ExoD - PFAM28P - GREMLIN Contacts

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ExoD - Exopolysaccharide synthesis, ExoD

PFAM:	PF06055	Sequences: LSDLLERLAAEAPGERVTLGELLDALGERSFGLLLLLLALPNLLPLPIPGVSTVFGLPLLLLALQLLLGRRTPWLPRRLARRSLPRARLRRLLRRLLPWLRRLERLSRPRLTFLTGRPARRLIGLLILLLALLLALPIPFTNTLPALAIVLLALGLLERDGLLVLLGLLLGLAALALFA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	179 (177)
Sequences:	6831 (5113)
Seq/√Len:	384.3
META:	0.848

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_R	81_R	3.700	1.00
20_G	80_A	3.681	1.00
155_G	164_V	3.662	1.00
16_R	83_S	3.164	1.00
78_R	82_R	2.853	1.00
36_L	150_V	2.500	1.00
20_G	81_R	2.452	1.00
138_I	141_T	2.380	1.00
99_W	102_R	2.344	1.00
111_L	165_L	2.292	1.00
85_P	88_R	2.274	1.00
91_R	95_R	2.268	1.00
123_I	164_V	2.216	1.00
151_L	170_L	2.183	1.00
36_L	153_A	2.146	1.00
60_L	128_L	2.139	1.00
6_E	97_L	2.099	1.00
102_R	106_L	1.972	1.00
2_S	104_E	1.933	1.00
98_P	102_R	1.918	1.00
110_R	162_L	1.895	1.00
20_G	24_D	1.786	1.00
18_T	21_E	1.771	1.00
6_E	101_R	1.733	1.00
63_A	128_L	1.710	1.00
130_L	171_G	1.704	1.00
148_A	170_L	1.667	1.00
111_L	161_G	1.667	1.00
63_A	124_G	1.664	1.00
117_R	121_R	1.660	1.00
67_L	125_L	1.635	1.00
162_L	166_L	1.632	1.00
123_I	168_L	1.601	1.00
116_G	119_A	1.568	1.00
95_R	98_P	1.554	1.00
39_A	150_V	1.546	1.00
64_L	68_L	1.490	1.00
152_L	171_G	1.475	1.00
39_A	59_L	1.465	1.00
174_A	178_F	1.453	1.00
145_P	148_A	1.422	1.00
86_R	90_R	1.394	1.00
90_R	94_R	1.393	1.00
35_L	63_A	1.366	1.00
60_L	132_L	1.359	1.00
118_P	121_R	1.354	1.00
133_L	137_P	1.343	1.00
59_L	131_A	1.342	1.00
32_G	153_A	1.341	1.00
75_L	80_A	1.340	1.00
107_S	158_E	1.337	1.00
44_L	47_P	1.336	1.00
151_L	163_L	1.294	1.00
67_L	124_G	1.293	1.00
78_R	81_R	1.287	1.00
111_L	162_L	1.262	1.00
20_G	77_R	1.232	1.00
63_A	127_I	1.230	1.00
63_A	131_A	1.222	1.00
134_L	137_P	1.222	1.00
148_A	174_A	1.208	1.00
88_R	91_R	1.204	1.00
77_R	80_A	1.190	1.00
95_R	99_W	1.137	1.00
126_L	168_L	1.134	1.00
67_L	128_L	1.131	1.00
39_A	146_A	1.130	1.00
60_L	131_A	1.121	1.00
39_A	153_A	1.118	1.00
18_T	83_S	1.117	1.00
69_G	121_R	1.116	1.00
148_A	167_G	1.114	1.00
115_T	118_P	1.111	1.00
4_L	29_R	1.098	1.00
107_S	163_L	1.098	1.00
137_P	142_N	1.082	1.00
35_L	149_I	1.082	1.00
11_E	25_A	1.077	1.00
152_L	167_G	1.075	1.00
173_A	176_A	1.064	1.00
133_L	136_L	1.061	1.00
31_F	65_Q	1.060	1.00
119_A	123_I	1.052	1.00
9_A	97_L	1.034	1.00
70_R	74_W	1.033	1.00
43_L	147_L	1.020	1.00
97_L	101_R	1.013	1.00
155_G	167_G	1.011	1.00
46_L	51_V	1.004	1.00
31_F	73_P	1.001	1.00
40_L	96_L	1.001	1.00
5_L	93_L	1.000	1.00
171_G	175_L	0.999	1.00
38_L	59_L	0.995	1.00
151_L	167_G	0.992	1.00
34_L	62_L	0.987	1.00
173_A	177_L	0.987	1.00
115_T	164_V	0.978	1.00
65_Q	70_R	0.958	1.00
64_L	67_L	0.954	1.00
7_R	11_E	0.953	1.00
54_V	58_P	0.953	1.00
42_N	49_P	0.951	1.00
66_L	156_L	0.949	1.00
161_G	165_L	0.935	1.00
6_E	10_A	0.933	1.00
16_R	85_P	0.927	1.00
127_I	149_I	0.921	1.00
107_S	154_L	0.900	1.00
126_L	171_G	0.896	1.00
35_L	153_A	0.892	1.00
153_A	157_L	0.891	1.00
115_T	159_R	0.888	1.00
98_P	101_R	0.879	1.00
129_L	175_L	0.875	1.00
87_A	91_R	0.875	1.00
23_L	34_L	0.871	1.00
131_A	149_I	0.868	1.00
171_G	174_A	0.851	1.00
42_N	55_F	0.851	1.00
38_L	55_F	0.836	1.00
117_R	120_R	0.834	1.00
102_R	105_R	0.825	1.00
131_A	137_P	0.824	1.00
34_L	73_P	0.823	1.00
123_I	152_L	0.823	1.00
136_L	142_N	0.821	1.00
172_L	176_A	0.820	1.00
41_P	92_L	0.819	1.00
9_A	94_R	0.819	1.00
131_A	134_L	0.817	1.00
155_G	163_L	0.816	1.00
18_T	81_R	0.812	1.00
96_L	99_W	0.811	1.00
100_L	104_E	0.805	1.00
69_G	72_T	0.799	1.00
43_L	48_I	0.798	1.00
165_L	169_L	0.798	1.00
148_A	171_G	0.795	1.00
56_G	131_A	0.789	1.00
79_L	82_R	0.788	1.00
61_L	64_L	0.786	1.00
62_L	73_P	0.785	1.00
9_A	12_A	0.774	1.00
87_A	90_R	0.774	1.00
168_L	172_L	0.774	1.00
52_S	56_G	0.772	1.00
42_N	56_G	0.771	1.00
166_L	170_L	0.770	1.00
59_L	134_L	0.770	1.00
12_A	86_R	0.764	1.00
134_L	142_N	0.762	1.00
30_S	73_P	0.759	1.00
11_E	14_G	0.754	1.00
39_A	149_I	0.753	1.00
131_A	135_A	0.752	1.00
114_L	165_L	0.744	1.00
42_N	146_A	0.743	1.00
152_L	168_L	0.743	1.00
132_L	136_L	0.741	1.00
23_L	80_A	0.737	1.00
19_L	79_L	0.736	1.00
35_L	62_L	0.730	1.00
144_L	174_A	0.728	1.00
66_L	124_G	0.723	1.00
110_R	161_G	0.720	1.00
24_D	80_A	0.719	1.00
36_L	154_L	0.718	1.00
28_E	120_R	0.713	1.00
40_L	150_V	0.710	1.00
19_L	38_L	0.709	1.00
133_L	178_F	0.704	1.00
59_L	63_A	0.701	1.00
112_T	115_T	0.699	1.00
91_R	94_R	0.699	1.00
3_D	7_R	0.697	0.99
45_P	49_P	0.696	0.99
144_L	177_L	0.696	0.99
143_T	147_L	0.694	0.99
41_P	142_N	0.694	0.99
29_R	32_G	0.691	0.99
110_R	160_D	0.689	0.99
53_T	135_A	0.688	0.99
8_L	25_A	0.675	0.99
32_G	157_L	0.674	0.99
15_E	85_P	0.673	0.99
8_L	12_A	0.672	0.99
35_L	127_I	0.667	0.99
7_R	10_A	0.666	0.99
61_L	79_L	0.657	0.99
49_P	52_S	0.656	0.99
109_P	112_T	0.656	0.99
61_L	74_W	0.653	0.99
36_L	40_L	0.649	0.99
60_L	64_L	0.646	0.99
64_L	128_L	0.644	0.99
89_L	92_L	0.643	0.99
106_L	109_P	0.640	0.99
93_L	96_L	0.635	0.99
153_A	156_L	0.629	0.99
42_N	51_V	0.626	0.99
84_L	89_L	0.625	0.99
136_L	141_T	0.624	0.99
24_D	72_T	0.618	0.99
42_N	52_S	0.613	0.99
53_T	142_N	0.609	0.99
44_L	48_I	0.609	0.99
55_F	58_P	0.606	0.99
162_L	165_L	0.604	0.99
58_P	62_L	0.602	0.99
138_I	142_N	0.598	0.98
161_G	164_V	0.598	0.98
130_L	149_I	0.597	0.98
56_G	135_A	0.595	0.98
36_L	39_A	0.595	0.98
28_E	71_R	0.595	0.98
115_T	119_A	0.595	0.98
159_R	165_L	0.594	0.98
47_P	143_T	0.593	0.98
93_L	135_A	0.593	0.98
63_A	67_L	0.593	0.98
43_L	149_I	0.584	0.98
21_E	24_D	0.582	0.98
145_P	174_A	0.582	0.98
42_N	48_I	0.582	0.98
123_I	156_L	0.581	0.98
127_I	152_L	0.581	0.98
42_N	46_L	0.575	0.98
70_R	73_P	0.575	0.98
168_L	171_G	0.571	0.98
148_A	152_L	0.568	0.98
8_L	15_E	0.567	0.98
94_R	98_P	0.567	0.98
65_Q	74_W	0.562	0.98
3_D	6_E	0.560	0.98
15_E	86_R	0.558	0.98
35_L	59_L	0.554	0.97
63_A	152_L	0.553	0.97
155_G	165_L	0.552	0.97
51_V	54_V	0.546	0.97
24_D	27_G	0.543	0.97
44_L	95_R	0.542	0.97
121_R	124_G	0.542	0.97
63_A	130_L	0.542	0.97
170_L	174_A	0.540	0.97
52_S	142_N	0.539	0.97
42_N	143_T	0.539	0.97
125_L	129_L	0.539	0.97
57_L	61_L	0.537	0.97
29_R	159_R	0.536	0.97
38_L	62_L	0.533	0.97
152_L	164_V	0.531	0.97
9_A	90_R	0.531	0.97
58_P	127_I	0.526	0.97
15_E	21_E	0.524	0.96
42_N	134_L	0.524	0.96
6_E	94_R	0.523	0.96
8_L	22_L	0.522	0.96
80_A	83_S	0.521	0.96
18_T	23_L	0.520	0.96
53_T	137_P	0.517	0.96
65_Q	73_P	0.511	0.96
75_L	79_L	0.510	0.96
129_L	133_L	0.509	0.96
35_L	66_L	0.500	0.95
14_G	21_E	0.500	0.95

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
3eqcA	2	0.2682	11.7	0.94	Contact Map
3comA	1	0.2626	10.8	0.941	Contact Map
4wv4B	1	0.2737	5.3	0.949	Contact Map
4wv4A	1	0.1788	4.6	0.95	Contact Map
3bpqA	2	0.1341	4.6	0.95	Contact Map
1ciiA	1	0.4022	4.2	0.951	Contact Map
3w9iA	3	0.9609	4	0.952	Contact Map
2yfwB	2	0.2123	3.7	0.952	Contact Map
4dx5A	3	0.9609	3.7	0.952	Contact Map
4a0dA	1	0.3073	3.5	0.953	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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