YLMD - BACSU - GREMLIN Contacts

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YLMD - Laccase domain protein YlmD

UniProt:	O31726	Sequences: MNTYHPFSLTTPSTLMIQDWAQTNQNNKEVIAGFTTKNGGVSQKPFESLNTGLHVHDKDADVVKNREYIADMFNTDLQSWVFADQTHDNRVQKVTQRDRGKGAREYHTALKATDGIYTNEKNVFLALCFADCVPLFFYDPVKSLVGVAHAGWKGTVKQIGREMVKQWTEKEGSNPSDIYAVIGPSISGACYTVDDRVMDAVRALPVSADLAANQTAKAQYQLDLKELNRLILMDSGLASEQISVSGLCTESEPSLFYSHRRDQGKTGRMMSFIGMKEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	278 (237)
Sequences:	3216 (2409)
Seq/√Len:	156.5

ECOLI - YFIH
BACSU - YLMD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
164_V	178_I	3.255	1.00
190_C	248_C	3.246	1.00
190_C	251_S	3.077	1.00
136_F	147_V	2.906	1.00
64_K	67_E	2.755	1.00
148_A	163_M	2.707	1.00
252_E	255_L	2.594	1.00
129_F	271_S	2.535	1.00
137_F	148_A	2.501	1.00
44_K	47_E	2.437	1.00
195_D	199_D	2.426	1.00
43_Q	61_D	2.420	1.00
64_K	68_Y	2.364	1.00
115_G	163_M	2.301	1.00
135_L	160_G	2.275	1.00
141_V	177_D	2.217	1.00
161_R	231_I	2.198	1.00
133_V	185_S	2.192	1.00
189_A	251_S	2.168	1.00
89_N	162_E	2.141	1.00
226_E	229_R	2.115	1.00
84_D	112_A	2.109	1.00
35_T	69_I	2.053	1.00
115_G	148_A	2.039	1.00
185_S	225_K	1.954	1.00
144_L	167_W	1.932	1.00
49_L	69_I	1.919	1.00
58_K	61_D	1.912	1.00
191_Y	222_L	1.909	1.00
137_F	180_A	1.901	1.00
53_L	63_V	1.858	1.00
187_S	190_C	1.791	1.00
216_A	219_Q	1.771	1.00
247_L	252_E	1.765	1.00
137_F	178_I	1.752	1.00
137_F	163_M	1.724	1.00
187_S	248_C	1.704	1.00
124_F	274_G	1.600	1.00
229_R	233_M	1.574	1.00
89_N	157_K	1.570	1.00
133_V	228_N	1.570	1.00
155_T	228_N	1.567	1.00
162_E	165_K	1.553	1.00
41_V	64_K	1.548	1.00
173_S	178_I	1.533	1.00
34_F	271_S	1.526	1.00
186_I	250_E	1.524	1.00
139_D	143_S	1.487	1.00
247_L	256_F	1.478	1.00
90_R	112_A	1.467	1.00
41_V	61_D	1.447	1.00
164_V	235_S	1.441	1.00
247_L	255_L	1.439	1.00
147_V	273_I	1.437	1.00
158_Q	161_R	1.431	1.00
140_P	177_D	1.428	1.00
48_S	257_Y	1.426	1.00
180_A	232_L	1.413	1.00
30_V	275_M	1.412	1.00
198_M	202_R	1.409	1.00
225_K	244_V	1.393	1.00
198_M	212_A	1.379	1.00
145_V	273_I	1.365	1.00
229_R	244_V	1.364	1.00
198_M	220_Y	1.359	1.00
59_D	63_V	1.340	1.00
194_D	197_V	1.339	1.00
46_F	265_K	1.334	1.00
93_K	119_N	1.317	1.00
41_V	68_Y	1.314	1.00
92_Q	113_T	1.304	1.00
116_I	125_L	1.291	1.00
156_V	201_V	1.291	1.00
117_Y	146_G	1.281	1.00
150_A	228_N	1.280	1.00
126_A	270_M	1.279	1.00
148_A	160_G	1.260	1.00
192_T	219_Q	1.259	1.00
190_C	250_E	1.258	1.00
96_Q	120_E	1.258	1.00
140_P	179_Y	1.256	1.00
136_F	271_S	1.250	1.00
80_W	126_A	1.246	1.00
86_T	112_A	1.245	1.00
142_K	173_S	1.243	1.00
136_F	273_I	1.235	1.00
83_A	116_I	1.223	1.00
144_L	173_S	1.198	1.00
226_E	230_L	1.196	1.00
160_G	228_N	1.196	1.00
238_A	241_Q	1.187	1.00
75_T	124_F	1.187	1.00
69_I	272_F	1.185	1.00
51_T	69_I	1.178	1.00
93_K	171_E	1.171	1.00
187_S	251_S	1.171	1.00
34_F	269_M	1.169	1.00
225_K	245_S	1.168	1.00
91_V	162_E	1.164	1.00
94_V	116_I	1.161	1.00
125_L	145_V	1.157	1.00
38_N	255_L	1.148	1.00
199_D	203_A	1.148	1.00
259_H	266_T	1.144	1.00
140_P	241_Q	1.138	1.00
83_A	127_L	1.128	1.00
83_A	113_T	1.125	1.00
51_T	270_M	1.123	1.00
134_P	183_G	1.122	1.00
82_F	126_A	1.121	1.00
248_C	251_S	1.120	1.00
117_Y	167_W	1.108	1.00
168_T	175_P	1.107	1.00
153_K	157_K	1.101	0.99
180_A	237_L	1.078	0.99
55_V	266_T	1.072	0.99
35_T	272_F	1.057	0.99
164_V	237_L	1.047	0.99
118_T	123_V	1.042	0.99
139_D	275_M	1.037	0.99
127_L	147_V	1.033	0.99
95_T	98_D	1.028	0.99
139_D	167_W	1.028	0.99
146_G	163_M	1.024	0.99
138_Y	179_Y	1.023	0.99
124_F	272_F	1.022	0.99
188_G	223_D	1.019	0.99
139_D	144_L	1.012	0.99
173_S	177_D	1.010	0.99
214_Q	221_Q	1.009	0.99
115_G	159_I	1.001	0.99
26_N	179_Y	0.992	0.99
223_D	226_E	0.984	0.99
54_H	84_D	0.968	0.99
118_T	125_L	0.966	0.99
76_D	79_S	0.957	0.99
27_N	30_V	0.954	0.99
79_S	99_R	0.947	0.98
179_Y	241_Q	0.944	0.98
211_A	226_E	0.944	0.98
165_K	169_E	0.939	0.98
39_G	42_S	0.936	0.98
49_L	68_Y	0.926	0.98
29_E	275_M	0.925	0.98
27_N	138_Y	0.924	0.98
133_V	182_I	0.923	0.98
34_F	181_V	0.921	0.98
166_Q	169_E	0.910	0.98
211_A	230_L	0.910	0.98
165_K	235_S	0.910	0.98
165_K	168_T	0.905	0.98
70_A	80_W	0.904	0.98
250_E	261_R	0.901	0.98
195_D	220_Y	0.898	0.98
128_C	270_M	0.897	0.98
93_K	117_Y	0.891	0.98
29_E	138_Y	0.890	0.98
262_D	266_T	0.884	0.98
253_P	261_R	0.880	0.98
81_V	123_V	0.879	0.97
75_T	274_G	0.873	0.97
156_V	200_A	0.871	0.97
224_L	250_E	0.869	0.97
135_L	148_A	0.867	0.97
54_H	128_C	0.860	0.97
94_V	125_L	0.860	0.97
129_F	147_V	0.857	0.97
208_A	227_L	0.856	0.97
91_V	163_M	0.852	0.97
55_V	268_R	0.848	0.97
117_Y	166_Q	0.848	0.97
137_F	160_G	0.844	0.97
139_D	173_S	0.843	0.97
158_Q	231_I	0.831	0.96
117_Y	144_L	0.821	0.96
201_V	205_P	0.820	0.96
207_S	230_L	0.817	0.96
153_K	200_A	0.814	0.96
83_A	128_C	0.814	0.96
95_T	120_E	0.811	0.96
214_Q	217_K	0.810	0.96
159_I	162_E	0.807	0.96
174_N	177_D	0.803	0.96
135_L	180_A	0.793	0.95
180_A	235_S	0.783	0.95
76_D	80_W	0.783	0.95
82_F	128_C	0.782	0.95
230_L	234_D	0.778	0.95
90_R	113_T	0.776	0.95
197_V	200_A	0.776	0.95
74_N	77_L	0.776	0.95
225_K	247_L	0.775	0.95
142_K	177_D	0.773	0.95
158_Q	234_D	0.761	0.94
253_P	262_D	0.760	0.94
81_V	98_D	0.755	0.94
30_V	138_Y	0.753	0.94
40_G	57_D	0.751	0.94
33_G	272_F	0.747	0.94
39_G	48_S	0.744	0.94
155_T	227_L	0.744	0.94
91_V	117_Y	0.743	0.94
94_V	123_V	0.743	0.94
67_E	71_D	0.742	0.93
88_D	157_K	0.741	0.93
119_N	171_E	0.740	0.93
120_E	123_V	0.738	0.93
233_M	242_I	0.735	0.93
33_G	73_F	0.735	0.93
55_V	62_V	0.730	0.93
54_H	66_R	0.729	0.93
143_S	275_M	0.728	0.93
156_V	197_V	0.728	0.93
158_Q	204_L	0.728	0.93
117_Y	163_M	0.727	0.93
52_G	55_V	0.727	0.93
119_N	144_L	0.726	0.93
93_K	169_E	0.721	0.92
191_Y	250_E	0.718	0.92
31_I	274_G	0.717	0.92
93_K	166_Q	0.716	0.92
213_N	221_Q	0.716	0.92
259_H	262_D	0.716	0.92
133_V	224_L	0.712	0.92
150_A	155_T	0.712	0.92
200_A	203_A	0.709	0.92
144_L	178_I	0.708	0.92
42_S	65_N	0.707	0.92
125_L	146_G	0.706	0.92
89_N	159_I	0.702	0.91
188_G	225_K	0.700	0.91
252_E	256_F	0.693	0.91
57_D	62_V	0.693	0.91
150_A	154_G	0.687	0.91
34_F	184_P	0.681	0.90
195_D	198_M	0.680	0.90
75_T	80_W	0.676	0.90
161_R	165_K	0.672	0.90
231_I	235_S	0.670	0.89
40_G	65_N	0.670	0.89
181_V	243_S	0.669	0.89
229_R	242_I	0.665	0.89
138_Y	143_S	0.664	0.89
95_T	119_N	0.662	0.89
138_Y	275_M	0.660	0.89
121_K	143_S	0.659	0.89
167_W	178_I	0.659	0.89
35_T	51_T	0.657	0.89
61_D	64_K	0.653	0.88
205_P	230_L	0.651	0.88
139_D	142_K	0.651	0.88
186_I	191_Y	0.648	0.88
215_T	219_Q	0.648	0.88
66_R	268_R	0.646	0.88
152_W	197_V	0.646	0.88
127_L	271_S	0.645	0.88
53_L	59_D	0.645	0.88
222_L	227_L	0.644	0.88
182_I	244_V	0.642	0.87
53_L	66_R	0.641	0.87
53_L	84_D	0.640	0.87
237_L	242_I	0.638	0.87
187_S	250_E	0.636	0.87
129_F	269_M	0.633	0.87
38_N	48_S	0.632	0.87
213_N	216_A	0.631	0.86
45_P	265_K	0.631	0.86
50_N	57_D	0.628	0.86
84_D	111_K	0.628	0.86
213_N	217_K	0.628	0.86
45_P	266_T	0.625	0.86
228_N	231_I	0.624	0.86
32_A	181_V	0.623	0.86
77_L	80_W	0.622	0.86
188_G	221_Q	0.622	0.86
133_V	155_T	0.618	0.85
215_T	221_Q	0.616	0.85
195_D	218_A	0.615	0.85
244_V	247_L	0.614	0.85
197_V	201_V	0.613	0.85
208_A	231_I	0.611	0.85
150_A	159_I	0.605	0.84
81_V	94_V	0.604	0.84
147_V	271_S	0.604	0.84
214_Q	219_Q	0.604	0.84
52_G	268_R	0.601	0.84
205_P	231_I	0.601	0.84
139_D	177_D	0.599	0.84
150_A	224_L	0.599	0.84
82_F	270_M	0.596	0.83
129_F	134_P	0.595	0.83
63_V	67_E	0.595	0.83
191_Y	219_Q	0.595	0.83
194_D	219_Q	0.593	0.83
230_L	233_M	0.592	0.83
76_D	124_F	0.588	0.82
185_S	244_V	0.584	0.82
39_G	65_N	0.582	0.82
69_I	270_M	0.580	0.82
90_R	162_E	0.579	0.81
121_K	275_M	0.577	0.81
157_K	200_A	0.575	0.81
93_K	144_L	0.573	0.81
144_L	171_E	0.568	0.80
205_P	234_D	0.564	0.80
91_V	166_Q	0.562	0.80
68_Y	71_D	0.561	0.79
192_T	221_Q	0.561	0.79
91_V	115_G	0.560	0.79
155_T	160_G	0.560	0.79
35_T	73_F	0.559	0.79
186_I	193_V	0.559	0.79
81_V	116_I	0.559	0.79
189_A	221_Q	0.558	0.79
259_H	265_K	0.558	0.79
186_I	224_L	0.557	0.79
36_T	256_F	0.557	0.79
75_T	272_F	0.554	0.79
126_A	272_F	0.551	0.78
210_L	230_L	0.549	0.78
115_G	129_F	0.548	0.78
110_L	113_T	0.546	0.78
208_A	230_L	0.545	0.77
88_D	112_A	0.543	0.77
70_A	79_S	0.537	0.76
75_T	79_S	0.537	0.76
168_T	174_N	0.531	0.76
88_D	154_G	0.531	0.76
152_W	221_Q	0.530	0.75
77_L	124_F	0.527	0.75
191_Y	221_Q	0.526	0.75
36_T	252_E	0.526	0.75
27_N	179_Y	0.525	0.75
43_Q	58_K	0.525	0.75
42_S	61_D	0.524	0.75
55_V	66_R	0.523	0.75
193_V	197_V	0.522	0.74
73_F	272_F	0.519	0.74
60_A	63_V	0.517	0.74
117_Y	171_E	0.517	0.74
196_R	200_A	0.515	0.73
207_S	234_D	0.515	0.73
156_V	204_L	0.515	0.73
136_F	269_M	0.512	0.73
189_A	250_E	0.512	0.73
195_D	219_Q	0.512	0.73
202_R	209_D	0.509	0.73
139_D	179_Y	0.509	0.73
161_R	235_S	0.508	0.72
195_D	217_K	0.507	0.72
92_Q	95_T	0.507	0.72
93_K	120_E	0.507	0.72
248_C	262_D	0.504	0.72
138_Y	142_K	0.501	0.71
179_Y	243_S	0.501	0.71
36_T	269_M	0.500	0.71

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
1t8hA	1	0.9748	100	0.103	Contact Map
1xfjA	1	0.9029	100	0.142	Contact Map
1z9tA	1	0.8633	100	0.158	Contact Map
1rv9A	1	0.8705	100	0.16	Contact Map
2f9zC	1	0.4784	34.5	0.965	Contact Map
1np7A	1	0.5827	23.3	0.968	Contact Map
1owlA	1	0.5647	14.5	0.971	Contact Map
3ch0A	1	0.3777	11.1	0.972	Contact Map
4g55A	1	0.2122	9.6	0.973	Contact Map
4k0rA	1	0.5144	7.8	0.974	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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