MODA - ECOLI - GREMLIN Contacts

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MODA - Molybdate-binding periplasmic protein

UniProt:	P37329	Sequences: MARKWLNLFAGAALSFAVAGNALADEGKITVFAAASLTNAMQDIATQFKKEKGVDVVSSFASSSTLARQIEAGAPADLFISADQKWMDYAVDKKAIDTATRQTLLGNSLVVVAPKASVQKDFTIDSKTNWTSLLNGGRLAVGDPEHVPAGIYAKEALQKLGAWDTLSPKLAPAEDVRGALALVERNEAPLGIVYGSDAVASKGVKVVATFPEDSHKKVEYPVAVVEGHNNATVKAFYDYLKGPQAAEIFKRYGFTIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12427
Length:	257 (238)
Sequences:	15970 (11567)
Seq/√Len:	749.8

ECOLI - MODA POTD THIB YDCS
BACSU - YVGL
HALSA - Y1595 Q9HMT5 Q9HR04 Q9HR87 Q9HNZ3 Q9HP00

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_Q	239_Y	3.311	1.00
28_K	57_V	3.196	1.00
140_A	188_A	2.935	1.00
30_T	57_V	2.924	1.00
54_V	232_T	2.767	1.00
115_K	207_V	2.762	1.00
71_E	93_K	2.645	1.00
97_D	231_A	2.543	1.00
222_V	237_Y	2.536	1.00
231_A	234_K	2.520	1.00
28_K	55_D	2.518	1.00
49_K	55_D	2.416	1.00
51_E	244_Q	2.271	1.00
51_E	242_G	2.155	1.00
61_A	65_T	2.120	1.00
45_A	236_F	2.053	1.00
138_R	189_P	2.043	1.00
96_I	223_A	2.027	1.00
116_A	205_K	1.998	1.00
234_K	238_D	1.976	1.00
27_G	232_T	1.965	1.00
117_S	189_P	1.957	1.00
242_G	245_A	1.938	1.00
42_Q	46_T	1.885	1.00
243_P	247_E	1.866	1.00
18_V	21_N	1.866	1.00
247_E	251_R	1.865	1.00
88_D	92_D	1.842	1.00
47_Q	248_I	1.812	1.00
48_F	54_V	1.811	1.00
232_T	235_A	1.807	1.00
47_Q	50_K	1.802	1.00
68_R	72_A	1.797	1.00
129_N	132_S	1.726	1.00
114_P	117_S	1.725	1.00
222_V	240_L	1.714	1.00
47_Q	51_E	1.708	1.00
45_A	49_K	1.698	1.00
224_V	234_K	1.655	1.00
235_A	238_D	1.649	1.00
125_D	212_E	1.645	1.00
90_A	96_I	1.595	1.00
47_Q	244_Q	1.554	1.00
224_V	233_V	1.550	1.00
29_I	232_T	1.538	1.00
46_T	50_K	1.538	1.00
43_D	251_R	1.534	1.00
45_A	58_S	1.534	1.00
45_A	56_V	1.496	1.00
80_I	222_V	1.481	1.00
154_K	158_Q	1.479	1.00
245_A	248_I	1.454	1.00
112_V	198_A	1.451	1.00
115_K	205_K	1.446	1.00
228_H	231_A	1.440	1.00
182_L	187_E	1.433	1.00
126_S	213_D	1.419	1.00
32_F	76_A	1.415	1.00
156_A	160_L	1.410	1.00
46_T	49_K	1.407	1.00
70_I	79_F	1.397	1.00
179_A	191_G	1.391	1.00
78_L	237_Y	1.368	1.00
224_V	237_Y	1.366	1.00
48_F	235_A	1.364	1.00
94_K	226_E	1.361	1.00
67_A	71_E	1.359	1.00
244_Q	247_E	1.359	1.00
45_A	55_D	1.349	1.00
97_D	226_E	1.342	1.00
38_T	42_Q	1.336	1.00
89_Y	93_K	1.311	1.00
155_E	216_K	1.306	1.00
248_I	251_R	1.284	1.00
14_L	17_A	1.283	1.00
157_L	162_A	1.274	1.00
149_A	152_Y	1.273	1.00
126_S	129_N	1.273	1.00
158_Q	162_A	1.269	1.00
164_D	168_P	1.268	1.00
16_F	19_A	1.266	1.00
49_K	52_K	1.261	1.00
193_V	198_A	1.243	1.00
103_T	219_E	1.239	1.00
91_V	96_I	1.237	1.00
54_V	235_A	1.233	1.00
52_K	235_A	1.229	1.00
125_D	129_N	1.228	1.00
164_D	167_S	1.220	1.00
165_T	168_P	1.203	1.00
48_F	239_Y	1.199	1.00
113_A	207_V	1.190	1.00
107_N	218_V	1.188	1.00
43_D	46_T	1.178	1.00
71_E	95_A	1.178	1.00
132_S	135_N	1.176	1.00
67_A	90_A	1.174	1.00
44_I	245_A	1.169	1.00
157_L	160_L	1.164	1.00
78_L	233_V	1.153	1.00
43_D	47_Q	1.145	1.00
44_I	239_Y	1.144	1.00
110_V	208_A	1.137	1.00
112_V	193_V	1.130	1.00
83_D	86_W	1.117	1.00
182_L	188_A	1.112	1.00
29_I	236_F	1.109	1.00
70_I	225_V	1.108	1.00
79_F	223_A	1.100	1.00
15_S	18_V	1.098	1.00
246_A	250_K	1.098	1.00
157_L	161_G	1.096	1.00
147_V	152_Y	1.095	1.00
47_Q	245_A	1.095	1.00
102_Q	241_K	1.091	1.00
239_Y	245_A	1.090	1.00
181_A	185_R	1.070	1.00
27_G	230_N	1.064	1.00
54_V	58_S	1.056	1.00
208_A	211_P	1.039	1.00
113_A	209_T	1.036	1.00
154_K	157_L	1.031	1.00
68_R	71_E	1.028	1.00
48_F	236_F	1.019	1.00
67_A	86_W	1.019	1.00
225_V	228_H	1.018	1.00
224_V	231_A	1.017	1.00
131_T	165_T	1.011	1.00
31_V	236_F	1.003	1.00
112_V	183_V	1.002	1.00
171_A	174_E	0.999	1.00
136_G	169_K	0.998	1.00
67_A	89_Y	0.998	1.00
156_A	162_A	0.985	1.00
148_P	151_I	0.982	1.00
124_I	129_N	0.979	1.00
156_A	159_K	0.976	1.00
87_M	223_A	0.974	1.00
48_F	232_T	0.971	1.00
131_T	166_L	0.968	1.00
12_A	15_S	0.964	1.00
148_P	152_Y	0.964	1.00
135_N	190_L	0.944	1.00
175_D	178_G	0.943	1.00
99_A	234_K	0.937	1.00
49_K	56_V	0.934	1.00
202_K	207_V	0.920	1.00
29_I	233_V	0.914	1.00
163_W	166_L	0.912	1.00
154_K	162_A	0.912	1.00
128_T	131_T	0.912	1.00
19_A	22_A	0.908	1.00
147_V	150_G	0.902	1.00
128_T	132_S	0.902	1.00
195_G	199_V	0.902	1.00
155_E	158_Q	0.899	1.00
69_Q	73_G	0.891	1.00
11_G	14_L	0.890	1.00
166_L	169_K	0.888	1.00
24_A	27_G	0.887	1.00
111_V	190_L	0.883	1.00
97_D	234_K	0.875	1.00
33_A	58_S	0.873	1.00
13_A	16_F	0.868	1.00
91_V	101_R	0.866	1.00
148_P	153_A	0.862	1.00
84_Q	219_E	0.861	1.00
108_S	195_G	0.861	1.00
51_E	239_Y	0.859	1.00
89_Y	92_D	0.856	1.00
126_S	212_E	0.856	1.00
173_A	182_L	0.852	1.00
29_I	56_V	0.850	1.00
113_A	123_T	0.846	1.00
163_W	167_S	0.839	1.00
238_D	241_K	0.828	1.00
159_K	162_A	0.827	1.00
174_E	178_G	0.824	1.00
245_A	249_F	0.824	1.00
27_G	54_V	0.821	1.00
19_A	23_L	0.816	1.00
240_L	245_A	0.810	1.00
78_L	236_F	0.809	1.00
155_E	159_K	0.809	1.00
41_M	44_I	0.807	1.00
59_S	69_Q	0.806	1.00
154_K	163_W	0.805	1.00
86_W	89_Y	0.800	1.00
79_F	90_A	0.799	1.00
63_S	81_S	0.792	1.00
228_H	233_V	0.792	1.00
105_L	249_F	0.791	1.00
118_V	135_N	0.785	1.00
165_T	169_K	0.782	1.00
147_V	151_I	0.781	1.00
184_E	201_S	0.779	1.00
194_Y	197_D	0.777	1.00
141_V	170_L	0.777	1.00
158_Q	161_G	0.776	1.00
77_D	228_H	0.774	1.00
132_S	136_G	0.769	1.00
206_V	211_P	0.766	1.00
77_D	230_N	0.766	1.00
119_Q	123_T	0.765	1.00
127_K	192_I	0.764	1.00
17_A	20_G	0.756	1.00
26_E	55_D	0.756	1.00
27_G	235_A	0.754	1.00
183_V	191_G	0.741	1.00
15_S	19_A	0.739	1.00
150_G	153_A	0.739	1.00
31_V	78_L	0.732	1.00
9_F	12_A	0.729	1.00
97_D	227_G	0.729	1.00
48_F	52_K	0.723	1.00
76_A	225_V	0.722	1.00
11_G	15_S	0.721	1.00
80_I	104_L	0.721	1.00
65_T	69_Q	0.717	1.00
10_A	14_L	0.716	1.00
10_A	13_A	0.715	1.00
112_V	206_V	0.715	1.00
90_A	95_A	0.714	1.00
99_A	238_D	0.714	1.00
32_F	59_S	0.713	1.00
71_E	89_Y	0.713	1.00
69_Q	72_A	0.711	1.00
156_A	161_G	0.708	1.00
178_G	181_A	0.707	1.00
97_D	228_H	0.707	1.00
31_V	58_S	0.706	1.00
70_I	95_A	0.704	1.00
100_T	234_K	0.704	1.00
12_A	16_F	0.703	1.00
114_P	205_K	0.702	1.00
43_D	248_I	0.699	1.00
23_L	26_E	0.698	1.00
180_L	184_E	0.695	1.00
224_V	228_H	0.694	1.00
103_T	107_N	0.692	1.00
22_A	26_E	0.691	1.00
25_D	28_K	0.689	1.00
118_V	123_T	0.687	1.00
103_T	221_P	0.686	1.00
149_A	153_A	0.681	1.00
42_Q	45_A	0.681	1.00
113_A	190_L	0.679	1.00
69_Q	74_A	0.675	1.00
139_L	190_L	0.675	1.00
52_K	232_T	0.670	1.00
172_P	176_V	0.667	1.00
173_A	178_G	0.665	1.00
181_A	184_E	0.664	1.00
247_E	250_K	0.664	1.00
22_A	25_D	0.663	1.00
199_V	202_K	0.662	1.00
87_M	221_P	0.661	1.00
44_I	47_Q	0.660	1.00
238_D	242_G	0.658	1.00
39_N	42_Q	0.656	1.00
21_N	25_D	0.653	1.00
84_Q	88_D	0.652	1.00
49_K	54_V	0.651	1.00
104_L	107_N	0.650	1.00
236_F	240_L	0.647	1.00
222_V	241_K	0.646	1.00
244_Q	248_I	0.645	1.00
141_V	153_A	0.640	1.00
67_A	93_K	0.636	1.00
119_Q	124_I	0.635	1.00
62_S	65_T	0.629	1.00
19_A	24_A	0.626	1.00
106_G	219_E	0.625	1.00
65_T	68_R	0.620	1.00
131_T	169_K	0.619	1.00
17_A	21_N	0.615	1.00
97_D	100_T	0.611	1.00
79_F	225_V	0.607	1.00
13_A	17_A	0.607	1.00
154_K	159_K	0.606	1.00
154_K	161_G	0.604	1.00
39_N	177_R	0.603	1.00
40_A	249_F	0.602	1.00
32_F	66_L	0.601	1.00
179_A	183_V	0.600	1.00
114_P	118_V	0.597	1.00
61_A	66_L	0.596	1.00
183_V	188_A	0.595	1.00
33_A	41_M	0.590	1.00
73_G	76_A	0.590	1.00
140_A	173_A	0.588	1.00
110_V	198_A	0.587	1.00
66_L	79_F	0.587	1.00
137_G	189_P	0.586	1.00
49_K	53_G	0.584	1.00
65_T	174_E	0.584	1.00
177_R	180_L	0.583	1.00
94_K	98_T	0.582	1.00
182_L	185_R	0.582	1.00
20_G	24_A	0.582	1.00
48_F	56_V	0.582	1.00
54_V	57_V	0.582	1.00
118_V	190_L	0.579	1.00
16_F	20_G	0.578	1.00
155_E	160_L	0.577	1.00
23_L	27_G	0.572	1.00
21_N	24_A	0.571	1.00
136_G	144_P	0.566	1.00
88_D	91_V	0.565	1.00
37_L	80_I	0.564	1.00
145_E	154_K	0.563	1.00
110_V	195_G	0.561	1.00
153_A	156_A	0.560	1.00
143_D	146_H	0.557	1.00
102_Q	238_D	0.555	1.00
26_E	230_N	0.553	1.00
31_V	56_V	0.553	1.00
66_L	81_S	0.551	1.00
51_E	235_A	0.550	1.00
52_K	56_V	0.545	1.00
237_Y	241_K	0.545	1.00
128_T	213_D	0.545	1.00
195_G	209_T	0.544	1.00
26_E	53_G	0.543	1.00
227_G	231_A	0.543	1.00
141_V	148_P	0.541	1.00
167_S	170_L	0.539	1.00
142_G	179_A	0.539	1.00
212_E	215_H	0.537	1.00
31_V	45_A	0.534	1.00
145_E	149_A	0.534	1.00
118_V	124_I	0.532	1.00
210_F	215_H	0.531	1.00
151_I	154_K	0.530	1.00
109_L	194_Y	0.530	1.00
61_A	69_Q	0.530	1.00
99_A	237_Y	0.529	1.00
71_E	90_A	0.526	1.00
105_L	220_Y	0.524	1.00
116_A	119_Q	0.524	1.00
103_T	106_G	0.522	1.00
106_G	217_K	0.522	1.00
42_Q	60_F	0.521	1.00
29_I	228_H	0.519	1.00
9_F	13_A	0.517	1.00
243_P	246_A	0.514	1.00
116_A	206_V	0.513	1.00
113_A	117_S	0.513	1.00
174_E	177_R	0.510	1.00
128_T	160_L	0.510	1.00
80_I	240_L	0.509	1.00
81_S	86_W	0.505	1.00
173_A	177_R	0.503	1.00
99_A	224_V	0.502	1.00
20_G	23_L	0.502	1.00
171_A	182_L	0.500	1.00
178_G	182_L	0.500	1.00

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
3r26A	1	0.8872	100	0.34	Contact Map
4rxlA	1	0.8755	100	0.365	Contact Map
3c9hA	1	0.9377	100	0.383	Contact Map
4edpA	1	0.8755	100	0.397	Contact Map
3rpwA	1	0.8833	100	0.414	Contact Map
3k6vA	1	0.8755	100	0.421	Contact Map
3gzgA	1	0.8988	100	0.425	Contact Map
3waeA	2	0.8872	100	0.429	Contact Map
2vozA	3	0.8755	100	0.437	Contact Map
4kd5C	3	0.8794	100	0.442	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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