UMUD - ECOLI - GREMLIN Contacts

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UMUD - Protein UmuD

UniProt:	P0AG11	Sequences: MLFIKPADLREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNQLLIQHPSATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11057
Length:	139 (123)
Sequences:	4013 (2589)
Seq/√Len:	233.5

ECOLI - UMUD LEXA COHE
BACSU - LEXA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_K	110_M	4.295	1.00
63_D	112_S	3.676	1.00
104_T	118_T	2.665	1.00
64_G	110_M	2.620	1.00
72_L	96_V	2.472	1.00
22_V	87_I	2.395	1.00
50_A	76_S	2.371	1.00
24_C	56_A	2.272	1.00
100_Q	108_I	2.248	1.00
95_T	109_P	2.216	1.00
67_S	136_K	2.143	1.00
108_I	116_P	2.118	1.00
84_D	130_V	2.065	1.00
59_D	114_Y	1.993	1.00
80_A	86_V	1.956	1.00
64_G	98_K	1.904	1.00
21_L	57_S	1.885	1.00
70_D	136_K	1.836	1.00
82_H	100_Q	1.813	1.00
119_I	125_L	1.810	1.00
100_Q	106_Q	1.754	1.00
56_A	72_L	1.727	1.00
91_D	123_D	1.700	1.00
55_K	71_L	1.675	1.00
96_V	131_V	1.675	1.00
15_F	53_F	1.667	1.00
53_F	71_L	1.602	1.00
102_R	106_Q	1.515	1.00
101_L	105_V	1.502	1.00
38_I	53_F	1.497	1.00
109_P	116_P	1.483	1.00
91_D	124_T	1.475	1.00
74_V	131_V	1.470	1.00
63_D	110_M	1.470	1.00
74_V	87_I	1.455	1.00
89_A	128_F	1.450	1.00
57_S	68_D	1.435	1.00
59_D	113_A	1.425	1.00
17_L	36_Q	1.421	1.00
64_G	85_I	1.394	1.00
72_L	131_V	1.385	1.00
49_S	75_D	1.318	1.00
86_V	99_L	1.313	1.00
14_T	39_D	1.305	1.00
85_I	98_K	1.293	1.00
106_Q	118_T	1.229	1.00
34_V	37_R	1.166	1.00
56_A	96_V	1.163	1.00
81_S	84_D	1.141	1.00
60_S	97_K	1.136	1.00
106_Q	116_P	1.098	1.00
67_S	70_D	1.075	1.00
21_L	55_K	1.073	1.00
59_D	68_D	1.072	1.00
82_H	101_L	1.066	1.00
12_I	42_Q	1.034	1.00
53_F	73_I	1.026	1.00
105_V	125_L	1.001	1.00
66_I	85_I	0.997	1.00
26_F	29_P	0.987	1.00
74_V	96_V	0.982	1.00
22_V	54_V	0.978	1.00
89_A	126_D	0.959	1.00
80_A	99_L	0.957	1.00
35_E	55_K	0.955	1.00
109_P	115_S	0.955	1.00
90_V	119_I	0.935	1.00
52_Y	76_S	0.931	1.00
102_R	108_I	0.926	1.00
51_T	73_I	0.919	1.00
133_H	137_A	0.912	1.00
51_T	132_I	0.911	1.00
87_I	96_V	0.907	1.00
48_P	75_D	0.902	1.00
72_L	134_V	0.887	0.99
23_Q	28_S	0.879	0.99
54_V	87_I	0.866	0.99
14_T	37_R	0.857	0.99
27_P	95_T	0.848	0.99
17_L	38_I	0.840	0.99
45_I	51_T	0.834	0.99
88_A	99_L	0.831	0.99
59_D	62_I	0.827	0.99
82_H	99_L	0.806	0.99
40_L	53_F	0.801	0.99
99_L	105_V	0.796	0.99
15_F	51_T	0.791	0.99
104_T	120_S	0.788	0.99
11_E	42_Q	0.780	0.99
23_Q	68_D	0.777	0.99
77_A	130_V	0.766	0.98
58_G	97_K	0.754	0.98
13_V	45_I	0.744	0.98
18_F	34_V	0.737	0.98
78_I	126_D	0.730	0.98
73_I	135_V	0.726	0.98
62_I	67_S	0.722	0.98
131_V	134_V	0.721	0.98
56_A	66_I	0.720	0.98
18_F	32_D	0.714	0.97
58_G	68_D	0.711	0.97
46_Q	49_S	0.707	0.97
87_I	131_V	0.702	0.97
85_I	110_M	0.697	0.97
13_V	42_Q	0.695	0.97
61_M	96_V	0.688	0.97
50_A	75_D	0.686	0.97
120_S	123_D	0.681	0.97
77_A	80_A	0.679	0.97
62_I	112_S	0.678	0.97
62_I	111_N	0.675	0.96
22_V	96_V	0.670	0.96
66_I	96_V	0.661	0.96
79_T	101_L	0.654	0.96
78_I	84_D	0.654	0.96
23_Q	27_P	0.652	0.96
109_P	117_I	0.646	0.95
40_L	45_I	0.643	0.95
40_L	44_L	0.639	0.95
30_A	89_A	0.638	0.95
44_L	133_H	0.638	0.95
80_A	88_A	0.637	0.95
89_A	94_F	0.637	0.95
65_G	70_D	0.637	0.95
133_H	136_K	0.635	0.95
65_G	136_K	0.635	0.95
42_Q	48_P	0.632	0.95
85_I	114_Y	0.629	0.95
73_I	133_H	0.622	0.94
41_N	44_L	0.620	0.94
62_I	114_Y	0.618	0.94
76_S	128_F	0.613	0.94
62_I	113_A	0.613	0.94
17_L	71_L	0.612	0.94
75_D	130_V	0.611	0.94
23_Q	95_T	0.599	0.93
51_T	75_D	0.598	0.93
102_R	118_T	0.591	0.93
66_I	134_V	0.590	0.93
30_A	93_E	0.588	0.93
108_I	118_T	0.587	0.93
25_G	58_G	0.586	0.92
109_P	114_Y	0.586	0.92
54_V	74_V	0.584	0.92
75_D	78_I	0.583	0.92
17_L	53_F	0.581	0.92
16_P	37_R	0.581	0.92
71_L	135_V	0.579	0.92
20_D	31_A	0.579	0.92
52_Y	87_I	0.573	0.92
100_Q	105_V	0.572	0.92
60_S	95_T	0.568	0.91
12_I	39_D	0.567	0.91
88_A	125_L	0.566	0.91
11_E	39_D	0.565	0.91
25_G	30_A	0.560	0.91
111_N	114_Y	0.560	0.91
82_H	105_V	0.556	0.90
51_T	76_S	0.553	0.90
29_P	33_Y	0.550	0.90
28_S	33_Y	0.548	0.90
73_I	132_I	0.547	0.90
86_V	130_V	0.544	0.89
43_L	71_L	0.543	0.89
92_G	126_D	0.542	0.89
85_I	131_V	0.542	0.89
54_V	94_F	0.541	0.89
54_V	97_K	0.541	0.89
43_L	137_A	0.540	0.89
26_F	32_D	0.536	0.89
26_F	57_S	0.536	0.89
30_A	94_F	0.534	0.89
20_D	32_D	0.533	0.88
52_Y	128_F	0.527	0.88
23_Q	57_S	0.520	0.87
38_I	43_L	0.516	0.87
118_T	125_L	0.516	0.87
38_I	44_L	0.514	0.87
94_F	128_F	0.514	0.87
120_S	124_T	0.509	0.86
98_K	108_I	0.507	0.86
21_L	93_E	0.506	0.86
77_A	81_S	0.503	0.85
29_P	32_D	0.500	0.85

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
1umuA	2	0.7626	100	0.357	Contact Map
1jhfA	2	0.9784	99.9	0.398	Contact Map
3k2zA	2	0.9784	99.9	0.406	Contact Map
2hnfA	1	0.8705	99.9	0.418	Contact Map
3bdnA	2	0.9424	99.9	0.441	Contact Map
1kcaA	6	0.6547	99.8	0.531	Contact Map
2fjrA	4	0.8417	99.7	0.575	Contact Map
4me8A	1	0.4101	98.7	0.75	Contact Map
4k8wA	2	0.518	98.5	0.765	Contact Map
4n31A	5	0.6835	98.3	0.777	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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