Query 032317
Match_columns 143
No_of_seqs 114 out of 1104
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 12:30:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032317hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0177 Nth Predicted EndoIII- 100.0 3.4E-43 7.4E-48 263.7 11.6 120 1-128 89-208 (211)
2 PRK10702 endonuclease III; Pro 100.0 1.7E-39 3.7E-44 245.4 12.3 120 1-128 89-208 (211)
3 PRK13910 DNA glycosylase MutY; 100.0 1.5E-38 3.3E-43 249.5 13.0 126 1-134 52-177 (289)
4 TIGR01084 mutY A/G-specific ad 100.0 9.4E-39 2E-43 249.7 11.7 137 1-140 85-223 (275)
5 PRK10880 adenine DNA glycosyla 100.0 1E-38 2.2E-43 256.2 11.0 138 1-141 89-228 (350)
6 COG1194 MutY A/G-specific DNA 100.0 1.2E-36 2.5E-41 241.0 11.0 138 1-141 93-233 (342)
7 KOG1921 Endonuclease III [Repl 100.0 1.7E-34 3.8E-39 218.1 6.8 127 1-132 139-266 (286)
8 TIGR01083 nth endonuclease III 100.0 1.3E-31 2.7E-36 199.9 11.4 106 1-114 86-191 (191)
9 KOG2457 A/G-specific adenine D 99.9 7.1E-28 1.5E-32 192.3 7.0 124 1-127 185-309 (555)
10 PRK13913 3-methyladenine DNA g 99.9 5E-25 1.1E-29 167.0 11.0 100 1-109 97-216 (218)
11 COG2231 Uncharacterized protei 99.9 6.3E-24 1.4E-28 157.4 8.6 115 4-127 94-214 (215)
12 smart00478 ENDO3c endonuclease 99.9 1.2E-23 2.7E-28 150.6 9.2 97 1-104 52-148 (149)
13 cd00056 ENDO3c endonuclease II 99.9 2.6E-21 5.7E-26 139.7 9.6 96 1-103 60-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.8 2E-19 4.3E-24 135.5 9.7 102 1-103 93-202 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 99.8 9.9E-19 2.1E-23 139.1 8.9 102 1-104 190-304 (310)
16 KOG2875 8-oxoguanine DNA glyco 99.6 2.2E-15 4.9E-20 116.4 5.5 100 1-102 188-298 (323)
17 PF00633 HHH: Helix-hairpin-he 99.3 4.9E-13 1.1E-17 71.0 0.6 29 12-40 2-30 (30)
18 PRK10308 3-methyl-adenine DNA 99.3 9.5E-12 2.1E-16 98.0 7.1 85 1-98 182-272 (283)
19 COG0122 AlkA 3-methyladenine D 99.2 5.5E-11 1.2E-15 93.8 6.0 66 18-89 195-261 (285)
20 TIGR03252 uncharacterized HhH- 99.1 1.4E-10 3.1E-15 85.2 4.6 56 1-59 84-150 (177)
21 PF10576 EndIII_4Fe-2S: Iron-s 98.2 2.8E-07 6E-12 42.5 0.4 17 107-123 1-17 (17)
22 PF00730 HhH-GPD: HhH-GPD supe 98.1 4.1E-05 8.8E-10 51.5 8.4 81 3-89 16-108 (108)
23 smart00525 FES FES domain. iro 97.8 8.3E-06 1.8E-10 41.6 0.8 22 106-127 1-22 (26)
24 COG1059 Thermostable 8-oxoguan 97.6 9.3E-05 2E-09 55.0 4.7 82 19-101 118-202 (210)
25 PF09674 DUF2400: Protein of u 97.6 2.7E-05 5.9E-10 59.8 1.8 54 48-104 177-230 (232)
26 TIGR02757 conserved hypothetic 97.5 3.7E-05 7.9E-10 59.0 1.6 54 48-104 174-227 (229)
27 KOG1918 3-methyladenine DNA gl 97.3 0.00022 4.7E-09 54.2 3.4 77 21-103 165-243 (254)
28 smart00278 HhH1 Helix-hairpin- 97.3 0.00019 4.1E-09 36.4 2.0 21 22-42 2-22 (26)
29 PF12826 HHH_2: Helix-hairpin- 97.2 0.00052 1.1E-08 42.4 3.8 39 3-41 14-55 (64)
30 PRK00116 ruvA Holliday junctio 95.9 0.0094 2E-07 44.5 3.5 41 3-43 84-130 (192)
31 PF12836 HHH_3: Helix-hairpin- 95.8 0.011 2.4E-07 36.4 2.9 24 18-41 11-34 (65)
32 COG1555 ComEA DNA uptake prote 95.7 0.011 2.3E-07 42.6 2.9 24 18-41 94-117 (149)
33 PRK14605 ruvA Holliday junctio 95.6 0.012 2.7E-07 44.0 3.1 40 3-42 84-129 (194)
34 COG0353 RecR Recombinational D 95.4 0.0064 1.4E-07 45.5 0.8 28 18-45 9-36 (198)
35 PRK00076 recR recombination pr 95.3 0.014 3E-07 43.9 2.6 27 19-45 9-35 (196)
36 TIGR00615 recR recombination p 95.3 0.014 3.1E-07 43.7 2.6 27 19-45 9-35 (195)
37 PF14716 HHH_8: Helix-hairpin- 95.3 0.031 6.8E-07 34.7 3.8 31 9-40 35-66 (68)
38 TIGR01259 comE comEA protein. 95.3 0.019 4.1E-07 39.8 3.0 24 18-41 65-88 (120)
39 PRK14601 ruvA Holliday junctio 95.1 0.019 4.2E-07 42.7 2.9 27 18-44 105-131 (183)
40 PRK13844 recombination protein 95.1 0.018 3.8E-07 43.4 2.6 28 18-45 12-39 (200)
41 COG1415 Uncharacterized conser 95.1 0.08 1.7E-06 43.0 6.3 70 17-89 274-346 (373)
42 PRK13901 ruvA Holliday junctio 94.9 0.025 5.4E-07 42.5 2.8 27 18-44 104-130 (196)
43 COG0632 RuvA Holliday junction 94.8 0.025 5.3E-07 42.7 2.6 27 18-44 105-131 (201)
44 PRK14606 ruvA Holliday junctio 94.8 0.028 6.1E-07 41.9 2.9 27 18-44 105-131 (188)
45 PRK14603 ruvA Holliday junctio 94.7 0.029 6.4E-07 42.1 2.9 27 18-44 104-130 (197)
46 PRK14602 ruvA Holliday junctio 94.7 0.03 6.5E-07 42.3 2.9 27 18-44 106-132 (203)
47 PRK14604 ruvA Holliday junctio 94.6 0.031 6.8E-07 41.9 2.9 27 18-44 105-131 (195)
48 PF14520 HHH_5: Helix-hairpin- 94.6 0.04 8.7E-07 33.2 2.8 39 3-41 16-58 (60)
49 PF02371 Transposase_20: Trans 94.6 0.034 7.3E-07 36.1 2.6 43 21-67 2-44 (87)
50 TIGR00426 competence protein C 94.6 0.1 2.2E-06 32.2 4.7 20 21-40 16-36 (69)
51 PF14520 HHH_5: Helix-hairpin- 94.5 0.034 7.4E-07 33.5 2.3 36 20-56 4-39 (60)
52 PRK00116 ruvA Holliday junctio 94.4 0.043 9.3E-07 41.0 3.2 20 21-40 73-92 (192)
53 PF05559 DUF763: Protein of un 94.4 0.041 9E-07 44.1 3.1 26 16-41 264-289 (319)
54 PRK02515 psbU photosystem II c 94.2 0.044 9.6E-07 38.5 2.6 31 11-41 48-81 (132)
55 PRK14600 ruvA Holliday junctio 94.1 0.038 8.2E-07 41.2 2.3 26 18-44 105-130 (186)
56 PF11731 Cdd1: Pathogenicity l 93.7 0.075 1.6E-06 35.3 2.8 27 19-45 10-36 (93)
57 TIGR01259 comE comEA protein. 93.6 0.12 2.5E-06 35.8 3.9 38 3-40 79-117 (120)
58 TIGR00084 ruvA Holliday juncti 93.6 0.068 1.5E-06 40.0 2.8 27 18-44 104-130 (191)
59 TIGR00084 ruvA Holliday juncti 93.0 0.084 1.8E-06 39.5 2.6 20 21-40 72-91 (191)
60 TIGR00426 competence protein C 93.0 0.12 2.7E-06 31.9 3.0 22 19-40 45-66 (69)
61 PF11798 IMS_HHH: IMS family H 92.8 0.078 1.7E-06 28.1 1.6 15 23-37 13-27 (32)
62 PRK00024 hypothetical protein; 92.7 0.17 3.7E-06 38.7 4.0 39 2-40 44-85 (224)
63 TIGR00608 radc DNA repair prot 92.6 0.18 3.9E-06 38.5 3.9 39 2-40 35-79 (218)
64 PRK02515 psbU photosystem II c 92.3 0.34 7.4E-06 34.1 4.7 36 3-41 72-107 (132)
65 PRK14605 ruvA Holliday junctio 92.3 0.13 2.7E-06 38.6 2.7 20 21-40 73-92 (194)
66 PRK13482 DNA integrity scannin 91.9 0.22 4.7E-06 40.7 3.8 39 3-41 298-339 (352)
67 smart00279 HhH2 Helix-hairpin- 91.8 0.14 3.1E-06 27.9 1.9 16 24-39 19-34 (36)
68 cd00141 NT_POLXc Nucleotidyltr 91.1 0.16 3.5E-06 40.6 2.3 28 15-42 79-106 (307)
69 smart00483 POLXc DNA polymeras 90.5 0.19 4.1E-06 40.7 2.2 29 13-41 81-109 (334)
70 KOG2534 DNA polymerase IV (fam 89.8 0.75 1.6E-05 37.1 5.0 26 18-43 53-78 (353)
71 PF10391 DNA_pol_lambd_f: Fing 89.1 0.39 8.5E-06 28.4 2.3 24 20-43 1-24 (52)
72 cd00080 HhH2_motif Helix-hairp 88.9 0.32 6.9E-06 30.8 1.9 19 22-40 23-41 (75)
73 PRK08609 hypothetical protein; 88.1 0.38 8.3E-06 41.7 2.5 24 15-38 82-105 (570)
74 COG4277 Predicted DNA-binding 87.5 0.48 1E-05 38.2 2.5 24 18-41 327-350 (404)
75 PF00416 Ribosomal_S13: Riboso 87.4 0.64 1.4E-05 31.4 2.8 29 14-42 5-36 (107)
76 COG2003 RadC DNA repair protei 87.1 1.1 2.5E-05 34.3 4.3 39 2-40 44-85 (224)
77 PRK12766 50S ribosomal protein 87.1 0.37 8E-06 37.1 1.6 24 21-44 3-26 (232)
78 PF12836 HHH_3: Helix-hairpin- 87.0 0.77 1.7E-05 28.0 2.8 35 3-38 25-61 (65)
79 PRK13901 ruvA Holliday junctio 87.0 0.53 1.2E-05 35.4 2.4 21 20-40 71-91 (196)
80 PRK14600 ruvA Holliday junctio 86.4 0.56 1.2E-05 34.9 2.3 20 21-40 73-92 (186)
81 PRK07956 ligA NAD-dependent DN 86.4 0.77 1.7E-05 40.6 3.4 39 3-42 522-564 (665)
82 cd00141 NT_POLXc Nucleotidyltr 86.2 1.6 3.4E-05 34.9 4.9 26 18-43 42-67 (307)
83 PF14229 DUF4332: Domain of un 85.9 1.4 3E-05 30.5 3.9 65 20-85 52-118 (122)
84 smart00483 POLXc DNA polymeras 85.8 1.7 3.8E-05 35.1 5.0 32 9-41 37-68 (334)
85 TIGR00575 dnlj DNA ligase, NAD 85.7 0.89 1.9E-05 40.1 3.5 40 3-43 509-552 (652)
86 PRK14601 ruvA Holliday junctio 85.7 0.66 1.4E-05 34.5 2.3 21 20-40 72-92 (183)
87 PRK14602 ruvA Holliday junctio 85.6 0.74 1.6E-05 34.7 2.6 20 21-40 74-93 (203)
88 PRK14606 ruvA Holliday junctio 85.3 0.7 1.5E-05 34.5 2.3 20 21-40 73-92 (188)
89 PF14490 HHH_4: Helix-hairpin- 85.1 0.93 2E-05 29.7 2.6 38 3-40 23-65 (94)
90 PRK14603 ruvA Holliday junctio 84.9 0.73 1.6E-05 34.6 2.3 23 21-43 72-95 (197)
91 PRK14604 ruvA Holliday junctio 84.2 0.81 1.8E-05 34.3 2.2 20 21-40 73-92 (195)
92 PRK14350 ligA NAD-dependent DN 83.7 1.5 3.2E-05 38.9 3.9 26 18-43 538-563 (669)
93 TIGR01448 recD_rel helicase, p 82.6 2 4.3E-05 38.4 4.4 13 26-38 89-101 (720)
94 TIGR01448 recD_rel helicase, p 82.6 1.4 3.1E-05 39.3 3.4 38 3-40 95-136 (720)
95 COG1491 Predicted RNA-binding 82.6 0.89 1.9E-05 33.9 1.8 40 20-64 129-168 (202)
96 PF03118 RNA_pol_A_CTD: Bacter 82.3 1.2 2.7E-05 27.4 2.2 21 18-38 41-61 (66)
97 COG1796 POL4 DNA polymerase IV 81.7 1.6 3.5E-05 35.2 3.1 32 10-41 40-73 (326)
98 COG0632 RuvA Holliday junction 81.7 1.1 2.4E-05 33.8 2.1 41 21-62 73-114 (201)
99 PF04919 DUF655: Protein of un 80.8 1.2 2.6E-05 33.0 2.0 21 21-41 116-136 (181)
100 COG1948 MUS81 ERCC4-type nucle 80.2 2.8 6E-05 32.8 3.9 22 19-40 212-233 (254)
101 COG0272 Lig NAD-dependent DNA 78.0 2.5 5.4E-05 37.4 3.3 40 3-42 522-564 (667)
102 PRK12766 50S ribosomal protein 77.8 3.4 7.4E-05 31.9 3.7 38 4-41 15-56 (232)
103 PF01367 5_3_exonuc: 5'-3' exo 77.4 0.43 9.3E-06 32.1 -1.2 23 19-41 16-38 (101)
104 PRK14976 5'-3' exonuclease; Pr 77.2 1.7 3.6E-05 34.4 1.9 18 23-40 193-210 (281)
105 PRK14351 ligA NAD-dependent DN 75.8 3.2 6.9E-05 37.0 3.5 39 3-42 539-581 (689)
106 PRK09482 flap endonuclease-lik 74.9 2 4.4E-05 33.6 1.8 19 23-41 184-202 (256)
107 PRK07758 hypothetical protein; 74.3 2.9 6.3E-05 27.8 2.2 23 17-39 63-85 (95)
108 PRK07945 hypothetical protein; 74.3 2.8 6E-05 33.9 2.5 21 22-42 50-70 (335)
109 cd00008 53EXOc 5'-3' exonuclea 74.3 2.2 4.7E-05 32.9 1.8 20 21-40 183-202 (240)
110 COG3547 Transposase and inacti 73.8 3.4 7.3E-05 32.1 2.9 32 5-38 174-205 (303)
111 PRK08097 ligB NAD-dependent DN 73.7 3.2 6.8E-05 36.1 2.8 26 18-43 517-542 (562)
112 smart00475 53EXOc 5'-3' exonuc 73.6 2.5 5.4E-05 33.0 2.0 18 23-40 188-205 (259)
113 PTZ00134 40S ribosomal protein 72.8 2.5 5.4E-05 30.6 1.7 35 7-41 13-50 (154)
114 PF00570 HRDC: HRDC domain Blo 72.2 3.9 8.5E-05 24.6 2.3 20 16-35 39-58 (68)
115 CHL00137 rps13 ribosomal prote 72.0 2.6 5.6E-05 29.3 1.6 28 14-41 7-37 (122)
116 PRK08609 hypothetical protein; 71.3 4.6 9.9E-05 35.1 3.3 24 19-42 46-69 (570)
117 PRK14670 uvrC excinuclease ABC 70.0 6.5 0.00014 34.3 3.9 37 5-41 527-566 (574)
118 PRK04053 rps13p 30S ribosomal 69.7 4.7 0.0001 29.0 2.6 36 6-41 7-45 (149)
119 COG1796 POL4 DNA polymerase IV 66.8 4.9 0.00011 32.5 2.4 30 12-41 84-114 (326)
120 PRK04301 radA DNA repair and r 66.7 6 0.00013 31.5 2.9 21 23-43 8-28 (317)
121 KOG2841 Structure-specific end 66.6 8.1 0.00018 30.0 3.4 37 5-41 208-247 (254)
122 PRK05179 rpsM 30S ribosomal pr 66.4 4 8.6E-05 28.4 1.6 28 14-41 7-37 (122)
123 COG0258 Exo 5'-3' exonuclease 65.7 7.7 0.00017 30.9 3.3 35 6-40 172-217 (310)
124 TIGR03631 bact_S13 30S ribosom 64.8 4 8.8E-05 27.9 1.4 21 21-41 15-35 (113)
125 TIGR03629 arch_S13P archaeal r 62.1 4.9 0.00011 28.8 1.4 29 13-41 10-41 (144)
126 PRK00254 ski2-like helicase; P 61.1 11 0.00024 33.5 3.8 29 16-44 640-668 (720)
127 COG0099 RpsM Ribosomal protein 61.0 7.2 0.00016 27.1 2.0 29 14-42 7-38 (121)
128 PRK14669 uvrC excinuclease ABC 59.5 7.7 0.00017 34.2 2.5 21 21-41 552-572 (624)
129 PRK14671 uvrC excinuclease ABC 58.2 8.3 0.00018 34.0 2.5 21 21-41 569-589 (621)
130 PRK14672 uvrC excinuclease ABC 58.1 16 0.00036 32.6 4.2 40 5-44 621-663 (691)
131 PF09171 DUF1886: Domain of un 58.0 2.9 6.3E-05 32.6 -0.3 62 47-109 168-232 (246)
132 PF11372 DUF3173: Domain of un 57.6 14 0.0003 22.4 2.6 22 19-41 5-26 (59)
133 PF14475 Mso1_Sec1_bdg: Sec1-b 57.2 6.9 0.00015 21.9 1.2 16 48-63 16-31 (41)
134 PHA00439 exonuclease 56.8 7.1 0.00015 31.1 1.7 17 23-40 190-206 (286)
135 cd00128 XPG Xeroderma pigmento 55.1 9.1 0.0002 30.4 2.1 17 24-40 226-242 (316)
136 PRK03980 flap endonuclease-1; 54.9 8.3 0.00018 30.7 1.8 16 25-40 193-208 (292)
137 TIGR00596 rad1 DNA repair prot 54.7 9.4 0.0002 34.7 2.3 24 20-44 756-779 (814)
138 PF13592 HTH_33: Winged helix- 54.6 17 0.00037 21.5 2.8 34 50-83 23-57 (60)
139 TIGR00194 uvrC excinuclease AB 54.2 11 0.00023 33.0 2.5 20 21-40 541-560 (574)
140 PF03686 UPF0146: Uncharacteri 53.4 2.3 5E-05 29.8 -1.4 93 2-106 2-94 (127)
141 PF14579 HHH_6: Helix-hairpin- 53.3 12 0.00027 24.1 2.1 22 21-42 27-48 (90)
142 smart00341 HRDC Helicase and R 52.3 15 0.00032 22.7 2.3 19 16-34 42-60 (81)
143 PRK14667 uvrC excinuclease ABC 51.6 11 0.00024 32.9 2.2 20 21-40 514-533 (567)
144 PF03755 YicC_N: YicC-like fam 51.1 19 0.00041 25.8 3.0 28 2-29 88-115 (159)
145 COG3743 Uncharacterized conser 50.7 8.1 0.00017 27.3 1.0 19 21-39 67-85 (133)
146 PF02961 BAF: Barrier to autoi 50.6 26 0.00056 23.0 3.3 53 17-86 15-67 (89)
147 COG1031 Uncharacterized Fe-S o 50.5 12 0.00026 32.0 2.1 22 19-40 514-535 (560)
148 PF12482 DUF3701: Phage integr 50.4 15 0.00032 24.5 2.1 24 21-44 50-73 (96)
149 COG1255 Uncharacterized protei 49.9 23 0.00049 24.7 3.1 91 2-107 2-95 (129)
150 COG1468 CRISPR-associated prot 49.7 18 0.00039 26.9 2.8 16 110-125 173-188 (190)
151 PF13523 Acetyltransf_8: Acety 49.7 18 0.00038 24.9 2.6 41 25-65 91-138 (152)
152 PRK00254 ski2-like helicase; P 49.2 16 0.00034 32.5 2.8 38 4-41 657-698 (720)
153 TIGR02236 recomb_radA DNA repa 49.1 12 0.00026 29.5 1.8 22 23-44 1-22 (310)
154 PTZ00217 flap endonuclease-1; 49.1 12 0.00026 31.1 1.9 17 23-39 237-253 (393)
155 TIGR00593 pola DNA polymerase 49.1 11 0.00024 34.6 1.8 17 24-40 188-204 (887)
156 PRK00558 uvrC excinuclease ABC 49.0 14 0.0003 32.4 2.4 22 20-41 542-563 (598)
157 PF13751 DDE_Tnp_1_6: Transpos 49.0 9 0.0002 25.9 1.0 18 111-128 30-47 (125)
158 TIGR03674 fen_arch flap struct 48.7 12 0.00025 30.4 1.8 17 24-40 239-255 (338)
159 PRK14670 uvrC excinuclease ABC 47.7 14 0.0003 32.3 2.1 21 20-40 513-533 (574)
160 PRK02362 ski2-like helicase; P 47.4 26 0.00055 31.3 3.8 29 16-44 647-675 (737)
161 PF02889 Sec63: Sec63 Brl doma 45.0 21 0.00045 28.0 2.7 33 3-39 134-166 (314)
162 TIGR00575 dnlj DNA ligase, NAD 43.8 26 0.00056 31.1 3.2 22 20-41 465-486 (652)
163 PF11842 DUF3362: Domain of un 43.5 50 0.0011 23.8 4.1 44 75-118 42-85 (150)
164 PRK05755 DNA polymerase I; Pro 42.9 17 0.00036 33.3 2.0 20 21-40 187-206 (880)
165 PF09288 UBA_3: Fungal ubiquit 42.8 44 0.00096 19.9 3.2 51 25-87 4-54 (55)
166 TIGR01954 nusA_Cterm_rpt trans 42.6 41 0.0009 18.6 3.0 24 18-41 23-46 (50)
167 COG1948 MUS81 ERCC4-type nucle 42.1 22 0.00048 27.8 2.3 32 21-52 182-213 (254)
168 PRK14668 uvrC excinuclease ABC 41.8 23 0.00049 31.0 2.5 22 20-41 524-545 (577)
169 PRK14666 uvrC excinuclease ABC 41.7 22 0.00047 31.9 2.5 23 21-44 637-659 (694)
170 smart00611 SEC63 Domain of unk 41.7 22 0.00048 27.8 2.3 33 3-39 137-169 (312)
171 PRK03352 DNA polymerase IV; Va 41.4 22 0.00048 28.5 2.3 21 23-43 179-199 (346)
172 PRK00783 DNA-directed RNA poly 39.8 15 0.00032 28.5 1.1 41 26-66 17-67 (263)
173 COG1561 Uncharacterized stress 39.8 31 0.00068 27.6 2.8 29 2-30 89-117 (290)
174 COG4892 Predicted heme/steroid 39.6 17 0.00038 22.9 1.1 30 2-31 45-74 (81)
175 PF09441 Abp2: ARS binding pro 39.5 84 0.0018 23.1 4.7 23 34-56 15-37 (175)
176 PF02467 Whib: Transcription f 39.0 5.1 0.00011 24.7 -1.3 20 103-129 28-47 (66)
177 PRK14672 uvrC excinuclease ABC 37.9 25 0.00054 31.5 2.2 20 21-40 608-627 (691)
178 PF04994 TfoX_C: TfoX C-termin 37.8 25 0.00053 22.5 1.7 42 21-63 3-44 (81)
179 TIGR03585 PseH pseudaminic aci 37.4 42 0.00092 22.8 3.0 39 27-65 90-135 (156)
180 COG1799 Uncharacterized protei 35.5 22 0.00047 26.1 1.3 44 21-66 99-142 (167)
181 PF11691 DUF3288: Protein of u 34.9 24 0.00052 23.2 1.3 11 54-64 51-61 (90)
182 TIGR00372 cas4 CRISPR-associat 34.6 23 0.0005 25.2 1.3 14 111-124 164-177 (178)
183 PRK14973 DNA topoisomerase I; 34.1 39 0.00084 31.4 2.9 46 18-64 874-919 (936)
184 cd01703 PolY_Pol_iota DNA Poly 33.7 28 0.0006 28.7 1.8 21 23-43 174-194 (379)
185 PF01930 Cas_Cas4: Domain of u 33.6 26 0.00057 24.7 1.5 14 111-124 148-161 (162)
186 PRK07757 acetyltransferase; Pr 33.1 57 0.0012 22.2 3.1 40 26-65 79-119 (152)
187 PF14261 DUF4351: Domain of un 32.5 36 0.00077 20.4 1.7 27 73-99 33-59 (59)
188 PF09796 QCR10: Ubiquinol-cyto 32.2 21 0.00045 22.0 0.6 21 12-32 31-52 (64)
189 PF06831 H2TH: Formamidopyrimi 32.0 42 0.0009 21.8 2.1 19 26-44 36-54 (92)
190 PRK07956 ligA NAD-dependent DN 31.9 52 0.0011 29.4 3.2 20 20-39 478-497 (665)
191 PRK01151 rps17E 30S ribosomal 31.7 29 0.00063 20.9 1.2 20 1-20 8-27 (58)
192 cd01701 PolY_Rev1 DNA polymera 31.3 42 0.0009 27.7 2.5 21 23-43 224-244 (404)
193 PF13932 GIDA_assoc_3: GidA as 30.9 68 0.0015 19.9 2.8 23 16-38 49-71 (72)
194 PRK03858 DNA polymerase IV; Va 30.6 46 0.001 27.1 2.6 21 23-43 175-195 (396)
195 KOG2518 5'-3' exonuclease [Rep 29.2 38 0.00082 29.4 1.9 21 21-41 225-245 (556)
196 PF14964 DUF4507: Domain of un 29.2 84 0.0018 26.0 3.8 37 2-38 147-183 (362)
197 PRK11057 ATP-dependent DNA hel 29.0 44 0.00096 29.2 2.3 21 16-36 570-590 (607)
198 cd01700 PolY_Pol_V_umuC umuC s 28.7 45 0.00098 26.7 2.2 21 23-43 178-198 (344)
199 PRK01810 DNA polymerase IV; Va 28.5 47 0.001 27.3 2.3 21 23-43 181-201 (407)
200 PRK02406 DNA polymerase IV; Va 28.3 41 0.0009 26.9 1.9 21 23-43 170-190 (343)
201 COG1670 RimL Acetyltransferase 28.1 69 0.0015 22.0 2.9 40 26-65 109-155 (187)
202 cd07030 RNAP_D D subunit of Ar 28.1 33 0.00072 26.5 1.3 41 26-66 17-67 (259)
203 PF07643 DUF1598: Protein of u 27.0 36 0.00078 22.1 1.1 22 38-59 36-61 (84)
204 PRK03609 umuC DNA polymerase V 26.7 51 0.0011 27.3 2.2 21 23-43 181-201 (422)
205 TIGR01766 tspaseT_teng_C trans 26.7 33 0.00071 21.3 0.9 44 1-44 9-57 (82)
206 PF04891 NifQ: NifQ; InterPro 26.6 77 0.0017 23.2 2.9 48 74-123 108-165 (167)
207 PRK03103 DNA polymerase IV; Re 26.2 57 0.0012 26.8 2.4 21 23-43 183-203 (409)
208 PRK01216 DNA polymerase IV; Va 26.0 57 0.0012 26.5 2.4 21 23-43 180-200 (351)
209 COG2406 Protein distantly rela 26.0 62 0.0013 23.5 2.2 20 11-30 75-94 (172)
210 PRK14133 DNA polymerase IV; Pr 25.5 56 0.0012 26.2 2.2 21 23-43 175-195 (347)
211 PTZ00205 DNA polymerase kappa; 24.9 42 0.0009 29.5 1.4 20 23-42 311-330 (571)
212 PRK04148 hypothetical protein; 24.8 69 0.0015 22.6 2.3 109 2-119 2-116 (134)
213 KOG1573 Aldehyde reductase [Ge 23.8 1.5E+02 0.0033 21.9 3.9 35 79-113 104-138 (204)
214 PRK10809 ribosomal-protein-S5- 23.6 77 0.0017 22.7 2.5 40 26-65 117-163 (194)
215 PF11575 FhuF_C: FhuF 2Fe-2S C 23.6 60 0.0013 15.5 1.3 10 111-120 13-22 (22)
216 cd03110 Fer4_NifH_child This p 23.5 48 0.001 23.5 1.4 29 26-56 8-36 (179)
217 PRK07571 bidirectional hydroge 23.3 52 0.0011 24.1 1.5 59 1-60 38-96 (169)
218 PF08833 Axin_b-cat_bind: Axin 23.3 28 0.00061 19.9 0.1 10 49-58 7-16 (45)
219 PRK02794 DNA polymerase IV; Pr 23.1 66 0.0014 26.6 2.3 21 23-43 211-231 (419)
220 PRK14351 ligA NAD-dependent DN 23.1 90 0.002 28.0 3.2 20 20-39 495-514 (689)
221 cd00424 PolY Y-family of DNA p 23.1 62 0.0014 25.9 2.0 21 23-43 175-195 (343)
222 PRK01177 hypothetical protein; 22.9 32 0.0007 24.5 0.3 14 111-124 24-37 (140)
223 PRK03348 DNA polymerase IV; Pr 22.5 71 0.0015 26.9 2.3 21 23-43 182-202 (454)
224 TIGR01896 cas_AF1879 CRISPR-as 22.2 44 0.00095 26.5 1.0 31 93-123 235-270 (271)
225 COG0322 UvrC Nuclease subunit 21.5 71 0.0015 28.1 2.2 21 21-41 530-550 (581)
226 PF08097 Toxin_26: Conotoxin T 21.4 36 0.00077 13.3 0.2 8 117-124 3-10 (11)
227 PF03684 UPF0179: Uncharacteri 21.4 35 0.00077 24.4 0.3 14 111-124 22-35 (142)
228 COG1587 HemD Uroporphyrinogen- 21.2 1.2E+02 0.0026 23.1 3.2 36 25-61 81-116 (248)
229 PRK13766 Hef nuclease; Provisi 21.2 77 0.0017 28.3 2.4 19 22-40 716-734 (773)
230 PF09821 AAA_assoc_C: C-termin 20.6 2.9E+02 0.0063 18.9 4.7 50 48-105 63-112 (120)
231 COG5452 Uncharacterized conser 20.5 57 0.0012 23.8 1.2 22 2-23 69-90 (180)
No 1
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.4e-43 Score=263.67 Aligned_cols=120 Identities=43% Similarity=0.828 Sum_probs=115.7
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|++|+++|||++|+++++|++|||||+|||++||+++||.+ +|+|||||.||+.||||.+ ..++++++
T Consensus 89 I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~-------~~~p~~ve 160 (211)
T COG0177 89 IKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVP-------GKTPEEVE 160 (211)
T ss_pred HHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHHHHHHHhhcCCC-cccccchHHHHHHHhCCCC-------CCCHHHHH
Confidence 578999999999999999999999999999999999999999996 9999999999999999986 47899999
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCccccc
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFK 128 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~ 128 (143)
+.+.+++|++.|..+|.+|+.|||.+|++++|+|+.|||+++|+++.+
T Consensus 161 ~~L~~~iP~~~~~~~h~~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~ 208 (211)
T COG0177 161 EALMKLIPKELWTDLHHWLILHGRYICKARKPRCEECPLADLCPSAGK 208 (211)
T ss_pred HHHHHHCCHHHHHHHHHHHHHhhhhhccCCCCCcCcccchhhCchhcc
Confidence 999999999999999999999999999999999999999999998765
No 2
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.7e-39 Score=245.44 Aligned_cols=120 Identities=34% Similarity=0.592 Sum_probs=112.5
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|++|+++|+|++|+++++|++|||||+|||++||+|+|++ ++|||||||+||+.|+|+.. ..++++++
T Consensus 89 l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~Rv~~r~g~~~-------~~~~~~~~ 160 (211)
T PRK10702 89 VIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIFRVCNRTQFAP-------GKNVEQVE 160 (211)
T ss_pred HHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHHHHHHHhCCCC-------CCCHHHHH
Confidence 57899999999999999999999999999999999999999998 58999999999999999864 35788999
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCccccc
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFK 128 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~ 128 (143)
+.+.+.+|.+.|.++|++||+||+.+|++++|+|+.|||++.|.++.+
T Consensus 161 ~~l~~~lp~~~~~~~~~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 161 EKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred HHHHHhCCchHHHHHHHHHHHHhHHHcCCCCCCCCCCcChhhcCcccc
Confidence 999999999999999999999999999999999999999999997654
No 3
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=1.5e-38 Score=249.53 Aligned_cols=126 Identities=26% Similarity=0.532 Sum_probs=112.8
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|++|+++|+|.+|.++++|++|||||+|||++||+|+||++ +++||+||+||+.|++.+.. ..++++++
T Consensus 52 L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~af~~~-~~~VD~nV~RVl~Rl~g~~~------~~~~~~l~ 124 (289)
T PRK13910 52 LKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFGFREK-SACVDANIKRVLLRLFGLDP------NIHAKDLQ 124 (289)
T ss_pred HHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHHCCCC-cCcccHHHHHHHHHHhcCCC------CccHHHHH
Confidence 578999999999999999999999999999999999999999985 78999999999999855543 23566788
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccccCCCCCC
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFKDSSSPS 134 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~~~~~~~ 134 (143)
...++++|.+.++++|++||+||+.+|++ +|+|+.|||++.|.++..+...+.
T Consensus 125 ~~~~~~l~~~~~~~~nqaLm~~Ga~iC~~-~P~C~~CPl~~~C~~~~~~~~~~~ 177 (289)
T PRK13910 125 IKANDFLNLNESFNHNQALIDLGALICSP-KPKCAICPLNPYCLGKNNPEKHTL 177 (289)
T ss_pred HHHHHhCCccchHHHHHHHHHHhHHHcCC-CCCCCCCcChhhhhhhhcCCcccc
Confidence 88888899999999999999999999999 799999999999998877655554
No 4
>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=9.4e-39 Score=249.65 Aligned_cols=137 Identities=24% Similarity=0.460 Sum_probs=117.9
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|+.|+++|+|.+|+++++|++|||||+|||++|++|+|+++ .++||+||.||+.|+++++.+... ....+.++
T Consensus 85 L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~-~~~vD~~v~RVl~Rl~~~~~~~~~--~~~~~~l~ 161 (275)
T TIGR01084 85 LHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKP-YPILDGNVKRVLSRLFAVEGWPGK--KKVENRLW 161 (275)
T ss_pred HHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCC-CCcchHhHHHHHHHHccCcCCCCH--HHHHHHHH
Confidence 578999999999999999999999999999999999999999995 678999999999999877532211 22344566
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccccC--CCCCCCccccc
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFKD--SSSPSSKSRKS 140 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~~--~~~~~~~~~~~ 140 (143)
+.+++++|.+.+++||++||+||+.+|++++|+|+.|||++.|.++..+ ..+|.+++|++
T Consensus 162 ~~~~~~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~~~~p~~~~~~~ 223 (275)
T TIGR01084 162 TLAESLLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAA 223 (275)
T ss_pred HHHHHHCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCHhhcCCCCCCCC
Confidence 6689999999999999999999999999999999999999999988765 36787665543
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1e-38 Score=256.23 Aligned_cols=138 Identities=22% Similarity=0.366 Sum_probs=117.3
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|++|+++|+|.+|+++++|++|||||+|||+||++|+||++ .++||+||.||+.|++.++.... .....+.++
T Consensus 89 L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~-~~iVD~nV~RV~~Rl~~i~~~~~--~~~~~~~l~ 165 (350)
T PRK10880 89 LHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKH-FPILDGNVKRVLARCYAVSGWPG--KKEVENRLW 165 (350)
T ss_pred HHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHCCCC-eecccHHHHHHHHHHhcccCCCC--hHHHHHHHH
Confidence 578999999999999999999999999999999999999999984 67799999999999977643221 112334556
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccccCC--CCCCCcccccc
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFKDS--SSPSSKSRKSA 141 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~~~--~~~~~~~~~~~ 141 (143)
+.+++++|.+.+++||++||+||+.+|++++|+|+.|||++.|.++..+. ..|++++|++.
T Consensus 166 ~~~~~l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~~~~P~k~~k~~~ 228 (350)
T PRK10880 166 QLSEQVTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQTL 228 (350)
T ss_pred HHHHHhCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCHhhCCCCCCCCCC
Confidence 67778889899999999999999999999999999999999999987653 57877655543
No 6
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-36 Score=240.99 Aligned_cols=138 Identities=25% Similarity=0.472 Sum_probs=120.2
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|+.|+++|+|.+|++.++|.+|||||+|||++|++|+||++ ...||+||.||+.|++.++.+... ..+..+++
T Consensus 93 L~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~-~~~lDgNV~RVl~R~f~i~~~~~~--~~~~~~~~ 169 (342)
T COG1194 93 LHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQP-EPVLDGNVKRVLSRLFAISGDIGK--PKTKKELW 169 (342)
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCC-Cceeecchheeehhhhcccccccc--cchhHHHH
Confidence 689999999999999999999999999999999999999999996 556999999999999988654332 34677899
Q ss_pred HHHHHhCCCCC-hhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccccCC--CCCCCcccccc
Q 032317 81 EVLQLWLPKEE-WVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAFKDS--SSPSSKSRKSA 141 (143)
Q Consensus 81 ~~l~~~~p~~~-~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~~~~--~~~~~~~~~~~ 141 (143)
+.+++++.++. +++||++|||+|+.||++++|+|+.|||++.|..+..+. .+|+++++++.
T Consensus 170 ~~~~~ll~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~ 233 (342)
T COG1194 170 ELAEQLLTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKL 233 (342)
T ss_pred HHHHHhcCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCcccCCCcCccccc
Confidence 99999665444 899999999999999999999999999999999887664 57777766554
No 7
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-34 Score=218.09 Aligned_cols=127 Identities=69% Similarity=1.288 Sum_probs=118.6
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|+++.++|+|++|++.++|++|||||||+|..+|..|+|.-..|.|||||+|+..||||++. +..++++.+
T Consensus 139 lkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~-----ktkspE~TR 213 (286)
T KOG1921|consen 139 LKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT-----KTKSPEQTR 213 (286)
T ss_pred HHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc-----ccCCHHHHH
Confidence 578999999999999999999999999999999999999999999999999999999999999974 357799999
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCc-CccCcccccCCCC
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSV-SELCPSAFKDSSS 132 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL-~~~C~~~~~~~~~ 132 (143)
..|+.|+|.+.|.++|..|+.||+.||++++|.|+.|-+ ++.|+++......
T Consensus 214 ~aLq~wLPk~lW~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~~~~~~ 266 (286)
T KOG1921|consen 214 VALQQWLPKSLWVEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSFKEASS 266 (286)
T ss_pred HHHHHhCcHHHHhhhhceeecccceeeecCCCCccccccCcccCchhhhhccc
Confidence 999999999999999999999999999999999999999 5999987654333
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=99.97 E-value=1.3e-31 Score=199.89 Aligned_cols=106 Identities=35% Similarity=0.702 Sum_probs=99.8
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|+++.++|+|++|+++++|++|||||+|||++||+|+++++ .||||+||+|++.|+|+.+ ..++++++
T Consensus 86 i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~Ri~~r~g~~~-------~~~~~~~~ 157 (191)
T TIGR01083 86 IIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVFRVSNRLGLSK-------GKDPDKVE 157 (191)
T ss_pred HHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHHHHHHHcCCCC-------CCCHHHHH
Confidence 578999999999999999999999999999999999999999985 7999999999999999874 35689999
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCC
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRC 114 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C 114 (143)
+.+++++|.+.|.+||++|++||+.+|++++|+|
T Consensus 158 ~~l~~~~p~~~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 158 EELLKLIPREFWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred HHHHHHCCchhHHHHHHHHHHHhHHhcCCCCCCC
Confidence 9999999999999999999999999999999998
No 9
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.94 E-value=7.1e-28 Score=192.33 Aligned_cols=124 Identities=24% Similarity=0.431 Sum_probs=114.6
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhc-CCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLL-LPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQT 79 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~-lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~ 79 (143)
|++.|+.+++..+|.+|.+-++|.+ +||||+|||.+|+++||+++.. +||+||.||+.|..-+..|.++ +.-...+
T Consensus 185 L~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tG-iVDGNVirvlsRalAIhsDcSk--gk~~q~~ 261 (555)
T KOG2457|consen 185 LLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTG-IVDGNVIRVLSRALAIHSDCSK--GKFFQSS 261 (555)
T ss_pred HHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhhcCccc-ccccchHHHhHHhHhhcCCcch--hhHHHHH
Confidence 5789999999999999999999999 9999999999999999999755 5999999999999888766654 4557789
Q ss_pred HHHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccc
Q 032317 80 REVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAF 127 (143)
Q Consensus 80 ~~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~ 127 (143)
+.++.+++++..+++||+++|++|+..|++-+|.|..||++..|.+++
T Consensus 262 wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q 309 (555)
T KOG2457|consen 262 WKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQ 309 (555)
T ss_pred HHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHh
Confidence 999999999999999999999999999999999999999999999987
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.92 E-value=5e-25 Score=166.98 Aligned_cols=100 Identities=13% Similarity=0.157 Sum_probs=88.5
Q ss_pred CHHHHHHHHHHcCC----CCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCH
Q 032317 1 MKKIAPICLTKYDG----DIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSP 76 (143)
Q Consensus 1 l~~~a~~i~~~~~g----~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~ 76 (143)
|+++|+.++++|+| ..|+++++|++|||||+|||++||+|++++ ++|+||||++||+.|+|+.. .+|
T Consensus 97 Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r-p~fvVDty~~Rv~~RlG~~~--------~~y 167 (218)
T PRK13913 97 LIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAK-EVMVVDKYSYLFLKKLGIEI--------EDY 167 (218)
T ss_pred HHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCC-CccccchhHHHHHHHcCCCC--------CCH
Confidence 57899999999987 357899999999999999999999999999 58999999999999999963 469
Q ss_pred HHHHHHHHHhCCC----------------CChhhHHHHHHHHHHHhccC
Q 032317 77 EQTREVLQLWLPK----------------EEWVPINPLLVGFGQTICTP 109 (143)
Q Consensus 77 ~~~~~~l~~~~p~----------------~~~~~~~~~l~~~G~~~C~~ 109 (143)
.+++++++..++. ..+.+||..|++||+..|..
T Consensus 168 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 168 DELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred HHHHHHHHHhhhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999987621 24899999999999999975
No 11
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.90 E-value=6.3e-24 Score=157.45 Aligned_cols=115 Identities=21% Similarity=0.386 Sum_probs=97.3
Q ss_pred HHHHHHHHcCC---CCcC-cHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHH
Q 032317 4 IAPICLTKYDG---DIPS-SLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQT 79 (143)
Q Consensus 4 ~a~~i~~~~~g---~~p~-~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~ 79 (143)
+.+.++..|.+ .-+. .|++|++++|||+.|||+||+|++++ ++|+||.+.+|++.|+|++.. .+|.++
T Consensus 94 l~k~l~~~~~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r-p~FVvD~Yt~R~l~rlg~i~~-------k~ydei 165 (215)
T COG2231 94 LSKNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYALDR-PVFVVDKYTRRLLSRLGGIEE-------KKYDEI 165 (215)
T ss_pred HHHHHHHHhhhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcC-cccchhHHHHHHHHHhccccc-------ccHHHH
Confidence 34445554433 2232 49999999999999999999999998 599999999999999999863 479999
Q ss_pred HHHHHHhCCCC--ChhhHHHHHHHHHHHhccCCCCCCCCCCcCccCcccc
Q 032317 80 REVLQLWLPKE--EWVPINPLLVGFGQTICTPIRPRCGMCSVSELCPSAF 127 (143)
Q Consensus 80 ~~~l~~~~p~~--~~~~~~~~l~~~G~~~C~~~~P~C~~CpL~~~C~~~~ 127 (143)
++.+++.+|.+ .+..||..|+.||+.+|+. +|.|+.|||...|.++.
T Consensus 166 k~~fe~~l~~~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 166 KELFEENLPENLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred HHHHHhcchhHHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 99999988864 3799999999999999995 79999999999998753
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=99.90 E-value=1.2e-23 Score=150.65 Aligned_cols=97 Identities=42% Similarity=0.758 Sum_probs=90.3
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTR 80 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~ 80 (143)
|+++|+.+++.|+|++|+++++|++|||||+|||++|++|++++ +.+|||+||.|++.|+|+.+. ..++++++
T Consensus 52 i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~------~~~~~~~~ 124 (149)
T smart00478 52 LIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHVLRIAKRLGLVDK------KSTPEEVE 124 (149)
T ss_pred HHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHHHHHHHHhCCCCC------CCCHHHHH
Confidence 57889999999999999999999999999999999999999998 689999999999999998853 35789999
Q ss_pred HHHHHhCCCCChhhHHHHHHHHHH
Q 032317 81 EVLQLWLPKEEWVPINPLLVGFGQ 104 (143)
Q Consensus 81 ~~l~~~~p~~~~~~~~~~l~~~G~ 104 (143)
+.+++++|...|..+|++++++|+
T Consensus 125 ~~~~~~~p~~~~~~~~~~~l~~g~ 148 (149)
T smart00478 125 KLLEKLLPKEDWRELNLLLIDFGR 148 (149)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHcC
Confidence 999999998889999999999996
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=99.86 E-value=2.6e-21 Score=139.67 Aligned_cols=96 Identities=35% Similarity=0.638 Sum_probs=87.5
Q ss_pred CHHHHHHHHHHcCCCC---cCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHH
Q 032317 1 MKKIAPICLTKYDGDI---PSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPE 77 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~---p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~ 77 (143)
|+++|+.+.+.|++.. ++.+++|++|||||+|||++|++|+++ .++||||+|+.|++.|+|+++. ..+++
T Consensus 60 i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~~~~------~~~~~ 132 (158)
T cd00056 60 LKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG-PDAFPVDTHVRRVLKRLGLIPK------KKTPE 132 (158)
T ss_pred HHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCccchhHHHHHHHhCCCCC------CCCHH
Confidence 4688999999999877 899999999999999999999999999 5799999999999999998642 46899
Q ss_pred HHHHHHHHhCCCCChhhHHHHHHHHH
Q 032317 78 QTREVLQLWLPKEEWVPINPLLVGFG 103 (143)
Q Consensus 78 ~~~~~l~~~~p~~~~~~~~~~l~~~G 103 (143)
++++.++.++|......+|+.|+++|
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~l~~~g 158 (158)
T cd00056 133 ELEELLEELLPKPYWGEANQALMDLG 158 (158)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHcC
Confidence 99999999998788899999999986
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.80 E-value=2e-19 Score=135.48 Aligned_cols=102 Identities=15% Similarity=0.090 Sum_probs=80.2
Q ss_pred CHHHHHH---HHHHc--CCCCcCcHHHHh-cCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCC
Q 032317 1 MKKIAPI---CLTKY--DGDIPSSLDELL-LLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTS 74 (143)
Q Consensus 1 l~~~a~~---i~~~~--~g~~p~~~~~L~-~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~ 74 (143)
|+++++. +.+.+ ++++|+++++|+ +|||||+|||++||++...+ ++|+|||||.|++.|+|+++....+.+..
T Consensus 93 I~~~~~~~~~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~-~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~ 171 (208)
T PRK01229 93 IVEARKLYGKLKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE-DLAILDRHILRFLKRYGLIEEIPKTLSKK 171 (208)
T ss_pred HHHHHHHHHHHHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC-CeeeeeHHHHHHHHHhCCCcccccccCcC
Confidence 3556665 66676 889999999999 99999999999999766555 68999999999999999987533344457
Q ss_pred CHHHHHHHHHHhCCCC--ChhhHHHHHHHHH
Q 032317 75 SPEQTREVLQLWLPKE--EWVPINPLLVGFG 103 (143)
Q Consensus 75 ~~~~~~~~l~~~~p~~--~~~~~~~~l~~~G 103 (143)
+|.+++..+.+..+.- ..+.+...|+...
T Consensus 172 ~y~~~E~~l~~~~~~~~~~~~~Ldl~~w~~~ 202 (208)
T PRK01229 172 RYLEIEEILREIAEELGISLGELDLYIWYKE 202 (208)
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 8999999999877642 2456666666544
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=99.77 E-value=9.9e-19 Score=139.12 Aligned_cols=102 Identities=21% Similarity=0.251 Sum_probs=81.3
Q ss_pred CHHHHHHHHHHcCCC----------CcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCC-
Q 032317 1 MKKIAPICLTKYDGD----------IPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGR- 69 (143)
Q Consensus 1 l~~~a~~i~~~~~g~----------~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~- 69 (143)
|+++|+.+++.+++. .++.+++|++|||||+|||++|++|+++++++||||+||+|++.|++.......
T Consensus 190 I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~ 269 (310)
T TIGR00588 190 IRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSR 269 (310)
T ss_pred HHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccc
Confidence 578999999988765 467799999999999999999999999998899999999999999975532221
Q ss_pred --CCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHH
Q 032317 70 --KQKTSSPEQTREVLQLWLPKEEWVPINPLLVGFGQ 104 (143)
Q Consensus 70 --~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 104 (143)
..+..+++++++...+.+.+ +..|.|+++.+-.
T Consensus 270 ~~~~~~~~~~~i~~~~~~~~g~--~ag~aq~~lf~~~ 304 (310)
T TIGR00588 270 AKGPSPFARKELGNFFRSLWGP--YAGWAQAVLFSAD 304 (310)
T ss_pred cccCChhHHHHHHHHHHHHhcC--cchHHHHHHHHHH
Confidence 12356788888888887853 7777777665543
No 16
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.58 E-value=2.2e-15 Score=116.43 Aligned_cols=100 Identities=19% Similarity=0.265 Sum_probs=74.7
Q ss_pred CHHHHHHHHHHcCC----------CCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCC
Q 032317 1 MKKIAPICLTKYDG----------DIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRK 70 (143)
Q Consensus 1 l~~~a~~i~~~~~g----------~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~ 70 (143)
|..+|+.|++++|| .+.+.++.|.+|||||+|+||||+++++++..++|||+||+|++.........+.+
T Consensus 188 I~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y~l~~~~g~k 267 (323)
T KOG2875|consen 188 ISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDYILPGLSGAK 267 (323)
T ss_pred HHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcccCCCccccc
Confidence 45789999999998 23468899999999999999999999999999999999999999954222222332
Q ss_pred -CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHH
Q 032317 71 -QKTSSPEQTREVLQLWLPKEEWVPINPLLVGF 102 (143)
Q Consensus 71 -~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~ 102 (143)
.+...+.++..+....+ +.+..|.++++.-
T Consensus 268 ~l~~ki~~ev~~~f~~~~--G~YAGwAQ~~lfs 298 (323)
T KOG2875|consen 268 ELTPKINGEVSNFFRSLW--GEYAGWAQAVLFS 298 (323)
T ss_pred cCCcchhHHHHHHHHHHh--cccccchhheeec
Confidence 34456777777666654 3355555655543
No 17
>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=99.30 E-value=4.9e-13 Score=71.00 Aligned_cols=29 Identities=52% Similarity=0.968 Sum_probs=26.2
Q ss_pred cCCCCcCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 12 YDGDIPSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 12 ~~g~~p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
|+|.+|.++++|++|||||+|||++|+.|
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 66889999999999999999999999986
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.28 E-value=9.5e-12 Score=98.04 Aligned_cols=85 Identities=21% Similarity=0.335 Sum_probs=63.2
Q ss_pred CHHHHHHHHH-HcCCCCc----CcHHHHhcCCCCcHHHHHHHHHHhcCCCccc-cccchHHHHHHHhcccCCCCCCCCCC
Q 032317 1 MKKIAPICLT-KYDGDIP----SSLDELLLLPGIGPKMAHLVMNVGWNNVQGI-CVDTHVHRICNRLGWVSQPGRKQKTS 74 (143)
Q Consensus 1 l~~~a~~i~~-~~~g~~p----~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~-pvD~~v~Rv~~Rl~~~~~~~~~~~~~ 74 (143)
|+++|+.+.+ +...+.+ +.+++|++|||||+|||++|++|+++++++| +.|.+++|.+ . ..
T Consensus 182 L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----------~~ 248 (283)
T PRK10308 182 LIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----------GM 248 (283)
T ss_pred HHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----------cC
Confidence 4677888776 2222112 2478999999999999999999999999999 7999999844 1 23
Q ss_pred CHHHHHHHHHHhCCCCChhhHHHH
Q 032317 75 SPEQTREVLQLWLPKEEWVPINPL 98 (143)
Q Consensus 75 ~~~~~~~~l~~~~p~~~~~~~~~~ 98 (143)
+++++++.++.+-|-..|..+|.|
T Consensus 249 ~~~~~~~~a~~w~P~rsya~~~LW 272 (283)
T PRK10308 249 TPAQIRRYAERWKPWRSYALLHIW 272 (283)
T ss_pred CHHHHHHHHHhcCCHHHHHHHHHH
Confidence 577888888887775555555554
No 19
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.16 E-value=5.5e-11 Score=93.77 Aligned_cols=66 Identities=24% Similarity=0.396 Sum_probs=51.3
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCCCcccc-ccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNNVQGIC-VDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPK 89 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~p-vD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~ 89 (143)
+.+|+|.+|+|||++||++||+|+++++++|| .|.++++.+.+++..+. ..+...+....+.+-|-
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~------~~~~~~~~~~~e~w~p~ 261 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPT------RPTEKEVRELAERWGPY 261 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCC------CchHHHHHHHHhcccCH
Confidence 45799999999999999999999999999999 78888888888873321 23344456666665553
No 20
>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=99.07 E-value=1.4e-10 Score=85.22 Aligned_cols=56 Identities=27% Similarity=0.457 Sum_probs=45.4
Q ss_pred CHHHHHHHHHHcCCCC--------cCc---HHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHH
Q 032317 1 MKKIAPICLTKYDGDI--------PSS---LDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICN 59 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~--------p~~---~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~ 59 (143)
|+++|++|+++|+|++ |++ +++|++|||||+|||++||++.-++ |-|----+|-+.
T Consensus 84 Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~---~~~~~~~~~~~~ 150 (177)
T TIGR03252 84 VQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQ---LGVTPEGWREAA 150 (177)
T ss_pred HHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHH---hCCCCcchHHhc
Confidence 5789999999999997 877 7899999999999999999988655 345444455443
No 21
>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=98.24 E-value=2.8e-07 Score=42.47 Aligned_cols=17 Identities=35% Similarity=1.226 Sum_probs=11.5
Q ss_pred ccCCCCCCCCCCcCccC
Q 032317 107 CTPIRPRCGMCSVSELC 123 (143)
Q Consensus 107 C~~~~P~C~~CpL~~~C 123 (143)
|++++|+|+.|||+++|
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 88999999999999988
No 22
>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=98.06 E-value=4.1e-05 Score=51.54 Aligned_cols=81 Identities=27% Similarity=0.372 Sum_probs=51.4
Q ss_pred HHHHHHHHHcCCCCc--------CcHHHHhcCCCCcHHHHHHHHHHh---cCCC-ccccccchHHHHHHHhcccCCCCCC
Q 032317 3 KIAPICLTKYDGDIP--------SSLDELLLLPGIGPKMAHLVMNVG---WNNV-QGICVDTHVHRICNRLGWVSQPGRK 70 (143)
Q Consensus 3 ~~a~~i~~~~~g~~p--------~~~~~L~~lpGIG~ktA~~Il~~~---~~~~-~~~pvD~~v~Rv~~Rl~~~~~~~~~ 70 (143)
.+-..+.+.||.--| ++++++++-=|.+.+=|..|...+ .+++ ..+++|+|+.|++.|+++++.
T Consensus 16 ~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~~~~d~~~~~D~~v~r~~~r~~~~~~---- 91 (108)
T PF00730_consen 16 KIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAILGRPDPFPPVDTHVRRVLQRLGGIPE---- 91 (108)
T ss_dssp HHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHHC-SSSS-TTSHHHHHHHHHHTSSSS----
T ss_pred HHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhhhcccceecCcHHHHHHHHHHcCCCC----
Confidence 344567777872111 223333444577755555554443 1433 378999999999999999874
Q ss_pred CCCCCHHHHHHHHHHhCCC
Q 032317 71 QKTSSPEQTREVLQLWLPK 89 (143)
Q Consensus 71 ~~~~~~~~~~~~l~~~~p~ 89 (143)
..+++++++.+++.+++
T Consensus 92 --~~~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 92 --KKTKEETEKKLEELWPP 108 (108)
T ss_dssp --STTHHHHHHHHHHHGTT
T ss_pred --CCCHHHHHHHHHhhCcC
Confidence 35789999999877753
No 23
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=97.78 E-value=8.3e-06 Score=41.57 Aligned_cols=22 Identities=45% Similarity=1.200 Sum_probs=19.6
Q ss_pred hccCCCCCCCCCCcCccCcccc
Q 032317 106 ICTPIRPRCGMCSVSELCPSAF 127 (143)
Q Consensus 106 ~C~~~~P~C~~CpL~~~C~~~~ 127 (143)
+|++++|+|+.|||...|.++.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999998643
No 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=97.63 E-value=9.3e-05 Score=54.97 Aligned_cols=82 Identities=16% Similarity=0.099 Sum_probs=58.8
Q ss_pred cHHHHh-cCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCC--CCChhhH
Q 032317 19 SLDELL-LLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLP--KEEWVPI 95 (143)
Q Consensus 19 ~~~~L~-~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p--~~~~~~~ 95 (143)
.||.|. .++|||.|-|+-+|...--. +..++|.|+.|.+.|.|.+...+...+.+.|.++++.+...-. ....+.+
T Consensus 118 aRE~Lv~nikGiGyKEASHFLRNVG~~-D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g~s~gel 196 (210)
T COG1059 118 ARELLVENIKGIGYKEASHFLRNVGFE-DLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVGISLGEL 196 (210)
T ss_pred HHHHHHHHcccccHHHHHHHHHhcChh-HHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 688888 79999999999999887444 5667999999999999998754433334567677766655421 2335556
Q ss_pred HHHHHH
Q 032317 96 NPLLVG 101 (143)
Q Consensus 96 ~~~l~~ 101 (143)
+..||.
T Consensus 197 DL~IWY 202 (210)
T COG1059 197 DLYIWY 202 (210)
T ss_pred HHHHHH
Confidence 555554
No 25
>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=97.61 E-value=2.7e-05 Score=59.84 Aligned_cols=54 Identities=24% Similarity=0.353 Sum_probs=42.5
Q ss_pred ccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHH
Q 032317 48 ICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPKEEWVPINPLLVGFGQ 104 (143)
Q Consensus 48 ~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 104 (143)
+|+||||.||+.+||++...... .++..++.+.+.++. ++++-.+..+|..+|.
T Consensus 177 iPLDtHv~~var~LGL~~rk~~d--~k~A~elT~~lr~~~-p~DPvKYDFAL~~~Gi 230 (232)
T PF09674_consen 177 IPLDTHVFRVARKLGLLKRKSAD--WKAARELTEALREFD-PDDPVKYDFALFRLGI 230 (232)
T ss_pred ccchHhHHHHHHHcCCccCCCcc--HHHHHHHHHHHHhcC-CCCCcchhhhcccCCc
Confidence 89999999999999999653322 345677777787755 5888899999988874
No 26
>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=97.54 E-value=3.7e-05 Score=58.97 Aligned_cols=54 Identities=26% Similarity=0.352 Sum_probs=41.9
Q ss_pred ccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHH
Q 032317 48 ICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPKEEWVPINPLLVGFGQ 104 (143)
Q Consensus 48 ~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~ 104 (143)
+|+||||.||+.+||++...... .++..++.+.+.+ +.++++-.+..||..+|.
T Consensus 174 iPLDtH~~rvar~LgL~~Rk~~d--~kaa~ElT~~Lr~-~dp~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 174 LPLDTHVFRIAKKLKLLKRKSYD--LKAAIEITEALRE-LNPEDPIKYDFALFRLGQ 227 (229)
T ss_pred eechHhHHHHHHHhCCcccCchh--HHHHHHHHHHHHh-cCCCCCcchhhhcccCCc
Confidence 89999999999999998653322 3456667777766 455889999999988885
No 27
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=97.32 E-value=0.00022 Score=54.23 Aligned_cols=77 Identities=10% Similarity=0.085 Sum_probs=51.6
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCCccccccc-hHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCCCC-hhhHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNNVQGICVDT-HVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPKEE-WVPINPL 98 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~-~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~~~-~~~~~~~ 98 (143)
+.|..++|||++|+.++|.|++++++++|+|- .|++=+..+..... -..+.+++++-+.+-|... ...+.+-
T Consensus 165 ~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~------~p~~~evekl~e~~kpyRtvaawYlWk 238 (254)
T KOG1918|consen 165 ERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP------LPLPKEVEKLCEKCKPYRTVAAWYLWK 238 (254)
T ss_pred HHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC------CCchHHHHHHhhhccchHHHHHHHHHh
Confidence 44667999999999999999999999999865 45555555554432 2346677776666555332 3344455
Q ss_pred HHHHH
Q 032317 99 LVGFG 103 (143)
Q Consensus 99 l~~~G 103 (143)
|.+..
T Consensus 239 i~~~~ 243 (254)
T KOG1918|consen 239 IIKLD 243 (254)
T ss_pred hhhhh
Confidence 55544
No 28
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=97.29 E-value=0.00019 Score=36.45 Aligned_cols=21 Identities=48% Similarity=0.808 Sum_probs=18.4
Q ss_pred HHhcCCCCcHHHHHHHHHHhc
Q 032317 22 ELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 22 ~L~~lpGIG~ktA~~Il~~~~ 42 (143)
.|.++||||+++|+.|+.+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~~ 22 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhcc
Confidence 688999999999999998653
No 29
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.22 E-value=0.00052 Score=42.39 Aligned_cols=39 Identities=31% Similarity=0.527 Sum_probs=29.2
Q ss_pred HHHHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 3 KIAPICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 3 ~~a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|+.|.+.|+. -.-.+.++|.++||||+.+|..|..|-
T Consensus 14 ~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 14 KTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp HHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHH
Confidence 468889999974 124578999999999999999999885
No 30
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.90 E-value=0.0094 Score=44.53 Aligned_cols=41 Identities=24% Similarity=0.238 Sum_probs=30.7
Q ss_pred HHHHHHHHHcCC------CCcCcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 3 KIAPICLTKYDG------DIPSSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 3 ~~a~~i~~~~~g------~~p~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+.|+.|++.|+. ..-.+.+.|.++||||+++|..|+...-+
T Consensus 84 k~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 84 KLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 467778888875 22457788889999999999998866543
No 31
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=95.77 E-value=0.011 Score=36.39 Aligned_cols=24 Identities=46% Similarity=0.743 Sum_probs=19.4
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+.++|.++||||++.|..|+.+-
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 467999999999999999999986
No 32
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.67 E-value=0.011 Score=42.64 Aligned_cols=24 Identities=46% Similarity=0.776 Sum_probs=21.9
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+.++|..|||||++.|.+|..+-
T Consensus 94 As~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 94 ASAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred cCHHHHHHCCCCCHHHHHHHHHHH
Confidence 366999999999999999999997
No 33
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.57 E-value=0.012 Score=44.04 Aligned_cols=40 Identities=23% Similarity=0.289 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCCC------cCcHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 3 KIAPICLTKYDGDI------PSSLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 3 ~~a~~i~~~~~g~~------p~~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
++|..|++.|+-+- -+|.+.|.++||||+|||.-|++-.-
T Consensus 84 K~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 84 KLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred HHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 35556666554321 35667788888888888888665443
No 34
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=95.35 E-value=0.0064 Score=45.52 Aligned_cols=28 Identities=32% Similarity=0.394 Sum_probs=24.0
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNNV 45 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~~ 45 (143)
.-.+.|.+|||||+|+|.-++.+.+.++
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 4468899999999999999988888764
No 35
>PRK00076 recR recombination protein RecR; Reviewed
Probab=95.33 E-value=0.014 Score=43.92 Aligned_cols=27 Identities=33% Similarity=0.393 Sum_probs=23.5
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHhcCCC
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVGWNNV 45 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~~~~~ 45 (143)
-.+.|.+|||||+|||.-++.+.+.++
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll~~~ 35 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLLQRD 35 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 357888999999999999999998764
No 36
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.31 E-value=0.014 Score=43.75 Aligned_cols=27 Identities=33% Similarity=0.398 Sum_probs=23.4
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHhcCCC
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVGWNNV 45 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~~~~~ 45 (143)
-.+.|.+|||||+|||.-++.+.+.++
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 357888999999999999999988764
No 37
>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=95.29 E-value=0.031 Score=34.67 Aligned_cols=31 Identities=32% Similarity=0.456 Sum_probs=21.4
Q ss_pred HHHcCCCCcCcHHH-HhcCCCCcHHHHHHHHHH
Q 032317 9 LTKYDGDIPSSLDE-LLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 9 ~~~~~g~~p~~~~~-L~~lpGIG~ktA~~Il~~ 40 (143)
+..+...+ .+.++ |.+|||||+.+|..|--|
T Consensus 35 i~~l~~~i-~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 35 IKALPYPI-TSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHSSS-H-HSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHhCCHhH-hhHHHHHhhCCCCCHHHHHHHHHH
Confidence 33444444 23365 999999999999998655
No 38
>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=95.26 E-value=0.019 Score=39.77 Aligned_cols=24 Identities=46% Similarity=0.772 Sum_probs=21.6
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+.++|.++||||+++|..|+.+-
T Consensus 65 A~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 65 ASLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHHH
Confidence 356899999999999999999985
No 39
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.14 E-value=0.019 Score=42.68 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=23.9
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|++-.-++
T Consensus 105 ~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 105 GDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 567999999999999999999887665
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=95.11 E-value=0.018 Score=43.43 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=23.7
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNNV 45 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~~ 45 (143)
+-.+.|.+|||||+|||.-++.+.+.++
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 39 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLALYLLDKS 39 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 3457788999999999999999988764
No 41
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=95.06 E-value=0.08 Score=42.95 Aligned_cols=70 Identities=23% Similarity=0.345 Sum_probs=48.4
Q ss_pred cCcHHHHhcCCCCcHHHHHHHHHHh---cCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCC
Q 032317 17 PSSLDELLLLPGIGPKMAHLVMNVG---WNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPK 89 (143)
Q Consensus 17 p~~~~~L~~lpGIG~ktA~~Il~~~---~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~ 89 (143)
|+|.++|+-.|||||+|+.|..+.| ||.++.+ =|-- +.+.-+|.-+..+......+|.++-+++++.+..
T Consensus 274 p~Df~elLl~~GiGpstvRALalVAEvIyg~~~s~-rDP~--~yafA~GGKDgvP~pV~~~~yde~I~~l~~~ve~ 346 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVAEVIYGEPPSF-RDPV--KYAFAVGGKDGVPFPVNRKTYDELIEFLEELVEK 346 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHHHHHhCCCCCc-CCch--hhhhhhcCCCCCCCCcchhhHHHHHHHHHHHHHh
Confidence 7899999999999999999998887 6654332 2221 1555566654433333456788888888777653
No 42
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.88 E-value=0.025 Score=42.53 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=23.8
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|.+-.-++
T Consensus 104 ~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 104 EDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 567999999999999999999887665
No 43
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.79 E-value=0.025 Score=42.72 Aligned_cols=27 Identities=26% Similarity=0.324 Sum_probs=23.9
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||.|||.-|++-.-++
T Consensus 105 ~d~~~L~k~PGIGkKtAerivleLk~K 131 (201)
T COG0632 105 EDVKALSKIPGIGKKTAERIVLELKGK 131 (201)
T ss_pred cChHhhhcCCCCCHHHHHHHHHHHhhh
Confidence 467999999999999999999987665
No 44
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.75 E-value=0.028 Score=41.94 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=23.7
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|.+-.-++
T Consensus 105 ~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 105 QDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 567999999999999999999887654
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.70 E-value=0.029 Score=42.14 Aligned_cols=27 Identities=19% Similarity=0.120 Sum_probs=23.6
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|..-.-++
T Consensus 104 ~D~~~L~kvpGIGkKtAerIilELkdK 130 (197)
T PRK14603 104 GDARLLTSASGVGKKLAERIALELKGK 130 (197)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 567999999999999999999877554
No 46
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.69 E-value=0.03 Score=42.26 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=23.6
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|+.-.-++
T Consensus 106 ~D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 106 EDVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred CCHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 577999999999999999999877554
No 47
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.64 E-value=0.031 Score=41.94 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=23.8
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.|.++||||+|||.-|+.-.-++
T Consensus 105 ~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 105 GDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 567999999999999999999887654
No 48
>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=94.61 E-value=0.04 Score=33.21 Aligned_cols=39 Identities=28% Similarity=0.372 Sum_probs=26.8
Q ss_pred HHHHHHHHH-cCC--C-CcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 3 KIAPICLTK-YDG--D-IPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 3 ~~a~~i~~~-~~g--~-~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
+.|+.|.+. |.. + .-.+.++|.++||||+++|+.|...+
T Consensus 16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 16 KRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 356677766 221 0 01356889999999999999987654
No 49
>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=94.58 E-value=0.034 Score=36.14 Aligned_cols=43 Identities=21% Similarity=0.412 Sum_probs=30.6
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCC
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQP 67 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~ 67 (143)
+.|+++||||+-||..++... +....|+ +...+..-+|+.+..
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~---~~~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFK---SAKQLASYAGLAPRP 44 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhcc---cchhhhhcccccccc
Confidence 468899999999999999998 4334553 445555556766543
No 50
>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=94.57 E-value=0.1 Score=32.24 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=10.1
Q ss_pred HHHhc-CCCCcHHHHHHHHHH
Q 032317 21 DELLL-LPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~-lpGIG~ktA~~Il~~ 40 (143)
++|.. +||||+++|..|+.+
T Consensus 16 ~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 16 EELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHhHCCCCCHHHHHHHHHH
Confidence 44444 555555555555544
No 51
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=94.50 E-value=0.034 Score=33.51 Aligned_cols=36 Identities=31% Similarity=0.649 Sum_probs=26.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHR 56 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~R 56 (143)
.++|.++||||+++|..+...++...+.+ .+.....
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~G~~t~~~l-~~a~~~~ 39 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEAGIKTLEDL-ANADPEE 39 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHTTCSSHHHH-HTSHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhcCCCcHHHH-HcCCHHH
Confidence 47899999999999999999877654333 4444433
No 52
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.44 E-value=0.043 Score=40.96 Aligned_cols=20 Identities=30% Similarity=0.609 Sum_probs=17.8
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|.++|||||+||..|+..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~ 92 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSG 92 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHh
Confidence 57889999999999999764
No 53
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=94.36 E-value=0.041 Score=44.09 Aligned_cols=26 Identities=38% Similarity=0.699 Sum_probs=24.2
Q ss_pred CcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 16 IPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
=|++.|+|+.++||||+|..++.+.|
T Consensus 264 ~p~~feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 264 QPSDFEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred CccCHHHHHhcCCCCHHHHHHHHHHH
Confidence 47999999999999999999999887
No 54
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.18 E-value=0.044 Score=38.53 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=24.3
Q ss_pred HcCCCCc---CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 11 KYDGDIP---SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 11 ~~~g~~p---~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+++.+. .+.++|.+||||||..|..|...+
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nG 81 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNA 81 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCC
Confidence 4555553 467889999999999999999643
No 55
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.11 E-value=0.038 Score=41.19 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=22.3
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|.+.| ++||||+|||.-|++-.-++
T Consensus 105 ~D~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 105 EDKAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCHhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 466889 99999999999999877654
No 56
>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=93.65 E-value=0.075 Score=35.30 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=23.6
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHhcCCC
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVGWNNV 45 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~~~~~ 45 (143)
...+|..|||||+.||.-+...++..+
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 357899999999999999999888764
No 57
>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=93.64 E-value=0.12 Score=35.83 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=29.5
Q ss_pred HHHHHHHHHcCCC-CcCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 3 KIAPICLTKYDGD-IPSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 3 ~~a~~i~~~~~g~-~p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|+.|++.++.. -..+.++|..++|||+++++-|.-|
T Consensus 79 ~~A~~Ii~~R~~~g~f~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 79 AKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred HHHHHHHHHHHhcCCcCCHHHHHcCCCCCHHHHHHHHhc
Confidence 4577788776422 2378999999999999999988765
No 58
>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=93.56 E-value=0.068 Score=39.97 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=22.3
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
+|.+.|.++||||+|||.-|++-.-++
T Consensus 104 ~d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 104 EEVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 567889999999999999999665443
No 59
>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=93.01 E-value=0.084 Score=39.46 Aligned_cols=20 Identities=35% Similarity=0.725 Sum_probs=18.0
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|++++|||||+|-+||..
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSN 91 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhc
Confidence 67999999999999999774
No 60
>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=93.01 E-value=0.12 Score=31.87 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=19.2
Q ss_pred cHHHHhcCCCCcHHHHHHHHHH
Q 032317 19 SLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.++|.+++|||.++|+-|..+
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4588999999999999999876
No 61
>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=92.84 E-value=0.078 Score=28.10 Aligned_cols=15 Identities=33% Similarity=0.388 Sum_probs=11.7
Q ss_pred HhcCCCCcHHHHHHH
Q 032317 23 LLLLPGIGPKMAHLV 37 (143)
Q Consensus 23 L~~lpGIG~ktA~~I 37 (143)
+.+++|||++|+.-+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 567999999999864
No 62
>PRK00024 hypothetical protein; Reviewed
Probab=92.70 E-value=0.17 Score=38.71 Aligned_cols=39 Identities=28% Similarity=0.413 Sum_probs=30.2
Q ss_pred HHHHHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 2 KKIAPICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 2 ~~~a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
.++|+.|.++||+ -+-.+.++|.+++|||+..|..|+..
T Consensus 44 ~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~ 85 (224)
T PRK00024 44 LDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85 (224)
T ss_pred HHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHH
Confidence 3688999999975 22457899999999999988666443
No 63
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.62 E-value=0.18 Score=38.51 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=30.2
Q ss_pred HHHHHHHHHHc---CC---CCcCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 2 KKIAPICLTKY---DG---DIPSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 2 ~~~a~~i~~~~---~g---~~p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
.++|+.|.++| |+ -+-.+.++|.+++|||+..|..|+..
T Consensus 35 ~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~ 79 (218)
T TIGR00608 35 LSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAA 79 (218)
T ss_pred HHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHH
Confidence 46899999998 54 23467899999999999877666543
No 64
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=92.33 E-value=0.34 Score=34.09 Aligned_cols=36 Identities=19% Similarity=0.334 Sum_probs=28.4
Q ss_pred HHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 3 KIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 3 ~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|+.|++ +|-+ .+.|+|+.+||||+++...+--+-
T Consensus 72 ~~A~~IV~--nGpf-~sveDL~~V~GIgekqk~~l~k~~ 107 (132)
T PRK02515 72 TLAGKIVK--NAPY-DSVEDVLNLPGLSERQKELLEANL 107 (132)
T ss_pred HHHHHHHH--CCCC-CCHHHHHcCCCCCHHHHHHHHHhh
Confidence 36778885 3533 789999999999999988887764
No 65
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.26 E-value=0.13 Score=38.63 Aligned_cols=20 Identities=30% Similarity=0.687 Sum_probs=18.4
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|++++||||++|-.|++.
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHh
Confidence 66899999999999999994
No 66
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=91.86 E-value=0.22 Score=40.66 Aligned_cols=39 Identities=15% Similarity=0.205 Sum_probs=31.3
Q ss_pred HHHHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 3 KIAPICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 3 ~~a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|+.|+++||+ .+-.+.++|.+.+|||++.|..|....
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l 339 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGL 339 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHH
Confidence 578999999985 345678999999999999999864443
No 67
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=91.84 E-value=0.14 Score=27.89 Aligned_cols=16 Identities=38% Similarity=0.526 Sum_probs=13.5
Q ss_pred hcCCCCcHHHHHHHHH
Q 032317 24 LLLPGIGPKMAHLVMN 39 (143)
Q Consensus 24 ~~lpGIG~ktA~~Il~ 39 (143)
-.+||||++||--++.
T Consensus 19 ~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 19 PGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCcccHHHHHHHHH
Confidence 4689999999988764
No 68
>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=91.11 E-value=0.16 Score=40.57 Aligned_cols=28 Identities=43% Similarity=0.775 Sum_probs=22.7
Q ss_pred CCcCcHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 15 DIPSSLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 15 ~~p~~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
+.|..+.+|+++|||||+||..+-..++
T Consensus 79 ~~~~~l~~l~~i~GiGpk~a~~l~~lGi 106 (307)
T cd00141 79 DVPPGLLLLLRVPGVGPKTARKLYELGI 106 (307)
T ss_pred cchHHHHHHHcCCCCCHHHHHHHHHcCC
Confidence 4678888999999999999988874333
No 69
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=90.48 E-value=0.19 Score=40.66 Aligned_cols=29 Identities=28% Similarity=0.382 Sum_probs=23.8
Q ss_pred CCCCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 13 DGDIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 13 ~g~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..++|..+.+|+++|||||+||..+-..+
T Consensus 81 ~~~~p~~l~~l~~i~GiGpk~a~~l~~lG 109 (334)
T smart00483 81 NDEVYKSLKLFTNVFGVGPKTAAKWYRKG 109 (334)
T ss_pred cCcHHHHHHHHHccCCcCHHHHHHHHHhC
Confidence 34567888999999999999998886633
No 70
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=89.79 E-value=0.75 Score=37.12 Aligned_cols=26 Identities=38% Similarity=0.516 Sum_probs=22.8
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
.+.+++.+|||||+++|..|--|.-.
T Consensus 53 ~S~~ea~~lP~iG~kia~ki~Eilet 78 (353)
T KOG2534|consen 53 TSGEEAEKLPGIGPKIAEKIQEILET 78 (353)
T ss_pred ccHHHhcCCCCCCHHHHHHHHHHHHc
Confidence 57899999999999999999888743
No 71
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=89.14 E-value=0.39 Score=28.36 Aligned_cols=24 Identities=29% Similarity=0.328 Sum_probs=17.0
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 20 LDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
++.+..+.|||+.||.-....++.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--
T ss_pred CcchhhcccccHHHHHHHHHhCCC
Confidence 357889999999999998886664
No 72
>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=88.94 E-value=0.32 Score=30.77 Aligned_cols=19 Identities=37% Similarity=0.627 Sum_probs=16.0
Q ss_pred HHhcCCCCcHHHHHHHHHH
Q 032317 22 ELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 22 ~L~~lpGIG~ktA~~Il~~ 40 (143)
-+-.+||||++||.-++.-
T Consensus 23 ~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCCCCcccHHHHHHHHHH
Confidence 3557999999999999866
No 73
>PRK08609 hypothetical protein; Provisional
Probab=88.13 E-value=0.38 Score=41.67 Aligned_cols=24 Identities=38% Similarity=0.627 Sum_probs=21.0
Q ss_pred CCcCcHHHHhcCCCCcHHHHHHHH
Q 032317 15 DIPSSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 15 ~~p~~~~~L~~lpGIG~ktA~~Il 38 (143)
++|....+|+++|||||+||..+-
T Consensus 82 ~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 82 EVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred hCcHHHHHHhcCCCCCHHHHHHHH
Confidence 578888899999999999998765
No 74
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=87.46 E-value=0.48 Score=38.20 Aligned_cols=24 Identities=38% Similarity=0.560 Sum_probs=20.7
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.++++|++.||||.++|.-|+..-
T Consensus 327 A~~~~llRVPGiG~ksa~rIv~~R 350 (404)
T COG4277 327 APYKELLRVPGIGVKSARRIVMTR 350 (404)
T ss_pred cCHHHhcccCCCChHHHHHHHHHh
Confidence 356999999999999999888764
No 75
>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=87.45 E-value=0.64 Score=31.40 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=22.6
Q ss_pred CCCcCc---HHHHhcCCCCcHHHHHHHHHHhc
Q 032317 14 GDIPSS---LDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 14 g~~p~~---~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
-++|.+ .-.|.++.|||+++|..|+..+-
T Consensus 5 ~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 5 TNLPGNKPIYIALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp TCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTT
T ss_pred CcCCCCcchHhHHhhhhccCHHHHHHHHHHcC
Confidence 345543 57899999999999999998873
No 76
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=87.14 E-value=1.1 Score=34.31 Aligned_cols=39 Identities=23% Similarity=0.287 Sum_probs=30.6
Q ss_pred HHHHHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 2 KKIAPICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 2 ~~~a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
..+|+.|.++||+ -...+.++|.++||||+.-|--+...
T Consensus 44 ~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~ 85 (224)
T COG2003 44 LDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAA 85 (224)
T ss_pred HHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHH
Confidence 4689999999986 34678999999999998766554443
No 77
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=87.13 E-value=0.37 Score=37.13 Aligned_cols=24 Identities=29% Similarity=0.612 Sum_probs=16.9
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
+.|..|||||++++..++..+|+-
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~S 26 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFES 26 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCC
Confidence 456677777777777777776653
No 78
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=87.00 E-value=0.77 Score=28.02 Aligned_cols=35 Identities=34% Similarity=0.450 Sum_probs=22.7
Q ss_pred HHHHHHHHH--cCCCCcCcHHHHhcCCCCcHHHHHHHH
Q 032317 3 KIAPICLTK--YDGDIPSSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 3 ~~a~~i~~~--~~g~~p~~~~~L~~lpGIG~ktA~~Il 38 (143)
+.|+.|++. -.|. -.+.++|..++|||+++.+-+.
T Consensus 25 ~~A~~Iv~~R~~~G~-f~s~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 25 KQAKAIVEYREKNGP-FKSLEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp HHHHHHHHHHHHH-S--SSGGGGGGSTT--HHHHHHHC
T ss_pred HHHHHHHHHHHhCcC-CCCHHHHhhCCCCCHHHHHHHH
Confidence 356666663 2243 3788999999999999988664
No 79
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.95 E-value=0.53 Score=35.41 Aligned_cols=21 Identities=38% Similarity=0.646 Sum_probs=18.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~ 40 (143)
.+.|++..|||||+|=+||+-
T Consensus 71 F~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 71 FEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred HHHHhCcCCcCHHHHHHHHcC
Confidence 367999999999999999964
No 80
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.44 E-value=0.56 Score=34.94 Aligned_cols=20 Identities=20% Similarity=0.290 Sum_probs=18.3
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|++..|||||+|=+||+-
T Consensus 73 ~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHhCcCCcCHHHHHHHHcc
Confidence 66899999999999999994
No 81
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=86.36 E-value=0.77 Score=40.60 Aligned_cols=39 Identities=21% Similarity=0.289 Sum_probs=30.8
Q ss_pred HHHHHHHHHcCCCC----cCcHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 3 KIAPICLTKYDGDI----PSSLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 3 ~~a~~i~~~~~g~~----p~~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
..|+.|.+.|+. + ..+.++|.+++|||+++|..|..|--
T Consensus 522 ~~ak~L~~~f~s-l~~l~~As~eeL~~i~GIG~~~A~sI~~ff~ 564 (665)
T PRK07956 522 KAAKALARHFGS-LEALRAASEEELAAVEGVGEVVAQSIVEFFA 564 (665)
T ss_pred HHHHHHHHHcCC-HHHHHhCCHHHHhccCCcCHHHHHHHHHHHh
Confidence 356778877753 3 35678999999999999999988853
No 82
>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=86.23 E-value=1.6 Score=34.94 Aligned_cols=26 Identities=38% Similarity=0.498 Sum_probs=22.0
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
.+.+++.+|||||+.+|+.|--+.-.
T Consensus 42 ~~~~~~~~ipgiG~~ia~kI~E~~~t 67 (307)
T cd00141 42 ESLEEAKKLPGIGKKIAEKIEEILET 67 (307)
T ss_pred CCHHHhcCCCCccHHHHHHHHHHHHc
Confidence 45678899999999999999888643
No 83
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=85.90 E-value=1.4 Score=30.51 Aligned_cols=65 Identities=23% Similarity=0.471 Sum_probs=43.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCC-CCCCC-CCHHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPG-RKQKT-SSPEQTREVLQL 85 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~-~~~~~-~~~~~~~~~l~~ 85 (143)
+.+|.++||||+..|..++.-++.-.+.+ ...+..++..+++-++... ..... .+.+++++++++
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~AGv~Tv~~L-A~~~p~~L~~~l~~~n~~~~~~r~~~p~~~~v~~WI~~ 118 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEHAGVDTVEEL-AQRNPQNLHQKLGRLNRKLKLRRQLCPSLEEVQEWIEQ 118 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHHhCcCcHHHH-HhCCHHHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHH
Confidence 57789999999999999988888764443 7788888888876542111 11111 455666666653
No 84
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=85.81 E-value=1.7 Score=35.10 Aligned_cols=32 Identities=31% Similarity=0.425 Sum_probs=24.2
Q ss_pred HHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 9 LTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 9 ~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
++.+.-.+ .+.++|.+|||||..+|+.|--+.
T Consensus 37 i~~l~~~i-~~~~~l~~lpgIG~~ia~kI~Eil 68 (334)
T smart00483 37 LKSLPFPI-NSMKDLKGLPGIGDKIKKKIEEII 68 (334)
T ss_pred HHhCCCCC-CCHHHHhcCCCccHHHHHHHHHHH
Confidence 44444444 456789999999999999998665
No 85
>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=85.74 E-value=0.89 Score=40.13 Aligned_cols=40 Identities=30% Similarity=0.484 Sum_probs=31.3
Q ss_pred HHHHHHHHHcCCCC----cCcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 3 KIAPICLTKYDGDI----PSSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 3 ~~a~~i~~~~~g~~----p~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+.|+.|.+.|+ .+ ..+.++|.+++|||+++|..|..|--+
T Consensus 509 ~~ak~L~~~f~-sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~ 552 (652)
T TIGR00575 509 VTAKNLAKHFG-TLDKLKAASLEELLSVEGVGPKVAESIVNFFHD 552 (652)
T ss_pred HHHHHHHHHhC-CHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhh
Confidence 45777888876 33 246789999999999999999988543
No 86
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.72 E-value=0.66 Score=34.51 Aligned_cols=21 Identities=33% Similarity=0.469 Sum_probs=18.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~ 40 (143)
.+.|++..|||||+|=+||+-
T Consensus 72 F~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 72 FEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHhccCCccHHHHHHHHcC
Confidence 366899999999999999974
No 87
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.63 E-value=0.74 Score=34.73 Aligned_cols=20 Identities=20% Similarity=0.307 Sum_probs=18.3
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|++..|||||+|=.||+.
T Consensus 74 ~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 74 IVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHhCCCCcCHHHHHHHHhh
Confidence 66899999999999999995
No 88
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.29 E-value=0.7 Score=34.47 Aligned_cols=20 Identities=25% Similarity=0.340 Sum_probs=18.0
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|++..|||||+|=+||+.
T Consensus 73 ~~Li~V~GIGpK~AL~iLs~ 92 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIISN 92 (188)
T ss_pred HHHhccCCccHHHHHHHHcC
Confidence 66899999999999999964
No 89
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=85.08 E-value=0.93 Score=29.75 Aligned_cols=38 Identities=34% Similarity=0.370 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCCcCcHHH----Hhc-CCCCcHHHHHHHHHH
Q 032317 3 KIAPICLTKYDGDIPSSLDE----LLL-LPGIGPKMAHLVMNV 40 (143)
Q Consensus 3 ~~a~~i~~~~~g~~p~~~~~----L~~-lpGIG~ktA~~Il~~ 40 (143)
+.|+.|.+.||.+.-+..++ |.. ++|||-++||.|..-
T Consensus 23 ~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 23 KLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp HHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT
T ss_pred HHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH
Confidence 56788888898744333322 555 899999999999885
No 90
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.92 E-value=0.73 Score=34.61 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=19.5
Q ss_pred HHHhcCCCCcHHHHHHHHHH-hcC
Q 032317 21 DELLLLPGIGPKMAHLVMNV-GWN 43 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~-~~~ 43 (143)
+.|++..|||||+|=+||+. ..+
T Consensus 72 ~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 72 ELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred HHHhCcCCcCHHHHHHHHcCCCHH
Confidence 66899999999999999994 443
No 91
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.18 E-value=0.81 Score=34.32 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=18.3
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|+++.||||++|=+||+.
T Consensus 73 ~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 73 ELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHhCcCCcCHHHHHHHHcC
Confidence 66899999999999999994
No 92
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=83.70 E-value=1.5 Score=38.93 Aligned_cols=26 Identities=31% Similarity=0.411 Sum_probs=22.6
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
.+.++|++++|||+.+|..|..|--+
T Consensus 538 ~~~e~l~~i~giG~~~a~si~~ff~~ 563 (669)
T PRK14350 538 FALSKLLKIKGIGEKIALNIIEAFND 563 (669)
T ss_pred CCHHHHhhCCCccHHHHHHHHHHHcC
Confidence 36789999999999999999998643
No 93
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=82.64 E-value=2 Score=38.36 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=8.6
Q ss_pred CCCCcHHHHHHHH
Q 032317 26 LPGIGPKMAHLVM 38 (143)
Q Consensus 26 lpGIG~ktA~~Il 38 (143)
+||||++||..|.
T Consensus 89 ~~GIG~~~A~~iv 101 (720)
T TIGR01448 89 IKGVGKKLAQRIV 101 (720)
T ss_pred CCCcCHHHHHHHH
Confidence 6666666666665
No 94
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=82.61 E-value=1.4 Score=39.27 Aligned_cols=38 Identities=18% Similarity=0.287 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCC----cCcHHHHhcCCCCcHHHHHHHHHH
Q 032317 3 KIAPICLTKYDGDI----PSSLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 3 ~~a~~i~~~~~g~~----p~~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.|+.|++.||.+. -++.+.|..+||||++.+..|..-
T Consensus 95 ~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~ 136 (720)
T TIGR01448 95 KLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQ 136 (720)
T ss_pred HHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHH
Confidence 57999999999764 456788999999999999888763
No 95
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=82.57 E-value=0.89 Score=33.93 Aligned_cols=40 Identities=28% Similarity=0.385 Sum_probs=27.0
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhccc
Q 032317 20 LDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWV 64 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~ 64 (143)
+-.|.-|||||.||...||---=.+ .| +...=|-.|++..
T Consensus 129 LH~LELLpGiGkK~m~~ILeERkkk--pF---eSFeDi~~Rv~~~ 168 (202)
T COG1491 129 LHQLELLPGIGKKTMWAILEERKKK--PF---ESFEDIKERVKGL 168 (202)
T ss_pred HHHHHhcccccHHHHHHHHHHHhcC--CC---cCHHHHHHHhcCC
Confidence 3668899999999999999875332 23 2233455566554
No 96
>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=82.26 E-value=1.2 Score=27.39 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=17.3
Q ss_pred CcHHHHhcCCCCcHHHHHHHH
Q 032317 18 SSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il 38 (143)
-+.++|++++|+|.++.+=|.
T Consensus 41 ~s~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 41 YSEEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp S-HHHHHTSTTSHHHHHHHHH
T ss_pred CCHHHHHhCCCCCHhHHHHHH
Confidence 356899999999999988764
No 97
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=81.72 E-value=1.6 Score=35.19 Aligned_cols=32 Identities=25% Similarity=0.344 Sum_probs=24.2
Q ss_pred HHcCCCCcCcHHH--HhcCCCCcHHHHHHHHHHh
Q 032317 10 TKYDGDIPSSLDE--LLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 10 ~~~~g~~p~~~~~--L~~lpGIG~ktA~~Il~~~ 41 (143)
+.-+-++|+..+- +..|||||+.||+.|.-|.
T Consensus 40 e~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 40 ENLTEDLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred hhcccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 3334456655555 8899999999999998876
No 98
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=81.70 E-value=1.1 Score=33.81 Aligned_cols=41 Identities=17% Similarity=0.318 Sum_probs=26.3
Q ss_pred HHHhcCCCCcHHHHHHHHHH-hcCCCccccccchHHHHHHHhc
Q 032317 21 DELLLLPGIGPKMAHLVMNV-GWNNVQGICVDTHVHRICNRLG 62 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~-~~~~~~~~pvD~~v~Rv~~Rl~ 62 (143)
..|+++-||||++|=+||+. ..+.- +-.|++.=...+.|+-
T Consensus 73 ~~LisVnGIGpK~ALaiLs~~~~~~l-~~aI~~~d~~~L~k~P 114 (201)
T COG0632 73 RLLISVNGIGPKLALAILSNLDPEEL-AQAIANEDVKALSKIP 114 (201)
T ss_pred HHHHccCCccHHHHHHHHcCCCHHHH-HHHHHhcChHhhhcCC
Confidence 66899999999999999987 33322 1224444444444443
No 99
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=80.82 E-value=1.2 Score=33.04 Aligned_cols=21 Identities=38% Similarity=0.586 Sum_probs=16.2
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
=.|.-|||||.|+...|+---
T Consensus 116 H~LeLLPGIGKK~m~~ILeER 136 (181)
T PF04919_consen 116 HSLELLPGIGKKTMWKILEER 136 (181)
T ss_dssp BGGGGSTT--HHHHHHHHHHH
T ss_pred HHHhhcccccHHHHHHHHHHH
Confidence 458889999999999999764
No 100
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=80.16 E-value=2.8 Score=32.84 Aligned_cols=22 Identities=36% Similarity=0.510 Sum_probs=12.0
Q ss_pred cHHHHhcCCCCcHHHHHHHHHH
Q 032317 19 SLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.++|++.+|||++.|..|--|
T Consensus 212 s~~eL~~v~gig~k~A~~I~~~ 233 (254)
T COG1948 212 SEEELMKVKGIGEKKAREIYRF 233 (254)
T ss_pred CHHHHHHhcCccHHHHHHHHHH
Confidence 3455555555555555555544
No 101
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=77.96 E-value=2.5 Score=37.37 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=30.9
Q ss_pred HHHHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 3 KIAPICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 3 ~~a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
.+|+.+...|+. -.-.+.++|.++||||..+|..|..|--
T Consensus 522 ~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~ 564 (667)
T COG0272 522 TTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFA 564 (667)
T ss_pred HHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHHHHHHHc
Confidence 356777776653 2246779999999999999999998853
No 102
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=77.80 E-value=3.4 Score=31.90 Aligned_cols=38 Identities=18% Similarity=0.147 Sum_probs=29.0
Q ss_pred HHHHHHHH-cCCC---CcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 4 IAPICLTK-YDGD---IPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 4 ~a~~i~~~-~~g~---~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
-++.|.+. |+.. .-.+.++|.++||||.++|..|..+.
T Consensus 15 rakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 15 KAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred HHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 35566666 5541 13578999999999999999998885
No 103
>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=77.35 E-value=0.43 Score=32.10 Aligned_cols=23 Identities=39% Similarity=0.544 Sum_probs=14.8
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHh
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
+-+-+--+||||+|||..++.--
T Consensus 16 ~sDNIPGV~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 16 SSDNIPGVPGIGPKTAAKLLQEY 38 (101)
T ss_dssp CCCTB---TTSTCHCCCCCHHHH
T ss_pred cccCCCCCCCCCHHHHHHHHHHc
Confidence 33445568999999998877654
No 104
>PRK14976 5'-3' exonuclease; Provisional
Probab=77.22 E-value=1.7 Score=34.42 Aligned_cols=18 Identities=39% Similarity=0.551 Sum_probs=14.6
Q ss_pred HhcCCCCcHHHHHHHHHH
Q 032317 23 LLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~ 40 (143)
+-.+||||+|||..++.-
T Consensus 193 ipGVpGIG~KtA~~LL~~ 210 (281)
T PRK14976 193 IKGVKGIGPKTAIKLLNK 210 (281)
T ss_pred CCCCCcccHHHHHHHHHH
Confidence 445899999999988854
No 105
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=75.82 E-value=3.2 Score=36.99 Aligned_cols=39 Identities=13% Similarity=0.132 Sum_probs=31.0
Q ss_pred HHHHHHHHHcCCCC----cCcHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 3 KIAPICLTKYDGDI----PSSLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 3 ~~a~~i~~~~~g~~----p~~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
..|+.|...|+. + ..+.++|.+++|||+++|..|..|--
T Consensus 539 ~~ak~L~~~F~s-i~~L~~As~eeL~~i~GIG~k~A~sI~~ff~ 581 (689)
T PRK14351 539 TTARNLAREFGT-FEAIMDADEEALRAVDDVGPTVAEEIREFFD 581 (689)
T ss_pred HHHHHHHHHhCC-HHHHHhCCHHHHhccCCcCHHHHHHHHHHHh
Confidence 457778888854 3 35678999999999999999988853
No 106
>PRK09482 flap endonuclease-like protein; Provisional
Probab=74.85 E-value=2 Score=33.59 Aligned_cols=19 Identities=37% Similarity=0.445 Sum_probs=15.2
Q ss_pred HhcCCCCcHHHHHHHHHHh
Q 032317 23 LLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~ 41 (143)
+--+||||+|||.-++.--
T Consensus 184 IpGVpGIG~KtA~~LL~~~ 202 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQF 202 (256)
T ss_pred CCCCCCcChHHHHHHHHHh
Confidence 4558999999999887653
No 107
>PRK07758 hypothetical protein; Provisional
Probab=74.33 E-value=2.9 Score=27.82 Aligned_cols=23 Identities=30% Similarity=0.387 Sum_probs=19.0
Q ss_pred cCcHHHHhcCCCCcHHHHHHHHH
Q 032317 17 PSSLDELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 17 p~~~~~L~~lpGIG~ktA~~Il~ 39 (143)
..+.++|++++|+|+++.+-|-.
T Consensus 63 ~~te~ELl~iknlGkKSL~EIke 85 (95)
T PRK07758 63 KYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred cCCHHHHHHccCCCHHHHHHHHH
Confidence 34679999999999999887653
No 108
>PRK07945 hypothetical protein; Provisional
Probab=74.32 E-value=2.8 Score=33.95 Aligned_cols=21 Identities=43% Similarity=0.632 Sum_probs=18.5
Q ss_pred HHhcCCCCcHHHHHHHHHHhc
Q 032317 22 ELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 22 ~L~~lpGIG~ktA~~Il~~~~ 42 (143)
+|.+|||||.-||..|.-+.-
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 688999999999999988764
No 109
>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=74.32 E-value=2.2 Score=32.87 Aligned_cols=20 Identities=35% Similarity=0.557 Sum_probs=15.2
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+-+-.+||||+|||.-++.-
T Consensus 183 DnipGv~GiG~ktA~~Ll~~ 202 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLKE 202 (240)
T ss_pred cCCCCCCccCHHHHHHHHHH
Confidence 33456899999999777754
No 110
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.83 E-value=3.4 Score=32.13 Aligned_cols=32 Identities=19% Similarity=0.212 Sum_probs=22.5
Q ss_pred HHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHH
Q 032317 5 APICLTKYDGDIPSSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 5 a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il 38 (143)
.+.+.+..+...+.+. |.++||||+-+|..|.
T Consensus 174 ~~~~~~~~~~~~~~~~--l~~~pgig~~~a~~i~ 205 (303)
T COG3547 174 DREIEARLGIGVVTDR--LASIPGIGELTAAAIA 205 (303)
T ss_pred HHHHHHhhcccchHHH--HHhCCCccHHHHHHHH
Confidence 3344444444444444 8899999999999999
No 111
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=73.67 E-value=3.2 Score=36.14 Aligned_cols=26 Identities=27% Similarity=0.297 Sum_probs=22.8
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcC
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~ 43 (143)
.+.++|.+++|||+++|..|..|--+
T Consensus 517 a~~e~l~~i~gIG~~~a~si~~~f~~ 542 (562)
T PRK08097 517 RSEQQWQQLPGIGEGRARQLIAFLQH 542 (562)
T ss_pred CCHHHHhcCCCchHHHHHHHHHHHcC
Confidence 56789999999999999999999643
No 112
>smart00475 53EXOc 5'-3' exonuclease.
Probab=73.62 E-value=2.5 Score=33.05 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=14.8
Q ss_pred HhcCCCCcHHHHHHHHHH
Q 032317 23 LLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~ 40 (143)
+-.+||||+|||.-++.-
T Consensus 188 ipGV~GIG~KtA~~Ll~~ 205 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKE 205 (259)
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 556899999999988754
No 113
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=72.77 E-value=2.5 Score=30.64 Aligned_cols=35 Identities=23% Similarity=0.289 Sum_probs=26.5
Q ss_pred HHHHHcCCCCcCcH---HHHhcCCCCcHHHHHHHHHHh
Q 032317 7 ICLTKYDGDIPSSL---DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 7 ~i~~~~~g~~p~~~---~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.++-=+|-++|.+. -.|..+.|||+.+|..|+.-+
T Consensus 13 ~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~l 50 (154)
T PTZ00134 13 HILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKA 50 (154)
T ss_pred hhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHc
Confidence 44444556677654 568899999999999999876
No 114
>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=72.23 E-value=3.9 Score=24.60 Aligned_cols=20 Identities=40% Similarity=0.951 Sum_probs=16.3
Q ss_pred CcCcHHHHhcCCCCcHHHHH
Q 032317 16 IPSSLDELLLLPGIGPKMAH 35 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~ 35 (143)
.|.+.++|.+++|+|+.-+.
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 69999999999999988665
No 115
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=72.02 E-value=2.6 Score=29.31 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=22.1
Q ss_pred CCCcCc---HHHHhcCCCCcHHHHHHHHHHh
Q 032317 14 GDIPSS---LDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 14 g~~p~~---~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
-++|.+ +-.|..+.|||+.+|..|+.-+
T Consensus 7 ~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~l 37 (122)
T CHL00137 7 VDLPRNKRIEYALTYIYGIGLTSAKEILEKA 37 (122)
T ss_pred ccCCCCCEeeeeecccccccHHHHHHHHHHc
Confidence 345544 3568899999999999999886
No 116
>PRK08609 hypothetical protein; Provisional
Probab=71.33 E-value=4.6 Score=35.11 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=20.0
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHhc
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
+.++|.+|||||+.+|+.|--+.-
T Consensus 46 ~~~~l~~ipgIG~~ia~kI~Eil~ 69 (570)
T PRK08609 46 EIDDFTKLKGIGKGTAEVIQEYRE 69 (570)
T ss_pred hhhhhccCCCcCHHHHHHHHHHHH
Confidence 446788999999999999987753
No 117
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=70.05 E-value=6.5 Score=34.33 Aligned_cols=37 Identities=22% Similarity=0.095 Sum_probs=25.0
Q ss_pred HHHHHHHcCCC---CcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 5 APICLTKYDGD---IPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 5 a~~i~~~~~g~---~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+.|.+.||+- --.+.++|.++||||.++|..|..+.
T Consensus 527 ~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l 566 (574)
T PRK14670 527 AKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFA 566 (574)
T ss_pred HHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 35566666651 13566888888888888888887665
No 118
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=69.68 E-value=4.7 Score=29.05 Aligned_cols=36 Identities=17% Similarity=0.141 Sum_probs=27.1
Q ss_pred HHHHHHcCCCCcCcH---HHHhcCCCCcHHHHHHHHHHh
Q 032317 6 PICLTKYDGDIPSSL---DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 6 ~~i~~~~~g~~p~~~---~~L~~lpGIG~ktA~~Il~~~ 41 (143)
+.++-=+|-++|.+. -.|.++.|||+.+|..|+.-+
T Consensus 7 ~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~l 45 (149)
T PRK04053 7 KYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKL 45 (149)
T ss_pred hhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHc
Confidence 344444566777654 568899999999999998776
No 119
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=66.85 E-value=4.9 Score=32.48 Aligned_cols=30 Identities=37% Similarity=0.832 Sum_probs=22.9
Q ss_pred cCCCCcCcHHHHhcCCCCcH-HHHHHHHHHh
Q 032317 12 YDGDIPSSLDELLLLPGIGP-KMAHLVMNVG 41 (143)
Q Consensus 12 ~~g~~p~~~~~L~~lpGIG~-ktA~~Il~~~ 41 (143)
..+.+|.....|+++||.|| |++..---++
T Consensus 84 lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elg 114 (326)
T COG1796 84 LKKEVPEGLEPLLKVPGLGPKKIVSLYKELG 114 (326)
T ss_pred HHHhCCcchHHHhhCCCCCcHHHHHHHHHHC
Confidence 34578999999999999999 5665554444
No 120
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=66.71 E-value=6 Score=31.47 Aligned_cols=21 Identities=38% Similarity=0.737 Sum_probs=10.9
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
|.++||||+++|+.....++.
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~ 28 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYD 28 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCC
Confidence 444555555555555555444
No 121
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=66.56 E-value=8.1 Score=30.02 Aligned_cols=37 Identities=30% Similarity=0.355 Sum_probs=27.1
Q ss_pred HHHHHHHcCC---CCcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 5 APICLTKYDG---DIPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 5 a~~i~~~~~g---~~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
|..|...||. -+-.++++|.+.||+|+--|.-|..|.
T Consensus 208 a~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l 247 (254)
T KOG2841|consen 208 AQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFL 247 (254)
T ss_pred HHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHH
Confidence 4455556653 224678999999999999998887775
No 122
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=66.39 E-value=4 Score=28.36 Aligned_cols=28 Identities=29% Similarity=0.374 Sum_probs=22.1
Q ss_pred CCCcCcH---HHHhcCCCCcHHHHHHHHHHh
Q 032317 14 GDIPSSL---DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 14 g~~p~~~---~~L~~lpGIG~ktA~~Il~~~ 41 (143)
-++|.+. -.|..+.|||+.+|..|+.-+
T Consensus 7 ~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~l 37 (122)
T PRK05179 7 VDIPRNKRVVIALTYIYGIGRTRAKEILAAA 37 (122)
T ss_pred ccCCCCcEEEeeecccccccHHHHHHHHHHh
Confidence 3455443 568899999999999999876
No 123
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=65.69 E-value=7.7 Score=30.87 Aligned_cols=35 Identities=31% Similarity=0.468 Sum_probs=22.2
Q ss_pred HHHHHHcCCCCcCc---HHHHh--------cCCCCcHHHHHHHHHH
Q 032317 6 PICLTKYDGDIPSS---LDELL--------LLPGIGPKMAHLVMNV 40 (143)
Q Consensus 6 ~~i~~~~~g~~p~~---~~~L~--------~lpGIG~ktA~~Il~~ 40 (143)
..+.+.|.|.-|.. +..|+ -+||||+|||--++.-
T Consensus 172 ~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~ 217 (310)
T COG0258 172 EEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQE 217 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHH
Confidence 34667776655542 22233 3899999999877654
No 124
>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=64.81 E-value=4 Score=27.92 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=18.8
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
-.|.++.|||+.+|..|+.-+
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~l 35 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKA 35 (113)
T ss_pred eeeeeeecccHHHHHHHHHHh
Confidence 568899999999999999876
No 125
>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=62.13 E-value=4.9 Score=28.77 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=22.5
Q ss_pred CCCCcCcH---HHHhcCCCCcHHHHHHHHHHh
Q 032317 13 DGDIPSSL---DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 13 ~g~~p~~~---~~L~~lpGIG~ktA~~Il~~~ 41 (143)
|-++|.+. -.|.++.|||+.+|..|+.-+
T Consensus 10 ~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~l 41 (144)
T TIGR03629 10 DTDLDGNKPVEYALTGIKGIGRRFARAIARKL 41 (144)
T ss_pred CccCCCCCEEEEeecceeccCHHHHHHHHHHc
Confidence 44566543 568899999999999998776
No 126
>PRK00254 ski2-like helicase; Provisional
Probab=61.14 E-value=11 Score=33.45 Aligned_cols=29 Identities=38% Similarity=0.562 Sum_probs=17.1
Q ss_pred CcCcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 16 IPSSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
++++.-.|.++||||+++|...+..+|+.
T Consensus 640 ~~~~~~~L~~ipgig~~~~~~l~~~g~~s 668 (720)
T PRK00254 640 VREELLELMRLPMIGRKRARALYNAGFRS 668 (720)
T ss_pred CCHHHhhhhcCCCCCHHHHHHHHHccCCC
Confidence 34444556666666666666666665543
No 127
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=60.98 E-value=7.2 Score=27.08 Aligned_cols=29 Identities=28% Similarity=0.301 Sum_probs=22.9
Q ss_pred CCCcCcH---HHHhcCCCCcHHHHHHHHHHhc
Q 032317 14 GDIPSSL---DELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 14 g~~p~~~---~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
-++|.+. =.|..+.|||..+|..|+.-+-
T Consensus 7 vdip~~K~v~iALt~IyGIG~~~a~~I~~~~g 38 (121)
T COG0099 7 VDIPGNKRVVIALTYIYGIGRRRAKEICKKAG 38 (121)
T ss_pred cCCCCCceEeehhhhhccccHHHHHHHHHHcC
Confidence 4566543 4588899999999999998773
No 128
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=59.49 E-value=7.7 Score=34.20 Aligned_cols=21 Identities=33% Similarity=0.575 Sum_probs=17.8
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|.++||||++++..+|..-
T Consensus 552 S~L~~IpGIG~kr~~~LL~~F 572 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHF 572 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 567899999999999988763
No 129
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=58.19 E-value=8.3 Score=33.97 Aligned_cols=21 Identities=33% Similarity=0.377 Sum_probs=17.8
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|..+||||+++|..++..-
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc
Confidence 567789999999999887764
No 130
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=58.10 E-value=16 Score=32.58 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=23.4
Q ss_pred HHHHHHHcCCC---CcCcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 5 APICLTKYDGD---IPSSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 5 a~~i~~~~~g~---~p~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.+.|.+.||+- -..+.++|.++||||.++|..|.--+-..
T Consensus 621 ~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~ 663 (691)
T PRK14672 621 AHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRS 663 (691)
T ss_pred HHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcc
Confidence 34555555541 13456677777777777777776665443
No 131
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=57.98 E-value=2.9 Score=32.58 Aligned_cols=62 Identities=15% Similarity=0.118 Sum_probs=33.0
Q ss_pred cccccchHHHHHHHhcccCCCCCC--CCCCCHHHHHHHHHHhCCCCChhhHHHHHH-HHHHHhccC
Q 032317 47 GICVDTHVHRICNRLGWVSQPGRK--QKTSSPEQTREVLQLWLPKEEWVPINPLLV-GFGQTICTP 109 (143)
Q Consensus 47 ~~pvD~~v~Rv~~Rl~~~~~~~~~--~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~-~~G~~~C~~ 109 (143)
.||||.+|.++..+.|+++..... ........+++.+.+. ..-.+-+++-.|+ -+|+.....
T Consensus 168 pIPvD~Rva~~T~~sGi~~~~~~~~~~~~~~v~~~W~~Va~~-sgIpplhLDs~lW~l~G~~~~~~ 232 (246)
T PF09171_consen 168 PIPVDYRVAKLTKRSGIIECEREEMMRTREEVQKAWREVAKE-SGIPPLHLDSLLWPLLGRARDVK 232 (246)
T ss_dssp -----HHHHHHHHCTTS-SS-HHHHHCTCCHHHHHHHHHHHH-HT--HHHHHHHHHHHHCCHHCCT
T ss_pred CCCccHHHHHHHHHhccccccHHhhhccHHHHHHHHHHHHhh-cCCCchhhhhHHHHhcccchhhh
Confidence 489999999999999997542211 1122233344433332 2344778888888 888877653
No 132
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=57.61 E-value=14 Score=22.43 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=19.5
Q ss_pred cHHHHhcCCCCcHHHHHHHHHHh
Q 032317 19 SLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
+.++|+.+ |.+++||.-|..-|
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 46899999 99999999998776
No 133
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=57.17 E-value=6.9 Score=21.95 Aligned_cols=16 Identities=38% Similarity=0.374 Sum_probs=13.4
Q ss_pred ccccchHHHHHHHhcc
Q 032317 48 ICVDTHVHRICNRLGW 63 (143)
Q Consensus 48 ~pvD~~v~Rv~~Rl~~ 63 (143)
=+=||||.|++..++-
T Consensus 16 teddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 16 TEDDTHVHRVLRKYYT 31 (41)
T ss_pred CcchhHHHHHHHHHHH
Confidence 3589999999999874
No 134
>PHA00439 exonuclease
Probab=56.84 E-value=7.1 Score=31.09 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=14.2
Q ss_pred HhcCCCCcHHHHHHHHHH
Q 032317 23 LLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~ 40 (143)
+--+|||| |||..+|.-
T Consensus 190 IPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 190 YSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCCCCcC-HHHHHHHhC
Confidence 44589999 999999876
No 135
>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=55.12 E-value=9.1 Score=30.44 Aligned_cols=17 Identities=35% Similarity=0.540 Sum_probs=14.6
Q ss_pred hcCCCCcHHHHHHHHHH
Q 032317 24 LLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 24 ~~lpGIG~ktA~~Il~~ 40 (143)
-.+||||++||--++.-
T Consensus 226 ~gv~giG~k~A~~li~~ 242 (316)
T cd00128 226 EGIPGIGPVTALKLIKK 242 (316)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 46999999999988865
No 136
>PRK03980 flap endonuclease-1; Provisional
Probab=54.92 E-value=8.3 Score=30.68 Aligned_cols=16 Identities=38% Similarity=0.563 Sum_probs=13.7
Q ss_pred cCCCCcHHHHHHHHHH
Q 032317 25 LLPGIGPKMAHLVMNV 40 (143)
Q Consensus 25 ~lpGIG~ktA~~Il~~ 40 (143)
.+||||++||--++.-
T Consensus 193 GI~GIG~ktA~kLi~~ 208 (292)
T PRK03980 193 GIKGIGPKTALKLIKK 208 (292)
T ss_pred CCCCccHHHHHHHHHH
Confidence 6899999999888754
No 137
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=54.66 E-value=9.4 Score=34.74 Aligned_cols=24 Identities=29% Similarity=0.271 Sum_probs=20.0
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 20 LDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.+.|.+|||||++.|..++.. |+.
T Consensus 756 q~~L~~lPgI~~~~a~~ll~~-f~s 779 (814)
T TIGR00596 756 QDFLLKLPGVTKKNYRNLRKK-VKS 779 (814)
T ss_pred HHHHHHCCCCCHHHHHHHHHH-cCC
Confidence 466889999999999999986 443
No 138
>PF13592 HTH_33: Winged helix-turn helix
Probab=54.61 E-value=17 Score=21.55 Aligned_cols=34 Identities=24% Similarity=0.288 Sum_probs=20.4
Q ss_pred ccchHHHHHHHhcccCCCCCC-CCCCCHHHHHHHH
Q 032317 50 VDTHVHRICNRLGWVSQPGRK-QKTSSPEQTREVL 83 (143)
Q Consensus 50 vD~~v~Rv~~Rl~~~~~~~~~-~~~~~~~~~~~~l 83 (143)
=..+|.|+|.|+|+.-..+.. ....+++..+++.
T Consensus 23 s~~~v~~lL~r~G~s~~kp~~~~~k~d~~~q~~f~ 57 (60)
T PF13592_consen 23 SPSGVYRLLKRLGFSYQKPRPRPPKADEEAQEAFK 57 (60)
T ss_pred cHHHHHHHHHHcCCccccCCCCcccCCHHHHHHHH
Confidence 667899999999986432221 1234555444433
No 139
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=54.17 E-value=11 Score=32.96 Aligned_cols=20 Identities=30% Similarity=0.619 Sum_probs=17.1
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|..+||||+++...+|..
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~ 560 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKY 560 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHH
Confidence 56778999999999988765
No 140
>PF03686 UPF0146: Uncharacterised protein family (UPF0146); InterPro: IPR005353 The function of this family of proteins is unknown.; PDB: 2K4M_A.
Probab=53.38 E-value=2.3 Score=29.81 Aligned_cols=93 Identities=11% Similarity=0.002 Sum_probs=42.2
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHHH
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTRE 81 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~ 81 (143)
.+.|..|.++..-. ... ==|||.++--|-.+--.|- +++.+|.|-..+-..+-++-.|.. .-..++.+
T Consensus 2 ~~~a~~ia~~~~~~--kiV-----EVGiG~~~~vA~~L~~~G~-dV~~tDi~~~~a~~g~~~v~DDif----~P~l~iY~ 69 (127)
T PF03686_consen 2 VDFAEYIARLNNYG--KIV-----EVGIGFNPEVAKKLKERGF-DVIATDINPRKAPEGVNFVVDDIF----NPNLEIYE 69 (127)
T ss_dssp HHHHHHHHHHS-SS--EEE-----EET-TT--HHHHHHHHHS--EEEEE-SS-S----STTEE---SS----S--HHHHT
T ss_pred chHHHHHHHhCCCC--cEE-----EECcCCCHHHHHHHHHcCC-cEEEEECcccccccCcceeeeccc----CCCHHHhc
Confidence 45677777543210 001 1289988655555555554 688999999966544433333321 11123333
Q ss_pred HHHHhCCCCChhhHHHHHHHHHHHh
Q 032317 82 VLQLWLPKEEWVPINPLLVGFGQTI 106 (143)
Q Consensus 82 ~l~~~~p~~~~~~~~~~l~~~G~~~ 106 (143)
.+.....-..+.++|..|+++++.+
T Consensus 70 ~a~lIYSiRPP~El~~~il~lA~~v 94 (127)
T PF03686_consen 70 GADLIYSIRPPPELQPPILELAKKV 94 (127)
T ss_dssp TEEEEEEES--TTSHHHHHHHHHHH
T ss_pred CCcEEEEeCCChHHhHHHHHHHHHh
Confidence 2222222234689999999999987
No 141
>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=53.28 E-value=12 Score=24.08 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=17.4
Q ss_pred HHHhcCCCCcHHHHHHHHHHhc
Q 032317 21 DELLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~ 42 (143)
=-|..++|||..+|..|+.---
T Consensus 27 ~gl~~Ikglg~~~a~~I~~~R~ 48 (90)
T PF14579_consen 27 LGLSAIKGLGEEVAEKIVEERE 48 (90)
T ss_dssp -BGGGSTTS-HHHHHHHHHHHH
T ss_pred ehHhhcCCCCHHHHHHHHHhHh
Confidence 3488999999999999988764
No 142
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=52.27 E-value=15 Score=22.67 Aligned_cols=19 Identities=37% Similarity=0.800 Sum_probs=16.2
Q ss_pred CcCcHHHHhcCCCCcHHHH
Q 032317 16 IPSSLDELLLLPGIGPKMA 34 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA 34 (143)
.|.+.++|.+++|+|..-.
T Consensus 42 ~P~~~~~L~~i~g~~~~~~ 60 (81)
T smart00341 42 LPTNVSELLAIDGVGEEKA 60 (81)
T ss_pred CCCCHHHHhcCCCCCHHHH
Confidence 5889999999999997644
No 143
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=51.61 E-value=11 Score=32.86 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=16.9
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|..+||||+++..++|..
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~ 533 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRN 533 (567)
T ss_pred CccccCCCCCHHHHHHHHHH
Confidence 55778999999999988765
No 144
>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=51.11 E-value=19 Score=25.80 Aligned_cols=28 Identities=32% Similarity=0.354 Sum_probs=21.6
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCC
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGI 29 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGI 29 (143)
++..+.+.+.++-..+-+.+.|+++|||
T Consensus 88 ~~~l~~l~~~~~~~~~~~~~~ll~~p~v 115 (159)
T PF03755_consen 88 YEALKELAEELGLAGPISLDDLLRLPGV 115 (159)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHcCCCc
Confidence 3556677778876677888999999987
No 145
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=50.71 E-value=8.1 Score=27.28 Aligned_cols=19 Identities=37% Similarity=0.786 Sum_probs=15.9
Q ss_pred HHHhcCCCCcHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~ 39 (143)
++|..|.||||+.+..+--
T Consensus 67 DDLt~I~GIGPk~e~~Ln~ 85 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNE 85 (133)
T ss_pred ccchhhcccCHHHHHHHHH
Confidence 6899999999999876543
No 146
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=50.62 E-value=26 Score=23.03 Aligned_cols=53 Identities=17% Similarity=0.245 Sum_probs=30.3
Q ss_pred cCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHh
Q 032317 17 PSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLW 86 (143)
Q Consensus 17 p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~ 86 (143)
|---+....|||||+..+.-...-+|++. . -|+.++.+. .++.+..++++...
T Consensus 15 PMGeK~V~~laGIG~~lg~~L~~~GfdKA-y--------~vLGqfLll--------~kde~~F~~WLk~~ 67 (89)
T PF02961_consen 15 PMGEKPVTELAGIGPVLGKRLEEKGFDKA-Y--------VVLGQFLLL--------KKDEELFQDWLKDT 67 (89)
T ss_dssp --TT-BGGGSTT--HHHHHHHHHTT--BH-H--------HHHHHHHHT--------TT-HHHHHHHHHHH
T ss_pred ccCCCCccccCCcCHHHHHHHHHCCCcHH-H--------HHhhhhhhc--------cCcHHHHHHHHHHH
Confidence 33346678899999999999888888762 2 245555444 34566667766653
No 147
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=50.48 E-value=12 Score=32.00 Aligned_cols=22 Identities=36% Similarity=0.517 Sum_probs=19.0
Q ss_pred cHHHHhcCCCCcHHHHHHHHHH
Q 032317 19 SLDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 19 ~~~~L~~lpGIG~ktA~~Il~~ 40 (143)
+.+.|..+||||.+|+.-|+.-
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~ 535 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAE 535 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhc
Confidence 4678999999999999988763
No 148
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=50.36 E-value=15 Score=24.51 Aligned_cols=24 Identities=17% Similarity=0.072 Sum_probs=21.1
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
.|-.++||||..-|..|..|.-..
T Consensus 50 ~Wwr~vpglG~~~A~~I~awLa~h 73 (96)
T PF12482_consen 50 RWWRAVPGLGAAGARRIEAWLAAH 73 (96)
T ss_pred hHHHhCcccchHHHHHHHHHHHHh
Confidence 678899999999999999997654
No 149
>COG1255 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.94 E-value=23 Score=24.69 Aligned_cols=91 Identities=13% Similarity=0.130 Sum_probs=51.7
Q ss_pred HHHHHHHH-HHcCCCCcCcHHHHhcCCCCcHHH--HHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHH
Q 032317 2 KKIAPICL-TKYDGDIPSSLDELLLLPGIGPKM--AHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQ 78 (143)
Q Consensus 2 ~~~a~~i~-~~~~g~~p~~~~~L~~lpGIG~kt--A~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~ 78 (143)
.+.|..|. +...|++=+ =|||.++ |+.+.-.+| +++.+|-|-.++=.-+-++-.|.. .-...
T Consensus 2 ~e~a~~iAre~~~gkVvE--------VGiG~~~~VA~~L~e~g~---dv~atDI~~~~a~~g~~~v~DDit----nP~~~ 66 (129)
T COG1255 2 IEVAEYIARENARGKVVE--------VGIGFFLDVAKRLAERGF---DVLATDINEKTAPEGLRFVVDDIT----NPNIS 66 (129)
T ss_pred ccHHHHHHHHhcCCcEEE--------EccchHHHHHHHHHHcCC---cEEEEecccccCcccceEEEccCC----CccHH
Confidence 45566665 444454422 3899885 444444443 578899988844422223322221 11224
Q ss_pred HHHHHHHhCCCCChhhHHHHHHHHHHHhc
Q 032317 79 TREVLQLWLPKEEWVPINPLLVGFGQTIC 107 (143)
Q Consensus 79 ~~~~l~~~~p~~~~~~~~~~l~~~G~~~C 107 (143)
+.+.+.....-..+.+++-+|+++.+.+=
T Consensus 67 iY~~A~lIYSiRpppEl~~~ildva~aVg 95 (129)
T COG1255 67 IYEGADLIYSIRPPPELQSAILDVAKAVG 95 (129)
T ss_pred HhhCccceeecCCCHHHHHHHHHHHHhhC
Confidence 44444444333457899999999999873
No 150
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=49.68 E-value=18 Score=26.95 Aligned_cols=16 Identities=25% Similarity=0.781 Sum_probs=14.1
Q ss_pred CCCCCCCCCcCccCcc
Q 032317 110 IRPRCGMCSVSELCPS 125 (143)
Q Consensus 110 ~~P~C~~CpL~~~C~~ 125 (143)
+++.|..|+++..|..
T Consensus 173 ~~~~C~~C~y~~iC~~ 188 (190)
T COG1468 173 KKKKCKKCAYREICFP 188 (190)
T ss_pred CCCcCCCCCcceeccC
Confidence 5789999999999963
No 151
>PF13523 Acetyltransf_8: Acetyltransferase (GNAT) domain; PDB: 2VQY_A 2BUE_A 1V0C_A 1YK3_D 2PR8_A 2QIR_A 2PRB_A 2QML_A 2PC1_A.
Probab=49.67 E-value=18 Score=24.86 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=30.7
Q ss_pred cCCCCcHHHHHHHHHHhcCC--Cccccccch-----HHHHHHHhcccC
Q 032317 25 LLPGIGPKMAHLVMNVGWNN--VQGICVDTH-----VHRICNRLGWVS 65 (143)
Q Consensus 25 ~lpGIG~ktA~~Il~~~~~~--~~~~pvD~~-----v~Rv~~Rl~~~~ 65 (143)
.=+|+|.....+++.+++.+ .+.+.+|+| +.++..++|+..
T Consensus 91 rg~G~g~~~~~~~~~~~~~~~~~~~i~~~~~~~N~~~~~~~~k~GF~~ 138 (152)
T PF13523_consen 91 RGQGLGKAMLRALIEFLFEDPGVDRIVLDPHEDNTRAIRLYEKAGFRK 138 (152)
T ss_dssp TTSSHHHHHHHHHHHHHHTSTT--EEEEEEBTT-HHHHHHHHHTT-EE
T ss_pred cCCCHHHHHHHHHHHHHHhCCCCCEEEEecCcCCHHHHHHHHHcCCEE
Confidence 45899999999999998865 456778885 588888888753
No 152
>PRK00254 ski2-like helicase; Provisional
Probab=49.19 E-value=16 Score=32.54 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=27.3
Q ss_pred HHHHHHHH-cCCC---CcCcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 4 IAPICLTK-YDGD---IPSSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 4 ~a~~i~~~-~~g~---~p~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.++.+.+. |+.. .-.+.++|.++||||.++|..|..+.
T Consensus 657 ~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~ 698 (720)
T PRK00254 657 RARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHL 698 (720)
T ss_pred HHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHh
Confidence 34555555 4431 13467999999999999999998874
No 153
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=49.13 E-value=12 Score=29.53 Aligned_cols=22 Identities=36% Similarity=0.711 Sum_probs=18.9
Q ss_pred HhcCCCCcHHHHHHHHHHhcCC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
|.++||||+++++.+...++..
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~t 22 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDT 22 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCC
Confidence 3578999999999999998774
No 154
>PTZ00217 flap endonuclease-1; Provisional
Probab=49.07 E-value=12 Score=31.09 Aligned_cols=17 Identities=35% Similarity=0.510 Sum_probs=13.9
Q ss_pred HhcCCCCcHHHHHHHHH
Q 032317 23 LLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~ 39 (143)
+-.+||||++||--++.
T Consensus 237 ~pgi~GIG~ktA~~Li~ 253 (393)
T PTZ00217 237 CDTIKGIGPKTAYKLIK 253 (393)
T ss_pred CCCCCCccHHHHHHHHH
Confidence 34699999999988774
No 155
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.06 E-value=11 Score=34.62 Aligned_cols=17 Identities=29% Similarity=0.329 Sum_probs=13.9
Q ss_pred hcCCCCcHHHHHHHHHH
Q 032317 24 LLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 24 ~~lpGIG~ktA~~Il~~ 40 (143)
-.+||||+|||.-++.-
T Consensus 188 pGVpGIG~KtA~kLL~~ 204 (887)
T TIGR00593 188 PGVKGIGEKTAAKLLQE 204 (887)
T ss_pred CCCCCcCHHHHHHHHHH
Confidence 34899999999988753
No 156
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=49.01 E-value=14 Score=32.41 Aligned_cols=22 Identities=32% Similarity=0.439 Sum_probs=18.2
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 032317 20 LDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.-+|..+||||++++..++..-
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F 563 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF 563 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc
Confidence 3668899999999999877754
No 157
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=48.99 E-value=9 Score=25.87 Aligned_cols=18 Identities=28% Similarity=0.709 Sum_probs=15.0
Q ss_pred CCCCCCCCcCccCccccc
Q 032317 111 RPRCGMCSVSELCPSAFK 128 (143)
Q Consensus 111 ~P~C~~CpL~~~C~~~~~ 128 (143)
...|..||+.+.|....+
T Consensus 30 ~~~C~~Cp~r~~C~~~~~ 47 (125)
T PF13751_consen 30 KEDCKNCPLREQCTKSKK 47 (125)
T ss_pred chhccCCCccccCCCccc
Confidence 578999999999997543
No 158
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=48.74 E-value=12 Score=30.40 Aligned_cols=17 Identities=35% Similarity=0.452 Sum_probs=14.4
Q ss_pred hcCCCCcHHHHHHHHHH
Q 032317 24 LLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 24 ~~lpGIG~ktA~~Il~~ 40 (143)
-.+||||++||--++.-
T Consensus 239 ~Gv~GIG~ktA~kli~~ 255 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE 255 (338)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 57999999999888754
No 159
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=47.70 E-value=14 Score=32.33 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=17.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~ 40 (143)
...|..+||||+++...+|..
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~ 533 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKS 533 (574)
T ss_pred ccccccCCCCCHHHHHHHHHH
Confidence 357889999999999887765
No 160
>PRK02362 ski2-like helicase; Provisional
Probab=47.42 E-value=26 Score=31.33 Aligned_cols=29 Identities=28% Similarity=0.400 Sum_probs=23.6
Q ss_pred CcCcHHHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 16 IPSSLDELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
+|.+.-.|++|||||+++|...-..++..
T Consensus 647 v~~~~~~L~~ip~i~~~~a~~l~~~gi~s 675 (737)
T PRK02362 647 VREELLDLVGLRGVGRVRARRLYNAGIES 675 (737)
T ss_pred CCHHHHHHhCCCCCCHHHHHHHHHcCCCC
Confidence 67777889999999999998877755543
No 161
>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=45.03 E-value=21 Score=27.96 Aligned_cols=33 Identities=21% Similarity=0.227 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHH
Q 032317 3 KIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 3 ~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~ 39 (143)
++++.|+. +.+ .+...|.+|||||+..+..+..
T Consensus 134 ~l~q~i~q---~~w-~~~~~L~Qlp~i~~~~~~~l~~ 166 (314)
T PF02889_consen 134 ELSQCIVQ---ALW-DSDSPLLQLPHIGEESLKKLEK 166 (314)
T ss_dssp HHHHHHHH---TS--TTS-GGGGSTT--HHHHHHHHH
T ss_pred HHHHHHHh---hcC-CCCChhhcCCCCCHHHHHHHhc
Confidence 45555554 334 4668999999999999988877
No 162
>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=43.77 E-value=26 Score=31.14 Aligned_cols=22 Identities=36% Similarity=0.487 Sum_probs=17.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 032317 20 LDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.++|.+|||+|.++|+-|+...
T Consensus 465 ~~~L~~L~GfG~Ksa~nIl~~I 486 (652)
T TIGR00575 465 KEDLLELEGFGEKSAQNLLNAI 486 (652)
T ss_pred HHHHhhccCccHHHHHHHHHHH
Confidence 4678899999999998776544
No 163
>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=43.54 E-value=50 Score=23.84 Aligned_cols=44 Identities=16% Similarity=0.280 Sum_probs=34.4
Q ss_pred CHHHHHHHHHHhCCCCChhhHHHHHHHHHHHhccCCCCCCCCCC
Q 032317 75 SPEQTREVLQLWLPKEEWVPINPLLVGFGQTICTPIRPRCGMCS 118 (143)
Q Consensus 75 ~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~C~~Cp 118 (143)
..+.++.+|-+.-.+++|..+..+|...|+.---..-|+|-.=|
T Consensus 42 ~er~lqkAll~Y~~PeN~~lvreAL~~~GR~DLIG~g~~cLip~ 85 (150)
T PF11842_consen 42 RERRLQKALLRYHDPENWPLVREALKKMGREDLIGNGPKCLIPP 85 (150)
T ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhhhhhcccCCCCccccC
Confidence 35578888888778899999999999999987655566665433
No 164
>PRK05755 DNA polymerase I; Provisional
Probab=42.86 E-value=17 Score=33.31 Aligned_cols=20 Identities=35% Similarity=0.556 Sum_probs=15.4
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
+-+-.+||||+|||.-++.-
T Consensus 187 DnipGv~GiG~ktA~~Ll~~ 206 (880)
T PRK05755 187 DNIPGVPGIGEKTAAKLLQE 206 (880)
T ss_pred CCCCCCCCccHHHHHHHHHH
Confidence 33556899999999987753
No 165
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=42.82 E-value=44 Score=19.93 Aligned_cols=51 Identities=27% Similarity=0.382 Sum_probs=26.2
Q ss_pred cCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhC
Q 032317 25 LLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWL 87 (143)
Q Consensus 25 ~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~ 87 (143)
++.||-+-..+-+..++|.+. - |..++.|+|+-..++ .+...-...+++++
T Consensus 4 ~~~Gi~~~lVd~F~~mGF~~d-k------Vvevlrrlgik~~n~-----~dn~t~~~ilEELL 54 (55)
T PF09288_consen 4 ALYGIDKDLVDQFENMGFERD-K------VVEVLRRLGIKSMNG-----VDNETENKILEELL 54 (55)
T ss_dssp S----SHHHHHHHHHHT--HH-H------HHHHHHHS--SS--S-----S--HHHHHHHHHHT
T ss_pred HHcCCCHHHHHHHHHcCCcHH-H------HHHHHHHhCCCCCCC-----ccchhHHHHHHHHh
Confidence 467999999999999998763 2 347899999765332 23344444555543
No 166
>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=42.58 E-value=41 Score=18.59 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=19.7
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHh
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.+.++|..++|++...|..+..-+
T Consensus 23 ~~~~eL~~i~g~~~e~a~~ii~~a 46 (50)
T TIGR01954 23 VPIDELLSIEGFDEETAKELINRA 46 (50)
T ss_pred cCHHHHhcCCCCCHHHHHHHHHHH
Confidence 456899999999999998887654
No 167
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=42.15 E-value=22 Score=27.84 Aligned_cols=32 Identities=25% Similarity=0.284 Sum_probs=21.1
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCCccccccc
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNNVQGICVDT 52 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~ 52 (143)
.-|.++||||+.+|.-++..-..-..++-++.
T Consensus 182 ~il~s~pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 182 YILESIPGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred HHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 34778999999999988865433223443444
No 168
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=41.79 E-value=23 Score=31.05 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=17.9
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 032317 20 LDELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~~~ 41 (143)
.-+|..+||||++++..++..-
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~F 545 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRF 545 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHc
Confidence 3567789999999999877753
No 169
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=41.68 E-value=22 Score=31.87 Aligned_cols=23 Identities=35% Similarity=0.589 Sum_probs=19.0
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCC
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~ 44 (143)
..|..+||||++++..++.. |+.
T Consensus 637 s~L~~IPGIGpkr~k~LL~~-FGS 659 (694)
T PRK14666 637 GELQRVEGIGPATARLLWER-FGS 659 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHH-hCC
Confidence 66889999999999988885 453
No 170
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=41.67 E-value=22 Score=27.85 Aligned_cols=33 Identities=15% Similarity=0.277 Sum_probs=22.2
Q ss_pred HHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHH
Q 032317 3 KIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 3 ~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~ 39 (143)
++++.|.. |.+++ ...|.+|||||+..+..+-.
T Consensus 137 ~L~q~i~q---~~w~~-~~~L~Qlp~i~~~~~~~l~~ 169 (312)
T smart00611 137 NLSQMIIQ---ALWPT-DSPLLQLPHLPEEILKRLEK 169 (312)
T ss_pred HHHHHHHH---hhCCC-CCccccCCCCCHHHHHHHHh
Confidence 45555553 33433 34699999999998887754
No 171
>PRK03352 DNA polymerase IV; Validated
Probab=41.36 E-value=22 Score=28.48 Aligned_cols=21 Identities=33% Similarity=0.441 Sum_probs=17.5
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
|..|||||++|+.....++..
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ 199 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGIT 199 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCc
Confidence 556899999999998887765
No 172
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=39.83 E-value=15 Score=28.52 Aligned_cols=41 Identities=20% Similarity=0.426 Sum_probs=34.6
Q ss_pred CCCCcHHHHHHHHHHhcCCCccccccc-hHHH---------HHHHhcccCC
Q 032317 26 LPGIGPKMAHLVMNVGWNNVQGICVDT-HVHR---------ICNRLGWVSQ 66 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~~~~pvD~-~v~R---------v~~Rl~~~~~ 66 (143)
+.|+|.-.|+++-...+..-+.++||. .+.- ++.|||+++.
T Consensus 17 ~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~ 67 (263)
T PRK00783 17 VEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPL 67 (263)
T ss_pred EeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCccc
Confidence 579999999999999988777888776 6666 9999999874
No 173
>COG1561 Uncharacterized stress-induced protein [Function unknown]
Probab=39.77 E-value=31 Score=27.56 Aligned_cols=29 Identities=31% Similarity=0.393 Sum_probs=24.7
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCCc
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGIG 30 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGIG 30 (143)
.++++.|.+.|+-.-|-+..+|+++|||=
T Consensus 89 ~~~~~~i~~~~~~~~~~~~~~lL~~~gVl 117 (290)
T COG1561 89 VTLLKELAAQFDLAAELSLDDLLRLPGVL 117 (290)
T ss_pred HHHHHHHHHHcCccCCCCHHHHhCCccee
Confidence 46788888898877789999999999983
No 174
>COG4892 Predicted heme/steroid binding protein [General function prediction only]
Probab=39.63 E-value=17 Score=22.90 Aligned_cols=30 Identities=17% Similarity=0.316 Sum_probs=23.6
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCCcH
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGIGP 31 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ 31 (143)
+.+.+-+.+.++..-|.-.+-|.++|-||-
T Consensus 45 hsaG~DLs~~~~~~aphg~eil~~~PvVG~ 74 (81)
T COG4892 45 HSAGKDLSSEFNSCAPHGMEILTSLPVVGA 74 (81)
T ss_pred cccchhHHHHHhhcCCchhHHHhcCchhhe
Confidence 345566777788888888999999998884
No 175
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=39.45 E-value=84 Score=23.06 Aligned_cols=23 Identities=9% Similarity=-0.019 Sum_probs=12.7
Q ss_pred HHHHHHHhcCCCccccccchHHH
Q 032317 34 AHLVMNVGWNNVQGICVDTHVHR 56 (143)
Q Consensus 34 A~~Il~~~~~~~~~~pvD~~v~R 56 (143)
-++...|.+-.++.+|.||...-
T Consensus 15 ~dAYv~FilyCNP~vP~~tdT~~ 37 (175)
T PF09441_consen 15 DDAYVAFILYCNPAVPLDTDTSE 37 (175)
T ss_pred hhhhheeeeecCCCCCCCCCHHH
Confidence 34555565555556666555543
No 176
>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=39.03 E-value=5.1 Score=24.67 Aligned_cols=20 Identities=30% Similarity=0.614 Sum_probs=15.2
Q ss_pred HHHhccCCCCCCCCCCcCccCcccccC
Q 032317 103 GQTICTPIRPRCGMCSVSELCPSAFKD 129 (143)
Q Consensus 103 G~~~C~~~~P~C~~CpL~~~C~~~~~~ 129 (143)
++.+|. .||+...|..+.-.
T Consensus 28 A~~iC~-------~CPVr~~C~~~Al~ 47 (66)
T PF02467_consen 28 ARAICA-------RCPVRAECLEYALD 47 (66)
T ss_pred HHHHHc-------CChhHHHHHHHHHH
Confidence 666665 49999999987643
No 177
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=37.89 E-value=25 Score=31.47 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=16.7
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 032317 21 DELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~ 40 (143)
..|..+||||+++...+|..
T Consensus 608 s~L~~IpGiG~kr~~~LL~~ 627 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAH 627 (691)
T ss_pred cccccCCCCCHHHHHHHHHH
Confidence 45778999999999887765
No 178
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=37.81 E-value=25 Score=22.48 Aligned_cols=42 Identities=29% Similarity=0.413 Sum_probs=24.1
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcc
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGW 63 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~ 63 (143)
..|..||+||+++....-..+-...+.+ -......++.|+--
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI~t~~~L-~~~Ga~~a~~~Lk~ 44 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGIHTVEDL-RELGAVEAYLRLKA 44 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT--SHHHH-HHHHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcCCCCHHHH-HHhCHHHHHHHHHH
Confidence 4678899999999998887776544332 44455555555543
No 179
>TIGR03585 PseH pseudaminic acid biosynthesis N-acetyl transferase. Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar.
Probab=37.36 E-value=42 Score=22.77 Aligned_cols=39 Identities=10% Similarity=0.502 Sum_probs=29.2
Q ss_pred CCCcHHHHHHHHHHhcCCC--cccc-----ccchHHHHHHHhcccC
Q 032317 27 PGIGPKMAHLVMNVGWNNV--QGIC-----VDTHVHRICNRLGWVS 65 (143)
Q Consensus 27 pGIG~ktA~~Il~~~~~~~--~~~p-----vD~~v~Rv~~Rl~~~~ 65 (143)
.|||.....+++.+++... ..+- -.....|+..++|+..
T Consensus 90 ~G~g~~~~~~~~~~a~~~~~~~~i~~~v~~~N~~s~~~y~k~Gf~~ 135 (156)
T TIGR03585 90 PGVGSVLEEAALEYAFEHLGLHKLSLEVLEFNNKALKLYEKFGFER 135 (156)
T ss_pred cCchHHHHHHHHHHHHhhCCeeEEEEEEeccCHHHHHHHHHcCCeE
Confidence 8999999999999987531 2232 2345689999999864
No 180
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.47 E-value=22 Score=26.13 Aligned_cols=44 Identities=7% Similarity=0.161 Sum_probs=38.4
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhcccCC
Q 032317 21 DELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWVSQ 66 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~~~ 66 (143)
--++-|--+++..|.=|+-|.-|- ++++++++.||....++..+
T Consensus 99 ~Vvinl~~m~~~qArRivDFlaG~--~~al~G~~qkVg~~ifL~tP 142 (167)
T COG1799 99 AVVINLQRMDPAQARRIVDFLAGA--VFALRGSIQKVGSKIFLLTP 142 (167)
T ss_pred eEEEEeeeCCHHHHHHHHHHhcch--hhhhcccHHhhcceeEEecc
Confidence 346778999999999999999884 79999999999999998643
No 181
>PF11691 DUF3288: Protein of unknown function (DUF3288); InterPro: IPR021705 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=34.91 E-value=24 Score=23.23 Aligned_cols=11 Identities=18% Similarity=0.486 Sum_probs=5.2
Q ss_pred HHHHHHHhccc
Q 032317 54 VHRICNRLGWV 64 (143)
Q Consensus 54 v~Rv~~Rl~~~ 64 (143)
+-+|+..|++.
T Consensus 51 L~kiL~~W~lt 61 (90)
T PF11691_consen 51 LDKILQKWGLT 61 (90)
T ss_pred HHHHHHHcCCC
Confidence 34455555544
No 182
>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=34.62 E-value=23 Score=25.23 Aligned_cols=14 Identities=29% Similarity=0.947 Sum_probs=12.3
Q ss_pred CCCCCCCCcCccCc
Q 032317 111 RPRCGMCSVSELCP 124 (143)
Q Consensus 111 ~P~C~~CpL~~~C~ 124 (143)
.+.|..|+.+..|.
T Consensus 164 ~~~C~~C~y~~~C~ 177 (178)
T TIGR00372 164 SRKCKFCPYREICL 177 (178)
T ss_pred CCcCCCCCCccccC
Confidence 46799999999996
No 183
>PRK14973 DNA topoisomerase I; Provisional
Probab=34.11 E-value=39 Score=31.42 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=33.2
Q ss_pred CcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHhccc
Q 032317 18 SSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRLGWV 64 (143)
Q Consensus 18 ~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl~~~ 64 (143)
..+.+|++++|||++|+...-.-+.-..+.+ +-....+++.+.|+-
T Consensus 874 ~~~~el~~vkg~ge~t~~~l~~ag~~~~e~l-~~~d~~~la~~~~i~ 919 (936)
T PRK14973 874 RGRAELLSVPGLGETTLEKLYLAGVYDGDLL-VSADPKKLAKVTGID 919 (936)
T ss_pred ccchhhhhccCCCHHHHHHHHHcCCCCHHHh-ccCCHHHHhhhcCCC
Confidence 3445699999999999987777666655554 333778888777753
No 184
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=33.73 E-value=28 Score=28.68 Aligned_cols=21 Identities=38% Similarity=0.469 Sum_probs=17.9
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||++|+.-+..++..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~ 194 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGIS 194 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCC
Confidence 567999999999999887754
No 185
>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=33.64 E-value=26 Score=24.69 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=12.5
Q ss_pred CCCCCCCCcCccCc
Q 032317 111 RPRCGMCSVSELCP 124 (143)
Q Consensus 111 ~P~C~~CpL~~~C~ 124 (143)
.+.|..|.+.+.|.
T Consensus 148 ~~~C~~C~y~~~C~ 161 (162)
T PF01930_consen 148 SKKCRRCSYREFCW 161 (162)
T ss_pred CCCCCCCCCcCcCC
Confidence 56899999999996
No 186
>PRK07757 acetyltransferase; Provisional
Probab=33.13 E-value=57 Score=22.18 Aligned_cols=40 Identities=15% Similarity=0.176 Sum_probs=29.3
Q ss_pred CCCCcHHHHHHHHHHhcCCC-ccccccchHHHHHHHhcccC
Q 032317 26 LPGIGPKMAHLVMNVGWNNV-QGICVDTHVHRICNRLGWVS 65 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~-~~~pvD~~v~Rv~~Rl~~~~ 65 (143)
=.|+|....+.+...+.... ..+.+.+...|+..|+|+..
T Consensus 79 g~Glg~~Ll~~l~~~a~~~g~~~i~~~~~~~~~Y~k~GF~~ 119 (152)
T PRK07757 79 GQGIGRMLVEACLEEARELGVKRVFALTYQPEFFEKLGFRE 119 (152)
T ss_pred CCCHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHCCCEE
Confidence 46899999898888885432 23445666789999999875
No 187
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=32.48 E-value=36 Score=20.39 Aligned_cols=27 Identities=19% Similarity=0.081 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHHhCCCCChhhHHHHH
Q 032317 73 TSSPEQTREVLQLWLPKEEWVPINPLL 99 (143)
Q Consensus 73 ~~~~~~~~~~l~~~~p~~~~~~~~~~l 99 (143)
..+.++++.+.++.+......++..||
T Consensus 33 ~l~~eqLE~l~e~ildf~~l~dL~~wL 59 (59)
T PF14261_consen 33 QLSLEQLEALAEAILDFNSLEDLENWL 59 (59)
T ss_pred cCCHHHHHHHHHHHhCCCCHHHHHhhC
Confidence 567788888888888877777776553
No 188
>PF09796 QCR10: Ubiquinol-cytochrome-c reductase complex subunit (QCR10); InterPro: IPR019182 This entry represents subunit 10 of the cytochrome b-c1 complex (also known as the ubiquinol-cytochrome c reductase complex or complex III). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. Subunit 10 is required for stable association of the iron-sulphur protein with the complex [].
Probab=32.16 E-value=21 Score=21.99 Aligned_cols=21 Identities=19% Similarity=0.506 Sum_probs=15.9
Q ss_pred cCCCCcCcHHHHh-cCCCCcHH
Q 032317 12 YDGDIPSSLDELL-LLPGIGPK 32 (143)
Q Consensus 12 ~~g~~p~~~~~L~-~lpGIG~k 32 (143)
|-+.+|.-+++++ ++|.+|.|
T Consensus 31 f~~~vPr~q~dil~KIP~~G~~ 52 (64)
T PF09796_consen 31 FTSGVPRFQRDILQKIPVFGSY 52 (64)
T ss_pred HhcCCcHHHHHHHHhCCccccc
Confidence 4457898887755 69999976
No 189
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=31.96 E-value=42 Score=21.83 Aligned_cols=19 Identities=21% Similarity=0.226 Sum_probs=13.8
Q ss_pred CCCCcHHHHHHHHHHhcCC
Q 032317 26 LPGIGPKMAHLVMNVGWNN 44 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~ 44 (143)
++|||++-++=||-.+-=.
T Consensus 36 iaGiGNiy~~EiLf~a~i~ 54 (92)
T PF06831_consen 36 IAGIGNIYADEILFRAGIH 54 (92)
T ss_dssp STT--HHHHHHHHHHTTB-
T ss_pred cccCcHHHHHHHHHHcCCC
Confidence 9999999999999877434
No 190
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.91 E-value=52 Score=29.37 Aligned_cols=20 Identities=35% Similarity=0.571 Sum_probs=16.3
Q ss_pred HHHHhcCCCCcHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~ 39 (143)
.+.|.+|||+|.|+|.-|+.
T Consensus 478 ~~~L~~l~gfG~Ksa~~ll~ 497 (665)
T PRK07956 478 AEDLLGLEGFGEKSAQNLLD 497 (665)
T ss_pred HHHHhcCcCcchHHHHHHHH
Confidence 36788999999999987754
No 191
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=31.67 E-value=29 Score=20.95 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHcCCCCcCcH
Q 032317 1 MKKIAPICLTKYDGDIPSSL 20 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~ 20 (143)
+.++|+.|+++|...+-.|.
T Consensus 8 IKr~a~~lieky~~~ft~DF 27 (58)
T PRK01151 8 IKRTAEELLEKYPDLFTTDF 27 (58)
T ss_pred HHHHHHHHHHHhHHHhcccH
Confidence 36789999998877665554
No 192
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=31.32 E-value=42 Score=27.74 Aligned_cols=21 Identities=24% Similarity=0.387 Sum_probs=17.6
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||++|+..+..++..
T Consensus 224 v~~l~GIG~~~~~~L~~~Gi~ 244 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLFGD 244 (404)
T ss_pred HhHhCCCCHHHHHHHHHcCCc
Confidence 456899999999999888765
No 193
>PF13932 GIDA_assoc_3: GidA associated domain 3; PDB: 3CES_C 3CP2_A 3G05_A 3CP8_A 2ZXI_B 2ZXH_A.
Probab=30.87 E-value=68 Score=19.94 Aligned_cols=23 Identities=22% Similarity=0.561 Sum_probs=16.8
Q ss_pred CcCcHHHHhcCCCCcHHHHHHHH
Q 032317 16 IPSSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~~Il 38 (143)
-|.+.....++|||-|-....+|
T Consensus 49 rP~Ti~~A~rI~GvtPa~i~~Ll 71 (72)
T PF13932_consen 49 RPRTIGQASRIPGVTPAAISLLL 71 (72)
T ss_dssp --SCHHHHTTSTTS-HHHHHHHH
T ss_pred CCCCHHHHHhCCCCCHHHHHHHh
Confidence 37888999999999998776654
No 194
>PRK03858 DNA polymerase IV; Validated
Probab=30.61 E-value=46 Score=27.15 Aligned_cols=21 Identities=29% Similarity=0.328 Sum_probs=17.2
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||+.|+.-+..++..
T Consensus 175 l~~l~Gig~~~~~~L~~~Gi~ 195 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHGIT 195 (396)
T ss_pred hhhcCCCCHHHHHHHHHhCCC
Confidence 445899999999998887764
No 195
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=29.24 E-value=38 Score=29.41 Aligned_cols=21 Identities=38% Similarity=0.517 Sum_probs=17.7
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
+-|-+|||||-.||-.++.--
T Consensus 225 DYl~slpGvGl~tA~k~l~k~ 245 (556)
T KOG2518|consen 225 DYLSSLPGVGLATAHKLLSKY 245 (556)
T ss_pred cccccCccccHHHHHHHHHhc
Confidence 457889999999999888764
No 196
>PF14964 DUF4507: Domain of unknown function (DUF4507)
Probab=29.21 E-value=84 Score=25.96 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=32.4
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHH
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVM 38 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il 38 (143)
.++|+.|+++|=--.|...+.|.+++.+.|--+..++
T Consensus 147 ~~La~~iv~dy~~l~p~~~~~L~~l~~~sP~F~a~fi 183 (362)
T PF14964_consen 147 LRLAQMIVEDYCCLSPGSQETLKQLPNVSPRFCANFI 183 (362)
T ss_pred HHHHHHHHHHHhccCCccHHHHHHhhccChHHHHHHH
Confidence 4789999999988889999999999999998666555
No 197
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=28.99 E-value=44 Score=29.16 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=18.3
Q ss_pred CcCcHHHHhcCCCCcHHHHHH
Q 032317 16 IPSSLDELLLLPGIGPKMAHL 36 (143)
Q Consensus 16 ~p~~~~~L~~lpGIG~ktA~~ 36 (143)
.|.+.++|++++|||.+-++-
T Consensus 570 ~P~t~~~l~~i~Gvg~~K~~~ 590 (607)
T PRK11057 570 MPITASEMLSVNGVGQRKLER 590 (607)
T ss_pred CCCCHHHHcCCCCCCHHHHHH
Confidence 588999999999999987654
No 198
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=28.74 E-value=45 Score=26.67 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=16.9
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
|..|||||++|+.-+..++..
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ 198 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIH 198 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCC
Confidence 445899999999998777654
No 199
>PRK01810 DNA polymerase IV; Validated
Probab=28.46 E-value=47 Score=27.29 Aligned_cols=21 Identities=29% Similarity=0.438 Sum_probs=17.0
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||+.|+.....++..
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~ 201 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQ 201 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCC
Confidence 445899999999998877664
No 200
>PRK02406 DNA polymerase IV; Validated
Probab=28.31 E-value=41 Score=26.88 Aligned_cols=21 Identities=24% Similarity=0.426 Sum_probs=16.9
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||+.|+.....++..
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ 190 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIY 190 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCC
Confidence 455899999999998777654
No 201
>COG1670 RimL Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]
Probab=28.10 E-value=69 Score=21.98 Aligned_cols=40 Identities=10% Similarity=0.165 Sum_probs=29.4
Q ss_pred CCCCcHHHHHHHHHHhcCCCc-------cccccchHHHHHHHhcccC
Q 032317 26 LPGIGPKMAHLVMNVGWNNVQ-------GICVDTHVHRICNRLGWVS 65 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~~-------~~pvD~~v~Rv~~Rl~~~~ 65 (143)
=.|+|.....+++.++|.... +.+-..-..||+.|+|+..
T Consensus 109 g~G~~tea~~~~l~~~f~~~~l~ri~~~~~~~N~~S~rv~ek~Gf~~ 155 (187)
T COG1670 109 GKGYATEALRALLDYAFEELGLHRIEATVDPENEASIRVYEKLGFRL 155 (187)
T ss_pred cCchHHHHHHHHHHHhhhhcCceEEEEEecCCCHHHHHHHHHcCChh
Confidence 468999999999999998431 1223334589999999764
No 202
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=28.10 E-value=33 Score=26.50 Aligned_cols=41 Identities=22% Similarity=0.463 Sum_probs=33.7
Q ss_pred CCCCcHHHHHHHHHHhcCCCccccccc-hHHH---------HHHHhcccCC
Q 032317 26 LPGIGPKMAHLVMNVGWNNVQGICVDT-HVHR---------ICNRLGWVSQ 66 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~~~~pvD~-~v~R---------v~~Rl~~~~~ 66 (143)
+.|+|.-.|+++-...+..-+.++||. .+.- ++.|+|.++.
T Consensus 17 ~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~ 67 (259)
T cd07030 17 LEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPL 67 (259)
T ss_pred EeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCccc
Confidence 459999999999999988877888776 5555 7899998864
No 203
>PF07643 DUF1598: Protein of unknown function (DUF1598); InterPro: IPR011487 This is a family of Rhodopirellula baltica hypothetical proteins of about 500 amino acids in length.
Probab=26.99 E-value=36 Score=22.11 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=15.1
Q ss_pred HHHhcCCCc----cccccchHHHHHH
Q 032317 38 MNVGWNNVQ----GICVDTHVHRICN 59 (143)
Q Consensus 38 l~~~~~~~~----~~pvD~~v~Rv~~ 59 (143)
|.-++|..+ .+|.|+|+.|++-
T Consensus 36 l~~~LG~QdV~V~Gip~~sh~ArvLV 61 (84)
T PF07643_consen 36 LRQALGPQDVTVYGIPADSHFARVLV 61 (84)
T ss_pred HHHHhCCceeEEEccCCccHHHHHHH
Confidence 344455443 3789999999974
No 204
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=26.74 E-value=51 Score=27.32 Aligned_cols=21 Identities=14% Similarity=0.314 Sum_probs=17.6
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||+.|+.-.-.++..
T Consensus 181 v~~l~GiG~~~~~~L~~lGi~ 201 (422)
T PRK03609 181 VEEVWGVGRRISKKLNAMGIK 201 (422)
T ss_pred hhhcCCccHHHHHHHHHcCCC
Confidence 445899999999999888765
No 205
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.
Probab=26.66 E-value=33 Score=21.29 Aligned_cols=44 Identities=7% Similarity=0.045 Sum_probs=22.1
Q ss_pred CHHHHHHHHHHc----CCCCcCcHHHHhcCCC-CcHHHHHHHHHHhcCC
Q 032317 1 MKKIAPICLTKY----DGDIPSSLDELLLLPG-IGPKMAHLVMNVGWNN 44 (143)
Q Consensus 1 l~~~a~~i~~~~----~g~~p~~~~~L~~lpG-IG~ktA~~Il~~~~~~ 44 (143)
++++|+.|++.+ +..+=++++.+...-+ .|.+.+..+..++|++
T Consensus 9 ~hk~a~~iv~~~~~~~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (82)
T TIGR01766 9 LHKIVKQIVEYAKENNGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRK 57 (82)
T ss_pred HHHHHHHHHHHHHHcCCEEEECCccchhhhcchhhHHHHHHHHhhhHHH
Confidence 367888888865 3222233332222222 4455565666555543
No 206
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=26.65 E-value=77 Score=23.24 Aligned_cols=48 Identities=23% Similarity=0.524 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHhCCC--------CChhhH--HHHHHHHHHHhccCCCCCCCCCCcCccC
Q 032317 74 SSPEQTREVLQLWLPK--------EEWVPI--NPLLVGFGQTICTPIRPRCGMCSVSELC 123 (143)
Q Consensus 74 ~~~~~~~~~l~~~~p~--------~~~~~~--~~~l~~~G~~~C~~~~P~C~~CpL~~~C 123 (143)
.+..++..++.+.||. -.|.+| -+.--.-|-.+|+ .|.|+.|.=...|
T Consensus 108 ~~R~eLs~Lm~r~Fp~Laa~N~~~MrWKKFfYrqlCe~eG~~~C~--aPsC~~C~D~~~C 165 (167)
T PF04891_consen 108 RSRAELSALMRRHFPPLAARNTRNMRWKKFFYRQLCEREGLYLCR--APSCEECSDYAVC 165 (167)
T ss_pred CCHHHHHHHHHHHhHHHHHhccCCCcHHHHHHHHHHHHcCCCcCC--CCCCCCcCCHhhc
Confidence 4577888999888873 235443 3444577888896 6999999865555
No 207
>PRK03103 DNA polymerase IV; Reviewed
Probab=26.25 E-value=57 Score=26.79 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=16.6
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||++|+.....++..
T Consensus 183 i~~l~gig~~~~~~L~~~Gi~ 203 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRRMGIR 203 (409)
T ss_pred HhhcCCccHHHHHHHHHcCCC
Confidence 345899999999998777654
No 208
>PRK01216 DNA polymerase IV; Validated
Probab=26.00 E-value=57 Score=26.53 Aligned_cols=21 Identities=33% Similarity=0.529 Sum_probs=17.3
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..+||||++|+.....++..
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~ 200 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVN 200 (351)
T ss_pred cccccCCCHHHHHHHHHcCCC
Confidence 456899999999988887765
No 209
>COG2406 Protein distantly related to bacterial ferritins [General function prediction only]
Probab=25.97 E-value=62 Score=23.48 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=17.5
Q ss_pred HcCCCCcCcHHHHhcCCCCc
Q 032317 11 KYDGDIPSSLDELLLLPGIG 30 (143)
Q Consensus 11 ~~~g~~p~~~~~L~~lpGIG 30 (143)
++||++|.+++.|-.+.|.-
T Consensus 75 elg~~~Prd~~~l~dISgC~ 94 (172)
T COG2406 75 ELGGDLPRDMKKLHDISGCK 94 (172)
T ss_pred HhCCCCchhHHHHHhhcCCC
Confidence 58999999999999988764
No 210
>PRK14133 DNA polymerase IV; Provisional
Probab=25.47 E-value=56 Score=26.20 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=17.0
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||+.|+.....++..
T Consensus 175 v~~l~gig~~~~~~L~~~Gi~ 195 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIGIY 195 (347)
T ss_pred ccccCCCCHHHHHHHHHcCCc
Confidence 446899999999998777655
No 211
>PTZ00205 DNA polymerase kappa; Provisional
Probab=24.89 E-value=42 Score=29.45 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=15.3
Q ss_pred HhcCCCCcHHHHHHHHHHhc
Q 032317 23 LLLLPGIGPKMAHLVMNVGW 42 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~ 42 (143)
+.++||||++|+.-.-.++.
T Consensus 311 V~ki~GIG~~t~~~L~~~GI 330 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGI 330 (571)
T ss_pred cceeCCcCHHHHHHHHHcCC
Confidence 44699999999987765543
No 212
>PRK04148 hypothetical protein; Provisional
Probab=24.79 E-value=69 Score=22.55 Aligned_cols=109 Identities=16% Similarity=0.174 Sum_probs=55.3
Q ss_pred HHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHH--HHhcc--cCCCCCCCCCCCHH
Q 032317 2 KKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRIC--NRLGW--VSQPGRKQKTSSPE 77 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~--~Rl~~--~~~~~~~~~~~~~~ 77 (143)
..+|++|.+++...-. .. .--=|+|.-.+-+..+...|. +++.+|.|-.++- ...+. +..+. .....
T Consensus 2 ~~i~~~l~~~~~~~~~--~k--ileIG~GfG~~vA~~L~~~G~-~ViaIDi~~~aV~~a~~~~~~~v~dDl----f~p~~ 72 (134)
T PRK04148 2 DTIAEFIAENYEKGKN--KK--IVELGIGFYFKVAKKLKESGF-DVIVIDINEKAVEKAKKLGLNAFVDDL----FNPNL 72 (134)
T ss_pred hHHHHHHHHhcccccC--CE--EEEEEecCCHHHHHHHHHCCC-EEEEEECCHHHHHHHHHhCCeEEECcC----CCCCH
Confidence 4577887777643211 11 122367753333333345565 6899998887653 22221 11111 11112
Q ss_pred HHHHHHHHhCCCCChhhHHHHHHHHHHHhccC--CCCCCCCCCc
Q 032317 78 QTREVLQLWLPKEEWVPINPLLVGFGQTICTP--IRPRCGMCSV 119 (143)
Q Consensus 78 ~~~~~l~~~~p~~~~~~~~~~l~~~G~~~C~~--~~P~C~~CpL 119 (143)
++.+.+.-...-..+.++|..|+++++.+=-. -+|...+=|.
T Consensus 73 ~~y~~a~liysirpp~el~~~~~~la~~~~~~~~i~~l~~e~~~ 116 (134)
T PRK04148 73 EIYKNAKLIYSIRPPRDLQPFILELAKKINVPLIIKPLSGEEPI 116 (134)
T ss_pred HHHhcCCEEEEeCCCHHHHHHHHHHHHHcCCCEEEEcCCCCCCC
Confidence 23333322222234789999999999988211 1455555443
No 213
>KOG1573 consensus Aldehyde reductase [General function prediction only]
Probab=23.78 E-value=1.5e+02 Score=21.93 Aligned_cols=35 Identities=23% Similarity=0.525 Sum_probs=26.2
Q ss_pred HHHHHHHhCCCCChhhHHHHHHHHHHHhccCCCCC
Q 032317 79 TREVLQLWLPKEEWVPINPLLVGFGQTICTPIRPR 113 (143)
Q Consensus 79 ~~~~l~~~~p~~~~~~~~~~l~~~G~~~C~~~~P~ 113 (143)
..+.+.+-.|.++|..+...|-++|+..-.-.-|.
T Consensus 104 tAE~iR~~~Pd~dWlHLtaLiHDLGKvl~f~GepQ 138 (204)
T KOG1573|consen 104 TAEAIRKDYPDEDWLHLTALIHDLGKVLAFGGEPQ 138 (204)
T ss_pred HHHHHHHhCCCccHHHHHHHHHHHHHHHHhcCCcc
Confidence 34456666899999999999999999874433443
No 214
>PRK10809 ribosomal-protein-S5-alanine N-acetyltransferase; Provisional
Probab=23.63 E-value=77 Score=22.65 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=29.4
Q ss_pred CCCCcHHHHHHHHHHhcCCC--c-----cccccchHHHHHHHhcccC
Q 032317 26 LPGIGPKMAHLVMNVGWNNV--Q-----GICVDTHVHRICNRLGWVS 65 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~--~-----~~pvD~~v~Rv~~Rl~~~~ 65 (143)
=.|+|...+..++.++++.. . +.+--.-..|++.++|+..
T Consensus 117 G~G~~~ea~~~ll~~~~~~l~l~~i~~~v~~~N~~S~~l~ek~Gf~~ 163 (194)
T PRK10809 117 GQGLMFEALQAAIRYMQRQQHMHRIMANYMPHNKRSGDLLARLGFEK 163 (194)
T ss_pred CCCHHHHHHHHHHHHHHhcCCceEEEEEeeCCCHHHHHHHHHCCCcE
Confidence 57999999999999998641 1 1222335689999999864
No 215
>PF11575 FhuF_C: FhuF 2Fe-2S C-terminal domain; InterPro: IPR024726 Ferric iron reductase (FhuF) is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B []. This entry represents the C-terminal domain that contains 4 conserved cysteine residues found to be part of a 2Fe-2S cluster [].; GO: 0051537 2 iron, 2 sulfur cluster binding
Probab=23.57 E-value=60 Score=15.49 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=7.1
Q ss_pred CCCCCCCCcC
Q 032317 111 RPRCGMCSVS 120 (143)
Q Consensus 111 ~P~C~~CpL~ 120 (143)
.-.|..||+.
T Consensus 13 ~~~C~~CP~~ 22 (22)
T PF11575_consen 13 GGYCGTCPLL 22 (22)
T ss_pred CCccCCCCCC
Confidence 4568889973
No 216
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=23.47 E-value=48 Score=23.49 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=25.1
Q ss_pred CCCCcHHHHHHHHHHhcCCCccccccchHHH
Q 032317 26 LPGIGPKMAHLVMNVGWNNVQGICVDTHVHR 56 (143)
Q Consensus 26 lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~R 56 (143)
-+|+|..|..+-|..++ . .++.||...++
T Consensus 8 kgG~GKSt~a~nLA~~l-~-~vlliD~D~~~ 36 (179)
T cd03110 8 KGGTGKTTVTAALAALL-K-NVVLADCDVDA 36 (179)
T ss_pred CCCCCHHHHHHHHHHHH-h-CcEEEECCCCC
Confidence 58999999999999999 5 57889999875
No 217
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=23.31 E-value=52 Score=24.07 Aligned_cols=59 Identities=7% Similarity=-0.139 Sum_probs=40.6
Q ss_pred CHHHHHHHHHHcCCCCcCcHHHHhcCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHH
Q 032317 1 MKKIAPICLTKYDGDIPSSLDELLLLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNR 60 (143)
Q Consensus 1 l~~~a~~i~~~~~g~~p~~~~~L~~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~R 60 (143)
|+.+.+.+++.||..-++..+.+-..=||-+--+..|+.|= .....-|+-.|+.||..-
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVatFY-~~f~~~P~Gk~~I~VC~g 96 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFY-HLFSLKPSGEHTCVVCTG 96 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHHHc-cccCcCCCCCEEEEEcCC
Confidence 35677888888876555677888888888888888888773 333234667777666543
No 218
>PF08833 Axin_b-cat_bind: Axin beta-catenin binding domain; InterPro: IPR014936 Proteins in this entry are found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin []. ; PDB: 1QZ7_B.
Probab=23.25 E-value=28 Score=19.89 Aligned_cols=10 Identities=40% Similarity=0.713 Sum_probs=8.3
Q ss_pred cccchHHHHH
Q 032317 49 CVDTHVHRIC 58 (143)
Q Consensus 49 pvD~~v~Rv~ 58 (143)
++|-||.||+
T Consensus 7 ILD~HvsRV~ 16 (45)
T PF08833_consen 7 ILDDHVSRVW 16 (45)
T ss_dssp HHHHHHHHH-
T ss_pred HHHHHHHHHh
Confidence 5999999997
No 219
>PRK02794 DNA polymerase IV; Provisional
Probab=23.14 E-value=66 Score=26.60 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=17.4
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
|..|||||+.|+.....++..
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~ 231 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIR 231 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccc
Confidence 456899999999999877754
No 220
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=23.12 E-value=90 Score=28.04 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=16.1
Q ss_pred HHHHhcCCCCcHHHHHHHHH
Q 032317 20 LDELLLLPGIGPKMAHLVMN 39 (143)
Q Consensus 20 ~~~L~~lpGIG~ktA~~Il~ 39 (143)
.++|..++|+|.|+|.-++.
T Consensus 495 ~~~L~~l~g~g~Ksa~~Ll~ 514 (689)
T PRK14351 495 VADLAELEGWGETSAENLLA 514 (689)
T ss_pred HHHHhcCcCcchhHHHHHHH
Confidence 46788999999999987653
No 221
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=23.06 E-value=62 Score=25.88 Aligned_cols=21 Identities=48% Similarity=0.601 Sum_probs=17.4
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+..|||||++|+..+..++..
T Consensus 175 i~~l~giG~~~~~~L~~~Gi~ 195 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAVGIN 195 (343)
T ss_pred hhhcCCCCHHHHHHHHHcCCC
Confidence 445999999999998887755
No 222
>PRK01177 hypothetical protein; Provisional
Probab=22.91 E-value=32 Score=24.52 Aligned_cols=14 Identities=21% Similarity=0.771 Sum_probs=13.1
Q ss_pred CCCCCCCCcCccCc
Q 032317 111 RPRCGMCSVSELCP 124 (143)
Q Consensus 111 ~P~C~~CpL~~~C~ 124 (143)
.+.|..|+|++.|.
T Consensus 24 ~~eCe~Cr~k~vC~ 37 (140)
T PRK01177 24 AEPCKTCRLANVCF 37 (140)
T ss_pred ccccCCCCchhHhh
Confidence 68999999999997
No 223
>PRK03348 DNA polymerase IV; Provisional
Probab=22.49 E-value=71 Score=26.93 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=17.2
Q ss_pred HhcCCCCcHHHHHHHHHHhcC
Q 032317 23 LLLLPGIGPKMAHLVMNVGWN 43 (143)
Q Consensus 23 L~~lpGIG~ktA~~Il~~~~~ 43 (143)
+.+|||||+.|+.-...++..
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~ 202 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIE 202 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCc
Confidence 446899999999998877654
No 224
>TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a particularly strongly conserved family found so only in the APERN subtype of CRISPR/Cas loci and represented by AF1879 from Archaeoglobus fulgidus. This family has four perfectly preserved Cys residues. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa1, for CRISPR/Cas Subtype Protein 1.
Probab=22.25 E-value=44 Score=26.47 Aligned_cols=31 Identities=19% Similarity=0.271 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHHhccC----CCCCCC-CCCcCccC
Q 032317 93 VPINPLLVGFGQTICTP----IRPRCG-MCSVSELC 123 (143)
Q Consensus 93 ~~~~~~l~~~G~~~C~~----~~P~C~-~CpL~~~C 123 (143)
..+...+-+.-+.+-.. ..++|. .|++..+|
T Consensus 235 ~~v~e~~dei~~iI~~g~~P~ps~KC~~~C~f~~vC 270 (271)
T TIGR01896 235 TEFLERRDEAIRIIEYGSDPGLPPKCPPTCPFLEHC 270 (271)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCcccccCCCCCcCcc
Confidence 33444444444444432 246897 99999999
No 225
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=21.45 E-value=71 Score=28.08 Aligned_cols=21 Identities=33% Similarity=0.483 Sum_probs=17.1
Q ss_pred HHHhcCCCCcHHHHHHHHHHh
Q 032317 21 DELLLLPGIGPKMAHLVMNVG 41 (143)
Q Consensus 21 ~~L~~lpGIG~ktA~~Il~~~ 41 (143)
..|..+||||++....+|-+-
T Consensus 530 s~Ld~I~GiG~~r~~~LL~~F 550 (581)
T COG0322 530 SSLDDIPGIGPKRRKALLKHF 550 (581)
T ss_pred CccccCCCcCHHHHHHHHHHh
Confidence 457789999999998877653
No 226
>PF08097 Toxin_26: Conotoxin T-superfamily; InterPro: IPR012631 This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species [].; GO: 0005576 extracellular region
Probab=21.39 E-value=36 Score=13.35 Aligned_cols=8 Identities=38% Similarity=0.928 Sum_probs=5.6
Q ss_pred CCcCccCc
Q 032317 117 CSVSELCP 124 (143)
Q Consensus 117 CpL~~~C~ 124 (143)
||+-.+|.
T Consensus 3 cpvirycc 10 (11)
T PF08097_consen 3 CPVIRYCC 10 (11)
T ss_pred cchhheec
Confidence 77777764
No 227
>PF03684 UPF0179: Uncharacterised protein family (UPF0179); InterPro: IPR005369 The function of this family is unknown, however the proteins contain two cysteine clusters that may be iron sulphur redox centres.
Probab=21.37 E-value=35 Score=24.36 Aligned_cols=14 Identities=21% Similarity=0.752 Sum_probs=13.2
Q ss_pred CCCCCCCCcCccCc
Q 032317 111 RPRCGMCSVSELCP 124 (143)
Q Consensus 111 ~P~C~~CpL~~~C~ 124 (143)
.+.|..|+|++.|.
T Consensus 22 ~~eCe~Crlk~~C~ 35 (142)
T PF03684_consen 22 AEECEGCRLKNVCL 35 (142)
T ss_pred ccccCCCCChHHhc
Confidence 68999999999998
No 228
>COG1587 HemD Uroporphyrinogen-III synthase [Coenzyme metabolism]
Probab=21.22 E-value=1.2e+02 Score=23.07 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=25.3
Q ss_pred cCCCCcHHHHHHHHHHhcCCCccccccchHHHHHHHh
Q 032317 25 LLPGIGPKMAHLVMNVGWNNVQGICVDTHVHRICNRL 61 (143)
Q Consensus 25 ~lpGIG~ktA~~Il~~~~~~~~~~pvD~~v~Rv~~Rl 61 (143)
.+--||++||..+-.+++-. +.+|-|....-++..+
T Consensus 81 ~i~aVG~~Ta~~l~~~G~~~-~~~p~~~~~~~l~~~l 116 (248)
T COG1587 81 KIAAVGEKTAEALRKLGIKV-DFIPEDGDSEGLLEEL 116 (248)
T ss_pred eEEEEcHHHHHHHHHhCCCC-CcCCCccchHHHHHHh
Confidence 46679999999999999864 4555555554444444
No 229
>PRK13766 Hef nuclease; Provisional
Probab=21.19 E-value=77 Score=28.33 Aligned_cols=19 Identities=26% Similarity=0.489 Sum_probs=16.1
Q ss_pred HHhcCCCCcHHHHHHHHHH
Q 032317 22 ELLLLPGIGPKMAHLVMNV 40 (143)
Q Consensus 22 ~L~~lpGIG~ktA~~Il~~ 40 (143)
.|..+||||+++|..++..
T Consensus 716 ~L~~ipgig~~~a~~Ll~~ 734 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH 734 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH
Confidence 3668999999999988875
No 230
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=20.61 E-value=2.9e+02 Score=18.88 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=36.0
Q ss_pred ccccchHHHHHHHhcccCCCCCCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHH
Q 032317 48 ICVDTHVHRICNRLGWVSQPGRKQKTSSPEQTREVLQLWLPKEEWVPINPLLVGFGQT 105 (143)
Q Consensus 48 ~pvD~~v~Rv~~Rl~~~~~~~~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~ 105 (143)
+|.=+|+.+++..-.. .+.....+.+.++..++++.....=..+++.|+.
T Consensus 63 ~Pl~~~I~~~L~~~~~--------~~~~~~~~~~~L~~~~~~~~ae~~l~~~i~WGrY 112 (120)
T PF09821_consen 63 VPLAAHIRRVLRERPN--------HRLPEERFLDELEDHFSPEEAERQLRTAIDWGRY 112 (120)
T ss_pred CCHHHHHHHHHHhCCC--------CCCCHHHHHHHHHHHCChhHHHHHHHHHHHHHHH
Confidence 5677888888876311 1456778888899989887777777777777764
No 231
>COG5452 Uncharacterized conserved protein [Function unknown]
Probab=20.49 E-value=57 Score=23.84 Aligned_cols=22 Identities=32% Similarity=0.401 Sum_probs=17.4
Q ss_pred HHHHHHHHHHcCCCCcCcHHHH
Q 032317 2 KKIAPICLTKYDGDIPSSLDEL 23 (143)
Q Consensus 2 ~~~a~~i~~~~~g~~p~~~~~L 23 (143)
.++||.|++.|=-++..+..||
T Consensus 69 qeiaQei~Daff~dvDhs~REl 90 (180)
T COG5452 69 QEIAQEIVDAFFKDVDHSLREL 90 (180)
T ss_pred HHHHHHHHHHHHhhhhHHHHHh
Confidence 4789999998877777777776
Done!