YGER - ECOLI - GREMLIN Contacts

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YGER - Uncharacterized lipoprotein YgeR

UniProt:	Q46798	Sequences: MSAGRLNKKSLGIVMLLSVGLLLAGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKLGGAKSSSITRKSTAKSTTKTASVTPSSAVPKSSWPPVGQRCWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAGKVVYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLPPQGSKPKC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13048
Length:	251 (204)
Sequences:	6709 (5589)
Seq/√Len:	391.3

ECOLI - YGER NLPD ENVC MEPM
BACSU - LYTH SP4FA SP2Q SAFA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_V	198_M	3.603	1.00
195_N	213_A	3.506	1.00
152_A	215_M	3.287	1.00
217_S	221_A	3.273	1.00
158_I	195_N	3.008	1.00
184_H	190_T	2.850	1.00
199_L	214_T	2.790	1.00
157_P	211_K	2.774	1.00
128_W	150_I	2.645	1.00
137_P	239_L	2.624	1.00
135_I	151_S	2.623	1.00
211_K	214_T	2.337	1.00
163_A	207_K	2.277	1.00
127_L	208_A	2.239	1.00
165_K	205_S	2.172	1.00
176_Y	193_A	2.110	1.00
154_R	223_V	2.047	1.00
149_D	226_H	2.023	1.00
200_V	204_Q	2.023	1.00
181_M	191_A	1.989	1.00
161_A	227_F	1.981	1.00
167_V	189_I	1.859	1.00
154_R	196_D	1.854	1.00
133_K	151_S	1.846	1.00
195_N	198_M	1.821	1.00
196_D	214_T	1.819	1.00
161_A	190_T	1.795	1.00
197_T	214_T	1.793	1.00
138_Y	235_A	1.782	1.00
152_A	156_T	1.776	1.00
160_A	182_I	1.747	1.00
215_M	223_V	1.743	1.00
42_Y	48_D	1.685	1.00
181_M	189_I	1.662	1.00
159_Y	211_K	1.653	1.00
190_T	229_I	1.638	1.00
179_L	191_A	1.596	1.00
167_V	183_K	1.551	1.00
90_S	94_R	1.526	1.00
207_K	210_Q	1.485	1.00
158_I	215_M	1.474	1.00
182_I	212_I	1.449	1.00
201_N	204_Q	1.443	1.00
188_Y	231_Y	1.438	1.00
230_R	235_A	1.430	1.00
132_G	150_I	1.427	1.00
153_P	156_T	1.414	1.00
162_G	208_A	1.401	1.00
78_V	82_L	1.392	1.00
171_N	178_N	1.381	1.00
136_M	141_A	1.379	1.00
42_Y	57_T	1.375	1.00
149_D	224_R	1.361	1.00
146_K	228_Q	1.353	1.00
148_I	239_L	1.347	1.00
237_D	240_R	1.342	1.00
89_S	93_T	1.325	1.00
168_Y	179_L	1.290	1.00
145_N	149_D	1.288	1.00
141_A	144_G	1.284	1.00
98_A	102_T	1.281	1.00
46_R	49_T	1.264	1.00
97_T	101_T	1.252	1.00
88_K	92_I	1.248	1.00
180_I	195_N	1.238	1.00
99_K	103_K	1.238	1.00
97_T	100_S	1.229	1.00
93_T	97_T	1.217	1.00
95_K	99_K	1.214	1.00
180_I	212_I	1.210	1.00
145_N	224_R	1.207	1.00
131_T	159_Y	1.179	1.00
86_G	90_S	1.167	1.00
95_K	98_A	1.142	1.00
63_E	67_L	1.129	1.00
164_G	182_I	1.128	1.00
57_T	60_S	1.120	1.00
199_L	211_K	1.119	1.00
199_L	213_A	1.116	1.00
179_L	193_A	1.114	1.00
130_T	152_A	1.102	1.00
92_I	96_S	1.088	1.00
86_G	89_S	1.085	1.00
188_Y	229_I	1.081	1.00
157_P	214_T	1.077	1.00
91_S	95_K	1.074	1.00
44_V	47_G	1.067	1.00
96_S	100_S	1.060	1.00
88_K	91_S	1.059	1.00
130_T	156_T	1.057	1.00
148_I	238_P	1.053	1.00
168_Y	181_M	1.051	1.00
161_A	192_Y	1.035	1.00
91_S	94_R	1.027	1.00
98_A	101_T	1.016	1.00
165_K	183_K	1.016	1.00
215_M	225_L	1.013	1.00
36_T	39_G	1.011	1.00
154_R	217_S	1.010	1.00
100_S	103_K	1.006	1.00
42_Y	45_K	1.001	1.00
87_A	91_S	0.996	1.00
92_I	95_K	0.995	1.00
77_E	80_Q	0.991	1.00
79_G	82_L	0.989	1.00
94_R	98_A	0.988	1.00
96_S	99_K	0.988	1.00
33_D	37_Y	0.986	1.00
236_I	241_Y	0.983	1.00
94_R	97_T	0.982	1.00
43_T	47_G	0.978	1.00
70_I	73_P	0.971	1.00
231_Y	236_I	0.969	1.00
40_S	44_V	0.962	1.00
193_A	228_Q	0.962	1.00
200_V	210_Q	0.960	1.00
52_R	56_T	0.960	1.00
76_I	80_Q	0.959	1.00
137_P	237_D	0.957	1.00
89_S	92_I	0.954	1.00
136_M	145_N	0.953	1.00
130_T	215_M	0.947	1.00
134_V	148_I	0.939	1.00
75_T	79_G	0.938	1.00
178_N	218_T	0.932	1.00
128_W	242_L	0.929	1.00
32_S	35_G	0.926	1.00
82_L	86_G	0.926	1.00
61_V	65_A	0.925	1.00
39_G	43_T	0.922	1.00
176_Y	230_R	0.907	1.00
194_H	219_D	0.906	1.00
163_A	208_A	0.896	1.00
49_T	52_R	0.888	1.00
90_S	93_T	0.885	1.00
183_K	187_D	0.884	1.00
99_K	102_T	0.882	1.00
126_W	188_Y	0.881	1.00
57_T	61_V	0.871	1.00
191_A	230_R	0.869	1.00
135_I	222_S	0.867	1.00
189_I	230_R	0.867	1.00
74_Y	78_V	0.866	1.00
74_Y	77_E	0.865	1.00
151_S	222_S	0.864	1.00
148_I	242_L	0.862	1.00
30_K	33_D	0.857	1.00
100_S	104_T	0.847	1.00
146_K	235_A	0.842	1.00
36_T	40_S	0.840	1.00
195_N	215_M	0.832	1.00
166_V	200_V	0.832	1.00
101_T	104_T	0.832	1.00
178_N	198_M	0.831	1.00
44_V	48_D	0.830	1.00
176_Y	191_A	0.830	1.00
54_S	57_T	0.830	1.00
87_A	90_S	0.827	1.00
68_N	71_S	0.824	1.00
156_T	215_M	0.823	1.00
194_H	218_T	0.821	1.00
85_G	88_K	0.817	1.00
125_C	162_G	0.814	1.00
221_A	224_R	0.811	1.00
35_G	38_S	0.799	1.00
176_Y	228_Q	0.796	1.00
168_Y	173_L	0.796	1.00
130_T	150_I	0.794	1.00
64_L	68_N	0.793	1.00
135_I	145_N	0.782	1.00
47_G	51_Y	0.781	1.00
63_E	66_R	0.777	1.00
38_S	42_Y	0.777	1.00
65_A	68_N	0.770	1.00
145_N	226_H	0.770	1.00
60_S	63_E	0.768	1.00
33_D	36_T	0.765	1.00
128_W	131_T	0.763	1.00
80_Q	84_L	0.757	1.00
143_G	220_A	0.752	1.00
217_S	223_V	0.746	1.00
194_H	224_R	0.741	1.00
35_G	39_G	0.735	1.00
195_N	225_L	0.734	1.00
62_K	66_R	0.731	1.00
80_Q	83_K	0.731	1.00
95_K	100_S	0.729	1.00
59_T	63_E	0.723	1.00
64_L	67_L	0.722	1.00
175_G	193_A	0.722	1.00
31_S	35_G	0.722	1.00
101_T	105_A	0.716	1.00
126_W	162_G	0.716	1.00
77_E	81_K	0.707	1.00
173_L	179_L	0.703	1.00
85_G	89_S	0.701	1.00
31_S	34_T	0.698	1.00
126_W	229_I	0.698	1.00
83_K	87_A	0.692	0.99
46_R	50_L	0.689	0.99
49_T	53_I	0.684	0.99
39_G	42_Y	0.682	0.99
92_I	99_K	0.678	0.99
163_A	205_S	0.676	0.99
124_R	162_G	0.672	0.99
155_G	196_D	0.670	0.99
162_G	184_H	0.668	0.99
58_G	61_V	0.665	0.99
40_S	43_T	0.665	0.99
48_D	52_R	0.665	0.99
139_S	144_G	0.662	0.99
93_T	96_S	0.658	0.99
169_V	200_V	0.657	0.99
138_Y	234_T	0.657	0.99
37_Y	40_S	0.653	0.99
45_K	49_T	0.653	0.99
135_I	224_R	0.653	0.99
126_W	190_T	0.652	0.99
176_Y	179_L	0.647	0.99
56_T	60_S	0.643	0.99
62_K	65_A	0.642	0.99
42_Y	46_R	0.642	0.99
134_V	137_P	0.641	0.99
134_V	239_L	0.637	0.99
76_I	79_G	0.636	0.99
127_L	161_A	0.636	0.99
228_Q	235_A	0.635	0.99
51_Y	55_R	0.634	0.99
81_K	84_L	0.631	0.99
95_K	103_K	0.630	0.99
91_S	98_A	0.628	0.99
181_M	230_R	0.627	0.99
149_D	194_H	0.627	0.99
140_T	143_G	0.626	0.99
191_A	228_Q	0.623	0.99
184_H	192_Y	0.623	0.99
127_L	159_Y	0.622	0.99
116_S	119_P	0.619	0.99
34_T	37_Y	0.614	0.99
188_Y	241_Y	0.610	0.99
91_S	99_K	0.607	0.99
30_K	34_T	0.607	0.99
183_K	189_I	0.606	0.99
190_T	227_F	0.605	0.99
121_V	125_C	0.603	0.99
155_G	214_T	0.602	0.99
227_F	242_L	0.602	0.99
58_G	62_K	0.602	0.99
183_K	232_R	0.598	0.99
187_D	231_Y	0.591	0.98
66_R	70_I	0.587	0.98
65_A	69_G	0.586	0.98
83_K	86_G	0.582	0.98
47_G	53_I	0.580	0.98
160_A	209_G	0.576	0.98
155_G	215_M	0.571	0.98
51_Y	54_S	0.571	0.98
43_T	81_K	0.569	0.98
195_N	199_L	0.569	0.98
139_S	143_G	0.567	0.98
180_I	200_V	0.567	0.98
123_Q	162_G	0.566	0.98
140_T	144_G	0.565	0.98
75_T	78_V	0.563	0.98
158_I	225_L	0.560	0.98
119_P	122_G	0.557	0.98
137_P	148_I	0.556	0.98
54_S	68_N	0.552	0.98
145_N	194_H	0.552	0.98
192_Y	227_F	0.551	0.98
39_G	46_R	0.548	0.97
54_S	58_G	0.545	0.97
136_M	149_D	0.545	0.97
32_S	36_T	0.544	0.97
79_G	83_K	0.544	0.97
119_P	124_R	0.539	0.97
140_T	146_K	0.539	0.97
41_V	44_V	0.539	0.97
134_V	150_I	0.538	0.97
152_A	155_G	0.537	0.97
167_V	202_N	0.536	0.97
118_W	121_V	0.535	0.97
122_G	162_G	0.535	0.97
41_V	81_K	0.532	0.97
46_R	60_S	0.531	0.97
99_K	104_T	0.531	0.97
168_Y	202_N	0.530	0.97
187_D	232_R	0.530	0.97
78_V	81_K	0.529	0.97
189_I	233_A	0.528	0.97
41_V	45_K	0.523	0.97
194_H	221_A	0.522	0.97
177_G	216_G	0.517	0.96
239_L	242_L	0.516	0.96
53_I	57_T	0.516	0.96
84_L	87_A	0.515	0.96
145_N	219_D	0.514	0.96
119_P	123_Q	0.511	0.96
158_I	213_A	0.510	0.96
53_I	60_S	0.509	0.96
88_K	95_K	0.508	0.96
102_T	105_A	0.507	0.96
193_A	230_R	0.506	0.96
231_Y	240_R	0.501	0.96
179_L	195_N	0.500	0.96
48_D	51_Y	0.500	0.96

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
4bh5A	4	0.502	100	0.372	Contact Map
2gu1A	1	0.9641	100	0.373	Contact Map
2hsiA	1	0.8008	100	0.379	Contact Map
3tufB	1	0.5139	100	0.392	Contact Map
1qwyA	1	0.7131	100	0.4	Contact Map
4rnzA	1	0.9562	100	0.41	Contact Map
3sluA	1	0.9761	100	0.413	Contact Map
3nyyA	2	0.8526	100	0.432	Contact Map
4qp5A	1	0.4821	100	0.448	Contact Map
4lxcA	4	0.5219	100	0.456	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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