YJDF - BACSU - GREMLIN Contacts

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YJDF - Uncharacterized protein YjdF

UniProt:	O31647	Sequences: MSVTFPSSGCPSFFNIFYEEGIVMKLTIYYDGQFWVGVVEVVDNGKLRAFRHLFGKEPRDSEVLEFVHNQLLNMMAQAEQEGVRLQGRRQKKINPKRLQRQVSKELKNAGVTSKAQEAIKLELEARKQKKKQIMKEQREHVKEQRYMLKKQKAKKKHRGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (132)
Sequences:	330 (268)
Seq/√Len:	23.3

BACSU - YJDF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_K	123_L	5.535	1.00
64_L	68_H	3.212	1.00
146_Y	150_K	3.062	1.00
30_Y	33_Q	2.879	0.99
47_L	115_A	2.657	0.99
70_Q	73_N	2.648	0.99
29_Y	36_V	2.479	0.98
24_M	71_L	2.438	0.98
39_V	52_H	2.346	0.98
144_Q	148_L	2.165	0.96
136_E	140_H	2.150	0.96
150_K	153_A	2.123	0.96
39_V	71_L	2.116	0.95
38_V	110_G	2.079	0.95
47_L	83_V	1.978	0.93
99_Q	114_K	1.944	0.93
28_I	63_V	1.746	0.88
112_T	117_E	1.726	0.88
52_H	66_F	1.722	0.87
123_L	126_R	1.720	0.87
114_K	146_Y	1.704	0.87
41_V	48_R	1.678	0.86
98_L	102_V	1.675	0.86
146_Y	153_A	1.637	0.85
59_R	63_V	1.636	0.85
113_S	116_Q	1.616	0.84
115_A	119_I	1.616	0.84
93_I	101_Q	1.518	0.80
98_L	132_Q	1.466	0.77
101_Q	105_E	1.441	0.76
37_G	54_F	1.433	0.76
67_V	123_L	1.403	0.74
141_V	144_Q	1.384	0.73
94_N	143_E	1.330	0.70
134_M	137_Q	1.311	0.69
85_L	89_R	1.286	0.67
24_M	39_V	1.270	0.66
39_V	67_V	1.259	0.66
39_V	146_Y	1.257	0.65
34_F	53_L	1.223	0.63
74_M	119_I	1.220	0.63
110_G	130_K	1.215	0.63
129_K	132_Q	1.202	0.62
36_V	50_F	1.197	0.62
115_A	147_M	1.188	0.61
31_D	131_K	1.176	0.60
46_K	104_K	1.174	0.60
133_I	137_Q	1.174	0.60
125_A	158_R	1.167	0.59
38_V	52_H	1.145	0.58
37_G	121_L	1.133	0.57
29_Y	128_Q	1.131	0.57
156_K	159_G	1.109	0.56
145_R	154_K	1.104	0.55
60_D	66_F	1.093	0.54
29_Y	47_L	1.070	0.53
143_E	147_M	1.065	0.52
151_Q	155_K	1.048	0.51
24_M	72_L	1.046	0.51
59_R	112_T	1.045	0.51
35_W	62_E	1.021	0.49
120_K	132_Q	1.018	0.49
85_L	115_A	1.015	0.49
29_Y	103_S	1.009	0.49
24_M	52_H	1.007	0.48
95_P	100_R	1.003	0.48
56_K	74_M	0.995	0.48
33_Q	153_A	0.992	0.47
50_F	119_I	0.987	0.47
73_N	140_H	0.987	0.47
47_L	89_R	0.986	0.47
42_V	115_A	0.981	0.47
76_A	122_E	0.964	0.45
67_V	106_L	0.958	0.45
68_H	74_M	0.953	0.45
51_R	74_M	0.953	0.45
98_L	101_Q	0.944	0.44
83_V	89_R	0.936	0.43
65_E	69_N	0.934	0.43
123_L	136_E	0.910	0.42
98_L	142_K	0.895	0.41
39_V	103_S	0.890	0.40
52_H	75_M	0.881	0.40
36_V	47_L	0.881	0.40
139_E	142_K	0.878	0.40
28_I	52_H	0.877	0.39
102_V	106_L	0.877	0.39
37_G	51_R	0.858	0.38
49_A	122_E	0.848	0.38
145_R	148_L	0.848	0.38
45_G	60_D	0.847	0.37
103_S	146_Y	0.845	0.37
99_Q	146_Y	0.844	0.37
49_A	151_Q	0.842	0.37
152_K	159_G	0.839	0.37
135_K	158_R	0.821	0.36
106_L	115_A	0.820	0.36
35_W	57_E	0.818	0.36
139_E	143_E	0.818	0.36
65_E	121_L	0.811	0.35
97_R	143_E	0.808	0.35
76_A	114_K	0.778	0.33
103_S	112_T	0.775	0.33
117_E	150_K	0.768	0.32
106_L	110_G	0.767	0.32
127_K	156_K	0.764	0.32
112_T	118_A	0.758	0.32
52_H	76_A	0.757	0.32
30_Y	150_K	0.756	0.32
28_I	136_E	0.747	0.31
38_V	47_L	0.746	0.31
44_N	126_R	0.743	0.31
90_Q	135_K	0.742	0.31
102_V	115_A	0.733	0.30
47_L	153_A	0.721	0.30
113_S	117_E	0.720	0.30
54_F	60_D	0.712	0.29
55_G	100_R	0.705	0.29
39_V	79_E	0.702	0.29
34_F	158_R	0.701	0.29
75_M	103_S	0.698	0.28
37_G	154_K	0.698	0.28
35_W	53_L	0.696	0.28
73_N	114_K	0.696	0.28
125_A	144_Q	0.692	0.28
33_Q	112_T	0.687	0.28
92_K	115_A	0.684	0.28
99_Q	150_K	0.681	0.27
24_M	145_R	0.678	0.27
51_R	119_I	0.673	0.27
71_L	106_L	0.672	0.27
29_Y	54_F	0.672	0.27
99_Q	142_K	0.666	0.27
109_A	153_A	0.662	0.26
46_K	60_D	0.661	0.26
119_I	132_Q	0.660	0.26
98_L	105_E	0.660	0.26
105_E	112_T	0.659	0.26
50_F	74_M	0.653	0.26
32_G	71_L	0.636	0.25
153_A	158_R	0.634	0.25
68_H	94_N	0.629	0.25
39_V	76_A	0.623	0.24
44_N	94_N	0.621	0.24
130_K	139_E	0.612	0.24
49_A	77_Q	0.612	0.24
49_A	119_I	0.611	0.24
91_K	142_K	0.609	0.24
94_N	104_K	0.604	0.23
65_E	125_A	0.603	0.23
64_L	102_V	0.603	0.23
103_S	153_A	0.601	0.23
37_G	118_A	0.598	0.23
85_L	117_E	0.597	0.23
43_D	48_R	0.596	0.23
137_Q	142_K	0.588	0.23
52_H	79_E	0.585	0.22
76_A	146_Y	0.585	0.22
107_K	143_E	0.576	0.22
64_L	153_A	0.573	0.22
86_Q	93_I	0.569	0.22
29_Y	92_K	0.569	0.22
66_F	149_K	0.568	0.22
59_R	102_V	0.566	0.21
70_Q	128_Q	0.564	0.21
92_K	126_R	0.558	0.21
90_Q	154_K	0.556	0.21
63_V	83_V	0.556	0.21
68_H	107_K	0.555	0.21
54_F	62_E	0.555	0.21
84_R	136_E	0.555	0.21
69_N	102_V	0.552	0.21
121_L	151_Q	0.552	0.21
152_K	156_K	0.550	0.21
93_I	134_M	0.548	0.21
120_K	145_R	0.543	0.20
107_K	138_R	0.539	0.20
26_L	37_G	0.538	0.20
35_W	60_D	0.538	0.20
34_F	114_K	0.536	0.20
74_M	150_K	0.535	0.20
68_H	127_K	0.533	0.20
154_K	158_R	0.532	0.20
104_K	108_N	0.530	0.20
27_T	115_A	0.528	0.20
30_Y	112_T	0.528	0.20
53_L	123_L	0.522	0.19
120_K	125_A	0.522	0.19
45_G	65_E	0.519	0.19
25_K	66_F	0.517	0.19
53_L	149_K	0.517	0.19
50_F	77_Q	0.515	0.19
30_Y	123_L	0.509	0.19
83_V	151_Q	0.509	0.19
60_D	135_K	0.509	0.19
32_G	112_T	0.504	0.19
108_N	120_K	0.501	0.19
94_N	156_K	0.500	0.19

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
4dooA	1	0.4375	21.1	0.953	Contact Map
2o8nA	2	0.45	20.3	0.953	Contact Map
4dokA	1	0.425	14.6	0.956	Contact Map
1f1eA	2	0.7875	13	0.957	Contact Map
3saoA	1	0.6	12.8	0.957	Contact Map
3idwA	1	0.3312	12.8	0.957	Contact Map
1jztA	2	0.475	12.8	0.957	Contact Map
4doiA	1	0.5	12.1	0.957	Contact Map
4b9pA	1	0.3375	11.4	0.958	Contact Map
2wnxA	2	0.325	11.1	0.958	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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