DSBA - ECOLI - GREMLIN Contacts

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DSBA - Thiol:disulfide interchange protein DsbA

UniProt:	P0AEG4	Sequences: MKKIWLALAGLVLAFSASAAQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11297
Length:	208 (179)
Sequences:	5832 (4673)
Seq/√Len:	349.2

ECOLI - DSBA DSBC
BACSU - BDBD
HALSA - Q9HN25

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_V	144_A	4.594	1.00
128_R	142_D	3.090	1.00
103_V	106_K	2.799	1.00
68_K	191_D	2.721	1.00
47_F	108_T	2.709	1.00
137_K	140_E	2.663	1.00
40_Q	74_K	2.393	1.00
41_V	73_V	2.326	1.00
191_D	195_Q	2.115	1.00
42_L	78_Y	2.090	1.00
138_G	142_D	2.069	1.00
64_N	185_M	2.018	1.00
90_D	124_A	2.013	1.00
47_F	95_W	2.003	1.00
41_V	174_V	1.980	1.00
89_K	155_A	1.940	1.00
80_V	161_A	1.939	1.00
40_Q	76_T	1.928	1.00
152_S	156_Q	1.924	1.00
124_A	146_N	1.910	1.00
93_Q	151_K	1.868	1.00
110_P	133_N	1.822	1.00
51_H	54_Q	1.814	1.00
126_D	129_D	1.772	1.00
79_H	96_A	1.767	1.00
64_N	68_K	1.750	1.00
30_T	33_K	1.723	1.00
140_E	144_A	1.685	1.00
55_F	172_M	1.674	1.00
159_K	163_D	1.601	1.00
53_Y	57_E	1.562	1.00
45_F	77_K	1.532	1.00
81_N	158_E	1.532	1.00
101_L	144_A	1.523	1.00
33_K	36_A	1.515	1.00
151_K	155_A	1.512	1.00
64_N	67_K	1.506	1.00
132_I	138_G	1.491	1.00
95_W	104_E	1.473	1.00
65_V	69_L	1.468	1.00
69_L	72_G	1.461	1.00
98_A	102_G	1.459	1.00
42_L	76_T	1.435	1.00
107_V	134_A	1.424	1.00
123_S	126_D	1.410	1.00
129_D	133_N	1.400	1.00
100_A	150_V	1.369	1.00
94_A	141_Y	1.356	1.00
173_F	178_Y	1.350	1.00
69_L	195_Q	1.349	1.00
101_L	140_E	1.348	1.00
159_K	162_A	1.344	1.00
128_R	138_G	1.324	1.00
44_F	160_A	1.320	1.00
193_F	197_Y	1.314	1.00
142_D	146_N	1.313	1.00
56_E	109_V	1.301	1.00
113_E	118_T	1.295	1.00
185_M	191_D	1.294	1.00
187_T	192_V	1.259	1.00
110_P	114_G	1.242	1.00
100_A	149_V	1.235	1.00
100_A	144_A	1.227	1.00
107_V	131_F	1.219	1.00
129_D	132_I	1.216	1.00
83_M	88_G	1.210	1.00
140_E	143_A	1.199	1.00
43_E	75_M	1.195	1.00
110_P	130_V	1.185	1.00
43_E	172_M	1.177	1.00
78_Y	160_A	1.161	1.00
15_F	18_S	1.160	1.00
171_A	178_Y	1.156	1.00
148_F	152_S	1.150	1.00
24_D	30_T	1.128	1.00
79_H	157_Q	1.121	1.00
107_V	111_L	1.113	1.00
139_E	142_D	1.107	1.00
184_G	187_T	1.099	1.00
54_Q	58_V	1.091	1.00
16_S	19_A	1.089	1.00
59_L	172_M	1.086	1.00
59_L	75_M	1.083	1.00
109_V	113_E	1.076	1.00
63_D	67_K	1.073	1.00
63_D	109_V	1.071	1.00
96_A	153_L	1.060	1.00
129_D	138_G	1.058	1.00
56_E	108_T	1.057	1.00
68_K	185_M	1.055	1.00
96_A	157_Q	1.052	1.00
89_K	93_Q	1.048	1.00
91_L	111_L	1.030	1.00
94_A	107_V	1.030	1.00
48_F	88_G	1.025	1.00
66_K	70_P	1.021	1.00
168_G	171_A	1.018	1.00
23_E	26_K	1.007	1.00
49_C	52_C	1.006	1.00
57_E	63_D	1.004	1.00
124_A	128_R	1.000	1.00
158_E	162_A	0.999	1.00
44_F	78_Y	0.999	1.00
47_F	79_H	0.989	1.00
93_Q	150_V	0.982	1.00
155_A	158_E	0.980	1.00
31_L	34_P	0.979	1.00
148_F	151_K	0.954	1.00
172_M	188_S	0.945	1.00
93_Q	148_F	0.938	1.00
139_E	143_A	0.933	1.00
90_D	93_Q	0.933	1.00
114_G	130_V	0.920	1.00
25_G	28_Y	0.900	1.00
107_V	141_Y	0.899	1.00
46_S	88_G	0.896	1.00
113_E	117_K	0.895	1.00
14_A	18_S	0.893	1.00
98_A	141_Y	0.885	1.00
155_A	159_K	0.884	1.00
39_P	175_N	0.877	1.00
101_L	137_K	0.866	1.00
46_S	91_L	0.865	1.00
90_D	127_I	0.862	1.00
95_W	107_V	0.854	1.00
48_F	87_L	0.854	1.00
192_V	196_Q	0.853	1.00
160_A	164_V	0.853	1.00
186_D	192_V	0.851	1.00
93_Q	145_W	0.849	1.00
98_A	107_V	0.846	1.00
69_L	191_D	0.841	1.00
68_K	72_G	0.836	1.00
29_T	33_K	0.831	1.00
18_S	21_Q	0.827	1.00
44_F	164_V	0.827	1.00
98_A	131_F	0.814	1.00
65_V	185_M	0.810	1.00
147_S	150_V	0.803	1.00
98_A	136_I	0.799	1.00
156_Q	160_A	0.793	1.00
53_Y	115_V	0.780	1.00
84_G	88_G	0.779	1.00
149_V	152_S	0.779	1.00
94_A	127_I	0.777	1.00
125_S	129_D	0.774	1.00
177_K	197_Y	0.774	1.00
55_F	59_L	0.774	1.00
66_K	71_E	0.771	1.00
66_K	72_G	0.770	1.00
95_W	99_M	0.769	1.00
124_A	142_D	0.768	1.00
47_F	92_T	0.766	1.00
175_N	197_Y	0.765	1.00
97_V	145_W	0.761	1.00
37_G	74_K	0.760	1.00
24_D	27_Q	0.757	1.00
101_L	138_G	0.756	1.00
128_R	132_I	0.756	1.00
152_S	155_A	0.753	1.00
13_L	16_S	0.747	1.00
79_H	104_E	0.742	1.00
143_A	147_S	0.741	1.00
28_Y	33_K	0.740	1.00
183_Q	187_T	0.740	1.00
96_A	100_A	0.737	1.00
84_G	87_L	0.735	1.00
42_L	173_F	0.734	1.00
80_V	158_E	0.732	0.99
166_L	173_F	0.731	0.99
174_V	193_F	0.726	0.99
110_P	134_A	0.724	0.99
16_S	20_A	0.717	0.99
51_H	168_G	0.716	0.99
130_V	134_A	0.712	0.99
77_K	108_T	0.709	0.99
160_A	163_D	0.707	0.99
77_K	105_D	0.697	0.99
14_A	17_A	0.697	0.99
94_A	111_L	0.690	0.99
105_D	109_V	0.688	0.99
91_L	127_I	0.688	0.99
22_Y	25_G	0.681	0.99
94_A	98_A	0.679	0.99
17_A	20_A	0.679	0.99
58_V	64_N	0.677	0.99
96_A	150_V	0.673	0.99
110_P	113_E	0.673	0.99
38_A	72_G	0.672	0.99
31_L	35_V	0.668	0.99
48_F	91_L	0.665	0.99
95_W	111_L	0.662	0.99
56_E	63_D	0.647	0.99
87_L	122_R	0.646	0.99
89_K	151_K	0.646	0.99
80_V	166_L	0.643	0.99
136_I	141_Y	0.640	0.99
187_T	193_F	0.639	0.99
95_W	108_T	0.635	0.99
149_V	153_L	0.632	0.99
166_L	171_A	0.630	0.98
24_D	28_Y	0.629	0.98
177_K	193_F	0.627	0.98
161_A	166_L	0.624	0.98
126_D	130_V	0.624	0.98
97_V	150_V	0.620	0.98
98_A	101_L	0.611	0.98
193_F	196_Q	0.607	0.98
26_K	33_K	0.603	0.98
16_S	21_Q	0.602	0.98
106_K	134_A	0.601	0.98
26_K	30_T	0.599	0.98
65_V	68_K	0.599	0.98
15_F	20_A	0.598	0.98
128_R	131_F	0.593	0.98
130_V	133_N	0.587	0.98
39_P	194_V	0.585	0.98
179_Q	193_F	0.584	0.98
90_D	145_W	0.583	0.97
45_F	112_F	0.582	0.97
23_E	27_Q	0.580	0.97
28_Y	31_L	0.580	0.97
66_K	69_L	0.578	0.97
81_N	169_V	0.577	0.97
38_A	74_K	0.575	0.97
22_Y	27_Q	0.574	0.97
25_G	29_T	0.569	0.97
81_N	92_T	0.568	0.97
131_F	136_I	0.567	0.97
26_K	29_T	0.566	0.97
28_Y	32_E	0.563	0.97
50_P	54_Q	0.558	0.97
39_P	73_V	0.557	0.97
43_E	56_E	0.557	0.97
82_F	88_G	0.554	0.97
167_R	178_Y	0.553	0.97
120_T	123_S	0.552	0.97
17_A	21_Q	0.549	0.96
122_R	126_D	0.545	0.96
96_A	154_V	0.545	0.96
44_F	161_A	0.543	0.96
99_M	153_L	0.541	0.96
94_A	131_F	0.538	0.96
89_K	158_E	0.538	0.96
103_V	134_A	0.536	0.96
101_L	136_I	0.535	0.96
108_T	112_F	0.535	0.96
67_K	70_P	0.534	0.96
111_L	127_I	0.533	0.96
184_G	188_S	0.533	0.96
63_D	66_K	0.532	0.96
29_T	32_E	0.532	0.96
48_F	121_I	0.532	0.96
131_F	141_Y	0.528	0.96
174_V	179_Q	0.527	0.96
65_V	73_V	0.524	0.95
79_H	95_W	0.521	0.95
30_T	36_A	0.519	0.95
31_L	74_K	0.518	0.95
81_N	88_G	0.516	0.95
158_E	161_A	0.515	0.95
45_F	105_D	0.513	0.95
124_A	145_W	0.507	0.94
27_Q	30_T	0.504	0.94
49_C	169_V	0.501	0.94
188_S	193_F	0.500	0.94
141_Y	145_W	0.500	0.94
96_A	99_M	0.500	0.94

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
3l9sA	1	0.8894	100	0.34	Contact Map
4od7A	1	0.8558	100	0.343	Contact Map
3l9vA	1	0.8702	100	0.362	Contact Map
4dvcA	1	0.8798	100	0.38	Contact Map
3f4sA	1	0.8798	100	0.4	Contact Map
2znmA	3	0.8606	100	0.405	Contact Map
4n30A	1	0.8221	100	0.405	Contact Map
4jrrA	1	0.8606	100	0.407	Contact Map
4pwoA	1	0.9615	100	0.408	Contact Map
3hz8A	1	0.8798	100	0.409	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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