MlaA - PFAM28P - GREMLIN Contacts

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MlaA - MlaA lipoprotein

PFAM:	PF04333	Sequences: VNDPLEPFNRAMFAFNDALDRAVLKPVAKGYRAVVPEPVRTGVSNFFSNLGEPVTFVNNLLQGKFKRAGSDLGRFLINSTVGLGGLFDVASEMGLPKHDEDFGQTLGVWGVGPGPYLVLPLLGPSTVRDAVGLVVDSFLDPVTYIDDDAVRYGLTALDAVDTRARLLDAEDLLEEASLDPYAFVRDAYLQRRRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	194 (193)
Sequences:	16097 (10628)
Seq/√Len:	765.0
META:	0.892

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_F	12_M	3.647	1.00
100_E	104_Q	2.790	1.00
20_D	163_R	2.615	1.00
56_F	72_L	2.433	1.00
60_L	68_A	2.402	1.00
58_N	105_T	2.399	1.00
148_D	152_Y	2.316	1.00
126_T	189_L	2.296	1.00
25_K	29_K	2.270	1.00
37_E	40_R	2.189	1.00
111_V	114_G	2.148	1.00
6_E	10_R	2.027	1.00
35_V	39_V	1.948	1.00
42_G	45_N	1.936	1.00
46_F	86_L	1.929	1.00
119_L	130_A	1.903	1.00
32_R	40_R	1.863	1.00
13_F	180_P	1.835	1.00
48_S	97_K	1.750	1.00
18_A	22_A	1.702	1.00
44_S	161_D	1.677	1.00
38_P	42_G	1.671	1.00
147_D	150_V	1.667	1.00
149_A	153_G	1.647	1.00
56_F	71_D	1.630	1.00
103_G	129_D	1.621	1.00
161_D	165_R	1.612	1.00
77_I	93_M	1.584	1.00
52_E	56_F	1.571	1.00
101_D	104_Q	1.568	1.00
64_K	100_E	1.544	1.00
67_R	98_H	1.544	1.00
170_E	174_E	1.542	1.00
113_P	126_T	1.538	1.00
11_A	14_A	1.536	1.00
42_G	86_L	1.529	1.00
83_L	87_F	1.512	1.00
102_F	135_V	1.498	1.00
70_S	98_H	1.459	1.00
131_V	134_V	1.448	1.00
113_P	193_R	1.441	1.00
59_N	71_D	1.423	1.00
59_N	67_R	1.421	1.00
56_F	68_A	1.420	1.00
5_L	8_F	1.413	1.00
72_L	76_L	1.408	1.00
16_N	118_V	1.399	1.00
127_V	130_A	1.368	1.00
49_N	79_S	1.367	1.00
54_V	139_L	1.335	1.00
53_P	75_F	1.333	1.00
32_R	164_A	1.330	1.00
59_N	98_H	1.327	1.00
30_G	33_A	1.323	1.00
64_K	67_R	1.322	1.00
170_E	173_L	1.321	1.00
152_Y	156_A	1.314	1.00
52_E	75_F	1.312	1.00
73_G	95_L	1.312	1.00
39_V	42_G	1.311	1.00
101_D	192_R	1.298	1.00
42_G	87_F	1.296	1.00
125_S	129_D	1.296	1.00
17_D	180_P	1.244	1.00
74_R	88_D	1.241	1.00
55_T	59_N	1.237	1.00
63_G	108_V	1.228	1.00
129_D	192_R	1.224	1.00
37_E	41_T	1.221	1.00
104_Q	108_V	1.213	1.00
52_E	71_D	1.211	1.00
55_T	71_D	1.207	1.00
166_L	169_A	1.197	1.00
70_S	95_L	1.190	1.00
52_E	55_T	1.185	1.00
153_G	156_A	1.185	1.00
80_T	84_G	1.183	1.00
57_V	139_L	1.178	1.00
113_P	189_L	1.177	1.00
150_V	153_G	1.176	1.00
17_D	21_R	1.171	1.00
73_G	76_L	1.142	1.00
8_F	11_A	1.140	1.00
5_L	115_P	1.139	1.00
64_K	108_V	1.138	1.00
44_S	165_R	1.135	1.00
8_F	117_L	1.133	1.00
19_L	23_V	1.120	1.00
149_A	152_Y	1.118	1.00
12_M	118_V	1.118	1.00
131_V	135_V	1.098	1.00
29_K	33_A	1.089	1.00
106_L	135_V	1.088	1.00
58_N	102_F	1.085	1.00
115_P	127_V	1.085	1.00
81_V	93_M	1.081	1.00
65_F	69_G	1.077	1.00
146_D	150_V	1.068	1.00
59_N	100_E	1.064	1.00
77_I	81_V	1.061	1.00
153_G	157_L	1.060	1.00
27_V	30_G	1.044	1.00
19_L	121_L	1.038	1.00
69_G	73_G	1.029	1.00
156_A	159_A	1.029	1.00
182_A	185_R	1.023	1.00
56_F	75_F	1.022	1.00
24_L	159_A	1.018	1.00
55_T	99_D	1.008	1.00
186_D	190_Q	1.006	1.00
5_L	11_A	1.001	1.00
130_A	134_V	0.997	1.00
162_T	166_L	0.993	1.00
30_G	34_V	0.985	1.00
71_D	98_H	0.982	1.00
140_D	154_L	0.981	1.00
81_V	89_V	0.980	1.00
66_K	70_S	0.977	1.00
52_E	97_K	0.975	1.00
106_L	111_V	0.971	1.00
89_V	93_M	0.969	1.00
18_A	21_R	0.967	1.00
7_P	11_A	0.961	1.00
32_R	168_D	0.961	1.00
17_D	174_E	0.958	1.00
80_T	83_L	0.956	1.00
81_V	84_G	0.949	1.00
125_S	130_A	0.946	1.00
111_V	115_P	0.943	1.00
19_L	24_L	0.942	1.00
182_A	186_D	0.941	1.00
130_A	133_L	0.933	1.00
76_L	80_T	0.924	1.00
107_G	128_R	0.915	1.00
13_F	118_V	0.909	1.00
4_P	115_P	0.905	1.00
167_L	170_E	0.905	1.00
11_A	15_F	0.904	1.00
25_K	170_E	0.888	1.00
174_E	180_P	0.886	1.00
35_V	40_R	0.883	1.00
88_D	91_S	0.883	1.00
56_F	59_N	0.875	1.00
119_L	125_S	0.875	1.00
180_P	184_V	0.875	1.00
12_M	15_F	0.861	1.00
55_T	98_H	0.857	1.00
14_A	18_A	0.853	1.00
102_F	136_D	0.853	1.00
19_L	22_A	0.852	1.00
127_V	131_V	0.844	1.00
12_M	16_N	0.840	1.00
15_F	118_V	0.837	1.00
28_A	167_L	0.836	1.00
183_F	187_A	0.835	1.00
54_V	136_D	0.834	1.00
169_A	172_L	0.834	1.00
155_T	159_A	0.832	1.00
38_P	87_F	0.829	1.00
63_G	109_W	0.824	1.00
100_E	107_G	0.824	1.00
87_F	92_E	0.816	1.00
44_S	48_S	0.816	1.00
5_L	127_V	0.812	1.00
138_F	141_P	0.812	1.00
18_A	23_V	0.809	1.00
161_D	164_A	0.807	1.00
53_P	57_V	0.806	1.00
40_R	164_A	0.802	1.00
144_Y	147_D	0.802	1.00
171_D	175_E	0.802	1.00
62_Q	100_E	0.801	1.00
29_K	167_L	0.796	1.00
77_I	80_T	0.796	1.00
68_A	72_L	0.791	1.00
13_F	184_V	0.788	1.00
117_L	130_A	0.785	1.00
60_L	65_F	0.785	1.00
170_E	180_P	0.783	1.00
61_L	105_T	0.776	1.00
14_A	17_D	0.764	1.00
57_V	61_L	0.761	1.00
155_T	158_D	0.760	1.00
89_V	92_E	0.758	1.00
77_I	90_A	0.755	1.00
25_K	167_L	0.741	1.00
132_G	136_D	0.741	1.00
56_F	60_L	0.737	1.00
15_F	19_L	0.736	1.00
21_R	174_E	0.729	1.00
40_R	165_R	0.729	1.00
73_G	77_I	0.718	1.00
135_V	138_F	0.717	1.00
74_R	90_A	0.714	1.00
125_S	133_L	0.713	1.00
51_G	55_T	0.707	1.00
3_D	9_N	0.707	1.00
35_V	38_P	0.706	1.00
29_K	32_R	0.705	1.00
102_F	106_L	0.699	1.00
122_L	133_L	0.698	1.00
191_R	194_A	0.698	1.00
140_D	158_D	0.693	1.00
152_Y	155_T	0.691	1.00
150_V	154_L	0.690	1.00
65_F	68_A	0.689	1.00
52_E	72_L	0.687	1.00
13_F	17_D	0.687	1.00
36_P	39_V	0.685	1.00
134_V	138_F	0.680	1.00
106_L	132_G	0.672	1.00
46_F	49_N	0.672	1.00
101_D	129_D	0.670	1.00
118_V	184_V	0.667	1.00
103_G	192_R	0.667	1.00
2_N	189_L	0.667	1.00
121_L	159_A	0.660	1.00
27_V	160_V	0.657	1.00
77_I	95_L	0.655	1.00
148_D	151_R	0.655	1.00
158_D	162_T	0.654	1.00
41_T	45_N	0.652	1.00
47_F	154_L	0.650	1.00
107_G	113_P	0.648	1.00
43_V	46_F	0.646	1.00
160_V	163_R	0.645	1.00
28_A	164_A	0.641	1.00
5_L	117_L	0.639	1.00
62_Q	104_Q	0.635	1.00
164_A	167_L	0.633	1.00
66_K	69_G	0.629	1.00
163_R	167_L	0.624	1.00
173_L	184_V	0.622	1.00
142_V	145_I	0.621	1.00
102_F	105_T	0.616	1.00
55_T	100_E	0.615	1.00
59_N	63_G	0.613	1.00
32_R	167_L	0.612	1.00
55_T	97_K	0.612	1.00
100_E	108_V	0.610	1.00
21_R	25_K	0.608	1.00
172_L	176_A	0.606	1.00
31_Y	43_V	0.603	1.00
116_Y	126_T	0.601	1.00
58_N	62_Q	0.597	1.00
25_K	171_D	0.595	1.00
172_L	175_E	0.595	1.00
135_V	139_L	0.593	1.00
126_T	129_D	0.592	1.00
12_M	119_L	0.591	1.00
142_V	146_D	0.589	1.00
43_V	157_L	0.588	1.00
59_N	64_K	0.588	1.00
28_A	32_R	0.584	1.00
134_V	137_S	0.582	1.00
69_G	72_L	0.581	1.00
65_F	72_L	0.580	1.00
159_A	162_T	0.577	1.00
83_L	86_L	0.577	1.00
112_G	115_P	0.577	1.00
111_V	131_V	0.577	1.00
157_L	161_D	0.572	1.00
145_I	150_V	0.566	1.00
22_A	30_G	0.564	1.00
179_D	182_A	0.563	1.00
189_L	193_R	0.562	1.00
84_G	87_F	0.561	1.00
48_S	52_E	0.560	1.00
176_A	183_F	0.559	1.00
57_V	60_L	0.552	1.00
51_G	54_V	0.551	1.00
70_S	73_G	0.550	1.00
62_Q	105_T	0.549	1.00
177_S	180_P	0.544	1.00
79_S	83_L	0.536	1.00
173_L	180_P	0.535	1.00
105_T	109_W	0.533	1.00
162_T	165_R	0.525	1.00
61_L	109_W	0.525	1.00
50_L	53_P	0.521	1.00
170_E	184_V	0.520	1.00
40_R	161_D	0.517	1.00
90_A	95_L	0.515	1.00
49_N	80_T	0.512	1.00
8_F	13_F	0.512	1.00
17_D	118_V	0.510	1.00
40_R	44_S	0.506	1.00
102_F	139_L	0.506	1.00
58_N	136_D	0.505	1.00
133_L	137_S	0.500	1.00

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
4aqnA	2	0.5155	42.7	0.945	Contact Map
3s88J	3	0.3918	31.8	0.949	Contact Map
2d7eA	4	0.2062	11	0.958	Contact Map
1vw41	1	0.3093	4.3	0.966	Contact Map
3zkvA	1	0.4124	4	0.966	Contact Map
1y2kA	2	0.299	3.4	0.967	Contact Map
3hdeA	2	0.4845	3.3	0.967	Contact Map
4e97A	1	0.5258	3	0.968	Contact Map
3hdfA	1	0.5103	3	0.968	Contact Map
1wjnA	1	0.3814	2.9	0.968	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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