YDHY - ECOLI - GREMLIN Contacts

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YDHY - Uncharacterized ferredoxin-like protein YdhY

UniProt:	P0AAL6	Sequences: MNPVDRPLLDIGLTRLEFLRISGKGLAGLTIAPALLSLLGCKQEDIDSGTVGLINTPKGVLVTQRARCTGCHRCEISCTNFNDGSVGTFFSRIKIHRNYFFGDNGVGSGGGLYGDLNYTADTCRQCKEPQCMNVCPIGAITWQQKEGCITVDHKRCIGCSACTTACPWMMATVNTESKKSSKCVLCGECANACPTGALKIIEWKDITV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13959
Length:	208 (157)
Sequences:	1092 (640)
Seq/√Len:	51.1

ECOLI - YDHY NRFC YDHX HYBA FDOH FDNH YNFG DMSB HYDN HYCB YSAA HYFA YGFS NAPG
HALSA - DMSB
SULSO - Q97V38 Q97XX9 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
68_C	74_C	4.318	1.00
68_C	193_C	3.994	1.00
68_C	71_C	3.896	1.00
61_L	185_L	3.504	1.00
71_C	74_C	3.353	1.00
143_Q	146_E	3.329	1.00
60_V	203_W	3.204	1.00
71_C	193_C	3.180	1.00
57_P	202_E	3.168	1.00
134_V	161_A	3.115	1.00
140_I	171_A	3.080	1.00
74_C	193_C	2.856	1.00
63_T	198_L	2.789	1.00
160_S	175_T	2.745	1.00
190_A	198_L	2.671	1.00
163_T	180_S	2.664	1.00
79_T	84_G	2.648	1.00
58_K	127_K	2.518	1.00
77_S	192_A	2.274	1.00
69_T	195_T	2.171	1.00
92_R	95_I	2.047	1.00
160_S	173_V	2.008	1.00
202_E	205_D	1.913	0.99
129_P	132_M	1.887	0.99
77_S	188_E	1.799	0.99
173_V	180_S	1.791	0.99
134_V	165_A	1.790	0.99
63_T	120_A	1.564	0.98
174_N	181_S	1.527	0.97
135_C	156_C	1.415	0.95
99_Y	103_D	1.408	0.95
73_R	76_I	1.372	0.95
163_T	173_V	1.362	0.94
182_K	194_P	1.357	0.94
160_S	163_T	1.351	0.94
174_N	177_S	1.337	0.94
125_Q	149_I	1.318	0.93
140_I	151_V	1.309	0.93
122_T	185_L	1.305	0.93
54_I	145_K	1.278	0.92
135_C	162_C	1.254	0.92
73_R	80_N	1.253	0.92
82_N	184_V	1.247	0.91
155_R	160_S	1.240	0.91
156_C	162_C	1.237	0.91
70_G	74_C	1.213	0.90
133_N	175_T	1.204	0.90
144_Q	148_C	1.193	0.89
54_I	129_P	1.176	0.89
99_Y	114_G	1.170	0.88
80_N	192_A	1.155	0.88
81_F	188_E	1.125	0.86
70_G	193_C	1.104	0.85
70_G	197_A	1.103	0.85
94_K	97_R	1.103	0.85
47_D	50_T	1.077	0.84
73_R	125_Q	1.072	0.84
150_T	187_G	1.069	0.83
45_D	48_S	1.065	0.83
172_T	181_S	1.060	0.83
132_M	140_I	1.056	0.83
143_Q	149_I	1.055	0.83
47_D	52_G	1.043	0.82
130_Q	165_A	1.035	0.81
95_I	99_Y	1.030	0.81
50_T	53_L	0.979	0.78
86_V	89_F	0.972	0.77
171_A	202_E	0.967	0.77
95_I	101_F	0.966	0.77
164_T	174_N	0.960	0.76
112_L	115_D	0.943	0.75
153_H	187_G	0.941	0.75
124_R	140_I	0.941	0.75
180_S	184_V	0.938	0.75
96_H	101_F	0.934	0.74
82_N	118_Y	0.933	0.74
97_R	101_F	0.927	0.74
152_D	155_R	0.924	0.73
83_D	174_N	0.916	0.73
151_V	171_A	0.916	0.73
76_I	80_N	0.906	0.72
47_D	54_I	0.906	0.72
111_G	115_D	0.904	0.72
77_S	81_F	0.901	0.72
171_A	206_I	0.894	0.71
137_I	154_K	0.889	0.70
130_Q	171_A	0.867	0.69
97_R	169_M	0.866	0.68
63_T	122_T	0.865	0.68
48_S	53_L	0.865	0.68
142_W	146_E	0.854	0.67
163_T	178_K	0.852	0.67
186_C	189_C	0.847	0.67
73_R	195_T	0.838	0.66
67_R	170_M	0.838	0.66
46_I	128_E	0.812	0.63
124_R	170_M	0.810	0.63
48_S	51_V	0.809	0.63
172_T	180_S	0.803	0.63
59_G	146_E	0.802	0.62
144_Q	187_G	0.790	0.61
66_A	161_A	0.790	0.61
120_A	151_V	0.782	0.61
129_P	190_A	0.779	0.60
109_G	112_L	0.775	0.60
137_I	140_I	0.775	0.60
87_G	90_F	0.774	0.60
92_R	96_H	0.769	0.59
56_T	204_K	0.768	0.59
122_T	168_W	0.766	0.59
110_G	113_Y	0.766	0.59
91_S	94_K	0.765	0.59
58_K	142_W	0.763	0.59
46_I	55_N	0.758	0.58
70_G	81_F	0.757	0.58
45_D	50_T	0.755	0.58
73_R	194_P	0.754	0.58
150_T	184_V	0.752	0.58
159_C	165_A	0.751	0.57
46_I	125_Q	0.746	0.57
63_T	157_I	0.743	0.57
97_R	102_G	0.731	0.55
139_A	148_C	0.730	0.55
51_V	55_N	0.728	0.55
158_G	182_K	0.727	0.55
171_A	181_S	0.719	0.54
133_N	151_V	0.716	0.54
45_D	52_G	0.713	0.54
128_E	197_A	0.711	0.53
53_L	113_Y	0.707	0.53
83_D	181_S	0.706	0.53
51_V	128_E	0.694	0.52
134_V	171_A	0.687	0.51
128_E	133_N	0.685	0.51
135_C	158_G	0.684	0.51
134_V	140_I	0.683	0.50
147_G	182_K	0.682	0.50
148_C	187_G	0.680	0.50
48_S	115_D	0.671	0.49
128_E	176_E	0.664	0.48
83_D	153_H	0.663	0.48
145_K	187_G	0.663	0.48
137_I	159_C	0.662	0.48
130_Q	140_I	0.659	0.48
87_G	165_A	0.659	0.48
81_F	93_I	0.655	0.48
93_I	100_F	0.649	0.47
127_K	190_A	0.647	0.47
70_G	170_M	0.646	0.47
145_K	150_T	0.639	0.46
109_G	114_G	0.637	0.46
124_R	130_Q	0.628	0.45
189_C	193_C	0.627	0.45
65_R	117_N	0.625	0.44
61_L	122_T	0.624	0.44
135_C	159_C	0.623	0.44
53_L	191_N	0.619	0.44
184_V	187_G	0.616	0.44
66_A	111_G	0.616	0.44
151_V	161_A	0.614	0.43
158_G	162_C	0.614	0.43
45_D	49_G	0.610	0.43
59_G	148_C	0.606	0.42
46_I	54_I	0.605	0.42
56_T	138_G	0.604	0.42
93_I	101_F	0.604	0.42
50_T	154_K	0.603	0.42
92_R	97_R	0.601	0.42
55_N	145_K	0.601	0.42
61_L	120_A	0.600	0.42
161_A	184_V	0.592	0.41
121_D	185_L	0.590	0.41
122_T	140_I	0.586	0.40
156_C	159_C	0.585	0.40
47_D	51_V	0.580	0.40
51_V	54_I	0.580	0.40
82_N	161_A	0.579	0.40
174_N	182_K	0.576	0.39
145_K	205_D	0.573	0.39
160_S	178_K	0.571	0.39
92_R	101_F	0.568	0.39
202_E	206_I	0.565	0.38
183_C	189_C	0.563	0.38
61_L	168_W	0.562	0.38
90_F	111_G	0.562	0.38
163_T	190_A	0.562	0.38
67_R	152_D	0.562	0.38
175_T	178_K	0.562	0.38
51_V	112_L	0.561	0.38
60_V	133_N	0.560	0.38
49_G	204_K	0.559	0.38
150_T	199_K	0.556	0.38
118_Y	195_T	0.554	0.37
154_K	157_I	0.553	0.37
136_P	162_C	0.547	0.37
121_D	124_R	0.546	0.37
149_I	159_C	0.546	0.37
60_V	163_T	0.545	0.36
111_G	114_G	0.539	0.36
45_D	53_L	0.539	0.36
152_D	165_A	0.538	0.36
48_S	191_N	0.536	0.36
72_H	136_P	0.534	0.35
50_T	54_I	0.534	0.35
121_D	176_E	0.534	0.35
149_I	201_I	0.534	0.35
50_T	57_P	0.534	0.35
125_Q	182_K	0.534	0.35
45_D	67_R	0.533	0.35
60_V	160_S	0.526	0.35
45_D	117_N	0.525	0.35
64_Q	169_M	0.525	0.35
168_W	206_I	0.524	0.34
68_C	194_P	0.522	0.34
56_T	145_K	0.518	0.34
62_V	93_I	0.518	0.34
59_G	171_A	0.517	0.34
84_G	200_I	0.516	0.34
151_V	181_S	0.514	0.34
48_S	52_G	0.513	0.33
46_I	51_V	0.512	0.33
51_V	196_G	0.511	0.33
67_R	115_D	0.510	0.33
103_D	145_K	0.509	0.33
67_R	195_T	0.507	0.33
126_C	131_C	0.506	0.33
126_C	166_C	0.506	0.33
131_C	166_C	0.506	0.33
123_C	131_C	0.506	0.33
123_C	126_C	0.506	0.33
123_C	166_C	0.506	0.33
140_I	174_N	0.505	0.33
88_T	195_T	0.502	0.32
134_V	170_M	0.502	0.32
69_T	74_C	0.500	0.32
52_G	157_I	0.500	0.32

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	0.7356	100	0.477	Contact Map
1kqfB	3	0.851	100	0.487	Contact Map
1ti6B	2	0.6779	100	0.489	Contact Map
1h0hB	1	0.726	100	0.506	Contact Map
2vpzB	2	0.6779	100	0.538	Contact Map
1q16B	2	0.7452	100	0.566	Contact Map
4z3xE	2	0.6202	100	0.617	Contact Map
3mm5B	2	0.9087	99.7	0.736	Contact Map
3gyxB	1	0.2933	99.4	0.787	Contact Map
2c42A	2	0.9183	99.4	0.792	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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