YDFG - BACSU - GREMLIN Contacts

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YDFG - Uncharacterized protein YdfG

UniProt:	P96684	Sequences: MSQRVSYYEIAPEGMKIMMDMEKYTKQSSINRTTRELIKIRVSQMNGCAFCIDMHTSDARKMGETEQRIYCLHAWNECDFYSPEEKAALELSEHITLIPSKRVPDELYHRVREHYDEEQYVDLVLIINQINSWNRISIAMGNRAASK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (139)
Sequences:	3133 (2008)
Seq/√Len:	170.3

ECOLI - YNJA
BACSU - YDFG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_R	66_E	3.656	1.00
42_V	92_S	3.426	1.00
64_E	68_R	3.217	1.00
66_E	70_Y	2.659	1.00
111_V	120_Y	2.548	1.00
116_D	119_Q	2.439	1.00
90_E	110_R	2.437	1.00
112_R	117_E	2.289	1.00
84_E	119_Q	2.238	1.00
128_N	132_S	2.219	1.00
91_L	124_V	2.037	1.00
95_I	139_A	1.960	1.00
38_I	123_L	1.930	1.00
35_R	126_I	1.904	1.00
94_H	107_L	1.878	1.00
60_R	70_Y	1.876	1.00
110_R	113_E	1.873	1.00
96_T	131_N	1.867	1.00
36_E	62_M	1.760	1.00
118_E	122_D	1.749	1.00
137_S	142_N	1.743	1.00
97_L	100_S	1.732	1.00
71_C	80_F	1.713	1.00
40_I	52_I	1.669	1.00
53_D	67_Q	1.668	1.00
18_M	132_S	1.624	1.00
14_G	125_L	1.615	1.00
44_Q	93_E	1.589	1.00
52_I	74_A	1.557	1.00
22_E	39_K	1.556	1.00
43_S	134_N	1.553	1.00
21_M	129_Q	1.533	1.00
68_R	85_E	1.531	1.00
53_D	57_S	1.457	1.00
40_I	56_T	1.419	1.00
42_V	130_I	1.397	1.00
71_C	78_C	1.381	1.00
34_T	115_Y	1.373	1.00
112_R	120_Y	1.370	1.00
94_H	104_P	1.365	1.00
84_E	114_H	1.359	1.00
34_T	88_A	1.344	1.00
104_P	107_L	1.330	1.00
48_C	51_C	1.325	1.00
71_C	81_Y	1.306	1.00
14_G	24_Y	1.305	1.00
57_S	61_K	1.298	1.00
29_S	122_D	1.278	1.00
33_T	68_R	1.273	1.00
6_S	9_E	1.257	1.00
65_T	68_R	1.249	1.00
84_E	115_Y	1.223	1.00
40_I	69_I	1.211	1.00
31_N	84_E	1.202	1.00
87_A	107_L	1.199	1.00
30_I	35_R	1.197	1.00
36_E	58_D	1.178	1.00
105_D	109_H	1.161	1.00
115_Y	123_L	1.151	1.00
95_I	124_V	1.149	1.00
112_R	116_D	1.145	1.00
105_D	141_G	1.137	1.00
11_A	122_D	1.130	1.00
8_Y	15_M	1.106	1.00
17_I	20_D	1.091	1.00
76_N	90_E	1.076	1.00
41_R	93_E	1.044	0.99
38_I	88_A	1.032	0.99
36_E	39_K	1.031	0.99
124_V	140_M	1.027	0.99
110_R	114_H	1.022	0.99
26_K	32_R	1.015	0.99
19_M	133_W	1.014	0.99
41_R	44_Q	0.992	0.99
98_I	138_I	0.991	0.99
107_L	110_R	0.976	0.99
90_E	107_L	0.968	0.99
91_L	139_A	0.964	0.99
90_E	94_H	0.957	0.99
83_P	113_E	0.935	0.99
56_T	70_Y	0.924	0.99
83_P	114_H	0.906	0.98
130_I	133_W	0.892	0.98
105_D	108_Y	0.884	0.98
22_E	133_W	0.876	0.98
101_K	141_G	0.867	0.98
71_C	79_D	0.866	0.98
107_L	111_V	0.865	0.98
46_N	134_N	0.865	0.98
58_D	61_K	0.857	0.98
109_H	113_E	0.857	0.98
32_R	62_M	0.856	0.98
79_D	86_K	0.852	0.98
29_S	118_E	0.835	0.97
10_I	121_V	0.829	0.97
87_A	90_E	0.828	0.97
129_Q	133_W	0.815	0.97
91_L	127_I	0.814	0.97
7_Y	142_N	0.814	0.97
121_V	140_M	0.811	0.97
91_L	103_V	0.802	0.97
59_A	69_I	0.795	0.96
103_V	139_A	0.793	0.96
131_N	135_R	0.791	0.96
55_H	130_I	0.789	0.96
49_A	74_A	0.789	0.96
11_A	121_V	0.788	0.96
15_M	19_M	0.784	0.96
54_M	133_W	0.780	0.96
74_A	77_E	0.758	0.95
88_A	115_Y	0.757	0.95
18_M	22_E	0.755	0.95
13_E	27_Q	0.754	0.95
132_S	137_S	0.752	0.95
39_K	130_I	0.745	0.95
18_M	133_W	0.744	0.95
109_H	112_R	0.741	0.95
67_Q	80_F	0.740	0.95
33_T	64_E	0.736	0.95
92_S	127_I	0.732	0.94
16_K	20_D	0.728	0.94
91_L	111_V	0.726	0.94
83_P	110_R	0.724	0.94
16_K	19_M	0.723	0.94
87_A	114_H	0.721	0.94
59_A	64_E	0.720	0.94
116_D	120_Y	0.717	0.94
40_I	59_A	0.716	0.94
45_M	93_E	0.716	0.94
103_V	107_L	0.713	0.94
24_Y	28_S	0.711	0.94
91_L	140_M	0.707	0.93
52_I	71_C	0.704	0.93
13_E	16_K	0.697	0.93
40_I	72_L	0.694	0.93
13_E	118_E	0.693	0.93
36_E	55_H	0.679	0.92
76_N	93_E	0.678	0.92
43_S	130_I	0.676	0.92
50_F	54_M	0.673	0.92
99_P	102_R	0.673	0.92
35_R	39_K	0.671	0.91
31_N	34_T	0.668	0.91
15_M	137_S	0.665	0.91
33_T	59_A	0.663	0.91
34_T	119_Q	0.662	0.91
83_P	86_K	0.657	0.91
20_D	24_Y	0.652	0.90
41_R	75_W	0.652	0.90
20_D	23_K	0.651	0.90
72_L	81_Y	0.647	0.90
98_I	102_R	0.644	0.90
88_A	123_L	0.635	0.89
70_Y	73_H	0.634	0.89
55_H	133_W	0.629	0.89
50_F	138_I	0.627	0.88
97_L	102_R	0.625	0.88
10_I	118_E	0.623	0.88
101_K	107_L	0.622	0.88
46_N	96_T	0.615	0.87
75_W	93_E	0.612	0.87
5_V	108_Y	0.612	0.87
5_V	120_Y	0.611	0.87
129_Q	132_S	0.610	0.87
22_E	130_I	0.598	0.86
43_S	51_C	0.597	0.86
34_T	38_I	0.590	0.85
103_V	111_V	0.580	0.84
57_S	67_Q	0.575	0.84
44_Q	72_L	0.574	0.84
7_Y	15_M	0.573	0.84
44_Q	75_W	0.568	0.83
23_K	26_K	0.566	0.83
6_S	142_N	0.563	0.82
52_I	70_Y	0.562	0.82
67_Q	79_D	0.561	0.82
71_C	74_A	0.557	0.82
7_Y	11_A	0.556	0.82
35_R	122_D	0.555	0.82
22_E	129_Q	0.550	0.81
28_S	122_D	0.544	0.80
19_M	22_E	0.542	0.80
103_V	108_Y	0.541	0.80
39_K	126_I	0.539	0.80
53_D	80_F	0.537	0.79
106_E	110_R	0.534	0.79
125_L	128_N	0.533	0.79
45_M	97_L	0.529	0.78
7_Y	121_V	0.527	0.78
11_A	24_Y	0.521	0.77
54_M	58_D	0.521	0.77
11_A	132_S	0.520	0.77
68_R	82_S	0.519	0.77
50_F	133_W	0.519	0.77
87_A	110_R	0.515	0.77
48_C	134_N	0.514	0.76
25_T	122_D	0.512	0.76
39_K	133_W	0.509	0.76
59_A	63_G	0.509	0.76
33_T	85_E	0.506	0.75
140_M	143_R	0.504	0.75
43_S	46_N	0.503	0.75
47_G	76_N	0.502	0.75
106_E	113_E	0.502	0.75
75_W	86_K	0.501	0.75
43_S	48_C	0.501	0.75
18_M	21_M	0.501	0.75
15_M	50_F	0.500	0.74

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
2o4dA	3	0.9796	100	0.261	Contact Map
2gmyA	3	1	100	0.269	Contact Map
2pfxA	3	0.9864	100	0.354	Contact Map
3c1lA	5	0.9864	100	0.357	Contact Map
2prrA	5	0.9864	100	0.362	Contact Map
2oyoA	4	0.9864	100	0.363	Contact Map
3lvyA	2	0.9728	100	0.401	Contact Map
2qeuA	6	0.7075	99.7	0.648	Contact Map
2ouwA	6	0.6531	99.7	0.662	Contact Map
1gu9A	3	0.6327	99.6	0.684	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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