YNFG - ECOLI - GREMLIN Contacts

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YNFG - Probable anaerobic dimethyl sulfoxide reductase chain YnfG

UniProt:	P0AAJ1	Sequences: MTTQYGFFIDSSRCTGCKTCELACKDFKDLGPEVSFRRIYEYAGGDWQEDNGVWHQNVFAYYLSISCNHCDDPACTKVCPSGAMHKREDGFVVVDEDVCIGCRYCHMACPYGAPQYNAEKGHMTKCDGCYSRVAEGKQPICVESCPLRALEFGPIEELRQKHGTLAAVAPLPRAHFTKPNIVIKPNANSRPTGDTTGYLANPEEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13845
Length:	205 (175)
Sequences:	3343 (1884)
Seq/√Len:	142.4

ECOLI - YNFG DMSB NRFC YDHX FDNH FDOH HYBA HYFA YDHY HYDN YSAA HYCB YGFS NARY NARH AEGA
BACSU - NARH
HALSA - DMSB
SULSO - Q97XX9 Q97V38 Q97V75

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_T	84_M	3.005	1.00
27_F	131_S	2.871	1.00
78_V	108_A	2.810	1.00
103_R	116_Y	2.772	1.00
71_D	180_N	2.531	1.00
139_P	142_V	2.477	1.00
106_H	123_M	2.382	1.00
84_M	114_P	2.373	1.00
73_P	86_K	2.305	1.00
7_F	128_G	2.271	1.00
84_M	94_V	2.159	1.00
130_Y	134_A	2.053	1.00
142_V	150_L	1.990	1.00
151_E	161_K	1.902	1.00
6_G	155_I	1.879	1.00
36_F	124_T	1.876	1.00
132_R	137_K	1.872	1.00
170_P	173_R	1.817	1.00
87_R	134_A	1.779	1.00
91_F	128_G	1.763	1.00
28_K	127_D	1.751	1.00
14_C	20_C	1.726	1.00
14_C	17_C	1.691	1.00
9_I	150_L	1.686	1.00
78_V	104_Y	1.680	1.00
79_C	99_C	1.665	1.00
103_R	106_H	1.663	1.00
85_H	93_V	1.662	1.00
18_K	21_E	1.653	1.00
17_C	20_C	1.650	1.00
15_T	147_L	1.636	1.00
79_C	105_C	1.631	1.00
132_R	143_E	1.629	1.00
117_N	124_T	1.617	1.00
91_F	133_V	1.609	1.00
27_F	132_R	1.607	1.00
4_Q	71_D	1.605	1.00
8_F	162_H	1.598	1.00
138_Q	143_E	1.585	1.00
72_D	77_K	1.577	1.00
103_R	118_A	1.573	1.00
155_I	159_R	1.569	1.00
116_Y	123_M	1.565	1.00
161_K	164_T	1.551	1.00
99_C	105_C	1.541	1.00
128_G	181_I	1.531	1.00
87_R	93_V	1.501	1.00
95_D	98_V	1.480	1.00
76_T	86_K	1.456	1.00
157_E	160_Q	1.453	1.00
23_A	144_S	1.448	1.00
85_H	95_D	1.440	1.00
153_G	157_E	1.407	1.00
114_P	123_M	1.404	1.00
170_P	178_K	1.375	1.00
14_C	145_C	1.358	1.00
36_F	39_I	1.355	1.00
117_N	120_K	1.350	1.00
8_F	184_K	1.347	1.00
161_K	165_L	1.332	1.00
93_V	130_Y	1.328	1.00
87_R	91_F	1.309	1.00
12_S	184_K	1.280	1.00
160_Q	163_G	1.278	1.00
159_R	164_T	1.266	1.00
66_S	181_I	1.266	1.00
28_K	131_S	1.263	1.00
53_V	56_Q	1.263	1.00
154_P	157_E	1.246	1.00
151_E	165_L	1.245	1.00
17_C	145_C	1.228	1.00
74_A	177_T	1.198	1.00
73_P	76_T	1.166	1.00
128_G	133_V	1.161	1.00
99_C	102_C	1.158	0.99
151_E	162_H	1.148	0.99
9_I	64_S	1.144	0.99
128_G	152_F	1.142	0.99
6_G	158_L	1.121	0.99
81_S	84_M	1.100	0.99
19_T	144_S	1.093	0.99
133_V	152_F	1.088	0.99
4_Q	180_N	1.053	0.99
20_C	145_C	1.053	0.99
170_P	182_V	1.043	0.99
172_P	175_H	1.040	0.99
163_G	167_A	1.029	0.99
66_S	150_L	1.021	0.99
11_S	64_S	1.014	0.99
72_D	178_K	1.011	0.99
163_G	166_A	1.005	0.99
74_A	108_A	1.000	0.99
27_F	140_I	0.992	0.98
7_F	142_V	0.990	0.98
103_R	123_M	0.986	0.98
39_I	45_G	0.978	0.98
137_K	143_E	0.978	0.98
83_A	98_V	0.975	0.98
79_C	102_C	0.974	0.98
170_P	175_H	0.966	0.98
102_C	105_C	0.961	0.98
65_I	171_L	0.953	0.98
64_S	150_L	0.938	0.98
104_Y	107_M	0.931	0.98
81_S	100_I	0.928	0.98
94_V	123_M	0.927	0.98
38_R	115_Q	0.923	0.97
96_E	122_H	0.922	0.97
53_V	57_N	0.915	0.97
93_V	127_D	0.901	0.97
132_R	140_I	0.899	0.97
176_F	183_I	0.899	0.97
37_R	150_L	0.887	0.97
166_A	182_V	0.886	0.97
160_Q	164_T	0.865	0.96
80_P	105_C	0.864	0.96
171_L	177_T	0.863	0.96
37_R	42_Y	0.853	0.96
39_I	42_Y	0.849	0.96
158_L	163_G	0.846	0.96
28_K	140_I	0.834	0.95
54_W	57_N	0.830	0.95
168_V	184_K	0.827	0.95
164_T	167_A	0.825	0.95
41_E	60_A	0.820	0.95
38_R	43_A	0.818	0.95
86_K	92_V	0.816	0.95
78_V	107_M	0.814	0.95
41_E	44_G	0.807	0.95
35_S	38_R	0.805	0.94
37_R	64_S	0.801	0.94
8_F	165_L	0.798	0.94
37_R	41_E	0.798	0.94
64_S	183_I	0.797	0.94
127_D	131_S	0.790	0.94
80_P	99_C	0.786	0.94
89_D	134_A	0.785	0.94
11_S	63_L	0.776	0.93
5_Y	152_F	0.775	0.93
9_I	66_S	0.771	0.93
116_Y	120_K	0.770	0.93
40_Y	44_G	0.770	0.93
106_H	118_A	0.769	0.93
30_L	36_F	0.765	0.93
176_F	179_P	0.764	0.93
91_F	130_Y	0.763	0.93
80_P	100_I	0.762	0.93
87_R	130_Y	0.759	0.93
13_R	149_A	0.757	0.92
139_P	150_L	0.752	0.92
6_G	180_N	0.751	0.92
38_R	42_Y	0.750	0.92
36_F	43_A	0.746	0.92
19_T	22_L	0.745	0.92
94_V	114_P	0.745	0.92
37_R	66_S	0.744	0.92
81_S	85_H	0.743	0.92
104_Y	108_A	0.740	0.92
5_Y	133_V	0.732	0.91
23_A	140_I	0.732	0.91
10_D	13_R	0.732	0.91
167_A	174_A	0.730	0.91
71_D	178_K	0.730	0.91
89_D	93_V	0.730	0.91
159_R	163_G	0.728	0.91
169_A	173_R	0.725	0.91
71_D	86_K	0.723	0.91
76_T	85_H	0.720	0.91
173_R	176_F	0.719	0.90
78_V	84_M	0.713	0.90
35_S	39_I	0.707	0.90
126_C	129_C	0.704	0.90
116_Y	121_G	0.699	0.89
39_I	43_A	0.691	0.89
43_A	60_A	0.690	0.89
15_T	146_P	0.687	0.88
138_Q	151_E	0.682	0.88
38_R	45_G	0.681	0.88
118_A	121_G	0.681	0.88
172_P	176_F	0.679	0.88
5_Y	91_F	0.679	0.88
162_H	165_L	0.677	0.88
19_T	26_D	0.663	0.87
117_N	121_G	0.656	0.86
45_G	56_Q	0.651	0.86
5_Y	89_D	0.648	0.85
81_S	94_V	0.646	0.85
158_L	162_H	0.635	0.84
19_T	140_I	0.634	0.84
35_S	40_Y	0.632	0.84
81_S	102_C	0.631	0.84
4_Q	86_K	0.625	0.83
86_K	91_F	0.625	0.83
100_I	104_Y	0.625	0.83
82_G	98_V	0.624	0.83
10_D	165_L	0.624	0.83
125_K	129_C	0.623	0.83
165_L	184_K	0.623	0.83
34_V	37_R	0.622	0.83
138_Q	142_V	0.617	0.82
27_F	127_D	0.616	0.82
8_F	160_Q	0.612	0.82
81_S	98_V	0.610	0.82
4_Q	156_E	0.608	0.81
25_K	30_L	0.600	0.81
148_R	151_E	0.599	0.80
9_I	181_I	0.598	0.80
45_G	58_V	0.596	0.80
115_Q	124_T	0.595	0.80
171_L	175_H	0.593	0.80
66_S	128_G	0.592	0.80
26_D	143_E	0.590	0.79
174_A	178_K	0.588	0.79
112_G	115_Q	0.587	0.79
73_P	114_P	0.587	0.79
96_E	120_K	0.586	0.79
38_R	65_I	0.585	0.79
19_T	146_P	0.585	0.79
64_S	68_N	0.584	0.79
45_G	55_H	0.582	0.79
37_R	44_G	0.581	0.78
100_I	105_C	0.570	0.77
36_F	41_E	0.569	0.77
16_G	20_C	0.568	0.77
68_N	113_A	0.567	0.77
37_R	43_A	0.566	0.77
7_F	64_S	0.561	0.76
65_I	68_N	0.560	0.76
175_H	178_K	0.558	0.76
44_G	61_Y	0.556	0.75
5_Y	154_P	0.556	0.75
111_Y	179_P	0.554	0.75
124_T	127_D	0.554	0.75
24_C	129_C	0.553	0.75
69_H	133_V	0.552	0.75
55_H	58_V	0.551	0.75
134_A	137_K	0.549	0.74
159_R	167_A	0.546	0.74
153_G	158_L	0.543	0.74
16_G	62_Y	0.541	0.73
87_R	133_V	0.538	0.73
39_I	44_G	0.538	0.73
16_G	149_A	0.537	0.73
169_A	172_P	0.537	0.73
158_L	161_K	0.535	0.73
12_S	182_V	0.532	0.72
103_R	124_T	0.531	0.72
103_R	107_M	0.526	0.71
162_H	166_A	0.525	0.71
7_F	66_S	0.523	0.71
169_A	184_K	0.523	0.71
33_E	36_F	0.522	0.71
80_P	102_C	0.521	0.71
85_H	98_V	0.521	0.71
15_T	18_K	0.513	0.69
179_P	183_I	0.511	0.69
69_H	92_V	0.507	0.69
35_S	42_Y	0.507	0.69
9_I	183_I	0.504	0.68
16_G	19_T	0.504	0.68
31_G	34_V	0.504	0.68
52_G	55_H	0.500	0.68

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
2ivfB	1	0.9902	100	0.349	Contact Map
1ti6B	2	0.9463	100	0.362	Contact Map
1kqfB	3	0.9902	100	0.403	Contact Map
2vpzB	2	0.922	100	0.408	Contact Map
1h0hB	1	0.9512	100	0.423	Contact Map
1q16B	2	1	100	0.436	Contact Map
4z3xE	2	0.8049	100	0.579	Contact Map
3mm5B	2	0.9756	99.8	0.684	Contact Map
1jnrB	1	0.678	99.5	0.761	Contact Map
3or1B	2	0.9463	99.4	0.771	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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