YGIV - ECOLI - GREMLIN Contacts

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YGIV - Probable transcriptional regulator YgiV

UniProt:	Q46866	Sequences: MTNLTLDVNIIDFPSIPVAMLPHRCSPELLNYSVAKFIMWRKETGLSPVNQSQTFGVAWDDPATTAPEAFRFDICGSVSEPIPDNRYGVSNGELTGGRYAVARHVGELDDISHTVWGIIRHWLPASGEKMRKAPILFHYTNLAEGVTEQRLETDVYVPLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13024
Length:	160 (151)
Sequences:	1193 (892)
Seq/√Len:	72.6

ECOLI - YGIV SBMC
BACSU - YOST

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_R	154_D	3.759	1.00
17_P	91_N	3.244	1.00
98_R	128_E	3.136	1.00
122_W	126_S	2.763	1.00
60_D	71_R	2.667	1.00
15_S	96_G	2.593	1.00
18_V	75_C	2.411	1.00
66_A	69_A	2.322	1.00
128_E	159_L	2.283	1.00
21_L	33_S	2.245	1.00
22_P	73_D	2.243	1.00
15_S	93_E	2.196	1.00
138_H	154_D	2.168	1.00
40_W	89_V	2.078	1.00
56_G	72_F	2.042	1.00
105_V	152_E	1.983	1.00
53_Q	77_S	1.962	1.00
53_Q	138_H	1.951	1.00
20_M	92_G	1.947	1.00
58_A	72_F	1.913	1.00
146_V	151_L	1.784	1.00
147_T	150_R	1.774	1.00
102_A	118_I	1.768	1.00
26_S	67_P	1.751	1.00
18_V	94_L	1.680	1.00
55_F	138_H	1.673	1.00
141_N	151_L	1.669	1.00
115_V	155_V	1.662	1.00
37_F	41_R	1.654	1.00
29_L	32_Y	1.598	0.99
56_G	74_I	1.570	0.99
123_L	126_S	1.563	0.99
8_V	122_W	1.520	0.99
115_V	137_F	1.511	0.99
140_T	152_E	1.506	0.99
73_D	92_G	1.475	0.99
106_G	153_T	1.471	0.99
136_L	156_Y	1.453	0.99
16_I	53_Q	1.448	0.99
41_R	76_G	1.443	0.99
59_W	92_G	1.437	0.99
19_A	89_V	1.433	0.99
27_P	70_F	1.422	0.99
33_S	74_I	1.421	0.99
95_T	133_A	1.405	0.98
104_H	114_T	1.398	0.98
58_A	137_F	1.394	0.98
21_L	37_F	1.381	0.98
103_R	152_E	1.362	0.98
20_M	90_S	1.332	0.98
34_V	72_F	1.299	0.97
107_E	148_E	1.254	0.97
102_A	114_T	1.213	0.96
13_F	136_L	1.210	0.96
142_L	145_G	1.210	0.96
24_R	69_A	1.209	0.96
11_I	101_V	1.204	0.96
59_W	73_D	1.197	0.96
36_K	88_G	1.189	0.96
19_A	78_V	1.182	0.95
101_V	156_Y	1.177	0.95
104_H	110_D	1.160	0.95
78_V	82_I	1.155	0.95
58_A	70_F	1.149	0.95
146_V	153_T	1.135	0.94
11_I	154_D	1.124	0.94
118_I	157_V	1.100	0.93
12_D	98_R	1.098	0.93
56_G	139_Y	1.083	0.93
44_T	85_N	1.046	0.92
62_P	71_R	1.042	0.91
121_H	125_A	1.040	0.91
114_T	155_V	1.040	0.91
111_I	115_V	1.030	0.91
21_L	36_K	1.027	0.91
34_V	70_F	1.023	0.91
22_P	59_W	1.023	0.91
100_A	122_W	0.999	0.90
123_L	130_M	0.983	0.89
108_L	153_T	0.974	0.88
106_G	111_I	0.973	0.88
33_S	37_F	0.969	0.88
37_F	76_G	0.966	0.88
108_L	151_L	0.956	0.87
34_V	74_I	0.953	0.87
143_A	151_L	0.951	0.87
8_V	102_A	0.933	0.86
146_V	150_R	0.922	0.85
84_D	91_N	0.910	0.85
30_L	74_I	0.907	0.85
34_V	106_G	0.904	0.84
8_V	118_I	0.901	0.84
97_G	131_R	0.891	0.83
61_D	64_T	0.882	0.83
105_V	150_R	0.879	0.83
30_L	34_V	0.875	0.82
36_K	69_A	0.874	0.82
115_V	135_I	0.865	0.82
60_D	65_T	0.861	0.81
27_P	60_D	0.852	0.81
57_V	158_P	0.849	0.80
138_H	156_Y	0.841	0.80
11_I	156_Y	0.838	0.79
131_R	156_Y	0.837	0.79
116_W	120_R	0.832	0.79
30_L	72_F	0.824	0.78
21_L	89_V	0.821	0.78
34_V	54_T	0.818	0.78
107_E	153_T	0.818	0.78
148_E	153_T	0.814	0.77
47_S	52_S	0.813	0.77
13_F	16_I	0.812	0.77
101_V	154_D	0.807	0.77
141_N	153_T	0.804	0.77
106_G	151_L	0.803	0.77
32_Y	35_A	0.795	0.76
85_N	88_G	0.794	0.76
61_D	65_T	0.785	0.75
103_R	136_L	0.783	0.75
18_V	92_G	0.776	0.74
119_I	123_L	0.772	0.74
117_G	121_H	0.768	0.73
99_Y	136_L	0.765	0.73
72_F	111_I	0.757	0.72
108_L	139_Y	0.755	0.72
24_R	60_D	0.755	0.72
17_P	81_P	0.755	0.72
20_M	73_D	0.755	0.72
113_H	117_G	0.743	0.71
87_Y	90_S	0.742	0.71
119_I	130_M	0.735	0.70
13_F	99_Y	0.723	0.69
12_D	96_G	0.719	0.68
74_I	142_L	0.715	0.68
124_P	127_G	0.713	0.68
19_A	40_W	0.712	0.68
39_M	43_E	0.711	0.67
108_L	115_V	0.708	0.67
31_N	35_A	0.708	0.67
32_Y	36_K	0.701	0.66
60_D	69_A	0.701	0.66
35_A	39_M	0.700	0.66
22_P	26_S	0.699	0.66
17_P	129_K	0.683	0.64
60_D	137_F	0.682	0.64
99_Y	133_A	0.682	0.64
108_L	143_A	0.682	0.64
19_A	101_V	0.666	0.62
106_G	115_V	0.665	0.62
27_P	137_F	0.662	0.62
15_S	95_T	0.657	0.61
19_A	38_I	0.643	0.60
141_N	148_E	0.641	0.59
57_V	75_C	0.637	0.59
34_V	58_A	0.633	0.58
8_V	100_A	0.629	0.58
20_M	87_Y	0.626	0.58
52_S	77_S	0.618	0.57
32_Y	125_A	0.606	0.55
20_M	75_C	0.606	0.55
62_P	94_L	0.606	0.55
24_R	71_R	0.604	0.55
39_M	145_G	0.603	0.55
48_P	52_S	0.602	0.55
78_V	110_D	0.602	0.55
116_W	121_H	0.593	0.54
23_H	30_L	0.592	0.53
20_M	74_I	0.591	0.53
30_L	37_F	0.590	0.53
41_R	47_S	0.588	0.53
20_M	70_F	0.588	0.53
17_P	78_V	0.587	0.53
35_A	44_T	0.586	0.53
40_W	44_T	0.586	0.53
100_A	123_L	0.584	0.53
36_K	126_S	0.584	0.53
79_S	96_G	0.581	0.52
23_H	33_S	0.581	0.52
94_L	113_H	0.581	0.52
16_I	94_L	0.580	0.52
59_W	65_T	0.576	0.52
48_P	51_Q	0.573	0.51
25_C	62_P	0.572	0.51
33_S	134_P	0.562	0.50
27_P	71_R	0.558	0.49
105_V	140_T	0.558	0.49
17_P	93_E	0.557	0.49
52_S	76_G	0.557	0.49
82_I	85_N	0.555	0.49
123_L	157_V	0.549	0.48
27_P	62_P	0.547	0.48
58_A	136_L	0.547	0.48
13_F	156_Y	0.546	0.48
113_H	120_R	0.546	0.48
110_D	113_H	0.544	0.48
73_D	96_G	0.538	0.47
7_D	158_P	0.536	0.47
61_D	146_V	0.536	0.47
28_E	58_A	0.534	0.46
140_T	156_Y	0.534	0.46
47_S	50_N	0.534	0.46
53_Q	154_D	0.533	0.46
36_K	51_Q	0.532	0.46
25_C	118_I	0.531	0.46
75_C	93_E	0.529	0.46
58_A	115_V	0.528	0.46
110_D	149_Q	0.527	0.45
34_V	102_A	0.526	0.45
19_A	76_G	0.524	0.45
78_V	91_N	0.519	0.45
18_V	55_F	0.518	0.44
58_A	110_D	0.516	0.44
35_A	101_V	0.515	0.44
102_A	117_G	0.511	0.44
34_V	108_L	0.511	0.44
109_D	149_Q	0.510	0.43
45_G	95_T	0.509	0.43
8_V	126_S	0.509	0.43
57_V	134_P	0.507	0.43
37_F	55_F	0.506	0.43
50_N	100_A	0.506	0.43
71_R	137_F	0.503	0.43
104_H	151_L	0.502	0.42
142_L	146_V	0.501	0.42
21_L	24_R	0.501	0.42
45_G	83_P	0.500	0.42

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
3b49A	1	0.9875	100	0.333	Contact Map
1jyhA	1	0.9375	100	0.341	Contact Map
3lurA	1	0.925	100	0.419	Contact Map
3e0hA	1	0.9187	100	0.425	Contact Map
3gk6A	1	0.8875	100	0.428	Contact Map
1d5yA	1	0.9313	99.9	0.457	Contact Map
1r8eA	2	0.9688	99.9	0.457	Contact Map
4b0yA	1	0.9187	98.7	0.775	Contact Map
3r8jA	1	0.9625	97.1	0.844	Contact Map
2govA	1	0.9625	96.9	0.849	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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