DKSA - ECOLI - GREMLIN Contacts

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DKSA - RNA polymerase-binding transcription factor DksA

UniProt:	P0ABS1	Sequences: MQEGQNRKTSSLSILAIAGVEPYQEKPGEEYMNEAQLAHFRRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10230
Length:	151 (121)
Sequences:	1859 (1005)
Seq/√Len:	91.4

ECOLI - DKSA
BACSU - G16O YTEA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_C	138_C	4.419	1.00
41_R	107_E	4.312	1.00
117_C	135_C	4.109	1.00
48_R	100_E	3.583	1.00
39_H	127_E	2.935	1.00
36_Q	123_I	2.932	1.00
135_C	138_C	2.920	1.00
37_L	106_V	2.802	1.00
115_E	133_D	2.785	1.00
48_R	96_I	2.423	1.00
43_I	127_E	2.129	1.00
102_T	105_K	2.114	1.00
41_R	45_E	2.006	1.00
116_S	134_L	1.919	1.00
38_A	41_R	1.879	1.00
139_K	142_A	1.845	1.00
47_W	95_L	1.798	1.00
31_Y	122_G	1.749	1.00
33_N	36_Q	1.728	1.00
32_M	40_F	1.727	1.00
48_R	52_R	1.666	1.00
37_L	109_E	1.609	1.00
44_L	99_I	1.607	1.00
40_F	123_I	1.582	1.00
101_K	105_K	1.582	1.00
98_K	133_D	1.500	1.00
81_E	84_L	1.473	1.00
104_K	108_D	1.440	0.99
116_S	138_C	1.429	0.99
42_R	46_A	1.427	0.99
38_A	45_E	1.381	0.99
34_E	38_A	1.367	0.99
40_F	106_V	1.366	0.99
52_R	100_E	1.340	0.99
124_R	127_E	1.336	0.99
45_E	49_N	1.322	0.99
49_N	53_D	1.274	0.99
51_L	96_I	1.268	0.99
47_W	50_Q	1.266	0.99
46_A	49_N	1.261	0.99
98_K	129_R	1.247	0.98
43_I	47_W	1.218	0.98
34_E	109_E	1.201	0.98
117_C	137_D	1.185	0.98
116_S	142_A	1.165	0.98
105_K	115_E	1.128	0.97
115_E	134_L	1.109	0.97
54_E	92_E	1.066	0.96
95_L	98_K	1.065	0.96
27_P	30_E	1.061	0.96
45_E	48_R	1.059	0.96
134_L	142_A	1.056	0.96
32_M	123_I	1.035	0.95
103_L	107_E	0.999	0.94
68_N	71_D	0.991	0.94
39_H	43_I	0.983	0.94
38_A	42_R	0.980	0.94
73_V	77_A	0.957	0.93
32_M	39_H	0.956	0.93
101_K	133_D	0.955	0.93
95_L	131_T	0.942	0.92
129_R	139_K	0.931	0.92
104_K	107_E	0.913	0.91
95_L	139_K	0.911	0.91
36_Q	40_F	0.893	0.90
45_E	103_L	0.892	0.90
42_R	45_E	0.889	0.90
114_C	138_C	0.879	0.89
58_T	89_R	0.878	0.89
53_D	57_R	0.876	0.89
56_D	60_T	0.868	0.89
105_K	133_D	0.865	0.88
26_K	29_E	0.857	0.88
51_L	92_E	0.854	0.88
66_A	71_D	0.835	0.87
32_M	36_Q	0.833	0.86
72_P	132_A	0.810	0.85
60_T	63_Q	0.807	0.85
96_I	100_E	0.803	0.84
48_R	99_I	0.791	0.83
90_D	93_R	0.786	0.83
72_P	76_A	0.785	0.83
102_T	126_L	0.779	0.83
88_N	92_E	0.777	0.82
98_K	146_E	0.772	0.82
76_A	80_E	0.761	0.81
95_L	129_R	0.755	0.81
31_Y	113_Y	0.752	0.80
136_I	140_T	0.744	0.80
81_E	106_V	0.742	0.79
26_K	30_E	0.738	0.79
139_K	146_E	0.719	0.77
70_P	74_D	0.716	0.77
119_V	137_D	0.712	0.77
70_P	80_E	0.708	0.76
90_D	94_K	0.707	0.76
30_E	34_E	0.701	0.75
72_P	78_Q	0.696	0.75
59_V	93_R	0.696	0.75
60_T	73_V	0.688	0.74
40_F	122_G	0.688	0.74
86_L	93_R	0.687	0.74
46_A	50_Q	0.683	0.74
73_V	80_E	0.682	0.73
49_N	52_R	0.680	0.73
101_K	104_K	0.679	0.73
75_R	87_R	0.679	0.73
53_D	56_D	0.675	0.73
75_R	79_E	0.673	0.72
37_L	41_R	0.666	0.72
141_L	144_I	0.664	0.71
80_E	83_S	0.663	0.71
87_R	95_L	0.661	0.71
93_R	97_K	0.658	0.71
51_L	54_E	0.656	0.70
91_R	95_L	0.651	0.70
46_A	52_R	0.651	0.70
41_R	106_V	0.647	0.69
62_M	65_E	0.642	0.69
72_P	96_I	0.639	0.69
47_W	59_V	0.636	0.68
92_E	101_K	0.635	0.68
68_N	72_P	0.632	0.68
138_C	143_E	0.628	0.67
69_F	72_P	0.628	0.67
134_L	139_K	0.624	0.67
111_F	132_A	0.618	0.66
70_P	73_V	0.618	0.66
28_G	42_R	0.610	0.65
79_E	87_R	0.602	0.64
91_R	139_K	0.600	0.64
87_R	98_K	0.600	0.64
41_R	103_L	0.595	0.63
52_R	55_V	0.591	0.62
82_F	122_G	0.586	0.62
38_A	136_I	0.584	0.62
102_T	133_D	0.582	0.61
137_D	141_L	0.581	0.61
26_K	77_A	0.581	0.61
129_R	146_E	0.580	0.61
54_E	57_R	0.580	0.61
72_P	77_A	0.577	0.61
47_W	75_R	0.575	0.60
132_A	139_K	0.575	0.60
72_P	82_F	0.568	0.59
40_F	126_L	0.558	0.58
87_R	129_R	0.557	0.58
110_D	113_Y	0.556	0.58
77_A	80_E	0.555	0.58
114_C	136_I	0.555	0.58
117_C	120_E	0.554	0.58
90_D	97_K	0.553	0.57
98_K	131_T	0.549	0.57
67_A	97_K	0.547	0.57
32_M	76_A	0.545	0.56
140_T	144_I	0.544	0.56
142_A	146_E	0.543	0.56
32_M	37_L	0.542	0.56
87_R	146_E	0.541	0.56
50_Q	54_E	0.540	0.56
103_L	124_R	0.540	0.56
117_C	140_T	0.535	0.55
65_E	73_V	0.535	0.55
57_R	64_D	0.531	0.54
77_A	84_L	0.530	0.54
73_V	76_A	0.527	0.54
71_D	84_L	0.525	0.54
79_E	90_D	0.522	0.53
113_Y	123_I	0.522	0.53
35_A	42_R	0.516	0.52
66_A	110_D	0.515	0.52
48_R	53_D	0.512	0.52
136_I	139_K	0.512	0.52
79_E	91_R	0.510	0.52
51_L	99_I	0.508	0.51
60_T	145_R	0.507	0.51
47_W	88_N	0.507	0.51
66_A	69_F	0.506	0.51
53_D	104_K	0.505	0.51
91_R	131_T	0.502	0.50
88_N	102_T	0.501	0.50
111_F	126_L	0.500	0.50

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
1tjlA	2	0.9603	100	0.189	Contact Map
4ijjA	1	0.8609	100	0.25	Contact Map
2kq9A	1	0.7417	99.9	0.359	Contact Map
2kgoA	1	0.4901	99.8	0.501	Contact Map
2lo3A	1	0.2914	43.5	0.914	Contact Map
3u6pA	1	0.8543	29.6	0.921	Contact Map
3mhsE	1	0.5629	26.5	0.923	Contact Map
1k82A	1	0.8808	25.5	0.924	Contact Map
3pwfA	4	0.7682	23.1	0.925	Contact Map
1lkoA	3	0.8609	19.7	0.928	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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