YHDJ - ECOLI - GREMLIN Contacts

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YHDJ - DNA adenine methyltransferase YhdJ

UniProt:	P28638	Sequences: MRTGCEPTRFGNEAKTIIHGDALAELKKIPAESVDLIFADPPYNIGKNFDGLIEAWKEDLFIDWLFEVIAECHRVLKKQGSMYIMNSTENMPFIDLQCRKLFTIKSRIVWSYDSSGVQAKKHYGSMYEPILMMVKDAKNYTFNGDAILVEAKTGSQRALIDYRKNPPQPYNHQKVPGNVWDFPRVRYLMDEYENHPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAIASGRKFIGIEINSEYIKMGLRRLDVASHYSAEELAKVKKRKTGNLSKRSRLSEVDPDLITK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11498
Length:	294 (241)
Sequences:	5201 (4277)
Seq/√Len:	275.5

ECOLI - YHDJ
HALSA - Q9HPN9

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
223_A	241_G	3.829	1.00
226_F	252_G	3.085	1.00
37_I	72_C	3.083	1.00
205_K	234_A	2.960	1.00
201_E	231_V	2.842	1.00
35_D	79_Q	2.840	1.00
84_I	98_C	2.794	1.00
109_V	127_Y	2.728	1.00
229_G	241_G	2.653	1.00
213_N	216_D	2.653	1.00
223_A	229_G	2.611	1.00
25_E	242_I	2.442	1.00
35_D	77_K	2.426	1.00
83_Y	211_S	2.424	1.00
254_R	258_V	2.305	1.00
233_I	239_F	2.275	1.00
127_Y	178_N	2.274	1.00
71_E	74_R	2.265	1.00
107_R	129_P	2.230	1.00
212_S	216_D	2.195	1.00
111_S	181_D	2.177	1.00
76_L	80_G	2.167	1.00
27_K	71_E	2.160	1.00
18_I	25_E	2.113	1.00
214_P	236_G	2.112	1.00
86_N	94_I	2.075	1.00
19_H	249_I	2.065	1.00
99_R	133_M	2.048	1.00
20_G	25_E	2.026	1.00
31_A	74_R	2.016	1.00
15_K	239_F	2.016	1.00
217_I	238_K	1.997	1.00
229_G	239_F	1.950	1.00
32_E	78_K	1.896	1.00
165_N	168_Q	1.881	1.00
223_A	252_G	1.849	1.00
35_D	216_D	1.790	1.00
108_I	180_W	1.786	1.00
205_K	209_L	1.784	1.00
38_F	85_M	1.767	1.00
230_A	234_A	1.675	1.00
17_I	252_G	1.670	1.00
104_I	107_R	1.662	1.00
34_V	217_I	1.662	1.00
37_I	76_L	1.649	1.00
59_D	63_D	1.635	1.00
201_E	230_A	1.628	1.00
254_R	257_D	1.625	1.00
141_T	213_N	1.591	1.00
212_S	237_R	1.569	1.00
34_V	240_I	1.562	1.00
166_P	169_P	1.560	1.00
82_M	98_C	1.554	1.00
113_D	117_V	1.550	1.00
123_Y	210_A	1.543	1.00
66_F	100_K	1.498	1.00
201_E	234_A	1.450	1.00
17_I	249_I	1.444	1.00
19_H	246_S	1.443	1.00
81_S	132_M	1.442	1.00
111_S	126_M	1.426	1.00
93_F	96_L	1.425	1.00
204_L	227_T	1.417	1.00
105_K	134_V	1.404	1.00
217_I	240_I	1.401	1.00
253_L	257_D	1.396	1.00
167_P	170_Y	1.389	1.00
109_V	179_V	1.382	1.00
205_K	235_S	1.366	1.00
165_N	170_Y	1.333	1.00
72_C	221_P	1.331	1.00
130_I	207_I	1.322	1.00
92_P	95_D	1.315	1.00
112_Y	128_E	1.310	1.00
104_I	133_M	1.308	1.00
110_W	200_P	1.306	1.00
83_Y	132_M	1.295	1.00
25_E	28_K	1.289	1.00
241_G	252_G	1.249	1.00
18_I	242_I	1.236	1.00
43_Y	85_M	1.233	1.00
145_D	148_L	1.231	1.00
17_I	223_A	1.224	1.00
229_G	256_L	1.218	1.00
108_I	132_M	1.209	1.00
106_S	123_Y	1.201	1.00
180_W	207_I	1.194	1.00
126_M	177_G	1.192	1.00
180_W	206_R	1.188	1.00
250_K	253_L	1.180	1.00
57_K	60_L	1.177	1.00
110_W	130_I	1.176	1.00
166_P	170_Y	1.157	1.00
95_D	104_I	1.157	1.00
91_M	107_R	1.156	1.00
78_K	136_D	1.156	1.00
95_D	99_R	1.155	1.00
92_P	99_R	1.150	1.00
209_L	235_S	1.144	1.00
202_A	205_K	1.137	1.00
249_I	253_L	1.127	1.00
204_L	207_I	1.124	1.00
91_M	131_L	1.116	1.00
43_Y	128_E	1.109	1.00
154_G	164_K	1.108	1.00
40_D	199_K	1.103	1.00
32_E	77_K	1.100	1.00
127_Y	179_V	1.091	1.00
65_L	68_V	1.086	1.00
184_R	187_Y	1.086	1.00
71_E	75_V	1.080	1.00
226_F	241_G	1.075	1.00
39_A	221_P	1.073	1.00
220_D	228_T	1.051	1.00
91_M	95_D	1.050	1.00
66_F	70_A	1.045	1.00
56_W	60_L	1.044	1.00
30_P	33_S	1.038	1.00
130_I	203_L	1.038	1.00
76_L	102_F	1.037	1.00
165_N	169_P	1.034	1.00
73_H	135_K	1.025	1.00
108_I	123_Y	1.015	1.00
63_D	67_E	1.015	1.00
26_L	75_V	1.009	1.00
36_L	212_S	1.003	1.00
31_A	71_E	0.990	1.00
93_F	99_R	0.980	1.00
36_L	207_I	0.980	1.00
92_P	96_L	0.966	1.00
219_L	242_I	0.960	1.00
249_I	252_G	0.959	1.00
84_I	94_I	0.958	1.00
75_V	219_L	0.957	1.00
243_E	249_I	0.953	1.00
38_F	204_L	0.947	1.00
108_I	130_I	0.944	1.00
60_L	63_D	0.939	1.00
247_E	250_K	0.929	1.00
98_C	133_M	0.910	1.00
190_D	202_A	0.909	1.00
34_V	219_L	0.904	1.00
117_V	120_K	0.902	1.00
218_V	228_T	0.894	1.00
16_T	30_P	0.893	1.00
73_H	102_F	0.892	1.00
14_A	238_K	0.884	1.00
186_R	189_M	0.874	1.00
112_Y	126_M	0.874	1.00
195_H	248_Y	0.864	1.00
245_N	248_Y	0.862	1.00
223_A	239_F	0.860	1.00
114_S	117_V	0.858	1.00
36_L	208_I	0.858	1.00
65_L	97_Q	0.857	1.00
168_Q	172_H	0.848	1.00
20_G	242_I	0.848	1.00
230_A	259_A	0.833	1.00
232_A	236_G	0.831	1.00
106_S	178_N	0.828	1.00
223_A	243_E	0.827	0.99
26_L	219_L	0.820	0.99
116_G	124_G	0.810	0.99
70_A	101_L	0.807	0.99
115_S	120_K	0.805	0.99
143_N	213_N	0.803	0.99
117_V	124_G	0.801	0.99
113_D	124_G	0.793	0.99
115_S	118_Q	0.792	0.99
24_A	27_K	0.790	0.99
112_Y	117_V	0.790	0.99
88_T	107_R	0.790	0.99
65_L	94_I	0.790	0.99
183_P	186_R	0.789	0.99
65_L	69_I	0.789	0.99
109_V	129_P	0.786	0.99
16_T	19_H	0.785	0.99
187_Y	190_D	0.782	0.99
108_I	207_I	0.781	0.99
200_P	203_L	0.779	0.99
232_A	239_F	0.777	0.99
58_E	90_N	0.776	0.99
115_S	124_G	0.776	0.99
171_N	174_K	0.775	0.99
250_K	254_R	0.775	0.99
44_N	90_N	0.773	0.99
29_I	75_V	0.773	0.99
69_I	82_M	0.772	0.99
31_A	75_V	0.769	0.99
182_F	185_V	0.766	0.99
83_Y	207_I	0.766	0.99
51_G	54_E	0.764	0.99
32_E	135_K	0.761	0.99
132_M	211_S	0.757	0.99
145_D	149_V	0.754	0.99
35_D	213_N	0.754	0.99
110_W	128_E	0.752	0.99
182_F	187_Y	0.744	0.99
24_A	31_A	0.744	0.99
117_V	126_M	0.742	0.99
81_S	211_S	0.737	0.99
86_N	91_M	0.737	0.99
246_S	250_K	0.736	0.99
83_Y	130_I	0.735	0.99
107_R	127_Y	0.735	0.99
199_K	204_L	0.723	0.99
134_V	140_Y	0.723	0.99
114_S	118_Q	0.719	0.99
103_T	137_A	0.718	0.99
33_S	74_R	0.718	0.99
116_G	126_M	0.717	0.99
122_H	140_Y	0.713	0.99
36_L	83_Y	0.713	0.99
111_S	179_V	0.711	0.98
227_T	231_V	0.708	0.98
110_W	203_L	0.704	0.98
144_G	147_I	0.703	0.98
79_Q	136_D	0.701	0.98
234_A	259_A	0.701	0.98
13_E	16_T	0.699	0.98
167_P	172_H	0.693	0.98
44_N	58_E	0.686	0.98
61_F	65_L	0.685	0.98
134_V	137_A	0.682	0.98
168_Q	171_N	0.681	0.98
182_F	206_R	0.679	0.98
191_E	198_Q	0.675	0.98
148_L	173_Q	0.674	0.98
113_D	116_G	0.671	0.98
26_L	72_C	0.670	0.98
167_P	171_N	0.668	0.98
252_G	256_L	0.668	0.98
144_G	148_L	0.667	0.98
212_S	218_V	0.666	0.98
118_Q	124_G	0.666	0.98
22_A	68_V	0.664	0.98
112_Y	125_S	0.664	0.98
108_I	206_R	0.663	0.98
15_K	238_K	0.662	0.98
143_N	146_A	0.661	0.98
34_V	75_V	0.660	0.98
223_A	249_I	0.660	0.98
66_F	97_Q	0.658	0.97
38_F	207_I	0.652	0.97
24_A	28_K	0.652	0.97
112_Y	115_S	0.652	0.97
15_K	229_G	0.652	0.97
72_C	82_M	0.651	0.97
136_D	139_N	0.650	0.97
78_K	135_K	0.650	0.97
243_E	248_Y	0.643	0.97
40_D	85_M	0.641	0.97
233_I	260_S	0.641	0.97
85_M	199_K	0.640	0.97
56_W	67_E	0.638	0.97
137_A	140_Y	0.637	0.97
40_D	204_L	0.635	0.97
113_D	118_Q	0.633	0.97
106_S	122_H	0.631	0.97
19_H	245_N	0.629	0.97
233_I	256_L	0.628	0.97
120_K	126_M	0.627	0.97
23_L	67_E	0.627	0.97
142_F	145_D	0.627	0.97
125_S	178_N	0.626	0.97
16_T	253_L	0.624	0.97
112_Y	118_Q	0.624	0.97
119_A	122_H	0.622	0.96
85_M	204_L	0.621	0.96
126_M	178_N	0.619	0.96
122_H	134_V	0.619	0.96
20_G	28_K	0.613	0.96
143_N	148_L	0.612	0.96
26_L	242_I	0.611	0.96
147_I	151_A	0.610	0.96
56_W	66_F	0.609	0.96
29_I	34_V	0.609	0.96
64_W	222_F	0.609	0.96
95_D	131_L	0.608	0.96
118_Q	122_H	0.606	0.96
23_L	68_V	0.605	0.96
147_I	150_E	0.605	0.96
205_K	231_V	0.599	0.96
148_L	151_A	0.598	0.96
19_H	243_E	0.598	0.96
114_S	126_M	0.594	0.95
166_P	171_N	0.591	0.95
21_D	27_K	0.591	0.95
258_V	261_H	0.591	0.95
20_G	24_A	0.590	0.95
22_A	26_L	0.590	0.95
32_E	75_V	0.588	0.95
124_G	177_G	0.583	0.95
37_I	80_G	0.583	0.95
14_A	17_I	0.583	0.95
98_C	101_L	0.580	0.95
182_F	186_R	0.580	0.95
17_I	226_F	0.579	0.95
107_R	131_L	0.575	0.95
33_S	217_I	0.574	0.95
35_D	217_I	0.574	0.95
117_V	122_H	0.574	0.95
16_T	28_K	0.573	0.94
19_H	252_G	0.573	0.94
24_A	60_L	0.572	0.94
182_F	202_A	0.566	0.94
112_Y	116_G	0.565	0.94
95_D	133_M	0.562	0.94
45_I	49_F	0.560	0.94
27_K	67_E	0.556	0.94
204_L	228_T	0.556	0.94
68_V	72_C	0.555	0.94
13_E	238_K	0.554	0.93
63_D	66_F	0.552	0.93
141_T	216_D	0.551	0.93
113_D	120_K	0.548	0.93
36_L	211_S	0.545	0.93
72_C	76_L	0.545	0.93
114_S	120_K	0.545	0.93
181_D	185_V	0.545	0.93
146_A	149_V	0.543	0.93
114_S	119_A	0.541	0.93
17_I	239_F	0.540	0.93
170_Y	174_K	0.539	0.93
113_D	119_A	0.536	0.92
119_A	124_G	0.534	0.92
50_D	55_A	0.533	0.92
88_T	129_P	0.531	0.92
23_L	27_K	0.531	0.92
114_S	189_M	0.529	0.92
20_G	23_L	0.529	0.92
144_G	149_V	0.528	0.92
208_I	235_S	0.528	0.92
122_H	142_F	0.528	0.92
231_V	235_S	0.528	0.92
62_I	97_Q	0.527	0.92
148_L	152_K	0.524	0.91
175_V	179_V	0.523	0.91
184_R	189_M	0.522	0.91
40_D	197_T	0.522	0.91
172_H	175_V	0.519	0.91
116_G	119_A	0.519	0.91
97_Q	101_L	0.518	0.91
85_M	130_I	0.518	0.91
21_D	24_A	0.516	0.91
105_K	140_Y	0.516	0.91
165_N	171_N	0.515	0.91
216_D	237_R	0.515	0.91
93_F	100_K	0.515	0.91
83_Y	123_Y	0.515	0.91
223_A	226_F	0.515	0.91
17_I	256_L	0.514	0.91
115_S	187_Y	0.512	0.90
111_S	177_G	0.512	0.90
26_L	29_I	0.510	0.90
28_K	56_W	0.510	0.90
221_P	242_I	0.507	0.90
73_H	101_L	0.502	0.90
170_Y	173_Q	0.501	0.90
175_V	180_W	0.501	0.90
115_S	126_M	0.500	0.89
21_D	244_I	0.500	0.89

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1eg2A	2	0.8639	100	0.332	Contact Map
1booA	1	0.8673	100	0.336	Contact Map
4zcfA	2	0.966	100	0.343	Contact Map
1g60A	2	0.7891	100	0.365	Contact Map
2zigA	2	0.7619	100	0.404	Contact Map
3v97A	1	0.4082	98	0.88	Contact Map
2b78A	1	0.4116	97.9	0.882	Contact Map
3lpmA	2	0.4728	97.9	0.883	Contact Map
2ozvA	2	0.5102	97.9	0.884	Contact Map
4dzrA	2	0.3163	97.8	0.884	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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