Query 016856
Match_columns 381
No_of_seqs 267 out of 1439
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 03:25:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016856.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016856hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00588 ogg 8-oxoguanine DNA 100.0 6.6E-44 1.4E-48 350.9 23.7 254 6-381 28-302 (310)
2 KOG2875 8-oxoguanine DNA glyco 100.0 5.3E-44 1.2E-48 340.9 19.7 238 34-380 47-296 (323)
3 PRK10308 3-methyl-adenine DNA 100.0 3.4E-39 7.4E-44 314.0 22.4 235 12-380 33-272 (283)
4 COG0122 AlkA 3-methyladenine D 100.0 1E-37 2.3E-42 303.8 17.3 206 66-380 60-270 (285)
5 cd00056 ENDO3c endonuclease II 99.9 1.9E-24 4.2E-29 191.4 10.5 106 253-370 31-142 (158)
6 TIGR01083 nth endonuclease III 99.9 7.1E-22 1.5E-26 182.0 14.9 105 251-370 54-164 (191)
7 KOG1918 3-methyladenine DNA gl 99.9 1.7E-22 3.6E-27 188.3 9.1 155 119-377 71-229 (254)
8 PRK10702 endonuclease III; Pro 99.9 9.7E-22 2.1E-26 184.4 14.3 105 251-370 57-167 (211)
9 PRK13913 3-methyladenine DNA g 99.9 3.2E-21 6.9E-26 181.8 15.0 108 251-369 65-177 (218)
10 COG0177 Nth Predicted EndoIII- 99.8 5.8E-20 1.2E-24 172.1 13.9 109 248-371 54-168 (211)
11 smart00478 ENDO3c endonuclease 99.8 3.9E-20 8.4E-25 162.6 11.1 110 252-376 21-139 (149)
12 TIGR01084 mutY A/G-specific ad 99.8 1.6E-19 3.4E-24 175.7 15.0 100 251-365 54-159 (275)
13 PRK10880 adenine DNA glycosyla 99.8 2.3E-18 4.9E-23 172.6 15.8 101 251-366 58-164 (350)
14 PRK01229 N-glycosylase/DNA lya 99.7 2.3E-17 5E-22 154.6 12.0 108 260-376 68-190 (208)
15 PRK13910 DNA glycosylase MutY; 99.7 1.3E-16 2.7E-21 156.3 8.1 96 246-356 16-115 (289)
16 PF00730 HhH-GPD: HhH-GPD supe 99.5 7.2E-14 1.6E-18 116.4 11.9 75 252-372 27-108 (108)
17 TIGR03252 uncharacterized HhH- 99.5 1.1E-13 2.5E-18 126.6 13.0 96 253-355 50-155 (177)
18 COG2231 Uncharacterized protei 99.4 4.6E-12 1E-16 117.9 13.5 103 255-368 63-171 (215)
19 COG1194 MutY A/G-specific DNA 99.3 1.5E-11 3.3E-16 122.5 11.1 89 249-356 60-156 (342)
20 KOG1921 Endonuclease III [Repl 99.2 3.4E-10 7.4E-15 107.9 12.9 108 254-376 110-225 (286)
21 PF07934 OGG_N: 8-oxoguanine D 98.4 2.8E-07 6E-12 78.6 5.1 80 34-127 38-117 (117)
22 PF06029 AlkA_N: AlkA N-termin 98.1 1.2E-05 2.7E-10 69.3 7.1 82 12-120 33-114 (116)
23 KOG2457 A/G-specific adenine D 97.9 4.5E-05 9.7E-10 77.5 9.2 93 249-356 151-249 (555)
24 COG1059 Thermostable 8-oxoguan 97.6 0.00054 1.2E-08 63.8 9.7 89 254-356 72-164 (210)
25 PF00633 HHH: Helix-hairpin-he 97.3 0.00019 4E-09 47.9 2.7 20 311-330 9-28 (30)
26 smart00278 HhH1 Helix-hairpin- 94.0 0.033 7.1E-07 35.5 1.6 17 314-330 2-18 (26)
27 PRK13901 ruvA Holliday junctio 93.1 0.28 6.2E-06 46.2 6.9 66 248-330 58-124 (196)
28 smart00483 POLXc DNA polymeras 91.9 0.9 2E-05 45.8 9.2 61 264-335 48-110 (334)
29 PRK14601 ruvA Holliday junctio 90.5 2 4.3E-05 40.1 9.3 106 248-369 59-166 (183)
30 PRK14606 ruvA Holliday junctio 89.9 2.8 6.2E-05 39.1 9.8 106 248-369 59-167 (188)
31 PF12826 HHH_2: Helix-hairpin- 89.3 0.52 1.1E-05 36.2 3.8 37 283-330 16-52 (64)
32 PF14716 HHH_8: Helix-hairpin- 89.3 1.6 3.5E-05 33.8 6.5 44 271-329 20-63 (68)
33 COG0632 RuvA Holliday junction 87.7 1.5 3.2E-05 41.6 6.3 67 248-330 59-125 (201)
34 TIGR00084 ruvA Holliday juncti 86.8 1.5 3.2E-05 41.0 5.8 106 248-370 58-172 (191)
35 PRK00076 recR recombination pr 86.4 0.6 1.3E-05 44.0 3.0 31 307-337 5-36 (196)
36 TIGR00615 recR recombination p 86.4 0.64 1.4E-05 43.8 3.1 31 307-337 5-36 (195)
37 PRK14605 ruvA Holliday junctio 86.3 8.6 0.00019 36.0 10.7 67 248-330 59-125 (194)
38 COG0353 RecR Recombinational D 86.2 0.64 1.4E-05 43.8 3.0 30 307-336 6-36 (198)
39 PF14520 HHH_5: Helix-hairpin- 85.6 2.9 6.4E-05 31.3 5.9 51 264-331 5-56 (60)
40 PRK13844 recombination protein 85.5 0.7 1.5E-05 43.7 3.0 31 307-337 9-40 (200)
41 PF02371 Transposase_20: Trans 84.6 0.77 1.7E-05 37.2 2.4 35 313-347 2-36 (87)
42 PRK14600 ruvA Holliday junctio 84.5 2.1 4.6E-05 39.9 5.6 66 248-330 59-124 (186)
43 PRK14602 ruvA Holliday junctio 84.0 1.4 3E-05 41.6 4.3 107 248-370 60-180 (203)
44 PRK14604 ruvA Holliday junctio 84.0 2 4.3E-05 40.4 5.2 67 248-330 59-125 (195)
45 PRK14603 ruvA Holliday junctio 82.8 1.8 3.9E-05 40.7 4.5 67 248-330 58-124 (197)
46 PRK14605 ruvA Holliday junctio 80.8 1.5 3.3E-05 41.0 3.2 29 307-335 67-95 (194)
47 PRK00116 ruvA Holliday junctio 80.3 12 0.00026 34.8 9.0 57 312-368 107-172 (192)
48 PRK08609 hypothetical protein; 80.1 2.4 5.3E-05 45.8 4.9 60 265-334 49-109 (570)
49 cd00141 NT_POLXc Nucleotidyltr 79.8 4.9 0.00011 40.0 6.6 61 265-336 46-107 (307)
50 TIGR00084 ruvA Holliday juncti 79.0 1.4 3.1E-05 41.1 2.4 24 307-330 66-89 (191)
51 PRK00116 ruvA Holliday junctio 76.8 2.4 5.3E-05 39.4 3.3 25 310-334 70-94 (192)
52 COG0632 RuvA Holliday junction 76.1 1.6 3.5E-05 41.3 1.9 68 307-376 67-135 (201)
53 PF03352 Adenine_glyco: Methyl 72.4 51 0.0011 30.8 10.7 31 121-151 24-54 (179)
54 PRK07956 ligA NAD-dependent DN 72.2 11 0.00024 41.7 7.4 79 252-335 467-565 (665)
55 PRK02515 psbU photosystem II c 71.0 7.8 0.00017 34.5 4.8 56 251-330 48-104 (132)
56 TIGR00608 radc DNA repair prot 70.4 4.4 9.6E-05 38.7 3.4 54 266-330 20-77 (218)
57 TIGR01259 comE comEA protein. 69.8 7.1 0.00015 33.7 4.2 58 253-330 57-115 (120)
58 PRK14601 ruvA Holliday junctio 69.4 3 6.4E-05 38.9 1.9 26 307-332 67-92 (183)
59 PF14520 HHH_5: Helix-hairpin- 69.2 7.3 0.00016 29.2 3.7 33 252-284 26-59 (60)
60 PRK00024 hypothetical protein; 67.4 6 0.00013 37.8 3.6 55 264-329 28-82 (224)
61 PF11731 Cdd1: Pathogenicity l 67.3 3.8 8.3E-05 34.3 2.0 30 308-337 7-37 (93)
62 PRK14350 ligA NAD-dependent DN 66.7 12 0.00027 41.4 6.3 23 313-335 541-563 (669)
63 PRK13901 ruvA Holliday junctio 66.5 3.9 8.5E-05 38.6 2.1 25 307-331 66-90 (196)
64 TIGR00575 dnlj DNA ligase, NAD 66.1 15 0.00032 40.6 6.8 78 253-335 455-552 (652)
65 PRK14603 ruvA Holliday junctio 65.9 3.6 7.8E-05 38.7 1.7 27 307-333 66-92 (197)
66 PRK14606 ruvA Holliday junctio 65.2 4.1 9E-05 38.0 2.0 25 307-331 67-91 (188)
67 PRK14602 ruvA Holliday junctio 65.1 4.5 9.8E-05 38.2 2.2 27 307-333 68-94 (203)
68 PRK14604 ruvA Holliday junctio 65.1 4 8.7E-05 38.3 1.9 25 307-331 67-91 (195)
69 PF11798 IMS_HHH: IMS family H 64.6 4.3 9.4E-05 27.2 1.5 16 314-329 12-27 (32)
70 PF10391 DNA_pol_lambd_f: Fing 64.2 5 0.00011 30.0 1.9 21 313-333 2-23 (52)
71 TIGR00426 competence protein C 62.1 8 0.00017 29.7 2.8 54 257-330 9-64 (69)
72 PRK14600 ruvA Holliday junctio 61.6 7.2 0.00016 36.4 2.9 27 307-333 67-93 (186)
73 cd00080 HhH2_motif Helix-hairp 60.1 5.4 0.00012 31.6 1.5 25 313-337 22-46 (75)
74 COG1555 ComEA DNA uptake prote 58.6 18 0.00039 32.6 4.8 52 258-329 91-143 (149)
75 PF12836 HHH_3: Helix-hairpin- 57.7 13 0.00028 28.4 3.2 52 258-329 8-60 (65)
76 PRK08097 ligB NAD-dependent DN 57.7 27 0.00059 38.0 6.8 83 251-335 446-542 (562)
77 PF12836 HHH_3: Helix-hairpin- 57.5 9.2 0.0002 29.2 2.4 19 312-330 13-31 (65)
78 PRK14351 ligA NAD-dependent DN 57.4 28 0.00061 38.8 7.0 82 253-336 485-583 (689)
79 smart00279 HhH2 Helix-hairpin- 56.2 8.2 0.00018 26.6 1.7 17 314-330 17-33 (36)
80 TIGR01259 comE comEA protein. 54.8 10 0.00022 32.7 2.5 20 312-331 67-86 (120)
81 COG1796 POL4 DNA polymerase IV 51.7 28 0.00061 35.4 5.3 46 270-330 22-70 (326)
82 COG1555 ComEA DNA uptake prote 51.6 10 0.00022 34.1 2.1 19 312-330 96-114 (149)
83 PRK07945 hypothetical protein; 51.2 27 0.00058 35.3 5.2 53 265-330 12-66 (335)
84 cd00141 NT_POLXc Nucleotidyltr 50.7 30 0.00065 34.5 5.4 44 271-330 19-62 (307)
85 smart00483 POLXc DNA polymeras 49.5 25 0.00055 35.5 4.7 47 273-335 24-72 (334)
86 PF00416 Ribosomal_S13: Riboso 49.3 18 0.00039 30.6 3.1 43 309-351 11-57 (107)
87 PRK02515 psbU photosystem II c 48.1 14 0.0003 32.9 2.3 19 312-330 60-78 (132)
88 PF01367 5_3_exonuc: 5'-3' exo 45.3 3 6.5E-05 35.3 -2.2 27 313-339 18-44 (101)
89 PF14475 Mso1_Sec1_bdg: Sec1-b 45.1 18 0.00039 26.0 2.0 16 339-354 16-31 (41)
90 COG1948 MUS81 ERCC4-type nucle 45.0 48 0.001 32.7 5.6 109 253-371 117-239 (254)
91 PRK14973 DNA topoisomerase I; 44.7 32 0.00069 39.7 5.0 82 250-340 821-905 (936)
92 KOG2534 DNA polymerase IV (fam 44.6 70 0.0015 32.7 6.8 40 274-329 33-72 (353)
93 PRK12766 50S ribosomal protein 42.5 39 0.00085 32.8 4.6 23 313-335 36-58 (232)
94 COG2003 RadC DNA repair protei 41.3 20 0.00042 34.7 2.3 49 270-329 34-82 (224)
95 KOG2534 DNA polymerase IV (fam 41.0 53 0.0011 33.6 5.3 65 263-336 55-121 (353)
96 TIGR00426 competence protein C 38.2 29 0.00062 26.6 2.5 19 312-330 15-34 (69)
97 PF09674 DUF2400: Protein of u 36.8 25 0.00054 34.1 2.3 18 338-355 176-193 (232)
98 PRK07758 hypothetical protein; 36.8 52 0.0011 27.8 3.9 39 280-329 44-83 (95)
99 COG4277 Predicted DNA-binding 36.1 26 0.00056 35.7 2.3 21 312-332 329-349 (404)
100 PF03118 RNA_pol_A_CTD: Bacter 35.3 35 0.00076 26.4 2.5 45 270-331 17-62 (66)
101 PF14229 DUF4332: Domain of un 35.1 1E+02 0.0022 26.6 5.6 32 289-330 39-70 (122)
102 KOG2841 Structure-specific end 35.0 39 0.00085 33.1 3.3 37 248-284 211-248 (254)
103 TIGR00624 tag DNA-3-methyladen 34.7 2.4E+02 0.0053 26.3 8.4 39 113-151 20-58 (179)
104 PRK09482 flap endonuclease-lik 34.5 25 0.00054 34.5 1.9 25 313-337 182-206 (256)
105 PRK14976 5'-3' exonuclease; Pr 34.3 26 0.00057 34.6 2.1 25 313-337 191-215 (281)
106 TIGR02757 conserved hypothetic 31.8 34 0.00073 33.2 2.3 17 338-354 173-189 (229)
107 TIGR01448 recD_rel helicase, p 31.2 48 0.0011 37.0 3.7 28 307-334 76-105 (720)
108 smart00475 53EXOc 5'-3' exonuc 30.8 32 0.00069 33.6 2.0 25 313-337 186-210 (259)
109 PRK08609 hypothetical protein; 30.5 98 0.0021 33.7 5.8 48 266-329 16-64 (570)
110 PRK14666 uvrC excinuclease ABC 30.4 41 0.00088 37.6 2.9 29 309-337 633-661 (694)
111 PRK14671 uvrC excinuclease ABC 29.6 79 0.0017 34.9 4.9 32 309-340 565-596 (621)
112 cd00008 53EXOc 5'-3' exonuclea 29.1 35 0.00076 32.7 1.9 25 313-337 183-207 (240)
113 PRK13482 DNA integrity scannin 28.2 78 0.0017 32.6 4.3 43 248-290 303-346 (352)
114 TIGR01954 nusA_Cterm_rpt trans 28.0 1.3E+02 0.0028 21.0 4.4 34 251-284 13-47 (50)
115 CHL00137 rps13 ribosomal prote 27.7 35 0.00076 29.8 1.5 26 309-334 13-38 (122)
116 PF12826 HHH_2: Helix-hairpin- 26.7 55 0.0012 24.9 2.3 33 249-281 20-53 (64)
117 PTZ00134 40S ribosomal protein 26.3 36 0.00078 31.0 1.4 26 310-335 27-52 (154)
118 PF09597 IGR: IGR protein moti 26.0 1.1E+02 0.0023 23.5 3.7 38 251-289 18-57 (57)
119 PRK13482 DNA integrity scannin 25.8 73 0.0016 32.8 3.6 39 281-330 298-336 (352)
120 cd08594 PI-PLCc_eta Catalytic 25.1 2.3E+02 0.005 27.5 6.7 41 114-154 62-117 (227)
121 PRK05179 rpsM 30S ribosomal pr 25.0 47 0.001 29.0 1.8 26 309-334 13-38 (122)
122 COG1415 Uncharacterized conser 24.0 1.9E+02 0.0041 30.0 6.1 20 310-329 275-294 (373)
123 TIGR00596 rad1 DNA repair prot 23.0 73 0.0016 36.3 3.3 29 307-335 751-779 (814)
124 TIGR03631 bact_S13 30S ribosom 22.7 51 0.0011 28.4 1.5 25 310-334 12-36 (113)
125 PRK10353 3-methyl-adenine DNA 22.6 6.5E+02 0.014 23.7 11.6 40 113-152 21-60 (187)
126 PRK10371 DNA-binding transcrip 22.1 5.7E+02 0.012 25.0 9.0 61 289-366 233-293 (302)
127 TIGR03629 arch_S13P archaeal r 21.6 49 0.0011 29.8 1.3 25 310-334 18-42 (144)
128 cd08633 PI-PLCc_eta2 Catalytic 21.0 3.1E+02 0.0068 27.0 6.8 41 114-154 62-117 (254)
129 PRK09685 DNA-binding transcrip 21.0 4.6E+02 0.01 25.0 8.0 84 262-364 216-299 (302)
130 PRK04053 rps13p 30S ribosomal 20.8 60 0.0013 29.4 1.7 25 310-334 22-46 (149)
No 1
>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=100.00 E-value=6.6e-44 Score=350.92 Aligned_cols=254 Identities=21% Similarity=0.274 Sum_probs=197.2
Q ss_pred ccc--cCCCccccceecCCCCCCCCCCCceeEEEEecCCCCCCcEEEEEeecCCCCCCCCCHHHHHHHHHHHHHHhcCCc
Q 016856 6 RWD--PLSRSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSE 83 (381)
Q Consensus 6 ~w~--~~~~~~~r~lrl~~~~~~~~~~~~~~~v~i~~~~~~~~~L~v~v~~~~~~~~~~~s~~~~~~i~~~v~r~l~Ld~ 83 (381)
+|. ...+.|.|++.+++. + .+.+.|. ++.+.+.+... .. .+.+.+.++|++||+||.
T Consensus 28 rw~~~~~~~~y~~~~~~~~~---------~-~~~~~q~---~~~~~~~~~~~------~~--~~~~~~~~~ir~~f~Ld~ 86 (310)
T TIGR00588 28 RWRWEESPAHWSGLLVIADQ---------P-VWTLTQT---EEQLLCTVYRG------DK--PTQDELETKLEKYFQLDV 86 (310)
T ss_pred cCceeCCCCeEEEEEEECCe---------e-EEEEEEc---CCceEEEEecC------CC--ccHHHHHHHHHHHhcCCC
Confidence 564 555789999999875 4 3445565 33454444432 11 245678899999999999
Q ss_pred cchHhHHHHHHHh-HHHHhhhccccccccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCC
Q 016856 84 ADERNVRDFKRIV-RQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSI 162 (381)
Q Consensus 84 d~~~~~~~f~~~~-~~~~~~~~~~~~~~~~~ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~~g~l~~~~~~~ 162 (381)
| +.++++.. ..++.+.....+ ..|.|++++ |+||++|++|||||+|++++.+|.++||+.||+
T Consensus 87 d----~~~i~~~~~~~D~~l~~~~~~---~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~-------- 150 (310)
T TIGR00588 87 S----LAQLYTHWGSVDKHFQYVAQK---FQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGP-------- 150 (310)
T ss_pred C----HHHHHHHHhhcCHHHHHHHHh---CCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCC--------
Confidence 9 66665542 223333211111 236699999 999999999999999999999999999999986
Q ss_pred CCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCC
Q 016856 163 SEDFIPQTPAGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDP 242 (381)
Q Consensus 163 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (381)
++. .++|
T Consensus 151 --------~~~--------------------------------------------------------~~~g--------- 157 (310)
T TIGR00588 151 --------RLI--------------------------------------------------------TLDG--------- 157 (310)
T ss_pred --------Ccc--------------------------------------------------------cCCC---------
Confidence 221 1222
Q ss_pred CCccccccCCCCHHHHhcCCH-HHHHHhCcCcHHHHHHHHHHHHHHhCCC---ChhHHHhhhhhcccCcHHHHHHHHhcC
Q 016856 243 PSARDRIGNFPSPRELANLDE-SFLAKRCNLGYRAGRILKLARGIVDGQI---QLRELEDMCNEASLTAYVKLAEQLSQI 318 (381)
Q Consensus 243 p~~~~~~~~FPTpe~La~~~~-e~Lr~~~g~GyRAkyI~~lA~~i~~G~l---~Le~L~~l~~~~~~~~~ee~~~~Ll~L 318 (381)
..++.||||++|+..+. +.|+. +|+||||+||+++|+++.+|.. +++.|..+ ++++++++|++|
T Consensus 158 ----~~~~~FPtp~~La~~~~e~~Lr~-~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~-------~~~~~~~~L~~l 225 (310)
T TIGR00588 158 ----VTYHGFPSLHALTGPEAEAHLRK-LGLGYRARYIRETARALLEEQGGRAWLQQIRGA-------SYEDAREALCEL 225 (310)
T ss_pred ----cccccCCCHHHHhCCChHHHHHH-cCCHHHHHHHHHHHHHHHhccCCchhHHhhccC-------ChHHHHHHHHhC
Confidence 25789999999998765 57887 9999999999999999998754 45566665 899999999999
Q ss_pred CccChHHHHHHH-HHhCCCCccccchHHHHHHHHhhccC-----------CChHHHHHHHHHHhccCCCc--ccccC
Q 016856 319 NGFGPFTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN-----------CTSKTVQMIAESIYGKYAPF--QFLAY 381 (381)
Q Consensus 319 ~GIGpwTAd~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~-----------~s~k~i~~~~~~~~g~~aGw--q~Lfy 381 (381)
||||||||+||| |+|+++|+||+|+||+|+++++|+.. .+++++++++++.|++|+|| +||||
T Consensus 226 ~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~~g~~ag~aq~~lf~ 302 (310)
T TIGR00588 226 PGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSLWGPYAGWAQAVLFS 302 (310)
T ss_pred CCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHHhcCcchHHHHHHHH
Confidence 999999999995 89999999999999999999998742 23467788899999999999 89986
No 2
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=5.3e-44 Score=340.92 Aligned_cols=238 Identities=21% Similarity=0.264 Sum_probs=191.7
Q ss_pred eEEEEecCCCCCCcEEEEEeecCCCCCCCCCHHHHHHHHHHHHHHhcCCccchHhHHHHHHHhHHHHhhhccccccccCC
Q 016856 34 VDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDF 113 (381)
Q Consensus 34 ~~v~i~~~~~~~~~L~v~v~~~~~~~~~~~s~~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ 113 (381)
-+|++.|. +++.+.+++..+ .....+ +++ ..|+.||+||.++..++..|-..|++|..+.+ -
T Consensus 47 ~v~~L~Q~--ee~~~~y~~~~s----~~~p~~---del-~~i~~yf~ldv~L~~l~~~W~~~D~~F~~la~--------q 108 (323)
T KOG2875|consen 47 QVWTLTQT--EEQCTVYRGDKS----ASRPTP---DEL-EAISKYFQLDVTLAQLYHHWGSVDDHFQELAQ--------Q 108 (323)
T ss_pred EEEEEEec--CCceEEEEeecC----CCCCCh---HHH-HHHHHHHhheeeHHHHHHHhCcCChHHHHHHH--------h
Confidence 36777777 344455555553 112222 222 25789999999999999999999988888773 3
Q ss_pred cccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCCCCCCCCCCCCcchhhhhhhhhhhhhhhhhhh
Q 016856 114 SGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSRI 193 (381)
Q Consensus 114 ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~~g~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 193 (381)
|+|++|+ ||||+|++||||+||||+||++|+++||..+|+. ++
T Consensus 109 gvRlLrQ-dP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~----------------i~-------------------- 151 (323)
T KOG2875|consen 109 GVRLLRQ-DPIECLFSFICSSNNNIARITGMVERFCQAFGPR----------------II-------------------- 151 (323)
T ss_pred hhHHHhc-CcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcc----------------eE--------------------
Confidence 7899997 9999999999999999999999999999999972 22
Q ss_pred hhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCCCCccccccCCCCHHHHhc-CCHHHHHHhCcC
Q 016856 194 AESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDPPSARDRIGNFPSPRELAN-LDESFLAKRCNL 272 (381)
Q Consensus 194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~FPTpe~La~-~~~e~Lr~~~g~ 272 (381)
.++|. .+|.|||.+.|+. ..+++||+ .|+
T Consensus 152 ------------------------------------~~dg~-------------~~h~FPsl~~L~g~~~Ea~LR~-~gf 181 (323)
T KOG2875|consen 152 ------------------------------------QLDGV-------------DYHGFPSLQALAGPEVEAELRK-LGF 181 (323)
T ss_pred ------------------------------------eecCc-------------ccccCccHHHhcCcHhHHHHHH-cCc
Confidence 45554 7999999999995 45678998 999
Q ss_pred cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH-HHHhCCCCccccchHHHHHHHH
Q 016856 273 GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV-LVCIGFYHVIPTDSETIRHLKQ 351 (381)
Q Consensus 273 GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V-L~~Lg~~dvfPvDt~v~Ril~r 351 (381)
||||+||.++|++|.+..--+.+|.++++ .+||++++.|+.+||||+|+|||| ||+|+.+.++|||+||.|+++.
T Consensus 182 GYRAkYI~~ta~~l~~~~g~~~wLqsl~~----~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~ 257 (323)
T KOG2875|consen 182 GYRAKYISATARALQEKQGGLAWLQSLRK----SSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQD 257 (323)
T ss_pred chhHHHHHHHHHHHHHhcccchHHHHHhc----ccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhc
Confidence 99999999999999975555555555532 499999999999999999999999 6999999999999999999995
Q ss_pred hhccC------C---ChHHHHHHHHHHhccCCCc-cccc
Q 016856 352 VHARN------C---TSKTVQMIAESIYGKYAPF-QFLA 380 (381)
Q Consensus 352 ly~~~------~---s~k~i~~~~~~~~g~~aGw-q~Lf 380 (381)
++... . -+.++..++.+.||+|||| |.+-
T Consensus 258 y~l~~~~g~k~l~~ki~~ev~~~f~~~~G~YAGwAQ~~l 296 (323)
T KOG2875|consen 258 YILPGLSGAKELTPKINGEVSNFFRSLWGEYAGWAQAVL 296 (323)
T ss_pred ccCCCccccccCCcchhHHHHHHHHHHhcccccchhhee
Confidence 54322 1 2467889999999999999 6543
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=3.4e-39 Score=313.99 Aligned_cols=235 Identities=18% Similarity=0.200 Sum_probs=187.2
Q ss_pred CccccceecCCCCCCCCCCCceeEEEEecCCCCCCcEEEEEeecCCCCCCCCCHHHHHHHHHHHHHHhcCCccchHhHHH
Q 016856 12 RSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRD 91 (381)
Q Consensus 12 ~~~~r~lrl~~~~~~~~~~~~~~~v~i~~~~~~~~~L~v~v~~~~~~~~~~~s~~~~~~i~~~v~r~l~Ld~d~~~~~~~ 91 (381)
++|.|+++++++ ...|+|++.+ ....|++++..+ + ......++++|+|||+||.| +..
T Consensus 33 ~~y~R~~~~~~~---------~~~~~v~~~~-~~~~l~~~~~~~-------~-~~~~~~~~~~vrr~fdLd~d----~~~ 90 (283)
T PRK10308 33 GYYARSLAVGEH---------RGVVTVIPDI-ARHTLHINLSAG-------L-EPVAAECLAKMSRLFDLQCN----PQI 90 (283)
T ss_pred CEEEEEEEECCc---------cEEEEEEEcC-CCceEEEEEcCC-------c-cccHHHHHHHHHHHcCCCCC----HHH
Confidence 689999999987 8899998762 233566666552 1 12455799999999999999 777
Q ss_pred HHHHhHHHHhhhccccccccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCCCCCCCCCCC
Q 016856 92 FKRIVRQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQTP 171 (381)
Q Consensus 92 f~~~~~~~~~~~~~~~~~~~~~ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~~g~l~~~~~~~~~~~~~~~p 171 (381)
|+........ ...|.|+++.+|+||++|++||+||+++.++.++.++||+.+|+ +
T Consensus 91 i~~~L~~~~~---------~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~----------------~ 145 (283)
T PRK10308 91 VNGALGKLGA---------ARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGE----------------R 145 (283)
T ss_pred HHHHHHHHHH---------hCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCc----------------c
Confidence 7643321111 12488999999999999999999999999999999999999987 2
Q ss_pred CcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCCCCccccccC
Q 016856 172 AGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDPPSARDRIGN 251 (381)
Q Consensus 172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 251 (381)
+. + +..++.
T Consensus 146 l~----------------------------------------------------------~-------------~~~~~~ 154 (283)
T PRK10308 146 LD----------------------------------------------------------D-------------FPEYVC 154 (283)
T ss_pred cc----------------------------------------------------------C-------------CCCccC
Confidence 21 0 013689
Q ss_pred CCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 252 FPSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 252 FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
||||++|+++++++|+. ||+++ |++||+++|+++.+|+++++... ++++++++|++|||||||||+||+
T Consensus 155 FPtpe~La~~~~~eL~~-~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~---------~~~~~~~~L~~LpGIGpwTA~~vl 224 (283)
T PRK10308 155 FPTPERLAAADPQALKA-LGMPLKRAEALIHLANAALEGTLPLTIPG---------DVEQAMKTLQTFPGIGRWTANYFA 224 (283)
T ss_pred CCCHHHHHcCCHHHHHH-CCCCHHHHHHHHHHHHHHHcCCCCccccC---------CHHHHHHHHhcCCCcCHHHHHHHH
Confidence 99999999999999998 88875 99999999999999999876532 678999999999999999999995
Q ss_pred -HHhCCCCccc-cchHHHHHHHHhhccCCChHHHHHHHHHHhccCCCc--cccc
Q 016856 331 -VCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPF--QFLA 380 (381)
Q Consensus 331 -~~Lg~~dvfP-vDt~v~Ril~rly~~~~s~k~i~~~~~~~~g~~aGw--q~Lf 380 (381)
|+||++|+|| +|+++++.+. + .+++++.+..+ .|.||++| .+|+
T Consensus 225 lr~lg~~D~fp~~D~~l~~~~~---~--~~~~~~~~~a~-~w~P~rsya~~~LW 272 (283)
T PRK10308 225 LRGWQAKDVFLPDDYLIKQRFP---G--MTPAQIRRYAE-RWKPWRSYALLHIW 272 (283)
T ss_pred HHhCCCCCCCCcccHHHHHhcc---c--CCHHHHHHHHH-hcCCHHHHHHHHHH
Confidence 7999999997 9999998652 2 35677776664 47777777 5544
No 4
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-37 Score=303.85 Aligned_cols=206 Identities=22% Similarity=0.321 Sum_probs=177.1
Q ss_pred HHHHHHHHHHHHHhcCCccchHhHHHHHHHhHHHHhhhccccccccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHH
Q 016856 66 EQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMA 145 (381)
Q Consensus 66 ~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~ 145 (381)
...+.+...++++|+||.+ +.++......+.... .+|+|++..+|+||+||++||+||+|++++.+|.
T Consensus 60 ~~~~~~~~~~~~~~~lD~~----l~~i~~~~~~~~~~~--------~~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~ 127 (285)
T COG0122 60 PVAEDIEAALRRLFDLDPD----LAPIIDALGPLPLLR--------APGLRLPLAPDPFEALVRAILSQQVSVAAAAKIW 127 (285)
T ss_pred hhhHHHHHHHHHHHhcCCc----HHHHHHhcCcccccc--------ccCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHH
Confidence 4667888999999999999 888887665444433 1588999889999999999999999999999999
Q ss_pred HHHHHHhhhhhcCCCCCCCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCC
Q 016856 146 RALCELQWELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQN 225 (381)
Q Consensus 146 ~~L~~~~g~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (381)
.+||+.+|+ ++
T Consensus 128 ~rl~~~~g~----------------~~----------------------------------------------------- 138 (285)
T COG0122 128 ARLVSLYGN----------------AL----------------------------------------------------- 138 (285)
T ss_pred HHHHHHhCC----------------cc-----------------------------------------------------
Confidence 999999886 11
Q ss_pred CcccccccccCCCCCCCCCccccccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhccc
Q 016856 226 DIESDLHGLNELSTTDPPSARDRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASL 305 (381)
Q Consensus 226 ~~~~~~~~~~~~~~~~~p~~~~~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~ 305 (381)
+.+|.|||||+|++++++.|+..+++++|++||+++|+++.+|.++++.+.++
T Consensus 139 ---------------------~~~~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~------ 191 (285)
T COG0122 139 ---------------------EIYHSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSELKPL------ 191 (285)
T ss_pred ---------------------ccccCCCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHcCCccHHHhccC------
Confidence 05789999999999999999986778999999999999999999999999988
Q ss_pred CcHHHHHHHHhcCCccChHHHHHHH-HHhCCCCccc-cchHHHHHHHHhhccCCCh-HHHHHHHHHHhccCCCc--cccc
Q 016856 306 TAYVKLAEQLSQINGFGPFTRNNVL-VCIGFYHVIP-TDSETIRHLKQVHARNCTS-KTVQMIAESIYGKYAPF--QFLA 380 (381)
Q Consensus 306 ~~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~dvfP-vDt~v~Ril~rly~~~~s~-k~i~~~~~~~~g~~aGw--q~Lf 380 (381)
+++++++.|++|+|||||||+|+| |+||++|+|| +|++++++++++|..+..+ +.......+.|+||++| .|||
T Consensus 192 -~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w~p~rs~A~~yLw 270 (285)
T COG0122 192 -SDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERWGPYRSYAALYLW 270 (285)
T ss_pred -CHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcccCHHHHHHHHHH
Confidence 999999999999999999999996 8999999999 8999999999999433222 22244556778888888 6665
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.91 E-value=1.9e-24 Score=191.43 Aligned_cols=106 Identities=29% Similarity=0.362 Sum_probs=88.6
Q ss_pred CCHHHHhcCCHHHHHHhCcC---cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 253 PSPRELANLDESFLAKRCNL---GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g~---GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|||++|+.+++++|++.+.. .+||++|+++|+.+.++..++.. +++++++.|++|||||||||+|+
T Consensus 31 pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~-----------~~~~~~~~L~~l~GIG~~tA~~~ 99 (158)
T cd00056 31 PTPEALAAADEEELRELIRSLGYRRKAKYLKELARAIVEGFGGLVL-----------DDPDAREELLALPGVGRKTANVV 99 (158)
T ss_pred CCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccC-----------CCcccHHHHHcCCCCCHHHHHHH
Confidence 89999999999999983322 37999999999999987764322 34778999999999999999999
Q ss_pred H-HHhCCCCccccchHHHHHHHHhhc--cCCChHHHHHHHHHHh
Q 016856 330 L-VCIGFYHVIPTDSETIRHLKQVHA--RNCTSKTVQMIAESIY 370 (381)
Q Consensus 330 L-~~Lg~~dvfPvDt~v~Ril~rly~--~~~s~k~i~~~~~~~~ 370 (381)
| ++++ .++||+|+|++|++++++. ...+++++.+.++.++
T Consensus 100 l~~~~~-~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (158)
T cd00056 100 LLFALG-PDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELL 142 (158)
T ss_pred HHHHCC-CCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHC
Confidence 6 8999 8899999999999999986 3456777777776555
No 6
>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=99.88 E-value=7.1e-22 Score=181.98 Aligned_cols=105 Identities=24% Similarity=0.277 Sum_probs=84.4
Q ss_pred CCCCHHHHhcCCHHHHHHh---CcC-cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHH
Q 016856 251 NFPSPRELANLDESFLAKR---CNL-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~---~g~-GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTA 326 (381)
.||||++|+++++++|.+. +|+ ..||+||+++|+.+.++.-. +.++.++.|++|||||+|||
T Consensus 54 ~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~--------------~~~~~~~~L~~l~GIG~ktA 119 (191)
T TIGR01083 54 VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG--------------EVPEDREELVKLPGVGRKTA 119 (191)
T ss_pred HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCC--------------CCchHHHHHHhCCCCcHHHH
Confidence 4899999999999999664 343 34999999999999874210 23457899999999999999
Q ss_pred HHHH-HHhCCCCccccchHHHHHHHHhhcc-CCChHHHHHHHHHHh
Q 016856 327 NNVL-VCIGFYHVIPTDSETIRHLKQVHAR-NCTSKTVQMIAESIY 370 (381)
Q Consensus 327 d~VL-~~Lg~~dvfPvDt~v~Ril~rly~~-~~s~k~i~~~~~~~~ 370 (381)
+||| |+++++ .||+|+|++|+++|++.. ..+++++++.+.+.+
T Consensus 120 ~~ill~~~~~~-~~~vD~~v~Ri~~r~g~~~~~~~~~~~~~l~~~~ 164 (191)
T TIGR01083 120 NVVLNVAFGIP-AIAVDTHVFRVSNRLGLSKGKDPDKVEEELLKLI 164 (191)
T ss_pred HHHHHHHcCCC-ccccchhHHHHHHHcCCCCCCCHHHHHHHHHHHC
Confidence 9996 899997 499999999999999643 346677777776554
No 7
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.87 E-value=1.7e-22 Score=188.27 Aligned_cols=155 Identities=23% Similarity=0.324 Sum_probs=133.1
Q ss_pred CCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCCCCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhc
Q 016856 119 RSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSRIAESKA 198 (381)
Q Consensus 119 r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~~g~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (381)
-..+|||.|+++|++||.+-.++-++-.|+|.++|.
T Consensus 71 ~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g-------------------------------------------- 106 (254)
T KOG1918|consen 71 ETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGG-------------------------------------------- 106 (254)
T ss_pred cccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------------------------------------
Confidence 346899999999999999988999999998887542
Q ss_pred chhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCCCCccccccCCCCHHHHhcCCHHHHHHhCcC-cHHHH
Q 016856 199 SSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDPPSARDRIGNFPSPRELANLDESFLAKRCNL-GYRAG 277 (381)
Q Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~FPTpe~La~~~~e~Lr~~~g~-GyRAk 277 (381)
-+.||+|+.+..++.++|++ ||+ ++|+.
T Consensus 107 --------------------------------------------------~~~~~~pe~i~~~~~~~lrk-cG~S~rK~~ 135 (254)
T KOG1918|consen 107 --------------------------------------------------AEKFPTPEFIDPLDCEELRK-CGFSKRKAS 135 (254)
T ss_pred --------------------------------------------------CcCCCCchhcCcCCHHHHHH-hCcchhhHH
Confidence 25799999999999999999 876 57899
Q ss_pred HHHHHHHHHHhCCCC-hhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH-HHhCCCCccc-cchHHHHHHHHhhc
Q 016856 278 RILKLARGIVDGQIQ-LRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL-VCIGFYHVIP-TDSETIRHLKQVHA 354 (381)
Q Consensus 278 yI~~lA~~i~~G~l~-Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~dvfP-vDt~v~Ril~rly~ 354 (381)
||+.+|++..+|.+. .+...+| +.+++++.|+.++|||+||++|+| |+|+|+|++| .|.+|++.++.+++
T Consensus 136 yLh~lA~~~~ng~I~s~~~i~~m-------seEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~g 208 (254)
T KOG1918|consen 136 YLHSLAEAYTNGYIPSKSGIEKM-------SEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLG 208 (254)
T ss_pred HHHHHHHHHhcCCCCchHHHhhc-------CHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhC
Confidence 999999999999654 5566777 889999999999999999999997 9999999999 89999999999998
Q ss_pred cCCChHHHHHHHHHHhccCCCcc
Q 016856 355 RNCTSKTVQMIAESIYGKYAPFQ 377 (381)
Q Consensus 355 ~~~s~k~i~~~~~~~~g~~aGwq 377 (381)
... .+...+++++.++|+||+
T Consensus 209 l~~--~p~~~evekl~e~~kpyR 229 (254)
T KOG1918|consen 209 LKP--LPLPKEVEKLCEKCKPYR 229 (254)
T ss_pred CCC--CCchHHHHHHhhhccchH
Confidence 753 333455666777888873
No 8
>PRK10702 endonuclease III; Provisional
Probab=99.87 E-value=9.7e-22 Score=184.43 Aligned_cols=105 Identities=17% Similarity=0.213 Sum_probs=85.7
Q ss_pred CCCCHHHHhcCCHHHHHHhC-cCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHH
Q 016856 251 NFPSPRELANLDESFLAKRC-NLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~-g~Gy---RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTA 326 (381)
.||||++|+++++++|++.+ +.|| ||++|+++|+.+.+..- .+.++.+++|++|||||+|||
T Consensus 57 ~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~--------------~~~p~~~~~Ll~lpGVG~ktA 122 (211)
T PRK10702 57 VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHN--------------GEVPEDRAALEALPGVGRKTA 122 (211)
T ss_pred HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcC--------------CCCCchHHHHhcCCcccHHHH
Confidence 59999999999999999854 4664 99999999999975321 033467899999999999999
Q ss_pred HHHH-HHhCCCCccccchHHHHHHHHhhcc-CCChHHHHHHHHHHh
Q 016856 327 NNVL-VCIGFYHVIPTDSETIRHLKQVHAR-NCTSKTVQMIAESIY 370 (381)
Q Consensus 327 d~VL-~~Lg~~dvfPvDt~v~Ril~rly~~-~~s~k~i~~~~~~~~ 370 (381)
+||| ++++++ +||||+||+|+++|++.. ..++.++++.+.+.+
T Consensus 123 ~~ill~a~~~~-~~~VDt~v~Rv~~r~g~~~~~~~~~~~~~l~~~l 167 (211)
T PRK10702 123 NVVLNTAFGWP-TIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVV 167 (211)
T ss_pred HHHHHHHcCCC-cccccchHHHHHHHhCCCCCCCHHHHHHHHHHhC
Confidence 9996 899995 899999999999999643 355667777766554
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.86 E-value=3.2e-21 Score=181.77 Aligned_cols=108 Identities=18% Similarity=0.137 Sum_probs=87.5
Q ss_pred CCCCHHHHhcCCHHHHHHhC---cCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHH
Q 016856 251 NFPSPRELANLDESFLAKRC---NLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~---g~G-yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTA 326 (381)
.||||+.|+++++++|++.+ |+. .||+||+++|+.+.++..+++. + ..++.++.|+++||||+|||
T Consensus 65 ~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~---~-------~~~~~re~Ll~l~GIG~kTA 134 (218)
T PRK13913 65 DEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFEN---F-------KQEVTREWLLDQKGIGKESA 134 (218)
T ss_pred cCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchh---c-------cCchHHHHHHcCCCccHHHH
Confidence 58999999999999999864 442 3899999999999875433332 2 22467899999999999999
Q ss_pred HHHH-HHhCCCCccccchHHHHHHHHhhccCCChHHHHHHHHHH
Q 016856 327 NNVL-VCIGFYHVIPTDSETIRHLKQVHARNCTSKTVQMIAESI 369 (381)
Q Consensus 327 d~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~~s~k~i~~~~~~~ 369 (381)
|+|| ++++++ +||||+|++|+++|++-...++.++++.+++.
T Consensus 135 d~iLlya~~rp-~fvVDty~~Rv~~RlG~~~~~y~~~~~~~~~~ 177 (218)
T PRK13913 135 DAILCYVCAKE-VMVVDKYSYLFLKKLGIEIEDYDELQHFFEKG 177 (218)
T ss_pred HHHHHHHcCCC-ccccchhHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 9996 799997 79999999999999854445677777777653
No 10
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.83 E-value=5.8e-20 Score=172.13 Aligned_cols=109 Identities=25% Similarity=0.272 Sum_probs=90.4
Q ss_pred cccCCCCHHHHhcCCHHHHHHhC---cCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccCh
Q 016856 248 RIGNFPSPRELANLDESFLAKRC---NLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGP 323 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~---g~G-yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGp 323 (381)
.+..||||++|+++++++|.+.+ |+- .||++|+++|+.|.+.-.. ..++.+++|++|||||+
T Consensus 54 Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g--------------~vP~~~~eL~~LPGVGr 119 (211)
T COG0177 54 LFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG--------------EVPDTREELLSLPGVGR 119 (211)
T ss_pred HHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC--------------CCCchHHHHHhCCCcch
Confidence 34569999999999999988754 443 4899999999999863211 33467899999999999
Q ss_pred HHHHHHH-HHhCCCCccccchHHHHHHHHhhc-cCCChHHHHHHHHHHhc
Q 016856 324 FTRNNVL-VCIGFYHVIPTDSETIRHLKQVHA-RNCTSKTVQMIAESIYG 371 (381)
Q Consensus 324 wTAd~VL-~~Lg~~dvfPvDt~v~Ril~rly~-~~~s~k~i~~~~~~~~g 371 (381)
|||++|| +++|.+ +|||||||.|+.+|+.. ...++.+++..+.+++.
T Consensus 120 KTAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~~~~p~~ve~~L~~~iP 168 (211)
T COG0177 120 KTANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVPGKTPEEVEEALMKLIP 168 (211)
T ss_pred HHHHHHHHhhcCCC-cccccchHHHHHHHhCCCCCCCHHHHHHHHHHHCC
Confidence 9999998 899999 99999999999999964 34788889888877664
No 11
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.82 E-value=3.9e-20 Score=162.63 Aligned_cols=110 Identities=28% Similarity=0.407 Sum_probs=86.9
Q ss_pred CCCHHHHhcCCHHHHHHh---CcC-cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 252 FPSPRELANLDESFLAKR---CNL-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 252 FPTpe~La~~~~e~Lr~~---~g~-GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
||||++|+++++++|.+. +|+ .+||+||+++|+.+.+... .+.++.++.|++|||||||||+
T Consensus 21 ~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~--------------~~~~~~~~~L~~l~GIG~~tA~ 86 (149)
T smart00478 21 FPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYG--------------GEVPDDREELLKLPGVGRKTAN 86 (149)
T ss_pred CCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHC--------------CCccHHHHHHHcCCCCcHHHHH
Confidence 789999999999988542 455 3599999999999886321 0234678999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CChHHHHHHHHHHhcc--CCCc
Q 016856 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIAESIYGK--YAPF 376 (381)
Q Consensus 328 ~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~--~s~k~i~~~~~~~~g~--~aGw 376 (381)
||| |++++ +++|+|+|+.|++++++..+ .+++.+++.+++++++ |.++
T Consensus 87 ~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 139 (149)
T smart00478 87 AVLSFALGK-PFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPKEDWREL 139 (149)
T ss_pred HHHHHHCCC-CCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHH
Confidence 995 89999 67889999999999998643 4567787777666542 6655
No 12
>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=99.82 E-value=1.6e-19 Score=175.67 Aligned_cols=100 Identities=26% Similarity=0.311 Sum_probs=79.2
Q ss_pred CCCCHHHHhcCCHHHHHHh-CcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 251 NFPSPRELANLDESFLAKR-CNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~-~g~Gy--RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
.||||++|+++++++|.+. .++|| ||++|+++|+.|.+.... ..++.++.|++|||||+|||+
T Consensus 54 ~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~A~~i~~~~~g--------------~~p~~~~~L~~LpGIG~~TA~ 119 (275)
T TIGR01084 54 RFPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQEVVEEFGG--------------EFPQDFEDLAALPGVGRYTAG 119 (275)
T ss_pred hCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHcCC--------------CCcHHHHHHHhCCCCCHHHHH
Confidence 4999999999999999764 25665 999999999999862110 123458999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CChHHHHHH
Q 016856 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMI 365 (381)
Q Consensus 328 ~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~--~s~k~i~~~ 365 (381)
||| ++|++++ +++|+||+|+++|+|+.+ .+.+.+++.
T Consensus 120 ~Il~~a~~~~~-~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~ 159 (275)
T TIGR01084 120 AILSFALNKPY-PILDGNVKRVLSRLFAVEGWPGKKKVENR 159 (275)
T ss_pred HHHHHHCCCCC-CcchHhHHHHHHHHccCcCCCCHHHHHHH
Confidence 996 8999984 559999999999998754 334445444
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.78 E-value=2.3e-18 Score=172.55 Aligned_cols=101 Identities=24% Similarity=0.268 Sum_probs=80.8
Q ss_pred CCCCHHHHhcCCHHHHHHhC-cCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 251 NFPSPRELANLDESFLAKRC-NLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~-g~Gy--RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
.|||+++|+++++++|.+.+ |+|| ||++|+++|+.+.+..- ...++.++.|++|||||+|||+
T Consensus 58 ~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~A~~i~~~~~--------------g~~p~~~~~L~~LpGIG~~TA~ 123 (350)
T PRK10880 58 RFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHG--------------GEFPETFEEVAALPGVGRSTAG 123 (350)
T ss_pred HCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhC--------------CCchhhHHHHhcCCCccHHHHH
Confidence 49999999999999998753 7888 99999999999975311 0334678999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CChHHHHHHH
Q 016856 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIA 366 (381)
Q Consensus 328 ~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~--~s~k~i~~~~ 366 (381)
||| ++++++ .+++|+||+|++.|+|+.. .+.+++++.+
T Consensus 124 aIl~~af~~~-~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l 164 (350)
T PRK10880 124 AILSLSLGKH-FPILDGNVKRVLARCYAVSGWPGKKEVENRL 164 (350)
T ss_pred HHHHHHCCCC-eecccHHHHHHHHHHhcccCCCChHHHHHHH
Confidence 996 899985 3338999999999998754 3344554444
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.73 E-value=2.3e-17 Score=154.64 Aligned_cols=108 Identities=20% Similarity=0.221 Sum_probs=78.6
Q ss_pred cCCHHHHHHh---Cc--C-cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHh-cCCccChHHHHHHHHH
Q 016856 260 NLDESFLAKR---CN--L-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLS-QINGFGPFTRNNVLVC 332 (381)
Q Consensus 260 ~~~~e~Lr~~---~g--~-GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll-~L~GIGpwTAd~VL~~ 332 (381)
.+++++|.+. +| + ..||++|+++++.+ |. +..+... ..+.+++++.|+ ++||||+|||+|||+.
T Consensus 68 ~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~--~~--l~~~~~~-----~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~ 138 (208)
T PRK01229 68 YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLY--GK--LKEIIKA-----DKDQFEAREFLVKNIKGIGYKEASHFLRN 138 (208)
T ss_pred CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHH--HH--HHHHHhc-----cCCchHHHHHHHHcCCCCcHHHHHHHHHH
Confidence 4555555554 33 3 23899999999976 22 1222100 125678999999 9999999999999864
Q ss_pred hCCCCccccchHHHHHHHHhhccC--------CChHHHHHHHHHHhccCCCc
Q 016856 333 IGFYHVIPTDSETIRHLKQVHARN--------CTSKTVQMIAESIYGKYAPF 376 (381)
Q Consensus 333 Lg~~dvfPvDt~v~Ril~rly~~~--------~s~k~i~~~~~~~~g~~aGw 376 (381)
.+..++|++|+|++|+++|++-.+ .++.+++..+++++.++..+
T Consensus 139 ~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~~ 190 (208)
T PRK01229 139 VGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGIS 190 (208)
T ss_pred ccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCCC
Confidence 555679999999999999996432 46888999988888776554
No 15
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.66 E-value=1.3e-16 Score=156.34 Aligned_cols=96 Identities=23% Similarity=0.251 Sum_probs=80.0
Q ss_pred cccccCCCCHHHHhcCCHHHHHHhC-cCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccC
Q 016856 246 RDRIGNFPSPRELANLDESFLAKRC-NLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFG 322 (381)
Q Consensus 246 ~~~~~~FPTpe~La~~~~e~Lr~~~-g~Gy--RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIG 322 (381)
......|||+++|+++++++|.+.+ |+|| ||++|+++|+.+.++... ...+.++.|++|||||
T Consensus 16 ~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g--------------~~P~~~~~L~~LpGIG 81 (289)
T PRK13910 16 SPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHS--------------QLPNDYQSLLKLPGIG 81 (289)
T ss_pred HHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCC--------------CCChhHHHHHhCCCCC
Confidence 3456799999999999999998854 7887 999999999999853210 1123479999999999
Q ss_pred hHHHHHHH-HHhCCCCccccchHHHHHHHHhhccC
Q 016856 323 PFTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN 356 (381)
Q Consensus 323 pwTAd~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~ 356 (381)
+|||++|| +++|++ ++|+|+||+|++.|+++..
T Consensus 82 ~kTA~aIl~~af~~~-~~~VD~nV~RVl~Rl~g~~ 115 (289)
T PRK13910 82 AYTANAILCFGFREK-SACVDANIKRVLLRLFGLD 115 (289)
T ss_pred HHHHHHHHHHHCCCC-cCcccHHHHHHHHHHhcCC
Confidence 99999996 899997 5789999999999998754
No 16
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.54 E-value=7.2e-14 Score=116.38 Aligned_cols=75 Identities=27% Similarity=0.374 Sum_probs=61.9
Q ss_pred CCCHHHHhcCCHHHHHHh---CcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 252 FPSPRELANLDESFLAKR---CNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 252 FPTpe~La~~~~e~Lr~~---~g~G-yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
||||++|+++++++|++. +|++ +||+||+++|+.+.
T Consensus 27 ~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~---------------------------------------- 66 (108)
T PF00730_consen 27 FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL---------------------------------------- 66 (108)
T ss_dssp CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH----------------------------------------
T ss_pred CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh----------------------------------------
Confidence 999999999999999984 4777 89999999998765
Q ss_pred HHHHHhCCCC-ccccchHHHHHHHHhhccC--CChHHHHHHHHHHhcc
Q 016856 328 NVLVCIGFYH-VIPTDSETIRHLKQVHARN--CTSKTVQMIAESIYGK 372 (381)
Q Consensus 328 ~VL~~Lg~~d-vfPvDt~v~Ril~rly~~~--~s~k~i~~~~~~~~g~ 372 (381)
|++| ++|+|+|++|+++++++.. .+++++++.+++.|.|
T Consensus 67 ------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 67 ------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWPP 108 (108)
T ss_dssp ------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGTT
T ss_pred ------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCcC
Confidence 7777 5569999999999999765 4678888888777764
No 17
>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=99.53 E-value=1.1e-13 Score=126.63 Aligned_cols=96 Identities=17% Similarity=0.095 Sum_probs=68.6
Q ss_pred CCHHHHhcCCHHHHHHhCc-C----c---HHHHHHHHHHHHHHh-CCCChhHHHhhhhhcccCcHHHHHHHHhcCCccCh
Q 016856 253 PSPRELANLDESFLAKRCN-L----G---YRAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGP 323 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g-~----G---yRAkyI~~lA~~i~~-G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGp 323 (381)
+||+.|++++.++|.+.+. . | .||++|+++|+.|.+ -.-+++.|.+. +.++..++++.|++||||||
T Consensus 50 ~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G~v~~L~~~----~~p~t~~lre~Ll~LpGVG~ 125 (177)
T TIGR03252 50 LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDGDATAVWTE----GDPDGKELLRRLKALPGFGK 125 (177)
T ss_pred CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCCChhhhhcc----cCCCcHHHHHHHHcCCCCCH
Confidence 6899999999999998773 1 5 489999999999974 22345555541 01256788999999999999
Q ss_pred HHHHHHHHHhCCCCccc-cchHHHHHHHHhhcc
Q 016856 324 FTRNNVLVCIGFYHVIP-TDSETIRHLKQVHAR 355 (381)
Q Consensus 324 wTAd~VL~~Lg~~dvfP-vDt~v~Ril~rly~~ 355 (381)
|||++||.-|++. |- .|-+-+.++ .-|+.
T Consensus 126 KTAnvVL~~l~~~--~~~~~~~~~~~~-~~~~~ 155 (177)
T TIGR03252 126 QKAKIFLALLGKQ--LGVTPEGWREAA-GPYGE 155 (177)
T ss_pred HHHHHHHHHHHHH--hCCCCcchHHhc-cccCC
Confidence 9999998656653 44 344444443 34443
No 18
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.39 E-value=4.6e-12 Score=117.93 Aligned_cols=103 Identities=24% Similarity=0.317 Sum_probs=84.1
Q ss_pred HHHHhcCCHHHHHHhCc-CcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 255 PRELANLDESFLAKRCN-LGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 255 pe~La~~~~e~Lr~~~g-~Gy---RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
++.|..++.++|.+++. .|+ ||++|+++.+.++..-..++...+ ...+++|++++|||+-|||.||
T Consensus 63 l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~----------~~~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 63 LKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKS----------EVLREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccch----------HHHHHHHHccCCcchhhHHHHH
Confidence 89999999999999764 453 899999999888875555554432 2379999999999999999996
Q ss_pred -HHhCCCCccccchHHHHHHHHhhccCC-ChHHHHHHHHH
Q 016856 331 -VCIGFYHVIPTDSETIRHLKQVHARNC-TSKTVQMIAES 368 (381)
Q Consensus 331 -~~Lg~~dvfPvDt~v~Ril~rly~~~~-s~k~i~~~~~~ 368 (381)
++++++ +|++|...+|.+.|++.... ++.++++.+++
T Consensus 133 lYa~~rp-~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~ 171 (215)
T COG2231 133 LYALDRP-VFVVDKYTRRLLSRLGGIEEKKYDEIKELFEE 171 (215)
T ss_pred HHHhcCc-ccchhHHHHHHHHHhcccccccHHHHHHHHHh
Confidence 899987 89999999999999987653 57777776654
No 19
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.29 E-value=1.5e-11 Score=122.46 Aligned_cols=89 Identities=30% Similarity=0.488 Sum_probs=74.7
Q ss_pred ccCCCCHHHHhcCCHHHHHH-hCcCcH--HHHHHHHHHHHHHh---CCCChhHHHhhhhhcccCcHHHHHHHHhcCCccC
Q 016856 249 IGNFPSPRELANLDESFLAK-RCNLGY--RAGRILKLARGIVD---GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFG 322 (381)
Q Consensus 249 ~~~FPTpe~La~~~~e~Lr~-~~g~Gy--RAkyI~~lA~~i~~---G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIG 322 (381)
...|||+++||+++++++.. ..|+|| ||+.|+..|+.+++ |.++ +..+.|.+|||||
T Consensus 60 l~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P-----------------~~~~~l~~LpGiG 122 (342)
T COG1194 60 LERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFP-----------------DDEEELAALPGVG 122 (342)
T ss_pred HHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCC-----------------CCHHHHHhCCCCc
Confidence 45799999999999887655 469996 99999999999985 4543 2246788899999
Q ss_pred hHHHHHHH-HHhCCCCccc-cchHHHHHHHHhhccC
Q 016856 323 PFTRNNVL-VCIGFYHVIP-TDSETIRHLKQVHARN 356 (381)
Q Consensus 323 pwTAd~VL-~~Lg~~dvfP-vDt~v~Ril~rly~~~ 356 (381)
++||..|| ++++++ +| +|.+|.|++.|++..+
T Consensus 123 ~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~ 156 (342)
T COG1194 123 PYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAIS 156 (342)
T ss_pred HHHHHHHHHHHhCCC--Cceeecchheeehhhhccc
Confidence 99999997 888875 78 8999999999999754
No 20
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.17 E-value=3.4e-10 Score=107.90 Aligned_cols=108 Identities=16% Similarity=0.134 Sum_probs=84.3
Q ss_pred CHHHHhcCCHHHHHHhC-cCc---HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 254 SPRELANLDESFLAKRC-NLG---YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 254 Tpe~La~~~~e~Lr~~~-g~G---yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|++.|.++++..|.+++ .+| +||+||+.+|+.+.+.-- .|..+..+.|++|||||||.|..+
T Consensus 110 T~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~--------------gDIP~~v~dLlsLPGVGPKMa~L~ 175 (286)
T KOG1921|consen 110 TLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFD--------------GDIPDTVEDLLSLPGVGPKMAHLT 175 (286)
T ss_pred CHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhC--------------CCCchhHHHHhcCCCCchHHHHHH
Confidence 89999999999998865 345 389999999998886421 134456889999999999999888
Q ss_pred H-HHhCCCCccccchHHHHHHHHhhcc---CCChHHHHHHHHHHhccCCCc
Q 016856 330 L-VCIGFYHVIPTDSETIRHLKQVHAR---NCTSKTVQMIAESIYGKYAPF 376 (381)
Q Consensus 330 L-~~Lg~~dvfPvDt~v~Ril~rly~~---~~s~k~i~~~~~~~~g~~aGw 376 (381)
| -+.|+-.-+-||+||+|+.+++.-. ..++++++.+++. |=|..=|
T Consensus 176 m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aLq~-wLPk~lW 225 (286)
T KOG1921|consen 176 MQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVALQQ-WLPKSLW 225 (286)
T ss_pred HHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHHHH-hCcHHHH
Confidence 7 5888877788999999999999632 2457888888854 4343333
No 21
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=98.43 E-value=2.8e-07 Score=78.56 Aligned_cols=80 Identities=16% Similarity=0.158 Sum_probs=47.9
Q ss_pred eEEEEecCCCCCCcEEEEEeecCCCCCCCCCHHHHHHHHHHHHHHhcCCccchHhHHHHHHHhHHHHhhhccccccccCC
Q 016856 34 VDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDF 113 (381)
Q Consensus 34 ~~v~i~~~~~~~~~L~v~v~~~~~~~~~~~s~~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ 113 (381)
.+|.|+|. ++.+.+++...+ ...+....+.+...+++||+||.|+...++.|.+.|+.++..-. . -.
T Consensus 38 ~~~~l~q~---~~~~~~~~~~~~----~~~~~~~~~~~~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~~~~~----~--~~ 104 (117)
T PF07934_consen 38 RVVQLRQD---DDNLLYRCLSSA----EPSNSSSEEDIEEFLRDYFDLDVDLEKLYEDWSKKDPRLAKAID----K--YR 104 (117)
T ss_dssp EEEEEEEE---TTEEEEECE--T----TS---S-HHHHHHCHHHHTTTTS-HHHHHHHHCCHSHHHHHHHH----C--TT
T ss_pred eEEEEEEC---CCEEEEEEecCC----CcccccchhhHHHHHHHHhcCCccHHHHHHHHhhhCHHHHHHHh----c--CC
Confidence 56678876 788999888731 23333566778888999999999977777777666765554431 1 13
Q ss_pred cccccCCCChHHHH
Q 016856 114 SGRVFRSPTLFEDM 127 (381)
Q Consensus 114 ggRv~r~p~~fE~l 127 (381)
|+||+|| ||||+|
T Consensus 105 GlRiLrQ-dp~E~L 117 (117)
T PF07934_consen 105 GLRILRQ-DPFETL 117 (117)
T ss_dssp T--------HHHHH
T ss_pred CcEEECC-ChhhhC
Confidence 7799996 999997
No 22
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=98.05 E-value=1.2e-05 Score=69.27 Aligned_cols=82 Identities=17% Similarity=0.184 Sum_probs=48.8
Q ss_pred CccccceecCCCCCCCCCCCceeEEEEecCCCCCCcEEEEEeecCCCCCCCCCHHHHHHHHHHHHHHhcCCccchHhHHH
Q 016856 12 RSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRD 91 (381)
Q Consensus 12 ~~~~r~lrl~~~~~~~~~~~~~~~v~i~~~~~~~~~L~v~v~~~~~~~~~~~s~~~~~~i~~~v~r~l~Ld~d~~~~~~~ 91 (381)
++|.|+++++++ ...|+|+.. ...++|.|++..+. ..+...++++||||||||.| +.++.+
T Consensus 33 ~~Y~Rt~~l~~~---------~g~v~v~~~-~~~~~l~v~~~~~~--------~~~l~~~~~rvRrlfDLdaD-p~~I~~ 93 (116)
T PF06029_consen 33 GSYRRTFRLGGG---------PGWVSVRHD-PEKNHLRVTLSLSD--------LRDLPAVIARVRRLFDLDAD-PQAIEA 93 (116)
T ss_dssp SEEEEEEEETTE---------EEEEEEEEE-TTTTEEEEEE-GGG--------GGGHHHHHHHHHHHTTTT---HHHHHH
T ss_pred CeEEEEEEeCCe---------EEEEEEEEc-CCCCEEEEEEEccc--------HHHHHHHHHHHHHHhCCCCC-HHHHHH
Confidence 489999999987 788888766 12478999998741 25778999999999999999 444444
Q ss_pred HHHHhHHHHhhhccccccccCCcccccCC
Q 016856 92 FKRIVRQVAQEEGEESQYMTDFSGRVFRS 120 (381)
Q Consensus 92 f~~~~~~~~~~~~~~~~~~~~~ggRv~r~ 120 (381)
-. ++...... ....|+|+++.
T Consensus 94 ~L--dp~l~p~~------~~~pGLRlPG~ 114 (116)
T PF06029_consen 94 HL--DPLLAPLV------AARPGLRLPGA 114 (116)
T ss_dssp HH------GGGG------TS-TT------
T ss_pred HH--hhcccccc------cCCCCCcCCCc
Confidence 33 33222221 12358899986
No 23
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=97.91 E-value=4.5e-05 Score=77.46 Aligned_cols=93 Identities=25% Similarity=0.383 Sum_probs=69.1
Q ss_pred ccCCCCHHHHhcCCHH-HHHH-hCcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhc-CCccCh
Q 016856 249 IGNFPSPRELANLDES-FLAK-RCNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQ-INGFGP 323 (381)
Q Consensus 249 ~~~FPTpe~La~~~~e-~Lr~-~~g~Gy--RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~-L~GIGp 323 (381)
....||..+++.++.+ +.-. +.|+|| |+++|++-|+.++.|.-. .....-+.|++ +||||+
T Consensus 151 MqkwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ega~~vv~~~~g--------------e~Prta~~l~kgvpGVG~ 216 (555)
T KOG2457|consen 151 MQKWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEGAKMVVAGTEG--------------EFPRTASSLMKGVPGVGQ 216 (555)
T ss_pred HHhCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCC--------------CCCChHHHHHhhCCCCCc
Confidence 4579999999998863 3333 358997 899999999999965321 11122356666 999999
Q ss_pred HHHHHHH-HHhCCCCccccchHHHHHHHHhhccC
Q 016856 324 FTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN 356 (381)
Q Consensus 324 wTAd~VL-~~Lg~~dvfPvDt~v~Ril~rly~~~ 356 (381)
+||..|+ .+++... =-||-+|.|++.|.....
T Consensus 217 YTAGAiaSIAf~q~t-GiVDGNVirvlsRalAIh 249 (555)
T KOG2457|consen 217 YTAGAIASIAFNQVT-GIVDGNVIRVLSRALAIH 249 (555)
T ss_pred cchhhhhhhhhcCcc-cccccchHHHhHHhHhhc
Confidence 9999997 6887642 128999999999887543
No 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=97.55 E-value=0.00054 Score=63.81 Aligned_cols=89 Identities=22% Similarity=0.216 Sum_probs=62.3
Q ss_pred CHHHHhcCCHHHHHHhCcC---cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHh-cCCccChHHHHHH
Q 016856 254 SPRELANLDESFLAKRCNL---GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLS-QINGFGPFTRNNV 329 (381)
Q Consensus 254 Tpe~La~~~~e~Lr~~~g~---GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll-~L~GIGpwTAd~V 329 (381)
+.++|. |.|+. +|- +.||+||...-+.+-+ +..+-+. .....-+++.|. .++|||.|-|..+
T Consensus 72 ~~eEL~----e~Lk~-~g~Rf~n~raeyIVeaR~~~~~----lk~~v~~-----~~~~~vaRE~Lv~nikGiGyKEASHF 137 (210)
T COG1059 72 SEEELR----EKLKE-VGYRFYNVRAEYIVEAREKFDD----LKIIVKA-----DENEKVARELLVENIKGIGYKEASHF 137 (210)
T ss_pred CHHHHH----HHHHH-hcchhcccchHHHHHHHHHHHH----HHHHHhc-----CcchHHHHHHHHHHcccccHHHHHHH
Confidence 556653 55665 443 3389999987776643 3333333 011223888888 9999999999999
Q ss_pred HHHhCCCCccccchHHHHHHHHhhccC
Q 016856 330 LVCIGFYHVIPTDSETIRHLKQVHARN 356 (381)
Q Consensus 330 L~~Lg~~dvfPvDt~v~Ril~rly~~~ 356 (381)
|+-.|..|.--.|-||.|-+.+++...
T Consensus 138 LRNVG~~D~AIlDrHIlr~l~r~g~i~ 164 (210)
T COG1059 138 LRNVGFEDLAILDRHILRWLVRYGLID 164 (210)
T ss_pred HHhcChhHHHHHHHHHHHHHHHhcccc
Confidence 988888664448999999999997543
No 25
>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=97.32 E-value=0.00019 Score=47.85 Aligned_cols=20 Identities=40% Similarity=0.657 Sum_probs=17.3
Q ss_pred HHHHHhcCCccChHHHHHHH
Q 016856 311 LAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 311 ~~~~Ll~L~GIGpwTAd~VL 330 (381)
.+++|+++|||||+||+.|+
T Consensus 9 s~eeL~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 9 SIEELMKLPGIGPKTANAIL 28 (30)
T ss_dssp SHHHHHTSTT-SHHHHHHHH
T ss_pred CHHHHHhCCCcCHHHHHHHH
Confidence 46899999999999999996
No 26
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=94.05 E-value=0.033 Score=35.51 Aligned_cols=17 Identities=35% Similarity=0.716 Sum_probs=15.8
Q ss_pred HHhcCCccChHHHHHHH
Q 016856 314 QLSQINGFGPFTRNNVL 330 (381)
Q Consensus 314 ~Ll~L~GIGpwTAd~VL 330 (381)
.|++++|||+|+|+.++
T Consensus 2 ~L~~i~GiG~k~A~~il 18 (26)
T smart00278 2 ELLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhhCCCCCHHHHHHHH
Confidence 68999999999999997
No 27
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.11 E-value=0.28 Score=46.17 Aligned_cols=66 Identities=24% Similarity=0.291 Sum_probs=41.0
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTA 326 (381)
..|-|.|.++..- -+.|...-|.|-| |-.|. +. ++.+.|... =..+..+.|.++||||+|||
T Consensus 58 ~LYGF~t~~Er~l--F~~LisVsGIGPK~ALaIL-------s~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKtA 120 (196)
T PRK13901 58 KLFGFLNSSEREV--FEELIGVDGIGPRAALRVL-------SG-IKYNEFRDA-------IDREDIELISKVKGIGNKMA 120 (196)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHHHHHHH-------cC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHH
Confidence 5688999888632 2445554588987 33333 22 233333332 11122579999999999999
Q ss_pred HHHH
Q 016856 327 NNVL 330 (381)
Q Consensus 327 d~VL 330 (381)
+-|.
T Consensus 121 eRII 124 (196)
T PRK13901 121 GKIF 124 (196)
T ss_pred HHHH
Confidence 9994
No 28
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=91.90 E-value=0.9 Score=45.83 Aligned_cols=61 Identities=20% Similarity=0.249 Sum_probs=40.5
Q ss_pred HHHHHhCcCcHH-HHHHHHHHHHHHhCCCC-hhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHHHhCC
Q 016856 264 SFLAKRCNLGYR-AGRILKLARGIVDGQIQ-LRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 264 e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~-Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
++|.++-|+|-+ |+-|..+ +..|.+. +..... .+.......|++++||||++|.-+-. +|.
T Consensus 48 ~~l~~lpgIG~~ia~kI~Ei---l~tG~~~~~~e~l~-------~~~p~~l~~l~~i~GiGpk~a~~l~~-lGi 110 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEI---IETGKSSKVLEILN-------DEVYKSLKLFTNVFGVGPKTAAKWYR-KGI 110 (334)
T ss_pred HHHhcCCCccHHHHHHHHHH---HHhCcHHHHHHHhc-------CcHHHHHHHHHccCCcCHHHHHHHHH-hCC
Confidence 356664588876 4444443 4468765 322222 26678899999999999999987743 554
No 29
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.53 E-value=2 Score=40.08 Aligned_cols=106 Identities=11% Similarity=0.172 Sum_probs=57.7
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++-.- -+.|...-|.|-|. |-++.+. ++.+.+... =..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~Li~VsGIGpK~------Al~ILs~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKtAe 122 (183)
T PRK14601 59 KLYGFLDKDEQKM--FEMLLKVNGIGANT------AMAVCSS-LDVNSFYKA-------LSLGDESVLKKVPGIGPKSAK 122 (183)
T ss_pred eeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHHH
Confidence 5688999887532 23455445788884 2233332 344444433 112235799999999999999
Q ss_pred HHHHHhC-CCCcc-ccchHHHHHHHHhhccCCChHHHHHHHHHH
Q 016856 328 NVLVCIG-FYHVI-PTDSETIRHLKQVHARNCTSKTVQMIAESI 369 (381)
Q Consensus 328 ~VL~~Lg-~~dvf-PvDt~v~Ril~rly~~~~s~k~i~~~~~~~ 369 (381)
-++.-|. +.... +.......++..+.....+.+++.+.+.+.
T Consensus 123 RIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 123 RIIAELSDAKTKLENVSDDKSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHhhccCCCCccHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 9943222 21011 112223445555544444556665555443
No 30
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.89 E-value=2.8 Score=39.11 Aligned_cols=106 Identities=17% Similarity=0.161 Sum_probs=56.5
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|.|.++-.- -+.|...-|.|-|. |-++.++ ++.+.|... =..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~Li~V~GIGpK~------AL~iLs~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKtAe 122 (188)
T PRK14606 59 TLYGFSNERKKEL--FLSLTKVSRLGPKT------ALKIISN-EDAETLVTM-------IASQDVEGLSKLPGISKKTAE 122 (188)
T ss_pred eeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHHH
Confidence 5788998887532 23444444788873 2233332 334444333 111225799999999999999
Q ss_pred HHHHHhCC-CCccc-cc-hHHHHHHHHhhccCCChHHHHHHHHHH
Q 016856 328 NVLVCIGF-YHVIP-TD-SETIRHLKQVHARNCTSKTVQMIAESI 369 (381)
Q Consensus 328 ~VL~~Lg~-~dvfP-vD-t~v~Ril~rly~~~~s~k~i~~~~~~~ 369 (381)
-|..-|.. ...+. .+ .....++..+-...-+++++...+.+.
T Consensus 123 rIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 123 RIVMELKDEFESAGIKDMRIYHESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 99433322 11111 11 123344444444444556666655554
No 31
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.34 E-value=0.52 Score=36.22 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=25.0
Q ss_pred HHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 283 ARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 283 A~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
|+.++..--+++.+... + .++|.+++|||+.+|+.|.
T Consensus 16 ak~L~~~f~sl~~l~~a-------~----~e~L~~i~gIG~~~A~si~ 52 (64)
T PF12826_consen 16 AKLLAKHFGSLEALMNA-------S----VEELSAIPGIGPKIAQSIY 52 (64)
T ss_dssp HHHHHHCCSCHHHHCC-------------HHHHCTSTT--HHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHc-------C----HHHHhccCCcCHHHHHHHH
Confidence 45556555567777654 3 4689999999999999996
No 32
>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=89.27 E-value=1.6 Score=33.79 Aligned_cols=44 Identities=16% Similarity=0.187 Sum_probs=32.8
Q ss_pred cCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 271 NLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 271 g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
+-.+|+..-...|..|.+-..++. +.++ .|.+|||||+.+|.-|
T Consensus 20 ~~~~r~~aY~~Aa~~i~~l~~~i~------------~~~~---~~~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 20 GDPFRARAYRRAAAAIKALPYPIT------------SGEE---DLKKLPGIGKSIAKKI 63 (68)
T ss_dssp TSHHHHHHHHHHHHHHHHSSS-HH------------SHHH---HHCTSTTTTHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHhCCHhHh------------hHHH---HHhhCCCCCHHHHHHH
Confidence 566899999999998887443322 2222 5999999999999987
No 33
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=87.69 E-value=1.5 Score=41.59 Aligned_cols=67 Identities=21% Similarity=0.232 Sum_probs=42.4
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|.|.++=.- -..|.+.-|.|-|. |-++.+. ++.+.|.+. =..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~ER~l--F~~LisVnGIGpK~------ALaiLs~-~~~~~l~~a-------I~~~d~~~L~k~PGIGkKtAe 122 (201)
T COG0632 59 LLYGFLTEEEREL--FRLLISVNGIGPKL------ALAILSN-LDPEELAQA-------IANEDVKALSKIPGIGKKTAE 122 (201)
T ss_pred HHcCCCCHHHHHH--HHHHHccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhcChHhhhcCCCCCHHHHH
Confidence 4677887766321 13344444788874 3334443 456666554 123346799999999999999
Q ss_pred HHH
Q 016856 328 NVL 330 (381)
Q Consensus 328 ~VL 330 (381)
-++
T Consensus 123 riv 125 (201)
T COG0632 123 RIV 125 (201)
T ss_pred HHH
Confidence 994
No 34
>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=86.84 E-value=1.5 Score=41.03 Aligned_cols=106 Identities=18% Similarity=0.172 Sum_probs=57.5
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTA 326 (381)
..|-|.|.++-.- -..|...-|.|-| |..| .+ ..+.+.|.... ..+....|.++||||+|||
T Consensus 58 ~LyGF~~~~Er~l--F~~L~~V~GIGpK~Al~i-------L~-~~~~~el~~aI-------~~~d~~~L~~ipGiGkKtA 120 (191)
T TIGR00084 58 LLFGFNTLEEREL--FKELIKVNGVGPKLALAI-------LS-NMSPEEFVYAI-------ETEEVKALVKIPGVGKKTA 120 (191)
T ss_pred eeeCCCCHHHHHH--HHHHhCCCCCCHHHHHHH-------Hh-cCCHHHHHHHH-------HhCCHHHHHhCCCCCHHHH
Confidence 5788999887532 2345544478876 4333 22 23444454330 1122467999999999999
Q ss_pred HHHHHHh-CCCC---cc----ccchHHHHHHHHhhccCCChHHHHHHHHHHh
Q 016856 327 NNVLVCI-GFYH---VI----PTDSETIRHLKQVHARNCTSKTVQMIAESIY 370 (381)
Q Consensus 327 d~VL~~L-g~~d---vf----PvDt~v~Ril~rly~~~~s~k~i~~~~~~~~ 370 (381)
+-|+.-| ++.. .+ +.......++..+-...-+.+++...+.+..
T Consensus 121 erIileLk~k~~~~~~~~~~~~~~~~~~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 121 ERLLLELKGKLKGNKNLEMFTPTEAARDELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHHHHHhhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 9994221 1111 01 1112234444455444445566666665543
No 35
>PRK00076 recR recombination protein RecR; Reviewed
Probab=86.43 E-value=0.6 Score=44.01 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=25.8
Q ss_pred cHHHHHHHHhcCCccChHHHHHHH-HHhCCCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFYH 337 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~d 337 (381)
+.+++.+.|.+|||||+|||.-+. +-+.+++
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~~ 36 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQRDR 36 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 568899999999999999999994 5665543
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=86.36 E-value=0.64 Score=43.84 Aligned_cols=31 Identities=23% Similarity=0.307 Sum_probs=25.7
Q ss_pred cHHHHHHHHhcCCccChHHHHHHH-HHhCCCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFYH 337 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~d 337 (381)
+.+++.+.|.+|||||+|||.-+. +-+..++
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~ 36 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDP 36 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 568899999999999999999994 5665543
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.33 E-value=8.6 Score=36.01 Aligned_cols=67 Identities=21% Similarity=0.262 Sum_probs=40.0
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++-.- -+.|...-|.|-|. |..|.+. ++.+.|...- ..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~ILs~-~~~~~l~~aI-------~~~D~~~L~~vpGIGkKtAe 122 (194)
T PRK14605 59 SLFGFATTEELSL--FETLIDVSGIGPKL------GLAMLSA-MNAEALASAI-------ISGNAELLSTIPGIGKKTAS 122 (194)
T ss_pred eeeCCCCHHHHHH--HHHHhCCCCCCHHH------HHHHHHh-CCHHHHHHHH-------HhCCHHHHHhCCCCCHHHHH
Confidence 5688998887532 23444434788873 3333332 3334433220 01225689999999999999
Q ss_pred HHH
Q 016856 328 NVL 330 (381)
Q Consensus 328 ~VL 330 (381)
-|.
T Consensus 123 rIi 125 (194)
T PRK14605 123 RIV 125 (194)
T ss_pred HHH
Confidence 973
No 38
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=86.18 E-value=0.64 Score=43.85 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=25.3
Q ss_pred cHHHHHHHHhcCCccChHHHHHHH-HHhCCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFY 336 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~ 336 (381)
+.+++++.|..|||||||+|.-+. +-+.+.
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 567889999999999999999995 456554
No 39
>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=85.57 E-value=2.9 Score=31.34 Aligned_cols=51 Identities=24% Similarity=0.342 Sum_probs=32.6
Q ss_pred HHHHHhCcCcHHHHHHHHHHHHHH-hCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHH
Q 016856 264 SFLAKRCNLGYRAGRILKLARGIV-DGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 264 e~Lr~~~g~GyRAkyI~~lA~~i~-~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~ 331 (381)
++|.+.-|+|.+ +|+.+. .|-.+++.|... + .+.|.+++|||+++|+-+..
T Consensus 5 ~~L~~I~Gig~~------~a~~L~~~G~~t~~~l~~a-------~----~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPK------RAEKLYEAGIKTLEDLANA-------D----PEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHH------HHHHHHHTTCSSHHHHHTS-------H----HHHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHH------HHHHHHhcCCCcHHHHHcC-------C----HHHHhcCCCCCHHHHHHHHH
Confidence 345543466654 223333 355566666654 2 45799999999999998853
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=85.54 E-value=0.7 Score=43.74 Aligned_cols=31 Identities=10% Similarity=0.099 Sum_probs=25.8
Q ss_pred cHHHHHHHHhcCCccChHHHHHHH-HHhCCCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFYH 337 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~d 337 (381)
..+++.+.|.+|||||+|+|.-+. +-|..++
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~~ 40 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDKSP 40 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 567889999999999999999994 5665543
No 41
>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=84.56 E-value=0.77 Score=37.15 Aligned_cols=35 Identities=29% Similarity=0.410 Sum_probs=27.6
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCCccccchHHHH
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYHVIPTDSETIR 347 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~dvfPvDt~v~R 347 (381)
+.|+++||||+-||..++--+++++.|+..-++..
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~~ 36 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLAS 36 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhhh
Confidence 46899999999999999866688778886555444
No 42
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.49 E-value=2.1 Score=39.91 Aligned_cols=66 Identities=20% Similarity=0.266 Sum_probs=40.4
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++-.- -+.|...-|.|.|. |-++.+. ++.+.|...-. .+..+.| ++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~LisV~GIGpK~------Al~iLs~-~~~~~l~~aI~-------~~D~~~L-~vpGIGkKtAe 121 (186)
T PRK14600 59 QLYGFLNREEQDC--LRMLVKVSGVNYKT------AMSILSK-LTPEQLFSAIV-------NEDKAAL-KVNGIGEKLIN 121 (186)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcc-CCHHHHHHHHH-------cCCHhhe-ECCCCcHHHHH
Confidence 5688999887532 24455545788874 2233332 34444443311 1123688 99999999999
Q ss_pred HHH
Q 016856 328 NVL 330 (381)
Q Consensus 328 ~VL 330 (381)
-++
T Consensus 122 rIi 124 (186)
T PRK14600 122 RII 124 (186)
T ss_pred HHH
Confidence 994
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.02 E-value=1.4 Score=41.57 Aligned_cols=107 Identities=12% Similarity=0.149 Sum_probs=56.5
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++..- -+.|...-|.|-|. |-.+.+. ++.+.|...- ..+..+.|.++||||+|||+
T Consensus 60 ~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~iLs~-~~~~~l~~aI-------~~~D~~~L~~ipGIGkKtAe 123 (203)
T PRK14602 60 ELFGFATWDERQT--FIVLISISKVGAKT------ALAILSQ-FRPDDLRRLV-------AEEDVAALTRVSGIGKKTAQ 123 (203)
T ss_pred eeeCCCCHHHHHH--HHHHhCCCCcCHHH------HHHHHhh-CCHHHHHHHH-------HhCCHHHHhcCCCcCHHHHH
Confidence 5688988887532 23444444788873 2223322 2333333321 11225799999999999999
Q ss_pred HHHHHhC-CCC--cc----------c-cchHHHHHHHHhhccCCChHHHHHHHHHHh
Q 016856 328 NVLVCIG-FYH--VI----------P-TDSETIRHLKQVHARNCTSKTVQMIAESIY 370 (381)
Q Consensus 328 ~VL~~Lg-~~d--vf----------P-vDt~v~Ril~rly~~~~s~k~i~~~~~~~~ 370 (381)
-|+.-|. +.. .+ + .+.....++..+-....+++++.+.+.+..
T Consensus 124 rIilELkdK~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~~LGy~~~ea~~av~~~~ 180 (203)
T PRK14602 124 HIFLELKYKLKVEGLPAAAVLAGTGAVPGSVFRDALAGLANLGYGEEEARPVLKEVL 180 (203)
T ss_pred HHHHHHHHhhccccccccccccccccCCCchHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 9942221 110 00 0 122334445555444455566666665553
No 44
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.98 E-value=2 Score=40.39 Aligned_cols=67 Identities=18% Similarity=0.208 Sum_probs=41.4
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++..- -..|...-|.|.|. |-++.+. ++.+.|... =..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~iLs~-~~~~el~~a-------I~~~D~~~L~kvpGIGkKtAe 122 (195)
T PRK14604 59 TLYGFSTPAQRQL--FELLIGVSGVGPKA------ALNLLSS-GTPDELQLA-------IAGGDVARLARVPGIGKKTAE 122 (195)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHHH
Confidence 5678888877532 23454445788874 2333332 344444433 112235799999999999999
Q ss_pred HHH
Q 016856 328 NVL 330 (381)
Q Consensus 328 ~VL 330 (381)
-++
T Consensus 123 rIi 125 (195)
T PRK14604 123 RIV 125 (195)
T ss_pred HHH
Confidence 994
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.83 E-value=1.8 Score=40.70 Aligned_cols=67 Identities=16% Similarity=0.178 Sum_probs=41.0
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
..|-|-|.++-.- -+.|...-|.|-|. |-++.++ ++.+.+... =..+..+.|.++||||+|||+
T Consensus 58 ~LyGF~~~~Er~l--F~~L~~V~GIGpK~------AL~iLs~-~~~~~l~~a-------I~~~D~~~L~kvpGIGkKtAe 121 (197)
T PRK14603 58 SLYGFPDEDSLEL--FELLLGVSGVGPKL------ALALLSA-LPPALLARA-------LLEGDARLLTSASGVGKKLAE 121 (197)
T ss_pred eeeCcCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHHH
Confidence 4678888777532 23454444788873 2333333 344444433 112235799999999999999
Q ss_pred HHH
Q 016856 328 NVL 330 (381)
Q Consensus 328 ~VL 330 (381)
-|.
T Consensus 122 rIi 124 (197)
T PRK14603 122 RIA 124 (197)
T ss_pred HHH
Confidence 994
No 46
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.82 E-value=1.5 Score=41.04 Aligned_cols=29 Identities=24% Similarity=0.348 Sum_probs=24.3
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHhCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
.-.++.+.|++++||||++|-.||-.++.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCH
Confidence 44678999999999999999999865553
No 47
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=80.30 E-value=12 Score=34.79 Aligned_cols=57 Identities=12% Similarity=0.134 Sum_probs=32.6
Q ss_pred HHHHhcCCccChHHHHHHHHHhCCCCc---------cccchHHHHHHHHhhccCCChHHHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVLVCIGFYHV---------IPTDSETIRHLKQVHARNCTSKTVQMIAES 368 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL~~Lg~~dv---------fPvDt~v~Ril~rly~~~~s~k~i~~~~~~ 368 (381)
.+.|.++||||+++|+-|+..|..... -+.+..+..++..+-..+.+.+.+...+.+
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~~ 172 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSALVALGYKPKEASKAVAK 172 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 458999999999999999633322110 011112455555554444455555555543
No 48
>PRK08609 hypothetical protein; Provisional
Probab=80.06 E-value=2.4 Score=45.81 Aligned_cols=60 Identities=17% Similarity=0.117 Sum_probs=36.6
Q ss_pred HHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHHHhC
Q 016856 265 FLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 265 ~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
+|.++-|.|-+ |+.|. +.+..|.+ ..|..++. ...+...+|++++||||++|.-+---+|
T Consensus 49 ~l~~ipgIG~~ia~kI~---Eil~tG~~--~~le~l~~-----~~p~~~~~l~~i~GiGpk~a~~l~~~lG 109 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQ---EYRETGES--SVLQELKK-----EVPEGLLPLLKLPGLGGKKIAKLYKELG 109 (570)
T ss_pred hhccCCCcCHHHHHHHH---HHHHhCCh--HHHHHHHh-----hCcHHHHHHhcCCCCCHHHHHHHHHHhC
Confidence 56665688877 44333 44456765 34444422 3344556889999999999877632333
No 49
>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=79.79 E-value=4.9 Score=40.04 Aligned_cols=61 Identities=23% Similarity=0.338 Sum_probs=39.9
Q ss_pred HHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHHHhCCC
Q 016856 265 FLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFY 336 (381)
Q Consensus 265 ~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~ 336 (381)
++.++=|.|-+ |+.|..+ +..|.+ ..+..+.. +.......|++++||||++|.-+- .+|..
T Consensus 46 ~~~~ipgiG~~ia~kI~E~---~~tG~~--~~le~l~~-----~~~~~l~~l~~i~GiGpk~a~~l~-~lGi~ 107 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEI---LETGKL--RKLEELRE-----DVPPGLLLLLRVPGVGPKTARKLY-ELGIR 107 (307)
T ss_pred HhcCCCCccHHHHHHHHHH---HHcCCH--HHHHHHhc-----cchHHHHHHHcCCCCCHHHHHHHH-HcCCC
Confidence 44443377875 5555544 445764 45555422 467788999999999999998885 55543
No 50
>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=78.99 E-value=1.4 Score=41.10 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=21.1
Q ss_pred cHHHHHHHHhcCCccChHHHHHHH
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
...++...|++++|||||+|-.+|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHH
Confidence 446789999999999999998886
No 51
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=76.80 E-value=2.4 Score=39.41 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=21.0
Q ss_pred HHHHHHhcCCccChHHHHHHHHHhC
Q 016856 310 KLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
+....|..++||||++|..+|-.++
T Consensus 70 ~~f~~L~~i~GIGpk~A~~il~~fg 94 (192)
T PRK00116 70 ELFRLLISVSGVGPKLALAILSGLS 94 (192)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHhCC
Confidence 4578999999999999999975454
No 52
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=76.14 E-value=1.6 Score=41.32 Aligned_cols=68 Identities=24% Similarity=0.313 Sum_probs=38.1
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHhCCCCccc-cchHHHHHHHHhhccCCChHHHHHHHHHHhccCCCc
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPF 376 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~dvfP-vDt~v~Ril~rly~~~~s~k~i~~~~~~~~g~~aGw 376 (381)
.-.+....|+++.|||||+|=.||-.+.-.+..- ++..=...+.++=| ..+|..++.+.++=+++..|
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PG--IGkKtAerivleLk~K~~~~ 135 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPG--IGKKTAERIVLELKGKLAAF 135 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCC--CCHHHHHHHHHHHhhhhhhh
Confidence 3457899999999999999988873332211111 22222233333323 23355555555555555554
No 53
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=72.37 E-value=51 Score=30.76 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=25.1
Q ss_pred CChHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 016856 121 PTLFEDMVKCMLLCNCQWPRTLSMARALCEL 151 (381)
Q Consensus 121 p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~ 151 (381)
..+||.|+-.+..+-.+|.-+++--..+.+.
T Consensus 24 ~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~a 54 (179)
T PF03352_consen 24 RKLFEMLTLEGFQAGLSWSTILKKREAFREA 54 (179)
T ss_dssp HHHHHHHHHHHHTTTS-HHHHHHTHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence 3699999999999999999998766666554
No 54
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=72.20 E-value=11 Score=41.72 Aligned_cols=79 Identities=16% Similarity=0.253 Sum_probs=44.9
Q ss_pred CCCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCC---------------CChhHHHhhhhhcccCcHHHH----
Q 016856 252 FPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQ---------------IQLRELEDMCNEASLTAYVKL---- 311 (381)
Q Consensus 252 FPTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~---------------l~Le~L~~l~~~~~~~~~ee~---- 311 (381)
--++++|..+..++|..+-|+|.| ++.|.+-.+.-.+.. .....|.+. -.+.+++
T Consensus 467 I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~-----f~sl~~l~~As 541 (665)
T PRK07956 467 IHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARH-----FGSLEALRAAS 541 (665)
T ss_pred CCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHH-----cCCHHHHHhCC
Confidence 358888888888888875588875 444443332222111 000011110 0122222
Q ss_pred HHHHhcCCccChHHHHHHHHHhCC
Q 016856 312 AEQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
.++|.+++|||+++|..|.-.|..
T Consensus 542 ~eeL~~i~GIG~~~A~sI~~ff~~ 565 (665)
T PRK07956 542 EEELAAVEGVGEVVAQSIVEFFAV 565 (665)
T ss_pred HHHHhccCCcCHHHHHHHHHHHhh
Confidence 357999999999999999644444
No 55
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=71.02 E-value=7.8 Score=34.48 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=40.4
Q ss_pred CCCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 251 NFPSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
.+-..=+|-.+++++|.+.=|.|- +|+.|. .+|... + .+.|++++|||+++.+.+
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV------~nGpf~--------------s----veDL~~V~GIgekqk~~l 103 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIV------KNAPYD--------------S----VEDVLNLPGLSERQKELL 103 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHH------HCCCCC--------------C----HHHHHcCCCCCHHHHHHH
Confidence 345556777888999988557885 677776 256542 2 468899999999988777
Q ss_pred H
Q 016856 330 L 330 (381)
Q Consensus 330 L 330 (381)
-
T Consensus 104 ~ 104 (132)
T PRK02515 104 E 104 (132)
T ss_pred H
Confidence 3
No 56
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.40 E-value=4.4 Score=38.70 Aligned_cols=54 Identities=26% Similarity=0.312 Sum_probs=39.5
Q ss_pred HHHhCcCcHHHH-HHHHHHHHHHhCC---CChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 266 LAKRCNLGYRAG-RILKLARGIVDGQ---IQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 266 Lr~~~g~GyRAk-yI~~lA~~i~~G~---l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
|.-+++.|.+-+ -...+|+.+.+.- -++..+... + .++|++++|||+-.|..++
T Consensus 20 LailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a-------~----~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 20 LAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSA-------P----PEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred HHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhC-------C----HHHHHhCcCCcHHHHHHHH
Confidence 333457787777 8889999998743 367777665 4 4679999999998777773
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=69.84 E-value=7.1 Score=33.74 Aligned_cols=58 Identities=14% Similarity=0.265 Sum_probs=40.4
Q ss_pred CCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 253 PSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
+.+-.|-.++.++|..+-|.|. +|+.|..--+. +|.+ . + .++|..++|||+++++-+.
T Consensus 57 ~~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f-----~---------s----~eeL~~V~GIg~k~~~~i~ 115 (120)
T TIGR01259 57 LAAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGAF-----K---------S----VDDLTKVSGIGEKSLEKLK 115 (120)
T ss_pred CCCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCc-----C---------C----HHHHHcCCCCCHHHHHHHH
Confidence 4456677888999988568886 57766554332 3332 1 2 4688999999999998874
No 58
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.36 E-value=3 Score=38.90 Aligned_cols=26 Identities=31% Similarity=0.308 Sum_probs=22.0
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHH
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVC 332 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~ 332 (381)
...+..+.|+++.|||||+|=.||-+
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcC
Confidence 44678999999999999999888743
No 59
>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=69.24 E-value=7.3 Score=29.17 Aligned_cols=33 Identities=33% Similarity=0.399 Sum_probs=27.6
Q ss_pred CCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHH
Q 016856 252 FPSPRELANLDESFLAKRCNLGY-RAGRILKLAR 284 (381)
Q Consensus 252 FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~ 284 (381)
|.|+++|+.+++++|.+.-|+|. +|+.|..-++
T Consensus 26 ~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 26 IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 88999999999999999668997 4777776554
No 60
>PRK00024 hypothetical protein; Reviewed
Probab=67.38 E-value=6 Score=37.83 Aligned_cols=55 Identities=31% Similarity=0.441 Sum_probs=39.6
Q ss_pred HHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 264 SFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 264 e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|-|.-.++.|.+-+-...+|+.+.+.--++..+... + .++|++++|||+..|..+
T Consensus 28 ELLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~a-------s----~~eL~~i~GIG~akA~~L 82 (224)
T PRK00024 28 ELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDA-------S----LEELQSIKGIGPAKAAQL 82 (224)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhC-------C----HHHHhhccCccHHHHHHH
Confidence 333334577777777788999888744456666655 4 457999999999988777
No 61
>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=67.30 E-value=3.8 Score=34.34 Aligned_cols=30 Identities=17% Similarity=0.072 Sum_probs=22.9
Q ss_pred HHHHHHHHhcCCccChHHHHHHH-HHhCCCC
Q 016856 308 YVKLAEQLSQINGFGPFTRNNVL-VCIGFYH 337 (381)
Q Consensus 308 ~ee~~~~Ll~L~GIGpwTAd~VL-~~Lg~~d 337 (381)
..+....|+.|||||+.+|.-+. .|+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~ 37 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLGIRSPA 37 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcCCCCHH
Confidence 34567899999999999999984 4554443
No 62
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=66.67 E-value=12 Score=41.40 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=18.6
Q ss_pred HHHhcCCccChHHHHHHHHHhCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
++|++++|||+.+|..|.-.|..
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~ 563 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFND 563 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcC
Confidence 47999999999999999633443
No 63
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.46 E-value=3.9 Score=38.60 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=21.6
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHH
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~ 331 (381)
.-.++.+.|+++.|||||+|=.||-
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4457899999999999999988873
No 64
>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=66.09 E-value=15 Score=40.60 Aligned_cols=78 Identities=19% Similarity=0.245 Sum_probs=44.1
Q ss_pred CCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCCC---------------ChhHHHhhhhhcccCcHHHH----H
Q 016856 253 PSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQI---------------QLRELEDMCNEASLTAYVKL----A 312 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l---------------~Le~L~~l~~~~~~~~~ee~----~ 312 (381)
-++++|..++.++|.++-|+|.| |+.|.+..+.-....+ ....|.+. -.+.+++ .
T Consensus 455 ~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~-----f~sl~~l~~As~ 529 (652)
T TIGR00575 455 RSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKH-----FGTLDKLKAASL 529 (652)
T ss_pred CCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHH-----hCCHHHHHhCCH
Confidence 47888888888888875578865 5555444432221110 00011100 0122222 3
Q ss_pred HHHhcCCccChHHHHHHHHHhCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
++|.+++|||+++|+.|+-.|..
T Consensus 530 eeL~~i~GIG~~~A~~I~~ff~~ 552 (652)
T TIGR00575 530 EELLSVEGVGPKVAESIVNFFHD 552 (652)
T ss_pred HHHhcCCCcCHHHHHHHHHHHhh
Confidence 47899999999999999744444
No 65
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.85 E-value=3.6 Score=38.67 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=22.3
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHh
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCI 333 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~L 333 (381)
.-.++.+.|+++.|||||+|=.||-.+
T Consensus 66 ~Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 66 DSLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 345789999999999999998887433
No 66
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.17 E-value=4.1 Score=38.02 Aligned_cols=25 Identities=20% Similarity=0.313 Sum_probs=21.6
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHH
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~ 331 (381)
...++.+.|+++.|||||+|=.||-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4467899999999999999988873
No 67
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.11 E-value=4.5 Score=38.17 Aligned_cols=27 Identities=19% Similarity=0.026 Sum_probs=22.4
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHh
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCI 333 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~L 333 (381)
.-.++.+.|+++.|||||+|=.||-.+
T Consensus 68 ~Er~lF~~Li~V~GIGpK~Al~iLs~~ 94 (203)
T PRK14602 68 DERQTFIVLISISKVGAKTALAILSQF 94 (203)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHhhC
Confidence 445789999999999999998887443
No 68
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.06 E-value=4 Score=38.34 Aligned_cols=25 Identities=36% Similarity=0.432 Sum_probs=21.6
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHH
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~ 331 (381)
.-.++.+.|+++.|||||+|=.||-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4467899999999999999988873
No 69
>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=64.58 E-value=4.3 Score=27.17 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=12.2
Q ss_pred HHhcCCccChHHHHHH
Q 016856 314 QLSQINGFGPFTRNNV 329 (381)
Q Consensus 314 ~Ll~L~GIGpwTAd~V 329 (381)
.+..++|||++|+.-+
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 3578999999998765
No 70
>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=64.23 E-value=5 Score=29.97 Aligned_cols=21 Identities=29% Similarity=0.332 Sum_probs=14.9
Q ss_pred HHHhcCCccChHHHHHHH-HHh
Q 016856 313 EQLSQINGFGPFTRNNVL-VCI 333 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL-~~L 333 (381)
+.++.+.||||.||.-.. +++
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~ 23 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGI 23 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT-
T ss_pred cchhhcccccHHHHHHHHHhCC
Confidence 578999999999999884 444
No 71
>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=62.06 E-value=8 Score=29.69 Aligned_cols=54 Identities=20% Similarity=0.274 Sum_probs=33.6
Q ss_pred HHhcCCHHHHHH-hCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 257 ELANLDESFLAK-RCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 257 ~La~~~~e~Lr~-~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
.|-.++.++|.. .-|+|.+ |+.|..-=. ..|.+ + ..++|.+++|||.++++-|+
T Consensus 9 nvNta~~~~L~~~ipgig~~~a~~Il~~R~--~~g~~-----------------~-s~~dL~~v~gi~~~~~~~i~ 64 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGLKKAEAIVSYRE--EYGPF-----------------K-TVEDLKQVPGIGNSLVEKNL 64 (69)
T ss_pred ECcCCCHHHHHhHCCCCCHHHHHHHHHHHH--HcCCc-----------------C-CHHHHHcCCCCCHHHHHHHH
Confidence 444567788887 4578874 443332211 01222 1 24688999999999999885
No 72
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.58 E-value=7.2 Score=36.40 Aligned_cols=27 Identities=15% Similarity=0.112 Sum_probs=22.5
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHh
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCI 333 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~L 333 (381)
...++.+.|+++.|||||+|=.||-.+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 445789999999999999998887433
No 73
>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=60.07 E-value=5.4 Score=31.61 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=19.5
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
+.+..+||||++||.-++.-++..+
T Consensus 22 D~i~gv~giG~k~A~~ll~~~~~~~ 46 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKEYGSLE 46 (75)
T ss_pred ccCCCCCcccHHHHHHHHHHhCCHH
Confidence 3677899999999999986555443
No 74
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=58.61 E-value=18 Score=32.57 Aligned_cols=52 Identities=19% Similarity=0.351 Sum_probs=35.6
Q ss_pred HhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 258 LANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 258 La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|-.++.|+|+.+-|.|- +|+.|++-- -.+|... ..+.|...+|||+++.+-+
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yR--e~~G~f~------------------sv~dL~~v~GiG~~~~ekl 143 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYR--EENGPFK------------------SVDDLAKVKGIGPKTLEKL 143 (149)
T ss_pred ccccCHHHHHHCCCCCHHHHHHHHHHH--HHcCCCC------------------cHHHHHhccCCCHHHHHHH
Confidence 45678899976557884 687775432 2345331 2468999999999998765
No 75
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.71 E-value=13 Score=28.44 Aligned_cols=52 Identities=21% Similarity=0.370 Sum_probs=29.8
Q ss_pred HhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 258 LANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 258 La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|-.++.++|...-|+|. .|+.|.+.=+. .|.+. + .++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~--~G~f~--------------s----~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREK--NGPFK--------------S----LEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHH--H-S-S--------------S----GGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHh--CcCCC--------------C----HHHHhhCCCCCHHHHHHH
Confidence 45678889987447776 46666554332 25432 1 458899999999998765
No 76
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=57.70 E-value=27 Score=38.03 Aligned_cols=83 Identities=13% Similarity=0.101 Sum_probs=45.9
Q ss_pred CCCCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHH-hh-----hhhc---ccCcHHH----HHHHHh
Q 016856 251 NFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELE-DM-----CNEA---SLTAYVK----LAEQLS 316 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~-~l-----~~~~---~~~~~ee----~~~~Ll 316 (381)
..-++.+|..++.++|.++-|+|.| ++.|.+..+. ....+|+.+- .+ .... .-.+.++ ..++|.
T Consensus 446 ~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~--sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~l~~a~~e~l~ 523 (562)
T PRK08097 446 LFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNL--ARQQPFSRWLKALGIPLPQAALNALDDRSWQQLLSRSEQQWQ 523 (562)
T ss_pred CcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHH--HcCCCHHHHHHHcCCccHHHHHHHHhcCCHHHHHcCCHHHHh
Confidence 4578889999898888874477764 4444333221 1222222210 00 0000 0001222 235799
Q ss_pred cCCccChHHHHHHHHHhCC
Q 016856 317 QINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 317 ~L~GIGpwTAd~VL~~Lg~ 335 (381)
+++|||+.+|+.|.-.|..
T Consensus 524 ~i~gIG~~~a~si~~~f~~ 542 (562)
T PRK08097 524 QLPGIGEGRARQLIAFLQH 542 (562)
T ss_pred cCCCchHHHHHHHHHHHcC
Confidence 9999999999999744544
No 77
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.47 E-value=9.2 Score=29.23 Aligned_cols=19 Identities=32% Similarity=0.648 Sum_probs=15.4
Q ss_pred HHHHhcCCccChHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL 330 (381)
.++|.++||||++.|..|+
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv 31 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIV 31 (65)
T ss_dssp HHHHHTSTT--HHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHH
Confidence 5689999999999999996
No 78
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=57.38 E-value=28 Score=38.80 Aligned_cols=82 Identities=17% Similarity=0.186 Sum_probs=43.0
Q ss_pred CCHHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHH-Hhhh----------hh-cccCcHHHH----HHHH
Q 016856 253 PSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLREL-EDMC----------NE-ASLTAYVKL----AEQL 315 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L-~~l~----------~~-~~~~~~ee~----~~~L 315 (381)
-++.+|..++.++|..+-|+|.| ++.|.+-.+.- ...+|+.+ ..+. .. ..-.+.+++ .++|
T Consensus 485 ~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~s--k~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL 562 (689)
T PRK14351 485 ESLADLYDLTVADLAELEGWGETSAENLLAELEAS--REPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEAL 562 (689)
T ss_pred CCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHH--ccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH
Confidence 47888888888888775577865 44333222211 11222211 0000 00 000122222 3579
Q ss_pred hcCCccChHHHHHHHHHhCCC
Q 016856 316 SQINGFGPFTRNNVLVCIGFY 336 (381)
Q Consensus 316 l~L~GIGpwTAd~VL~~Lg~~ 336 (381)
.+++|||+++|+.|.-.|..+
T Consensus 563 ~~i~GIG~k~A~sI~~ff~~~ 583 (689)
T PRK14351 563 RAVDDVGPTVAEEIREFFDSE 583 (689)
T ss_pred hccCCcCHHHHHHHHHHHhhh
Confidence 999999999999986444443
No 79
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=56.16 E-value=8.2 Score=26.63 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=14.0
Q ss_pred HHhcCCccChHHHHHHH
Q 016856 314 QLSQINGFGPFTRNNVL 330 (381)
Q Consensus 314 ~Ll~L~GIGpwTAd~VL 330 (381)
-+..+||||++||--+|
T Consensus 17 ni~Gv~giG~ktA~~ll 33 (36)
T smart00279 17 NIPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCCcccHHHHHHHH
Confidence 45689999999997665
No 80
>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=54.82 E-value=10 Score=32.75 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=18.0
Q ss_pred HHHHhcCCccChHHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL~ 331 (381)
.++|+++||||++.|.-|+.
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~ 86 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIE 86 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 56899999999999999973
No 81
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=51.69 E-value=28 Score=35.35 Aligned_cols=46 Identities=13% Similarity=0.188 Sum_probs=33.4
Q ss_pred CcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHH--HhcCCccChHHHHHHH
Q 016856 270 CNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQ--LSQINGFGPFTRNNVL 330 (381)
Q Consensus 270 ~g~G-yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~--Ll~L~GIGpwTAd~VL 330 (381)
.|-. +|+..-...|+.+.+-.- +++++.+. ++.|||||+-+|+.|-
T Consensus 22 ~Gen~fk~~aYr~Aa~sle~~~e---------------~~~ei~e~~~~t~l~gIGk~ia~~I~ 70 (326)
T COG1796 22 EGENPFKIRAYRKAAQSLENLTE---------------DLEEIEERGRLTELPGIGKGIAEKIS 70 (326)
T ss_pred cCCCccchHHHHHHHHhhhhccc---------------chHHHHhhcccCCCCCccHHHHHHHH
Confidence 3433 787777777887765433 44555555 9999999999999993
No 82
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=51.61 E-value=10 Score=34.09 Aligned_cols=19 Identities=32% Similarity=0.665 Sum_probs=16.7
Q ss_pred HHHHhcCCccChHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL 330 (381)
-++|..|||||++.|..|.
T Consensus 96 ~eeL~~lpgIG~~kA~aIi 114 (149)
T COG1555 96 AEELQALPGIGPKKAQAII 114 (149)
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 3567999999999999996
No 83
>PRK07945 hypothetical protein; Provisional
Probab=51.17 E-value=27 Score=35.30 Aligned_cols=53 Identities=23% Similarity=0.280 Sum_probs=35.8
Q ss_pred HHHHhCc-CcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHH-HHhcCCccChHHHHHHH
Q 016856 265 FLAKRCN-LGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAE-QLSQINGFGPFTRNNVL 330 (381)
Q Consensus 265 ~Lr~~~g-~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~-~Ll~L~GIGpwTAd~VL 330 (381)
+|-+..| .-||++.-.+.|+.|..-.-+ .+..+ ..+ .|.+|||||.-+|+.|.
T Consensus 12 ~lle~~~~n~frv~ayr~aa~~~~~~~~~--~~~~~-----------~~~g~l~~~~giG~~~a~~i~ 66 (335)
T PRK07945 12 FLLERARADTYRVRAFRRAADVVEALDAA--ERARR-----------ARAGSLTSLPGIGPKTAKVIA 66 (335)
T ss_pred HHHHHcCCChhhHHHHHHHHHHHHhcChh--HHHHH-----------HhcCCcccCCCcCHHHHHHHH
Confidence 3444344 358999999999988763322 23322 012 69999999999999883
No 84
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=50.70 E-value=30 Score=34.49 Aligned_cols=44 Identities=16% Similarity=0.203 Sum_probs=32.6
Q ss_pred cCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 271 NLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 271 g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
+--||+..-...|..|.+-..++. + .+++.+|||||+.+|+.|-
T Consensus 19 ~~~~r~~aY~~Aa~~l~~l~~~i~------------~----~~~~~~ipgiG~~ia~kI~ 62 (307)
T cd00141 19 GNPFRVRAYRKAARALESLPEPIE------------S----LEEAKKLPGIGKKIAEKIE 62 (307)
T ss_pred CCcchHHHHHHHHHHHHhCCcccC------------C----HHHhcCCCCccHHHHHHHH
Confidence 355888888888888876544322 2 2366899999999999993
No 85
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=49.52 E-value=25 Score=35.45 Aligned_cols=47 Identities=13% Similarity=0.215 Sum_probs=33.8
Q ss_pred cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH--HHHhCC
Q 016856 273 GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV--LVCIGF 335 (381)
Q Consensus 273 GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V--L~~Lg~ 335 (381)
-||+.+....|..|..-..++. +. ++|.+|||||+.+|+-| +..-|.
T Consensus 24 ~~k~~ay~~Aa~~i~~l~~~i~------------~~----~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 24 KRKCSYFRKAASVLKSLPFPIN------------SM----KDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HHHHHHHHHHHHHHHhCCCCCC------------CH----HHHhcCCCccHHHHHHHHHHHHhCc
Confidence 4788888888888876544332 21 36889999999999999 334454
No 86
>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=49.29 E-value=18 Score=30.58 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=27.9
Q ss_pred HHHHHHHhcCCccChHHHHHHHHHhCCCCccc----cchHHHHHHHH
Q 016856 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYHVIP----TDSETIRHLKQ 351 (381)
Q Consensus 309 ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~dvfP----vDt~v~Ril~r 351 (381)
..+.-.|.+|.|||+.+|..|+.-+|...-.. .|..+.++.+.
T Consensus 11 k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~ 57 (107)
T PF00416_consen 11 KPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKI 57 (107)
T ss_dssp SBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHH
T ss_pred cchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHH
Confidence 34678999999999999999975444333222 35455444443
No 87
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=48.13 E-value=14 Score=32.93 Aligned_cols=19 Identities=16% Similarity=0.329 Sum_probs=16.9
Q ss_pred HHHHhcCCccChHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL 330 (381)
.++|.++|||||..|.-|.
T Consensus 60 ~~el~~lpGigP~~A~~IV 78 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIV 78 (132)
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 4568899999999999997
No 88
>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=45.34 E-value=3 Score=35.30 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=18.2
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCCcc
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYHVI 339 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~dvf 339 (381)
+-+..+||||+|||.-+|.-+|-.+.+
T Consensus 18 DNIPGV~GIG~KtA~~LL~~ygsle~i 44 (101)
T PF01367_consen 18 DNIPGVPGIGPKTAAKLLQEYGSLENI 44 (101)
T ss_dssp CTB---TTSTCHCCCCCHHHHTSCHCC
T ss_pred cCCCCCCCCCHHHHHHHHHHcCCHHHH
Confidence 367789999999999988666655533
No 89
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=45.08 E-value=18 Score=26.02 Aligned_cols=16 Identities=19% Similarity=0.241 Sum_probs=13.8
Q ss_pred cccchHHHHHHHHhhc
Q 016856 339 IPTDSETIRHLKQVHA 354 (381)
Q Consensus 339 fPvDt~v~Ril~rly~ 354 (381)
=+.|+||.|++.++|.
T Consensus 16 teddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 16 TEDDTHVHRVLRKYYT 31 (41)
T ss_pred CcchhHHHHHHHHHHH
Confidence 3579999999999985
No 90
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=44.95 E-value=48 Score=32.68 Aligned_cols=109 Identities=18% Similarity=0.189 Sum_probs=56.6
Q ss_pred CCHHHHhcCCHHHHHHhCcCc--------HHHHHHHHHHHHHHh-CCCC--hhHHHhhhhhcccCcHHHHH-HHHhcCCc
Q 016856 253 PSPRELANLDESFLAKRCNLG--------YRAGRILKLARGIVD-GQIQ--LRELEDMCNEASLTAYVKLA-EQLSQING 320 (381)
Q Consensus 253 PTpe~La~~~~e~Lr~~~g~G--------yRAkyI~~lA~~i~~-G~l~--Le~L~~l~~~~~~~~~ee~~-~~Ll~L~G 320 (381)
-.|+++..+-....-+ .|+. .=+..|..+|+.... ++-. ...... ..++.+.. ..|.++||
T Consensus 117 i~~~av~~al~s~~vd-fg~~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~------~~t~~e~q~~il~s~pg 189 (254)
T COG1948 117 IHPNAVRGALASLAVD-FGLPVIWTRSPEETAELIHELARREQEERKRSVNPHGKKK------AKTLKELQLYILESIPG 189 (254)
T ss_pred cCHHHHHHHHHHHHhh-cCceEEEeCCHHHHHHHHHHHHHHHHHhcccccccccccc------ccchHHHHHHHHHcCCC
Confidence 3677776543333332 2321 248889999998872 2211 111111 12555554 45679999
Q ss_pred cChHHHHHHHHHhCCC-CccccchHHHHHHHHhhccC-CChHHHHHHHHHHhc
Q 016856 321 FGPFTRNNVLVCIGFY-HVIPTDSETIRHLKQVHARN-CTSKTVQMIAESIYG 371 (381)
Q Consensus 321 IGpwTAd~VL~~Lg~~-dvfPvDt~v~Ril~rly~~~-~s~k~i~~~~~~~~g 371 (381)
||+..|.-+|-.+|-. +++-.+. .-+.+.-|.+ .....|.+.+...|+
T Consensus 190 ig~~~a~~ll~~fgS~~~~~tas~---~eL~~v~gig~k~A~~I~~~~~t~~~ 239 (254)
T COG1948 190 IGPKLAERLLKKFGSVEDVLTASE---EELMKVKGIGEKKAREIYRFLRTEYK 239 (254)
T ss_pred ccHHHHHHHHHHhcCHHHHhhcCH---HHHHHhcCccHHHHHHHHHHHhchhh
Confidence 9999999997433322 2333333 3333333332 223455555554444
No 91
>PRK14973 DNA topoisomerase I; Provisional
Probab=44.68 E-value=32 Score=39.74 Aligned_cols=82 Identities=16% Similarity=0.242 Sum_probs=48.6
Q ss_pred cCCCCHHHHhcCCHHHHHHhCcCc-HHHHHHHHHHH-HHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHH
Q 016856 250 GNFPSPRELANLDESFLAKRCNLG-YRAGRILKLAR-GIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (381)
Q Consensus 250 ~~FPTpe~La~~~~e~Lr~~~g~G-yRAkyI~~lA~-~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd 327 (381)
.-|-++++++.++++.|...-|++ -.+..+...|. .+.. -+-....+. -.+.-+.+|+.++|||++|++
T Consensus 821 ~G~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-------~~~~~~~el~~vkg~ge~t~~ 891 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGR--PVPEKISKA-------AFERGRAELLSVPGLGETTLE 891 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcC--CCchhhhhh-------hhcccchhhhhccCCCHHHHH
Confidence 359999999999999999755554 24444433333 2221 111111121 223345559999999999997
Q ss_pred HH-HHHhCCCCccc
Q 016856 328 NV-LVCIGFYHVIP 340 (381)
Q Consensus 328 ~V-L~~Lg~~dvfP 340 (381)
-. +-+.-..+.+-
T Consensus 892 ~l~~ag~~~~e~l~ 905 (936)
T PRK14973 892 KLYLAGVYDGDLLV 905 (936)
T ss_pred HHHHcCCCCHHHhc
Confidence 76 44444444333
No 92
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=44.64 E-value=70 Score=32.71 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 274 YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 274 yRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
.|+..-...|..+.+=..+.. + .+++..||||||++|.-|
T Consensus 33 ~r~~~y~~Aasvlk~~p~~I~------------S----~~ea~~lP~iG~kia~ki 72 (353)
T KOG2534|consen 33 DRARAYRRAASVLKSLPFPIT------------S----GEEAEKLPGIGPKIAEKI 72 (353)
T ss_pred HHHHHHHHHHHHHHhCCCCcc------------c----HHHhcCCCCCCHHHHHHH
Confidence 466666666666655332211 2 356778999999999999
No 93
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=42.51 E-value=39 Score=32.83 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=11.5
Q ss_pred HHHhcCCccChHHHHHHHHHhCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
++|.+++|||..+|+-|.-.|+.
T Consensus 36 eEL~~V~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 36 SELAEVDGIGNALAARIKADVGG 58 (232)
T ss_pred HHHHHccCCCHHHHHHHHHHhcc
Confidence 44555555555555555433333
No 94
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=41.34 E-value=20 Score=34.71 Aligned_cols=49 Identities=24% Similarity=0.362 Sum_probs=37.9
Q ss_pred CcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 270 CNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 270 ~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
++.|-|-+-...+|+.+.+.--.|..|.+. + .++|++++|||+-.|--+
T Consensus 34 LrtG~~~~~~~~la~~lL~~fg~L~~l~~a-------~----~~el~~v~GiG~aka~~l 82 (224)
T COG2003 34 LRTGTKGESVLDLAKELLQEFGSLAELLKA-------S----VEELSSVKGIGLAKAIQI 82 (224)
T ss_pred HhcCCCCCCHHHHHHHHHHHcccHHHHHhC-------C----HHHHhhCCCccHHHHHHH
Confidence 578888888899999999865556666654 3 579999999998766555
No 95
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=41.00 E-value=53 Score=33.56 Aligned_cols=65 Identities=22% Similarity=0.189 Sum_probs=41.2
Q ss_pred HHHHHHhCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH-HHHhCCC
Q 016856 263 ESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV-LVCIGFY 336 (381)
Q Consensus 263 ~e~Lr~~~g~GyR-AkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V-L~~Lg~~ 336 (381)
-+++..+=|+|-| |+-|..++ ..|.+ ..+...++ .+..+..+.+..+-|||++||+.- .+++.-.
T Consensus 55 ~~ea~~lP~iG~kia~ki~Eil---etG~l--~ele~v~~----de~~~~lklFtnifGvG~ktA~~Wy~~GfrTl 121 (353)
T KOG2534|consen 55 GEEAEKLPGIGPKIAEKIQEIL---ETGVL--RELEAVRN----DERSQSLKLFTNIFGVGLKTAEKWYREGFRTL 121 (353)
T ss_pred HHHhcCCCCCCHHHHHHHHHHH---HcCCc--hhHHHHhc----chhHHHHHHHHHHhccCHHHHHHHHHhhhhHH
Confidence 3455543378877 55555443 35664 34443322 245677899999999999999998 5665543
No 96
>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=38.24 E-value=29 Score=26.55 Aligned_cols=19 Identities=32% Similarity=0.569 Sum_probs=16.5
Q ss_pred HHHHhc-CCccChHHHHHHH
Q 016856 312 AEQLSQ-INGFGPFTRNNVL 330 (381)
Q Consensus 312 ~~~Ll~-L~GIGpwTAd~VL 330 (381)
.+.|.. ++|||+.+|..|+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il 34 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIV 34 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHH
Confidence 347777 9999999999997
No 97
>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=36.79 E-value=25 Score=34.08 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=15.5
Q ss_pred ccccchHHHHHHHHhhcc
Q 016856 338 VIPTDSETIRHLKQVHAR 355 (381)
Q Consensus 338 vfPvDt~v~Ril~rly~~ 355 (381)
++|.||||.|+.++++..
T Consensus 176 iiPLDtHv~~var~LGL~ 193 (232)
T PF09674_consen 176 IIPLDTHVFRVARKLGLL 193 (232)
T ss_pred cccchHhHHHHHHHcCCc
Confidence 489999999999999654
No 98
>PRK07758 hypothetical protein; Provisional
Probab=36.77 E-value=52 Score=27.81 Aligned_cols=39 Identities=18% Similarity=0.376 Sum_probs=0.0
Q ss_pred HHHHHHHH-hCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 280 LKLARGIV-DGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 280 ~~lA~~i~-~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
.....++. .|--.++.|.++ -.++|++|+|+|+++.+-|
T Consensus 44 vRA~N~Lk~AGI~TL~dLv~~-----------te~ELl~iknlGkKSL~EI 83 (95)
T PRK07758 44 APARRALEHHGIHTVEELSKY-----------SEKEILKLHGMGPASLPKL 83 (95)
T ss_pred HHHHHHHHHcCCCcHHHHHcC-----------CHHHHHHccCCCHHHHHHH
No 99
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=36.06 E-value=26 Score=35.69 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.6
Q ss_pred HHHHhcCCccChHHHHHHHHH
Q 016856 312 AEQLSQINGFGPFTRNNVLVC 332 (381)
Q Consensus 312 ~~~Ll~L~GIGpwTAd~VL~~ 332 (381)
.++|+.+||||+++|.-|+|.
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 578999999999999999753
No 100
>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=35.35 E-value=35 Score=26.45 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=28.1
Q ss_pred CcCcHHHHHHHHHHHHHHh-CCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHH
Q 016856 270 CNLGYRAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLV 331 (381)
Q Consensus 270 ~g~GyRAkyI~~lA~~i~~-G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~ 331 (381)
+++..|+... +.. |--.++.|..+ + .+.|+.++|+|+++.+-|..
T Consensus 17 L~LS~Ra~n~------L~~~~I~tv~dL~~~-------s----~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 17 LGLSVRAYNC------LKRAGIHTVGDLVKY-------S----EEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp STSBHHHHHH------HHCTT--BHHHHHCS------------HHHHHTSTTSHHHHHHHHHH
T ss_pred hCCCHHHHHH------HHHhCCcCHHHHHhC-------C----HHHHHhCCCCCHhHHHHHHH
Confidence 3566665332 222 33345566655 2 36899999999999988753
No 101
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=35.11 E-value=1e+02 Score=26.62 Aligned_cols=32 Identities=25% Similarity=0.201 Sum_probs=25.4
Q ss_pred CCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 289 GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 289 G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
..++...+.++ ..+..|+.++|||+..|..++
T Consensus 39 ~~i~~~~l~~w----------~~~AdL~ri~gi~~~~a~LL~ 70 (122)
T PF14229_consen 39 LGISERNLLKW----------VNQADLMRIPGIGPQYAELLE 70 (122)
T ss_pred cCCCHHHHHHH----------HhHHHhhhcCCCCHHHHHHHH
Confidence 45777777776 347899999999999987774
No 102
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=35.04 E-value=39 Score=33.06 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=31.8
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHH
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGY-RAGRILKLAR 284 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~ 284 (381)
....|+|.++|.+++.++|...-|+|- ||+.|+..-.
T Consensus 211 LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 211 LLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred HHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence 467899999999999999998669995 7999987654
No 103
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.66 E-value=2.4e+02 Score=26.30 Aligned_cols=39 Identities=18% Similarity=0.159 Sum_probs=29.6
Q ss_pred CcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 016856 113 FSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCEL 151 (381)
Q Consensus 113 ~ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~ 151 (381)
+|.-+--...|||.|+-.+..+-.+|.-+++--..+.+.
T Consensus 20 WG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~a 58 (179)
T TIGR00624 20 WGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRA 58 (179)
T ss_pred CCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHH
Confidence 544444445799999999999999999998766666554
No 104
>PRK09482 flap endonuclease-like protein; Provisional
Probab=34.50 E-value=25 Score=34.51 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=20.3
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
+-+..+||||||||.-+|.-+|..+
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~gsle 206 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFRSLE 206 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhCCHH
Confidence 3678899999999999986666544
No 105
>PRK14976 5'-3' exonuclease; Provisional
Probab=34.27 E-value=26 Score=34.58 Aligned_cols=25 Identities=24% Similarity=0.413 Sum_probs=19.9
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
+.+..+||||||||.-+|--+|..+
T Consensus 191 DnipGVpGIG~KtA~~LL~~~gsle 215 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLNKYGNIE 215 (281)
T ss_pred CCCCCCCcccHHHHHHHHHHcCCHH
Confidence 3678899999999999986666544
No 106
>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=31.78 E-value=34 Score=33.17 Aligned_cols=17 Identities=24% Similarity=0.530 Sum_probs=14.7
Q ss_pred ccccchHHHHHHHHhhc
Q 016856 338 VIPTDSETIRHLKQVHA 354 (381)
Q Consensus 338 vfPvDt~v~Ril~rly~ 354 (381)
++|.|||+.|++.++.-
T Consensus 173 iiPLDtH~~rvar~LgL 189 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKL 189 (229)
T ss_pred eeechHhHHHHHHHhCC
Confidence 38999999999998854
No 107
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=31.23 E-value=48 Score=37.00 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=17.7
Q ss_pred cHHHHHHHHhc--CCccChHHHHHHHHHhC
Q 016856 307 AYVKLAEQLSQ--INGFGPFTRNNVLVCIG 334 (381)
Q Consensus 307 ~~ee~~~~Ll~--L~GIGpwTAd~VL~~Lg 334 (381)
+.+.+...|.+ ++||||++|.-|...||
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg 105 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFG 105 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhC
Confidence 44556666654 77777777777754444
No 108
>smart00475 53EXOc 5'-3' exonuclease.
Probab=30.77 E-value=32 Score=33.60 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=19.7
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
+.+..+||||||||.-+|.-+|-.+
T Consensus 186 DnipGV~GIG~KtA~~Ll~~ygsle 210 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLKEFGSLE 210 (259)
T ss_pred cCCCCCCCCCHHHHHHHHHHhCCHH
Confidence 3578899999999999986666444
No 109
>PRK08609 hypothetical protein; Provisional
Probab=30.52 E-value=98 Score=33.67 Aligned_cols=48 Identities=13% Similarity=0.193 Sum_probs=34.3
Q ss_pred HHHhCc-CcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHH
Q 016856 266 LAKRCN-LGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 266 Lr~~~g-~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~V 329 (381)
|-+..| ..||++.-...|+.|.+-.-++ .+ ...|.+|||||+.+|+.|
T Consensus 16 ~le~~g~n~fr~~aYr~Aa~~i~~l~~~i---------------~~-~~~l~~ipgIG~~ia~kI 64 (570)
T PRK08609 16 YMELKGENPFKISAFRKAAQALELDERSL---------------SE-IDDFTKLKGIGKGTAEVI 64 (570)
T ss_pred HHHhcCCCcHHHHHHHHHHHHHHhCchhh---------------hh-hhhhccCCCcCHHHHHHH
Confidence 333344 4589999999999887643321 11 247899999999999999
No 110
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=30.44 E-value=41 Score=37.62 Aligned_cols=29 Identities=24% Similarity=0.422 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCccChHHHHHHHHHhCCCC
Q 016856 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 309 ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
......|..+|||||+++.-+|..||-.+
T Consensus 633 ~~~~s~L~~IPGIGpkr~k~LL~~FGSle 661 (694)
T PRK14666 633 AALTGELQRVEGIGPATARLLWERFGSLQ 661 (694)
T ss_pred hhhHhHHhhCCCCCHHHHHHHHHHhCCHH
Confidence 34568899999999999999986677544
No 111
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=29.56 E-value=79 Score=34.87 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCccChHHHHHHHHHhCCCCccc
Q 016856 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYHVIP 340 (381)
Q Consensus 309 ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~dvfP 340 (381)
......|..|+|||+++|..+|..+|-.+.+-
T Consensus 565 ~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~ 596 (621)
T PRK14671 565 RTLQTELTDIAGIGEKTAEKLLEHFGSVEKVA 596 (621)
T ss_pred HHhhhhhhcCCCcCHHHHHHHHHHcCCHHHHH
Confidence 45678899999999999999987776544443
No 112
>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=29.07 E-value=35 Score=32.72 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=19.6
Q ss_pred HHHhcCCccChHHHHHHHHHhCCCC
Q 016856 313 EQLSQINGFGPFTRNNVLVCIGFYH 337 (381)
Q Consensus 313 ~~Ll~L~GIGpwTAd~VL~~Lg~~d 337 (381)
+.+..+||||||||.-+|.-+|-.+
T Consensus 183 DnipGv~GiG~ktA~~Ll~~~gsle 207 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLKEYGSLE 207 (240)
T ss_pred cCCCCCCccCHHHHHHHHHHhCCHH
Confidence 3678899999999988886555544
No 113
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=28.25 E-value=78 Score=32.63 Aligned_cols=43 Identities=19% Similarity=0.123 Sum_probs=36.8
Q ss_pred cccCCCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHHHHHhCC
Q 016856 248 RIGNFPSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQ 290 (381)
Q Consensus 248 ~~~~FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~~G~ 290 (381)
....|.+.+.|.+++.++|.+.-|.|- ||+.|.+.++.+.+..
T Consensus 303 Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~~ 346 (352)
T PRK13482 303 LVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQS 346 (352)
T ss_pred HHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 466799999999999999998668985 8999999998887654
No 114
>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=28.04 E-value=1.3e+02 Score=20.99 Aligned_cols=34 Identities=21% Similarity=0.202 Sum_probs=27.4
Q ss_pred CCCCHHHHhcCCHHHHHHhCcCcH-HHHHHHHHHH
Q 016856 251 NFPSPRELANLDESFLAKRCNLGY-RAGRILKLAR 284 (381)
Q Consensus 251 ~FPTpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~ 284 (381)
-|=|.++|+.+++++|....|++. ++..|+..|+
T Consensus 13 G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 13 GFTTVEDLAYVPIDELLSIEGFDEETAKELINRAR 47 (50)
T ss_pred CCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 477999999999999998667764 7777776665
No 115
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=27.74 E-value=35 Score=29.84 Aligned_cols=26 Identities=19% Similarity=0.278 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCccChHHHHHHHHHhC
Q 016856 309 VKLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 309 ee~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
..+.-.|..|.|||+.+|..|+.-+|
T Consensus 13 k~v~~aLt~i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 13 KRIEYALTYIYGIGLTSAKEILEKAN 38 (122)
T ss_pred CEeeeeecccccccHHHHHHHHHHcC
Confidence 34566899999999999999974444
No 116
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=26.71 E-value=55 Score=24.94 Aligned_cols=33 Identities=24% Similarity=0.212 Sum_probs=22.4
Q ss_pred ccCCCCHHHHhcCCHHHHHHhCcCcHH-HHHHHH
Q 016856 249 IGNFPSPRELANLDESFLAKRCNLGYR-AGRILK 281 (381)
Q Consensus 249 ~~~FPTpe~La~~~~e~Lr~~~g~GyR-AkyI~~ 281 (381)
...|+|.+.|.+++.|+|...-|.|.+ |+.|.+
T Consensus 20 ~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 20 AKHFGSLEALMNASVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp HHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHH
T ss_pred HHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHH
Confidence 456999999999999999875588875 655544
No 117
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=26.29 E-value=36 Score=31.04 Aligned_cols=26 Identities=27% Similarity=0.253 Sum_probs=21.1
Q ss_pred HHHHHHhcCCccChHHHHHHHHHhCC
Q 016856 310 KLAEQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
.+.-.|..|.|||+.+|..|+..+|-
T Consensus 27 ~v~~aLt~I~GIG~~~A~~I~~~lgi 52 (154)
T PTZ00134 27 KVPYALTAIKGIGRRFAYLVCKKAGI 52 (154)
T ss_pred EEEEeecccccccHHHHHHHHHHcCc
Confidence 35568999999999999999855553
No 118
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=26.05 E-value=1.1e+02 Score=23.46 Aligned_cols=38 Identities=21% Similarity=0.211 Sum_probs=30.5
Q ss_pred CCCC-HHHHhcCCHHHHHHhCcCcHH-HHHHHHHHHHHHhC
Q 016856 251 NFPS-PRELANLDESFLAKRCNLGYR-AGRILKLARGIVDG 289 (381)
Q Consensus 251 ~FPT-pe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~~G 289 (381)
.|++ +++|-..+-.+|++ .|.--| -+||..-.+.+..|
T Consensus 18 kf~~~w~~lf~~~s~~LK~-~GIp~r~RryiL~~~ek~r~G 57 (57)
T PF09597_consen 18 KFESDWEKLFTTSSKQLKE-LGIPVRQRRYILRWREKYRQG 57 (57)
T ss_pred HHHHHHHHHHhcCHHHHHH-CCCCHHHHHHHHHHHHHHhCc
Confidence 6899 99999999999998 565544 68998888776654
No 119
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=25.82 E-value=73 Score=32.82 Aligned_cols=39 Identities=18% Similarity=0.308 Sum_probs=28.1
Q ss_pred HHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHH
Q 016856 281 KLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (381)
Q Consensus 281 ~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL 330 (381)
.+|+.+.+.--++..+... + .++|.+++|||+..|..|.
T Consensus 298 ~iAk~Ll~~FGSL~~Il~A-------s----~eeL~~VeGIGe~rA~~I~ 336 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAA-------S----IEDLDEVEGIGEVRARAIR 336 (352)
T ss_pred HHHHHHHHHcCCHHHHHcC-------C----HHHHhhCCCcCHHHHHHHH
Confidence 4667777655566666544 3 4579999999999998873
No 120
>cd08594 PI-PLCc_eta Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif,
Probab=25.07 E-value=2.3e+02 Score=27.49 Aligned_cols=41 Identities=24% Similarity=0.360 Sum_probs=35.4
Q ss_pred cccccCCCChHHHHHHHHH---------------hcCCCHHHHHHHHHHHHHHhhh
Q 016856 114 SGRVFRSPTLFEDMVKCML---------------LCNCQWPRTLSMARALCELQWE 154 (381)
Q Consensus 114 ggRv~r~p~~fE~lv~~I~---------------~~n~~~~r~~~m~~~L~~~~g~ 154 (381)
.|+-+-++=+|++.+++|= .-.|+......||+-|.+.+|+
T Consensus 62 HG~tlts~i~f~dv~~aI~~~AF~~s~yPvIlSlE~Hcs~~qQ~~ma~~l~~~lGd 117 (227)
T cd08594 62 HGYTLTSKILFRDVIETINKYAFIKNEYPVILSIENHCSVQQQKKMAQYLKEILGD 117 (227)
T ss_pred eCCCcccCcCHHHHHHHHHHhhccCCCCCEEEEecccCCHHHHHHHHHHHHHHHhH
Confidence 4677878889999999986 3489999999999999999988
No 121
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=24.97 E-value=47 Score=29.03 Aligned_cols=26 Identities=23% Similarity=0.410 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCccChHHHHHHHHHhC
Q 016856 309 VKLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 309 ee~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
..+.-.|..|.|||+.+|..|+.-+|
T Consensus 13 k~v~~aL~~I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 13 KRVVIALTYIYGIGRTRAKEILAAAG 38 (122)
T ss_pred cEEEeeecccccccHHHHHHHHHHhC
Confidence 34566899999999999999974444
No 122
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=24.03 E-value=1.9e+02 Score=29.96 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=16.9
Q ss_pred HHHHHHhcCCccChHHHHHH
Q 016856 310 KLAEQLSQINGFGPFTRNNV 329 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~V 329 (381)
+..++|+-+|||||.|+..+
T Consensus 275 ~Df~elLl~~GiGpstvRAL 294 (373)
T COG1415 275 DDFEELLLVPGIGPSTVRAL 294 (373)
T ss_pred ccHHHHHhccCCCHHHHHHH
Confidence 34678999999999998776
No 123
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=23.03 E-value=73 Score=36.32 Aligned_cols=29 Identities=10% Similarity=-0.066 Sum_probs=23.5
Q ss_pred cHHHHHHHHhcCCccChHHHHHHHHHhCC
Q 016856 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (381)
Q Consensus 307 ~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~ 335 (381)
...+..+.|.+|||||++.|..+|..+|-
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~f~s 779 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKKVKS 779 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHHcCC
Confidence 44567888999999999999999855543
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=22.70 E-value=51 Score=28.41 Aligned_cols=25 Identities=24% Similarity=0.369 Sum_probs=20.3
Q ss_pred HHHHHHhcCCccChHHHHHHHHHhC
Q 016856 310 KLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
.+.-.|.+|.|||+.+|..|+.-+|
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEKAG 36 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHHhC
Confidence 4566899999999999999974444
No 125
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=22.64 E-value=6.5e+02 Score=23.67 Aligned_cols=40 Identities=15% Similarity=0.055 Sum_probs=30.3
Q ss_pred CcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 016856 113 FSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQ 152 (381)
Q Consensus 113 ~ggRv~r~p~~fE~lv~~I~~~n~~~~r~~~m~~~L~~~~ 152 (381)
+|.-+--...+||.|+=-+..+-.+|.-+++--..+.+.|
T Consensus 21 WG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF 60 (187)
T PRK10353 21 WGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACF 60 (187)
T ss_pred CCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHH
Confidence 5444555557999999999999999999987666665543
No 126
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.07 E-value=5.7e+02 Score=24.98 Aligned_cols=61 Identities=10% Similarity=0.072 Sum_probs=38.5
Q ss_pred CCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHHHhCCCCccccchHHHHHHHHhhccCCChHHHHHHH
Q 016856 289 GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIPTDSETIRHLKQVHARNCTSKTVQMIA 366 (381)
Q Consensus 289 G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~dvfPvDt~v~Ril~rly~~~~s~k~i~~~~ 366 (381)
|.-..+.+... -.+.+.+.|.. |..+..-|.+.+|+.+. .+..|.+++.+|. +|.+.++..
T Consensus 233 G~t~~~~l~~~-------Rl~~A~~lL~~----~~~si~eIA~~~Gf~~~----s~F~r~Fk~~~G~--tP~~yr~~~ 293 (302)
T PRK10371 233 QLTMKQYITAM-------RINHVRALLSD----TDKSILDIALTAGFRSS----SRFYSTFGKYVGM--SPQQYRKLS 293 (302)
T ss_pred CCCHHHHHHHH-------HHHHHHHHHhc----CCCCHHHHHHHcCCCCH----HHHHHHHHHHHCc--CHHHHHHHh
Confidence 54444555555 34566666655 34455666566676655 8999999999974 556655544
No 127
>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=21.61 E-value=49 Score=29.78 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=20.1
Q ss_pred HHHHHHhcCCccChHHHHHHHHHhC
Q 016856 310 KLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
.+.-.|..|.|||+.+|..|+.-+|
T Consensus 18 ~v~~aLt~I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 18 PVEYALTGIKGIGRRFARAIARKLG 42 (144)
T ss_pred EEEEeecceeccCHHHHHHHHHHcC
Confidence 3456899999999999999974444
No 128
>cd08633 PI-PLCc_eta2 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozyme 2. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding m
Probab=20.98 E-value=3.1e+02 Score=27.05 Aligned_cols=41 Identities=27% Similarity=0.448 Sum_probs=35.5
Q ss_pred cccccCCCChHHHHHHHHH---------------hcCCCHHHHHHHHHHHHHHhhh
Q 016856 114 SGRVFRSPTLFEDMVKCML---------------LCNCQWPRTLSMARALCELQWE 154 (381)
Q Consensus 114 ggRv~r~p~~fE~lv~~I~---------------~~n~~~~r~~~m~~~L~~~~g~ 154 (381)
.|+-+-++=+|++.+++|- .-.|+......|++-|.+.+|+
T Consensus 62 HG~tlts~i~f~~v~~~I~~~AF~~s~yPvIlslE~Hcs~~qQ~~ma~~l~~~lGd 117 (254)
T cd08633 62 HGYTLTSKILFKDVIETINKYAFIKNEYPVILSIENHCSVPQQKKMAQYLTEILGD 117 (254)
T ss_pred eCCCcccCcCHHHHHHHHHHHhccCCCCCEEEEecccCCHHHHHHHHHHHHHHHhH
Confidence 4777888899999999986 3488999999999999999887
No 129
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=20.96 E-value=4.6e+02 Score=24.99 Aligned_cols=84 Identities=13% Similarity=0.150 Sum_probs=47.4
Q ss_pred CHHHHHHhCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccCcHHHHHHHHhcCCccChHHHHHHHHHhCCCCcccc
Q 016856 262 DESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIPT 341 (381)
Q Consensus 262 ~~e~Lr~~~g~GyRAkyI~~lA~~i~~G~l~Le~L~~l~~~~~~~~~ee~~~~Ll~L~GIGpwTAd~VL~~Lg~~dvfPv 341 (381)
++++|.+.+|...| ||..+-+. .|.-..+++... -.+.+++.| . ++--..+..-|.+.+|+.|.
T Consensus 216 s~~~lA~~~giS~r--~L~r~Fk~--~G~T~~~yi~~~-------RL~~A~~lL-~-~~~~~~sI~eIA~~~GF~d~--- 279 (302)
T PRK09685 216 RPEWIAGELGISVR--SLYRLFAE--QGLVVAQYIRNR-------RLDRCADDL-R-PAADDEKITSIAYKWGFSDS--- 279 (302)
T ss_pred CHHHHHHHHCCCHH--HHHHHHHH--cCCCHHHHHHHH-------HHHHHHHHh-h-hhccCCCHHHHHHHhCCCCH---
Confidence 45556655666654 34444433 254445666655 335566666 2 22122344555456666554
Q ss_pred chHHHHHHHHhhccCCChHHHHH
Q 016856 342 DSETIRHLKQVHARNCTSKTVQM 364 (381)
Q Consensus 342 Dt~v~Ril~rly~~~~s~k~i~~ 364 (381)
.|..|.+++.||. +|.+.++
T Consensus 280 -s~Fsr~Fkk~~G~--sP~~yR~ 299 (302)
T PRK09685 280 -SHFSTAFKQRFGV--SPGEYRR 299 (302)
T ss_pred -HHHHHHHHHHHCc--CHHHHHh
Confidence 8999999999984 4565543
No 130
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=20.81 E-value=60 Score=29.42 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=20.4
Q ss_pred HHHHHHhcCCccChHHHHHHHHHhC
Q 016856 310 KLAEQLSQINGFGPFTRNNVLVCIG 334 (381)
Q Consensus 310 e~~~~Ll~L~GIGpwTAd~VL~~Lg 334 (381)
.+.-.|..|.|||+.+|..|+--+|
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred EEeeeccccccccHHHHHHHHHHcC
Confidence 3566899999999999999974444
Done!