YFJP - BACSU - GREMLIN Contacts

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YFJP - Putative DNA-3-methyladenine glycosylase YfjP

UniProt:	O31544	Sequences: MWKEKVSVTPPYHFDRVLDRLSLDPLNAVDREAREVRVPIRNQAGDVCIVKVQALGHAGEPEFLVSGETDQGEMMKEIKRIFQWENHLQHVLDHFSKTSLSAIFEEHAGTPLVLDYSVYNCMMKCIIHQQLNLSFAYTLTERFVHAFGEQKDGVWCYPKPETIAELDYQDLRDLQFSMRKAEYTIDTSRMIAEGTLSLSELPHMADEDIMKKLIKIRGIGPWTVQNVLMFGLGRPNLFPLADIGLQNAIKRHFQLDDKPAKDVMLAMSKEWEPYLSYASLYLWRSIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	287 (272)
Sequences:	2589 (1856)
Seq/√Len:	112.5

ECOLI - 3MG2
BACSU - YFJP 3MGA
HALSA - Q9HQ94 Q9HQ62

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_K	162_T	4.253	1.00
79_K	85_E	3.852	1.00
269_K	272_E	3.558	1.00
149_E	162_T	3.339	1.00
138_T	142_R	3.211	1.00
210_M	225_Q	2.834	1.00
122_M	227_V	2.720	1.00
214_I	224_V	2.682	1.00
38_V	51_K	2.625	1.00
243_I	247_N	2.581	1.00
205_A	208_D	2.567	1.00
167_D	170_D	2.456	1.00
119_Y	160_P	2.443	1.00
260_A	263_V	2.423	1.00
182_E	186_D	2.343	1.00
236_N	275_L	2.296	1.00
122_M	187_T	2.283	1.00
179_R	182_E	2.280	1.00
143_F	163_I	2.277	1.00
210_M	214_I	2.263	1.00
42_N	149_E	2.226	1.00
185_I	189_R	2.169	1.00
126_I	187_T	2.161	1.00
97_K	271_W	2.116	1.00
132_N	135_F	2.105	1.00
127_I	140_T	2.068	1.00
87_H	90_H	2.040	1.00
36_V	51_K	2.038	1.00
214_I	221_P	2.024	1.00
212_K	215_K	1.947	1.00
119_Y	188_S	1.942	1.00
141_E	145_H	1.814	1.00
123_M	157_Y	1.798	1.00
33_A	36_V	1.773	1.00
189_R	193_E	1.761	1.00
29_V	144_V	1.715	1.00
146_A	170_D	1.702	1.00
206_D	234_R	1.701	1.00
190_M	216_I	1.691	1.00
210_M	224_V	1.674	1.00
229_M	276_S	1.659	1.00
83_Q	86_N	1.642	1.00
240_L	265_L	1.620	1.00
123_M	184_T	1.608	1.00
27_N	30_D	1.606	1.00
39_P	120_N	1.581	1.00
119_Y	123_M	1.574	1.00
127_I	139_L	1.573	1.00
186_D	189_R	1.572	1.00
59_G	65_V	1.572	1.00
249_I	264_M	1.568	1.00
177_S	180_K	1.567	1.00
147_F	170_D	1.566	1.00
13_H	16_R	1.556	1.00
132_N	243_I	1.552	1.00
237_L	276_S	1.545	1.00
130_Q	135_F	1.534	1.00
80_R	85_E	1.530	1.00
125_C	226_N	1.524	1.00
200_E	212_K	1.474	1.00
86_N	91_V	1.461	1.00
8_V	12_Y	1.456	1.00
186_D	216_I	1.451	1.00
245_L	279_S	1.441	1.00
12_Y	17_V	1.438	1.00
191_I	198_L	1.422	1.00
182_E	217_R	1.418	1.00
31_R	38_V	1.410	1.00
75_M	79_K	1.409	1.00
145_H	155_W	1.400	1.00
139_L	176_F	1.394	1.00
271_W	278_A	1.393	1.00
130_Q	177_S	1.371	1.00
89_Q	93_D	1.368	1.00
210_M	228_L	1.367	1.00
244_G	248_A	1.355	1.00
26_L	30_D	1.349	1.00
129_Q	222_W	1.330	1.00
119_Y	191_I	1.328	1.00
204_M	208_D	1.315	1.00
208_D	212_K	1.314	1.00
18_L	32_E	1.308	1.00
183_Y	186_D	1.302	0.99
228_L	234_R	1.283	0.99
115_D	121_C	1.282	0.99
168_Y	185_I	1.280	0.99
55_L	60_E	1.266	0.99
51_K	62_E	1.264	0.99
148_G	156_C	1.257	0.99
139_L	142_R	1.254	0.99
131_L	222_W	1.254	0.99
128_H	131_L	1.250	0.99
186_D	190_M	1.241	0.99
40_I	156_C	1.237	0.99
101_S	105_E	1.229	0.99
208_D	211_K	1.223	0.99
135_F	138_T	1.222	0.99
190_M	195_T	1.209	0.99
59_G	66_S	1.209	0.99
14_F	54_A	1.204	0.99
209_I	232_L	1.203	0.99
147_F	166_L	1.199	0.99
102_A	106_E	1.187	0.99
239_P	245_L	1.186	0.99
164_A	189_R	1.184	0.99
259_P	263_V	1.181	0.99
44_A	73_E	1.173	0.99
43_Q	46_D	1.171	0.99
41_R	116_Y	1.168	0.99
239_P	279_S	1.165	0.99
266_A	269_K	1.155	0.99
83_Q	277_Y	1.151	0.99
36_V	53_Q	1.150	0.99
238_F	268_S	1.144	0.99
144_V	155_W	1.143	0.99
161_E	192_A	1.122	0.98
234_R	237_L	1.121	0.98
209_I	228_L	1.119	0.98
136_A	222_W	1.117	0.98
15_D	35_E	1.116	0.98
264_M	268_S	1.103	0.98
147_F	163_I	1.100	0.98
142_R	175_Q	1.098	0.98
61_P	64_L	1.069	0.98
168_Y	181_A	1.065	0.98
131_L	136_A	1.064	0.98
127_I	176_F	1.062	0.98
26_L	29_V	1.061	0.98
247_N	250_K	1.057	0.98
164_A	192_A	1.046	0.98
120_N	157_Y	1.045	0.98
268_S	271_W	1.034	0.97
204_M	212_K	1.020	0.97
24_D	125_C	1.014	0.97
8_V	14_F	1.011	0.97
19_D	23_L	1.003	0.97
52_V	61_P	1.000	0.97
265_L	268_S	0.996	0.97
73_E	76_K	0.983	0.96
128_H	226_N	0.980	0.96
272_E	275_L	0.977	0.96
245_L	282_L	0.976	0.96
115_D	233_G	0.972	0.96
46_D	70_D	0.965	0.96
103_I	281_Y	0.965	0.96
121_C	231_G	0.959	0.96
228_L	237_L	0.957	0.96
178_M	181_A	0.957	0.96
130_Q	222_W	0.957	0.96
42_N	47_V	0.957	0.96
59_G	64_L	0.956	0.96
239_P	276_S	0.953	0.96
165_E	185_I	0.950	0.96
197_S	200_E	0.948	0.96
80_R	233_G	0.942	0.95
228_L	232_L	0.941	0.95
222_W	242_D	0.934	0.95
47_V	149_E	0.932	0.95
62_E	262_D	0.930	0.95
134_S	137_Y	0.928	0.95
8_V	54_A	0.920	0.95
129_Q	223_T	0.919	0.95
95_F	104_F	0.917	0.95
57_H	61_P	0.913	0.95
56_G	61_P	0.911	0.95
150_Q	155_W	0.910	0.95
88_L	92_L	0.906	0.94
52_V	59_G	0.905	0.94
66_S	74_M	0.904	0.94
135_F	175_Q	0.904	0.94
122_M	219_I	0.902	0.94
91_V	95_F	0.899	0.94
204_M	209_I	0.898	0.94
81_I	116_Y	0.898	0.94
52_V	78_I	0.897	0.94
124_K	140_T	0.893	0.94
276_S	279_S	0.888	0.94
97_K	278_A	0.887	0.94
131_L	223_T	0.876	0.93
236_N	272_E	0.875	0.93
225_Q	239_P	0.874	0.93
61_P	65_V	0.872	0.93
131_L	180_K	0.869	0.93
55_L	58_A	0.865	0.93
192_A	216_I	0.861	0.93
19_D	22_S	0.857	0.93
126_I	183_Y	0.855	0.92
206_D	209_I	0.854	0.92
121_C	124_K	0.854	0.92
186_D	217_R	0.853	0.92
181_A	185_I	0.848	0.92
123_M	187_T	0.847	0.92
80_R	114_L	0.846	0.92
176_F	180_K	0.844	0.92
244_G	281_Y	0.837	0.92
262_D	266_A	0.836	0.92
53_Q	60_E	0.834	0.92
133_L	226_N	0.834	0.92
18_L	22_S	0.833	0.92
209_I	234_R	0.828	0.91
240_L	279_S	0.827	0.91
226_N	239_P	0.827	0.91
83_Q	235_P	0.825	0.91
160_P	188_S	0.825	0.91
254_Q	259_P	0.825	0.91
226_N	230_F	0.820	0.91
246_Q	258_K	0.813	0.90
22_S	34_R	0.808	0.90
25_P	137_Y	0.805	0.90
128_H	283_W	0.804	0.90
178_M	182_E	0.804	0.90
160_P	191_I	0.798	0.90
122_M	126_I	0.798	0.90
250_K	259_P	0.797	0.90
140_T	157_Y	0.790	0.89
30_D	33_A	0.787	0.89
125_C	223_T	0.785	0.89
97_K	253_F	0.779	0.89
221_P	225_Q	0.777	0.88
135_F	180_K	0.776	0.88
145_H	150_Q	0.774	0.88
65_V	70_D	0.773	0.88
169_Q	173_D	0.771	0.88
107_H	284_R	0.768	0.88
63_F	74_M	0.766	0.88
142_R	145_H	0.762	0.87
206_D	236_N	0.762	0.87
172_R	178_M	0.758	0.87
206_D	228_L	0.757	0.87
95_F	101_S	0.757	0.87
136_A	223_T	0.751	0.87
199_S	211_K	0.750	0.87
130_Q	244_G	0.750	0.87
195_T	215_K	0.747	0.86
131_L	243_I	0.744	0.86
131_L	176_F	0.739	0.86
49_I	154_V	0.737	0.86
139_L	175_Q	0.735	0.85
170_D	173_D	0.731	0.85
121_C	125_C	0.731	0.85
228_L	231_G	0.731	0.85
82_F	243_I	0.730	0.85
236_N	273_P	0.728	0.85
91_V	277_Y	0.728	0.85
206_D	237_L	0.725	0.85
71_Q	75_M	0.718	0.84
182_E	216_I	0.718	0.84
131_L	135_F	0.716	0.84
172_R	176_F	0.715	0.84
166_L	173_D	0.714	0.84
179_R	183_Y	0.713	0.84
77_E	80_R	0.712	0.84
61_P	67_G	0.711	0.84
267_M	270_E	0.709	0.83
114_L	233_G	0.708	0.83
41_R	157_Y	0.706	0.83
229_M	239_P	0.706	0.83
132_N	176_F	0.705	0.83
135_F	139_L	0.703	0.83
278_A	282_L	0.697	0.82
190_M	193_E	0.695	0.82
130_Q	243_I	0.691	0.82
66_S	69_T	0.689	0.82
128_H	136_A	0.688	0.82
207_E	211_K	0.686	0.81
118_V	231_G	0.685	0.81
24_D	37_R	0.684	0.81
148_G	162_T	0.684	0.81
61_P	66_S	0.684	0.81
193_E	200_E	0.684	0.81
24_D	226_N	0.681	0.81
143_F	146_A	0.680	0.81
16_R	19_D	0.679	0.81
88_L	232_L	0.676	0.80
10_P	17_V	0.676	0.80
196_L	199_S	0.674	0.80
167_D	172_R	0.672	0.80
247_N	258_K	0.665	0.79
235_P	274_Y	0.664	0.79
86_N	277_Y	0.662	0.79
214_I	225_Q	0.662	0.79
176_F	181_A	0.661	0.79
130_Q	248_A	0.659	0.79
44_A	47_V	0.658	0.79
15_D	55_L	0.657	0.78
199_S	204_M	0.653	0.78
129_Q	220_G	0.650	0.78
90_H	274_Y	0.645	0.77
108_A	273_P	0.644	0.77
200_E	204_M	0.641	0.77
176_F	184_T	0.640	0.77
56_G	62_E	0.634	0.76
194_G	197_S	0.631	0.76
186_D	191_I	0.630	0.76
239_P	246_Q	0.629	0.75
147_F	171_L	0.628	0.75
128_H	222_W	0.627	0.75
40_I	43_Q	0.627	0.75
8_V	57_H	0.624	0.75
162_T	165_E	0.621	0.74
126_I	139_L	0.620	0.74
60_E	63_F	0.620	0.74
166_L	170_D	0.618	0.74
238_F	241_A	0.617	0.74
229_M	279_S	0.616	0.74
246_Q	250_K	0.616	0.74
169_Q	178_M	0.615	0.74
222_W	226_N	0.614	0.74
88_L	274_Y	0.612	0.73
149_E	156_C	0.611	0.73
121_C	233_G	0.611	0.73
49_I	55_L	0.608	0.73
59_G	69_T	0.608	0.73
52_V	82_F	0.607	0.73
131_L	139_L	0.606	0.73
54_A	58_A	0.605	0.73
26_L	32_E	0.604	0.72
221_P	278_A	0.601	0.72
222_W	283_W	0.599	0.72
37_R	48_C	0.597	0.72
264_M	267_M	0.597	0.72
129_Q	136_A	0.594	0.71
128_H	133_L	0.592	0.71
108_A	236_N	0.591	0.71
180_K	220_G	0.590	0.71
231_G	280_L	0.584	0.70
32_E	36_V	0.583	0.70
224_V	228_L	0.582	0.70
80_R	115_D	0.582	0.70
65_V	69_T	0.581	0.70
105_E	165_E	0.580	0.69
101_S	108_A	0.580	0.69
119_Y	181_A	0.579	0.69
124_K	136_A	0.579	0.69
164_A	188_S	0.578	0.69
113_V	133_L	0.577	0.69
168_Y	182_E	0.576	0.69
40_I	154_V	0.574	0.69
280_L	284_R	0.574	0.69
92_L	104_F	0.573	0.68
84_W	111_P	0.569	0.68
131_L	177_S	0.569	0.68
206_D	210_M	0.567	0.68
83_Q	128_H	0.566	0.68
222_W	244_G	0.562	0.67
193_E	212_K	0.562	0.67
223_T	283_W	0.561	0.67
24_D	133_L	0.560	0.67
72_G	76_K	0.560	0.67
110_T	148_G	0.559	0.67
43_Q	48_C	0.557	0.66
29_V	32_E	0.557	0.66
24_D	29_V	0.555	0.66
67_G	74_M	0.552	0.66
47_V	156_C	0.550	0.65
55_L	62_E	0.547	0.65
27_N	31_R	0.547	0.65
164_A	185_I	0.546	0.65
277_Y	281_Y	0.546	0.65
122_M	216_I	0.546	0.65
121_C	230_F	0.544	0.65
45_G	57_H	0.544	0.65
68_E	71_Q	0.543	0.64
143_F	174_L	0.542	0.64
180_K	217_R	0.541	0.64
52_V	56_G	0.540	0.64
17_V	20_R	0.540	0.64
120_N	230_F	0.538	0.64
120_N	125_C	0.537	0.64
104_F	108_A	0.536	0.63
50_V	107_H	0.536	0.63
144_V	158_P	0.535	0.63
161_E	195_T	0.535	0.63
187_T	216_I	0.534	0.63
227_V	231_G	0.532	0.63
172_R	181_A	0.529	0.62
149_E	153_G	0.529	0.62
222_W	243_I	0.528	0.62
163_I	167_D	0.523	0.62
110_T	281_Y	0.522	0.61
8_V	11_P	0.522	0.61
20_R	226_N	0.521	0.61
64_L	151_K	0.519	0.61
189_R	212_K	0.519	0.61
92_L	107_H	0.519	0.61
43_Q	73_E	0.517	0.61
173_D	181_A	0.517	0.61
83_Q	88_L	0.515	0.60
132_N	247_N	0.515	0.60
246_Q	264_M	0.514	0.60
107_H	281_Y	0.512	0.60
21_L	113_V	0.512	0.60
128_H	223_T	0.510	0.60
78_I	82_F	0.510	0.60
112_L	280_L	0.508	0.59
20_R	230_F	0.508	0.59
240_L	261_K	0.507	0.59
129_Q	139_L	0.507	0.59
115_D	230_F	0.507	0.59
211_K	215_K	0.507	0.59
20_R	280_L	0.506	0.59
81_I	245_L	0.504	0.59
123_M	188_S	0.504	0.59
142_R	271_W	0.503	0.59
72_G	75_M	0.502	0.58
95_F	278_A	0.502	0.58
152_D	195_T	0.501	0.58
47_V	66_S	0.500	0.58

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
1mpgA	1	0.9443	100	0.234	Contact Map
2jhnA	1	0.9652	100	0.238	Contact Map
4ejyA	1	0.9443	100	0.291	Contact Map
3i0wA	1	0.9443	100	0.295	Contact Map
2xhiA	1	0.9652	100	0.31	Contact Map
4b21A	2	0.7003	100	0.372	Contact Map
2yg9A	1	0.6864	100	0.423	Contact Map
2h56A	1	0.7003	100	0.434	Contact Map
3s6iA	1	0.676	100	0.445	Contact Map
3fhfA	1	0.6655	100	0.593	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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