YGBL - ECOLI - GREMLIN Contacts

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YGBL - Putative aldolase class 2 protein YgbL

UniProt:	Q46890	Sequences: MSDFAKVEQSLREEMTRIASSFFQRGYATGSAGNLSLLLPDGNLLATPTGSCLGNLDPQRLSKVAADGEWLSGDKPSKEVLFHLALYRNNPRCKAVVHLHSTWSTALSCLQGLDSSNVIRPFTPYVVMRMGNVPLVPYYRPGDKRIAQDLAELAADNQAFLLANHGPVVCGESLQEAANNMEELEETAKLIFILGDRPIRYLTAGEIAELRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13106
Length:	212 (188)
Sequences:	6371 (3774)
Seq/√Len:	275.2

ECOLI - YGBL FUCA ULAF ARAD SGBE RHAD
BACSU - ARAD MTNB
HALSA - Q9HQE3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_A	69_E	4.933	1.00
172_E	176_E	3.243	1.00
189_K	193_I	3.165	1.00
103_W	193_I	3.122	1.00
43_N	63_K	3.020	1.00
112_G	195_G	2.685	1.00
11_L	37_L	2.626	1.00
44_L	84_L	2.537	1.00
45_L	61_L	2.534	1.00
14_E	175_Q	2.418	1.00
144_K	148_Q	2.291	1.00
93_C	170_C	2.217	1.00
106_A	193_I	2.106	1.00
102_T	189_K	2.095	1.00
43_N	71_L	2.094	1.00
85_A	148_Q	2.089	1.00
103_W	189_K	2.087	1.00
9_Q	13_E	2.076	1.00
103_W	192_F	1.993	1.00
16_T	58_P	1.909	1.00
37_L	174_L	1.882	1.00
13_E	17_R	1.877	1.00
85_A	88_R	1.844	1.00
57_D	60_R	1.829	1.00
159_A	184_L	1.811	1.00
45_L	63_K	1.809	1.00
97_V	177_A	1.797	1.00
137_P	163_A	1.793	1.00
39_L	45_L	1.768	1.00
94_K	173_S	1.711	1.00
193_I	196_D	1.711	1.00
21_S	25_R	1.699	1.00
95_A	174_L	1.673	1.00
173_S	176_E	1.666	1.00
15_M	35_L	1.646	1.00
90_N	93_C	1.638	1.00
64_V	80_V	1.626	1.00
10_S	14_E	1.586	1.00
18_I	178_A	1.577	1.00
139_Y	149_D	1.576	1.00
111_Q	163_A	1.533	1.00
25_R	182_E	1.493	1.00
13_E	58_P	1.491	1.00
16_T	20_S	1.485	1.00
171_G	176_E	1.483	1.00
134_P	157_N	1.472	1.00
67_D	88_R	1.434	1.00
167_P	184_L	1.419	1.00
102_T	106_A	1.403	1.00
37_L	95_A	1.389	1.00
89_N	151_A	1.389	1.00
15_M	61_L	1.365	1.00
89_N	155_A	1.332	1.00
99_L	181_M	1.328	1.00
100_H	165_H	1.318	1.00
85_A	89_N	1.297	1.00
20_S	24_Q	1.273	1.00
169_V	181_M	1.248	1.00
107_L	195_G	1.242	1.00
40_P	43_N	1.232	1.00
44_L	66_A	1.230	1.00
46_A	77_S	1.230	1.00
84_L	88_R	1.225	1.00
98_H	165_H	1.218	1.00
21_S	24_Q	1.214	1.00
137_P	152_E	1.208	1.00
36_S	96_V	1.197	1.00
36_S	87_Y	1.187	1.00
38_L	94_K	1.175	1.00
102_T	186_E	1.162	1.00
158_Q	180_N	1.158	1.00
111_Q	200_R	1.151	1.00
105_T	108_S	1.150	1.00
16_T	61_L	1.144	1.00
162_L	168_V	1.141	1.00
103_W	185_E	1.133	1.00
149_D	152_E	1.131	1.00
104_S	167_P	1.130	1.00
191_I	195_G	1.120	1.00
185_E	189_K	1.111	1.00
22_F	35_L	1.103	1.00
87_Y	96_V	1.100	1.00
48_P	51_S	1.092	1.00
51_S	60_R	1.081	1.00
23_F	54_G	1.079	1.00
99_L	167_P	1.078	1.00
39_L	63_K	1.070	1.00
148_Q	152_E	1.067	1.00
22_F	97_V	1.066	1.00
197_R	200_R	1.063	1.00
150_L	162_L	1.048	1.00
18_I	174_L	1.046	1.00
192_F	196_D	1.045	1.00
186_E	189_K	1.044	1.00
137_P	149_D	1.032	1.00
104_S	184_L	1.032	1.00
159_A	169_V	1.012	1.00
154_A	170_C	1.005	1.00
70_W	73_G	0.997	1.00
65_A	71_L	0.993	1.00
44_L	80_V	0.992	1.00
19_A	35_L	0.977	1.00
136_V	149_D	0.963	1.00
195_G	198_P	0.962	1.00
25_R	178_A	0.939	1.00
60_R	74_D	0.928	1.00
145_R	148_Q	0.927	1.00
120_R	191_I	0.924	1.00
109_C	122_F	0.923	1.00
56_L	60_R	0.909	1.00
63_K	72_S	0.909	1.00
66_A	88_R	0.908	1.00
102_T	193_I	0.907	1.00
22_F	178_A	0.907	1.00
14_E	17_R	0.901	1.00
16_T	56_L	0.900	1.00
90_N	170_C	0.897	1.00
136_V	139_Y	0.893	1.00
18_I	35_L	0.891	1.00
125_Y	130_M	0.889	1.00
14_E	37_L	0.887	1.00
138_Y	142_G	0.885	1.00
171_G	180_N	0.882	1.00
44_L	64_V	0.880	1.00
62_S	75_K	0.871	1.00
154_A	160_F	0.867	1.00
11_L	39_L	0.863	1.00
39_L	43_N	0.856	1.00
97_V	181_M	0.855	1.00
101_S	104_S	0.855	1.00
86_L	93_C	0.840	1.00
133_V	184_L	0.838	1.00
48_P	61_L	0.838	1.00
47_T	56_L	0.835	1.00
167_P	181_M	0.827	0.99
106_A	192_F	0.826	0.99
139_Y	142_G	0.824	0.99
198_P	201_Y	0.823	0.99
176_E	180_N	0.817	0.99
82_F	150_L	0.815	0.99
55_N	175_Q	0.815	0.99
85_A	151_A	0.812	0.99
38_L	66_A	0.809	0.99
136_V	153_L	0.805	0.99
101_S	181_M	0.805	0.99
136_V	162_L	0.799	0.99
86_L	154_A	0.792	0.99
89_N	152_E	0.791	0.99
12_R	72_S	0.787	0.99
82_F	168_V	0.781	0.99
112_G	198_P	0.780	0.99
46_A	79_E	0.773	0.99
152_E	155_A	0.766	0.99
21_S	178_A	0.764	0.99
17_R	55_N	0.762	0.99
94_K	172_E	0.746	0.99
118_V	188_A	0.743	0.99
145_R	149_D	0.743	0.99
88_R	151_A	0.739	0.99
10_S	13_E	0.730	0.99
101_S	185_E	0.725	0.99
11_L	14_E	0.724	0.99
134_P	160_F	0.723	0.99
36_S	46_A	0.719	0.99
49_T	75_K	0.716	0.99
79_E	146_I	0.715	0.99
127_V	131_G	0.712	0.98
47_T	87_Y	0.710	0.98
119_I	191_I	0.705	0.98
108_S	161_L	0.704	0.98
26_G	189_K	0.703	0.98
30_G	179_N	0.702	0.98
197_R	201_Y	0.702	0.98
85_A	144_K	0.701	0.98
107_L	191_I	0.700	0.98
132_N	157_N	0.692	0.98
42_G	66_A	0.692	0.98
38_L	42_G	0.686	0.98
19_A	53_L	0.683	0.98
22_F	27_Y	0.681	0.98
176_E	179_N	0.679	0.98
12_R	45_L	0.679	0.98
68_G	84_L	0.674	0.98
120_R	201_Y	0.672	0.98
81_L	144_K	0.670	0.98
80_V	84_L	0.664	0.98
163_A	200_R	0.664	0.98
105_T	190_L	0.663	0.98
31_S	49_T	0.659	0.98
140_R	145_R	0.658	0.97
49_T	77_S	0.654	0.97
153_L	160_F	0.653	0.97
34_N	79_E	0.652	0.97
34_N	77_S	0.651	0.97
110_L	194_L	0.645	0.97
124_P	127_V	0.644	0.97
125_Y	128_M	0.644	0.97
184_L	188_A	0.643	0.97
90_N	158_Q	0.640	0.97
151_A	154_A	0.636	0.97
127_V	130_M	0.635	0.97
63_K	71_L	0.635	0.97
33_G	53_L	0.634	0.97
95_A	177_A	0.634	0.97
51_S	56_L	0.632	0.97
29_T	186_E	0.626	0.97
90_N	154_A	0.624	0.97
86_L	168_V	0.617	0.96
43_N	66_A	0.615	0.96
15_M	45_L	0.613	0.96
128_M	131_G	0.610	0.96
38_L	44_L	0.609	0.96
55_N	60_R	0.607	0.96
169_V	180_N	0.606	0.96
107_L	188_A	0.603	0.96
105_T	166_G	0.603	0.96
12_R	58_P	0.599	0.96
23_F	29_T	0.598	0.96
133_V	159_A	0.596	0.96
97_V	169_V	0.595	0.95
28_A	35_L	0.593	0.95
101_S	167_P	0.592	0.95
160_F	168_V	0.588	0.95
24_Q	54_G	0.586	0.95
21_S	30_G	0.586	0.95
23_F	28_A	0.585	0.95
118_V	132_N	0.584	0.95
110_L	192_F	0.580	0.95
121_P	195_G	0.578	0.95
11_L	45_L	0.575	0.95
62_S	70_W	0.573	0.94
194_L	197_R	0.570	0.94
110_L	198_P	0.568	0.94
17_R	20_S	0.564	0.94
23_F	53_L	0.561	0.94
118_V	135_L	0.560	0.94
52_C	55_N	0.558	0.94
15_M	19_A	0.558	0.94
122_F	191_I	0.557	0.94
128_M	179_N	0.556	0.94
104_S	188_A	0.556	0.94
158_Q	176_E	0.555	0.93
29_T	32_A	0.555	0.93
66_A	84_L	0.553	0.93
12_R	61_L	0.551	0.93
158_Q	172_E	0.547	0.93
103_W	106_A	0.545	0.93
149_D	153_L	0.544	0.93
92_R	172_E	0.544	0.93
123_T	126_V	0.544	0.93
161_L	167_P	0.544	0.93
106_A	190_L	0.543	0.93
25_R	30_G	0.543	0.93
107_L	192_F	0.542	0.93
32_A	186_E	0.541	0.93
9_Q	12_R	0.539	0.92
151_A	155_A	0.538	0.92
14_E	174_L	0.536	0.92
104_S	161_L	0.534	0.92
81_L	85_A	0.532	0.92
87_Y	95_A	0.530	0.92
49_T	78_K	0.530	0.92
89_N	160_F	0.528	0.92
104_S	181_M	0.526	0.92
12_R	48_P	0.523	0.91
144_K	147_A	0.518	0.91
19_A	56_L	0.515	0.91
64_V	84_L	0.515	0.91
65_A	68_G	0.514	0.91
179_N	186_E	0.513	0.91
9_Q	58_P	0.512	0.90
164_N	200_R	0.511	0.90
153_L	156_D	0.509	0.90
86_L	96_V	0.509	0.90
15_M	37_L	0.508	0.90
12_R	63_K	0.506	0.90
138_Y	162_L	0.505	0.90
126_V	130_M	0.505	0.90
35_L	174_L	0.505	0.90
34_N	49_T	0.502	0.90
128_M	180_N	0.500	0.89
119_I	122_F	0.500	0.89

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
3ocrA	4	0.9764	100	0.149	Contact Map
4c24A	3	0.9623	100	0.163	Contact Map
1e4cP	3	0.9434	100	0.165	Contact Map
2opiA	3	0.9528	100	0.173	Contact Map
4xxfA	3	0.9434	100	0.192	Contact Map
2z7bA	3	0.9481	100	0.197	Contact Map
2v9lA	3	0.967	100	0.205	Contact Map
1k0wA	3	0.9481	100	0.212	Contact Map
2fk5A	4	0.8821	100	0.217	Contact Map
2irpA	4	0.9057	100	0.22	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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