YDFE - BACSU - GREMLIN Contacts

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YDFE - Uncharacterized protein YdfE

UniProt:	P96682	Sequences: MDIKKQDTRRFKEIKPKIMYYGTSTFLLTTLNEDGTTNISPMSSSWALGHYIILGVGLGGKAIDNLERHKECVINLPGPDLWENVERISSYSGKKSIPPLKKQIGFTYKKEKYEAAGLTPLQSKTVSPTRIKECPIQIEAEVKHIRLPEYESSFAIVETQALHFHAEESIILDENHINPSKWSPLIYNFRHYFGLGREVGKTFRSET	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	207 (170)
Sequences:	3523 (2540)
Seq/√Len:	194.8

ECOLI - YDDH
BACSU - YDFE YWRF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
119_T	133_E	3.893	1.00
125_T	162_L	3.451	1.00
72_C	159_T	3.353	1.00
141_E	160_Q	3.337	1.00
32_N	36_T	3.255	1.00
79_P	183_S	2.948	1.00
33_E	68_R	2.770	1.00
141_E	162_L	2.637	1.00
111_E	114_E	2.555	1.00
143_K	160_Q	2.427	1.00
106_F	115_A	2.307	1.00
29_T	73_V	2.278	1.00
121_L	132_K	2.269	1.00
37_T	120_P	2.160	1.00
79_P	194_G	2.149	1.00
67_E	145_I	2.144	1.00
77_P	85_V	2.088	1.00
31_L	37_T	2.061	1.00
71_E	141_E	1.995	1.00
73_V	126_V	1.963	1.00
39_I	131_I	1.962	1.00
119_T	132_K	1.958	1.00
31_L	127_S	1.881	1.00
113_Y	120_P	1.877	1.00
123_S	130_R	1.803	1.00
130_R	137_Q	1.776	1.00
106_F	110_K	1.676	1.00
71_E	127_S	1.643	1.00
52_I	55_G	1.641	1.00
37_T	129_T	1.620	1.00
123_S	139_E	1.615	1.00
172_L	178_N	1.507	1.00
123_S	128_P	1.498	1.00
145_I	155_A	1.477	1.00
66_L	142_V	1.477	1.00
124_K	163_H	1.476	1.00
27_L	39_I	1.405	1.00
126_V	139_E	1.391	1.00
186_I	193_F	1.380	1.00
77_P	185_L	1.374	1.00
27_L	88_I	1.372	1.00
48_L	55_G	1.368	1.00
123_S	126_V	1.354	1.00
72_C	140_A	1.353	1.00
178_N	181_K	1.341	1.00
194_G	197_R	1.335	1.00
78_G	81_L	1.335	1.00
90_S	106_F	1.332	1.00
16_P	47_A	1.313	1.00
125_T	163_H	1.312	1.00
111_E	120_P	1.299	1.00
19_M	136_I	1.292	1.00
48_L	158_E	1.284	1.00
29_T	39_I	1.271	1.00
40_S	62_A	1.247	1.00
130_R	165_H	1.240	1.00
66_L	72_C	1.232	1.00
81_L	133_E	1.222	1.00
30_T	66_L	1.214	1.00
172_L	181_K	1.204	1.00
138_I	164_F	1.199	1.00
191_H	198_E	1.197	1.00
121_L	130_R	1.181	1.00
39_I	113_Y	1.177	1.00
82_W	185_L	1.159	1.00
77_P	134_C	1.144	1.00
37_T	111_E	1.112	1.00
71_E	126_V	1.106	1.00
52_I	56_V	1.097	1.00
64_D	68_R	1.094	1.00
63_I	157_V	1.085	1.00
142_V	157_V	1.082	1.00
63_I	67_E	1.072	1.00
75_N	137_Q	1.069	1.00
140_A	159_T	1.065	1.00
27_L	81_L	1.064	1.00
146_R	158_E	1.060	1.00
78_G	135_P	1.056	1.00
26_F	45_S	1.053	1.00
52_I	74_I	1.049	1.00
170_I	182_W	1.036	1.00
30_T	65_N	1.025	1.00
142_V	145_I	1.023	1.00
73_V	130_R	1.016	1.00
69_H	127_S	1.009	1.00
64_D	108_Y	0.994	1.00
82_W	199_V	0.993	1.00
31_L	128_P	0.982	0.99
186_I	195_L	0.980	0.99
183_S	194_G	0.975	0.99
80_D	183_S	0.973	0.99
79_P	82_W	0.972	0.99
48_L	53_I	0.971	0.99
36_T	109_K	0.968	0.99
84_N	118_L	0.963	0.99
73_V	123_S	0.953	0.99
61_K	64_D	0.949	0.99
166_A	170_I	0.946	0.99
84_N	116_A	0.939	0.99
63_I	155_A	0.935	0.99
30_T	62_A	0.923	0.99
49_G	154_F	0.922	0.99
29_T	128_P	0.905	0.99
110_K	115_A	0.903	0.99
85_V	185_L	0.897	0.99
191_H	200_G	0.893	0.99
88_I	116_A	0.887	0.99
145_I	157_V	0.885	0.99
67_E	70_K	0.881	0.99
170_I	177_I	0.873	0.99
167_E	170_I	0.872	0.99
179_P	184_P	0.871	0.99
87_R	115_A	0.868	0.99
53_I	158_E	0.863	0.99
29_T	131_I	0.862	0.99
138_I	161_A	0.859	0.99
172_L	176_H	0.842	0.98
76_L	184_P	0.839	0.98
20_Y	47_A	0.836	0.98
85_V	134_C	0.832	0.98
29_T	75_N	0.829	0.98
55_G	156_I	0.823	0.98
36_T	108_Y	0.820	0.98
58_L	155_A	0.816	0.98
76_L	182_W	0.809	0.98
37_T	113_Y	0.807	0.98
32_N	108_Y	0.792	0.98
32_N	68_R	0.786	0.97
121_L	137_Q	0.784	0.97
73_V	137_Q	0.783	0.97
18_I	188_N	0.780	0.97
31_L	69_H	0.779	0.97
53_I	143_K	0.777	0.97
29_T	113_Y	0.777	0.97
143_K	158_E	0.773	0.97
87_R	106_F	0.772	0.97
27_L	131_I	0.768	0.97
71_E	128_P	0.766	0.97
70_K	142_V	0.762	0.97
48_L	156_I	0.756	0.97
49_G	151_E	0.752	0.97
90_S	105_G	0.748	0.97
125_T	139_E	0.744	0.97
135_P	167_E	0.743	0.96
44_S	47_A	0.739	0.96
80_D	135_P	0.737	0.96
70_K	141_E	0.735	0.96
84_N	133_E	0.734	0.96
31_L	122_Q	0.730	0.96
61_K	65_N	0.726	0.96
45_S	76_L	0.726	0.96
122_Q	127_S	0.720	0.96
170_I	179_P	0.712	0.96
73_V	128_P	0.705	0.95
177_I	182_W	0.702	0.95
121_L	124_K	0.700	0.95
170_I	181_K	0.699	0.95
87_R	116_A	0.698	0.95
21_Y	184_P	0.697	0.95
21_Y	179_P	0.691	0.95
74_I	140_A	0.681	0.94
37_T	128_P	0.679	0.94
190_R	193_F	0.678	0.94
65_N	69_H	0.677	0.94
27_L	118_L	0.674	0.94
137_Q	165_H	0.673	0.94
27_L	85_V	0.669	0.94
66_L	157_V	0.669	0.94
120_P	133_E	0.668	0.94
19_M	138_I	0.659	0.93
42_M	54_L	0.658	0.93
118_L	131_I	0.658	0.93
76_L	136_I	0.655	0.93
180_S	198_E	0.655	0.93
136_I	166_A	0.654	0.93
27_L	134_C	0.651	0.93
81_L	134_C	0.650	0.93
66_L	159_T	0.649	0.93
61_K	108_Y	0.643	0.92
26_F	74_I	0.643	0.92
87_R	90_S	0.643	0.92
81_L	118_L	0.641	0.92
184_P	195_L	0.637	0.92
75_N	131_I	0.634	0.92
53_I	156_I	0.632	0.92
107_T	110_K	0.628	0.92
136_I	182_W	0.619	0.91
54_L	74_I	0.618	0.91
63_I	145_I	0.618	0.91
16_P	20_Y	0.614	0.91
83_E	87_R	0.613	0.91
28_L	42_M	0.608	0.90
61_K	112_K	0.606	0.90
56_V	157_V	0.602	0.90
28_L	72_C	0.601	0.90
114_E	117_G	0.595	0.89
32_N	35_G	0.591	0.89
75_N	128_P	0.588	0.89
66_L	70_K	0.585	0.88
142_V	159_T	0.584	0.88
52_I	138_I	0.584	0.88
24_S	46_W	0.584	0.88
169_S	181_K	0.583	0.88
114_E	120_P	0.583	0.88
180_S	197_R	0.580	0.88
89_S	105_G	0.579	0.88
71_E	139_E	0.578	0.88
116_A	131_I	0.577	0.88
120_P	129_T	0.575	0.88
113_Y	131_I	0.570	0.87
143_K	146_R	0.565	0.87
31_L	35_G	0.559	0.86
17_K	50_H	0.557	0.86
129_T	161_A	0.555	0.86
118_L	133_E	0.555	0.86
31_L	123_S	0.553	0.85
193_F	198_E	0.553	0.85
32_N	65_N	0.551	0.85
64_D	67_E	0.548	0.85
62_A	65_N	0.547	0.85
171_I	177_I	0.544	0.85
42_M	62_A	0.544	0.85
82_W	85_V	0.543	0.84
75_N	134_C	0.543	0.84
193_F	199_V	0.541	0.84
27_L	40_S	0.541	0.84
45_S	53_I	0.539	0.84
25_T	41_P	0.537	0.84
41_P	77_P	0.537	0.84
68_R	108_Y	0.536	0.84
60_G	187_Y	0.536	0.84
136_I	170_I	0.533	0.83
122_Q	129_T	0.530	0.83
69_H	128_P	0.530	0.83
124_K	165_H	0.530	0.83
124_K	139_E	0.529	0.83
119_T	131_I	0.528	0.83
28_L	40_S	0.527	0.83
30_T	40_S	0.526	0.83
20_Y	26_F	0.525	0.82
76_L	134_C	0.524	0.82
50_H	57_G	0.516	0.81
84_N	87_R	0.516	0.81
190_R	200_G	0.514	0.81
27_L	41_P	0.512	0.81
54_L	159_T	0.511	0.81
113_Y	116_A	0.510	0.81
25_T	45_S	0.509	0.80
89_S	106_F	0.507	0.80
82_W	86_E	0.506	0.80
39_I	88_I	0.506	0.80
79_P	197_R	0.505	0.80
14_I	171_I	0.504	0.80
188_N	191_H	0.503	0.80
70_K	144_H	0.500	0.79

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
2d5mA	2	0.8599	100	0.374	Contact Map
3bpkA	2	0.8841	100	0.379	Contact Map
3fgeA	2	0.9082	100	0.387	Contact Map
3bnkA	2	0.8599	100	0.408	Contact Map
1ejeA	2	0.8744	100	0.408	Contact Map
3hmzA	2	0.8502	100	0.419	Contact Map
2r6vA	2	0.8309	100	0.44	Contact Map
3e4vA	2	0.8357	100	0.465	Contact Map
1uscA	2	0.8406	100	0.476	Contact Map
4r82A	2	0.7585	100	0.511	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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