YXEM - BACSU - GREMLIN Contacts

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YXEM - Probable amino-acid-binding protein YxeM

UniProt:	P54952	Sequences: MKMKKWTVLVVAALLAVLSACGNGNSSSKEDDNVLHVGATGQSYPFAYKENGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIAQIKKTGLPLKLAGDPIVYEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	264 (241)
Sequences:	23361 (17022)
Seq/√Len:	1096.5

ECOLI - GLTI FLIY YHDW GLNH ARGT HISJ ARTJ ARTI MLTF EVGS
BACSU - YXEM TCYJ GLNH YCKB TCYK ARTP TCYA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_G	92_L	3.899	1.00
143_A	183_V	3.715	1.00
34_V	74_D	3.639	1.00
68_K	239_E	2.954	1.00
151_A	167_T	2.495	1.00
168_Y	177_D	2.472	1.00
50_E	55_T	2.389	1.00
86_E	92_L	2.322	1.00
113_K	238_D	2.320	1.00
101_V	106_K	2.318	1.00
36_H	74_D	2.286	1.00
170_T	173_G	2.232	1.00
34_V	72_K	2.225	1.00
101_V	217_A	2.173	1.00
36_H	76_K	2.141	1.00
151_A	155_E	2.112	1.00
245_T	248_K	2.109	1.00
103_D	106_K	2.108	1.00
247_K	251_E	2.081	1.00
64_A	67_K	2.060	1.00
66_A	73_L	2.045	1.00
88_Q	108_T	2.043	1.00
109_Y	219_P	2.010	1.00
141_T	166_K	2.007	1.00
220_F	230_R	1.972	1.00
230_R	234_N	1.971	1.00
238_D	242_K	1.967	1.00
110_N	230_R	1.962	1.00
133_S	136_D	1.951	1.00
68_K	236_A	1.944	1.00
188_N	193_L	1.880	1.00
174_T	186_Y	1.855	1.00
220_F	233_V	1.836	1.00
64_A	245_T	1.819	1.00
113_K	234_N	1.814	1.00
123_V	193_L	1.740	1.00
227_D	231_K	1.725	1.00
37_V	62_M	1.723	1.00
141_T	164_N	1.721	1.00
96_S	218_F	1.701	1.00
86_E	91_K	1.680	1.00
132_K	136_D	1.680	1.00
177_D	182_R	1.660	1.00
112_T	234_N	1.636	1.00
64_A	68_K	1.606	1.00
125_K	181_G	1.590	1.00
146_L	169_E	1.573	1.00
64_A	240_L	1.557	1.00
221_A	224_D	1.547	1.00
50_E	53_K	1.499	1.00
78_L	86_E	1.485	1.00
60_E	252_K	1.483	1.00
231_K	235_K	1.467	1.00
117_Y	215_Q	1.457	1.00
127_D	205_K	1.416	1.00
126_K	203_P	1.414	1.00
68_K	243_D	1.414	1.00
179_A	203_P	1.414	1.00
83_L	95_I	1.412	1.00
152_K	156_S	1.405	1.00
48_Y	55_T	1.402	1.00
223_D	227_D	1.395	1.00
232_K	235_K	1.377	1.00
84_M	109_Y	1.370	1.00
110_N	223_D	1.363	1.00
141_T	184_D	1.355	1.00
37_V	94_T	1.348	1.00
65_V	236_A	1.345	1.00
63_E	75_W	1.341	1.00
190_R	194_I	1.333	1.00
59_V	63_E	1.330	1.00
69_I	236_A	1.322	1.00
177_D	183_V	1.319	1.00
140_K	184_D	1.300	1.00
99_V	219_P	1.299	1.00
155_E	167_T	1.298	1.00
121_Q	190_R	1.293	1.00
58_D	115_Y	1.256	1.00
49_K	77_L	1.250	1.00
124_V	185_A	1.244	1.00
236_A	239_E	1.243	1.00
176_K	180_Y	1.243	1.00
27_S	31_D	1.229	1.00
126_K	205_K	1.228	1.00
120_T	150_H	1.226	1.00
169_E	173_G	1.212	1.00
41_G	77_L	1.208	1.00
178_V	204_L	1.207	1.00
122_I	185_A	1.201	1.00
239_E	243_D	1.188	1.00
62_M	96_S	1.186	1.00
144_A	151_A	1.183	1.00
90_G	221_A	1.178	1.00
143_A	168_Y	1.166	1.00
85_G	89_T	1.166	1.00
85_G	88_Q	1.164	1.00
142_V	185_A	1.164	1.00
236_A	240_L	1.158	1.00
110_N	227_D	1.155	1.00
104_E	107_E	1.154	1.00
79_E	82_G	1.153	1.00
26_S	29_K	1.149	1.00
95_I	99_V	1.148	1.00
153_N	157_K	1.142	1.00
33_N	71_M	1.131	1.00
241_R	246_L	1.129	1.00
57_F	249_L	1.117	1.00
78_L	92_L	1.106	1.00
121_Q	206_L	1.099	1.00
232_K	236_A	1.092	1.00
124_V	207_A	1.088	1.00
176_K	179_A	1.087	1.00
168_Y	174_T	1.061	1.00
57_F	254_F	1.052	1.00
57_F	250_S	1.050	1.00
178_V	186_Y	1.042	1.00
60_E	253_Y	1.039	1.00
63_E	67_K	1.039	1.00
227_D	230_R	1.038	1.00
71_M	232_K	1.035	1.00
28_S	32_D	1.029	1.00
37_V	73_L	1.023	1.00
235_K	239_E	1.018	1.00
62_M	75_W	1.018	1.00
110_N	222_K	1.009	1.00
178_V	183_V	1.009	1.00
68_K	245_T	1.000	1.00
145_V	148_S	1.000	1.00
62_M	73_L	1.000	1.00
49_K	52_G	1.000	1.00
18_L	21_C	0.995	1.00
102_T	105_R	0.994	1.00
245_T	249_L	0.992	1.00
94_T	233_V	0.990	1.00
55_T	60_E	0.988	1.00
61_V	246_L	0.988	1.00
146_L	167_T	0.986	1.00
53_K	63_E	0.974	1.00
61_V	240_L	0.970	1.00
60_E	63_E	0.965	1.00
143_A	174_T	0.965	1.00
228_K	232_K	0.954	1.00
24_G	228_K	0.951	1.00
173_G	176_K	0.941	1.00
94_T	220_F	0.937	1.00
54_L	59_V	0.936	1.00
65_V	233_V	0.935	1.00
195_A	199_K	0.925	1.00
27_S	30_E	0.925	1.00
84_M	99_V	0.923	1.00
32_D	36_H	0.919	1.00
152_K	155_E	0.907	1.00
88_Q	109_Y	0.904	1.00
240_L	245_T	0.898	1.00
234_N	238_D	0.894	1.00
111_F	219_P	0.892	1.00
248_K	251_E	0.889	1.00
82_G	86_E	0.888	1.00
57_F	246_L	0.885	1.00
251_E	255_N	0.881	1.00
13_A	16_A	0.870	1.00
153_N	156_S	0.868	1.00
80_F	83_L	0.865	1.00
234_N	237_L	0.861	1.00
49_K	54_L	0.860	1.00
112_T	233_V	0.860	1.00
44_Y	48_Y	0.858	1.00
135_D	138_K	0.856	1.00
224_D	227_D	0.853	1.00
246_L	250_S	0.852	1.00
248_K	252_K	0.848	1.00
113_K	241_R	0.847	1.00
41_G	54_L	0.845	1.00
118_A	191_T	0.844	1.00
119_G	190_R	0.841	1.00
158_D	163_I	0.840	1.00
25_N	28_S	0.836	1.00
172_E	176_K	0.835	1.00
62_M	218_F	0.835	1.00
103_D	107_E	0.832	1.00
124_V	205_K	0.828	1.00
166_K	177_D	0.823	1.00
159_P	163_I	0.821	1.00
35_L	71_M	0.819	1.00
46_F	116_A	0.814	1.00
95_I	219_P	0.810	1.00
94_T	218_F	0.802	1.00
122_I	187_V	0.799	1.00
106_K	222_K	0.796	1.00
17_V	20_A	0.795	1.00
39_A	75_W	0.795	1.00
29_K	32_D	0.793	1.00
240_L	243_D	0.792	1.00
100_A	214_E	0.791	1.00
239_E	242_K	0.790	1.00
69_I	232_K	0.787	1.00
30_E	33_N	0.785	1.00
171_Q	188_N	0.780	1.00
14_L	17_V	0.777	1.00
35_L	94_T	0.771	1.00
48_Y	253_Y	0.770	1.00
68_K	240_L	0.769	1.00
39_A	59_V	0.768	1.00
62_M	94_T	0.766	1.00
65_V	69_I	0.759	1.00
39_A	97_N	0.758	1.00
24_G	27_S	0.755	1.00
87_L	95_I	0.754	1.00
64_A	236_A	0.750	1.00
123_V	204_L	0.750	1.00
19_S	22_G	0.749	1.00
247_K	250_S	0.747	1.00
137_L	185_A	0.742	1.00
29_K	33_N	0.737	1.00
36_H	93_D	0.734	1.00
105_R	111_F	0.730	1.00
87_L	92_L	0.727	1.00
84_M	88_Q	0.716	1.00
24_G	28_S	0.713	1.00
235_K	238_D	0.712	1.00
76_K	91_K	0.712	1.00
175_L	179_A	0.711	1.00
194_I	206_L	0.710	1.00
63_E	73_L	0.709	1.00
250_S	254_F	0.709	1.00
125_K	203_P	0.708	1.00
34_V	71_M	0.707	1.00
240_L	246_L	0.705	1.00
240_L	244_G	0.705	1.00
143_A	177_D	0.704	1.00
228_K	231_K	0.704	1.00
118_A	190_R	0.702	1.00
29_K	71_M	0.702	1.00
40_T	47_A	0.696	1.00
35_L	66_A	0.696	1.00
38_G	83_L	0.695	1.00
175_L	204_L	0.691	1.00
87_L	109_Y	0.690	1.00
121_Q	208_G	0.688	1.00
100_A	105_R	0.685	1.00
101_V	114_P	0.684	1.00
119_G	213_Y	0.682	1.00
37_V	75_W	0.680	1.00
64_A	249_L	0.678	1.00
168_Y	183_V	0.674	1.00
26_S	30_E	0.672	1.00
112_T	220_F	0.672	1.00
78_L	83_L	0.671	1.00
112_T	218_F	0.670	1.00
218_F	233_V	0.670	1.00
11_V	14_L	0.668	1.00
194_I	198_K	0.666	1.00
119_G	212_V	0.661	1.00
43_S	98_Q	0.661	1.00
40_T	80_F	0.658	1.00
16_A	19_S	0.655	1.00
111_F	217_A	0.655	1.00
61_V	237_L	0.653	1.00
224_D	229_L	0.652	1.00
173_G	177_D	0.651	1.00
155_E	165_I	0.649	1.00
65_V	96_S	0.648	1.00
130_D	205_K	0.648	1.00
154_L	165_I	0.646	1.00
55_T	253_Y	0.644	1.00
123_V	175_L	0.642	1.00
121_Q	193_L	0.640	1.00
59_V	75_W	0.639	1.00
41_G	47_A	0.639	1.00
90_G	223_D	0.638	1.00
14_L	18_L	0.633	1.00
82_G	85_G	0.632	1.00
112_T	237_L	0.631	1.00
80_F	99_V	0.628	1.00
18_L	22_G	0.628	1.00
131_I	136_D	0.624	1.00
23_N	28_S	0.622	1.00
25_N	29_K	0.620	1.00
149_N	214_E	0.619	1.00
101_V	111_F	0.619	1.00
39_A	54_L	0.618	1.00
10_V	13_A	0.617	1.00
117_Y	213_Y	0.614	1.00
45_P	48_Y	0.612	1.00
141_T	183_V	0.611	1.00
201_G	204_L	0.605	1.00
10_V	14_L	0.604	1.00
156_S	159_P	0.603	1.00
16_A	21_C	0.602	1.00
144_A	167_T	0.601	1.00
66_A	71_M	0.600	1.00
238_D	241_R	0.598	1.00
231_K	234_N	0.597	1.00
114_P	117_Y	0.596	1.00
66_A	69_I	0.594	1.00
43_S	80_F	0.591	1.00
110_N	224_D	0.591	1.00
76_K	92_L	0.589	1.00
166_K	183_V	0.589	1.00
99_V	109_Y	0.588	1.00
88_Q	221_A	0.587	1.00
193_L	197_I	0.583	1.00
113_K	237_L	0.582	1.00
65_V	218_F	0.581	1.00
62_M	66_A	0.576	1.00
244_G	247_K	0.574	1.00
47_A	97_N	0.573	1.00
87_L	221_A	0.573	1.00
204_L	207_A	0.571	1.00
224_D	228_K	0.569	1.00
40_T	97_N	0.567	1.00
130_D	140_K	0.567	1.00
123_V	197_I	0.564	1.00
43_S	46_F	0.564	1.00
195_A	198_K	0.563	1.00
179_A	201_G	0.559	1.00
188_N	192_V	0.556	1.00
244_G	248_K	0.556	1.00
154_L	187_V	0.552	1.00
26_S	71_M	0.552	1.00
12_A	15_L	0.550	1.00
30_E	232_K	0.549	1.00
179_A	204_L	0.549	1.00
120_T	187_V	0.547	1.00
40_T	145_V	0.546	1.00
193_L	206_L	0.545	1.00
67_K	245_T	0.543	1.00
38_G	95_I	0.541	1.00
26_S	32_D	0.538	1.00
23_N	27_S	0.537	1.00
220_F	224_D	0.533	1.00
122_I	137_L	0.533	1.00
25_N	221_A	0.531	1.00
80_F	105_R	0.530	1.00
116_A	216_V	0.530	1.00
126_K	202_L	0.530	1.00
198_K	255_N	0.530	1.00
58_D	98_Q	0.528	1.00
197_I	204_L	0.526	1.00
123_V	206_L	0.525	1.00
112_T	230_R	0.523	1.00
138_K	160_D	0.522	1.00
66_A	70_D	0.521	1.00
119_G	210_P	0.521	1.00
240_L	249_L	0.521	1.00
106_K	110_N	0.521	1.00
69_I	229_L	0.520	1.00
183_V	186_Y	0.519	1.00
154_L	158_D	0.518	1.00
28_S	31_D	0.518	1.00
54_L	77_L	0.517	1.00
33_N	232_K	0.516	1.00
127_D	181_G	0.516	1.00
145_V	171_Q	0.513	1.00
11_V	15_L	0.511	1.00
83_L	99_V	0.510	1.00
38_G	78_L	0.509	1.00
36_H	90_G	0.506	1.00
177_D	180_Y	0.505	1.00
76_K	86_E	0.501	1.00
51_N	55_T	0.501	1.00
174_T	177_D	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
1xt8A	1	0.8598	100	0.282	Contact Map
4powA	1	0.8485	100	0.283	Contact Map
4ohnA	1	0.8939	100	0.285	Contact Map
3hv1A	2	0.9242	100	0.287	Contact Map
2ylnA	1	0.875	100	0.289	Contact Map
3kbrA	4	0.8523	100	0.29	Contact Map
1pb7A	1	0.9167	100	0.293	Contact Map
2vhaA	2	0.9205	100	0.294	Contact Map
3delB	1	0.8485	100	0.299	Contact Map
2yjpA	1	0.8826	100	0.299	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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