YMAD - BACSU - GREMLIN Contacts

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YMAD - Uncharacterized protein YmaD

UniProt:	O31790	Sequences: MADHHFYLKANWPGNRNDVGTIESGNLITSISIPKEMDGPGEGTNPDEMLLGAAATCYIITLAAMMERSGLEKEDLQMESEGIVNVTKGVFTYKKIIHRPSVVLKHDASQDDVALAHKLCKKAESSCMISRAIQGNVELQLEASVKLGGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	150 (135)
Sequences:	1028 (770)
Seq/√Len:	66.3

BACSU - YMAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_A	96_I	3.363	1.00
95_K	138_E	3.259	1.00
99_R	140_Q	2.866	1.00
96_I	133_I	2.768	1.00
54_A	137_V	2.632	1.00
62_L	116_A	2.582	1.00
121_K	125_S	2.516	1.00
51_L	82_G	2.408	1.00
16_R	28_I	2.379	1.00
92_T	131_R	2.170	1.00
112_D	115_L	2.127	1.00
124_E	139_L	2.084	1.00
64_A	68_R	1.995	1.00
9_K	79_E	1.975	1.00
75_D	103_V	1.954	1.00
82_G	96_I	1.901	1.00
51_L	96_I	1.873	1.00
87_T	92_T	1.844	1.00
65_M	119_L	1.790	1.00
122_K	125_S	1.726	1.00
5_H	81_E	1.725	1.00
15_N	18_D	1.632	0.99
106_H	112_D	1.631	0.99
61_T	65_M	1.605	0.99
87_T	90_V	1.586	0.99
66_M	71_L	1.579	0.99
104_L	112_D	1.575	0.99
113_V	117_H	1.561	0.99
23_E	26_N	1.522	0.99
83_I	97_I	1.521	0.99
50_L	135_G	1.502	0.99
19_V	22_I	1.493	0.99
65_M	126_S	1.492	0.99
14_G	74_E	1.484	0.99
22_I	26_N	1.438	0.98
53_A	61_T	1.432	0.98
44_T	48_E	1.400	0.98
54_A	133_I	1.397	0.98
97_I	140_Q	1.395	0.98
58_Y	120_C	1.383	0.98
107_D	111_D	1.355	0.97
79_E	101_S	1.334	0.97
90_V	131_R	1.329	0.97
77_Q	101_S	1.325	0.97
8_L	80_S	1.314	0.97
104_L	113_V	1.309	0.97
71_L	104_L	1.298	0.97
64_A	67_E	1.283	0.96
97_I	138_E	1.266	0.96
10_A	59_I	1.248	0.96
18_D	21_T	1.245	0.96
74_E	105_K	1.216	0.95
83_I	95_K	1.205	0.95
69_S	115_L	1.155	0.93
85_N	94_K	1.132	0.93
69_S	122_K	1.127	0.93
11_N	77_Q	1.121	0.92
81_E	99_R	1.119	0.92
115_L	118_K	1.107	0.92
48_E	56_T	1.097	0.92
31_I	56_T	1.094	0.91
54_A	128_M	1.081	0.91
122_K	126_S	1.065	0.90
40_P	61_T	1.054	0.90
119_L	123_A	1.052	0.90
6_F	93_Y	1.037	0.89
50_L	133_I	1.026	0.89
7_Y	81_E	1.026	0.89
8_L	44_T	1.018	0.88
58_Y	78_M	1.015	0.88
32_S	48_E	1.014	0.88
5_H	83_I	1.013	0.88
6_F	84_V	1.010	0.88
65_M	69_S	1.003	0.87
61_T	68_R	0.985	0.87
82_G	93_Y	0.974	0.86
114_A	117_H	0.958	0.85
10_A	55_A	0.956	0.85
9_K	77_Q	0.949	0.84
30_S	43_G	0.931	0.83
24_S	28_I	0.912	0.82
90_V	126_S	0.892	0.81
27_L	30_S	0.886	0.80
58_Y	130_S	0.885	0.80
66_M	131_R	0.870	0.79
34_P	37_M	0.868	0.79
44_T	56_T	0.866	0.79
40_P	43_G	0.864	0.78
106_H	111_D	0.861	0.78
11_N	75_D	0.861	0.78
59_I	78_M	0.861	0.78
22_I	28_I	0.856	0.78
44_T	52_G	0.855	0.78
39_G	45_N	0.853	0.77
18_D	29_T	0.843	0.77
101_S	142_E	0.812	0.74
53_A	86_V	0.809	0.74
56_T	59_I	0.809	0.74
50_L	137_V	0.805	0.73
92_T	134_Q	0.804	0.73
104_L	116_A	0.801	0.73
73_K	76_L	0.798	0.73
50_L	93_Y	0.798	0.73
14_G	20_G	0.784	0.71
117_H	121_K	0.783	0.71
50_L	54_A	0.759	0.69
101_S	121_K	0.758	0.69
7_Y	79_E	0.757	0.69
57_C	127_C	0.756	0.69
100_P	141_L	0.754	0.68
107_D	112_D	0.754	0.68
50_L	129_I	0.750	0.68
25_G	28_I	0.748	0.68
31_I	35_K	0.747	0.68
114_A	118_K	0.729	0.66
50_L	96_I	0.722	0.65
32_S	45_N	0.722	0.65
95_K	136_N	0.717	0.64
19_V	26_N	0.714	0.64
21_T	27_L	0.709	0.64
77_Q	103_V	0.709	0.64
67_E	119_L	0.709	0.64
21_T	26_N	0.706	0.63
129_I	137_V	0.706	0.63
63_A	76_L	0.700	0.63
24_S	64_A	0.698	0.62
46_P	57_C	0.697	0.62
8_L	59_I	0.693	0.62
129_I	133_I	0.692	0.62
78_M	98_H	0.680	0.60
34_P	39_G	0.677	0.60
74_E	103_V	0.673	0.60
63_A	73_K	0.665	0.59
27_L	40_P	0.651	0.57
76_L	120_C	0.650	0.57
19_V	23_E	0.646	0.56
6_F	34_P	0.646	0.56
61_T	64_A	0.642	0.56
61_T	93_Y	0.635	0.55
81_E	95_K	0.633	0.55
105_K	111_D	0.633	0.55
92_T	136_N	0.630	0.55
65_M	122_K	0.628	0.54
12_W	63_A	0.627	0.54
46_P	127_C	0.625	0.54
83_I	138_E	0.625	0.54
50_L	53_A	0.619	0.53
35_K	41_G	0.617	0.53
33_I	37_M	0.615	0.53
104_L	111_D	0.613	0.53
71_L	111_D	0.612	0.52
75_D	102_V	0.612	0.52
80_S	98_H	0.610	0.52
61_T	84_V	0.607	0.52
62_L	66_M	0.595	0.50
86_V	90_V	0.591	0.50
71_L	103_V	0.588	0.50
47_D	84_V	0.586	0.49
30_S	49_M	0.585	0.49
78_M	120_C	0.583	0.49
33_I	60_I	0.582	0.49
35_K	48_E	0.580	0.49
34_P	64_A	0.577	0.48
83_I	94_K	0.576	0.48
14_G	34_P	0.574	0.48
93_Y	135_G	0.573	0.48
130_S	139_L	0.572	0.48
81_E	138_E	0.571	0.48
103_V	142_E	0.569	0.47
33_I	63_A	0.567	0.47
12_W	100_P	0.565	0.47
71_L	115_L	0.561	0.46
73_K	78_M	0.560	0.46
66_M	73_K	0.560	0.46
13_P	103_V	0.558	0.46
6_F	33_I	0.556	0.46
59_I	76_L	0.554	0.46
111_D	116_A	0.552	0.45
113_V	116_A	0.548	0.45
72_E	105_K	0.547	0.45
21_T	24_S	0.543	0.44
22_I	68_R	0.543	0.44
106_H	113_V	0.538	0.44
72_E	83_I	0.534	0.43
34_P	128_M	0.531	0.43
45_N	51_L	0.530	0.43
33_I	39_G	0.530	0.43
48_E	89_G	0.528	0.43
37_M	84_V	0.527	0.42
69_S	118_K	0.526	0.42
117_H	142_E	0.524	0.42
7_Y	99_R	0.518	0.41
79_E	83_I	0.514	0.41
6_F	43_G	0.513	0.41
34_P	38_D	0.512	0.41
103_V	106_H	0.511	0.41
12_W	73_K	0.509	0.40
20_G	24_S	0.506	0.40
47_D	98_H	0.503	0.40
26_N	30_S	0.501	0.39
7_Y	142_E	0.501	0.39
15_N	21_T	0.500	0.39

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
2d7vA	2	0.9133	100	0.483	Contact Map
2onfA	2	0.9267	100	0.489	Contact Map
1nyeA	5	0.9333	99.9	0.5	Contact Map
2oplA	2	0.94	99.9	0.508	Contact Map
1qwiA	2	0.92	99.9	0.509	Contact Map
4nozA	2	0.9133	99.9	0.512	Contact Map
1ukkA	2	0.9133	99.9	0.513	Contact Map
1n2fA	2	0.92	99.9	0.516	Contact Map
3eerA	2	0.9133	99.9	0.518	Contact Map
1uspA	2	0.9067	99.9	0.518	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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