 121 (341)
..|.+ +||||++||..|. -.||...+ ++|.+.
T Consensus 82 ~yL~s~~~~GIG~~~A~~iv-~~fg~~~~~~i~~~~ 116 (720)
T TIGR01448 82 AYLSSRSIKGVGKKLAQRIV-KTFGEAAFDVLDDDP 116 (720)
T ss_pred HHHhcCCCCCcCHHHHHHHH-HHhCHhHHHHHHhCH
Confidence 44553 9999999999987 44565422 344443
No 250
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=30.85 E-value=36 Score=29.43 Aligned_cols=27 Identities=37% Similarity=0.293 Sum_probs=19.1
Q ss_pred chHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 87 NFISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
-.-.|.-|||||.|+...||--=-..|
T Consensus 114 RlH~LeLLPGIGKK~m~~ILeERkkkp 140 (181)
T PF04919_consen 114 RLHSLELLPGIGKKTMWKILEERKKKP 140 (181)
T ss_dssp SSBGGGGSTT--HHHHHHHHHHHHHS-
T ss_pred HHHHHhhcccccHHHHHHHHHHHccCC
Confidence 357888999999999999997654444
No 251
>PRK04460 nickel responsive regulator; Provisional
Probab=30.59 E-value=62 Score=26.68 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=24.0
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHH
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFK 79 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~ 79 (341)
+++.+.++..||.+|++.|+++.+....+
T Consensus 15 ~~lD~~~~~~gy~sRSe~ird~ir~~l~e 43 (137)
T PRK04460 15 EKFDELIEEKGYQNRSEAIRDLIRDFLVE 43 (137)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 56777888999999999999998866654
No 252
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=29.62 E-value=91 Score=20.10 Aligned_cols=39 Identities=18% Similarity=0.344 Sum_probs=28.1
Q ss_pred HHH-HhCCCHHHHHhCCHHHHHHHHhhcCcH-HHHHHHHHHHHH
Q psy8564 34 RFL-KKFPNIMSLAQAKLENVMELWSGLGYY-SRARNLHICAKL 75 (341)
Q Consensus 34 ~l~-~~~pt~~~la~~~~~~l~~~l~~~G~~-~rA~~i~~~a~~ 75 (341)
.|. ..|-|.++++.++++++... -|+. .+|..|+..++.
T Consensus 8 ~L~~~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 8 LLVEEGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred HHHHcCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 444 35789999999999998664 4666 477777776653
No 253
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=29.59 E-value=4.1e+02 Score=23.73 Aligned_cols=98 Identities=15% Similarity=0.208 Sum_probs=54.3
Q ss_pred CChHHHHHHHHHhhhc------C-------hhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQT------Q-------VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAK 74 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt------~-------~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~ 74 (341)
..-|..+|-++|.++- + .-=+..++.+|++.||..++.. .-...++..+|+ -+..+++-|+
T Consensus 18 ~siYrrvv~ELLVe~HLl~~n~~F~yD~lfalG~vt~fd~fm~GY~p~~~~~----~If~Alc~a~~~--dp~~~r~dA~ 91 (216)
T PF11264_consen 18 PSIYRRVVDELLVELHLLSVNKDFQYDPLFALGLVTVFDRFMQGYPPEEDKD----SIFNALCQALGF--DPEQYRQDAE 91 (216)
T ss_pred cHHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHhcCCCChhHHH----HHHHHHHHHcCC--CHHHHHHHHH
Confidence 4557777777776654 1 1124678999999998766543 233456778898 3344555555
Q ss_pred HhHHHhCCCCccch-HHHhcCCCCCH-HHHHHHHHHHhC
Q psy8564 75 LVFFKYNGIFPKNF-ISLINLPGIGQ-STASAIRVFAYG 111 (341)
Q Consensus 75 ~i~~~~~g~~p~~~-~~L~~l~GIG~-~tA~~il~~~~~ 111 (341)
.+.+-..|.-..++ ++|.+=.|-|+ ..++.+..++-+
T Consensus 92 ~l~~~a~~~s~~~l~~~l~~~~~~~~~~l~~~~~~ia~~ 130 (216)
T PF11264_consen 92 KLEEWAKGKSIEDLLSWLSQKGGEGDNPLAAILQAIASN 130 (216)
T ss_pred HHHHHHHcCCHHHHHHHHhccccccchHHHHHHHHHhcC
Confidence 55543334334444 34443244444 444444455443
No 254
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=29.52 E-value=27 Score=27.76 Aligned_cols=23 Identities=35% Similarity=0.632 Sum_probs=17.8
Q ss_pred CCCCCCCCCccccccccccCccc
Q psy8564 175 IKPKCKVCPLQLCCISYKTNKIN 197 (341)
Q Consensus 175 ~~P~C~~Cpl~~~C~~~~~~~~~ 197 (341)
....|..||+++.|.....+...
T Consensus 29 ~~~~C~~Cp~r~~C~~~~~~r~i 51 (125)
T PF13751_consen 29 SKEDCKNCPLREQCTKSKKGRRI 51 (125)
T ss_pred echhccCCCccccCCCcccceee
Confidence 35789999999999988555433
No 255
>PRK13266 Thf1-like protein; Reviewed
Probab=29.39 E-value=4.2e+02 Score=23.81 Aligned_cols=97 Identities=13% Similarity=0.202 Sum_probs=57.0
Q ss_pred CChHHHHHHHHHhhhc------C-------hhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQT------Q-------VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAK 74 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt------~-------~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~ 74 (341)
..-|..+|-++|.++- + .--+..++.+|++.|+..++.. .-+..++..+|+ -+..+++-|+
T Consensus 23 ~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~----~IF~Alc~a~~~--dp~~~r~dA~ 96 (225)
T PRK13266 23 NSIYRRVVDELLVELHLLSVNSDFKYDPLFALGLVTVFDRFMQGYRPEEHKD----SIFNALCQAVGF--DPEQLRQDAE 96 (225)
T ss_pred chHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHH----HHHHHHHHHcCC--CHHHHHHHHH
Confidence 4456777777766653 1 1124678999999998777543 234456778898 4556666777
Q ss_pred HhHHHhCCCCccchHHHhcCC---CCCHHHHHHHHHHHhC
Q psy8564 75 LVFFKYNGIFPKNFISLINLP---GIGQSTASAIRVFAYG 111 (341)
Q Consensus 75 ~i~~~~~g~~p~~~~~L~~l~---GIG~~tA~~il~~~~~ 111 (341)
.+.+...|.-++++..+++-. +++. ..+.+..++-+
T Consensus 97 ~l~~~a~~~s~~~i~~~l~~~~~~~~~~-l~~~l~~ia~~ 135 (225)
T PRK13266 97 RLLELAKGKSLKEILSWLTQKALGEPGG-LLATLLAIANN 135 (225)
T ss_pred HHHHHHhcCCHHHHHHHHhccccccchh-HHHHHHHHhcC
Confidence 766655555555544444333 2333 44445555433
No 256
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=28.85 E-value=1.1e+02 Score=33.08 Aligned_cols=40 Identities=28% Similarity=0.305 Sum_probs=30.4
Q ss_pred HHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHH
Q psy8564 31 YYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICA 73 (341)
Q Consensus 31 ~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a 73 (341)
.+.+++++|.|.++|++++.++|.+. +|-..+|+.|++..
T Consensus 769 ~a~~ll~~f~si~~l~~as~eeL~~~---iG~~~~A~~i~~fl 808 (814)
T TIGR00596 769 NYRNLRKKVKSIRELAKLSQNELNEL---IGDEEAAKRLYDFL 808 (814)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHHHHH---hCCHHHHHHHHHHh
Confidence 34567888999999999999998774 67335788877664
No 257
>PRK00630 nickel responsive regulator; Provisional
Probab=28.81 E-value=70 Score=26.77 Aligned_cols=29 Identities=14% Similarity=0.107 Sum_probs=23.7
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHH
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFK 79 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~ 79 (341)
+++.++++..||.+|++.|+++.+..+.+
T Consensus 23 ~~lD~~~~~~gy~sRSe~Ir~~iR~~l~e 51 (148)
T PRK00630 23 DELDNRIIKNGYSSRSELVRDLIREKLVE 51 (148)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 56777788899989999999998866543
No 258
>PRK02967 nickel responsive regulator; Provisional
Probab=28.76 E-value=70 Score=26.44 Aligned_cols=30 Identities=17% Similarity=0.221 Sum_probs=24.6
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHHh
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFKY 80 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~ 80 (341)
+++.+.+...||.+|++.|+++.+..+..+
T Consensus 14 ~~lD~~~~~~gy~sRSeaIrd~iR~~l~~~ 43 (139)
T PRK02967 14 ETLDSLIARRGYQNRSEAIRDLLRAALAQE 43 (139)
T ss_pred HHHHHHHHHcCCCCHhHHHHHHHHHHHHHh
Confidence 566677888999999999999988776643
No 259
>KOG2841|consensus
Probab=28.74 E-value=63 Score=29.17 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=17.1
Q ss_pred ccchHHHhcCCCCCHHHHHHHHHH
Q psy8564 85 PKNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 85 p~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
..++++|.++||+|+-.|.-+..|
T Consensus 223 ~AS~~ele~~~G~G~~kak~l~~~ 246 (254)
T KOG2841|consen 223 NASEGELEQCPGLGPAKAKRLHKF 246 (254)
T ss_pred hcCHhHHHhCcCcCHHHHHHHHHH
Confidence 345778888888888777766554
No 260
>PF11480 ImmE5: Colicin-E5 Imm protein; InterPro: IPR020127 The proteins in this entry are able to protect a cell, which harbors the ColE5 plasmid encoding colicin E5, against colicin E5.; PDB: 2DFX_I 2FHZ_A.
Probab=28.49 E-value=20 Score=26.59 Aligned_cols=15 Identities=27% Similarity=0.377 Sum_probs=9.2
Q ss_pred ccccccccccccccc
Q psy8564 233 IWGGLLSFPEWILKD 247 (341)
Q Consensus 233 ~~~GlWEFPgvE~~E 247 (341)
+=+|.|.+||+|+.-
T Consensus 25 IEGGiWh~pGFear~ 39 (83)
T PF11480_consen 25 IEGGIWHNPGFEARL 39 (83)
T ss_dssp EEEEEE-SS-EEE-G
T ss_pred EecceecCCCccccc
Confidence 447899999987654
No 261
>PF02467 Whib: Transcription factor WhiB; InterPro: IPR003482 WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. The process of mycelium formation in Streptomyces, which occurs in response to nutrient limitation, is controlled by a number of whi genes, named for the white colour of aerial hyphae when mutations occur in these genes. The normal colour is grey. The exact role of WhiB is not clear, but a mutation in the gene results in white, tightly coiled aerial hyphae.
Probab=28.30 E-value=13 Score=26.49 Aligned_cols=17 Identities=29% Similarity=0.940 Sum_probs=13.8
Q ss_pred CCCCCCccccccccccC
Q psy8564 178 KCKVCPLQLCCISYKTN 194 (341)
Q Consensus 178 ~C~~Cpl~~~C~~~~~~ 194 (341)
.|..||++..|..+...
T Consensus 31 iC~~CPVr~~C~~~Al~ 47 (66)
T PF02467_consen 31 ICARCPVRAECLEYALD 47 (66)
T ss_pred HHcCChhHHHHHHHHHH
Confidence 46789999999998643
No 262
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=28.23 E-value=72 Score=25.99 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=23.6
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHH
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFK 79 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~ 79 (341)
+++.+.+...||.+|++.|+++.+..+.+
T Consensus 13 ~~lD~~~~~~g~~~RSe~ir~~ir~~l~e 41 (129)
T TIGR02793 13 ETLDRLIARRGYQNRSEAIRDLLRSGLQQ 41 (129)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 46667788899999999999998866654
No 263
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=28.16 E-value=32 Score=30.08 Aligned_cols=16 Identities=38% Similarity=0.812 Sum_probs=14.4
Q ss_pred CCCCCCCCCccccccc
Q psy8564 175 IKPKCKVCPLQLCCIS 190 (341)
Q Consensus 175 ~~P~C~~Cpl~~~C~~ 190 (341)
++++|..|+++..|..
T Consensus 173 ~~~~C~~C~y~~iC~~ 188 (190)
T COG1468 173 KKKKCKKCAYREICFP 188 (190)
T ss_pred CCCcCCCCCcceeccC
Confidence 5899999999999974
No 264
>PRK01002 nickel responsive regulator; Provisional
Probab=27.52 E-value=75 Score=26.30 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=24.5
Q ss_pred HHHHHHHhhcCcHHHHHHHHHHHHHhHHHh
Q psy8564 51 ENVMELWSGLGYYSRARNLHICAKLVFFKY 80 (341)
Q Consensus 51 ~~l~~~l~~~G~~~rA~~i~~~a~~i~~~~ 80 (341)
++|.++++..||.+|++.|+++.+..+.++
T Consensus 17 ~~lD~~~~~~g~~sRSe~Ir~air~~l~~~ 46 (141)
T PRK01002 17 GEFDEIIEERGYASRSEGIRDAIRDYIIKY 46 (141)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 566677888999899999999988776644
No 265
>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=26.73 E-value=51 Score=24.76 Aligned_cols=26 Identities=19% Similarity=0.201 Sum_probs=18.6
Q ss_pred hHHHhcCCCCCHHHHHHHHHHHhCCe
Q psy8564 88 FISLINLPGIGQSTASAIRVFAYGKR 113 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~~~~~ 113 (341)
+--|..|+|||..+|..|+.---+.+
T Consensus 26 r~gl~~Ikglg~~~a~~I~~~R~~g~ 51 (90)
T PF14579_consen 26 RLGLSAIKGLGEEVAEKIVEERENGP 51 (90)
T ss_dssp E-BGGGSTTS-HHHHHHHHHHHHCSS
T ss_pred eehHhhcCCCCHHHHHHHHHhHhcCC
Confidence 44588999999999999886654434
No 266
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=26.68 E-value=91 Score=24.33 Aligned_cols=49 Identities=12% Similarity=0.017 Sum_probs=32.6
Q ss_pred HHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHHHhHHH
Q psy8564 31 YYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAKLVFFK 79 (341)
Q Consensus 31 ~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~~i~~~ 79 (341)
...++.+...|.++|...+...+..+++.++...=|..|+.+...+.+.
T Consensus 11 la~~ir~~~f~F~dl~~l~~~~l~~ll~~v~~~~la~ALkga~~e~~~~ 59 (110)
T PF01706_consen 11 LAEKIREKMFTFDDLVRLDDRDLQKLLREVDPDDLALALKGASEELREK 59 (110)
T ss_dssp HHHHHHHHCS-GGGGGGS-HHHHHHHHTTS-HHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHhhhHHHHHcCCHHHHHHHHHHCCHhHHHHHHccCCHHHHHH
Confidence 4456778899999999999999999999888544444455554444443
No 267
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=26.12 E-value=94 Score=29.09 Aligned_cols=38 Identities=21% Similarity=0.440 Sum_probs=19.1
Q ss_pred HHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHH
Q psy8564 33 QRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHIC 72 (341)
Q Consensus 33 ~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~ 72 (341)
+++...|.+..+|.+|+.+++.+. .|.|= -||+.|++-
T Consensus 307 ~nlV~~F~~l~~il~As~edL~~V-eGIGe-~rAr~i~~G 344 (349)
T COG1623 307 ENLVRAFGTLDGILEASAEDLDAV-EGIGE-ARARAIKEG 344 (349)
T ss_pred HHHHHHHhhHHHHHHhcHhHHhhh-cchhH-HHHHHHHHh
Confidence 344455566666666666665332 33431 255555443
No 268
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=25.42 E-value=55 Score=22.79 Aligned_cols=23 Identities=22% Similarity=0.434 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhHHHhCCCCccc
Q psy8564 65 RARNLHICAKLVFFKYNGIFPKN 87 (341)
Q Consensus 65 rA~~i~~~a~~i~~~~~g~~p~~ 87 (341)
|.++|+++|..|+++|...+..+
T Consensus 4 r~k~IKr~a~~lieky~~~ft~D 26 (58)
T PRK01151 4 RPKYIKRTAEELLEKYPDLFTTD 26 (58)
T ss_pred chHHHHHHHHHHHHHhHHHhccc
Confidence 67899999999999876655443
No 269
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=24.91 E-value=1e+02 Score=28.87 Aligned_cols=57 Identities=28% Similarity=0.359 Sum_probs=0.0
Q ss_pred HhcCCCCCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhCC
Q psy8564 91 LINLPGIGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLLP 153 (341)
Q Consensus 91 L~~l~GIG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~p 153 (341)
|.++||||+++|+.+...++.--.-..+.-...+...+ |+. .+.-..+++.+...++
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~-g~~-----~~~a~~l~~~a~~~~~ 64 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAA-GIG-----ESTAAKIIEAAREAAD 64 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhc-CCC-----HHHHHHHHHHHHHhhc
No 270
>PF05166 YcgL: YcgL domain; InterPro: IPR007840 This family of proteins formerly called DUF709 includes the Escherichia coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure []. The proteins in this entry are functionally uncharacterised.; PDB: 2H7A_A.
Probab=24.29 E-value=44 Score=24.50 Aligned_cols=21 Identities=33% Similarity=0.540 Sum_probs=16.3
Q ss_pred HHHHhCCHHHHHHHHhhcCcH
Q psy8564 43 MSLAQAKLENVMELWSGLGYY 63 (341)
Q Consensus 43 ~~la~~~~~~l~~~l~~~G~~ 63 (341)
..||.++.++|.+.|+.-|||
T Consensus 48 r~La~~d~~~V~~~l~~~Gfy 68 (74)
T PF05166_consen 48 RKLARADAEKVLAALEEQGFY 68 (74)
T ss_dssp ---SSS-HHHHHHHHHHTSEE
T ss_pred ceeccCCHHHHHHHHHhCCEE
Confidence 459999999999999999996
No 271
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=24.21 E-value=83 Score=32.48 Aligned_cols=17 Identities=29% Similarity=0.571 Sum_probs=8.0
Q ss_pred HHhcCCCCCHHHHHHHH
Q psy8564 90 SLINLPGIGQSTASAIR 106 (341)
Q Consensus 90 ~L~~l~GIG~~tA~~il 106 (341)
.|..+||||++++..++
T Consensus 526 ~L~~IpGIG~kr~~~LL 542 (577)
T PRK14668 526 VLDDVPGVGPETRKRLL 542 (577)
T ss_pred HHhcCCCCCHHHHHHHH
Confidence 34445555555554333
No 272
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=24.10 E-value=42 Score=27.97 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=13.1
Q ss_pred CCCCCCCCCcccccc
Q psy8564 175 IKPKCKVCPLQLCCI 189 (341)
Q Consensus 175 ~~P~C~~Cpl~~~C~ 189 (341)
.+++|..|.+++.|.
T Consensus 147 ~~~~C~~C~y~~~C~ 161 (162)
T PF01930_consen 147 NSKKCRRCSYREFCW 161 (162)
T ss_pred CCCCCCCCCCcCcCC
Confidence 357899999999996
No 273
>PHA00439 exonuclease
Probab=24.03 E-value=47 Score=31.01 Aligned_cols=19 Identities=32% Similarity=0.331 Sum_probs=15.5
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~ 108 (341)
+-+--+|||| |||.-+|.-
T Consensus 188 DNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 188 DGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred cCCCCCCCcC-HHHHHHHhC
Confidence 3455789999 999999876
No 274
>PRK00254 ski2-like helicase; Provisional
Probab=23.93 E-value=1.2e+02 Score=32.08 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=18.9
Q ss_pred cchHHHhcCCCCCHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
.+.++|.+++|||+++|..|..+
T Consensus 675 a~~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 675 AKPSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHH
Confidence 35788888999999998888766
No 275
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=23.75 E-value=1.6e+02 Score=26.20 Aligned_cols=80 Identities=15% Similarity=0.220 Sum_probs=48.7
Q ss_pred CChHHHHHHHHHhhhc------C-------hhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQT------Q-------VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAK 74 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt------~-------~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~ 74 (341)
..-|..+|-++|.++- + .--+..++.+|++.|+..++... -+..++..+|+ -+..+++-|+
T Consensus 23 ~siYrrvv~ELLVElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~----IF~Alc~a~~~--dp~~~r~dA~ 96 (214)
T TIGR03060 23 PPLYRRVVDELLVELHLLSHQSDFKYDPLFALGLVTVFDRFMEGYRPEEHLDA----LFDALCNSNGF--DPEQLREDAK 96 (214)
T ss_pred chHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHH----HHHHHHHhcCC--CHHHHHHHHH
Confidence 4456777777766654 1 11246789999999987765432 33456778898 4455666666
Q ss_pred HhHHHhCCCCccchHHHhc
Q psy8564 75 LVFFKYNGIFPKNFISLIN 93 (341)
Q Consensus 75 ~i~~~~~g~~p~~~~~L~~ 93 (341)
.+.+...|.-.+++..+++
T Consensus 97 ~l~~~a~~~s~~~i~~~l~ 115 (214)
T TIGR03060 97 QLLEQAKGKGLDEILSWLT 115 (214)
T ss_pred HHHHHHhcCCHHHHHHHHh
Confidence 6665555544444444443
No 276
>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=23.48 E-value=1.3e+02 Score=28.28 Aligned_cols=18 Identities=33% Similarity=0.383 Sum_probs=14.8
Q ss_pred HhcCCCCCHHHHHHHHHH
Q psy8564 91 LINLPGIGQSTASAIRVF 108 (341)
Q Consensus 91 L~~l~GIG~~tA~~il~~ 108 (341)
+-.+||||++||--++.-
T Consensus 225 ~~gv~giG~k~A~~li~~ 242 (316)
T cd00128 225 TEGIPGIGPVTALKLIKK 242 (316)
T ss_pred CCCCCCccHHHHHHHHHH
Confidence 457899999999888755
No 277
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=23.37 E-value=65 Score=23.51 Aligned_cols=25 Identities=32% Similarity=0.425 Sum_probs=18.2
Q ss_pred CCHHHHHhCCH---HHHHHHHhhcCcHH
Q psy8564 40 PNIMSLAQAKL---ENVMELWSGLGYYS 64 (341)
Q Consensus 40 pt~~~la~~~~---~~l~~~l~~~G~~~ 64 (341)
|.|+++...+. .+|+++|+.+|||.
T Consensus 5 ~~p~~~~~l~~~~~~evq~~L~~lGyy~ 32 (74)
T PF08823_consen 5 PRPEELLPLDGDVAREVQEALKRLGYYK 32 (74)
T ss_pred CCchhhccCcHHHHHHHHHHHHHcCCcc
Confidence 56666666655 47888899999963
No 278
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=23.24 E-value=1.6e+02 Score=31.12 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=19.7
Q ss_pred cchHHHhcCCCCCHHHHHHHHHH
Q psy8564 86 KNFISLINLPGIGQSTASAIRVF 108 (341)
Q Consensus 86 ~~~~~L~~l~GIG~~tA~~il~~ 108 (341)
.+.++|.+++|||+++|..|+.+
T Consensus 666 AS~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 666 AGEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred cCHHHHHhcCCcCHHHHHHHHHH
Confidence 46788999999999999998765
No 279
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=23.16 E-value=1.6e+02 Score=27.30 Aligned_cols=43 Identities=21% Similarity=0.352 Sum_probs=29.5
Q ss_pred CcHHHHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHH
Q psy8564 61 GYYSRARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 61 G~~~rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
|+.+=+.++..+++.|.. +.+ .+...|.+|||||+..+..+..
T Consensus 124 ~~~~~~~~~l~l~q~i~q---~~w-~~~~~L~Qlp~i~~~~~~~l~~ 166 (314)
T PF02889_consen 124 GWLSTALNALELSQCIVQ---ALW-DSDSPLLQLPHIGEESLKKLEK 166 (314)
T ss_dssp TBCCHHHHHHHHHHHHHH---TS--TTS-GGGGSTT--HHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHh---hcC-CCCChhhcCCCCCHHHHHHHhc
Confidence 443456788888888876 444 4668899999999999887766
No 280
>PRK01172 ski2-like helicase; Provisional
Probab=23.12 E-value=5.5e+02 Score=26.83 Aligned_cols=119 Identities=12% Similarity=0.188 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhCC--CHHHHHhCCHHHHHHHHhhcCcHH---HH------HHHHHHHHHhHHHhCCCCccchHHHhcCCC
Q psy8564 28 VIPYYQRFLKKFP--NIMSLAQAKLENVMELWSGLGYYS---RA------RNLHICAKLVFFKYNGIFPKNFISLINLPG 96 (341)
Q Consensus 28 ~~~~~~~l~~~~p--t~~~la~~~~~~l~~~l~~~G~~~---rA------~~i~~~a~~i~~~~~g~~p~~~~~L~~l~G 96 (341)
+.-....++.+.+ ..+.....+...|..++...|+.. .+ --+.++...+..+-.--+++..-.|++|||
T Consensus 540 ~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~~~~~rl~~gv~~~~~~L~~ip~ 619 (674)
T PRK01172 540 TAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIYKPEMRRKLEILNIRIKEGIREDLIDLVLIPK 619 (674)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcCCCHHHHhhcCCCC
Q ss_pred CCHHHHHHHHHHHhCCeeeccChhHHHHHHHHhcccCCcchHHHHHHHHHHHHhhC
Q psy8564 97 IGQSTASAIRVFAYGKRNAILDGNVKRILIRVLGINCSLNIKFIEKKLWRYAIDLL 152 (341)
Q Consensus 97 IG~~tA~~il~~~~~~~~~~vD~~v~Rvl~Rl~~~~~~~~~~~~~~~l~~~~~~~~ 152 (341)
||+..|......++.-..-+.+...... .++.++. ...-+.+.+.+..++
T Consensus 620 ~~~~~a~~l~~~g~~~~~di~~~~~~~~-~~i~~~~-----~~~~~~i~~~~~~~~ 669 (674)
T PRK01172 620 VGRVRARRLYDAGFKTVDDIARSSPERI-KKIYGFS-----DTLANAIVNRAMKIS 669 (674)
T ss_pred CCHHHHHHHHHcCCCCHHHHHhCCHHHH-HHHhccC-----HHHHHHHHHHHHHHH
No 281
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=23.10 E-value=82 Score=32.49 Aligned_cols=22 Identities=23% Similarity=0.306 Sum_probs=17.9
Q ss_pred hHHHhcCCCCCHHHHHHHHHHH
Q psy8564 88 FISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~ 109 (341)
...|..|||||+++...+|..-
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~F 534 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSL 534 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHh
Confidence 4578899999999998877543
No 282
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=23.08 E-value=98 Score=32.61 Aligned_cols=23 Identities=30% Similarity=0.387 Sum_probs=19.3
Q ss_pred hHHHhcCCCCCHHHHHHHHHHHhC
Q psy8564 88 FISLINLPGIGQSTASAIRVFAYG 111 (341)
Q Consensus 88 ~~~L~~l~GIG~~tA~~il~~~~~ 111 (341)
...|..+||||++++..++.. ||
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~-FG 658 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWER-FG 658 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHH-hC
Confidence 467889999999999888875 55
No 283
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=22.78 E-value=1.8e+02 Score=19.02 Aligned_cols=33 Identities=12% Similarity=-0.002 Sum_probs=25.7
Q ss_pred HHHhCCHHHHHHHHhhcCcH-------HHHHHHHHHHHHh
Q psy8564 44 SLAQAKLENVMELWSGLGYY-------SRARNLHICAKLV 76 (341)
Q Consensus 44 ~la~~~~~~l~~~l~~~G~~-------~rA~~i~~~a~~i 76 (341)
++...+.+||.+.+...|+. .|.-|++++.+.+
T Consensus 2 d~~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 2 DVDRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred chhHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 45667889999999999973 3777888877765
No 284
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=22.38 E-value=63 Score=20.79 Aligned_cols=17 Identities=24% Similarity=0.292 Sum_probs=14.2
Q ss_pred eeccChhHHHHHHHHhc
Q psy8564 114 NAILDGNVKRILIRVLG 130 (341)
Q Consensus 114 ~~~vD~~v~Rvl~Rl~~ 130 (341)
.-.-|+||.|+|...|-
T Consensus 15 dteddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 15 DTEDDTHVHRVLRKYYT 31 (41)
T ss_pred CCcchhHHHHHHHHHHH
Confidence 45679999999999874
No 285
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=22.07 E-value=2.9e+02 Score=20.85 Aligned_cols=17 Identities=6% Similarity=0.051 Sum_probs=8.9
Q ss_pred CCCCCHHHHHHHHHHHh
Q psy8564 152 LPKKNIEIYTQGLMDFG 168 (341)
Q Consensus 152 ~p~~~~~~~~~~l~~~G 168 (341)
..++.+..++..+..|.
T Consensus 67 T~p~ta~~vn~Lf~qf~ 83 (85)
T PF11116_consen 67 TSPQTAKQVNELFEQFT 83 (85)
T ss_pred cCHHHHHHHHHHHHHHh
Confidence 34445555565555543
No 286
>TIGR00372 cas4 CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Probab=21.46 E-value=50 Score=27.84 Aligned_cols=14 Identities=43% Similarity=1.146 Sum_probs=12.7
Q ss_pred CCCCCCCCcccccc
Q psy8564 176 KPKCKVCPLQLCCI 189 (341)
Q Consensus 176 ~P~C~~Cpl~~~C~ 189 (341)
++.|..|+++..|.
T Consensus 164 ~~~C~~C~y~~~C~ 177 (178)
T TIGR00372 164 SRKCKFCPYREICL 177 (178)
T ss_pred CCcCCCCCCccccC
Confidence 57899999999996
No 287
>PF14964 DUF4507: Domain of unknown function (DUF4507)
Probab=21.43 E-value=3.5e+02 Score=26.23 Aligned_cols=42 Identities=14% Similarity=0.169 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHH
Q psy8564 66 ARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRV 107 (341)
Q Consensus 66 A~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~ 107 (341)
..+-.++|+.|+++|=.-.|...+.|..++.+.|--+..++.
T Consensus 143 s~~s~~La~~iv~dy~~l~p~~~~~L~~l~~~sP~F~a~fit 184 (362)
T PF14964_consen 143 SSYSLRLAQMIVEDYCCLSPGSQETLKQLPNVSPRFCANFIT 184 (362)
T ss_pred cHHHHHHHHHHHHHHhccCCccHHHHHHhhccChHHHHHHHH
Confidence 568899999999998777899999999999999976666653
No 288
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=21.37 E-value=1.4e+02 Score=24.98 Aligned_cols=34 Identities=21% Similarity=0.132 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhHHHhCCCCccchHHHhcCCCCC
Q psy8564 65 RARNLHICAKLVFFKYNGIFPKNFISLINLPGIG 98 (341)
Q Consensus 65 rA~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG 98 (341)
.++.+.++.+.+.+.++-..+.+.+.|+++|||=
T Consensus 83 l~~~y~~~l~~l~~~~~~~~~~~~~~ll~~p~v~ 116 (159)
T PF03755_consen 83 LAKAYYEALKELAEELGLAGPISLDDLLRLPGVL 116 (159)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHcCCCcc
Confidence 6777888888888887666677899999999974
No 289
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=20.95 E-value=2.4e+02 Score=26.27 Aligned_cols=88 Identities=13% Similarity=0.115 Sum_probs=51.9
Q ss_pred CChHHHHHHHHHhhhc------C-------hhhHHHHHHHHHHhCCCHHHHHhCCHHHHHHHHhhcCcHHHHHHHHHHHH
Q psy8564 8 KNTYYIWLSEIMLQQT------Q-------VNTVIPYYQRFLKKFPNIMSLAQAKLENVMELWSGLGYYSRARNLHICAK 74 (341)
Q Consensus 8 ~~p~~~lv~~il~qqt------~-------~~~~~~~~~~l~~~~pt~~~la~~~~~~l~~~l~~~G~~~rA~~i~~~a~ 74 (341)
..-|..+|-++|.|+- + .--...+|.+|++.||..++... -+..+++.+|+ -+..+++-|+
T Consensus 74 psiYrrvvdELLVElHLLs~n~~F~yDplFALGlVtvfd~fm~GY~Pee~~~~----IF~Alc~a~g~--Dp~qyr~dA~ 147 (283)
T PLN00047 74 PSIYSTVLQELLVQQHLMRYKKTYRYDPVFALGFVTVYDQLMEGYPSDEDRDA----IFKAYIKALGE--DPEQYRKDAA 147 (283)
T ss_pred cHHHHHHHHHHHHHHHHHHhccCceeCchhhhhhHHHHHHHHccCCChHHHHH----HHHHHHHHcCC--CHHHHHHHHH
Confidence 4567778888877764 1 11236789999999987775432 33456778898 3444555555
Q ss_pred HhHHHhCCCCccchHHHhcCCCCCHHH
Q psy8564 75 LVFFKYNGIFPKNFISLINLPGIGQST 101 (341)
Q Consensus 75 ~i~~~~~g~~p~~~~~L~~l~GIG~~t 101 (341)
.+.+...+.-.++...+....|-...+
T Consensus 148 ~l~~~A~~~s~~~l~~~l~~~~~l~~~ 174 (283)
T PLN00047 148 KLEEWARSQTGSSLVDFSSKEGEIEGI 174 (283)
T ss_pred HHHHHHhcCCHHHHHHHHhcchHHHHH
Confidence 555544444444444444444444443
No 290
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.89 E-value=1.1e+02 Score=21.36 Aligned_cols=22 Identities=41% Similarity=0.368 Sum_probs=17.9
Q ss_pred chHHHhcCCCCCHHHHHHHHHHH
Q psy8564 87 NFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 87 ~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+.++|+++ |.+++||.-|..-|
T Consensus 5 ~k~dLi~l-Gf~~~tA~~IIrqA 26 (59)
T PF11372_consen 5 TKKDLIEL-GFSESTARDIIRQA 26 (59)
T ss_pred CHHHHHHc-CCCHHHHHHHHHHH
Confidence 46788888 99999998887665
No 291
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=20.77 E-value=69 Score=33.41 Aligned_cols=18 Identities=28% Similarity=0.658 Sum_probs=0.0
Q ss_pred HHHhcCCCCCHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIR 106 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il 106 (341)
..|.+|||||++++..+|
T Consensus 552 S~L~~IpGIG~kr~~~LL 569 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLL 569 (624)
T ss_pred HHHhcCCCCCHHHHHHHH
No 292
>PRK02362 ski2-like helicase; Provisional
Probab=20.65 E-value=1.3e+02 Score=32.01 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhHHHhCCCCccchHHHhcCCCCCHHHHHHHHHHH
Q psy8564 66 ARNLHICAKLVFFKYNGIFPKNFISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 66 A~~i~~~a~~i~~~~~g~~p~~~~~L~~l~GIG~~tA~~il~~~ 109 (341)
+..+..+++.+.. -++...-.|++|||||++.|......+
T Consensus 633 ~~~~~~l~~~l~~----gv~~~~~~L~~ip~i~~~~a~~l~~~g 672 (737)
T PRK02362 633 ARAARELEKRVEY----GVREELLDLVGLRGVGRVRARRLYNAG 672 (737)
T ss_pred HHHHHHHHHHHHh----CCCHHHHHHhCCCCCCHHHHHHHHHcC
Confidence 4445555555543 256667789999999999887666533
No 293
>PF11842 DUF3362: Domain of unknown function (DUF3362); InterPro: IPR024560 This domain tends to occur to the C terminus of a radical SAM domain (PF04055 from PFAM) in members of the uncharacterised protein family UPF0313. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=20.30 E-value=1.8e+02 Score=24.43 Aligned_cols=47 Identities=21% Similarity=0.245 Sum_probs=37.0
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHhhhhcccCCCCCCCCCccc
Q psy8564 140 IEKKLWRYAIDLLPKKNIEIYTQGLMDFGSIICKKIKPKCKVCPLQL 186 (341)
Q Consensus 140 ~~~~l~~~~~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~Cpl~~ 186 (341)
-++.|++..-.+-.+++|..+..||...|+.--.-..|+|-.=|-..
T Consensus 42 ~er~lqkAll~Y~~PeN~~lvreAL~~~GR~DLIG~g~~cLip~~~~ 88 (150)
T PF11842_consen 42 RERRLQKALLRYHDPENWPLVREALKKMGREDLIGNGPKCLIPPEQP 88 (150)
T ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhhhhhcccCCCCccccCCCc
Confidence 34566666666777889999999999999998877788887765543
No 294
>PRK13766 Hef nuclease; Provisional
Probab=20.17 E-value=1.1e+02 Score=32.49 Aligned_cols=17 Identities=24% Similarity=0.384 Sum_probs=9.9
Q ss_pred HhcCCCCCHHHHHHHHH
Q psy8564 91 LINLPGIGQSTASAIRV 107 (341)
Q Consensus 91 L~~l~GIG~~tA~~il~ 107 (341)
|..+||||+++|..++.
T Consensus 717 L~~ipgig~~~a~~Ll~ 733 (773)
T PRK13766 717 VESLPDVGPVLARNLLE 733 (773)
T ss_pred HhcCCCCCHHHHHHHHH
Confidence 44666666666655554
No 295
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=20.02 E-value=75 Score=33.14 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=17.3
Q ss_pred HHHhcCCCCCHHHHHHHHHHH
Q psy8564 89 ISLINLPGIGQSTASAIRVFA 109 (341)
Q Consensus 89 ~~L~~l~GIG~~tA~~il~~~ 109 (341)
..|..|||||+++|..++..-
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc
Confidence 458899999999999777554
Done!