YGFM - ECOLI - GREMLIN Contacts

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YGFM - Uncharacterized protein YgfM

UniProt:	P64557	Sequences: MIEQFFRPDSVEQALELKRRYQDEAVWFAGGSKLNATPTRTDKKIAISLQDLELDWVDWDNGALRIGAMSRLQPLRDARFIPAALREALGFVYSRHVRNQSTIGGEIAARQEESVLLPVLLALDAELVFGNGETLSIEDYLACPCDRLLTEIIIKDPYRTCATRKISRSQAGLTVVTAAVAMTDHDGMRIALDGVASKALRLHDVEKQNLEGNALEQAVANAIFPQEDLRGSVAYKRYITGVLVADLYADCQQAGEEAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13063
Length:	259 (246)
Sequences:	5958 (4071)
Seq/√Len:	259.6

ECOLI - YGFM XDHB YAGS
BACSU - XDHC
SULSO - Q97VI7 Q97W13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_E	134_T	3.861	1.00
201_R	206_E	3.705	1.00
65_R	151_E	3.495	1.00
128_V	153_I	3.465	1.00
129_F	135_L	3.155	1.00
128_V	151_E	3.119	1.00
133_E	147_R	3.021	1.00
56_W	70_S	2.700	1.00
18_K	27_W	2.558	1.00
108_A	149_L	2.553	1.00
128_V	132_G	2.494	1.00
134_T	153_I	2.405	1.00
63_A	153_I	2.249	1.00
136_S	139_D	2.166	1.00
220_A	241_G	2.165	1.00
55_D	74_P	2.113	1.00
59_W	156_D	2.077	1.00
128_V	134_T	1.971	1.00
6_F	45_I	1.970	1.00
7_R	51_D	1.948	1.00
70_S	75_L	1.920	1.00
10_S	13_Q	1.881	1.00
130_G	150_T	1.879	1.00
73_Q	99_N	1.860	1.00
12_E	130_G	1.822	1.00
65_R	153_I	1.814	1.00
127_L	149_L	1.804	1.00
9_D	13_Q	1.775	1.00
183_T	187_G	1.763	1.00
124_D	138_E	1.739	1.00
21_Y	45_I	1.738	1.00
16_E	20_R	1.716	1.00
126_E	153_I	1.704	1.00
15_L	131_N	1.694	1.00
177_T	193_D	1.693	1.00
49_L	69_M	1.690	1.00
71_R	74_P	1.674	1.00
210_L	215_L	1.652	1.00
104_G	149_L	1.645	1.00
58_D	65_R	1.641	1.00
73_Q	77_D	1.625	1.00
164_R	250_D	1.615	1.00
66_I	75_L	1.604	1.00
216_E	245_A	1.575	1.00
126_E	136_S	1.564	1.00
6_F	17_L	1.563	1.00
18_K	47_I	1.557	1.00
132_G	150_T	1.556	1.00
192_L	202_L	1.538	1.00
182_M	188_M	1.538	1.00
63_A	156_D	1.470	1.00
27_W	148_L	1.466	1.00
138_E	203_H	1.464	1.00
59_W	80_F	1.438	1.00
17_L	47_I	1.437	1.00
28_F	46_A	1.433	1.00
115_V	165_K	1.423	1.00
180_V	247_L	1.419	1.00
127_L	137_I	1.419	1.00
27_W	49_L	1.417	1.00
64_L	81_I	1.415	1.00
212_G	249_A	1.396	1.00
118_P	193_D	1.388	1.00
204_D	207_K	1.373	1.00
204_D	222_A	1.371	1.00
238_Y	242_V	1.370	1.00
208_Q	214_A	1.351	1.00
14_A	148_L	1.347	1.00
24_E	44_K	1.339	1.00
180_V	190_I	1.331	1.00
164_R	246_D	1.325	1.00
26_V	41_T	1.324	1.00
212_G	216_E	1.324	1.00
219_V	244_V	1.311	1.00
11_V	148_L	1.304	1.00
211_E	214_A	1.294	1.00
25_A	47_I	1.294	1.00
192_L	240_T	1.288	1.00
11_V	130_G	1.288	1.00
29_A	69_M	1.280	1.00
103_I	152_I	1.266	1.00
50_Q	71_R	1.266	1.00
121_L	137_I	1.259	1.00
15_L	130_G	1.248	1.00
223_I	240_T	1.238	1.00
65_R	128_V	1.233	1.00
72_L	101_S	1.232	1.00
107_I	152_I	1.225	1.00
62_G	156_D	1.224	1.00
72_L	116_L	1.221	1.00
15_L	148_L	1.215	1.00
202_L	205_V	1.212	1.00
114_S	117_L	1.189	1.00
245_A	249_A	1.174	1.00
8_P	49_L	1.173	1.00
66_I	154_I	1.169	1.00
166_I	239_I	1.167	1.00
203_H	207_K	1.159	1.00
7_R	48_S	1.158	1.00
8_P	13_Q	1.157	1.00
122_A	191_A	1.155	1.00
13_Q	16_E	1.151	1.00
208_Q	217_Q	1.140	1.00
79_R	83_A	1.135	1.00
85_L	116_L	1.132	1.00
88_A	119_V	1.128	1.00
142_A	146_D	1.125	1.00
75_L	103_I	1.123	1.00
55_D	71_R	1.114	1.00
5_F	48_S	1.107	1.00
227_E	233_V	1.106	1.00
11_V	15_L	1.103	1.00
107_I	120_L	1.102	1.00
192_L	195_V	1.095	1.00
68_A	104_G	1.090	1.00
29_A	102_T	1.079	1.00
209_N	214_A	1.065	1.00
27_W	47_I	1.064	1.00
60_D	65_R	1.063	1.00
108_A	140_Y	1.063	1.00
57_V	70_S	1.060	1.00
117_L	141_L	1.053	1.00
73_Q	76_R	1.051	1.00
129_F	147_R	1.048	1.00
160_T	183_T	1.046	1.00
218_A	221_N	1.043	1.00
72_L	92_V	1.034	1.00
233_V	237_R	1.031	1.00
92_V	101_S	1.029	1.00
131_N	147_R	1.008	1.00
120_L	127_L	1.003	1.00
13_Q	17_L	0.999	1.00
85_L	119_V	0.997	1.00
56_W	151_E	0.995	1.00
87_E	250_D	0.994	1.00
28_F	31_G	0.993	1.00
31_G	35_N	0.993	1.00
174_T	177_T	0.988	1.00
242_V	246_D	0.986	1.00
205_V	222_A	0.976	1.00
202_L	222_A	0.975	1.00
63_A	155_K	0.957	1.00
247_L	251_C	0.950	1.00
9_D	51_D	0.948	1.00
55_D	69_M	0.942	1.00
238_Y	241_G	0.942	1.00
181_A	189_R	0.936	1.00
71_R	102_T	0.924	1.00
59_W	64_L	0.921	1.00
229_L	237_R	0.918	1.00
215_L	248_Y	0.916	1.00
210_L	214_A	0.913	1.00
158_Y	183_T	0.909	1.00
121_L	138_E	0.907	1.00
165_K	239_I	0.907	1.00
33_K	109_A	0.903	1.00
164_R	247_L	0.894	1.00
121_L	141_L	0.891	1.00
73_Q	95_R	0.881	1.00
127_L	140_Y	0.880	1.00
12_E	53_E	0.880	1.00
138_E	201_R	0.877	1.00
72_L	89_L	0.872	1.00
120_L	125_A	0.866	1.00
80_F	83_A	0.866	1.00
203_H	206_E	0.866	1.00
213_N	217_Q	0.865	1.00
190_I	205_V	0.864	1.00
66_I	103_I	0.862	1.00
195_V	240_T	0.855	1.00
79_R	82_P	0.847	0.99
178_A	243_L	0.846	0.99
214_A	217_Q	0.846	0.99
59_W	63_A	0.845	0.99
120_L	154_I	0.843	0.99
60_D	63_A	0.842	0.99
228_D	236_K	0.841	0.99
128_V	150_T	0.840	0.99
21_Y	24_E	0.836	0.99
49_L	148_L	0.833	0.99
192_L	244_V	0.832	0.99
28_F	34_L	0.831	0.99
157_P	160_T	0.829	0.99
103_I	116_L	0.829	0.99
231_G	236_K	0.826	0.99
11_V	53_E	0.826	0.99
137_I	141_L	0.823	0.99
129_F	133_E	0.818	0.99
124_D	201_R	0.815	0.99
22_Q	25_A	0.814	0.99
21_Y	25_A	0.812	0.99
70_S	103_I	0.812	0.99
166_I	243_L	0.812	0.99
54_L	69_M	0.810	0.99
164_R	243_L	0.807	0.99
204_D	221_N	0.806	0.99
87_E	161_C	0.804	0.99
76_R	90_G	0.796	0.99
84_A	161_C	0.796	0.99
87_E	162_A	0.796	0.99
12_E	16_E	0.796	0.99
11_V	54_L	0.795	0.99
50_Q	69_M	0.794	0.99
106_E	116_L	0.787	0.99
118_P	177_T	0.786	0.99
190_I	202_L	0.786	0.99
19_R	131_N	0.783	0.99
57_V	78_A	0.782	0.99
233_V	236_K	0.780	0.99
37_T	94_S	0.779	0.99
14_A	52_L	0.778	0.99
89_L	92_V	0.775	0.99
122_A	179_A	0.768	0.99
115_V	163_T	0.763	0.99
163_T	177_T	0.761	0.99
191_A	201_R	0.759	0.99
205_V	218_A	0.755	0.99
237_R	241_G	0.754	0.99
124_D	189_R	0.751	0.99
18_K	21_Y	0.751	0.99
33_K	111_Q	0.750	0.99
209_N	212_G	0.749	0.99
227_E	234_A	0.745	0.99
64_L	156_D	0.743	0.99
70_S	74_P	0.733	0.98
143_C	146_D	0.725	0.98
231_G	234_A	0.722	0.98
6_F	21_Y	0.721	0.98
14_A	27_W	0.717	0.98
109_A	114_S	0.715	0.98
17_L	21_Y	0.707	0.98
153_I	156_D	0.707	0.98
123_L	154_I	0.705	0.98
168_R	172_G	0.705	0.98
228_D	232_S	0.702	0.98
143_C	197_S	0.701	0.98
138_E	189_R	0.699	0.98
75_L	116_L	0.698	0.98
78_A	82_P	0.697	0.98
25_A	45_I	0.696	0.98
58_D	151_E	0.696	0.98
32_S	106_E	0.695	0.98
161_C	181_A	0.695	0.98
28_F	35_N	0.693	0.98
84_A	181_A	0.688	0.98
137_I	140_Y	0.687	0.98
76_R	89_L	0.687	0.98
103_I	120_L	0.685	0.98
208_Q	211_E	0.684	0.98
55_D	70_S	0.684	0.98
124_D	136_S	0.679	0.98
60_D	156_D	0.677	0.97
56_W	74_P	0.671	0.97
93_Y	97_V	0.670	0.97
229_L	234_A	0.670	0.97
111_Q	173_L	0.668	0.97
57_V	66_I	0.667	0.97
228_D	231_G	0.665	0.97
61_N	156_D	0.665	0.97
63_A	154_I	0.662	0.97
26_V	34_L	0.662	0.97
107_I	117_L	0.660	0.97
196_A	200_L	0.660	0.97
11_V	27_W	0.660	0.97
107_I	137_I	0.658	0.97
125_A	152_I	0.657	0.97
18_K	22_Q	0.654	0.97
168_R	173_L	0.645	0.97
76_R	95_R	0.644	0.97
141_L	199_A	0.642	0.97
8_P	11_V	0.641	0.96
84_A	123_L	0.640	0.96
94_S	165_K	0.634	0.96
125_A	154_I	0.632	0.96
200_L	223_I	0.626	0.96
176_V	195_V	0.624	0.96
11_V	14_A	0.623	0.96
70_S	104_G	0.619	0.96
29_A	49_L	0.618	0.96
189_R	201_R	0.618	0.96
72_L	93_Y	0.616	0.96
53_E	56_W	0.614	0.96
87_E	91_F	0.613	0.95
113_E	194_G	0.612	0.95
49_L	54_L	0.610	0.95
219_V	222_A	0.608	0.95
12_E	132_G	0.607	0.95
33_K	172_G	0.599	0.95
135_L	140_Y	0.598	0.95
102_T	105_G	0.596	0.95
242_V	245_A	0.593	0.95
196_A	199_A	0.592	0.95
32_S	94_S	0.591	0.94
54_L	68_A	0.590	0.94
21_Y	47_I	0.589	0.94
76_R	86_R	0.588	0.94
26_V	109_A	0.586	0.94
66_I	70_S	0.584	0.94
75_L	89_L	0.584	0.94
225_P	228_D	0.583	0.94
218_A	222_A	0.583	0.94
59_W	62_G	0.583	0.94
72_L	75_L	0.583	0.94
162_A	250_D	0.581	0.94
234_A	238_Y	0.580	0.94
188_M	206_E	0.580	0.94
109_A	145_C	0.579	0.94
239_I	243_L	0.578	0.94
212_G	245_A	0.577	0.94
6_F	13_Q	0.574	0.94
94_S	171_A	0.572	0.93
72_L	103_I	0.568	0.93
121_L	199_A	0.567	0.93
74_P	77_D	0.565	0.93
109_A	173_L	0.563	0.93
124_D	187_G	0.562	0.93
15_L	19_R	0.558	0.93
119_V	179_A	0.554	0.92
111_Q	145_C	0.553	0.92
173_L	194_G	0.552	0.92
37_T	115_V	0.552	0.92
157_P	181_A	0.551	0.92
114_S	173_L	0.551	0.92
48_S	100_Q	0.550	0.92
210_L	251_C	0.549	0.92
134_T	151_E	0.547	0.92
78_A	81_I	0.546	0.92
74_P	78_A	0.546	0.92
33_K	173_L	0.545	0.92
106_E	173_L	0.544	0.92
124_D	155_K	0.544	0.92
110_R	141_L	0.543	0.92
121_L	191_A	0.543	0.92
53_E	69_M	0.540	0.91
93_Y	171_A	0.539	0.91
143_C	198_K	0.538	0.91
234_A	237_R	0.538	0.91
21_Y	44_K	0.537	0.91
86_R	90_G	0.536	0.91
167_S	175_V	0.536	0.91
216_E	241_G	0.535	0.91
182_M	251_C	0.535	0.91
88_A	92_V	0.533	0.91
239_I	242_V	0.531	0.91
107_I	127_L	0.524	0.90
18_K	25_A	0.523	0.90
50_Q	100_Q	0.522	0.90
64_L	80_F	0.522	0.90
63_A	126_E	0.522	0.90
75_L	120_L	0.519	0.90
15_L	18_K	0.518	0.90
127_L	135_L	0.517	0.90
127_L	152_I	0.516	0.89
169_S	172_G	0.515	0.89
97_V	171_A	0.515	0.89
18_K	26_V	0.514	0.89
228_D	233_V	0.513	0.89
138_E	141_L	0.512	0.89
161_C	165_K	0.512	0.89
212_G	215_L	0.512	0.89
114_S	174_T	0.510	0.89
129_F	140_Y	0.510	0.89
43_K	46_A	0.507	0.89
142_A	197_S	0.506	0.89
144_P	196_A	0.505	0.88
94_S	97_V	0.502	0.88
141_L	198_K	0.501	0.88
127_L	141_L	0.500	0.88
112_E	228_D	0.500	0.88

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
1n62C	1	0.9846	100	0.2	Contact Map
1t3qC	1	0.9884	100	0.209	Contact Map
1rm6B	1	0.9691	100	0.218	Contact Map
1ffvC	1	0.9884	100	0.236	Contact Map
3hrdC	1	0.9884	100	0.246	Contact Map
3zyvA	3	0.9923	100	0.252	Contact Map
2w3sA	1	0.9807	100	0.258	Contact Map
3nvzB	1	0.9846	100	0.273	Contact Map
3uncA	2	0.9923	100	0.291	Contact Map
3tx1A	1	0.7722	98	0.872	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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