YAIL - ECOLI - GREMLIN Contacts

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YAIL - Uncharacterized protein YaiL

UniProt:	P51024	Sequences: MAKLTLQEQLLKAGLVTSKKAAKVERTAKKSRVQAREARAAVEENKKAQLERDKQLSEQQKQAALAKEYKAQVKQLIEMNRITIANGDIGFNFTDGNLIKKIFVDKLTQAQLINGRLAIARLLVDNNSEGEYAIIPASVADKIAQRDASSIVLHSALSAEEQDEDDPYADFKVPDDLMW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13294
Length:	179 (170)
Sequences:	475 (290)
Seq/√Len:	22.2

ECOLI - YAIL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_Q	58_E	4.245	1.00
95_D	132_Y	3.925	1.00
44_E	48_A	3.542	1.00
95_D	121_R	3.488	1.00
81_R	133_A	2.983	0.99
43_E	46_K	2.852	0.99
58_E	62_Q	2.721	0.99
120_A	135_I	2.697	0.99
73_V	147_D	2.674	0.99
88_D	106_K	2.562	0.98
55_Q	59_Q	2.450	0.98
4_L	8_E	2.430	0.98
73_V	149_S	2.381	0.97
90_G	103_F	2.360	0.97
118_A	140_A	2.333	0.97
105_D	108_T	2.227	0.96
42_V	45_N	2.172	0.95
90_G	101_K	2.162	0.95
120_A	151_I	2.097	0.95
45_N	49_Q	2.083	0.94
49_Q	53_D	2.080	0.94
64_A	68_E	1.995	0.93
17_T	20_K	1.943	0.92
61_K	65_L	1.920	0.91
57_S	68_E	1.885	0.91
91_F	153_L	1.849	0.90
59_Q	63_A	1.812	0.89
47_K	50_L	1.795	0.88
72_Q	146_R	1.764	0.87
82_I	117_L	1.747	0.87
93_F	132_Y	1.697	0.85
169_A	172_K	1.675	0.84
141_D	154_H	1.671	0.84
104_V	112_L	1.621	0.82
135_I	151_I	1.613	0.82
62_Q	99_I	1.613	0.82
52_R	173_V	1.504	0.77
138_S	141_D	1.447	0.74
73_V	99_I	1.430	0.74
48_A	52_R	1.421	0.73
71_A	142_K	1.409	0.72
51_E	55_Q	1.396	0.72
51_E	54_K	1.367	0.70
58_E	61_K	1.365	0.70
72_Q	142_K	1.344	0.69
7_Q	11_L	1.341	0.69
108_T	134_I	1.325	0.68
142_K	146_R	1.324	0.68
120_A	133_A	1.291	0.66
167_P	170_D	1.271	0.64
174_P	179_W	1.250	0.63
57_S	60_Q	1.245	0.63
20_K	24_V	1.210	0.60
4_L	12_K	1.201	0.60
40_A	43_E	1.191	0.59
68_E	173_V	1.189	0.59
63_A	84_I	1.180	0.58
173_V	178_M	1.176	0.58
65_L	68_E	1.169	0.58
54_K	58_E	1.165	0.57
104_V	142_K	1.163	0.57
84_I	133_A	1.162	0.57
175_D	179_W	1.128	0.55
122_L	165_D	1.115	0.54
167_P	178_M	1.103	0.53
38_A	42_V	1.094	0.53
176_D	179_W	1.071	0.51
64_A	99_I	1.058	0.50
6_L	10_L	1.057	0.50
89_I	109_Q	1.052	0.50
174_P	177_L	1.051	0.50
99_I	102_I	1.047	0.49
19_K	26_R	1.034	0.49
37_E	41_A	1.031	0.48
83_T	86_N	1.025	0.48
67_K	163_D	1.023	0.48
33_V	36_R	1.021	0.48
8_E	21_A	1.004	0.46
168_Y	175_D	0.991	0.46
68_E	72_Q	0.989	0.45
60_Q	63_A	0.976	0.45
167_P	172_K	0.975	0.45
22_A	57_S	0.967	0.44
118_A	137_A	0.960	0.43
59_Q	102_I	0.956	0.43
23_K	38_A	0.954	0.43
107_L	173_V	0.951	0.43
87_G	164_E	0.946	0.43
41_A	44_E	0.940	0.42
64_A	72_Q	0.939	0.42
71_A	146_R	0.938	0.42
13_A	88_D	0.928	0.41
163_D	167_P	0.908	0.40
162_Q	167_P	0.895	0.39
164_E	167_P	0.894	0.39
69_Y	72_Q	0.890	0.39
74_K	99_I	0.886	0.39
65_L	72_Q	0.881	0.38
168_Y	174_P	0.870	0.38
168_Y	179_W	0.870	0.38
76_L	79_M	0.865	0.37
6_L	9_Q	0.860	0.37
80_N	102_I	0.854	0.37
72_Q	139_V	0.849	0.36
61_K	64_A	0.845	0.36
25_E	33_V	0.840	0.36
4_L	21_A	0.838	0.36
109_Q	173_V	0.831	0.35
101_K	130_G	0.829	0.35
103_F	131_E	0.824	0.35
106_K	110_A	0.823	0.35
8_E	94_T	0.817	0.34
134_I	148_A	0.806	0.34
7_Q	25_E	0.798	0.33
42_V	142_K	0.795	0.33
60_Q	101_K	0.795	0.33
105_D	117_L	0.794	0.33
112_L	119_I	0.794	0.33
162_Q	172_K	0.791	0.33
82_I	112_L	0.790	0.33
136_P	146_R	0.788	0.32
73_V	143_I	0.787	0.32
57_S	61_K	0.785	0.32
119_I	158_S	0.780	0.32
102_I	158_S	0.777	0.32
106_K	134_I	0.770	0.31
20_K	94_T	0.770	0.31
41_A	45_N	0.770	0.31
109_Q	113_I	0.769	0.31
80_N	138_S	0.768	0.31
135_I	143_I	0.766	0.31
37_E	66_A	0.764	0.31
16_V	163_D	0.758	0.31
21_A	24_V	0.755	0.31
138_S	162_Q	0.751	0.30
107_L	110_A	0.750	0.30
25_E	28_A	0.749	0.30
30_K	34_Q	0.748	0.30
76_L	139_V	0.746	0.30
101_K	109_Q	0.746	0.30
22_A	26_R	0.738	0.30
92_N	101_K	0.734	0.29
152_V	155_S	0.729	0.29
73_V	150_S	0.725	0.29
85_A	88_D	0.724	0.29
23_K	29_K	0.723	0.29
161_E	164_E	0.723	0.29
90_G	135_I	0.723	0.29
49_Q	100_K	0.722	0.29
42_V	159_A	0.711	0.28
98_L	166_D	0.711	0.28
56_L	169_A	0.708	0.28
7_Q	20_K	0.704	0.28
23_K	80_N	0.701	0.27
34_Q	102_I	0.697	0.27
5_T	21_A	0.696	0.27
9_Q	14_G	0.695	0.27
8_E	31_S	0.691	0.27
66_A	108_T	0.690	0.27
106_K	156_A	0.690	0.27
77_I	120_A	0.683	0.27
50_L	134_I	0.683	0.27
21_A	49_Q	0.681	0.26
43_E	47_K	0.680	0.26
166_D	169_A	0.676	0.26
59_Q	62_Q	0.674	0.26
44_E	82_I	0.673	0.26
167_P	171_F	0.672	0.26
87_G	105_D	0.666	0.26
12_K	16_V	0.663	0.25
28_A	32_R	0.661	0.25
67_K	173_V	0.660	0.25
168_Y	176_D	0.656	0.25
115_G	166_D	0.652	0.25
168_Y	171_F	0.650	0.25
77_I	81_R	0.643	0.24
26_R	71_A	0.643	0.24
101_K	173_V	0.639	0.24
50_L	163_D	0.638	0.24
139_V	142_K	0.637	0.24
33_V	63_A	0.632	0.24
148_A	156_A	0.632	0.24
39_R	131_E	0.632	0.24
121_R	171_F	0.629	0.24
168_Y	177_L	0.623	0.23
15_L	21_A	0.623	0.23
70_K	99_I	0.615	0.23
8_E	170_D	0.615	0.23
25_E	137_A	0.614	0.23
52_R	56_L	0.610	0.23
25_E	34_Q	0.608	0.23
139_V	146_R	0.608	0.23
32_R	97_N	0.601	0.22
4_L	7_Q	0.598	0.22
12_K	15_L	0.598	0.22
71_A	93_F	0.597	0.22
20_K	23_K	0.597	0.22
29_K	67_K	0.597	0.22
71_A	99_I	0.594	0.22
105_D	158_S	0.593	0.22
102_I	118_A	0.593	0.22
135_I	139_V	0.593	0.22
79_M	171_F	0.591	0.22
119_I	152_V	0.590	0.22
70_K	147_D	0.589	0.22
8_E	33_V	0.585	0.22
20_K	164_E	0.580	0.21
141_D	145_Q	0.576	0.21
42_V	52_R	0.567	0.21
69_Y	143_I	0.564	0.21
10_L	14_G	0.562	0.21
162_Q	166_D	0.561	0.21
90_G	172_K	0.561	0.21
56_L	75_Q	0.560	0.21
18_S	24_V	0.560	0.21
16_V	91_F	0.550	0.20
49_Q	59_Q	0.550	0.20
7_Q	94_T	0.542	0.20
23_K	33_V	0.542	0.20
37_E	51_E	0.540	0.20
59_Q	110_A	0.539	0.20
43_E	50_L	0.538	0.20
73_V	155_S	0.538	0.20
72_Q	136_P	0.538	0.20
71_A	143_I	0.536	0.19
6_L	14_G	0.533	0.19
47_K	51_E	0.533	0.19
47_K	58_E	0.530	0.19
65_L	162_Q	0.529	0.19
102_I	120_A	0.528	0.19
52_R	93_F	0.527	0.19
58_E	171_F	0.527	0.19
73_V	134_I	0.526	0.19
24_V	106_K	0.526	0.19
69_Y	114_N	0.525	0.19
59_Q	87_G	0.525	0.19
74_K	92_N	0.525	0.19
38_A	41_A	0.524	0.19
41_A	83_T	0.522	0.19
77_I	155_S	0.518	0.19
49_Q	109_Q	0.517	0.19
137_A	154_H	0.516	0.19
50_L	160_E	0.515	0.19
46_K	129_E	0.515	0.19
110_A	114_N	0.511	0.18
98_L	114_N	0.509	0.18
74_K	78_E	0.508	0.18
53_D	56_L	0.508	0.18
84_I	108_T	0.508	0.18
54_K	66_A	0.506	0.18
74_K	129_E	0.506	0.18
22_A	27_T	0.502	0.18
18_S	33_V	0.501	0.18
50_L	64_A	0.500	0.18
46_K	114_N	0.500	0.18

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
1pkhA	5	0.3631	11.1	0.96	Contact Map
4ogeA	1	0.8715	8.5	0.962	Contact Map
3vhjA	1	0.4581	6.7	0.964	Contact Map
4ujrT	1	0.1844	6.3	0.964	Contact Map
4a18L	1	0.1508	5.6	0.965	Contact Map
2id0A	1	0.5754	5.3	0.965	Contact Map
3lzdA	2	0.1788	4.7	0.966	Contact Map
1n81A	1	0.5866	4.7	0.966	Contact Map
3u5eg	1	0.1844	4.5	0.966	Contact Map
1tj7A	4	0.514	4.5	0.967	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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