YGCQ - ECOLI - GREMLIN Contacts

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YGCQ - Putative electron transfer flavoprotein subunit YgcQ

UniProt:	Q46907	Sequences: MNIAIVTINQENAAIASWLAAQDFSGCTLAHWQIEPQPVVAEQVLDALVEQWQRTPADVVLFPPGTFGDELSTRLAWRLHGASICQVTSLDIPTVSVRKSHWGNALTATLQTEKRPLCLSLARQAGAAKNATLPSGMQQLNIVPGALPDWLVSTEDLKNVTRDPLAEARRVLVVGQGGEADNQEIAMLAEKLGAEVGYSRARVMNGGVDAEKVIGISGHLLAPEVCIVVGASGAAALMAGVRNSKFVVAINHDASAAVFSQADVGVVDDWKVVLEALVTNIHADCQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13124
Length:	286 (274)
Sequences:	4076 (2432)
Seq/√Len:	146.9

ECOLI - YGCQ YDIR FIXB
BACSU - ETFA
HALSA - Q9HND2
SULSO - Q97V19 Q97V72

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
268_D	273_V	4.944	1.00
259_F	265_G	3.653	1.00
169_R	224_E	3.535	1.00
229_V	250_I	3.496	1.00
173_V	231_A	3.321	1.00
62_F	72_S	3.266	1.00
27_C	138_Q	3.168	1.00
171_V	221_L	2.720	1.00
229_V	274_L	2.622	1.00
174_V	183_Q	2.597	1.00
191_K	278_V	2.540	1.00
4_A	29_L	2.417	1.00
52_W	60_V	2.383	1.00
184_E	187_M	2.254	1.00
10_Q	32_W	2.233	1.00
246_F	264_V	2.197	1.00
208_V	212_K	2.156	1.00
198_Y	208_V	2.154	1.00
187_M	278_V	2.140	1.00
238_M	261_Q	2.094	1.00
153_S	156_D	2.089	1.00
249_A	262_A	2.070	1.00
10_Q	34_I	2.028	1.00
199_S	231_A	2.021	1.00
170_R	194_A	1.988	1.00
10_Q	37_Q	1.975	1.00
182_N	271_K	1.969	1.00
174_V	185_I	1.965	1.00
186_A	196_V	1.946	1.00
97_V	106_L	1.944	1.00
87_V	119_L	1.904	1.00
229_V	270_W	1.897	1.00
188_L	278_V	1.896	1.00
89_S	97_V	1.858	1.00
225_V	248_V	1.847	1.00
11_E	32_W	1.831	1.00
173_V	228_V	1.818	1.00
178_G	185_I	1.803	1.00
164_P	167_E	1.776	1.00
224_E	245_K	1.775	1.00
132_T	135_S	1.770	1.00
45_L	78_R	1.763	1.00
226_C	237_L	1.753	1.00
185_I	229_V	1.740	1.00
13_A	17_S	1.723	1.00
188_L	274_L	1.720	1.00
249_A	258_V	1.713	1.00
173_V	214_I	1.699	1.00
4_A	26_G	1.698	1.00
49_V	78_R	1.697	1.00
20_A	137_M	1.694	1.00
276_A	279_T	1.688	1.00
188_L	192_L	1.688	1.00
36_P	47_A	1.665	1.00
49_V	75_L	1.664	1.00
61_L	119_L	1.659	1.00
221_L	241_V	1.649	1.00
172_L	188_L	1.592	1.00
165_L	171_V	1.572	1.00
171_V	197_G	1.564	1.00
14_A	17_S	1.536	1.00
4_A	57_A	1.533	1.00
72_S	120_S	1.529	1.00
241_V	244_S	1.522	1.00
40_V	43_Q	1.491	1.00
209_D	212_K	1.471	1.00
41_A	70_E	1.464	1.00
50_E	54_R	1.456	1.00
183_Q	196_V	1.441	1.00
198_Y	202_R	1.434	1.00
20_A	28_T	1.409	1.00
186_A	190_E	1.404	1.00
7_T	15_I	1.388	1.00
187_M	191_K	1.355	1.00
178_G	182_N	1.343	1.00
21_A	131_A	1.339	1.00
162_R	190_E	1.336	1.00
191_K	281_I	1.327	1.00
44_V	71_L	1.323	1.00
20_A	135_S	1.320	1.00
91_D	97_V	1.320	1.00
75_L	118_C	1.314	1.00
228_V	231_A	1.309	1.00
178_G	270_W	1.305	1.00
18_W	21_A	1.300	1.00
13_A	139_Q	1.294	1.00
228_V	237_L	1.286	1.00
34_I	37_Q	1.282	1.00
48_L	75_L	1.280	1.00
197_G	214_I	1.278	1.00
276_A	280_N	1.267	1.00
84_I	112_T	1.264	1.00
31_H	47_A	1.258	1.00
198_Y	203_V	1.253	1.00
33_Q	36_P	1.252	1.00
266_V	273_V	1.238	1.00
88_T	97_V	1.235	1.00
180_A	184_E	1.231	1.00
272_V	276_A	1.229	1.00
38_P	154_T	1.225	1.00
58_D	116_P	1.219	1.00
16_A	20_A	1.214	1.00
86_Q	122_A	1.214	1.00
17_S	21_A	1.212	1.00
87_V	121_L	1.193	1.00
173_V	221_L	1.190	1.00
174_V	202_R	1.189	1.00
88_T	106_L	1.161	1.00
166_A	219_H	1.157	1.00
48_L	71_L	1.157	1.00
100_S	105_A	1.148	1.00
23_D	130_N	1.137	0.99
21_A	132_T	1.131	0.99
181_D	184_E	1.129	0.99
46_D	146_A	1.123	0.99
4_A	27_C	1.119	0.99
39_V	44_V	1.115	0.99
183_Q	202_R	1.110	0.99
29_L	140_L	1.110	0.99
45_L	75_L	1.101	0.99
173_V	199_S	1.100	0.99
13_A	32_W	1.099	0.99
259_F	267_V	1.092	0.99
18_W	131_A	1.084	0.99
8_I	44_V	1.084	0.99
29_L	55_T	1.080	0.99
270_W	275_E	1.067	0.99
268_D	272_V	1.066	0.99
165_L	197_G	1.060	0.99
151_L	154_T	1.059	0.99
177_G	207_G	1.057	0.99
274_L	278_V	1.047	0.99
12_N	30_A	1.047	0.99
203_V	213_V	1.041	0.99
199_S	214_I	1.040	0.99
190_E	193_G	1.023	0.99
179_E	271_K	1.023	0.99
79_L	118_C	1.017	0.99
174_V	178_G	1.014	0.99
91_D	109_T	1.012	0.99
8_I	47_A	1.012	0.99
180_A	208_V	1.011	0.99
45_L	74_R	1.008	0.99
201_A	205_N	1.003	0.99
72_S	83_S	1.002	0.99
5_I	19_L	1.002	0.99
173_V	197_G	0.996	0.99
250_I	273_V	0.995	0.99
15_I	18_W	0.985	0.99
84_I	87_V	0.983	0.98
49_V	79_L	0.977	0.98
222_A	243_N	0.974	0.98
214_I	228_V	0.968	0.98
189_A	196_V	0.965	0.98
174_V	208_V	0.964	0.98
52_W	79_L	0.964	0.98
26_G	135_S	0.963	0.98
180_A	207_G	0.963	0.98
123_R	220_L	0.955	0.98
22_Q	131_A	0.954	0.98
51_Q	140_L	0.954	0.98
195_E	212_K	0.954	0.98
94_T	111_Q	0.947	0.98
12_N	32_W	0.947	0.98
202_R	207_G	0.945	0.98
29_L	51_Q	0.944	0.98
202_R	208_V	0.940	0.98
81_G	118_C	0.939	0.98
165_L	219_H	0.929	0.98
185_I	196_V	0.924	0.98
74_R	78_R	0.922	0.98
46_D	50_E	0.918	0.98
83_S	120_S	0.917	0.98
6_V	48_L	0.915	0.98
83_S	118_C	0.914	0.98
183_Q	208_V	0.913	0.98
9_N	12_N	0.904	0.97
76_A	83_S	0.895	0.97
96_S	119_L	0.893	0.97
69_D	86_Q	0.892	0.97
227_I	250_I	0.877	0.97
20_A	132_T	0.872	0.97
12_N	15_I	0.868	0.97
82_A	114_K	0.855	0.96
46_D	143_V	0.854	0.96
90_L	96_S	0.843	0.96
6_V	51_Q	0.835	0.96
62_F	120_S	0.835	0.96
64_P	86_Q	0.834	0.96
22_Q	129_K	0.832	0.96
35_E	144_P	0.832	0.96
197_G	212_K	0.832	0.96
136_G	139_Q	0.830	0.96
8_I	36_P	0.830	0.96
87_V	90_L	0.827	0.96
54_R	138_Q	0.825	0.96
30_A	139_Q	0.825	0.96
177_G	182_N	0.818	0.95
178_G	271_K	0.816	0.95
64_P	68_G	0.809	0.95
177_G	180_A	0.807	0.95
5_I	25_S	0.806	0.95
187_M	196_V	0.798	0.95
13_A	30_A	0.789	0.94
87_V	96_S	0.789	0.94
52_W	116_P	0.785	0.94
99_K	122_A	0.783	0.94
58_D	115_R	0.781	0.94
39_V	70_E	0.780	0.94
223_P	244_S	0.778	0.94
17_S	20_A	0.773	0.94
94_T	117_L	0.773	0.94
39_V	71_L	0.771	0.94
41_A	74_R	0.769	0.94
96_S	117_L	0.767	0.93
178_G	183_Q	0.763	0.93
62_F	68_G	0.763	0.93
241_V	261_Q	0.761	0.93
204_M	213_V	0.756	0.93
108_A	112_T	0.756	0.93
16_A	28_T	0.750	0.93
9_N	32_W	0.747	0.93
16_A	139_Q	0.740	0.92
178_G	207_G	0.738	0.92
43_Q	147_L	0.737	0.92
21_A	134_P	0.734	0.92
20_A	25_S	0.730	0.92
199_S	238_M	0.730	0.92
137_M	140_L	0.729	0.92
7_T	28_T	0.727	0.92
21_A	130_N	0.724	0.91
23_D	132_T	0.720	0.91
35_E	147_L	0.719	0.91
18_W	22_Q	0.718	0.91
82_A	112_T	0.718	0.91
44_V	67_F	0.717	0.91
42_E	148_P	0.716	0.91
50_E	143_V	0.714	0.91
19_L	22_Q	0.713	0.91
68_G	71_L	0.712	0.91
171_V	195_E	0.711	0.91
21_A	133_L	0.711	0.91
132_T	137_M	0.708	0.90
109_T	112_T	0.708	0.90
176_Q	201_A	0.704	0.90
79_L	116_P	0.701	0.90
72_S	75_L	0.699	0.90
228_V	258_V	0.694	0.90
227_I	248_V	0.694	0.90
258_V	265_G	0.692	0.89
102_W	122_A	0.687	0.89
97_V	109_T	0.686	0.89
143_V	146_A	0.677	0.88
45_L	49_V	0.672	0.88
83_S	87_V	0.668	0.88
5_I	8_I	0.667	0.88
28_T	135_S	0.667	0.88
48_L	52_W	0.663	0.87
214_I	241_V	0.660	0.87
174_V	198_Y	0.660	0.87
52_W	57_A	0.660	0.87
183_Q	198_Y	0.656	0.87
170_R	193_G	0.654	0.87
269_D	272_V	0.653	0.87
40_V	151_L	0.653	0.87
182_N	187_M	0.652	0.86
27_C	136_G	0.652	0.86
95_V	109_T	0.652	0.86
50_E	141_N	0.650	0.86
246_F	263_D	0.647	0.86
173_V	237_L	0.645	0.86
8_I	48_L	0.645	0.86
19_L	28_T	0.641	0.86
43_Q	46_D	0.641	0.86
238_M	260_S	0.640	0.85
273_V	276_A	0.636	0.85
238_M	241_V	0.636	0.85
179_E	182_N	0.632	0.85
47_A	50_E	0.632	0.85
226_C	231_A	0.632	0.85
122_A	216_I	0.630	0.85
14_A	18_W	0.628	0.84
87_V	92_I	0.625	0.84
200_R	213_V	0.624	0.84
56_P	116_P	0.622	0.84
180_A	186_A	0.622	0.84
217_S	235_A	0.620	0.84
74_R	77_W	0.620	0.84
21_A	135_S	0.618	0.83
174_V	229_V	0.617	0.83
199_S	228_V	0.617	0.83
163_D	195_E	0.616	0.83
7_T	12_N	0.615	0.83
135_S	214_I	0.614	0.83
182_N	186_A	0.613	0.83
92_I	111_Q	0.613	0.83
177_G	199_S	0.609	0.83
38_P	151_L	0.608	0.82
191_K	194_A	0.607	0.82
178_G	274_L	0.606	0.82
62_F	75_L	0.605	0.82
112_T	117_L	0.605	0.82
96_S	121_L	0.604	0.82
20_A	134_P	0.604	0.82
221_L	244_S	0.604	0.82
164_P	219_H	0.603	0.82
39_V	67_F	0.601	0.82
92_I	95_V	0.599	0.82
158_K	254_A	0.597	0.81
257_A	260_S	0.596	0.81
172_L	196_V	0.596	0.81
183_Q	216_I	0.596	0.81
178_G	202_R	0.593	0.81
142_I	147_L	0.592	0.81
60_V	116_P	0.590	0.81
98_R	236_A	0.590	0.81
112_T	115_R	0.588	0.80
271_K	275_E	0.587	0.80
188_L	191_K	0.587	0.80
43_Q	145_G	0.587	0.80
144_P	147_L	0.585	0.80
84_I	96_S	0.584	0.80
192_L	227_I	0.584	0.80
162_R	186_A	0.583	0.80
25_S	28_T	0.582	0.80
199_S	239_A	0.581	0.80
172_L	191_K	0.578	0.79
172_L	274_L	0.578	0.79
36_P	43_Q	0.577	0.79
31_H	51_Q	0.576	0.79
249_A	259_F	0.576	0.79
173_V	226_C	0.574	0.79
264_V	271_K	0.572	0.78
172_L	278_V	0.572	0.78
170_R	192_L	0.571	0.78
31_H	50_E	0.571	0.78
62_F	71_L	0.571	0.78
60_V	118_C	0.570	0.78
52_W	118_C	0.569	0.78
81_G	114_K	0.568	0.78
69_D	85_C	0.567	0.78
156_D	159_N	0.566	0.78
51_Q	55_T	0.565	0.78
46_D	147_L	0.563	0.77
127_A	130_N	0.561	0.77
177_G	270_W	0.559	0.77
247_V	261_Q	0.558	0.77
170_R	224_E	0.556	0.77
204_M	210_A	0.554	0.76
254_A	257_A	0.554	0.76
7_T	16_A	0.552	0.76
59_V	117_L	0.551	0.76
198_Y	213_V	0.551	0.76
142_I	145_G	0.549	0.76
274_L	281_I	0.546	0.75
196_V	212_K	0.546	0.75
174_V	196_V	0.546	0.75
80_H	114_K	0.544	0.75
204_M	217_S	0.544	0.75
16_A	137_M	0.544	0.75
185_I	214_I	0.543	0.75
186_A	212_K	0.542	0.75
184_E	272_V	0.541	0.75
249_A	265_G	0.541	0.75
54_R	140_L	0.540	0.74
85_C	121_L	0.540	0.74
145_G	148_P	0.536	0.74
95_V	111_Q	0.534	0.74
154_T	157_L	0.533	0.74
67_F	71_L	0.533	0.74
46_D	71_L	0.533	0.74
84_I	194_A	0.531	0.73
253_D	256_A	0.531	0.73
106_L	109_T	0.530	0.73
171_V	214_I	0.529	0.73
177_G	267_V	0.529	0.73
29_L	138_Q	0.526	0.73
35_E	142_I	0.524	0.72
67_F	194_A	0.523	0.72
235_A	263_D	0.523	0.72
162_R	165_L	0.521	0.72
13_A	16_A	0.519	0.72
133_L	136_G	0.517	0.71
76_A	118_C	0.516	0.71
67_F	70_E	0.516	0.71
210_A	214_I	0.514	0.71
241_V	258_V	0.514	0.71
165_L	168_A	0.514	0.71
244_S	247_V	0.513	0.71
22_Q	130_N	0.513	0.71
90_L	109_T	0.512	0.71
173_V	241_V	0.511	0.70
14_A	141_N	0.511	0.70
221_L	261_Q	0.511	0.70
187_M	279_T	0.510	0.70
91_D	94_T	0.510	0.70
202_R	270_W	0.509	0.70
8_I	31_H	0.509	0.70
91_D	95_V	0.505	0.70
211_E	222_A	0.505	0.70
231_A	237_L	0.505	0.70
258_V	264_V	0.505	0.70
186_A	194_A	0.504	0.69
271_K	274_L	0.503	0.69
32_W	139_Q	0.502	0.69
170_R	225_V	0.502	0.69
12_N	37_Q	0.502	0.69
179_E	188_L	0.500	0.69
170_R	227_I	0.500	0.69
242_R	260_S	0.500	0.69
95_V	108_A	0.500	0.69

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
4l2iA	1	0.9895	100	0.06	Contact Map
1efvA	1	0.9755	100	0.068	Contact Map
1efpA	1	0.965	100	0.073	Contact Map
1o97D	1	0.958	100	0.075	Contact Map
3ih5A	6	0.5594	99.9	0.702	Contact Map
1efvB	1	0.6189	99.9	0.747	Contact Map
1efpB	1	0.5979	99.9	0.753	Contact Map
4l2iB	1	0.6434	99.8	0.761	Contact Map
1o97C	1	0.6154	99.8	0.761	Contact Map
3fetA	2	0.4755	99.8	0.769	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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