YHDN - ECOLI - GREMLIN Contacts

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YHDN - Uncharacterized protein YhdN

UniProt:	P36677	Sequences: MWLLDQWAERHIAEAQAKGEFDNLAGSGEPLILDDDSHVPPELRAGYRLLKNAGCLPPELEQRREAIQLLDILKGIRHDDPQYQEVSRRLSLLELKLRQAGLSTDFLRGDYADKLLDKINDN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11970
Length:	122 (118)
Sequences:	375 (279)
Seq/√Len:	25.6

ECOLI - YHDN
BACSU - YFLB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_D	48_R	5.281	1.00
34_D	37_S	3.282	1.00
46_G	49_L	3.163	1.00
16_Q	21_F	3.092	1.00
58_P	61_E	2.920	1.00
43_L	72_I	2.746	0.99
94_E	98_R	2.490	0.99
56_L	60_L	2.335	0.98
93_L	97_L	2.166	0.97
61_E	64_R	2.117	0.97
57_P	60_L	1.953	0.95
15_A	20_E	1.912	0.94
58_P	100_A	1.864	0.93
14_E	18_K	1.832	0.92
22_D	27_S	1.821	0.92
56_L	73_L	1.784	0.91
14_E	69_L	1.761	0.91
7_W	10_R	1.756	0.91
80_D	86_V	1.704	0.89
91_S	98_R	1.703	0.89
43_L	47_Y	1.624	0.87
71_D	74_K	1.553	0.84
8_A	65_E	1.518	0.83
92_L	96_K	1.499	0.82
18_K	27_S	1.492	0.82
112_A	116_L	1.452	0.80
13_A	17_A	1.394	0.77
26_G	31_L	1.387	0.77
21_F	53_A	1.344	0.75
80_D	107_L	1.342	0.74
15_A	97_L	1.325	0.73
10_R	14_E	1.301	0.72
66_A	90_L	1.301	0.72
21_F	27_S	1.300	0.72
47_Y	72_I	1.272	0.70
9_E	23_N	1.261	0.70
97_L	101_G	1.255	0.69
46_G	50_L	1.249	0.69
33_L	37_S	1.246	0.69
39_V	57_P	1.224	0.67
16_Q	56_L	1.221	0.67
21_F	76_I	1.178	0.64
91_S	94_E	1.167	0.64
59_E	90_L	1.164	0.63
8_A	12_I	1.159	0.63
78_H	82_Q	1.155	0.63
4_L	70_L	1.152	0.62
10_R	13_A	1.143	0.62
89_R	93_L	1.142	0.62
113_D	117_D	1.133	0.61
37_S	40_P	1.129	0.61
31_L	35_D	1.100	0.59
8_A	45_A	1.098	0.59
18_K	29_E	1.062	0.56
104_T	107_L	1.059	0.56
116_L	119_I	1.059	0.56
7_W	11_H	1.045	0.55
17_A	64_R	1.033	0.54
32_I	37_S	1.010	0.52
38_H	45_A	0.991	0.51
7_W	62_Q	0.973	0.50
10_R	49_L	0.970	0.49
92_L	95_L	0.961	0.49
12_I	29_E	0.951	0.48
2_W	5_D	0.948	0.48
108_R	112_A	0.928	0.46
60_L	64_R	0.924	0.46
38_H	63_R	0.923	0.46
30_P	50_L	0.923	0.46
39_V	43_L	0.922	0.46
60_L	67_I	0.920	0.46
29_E	119_I	0.911	0.45
36_D	99_Q	0.909	0.45
11_H	45_A	0.901	0.44
109_G	114_K	0.895	0.44
20_E	28_G	0.871	0.42
89_R	113_D	0.836	0.40
33_L	48_R	0.835	0.40
35_D	59_E	0.830	0.39
30_P	76_I	0.830	0.39
23_N	48_R	0.830	0.39
79_D	82_Q	0.828	0.39
8_A	21_F	0.821	0.39
90_L	96_K	0.818	0.38
36_D	48_R	0.815	0.38
50_L	61_E	0.802	0.37
65_E	89_R	0.800	0.37
33_L	36_D	0.798	0.37
16_Q	104_T	0.793	0.37
4_L	49_L	0.792	0.37
37_S	60_L	0.789	0.36
35_D	52_N	0.779	0.36
106_F	110_D	0.777	0.36
13_A	16_Q	0.760	0.34
47_Y	90_L	0.753	0.34
31_L	38_H	0.750	0.34
46_G	108_R	0.741	0.33
115_L	119_I	0.733	0.33
44_R	107_L	0.729	0.32
104_T	110_D	0.720	0.32
21_F	24_L	0.712	0.31
46_G	77_R	0.712	0.31
98_R	101_G	0.709	0.31
14_E	118_K	0.703	0.31
38_H	44_R	0.702	0.31
23_N	84_Q	0.700	0.31
4_L	91_S	0.698	0.31
46_G	98_R	0.697	0.30
14_E	74_K	0.692	0.30
13_A	29_E	0.687	0.30
22_D	112_A	0.683	0.30
29_E	50_L	0.683	0.30
60_L	97_L	0.675	0.29
25_A	28_G	0.672	0.29
10_R	77_R	0.672	0.29
79_D	87_S	0.670	0.29
34_D	73_L	0.668	0.29
49_L	53_A	0.664	0.28
55_C	69_L	0.654	0.28
84_Q	99_Q	0.651	0.28
37_S	48_R	0.648	0.27
61_E	65_E	0.641	0.27
42_E	63_R	0.638	0.27
62_Q	96_K	0.638	0.27
34_D	86_V	0.636	0.27
58_P	108_R	0.634	0.27
7_W	64_R	0.622	0.26
23_N	27_S	0.620	0.26
39_V	97_L	0.619	0.26
34_D	39_V	0.619	0.26
90_L	113_D	0.614	0.26
16_Q	106_F	0.606	0.25
3_L	14_E	0.605	0.25
49_L	84_Q	0.598	0.25
24_L	28_G	0.596	0.25
99_Q	106_F	0.594	0.24
5_D	11_H	0.594	0.24
112_A	119_I	0.589	0.24
77_R	81_P	0.587	0.24
18_K	30_P	0.587	0.24
4_L	62_Q	0.584	0.24
70_L	74_K	0.582	0.24
45_A	119_I	0.582	0.24
8_A	63_R	0.575	0.23
58_P	82_Q	0.574	0.23
31_L	84_Q	0.573	0.23
4_L	7_W	0.573	0.23
74_K	116_L	0.573	0.23
7_W	66_A	0.572	0.23
105_D	119_I	0.567	0.23
50_L	77_R	0.565	0.23
7_W	89_R	0.562	0.23
33_L	47_Y	0.555	0.22
87_S	110_D	0.551	0.22
85_E	112_A	0.545	0.22
68_Q	85_E	0.543	0.22
101_G	104_T	0.541	0.22
62_Q	81_P	0.540	0.22
76_I	100_A	0.539	0.22
67_I	71_D	0.538	0.22
21_F	77_R	0.535	0.21
63_R	107_L	0.533	0.21
113_D	119_I	0.530	0.21
76_I	97_L	0.524	0.21
8_A	85_E	0.523	0.21
62_Q	97_L	0.519	0.21
114_K	118_K	0.517	0.21
8_A	16_Q	0.516	0.20
50_L	66_A	0.515	0.20
85_E	88_R	0.514	0.20
39_V	72_I	0.513	0.20
55_C	94_E	0.511	0.20
36_D	93_L	0.505	0.20
51_K	98_R	0.504	0.20
5_D	58_P	0.502	0.20
6_Q	16_Q	0.501	0.20
31_L	42_E	0.500	0.20

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
4uxvA	1	0.918	47.7	0.924	Contact Map
1bh9B	1	0.3525	29.8	0.932	Contact Map
1mhqA	1	0.3852	15.6	0.941	Contact Map
3ca8A	1	0.4836	14.4	0.942	Contact Map
4ad8A	1	0.9754	12.3	0.943	Contact Map
3nl9A	2	0.4672	10.4	0.945	Contact Map
3g06A	1	0.8197	8.4	0.948	Contact Map
4h0eA	2	0.5082	7.9	0.948	Contact Map
4y21A	1	0.6393	7.7	0.948	Contact Map
1g6uA	3	0.3934	7.7	0.948	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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