PGSA - BACSU - GREMLIN Contacts

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PGSA - CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase

UniProt:	P46322	Sequences: MFNLPNKITLARIALIPIFMIIMLAPFDWGRLEVGDESIPVAHLAGAILFIIASTTDWVDGYYARKLNLVTNFGKFLDPLADKLLVSAALIILVQFDLAPAWMVIVIISREFAVTGLRLVLAGTGEVVAANMLGKIKTWAQIIAVSALLLHNLPFELVSFPFADLALWVAVFFTVVSGWEYFSKNWEALKTSN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	193 (175)
Sequences:	4396 (2909)
Seq/√Len:	219.9

ECOLI - PGSA
BACSU - PGSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_Y	67_L	3.305	1.00
73_F	77_L	3.248	1.00
131_N	180_E	2.948	1.00
94_V	104_V	2.910	1.00
8_I	56_T	2.838	1.00
20_M	92_I	2.402	1.00
140_A	173_F	2.357	1.00
51_I	146_S	2.298	1.00
19_F	89_A	2.262	1.00
133_L	176_V	2.244	1.00
3_N	71_T	2.196	1.00
20_M	88_A	2.141	1.00
16_I	84_L	2.118	1.00
22_I	49_L	2.107	1.00
113_A	182_F	2.093	1.00
41_V	45_A	2.052	1.00
144_A	170_A	2.049	1.00
132_M	136_I	2.042	1.00
54_S	142_I	1.916	1.00
179_W	183_S	1.913	1.00
72_N	75_K	1.884	1.00
3_N	69_L	1.875	1.00
183_S	186_W	1.872	1.00
23_M	92_I	1.835	1.00
70_V	75_K	1.828	1.00
62_Y	66_K	1.810	1.00
55_T	58_W	1.805	1.00
103_M	168_W	1.802	1.00
22_I	45_A	1.758	1.00
15_L	49_L	1.753	1.00
140_A	169_V	1.691	1.00
2_F	7_K	1.652	1.00
53_A	85_L	1.634	1.00
136_I	139_W	1.612	1.00
141_Q	174_T	1.606	1.00
44_L	48_I	1.605	1.00
9_T	77_L	1.602	1.00
148_L	163_A	1.526	1.00
5_P	69_L	1.505	1.00
103_M	171_V	1.500	1.00
47_A	146_S	1.485	1.00
147_A	166_A	1.462	1.00
180_E	184_K	1.461	1.00
23_M	96_F	1.457	1.00
8_I	59_V	1.456	1.00
107_I	174_T	1.423	1.00
55_T	59_V	1.412	1.00
161_P	165_L	1.407	1.00
63_Y	69_L	1.402	1.00
148_L	167_L	1.396	1.00
13_I	81_A	1.396	1.00
10_L	14_A	1.343	1.00
58_W	62_Y	1.339	1.00
147_A	163_A	1.331	1.00
15_L	52_I	1.319	1.00
139_W	143_I	1.316	1.00
47_A	150_L	1.311	1.00
138_T	142_I	1.302	1.00
18_I	22_I	1.302	1.00
121_L	128_V	1.266	1.00
175_V	179_W	1.246	1.00
13_I	84_L	1.242	1.00
48_I	52_I	1.229	1.00
2_F	10_L	1.222	1.00
43_H	98_L	1.218	1.00
114_V	182_F	1.215	1.00
133_L	180_E	1.213	1.00
4_L	7_K	1.189	1.00
18_I	49_L	1.184	1.00
7_K	11_A	1.184	1.00
118_R	137_K	1.183	1.00
144_A	167_L	1.173	1.00
15_L	18_I	1.169	1.00
8_I	55_T	1.155	1.00
121_L	185_N	1.148	1.00
22_I	42_A	1.146	1.00
89_A	145_V	1.130	1.00
22_I	46_G	1.129	1.00
24_L	92_I	1.128	1.00
19_F	49_L	1.117	1.00
27_F	41_V	1.117	1.00
5_P	63_Y	1.101	1.00
106_V	175_V	1.090	1.00
99_A	167_L	1.080	1.00
106_V	171_V	1.066	1.00
101_A	105_I	1.063	1.00
90_L	145_V	1.059	1.00
87_S	108_I	1.020	1.00
105_I	109_S	1.019	1.00
87_S	91_I	1.015	1.00
131_N	184_K	1.006	1.00
174_T	178_G	0.991	1.00
59_V	63_Y	0.977	1.00
139_W	142_I	0.977	1.00
165_L	169_V	0.971	1.00
86_V	145_V	0.965	1.00
94_V	101_A	0.963	1.00
114_V	178_G	0.957	1.00
136_I	173_F	0.957	1.00
103_M	167_L	0.956	1.00
66_K	70_V	0.951	1.00
5_P	8_I	0.951	1.00
88_A	92_I	0.947	1.00
51_I	55_T	0.928	0.99
134_G	177_S	0.924	0.99
44_L	150_L	0.922	0.99
23_M	149_L	0.922	0.99
134_G	137_K	0.919	0.99
21_I	25_A	0.911	0.99
144_A	166_A	0.908	0.99
86_V	90_L	0.907	0.99
51_I	143_I	0.904	0.99
144_A	163_A	0.900	0.99
14_A	17_P	0.899	0.99
50_F	85_L	0.890	0.99
75_K	129_A	0.885	0.99
75_K	127_V	0.882	0.99
172_F	176_V	0.879	0.99
7_K	10_L	0.871	0.99
131_N	134_G	0.870	0.99
176_V	180_E	0.865	0.99
164_D	168_W	0.861	0.99
158_V	162_F	0.857	0.99
14_A	18_I	0.848	0.99
45_A	49_L	0.846	0.99
11_A	56_T	0.835	0.99
110_R	177_S	0.828	0.99
8_I	11_A	0.828	0.99
11_A	52_I	0.826	0.99
151_H	163_A	0.826	0.99
158_V	161_P	0.826	0.99
160_F	164_D	0.821	0.99
161_P	164_D	0.813	0.99
54_S	85_L	0.806	0.99
133_L	177_S	0.803	0.99
79_P	138_T	0.802	0.99
15_L	19_F	0.801	0.99
141_Q	170_A	0.790	0.98
76_F	119_L	0.781	0.98
115_T	118_R	0.781	0.98
87_S	111_E	0.774	0.98
90_L	107_I	0.771	0.98
119_L	122_A	0.768	0.98
4_L	67_L	0.766	0.98
16_I	88_A	0.763	0.98
25_A	42_A	0.760	0.98
43_H	96_F	0.755	0.98
2_F	6_N	0.742	0.98
95_Q	101_A	0.737	0.97
62_Y	67_L	0.734	0.97
97_D	101_A	0.726	0.97
88_A	105_I	0.724	0.97
27_F	42_A	0.721	0.97
113_A	116_G	0.721	0.97
111_E	174_T	0.720	0.97
17_P	79_P	0.719	0.97
121_L	124_T	0.719	0.97
133_L	136_I	0.716	0.97
70_V	130_A	0.714	0.97
111_E	115_T	0.712	0.97
17_P	81_A	0.705	0.97
19_F	46_G	0.702	0.97
169_V	173_F	0.697	0.96
110_R	137_K	0.690	0.96
170_A	174_T	0.681	0.96
47_A	149_L	0.680	0.96
91_I	104_V	0.679	0.96
86_V	142_I	0.678	0.96
45_A	48_I	0.672	0.96
91_I	94_V	0.668	0.95
84_L	109_S	0.666	0.95
117_L	137_K	0.664	0.95
4_L	63_Y	0.662	0.95
83_K	141_Q	0.661	0.95
111_E	137_K	0.660	0.95
5_P	67_L	0.660	0.95
100_P	103_M	0.657	0.95
46_G	53_A	0.653	0.95
11_A	15_L	0.648	0.95
23_M	43_H	0.648	0.95
104_V	108_I	0.644	0.95
8_I	77_L	0.644	0.95
8_I	63_Y	0.644	0.95
130_A	133_L	0.636	0.94
46_G	92_I	0.632	0.94
47_A	51_I	0.629	0.94
137_K	177_S	0.626	0.94
19_F	92_I	0.624	0.94
15_L	53_A	0.624	0.94
93_L	98_L	0.623	0.93
65_R	134_G	0.619	0.93
110_R	114_V	0.619	0.93
132_M	139_W	0.618	0.93
137_K	173_F	0.617	0.93
20_M	105_I	0.614	0.93
136_I	140_A	0.601	0.92
121_L	125_G	0.600	0.92
148_L	164_D	0.600	0.92
90_L	170_A	0.598	0.92
183_S	187_E	0.597	0.92
147_A	162_F	0.596	0.92
166_A	170_A	0.593	0.92
143_I	147_A	0.593	0.92
13_I	77_L	0.593	0.92
86_V	141_Q	0.592	0.92
87_S	112_F	0.591	0.92
103_M	164_D	0.590	0.92
140_A	166_A	0.589	0.91
20_M	24_L	0.587	0.91
92_I	96_F	0.587	0.91
115_T	137_K	0.581	0.91
161_P	166_A	0.578	0.91
54_S	58_W	0.576	0.91
4_L	69_L	0.576	0.91
143_I	166_A	0.575	0.90
121_L	126_E	0.571	0.90
98_L	152_N	0.569	0.90
83_K	174_T	0.561	0.89
72_N	124_T	0.560	0.89
159_S	163_A	0.560	0.89
83_K	130_A	0.559	0.89
157_L	161_P	0.556	0.89
90_L	141_Q	0.552	0.89
9_T	13_I	0.551	0.89
182_F	186_W	0.551	0.89
24_L	95_Q	0.549	0.88
67_L	71_T	0.545	0.88
75_K	130_A	0.544	0.88
55_T	159_S	0.543	0.88
130_A	134_G	0.541	0.88
110_R	141_Q	0.541	0.88
108_I	112_F	0.534	0.87
118_R	125_G	0.531	0.87
137_K	141_Q	0.531	0.87
116_G	120_V	0.531	0.87
58_W	139_W	0.530	0.87
115_T	122_A	0.528	0.86
152_N	160_F	0.527	0.86
42_A	45_A	0.527	0.86
155_F	159_S	0.525	0.86
97_D	100_P	0.524	0.86
43_H	151_H	0.521	0.86
83_K	111_E	0.517	0.85
44_L	47_A	0.516	0.85
143_I	146_S	0.516	0.85
80_L	116_G	0.516	0.85
152_N	155_F	0.514	0.85
141_Q	178_G	0.513	0.85
86_V	115_T	0.513	0.85
184_K	188_A	0.512	0.85
172_F	175_V	0.510	0.84
184_K	187_E	0.510	0.84
115_T	178_G	0.509	0.84
27_F	40_P	0.507	0.84
99_A	106_V	0.506	0.84
185_N	188_A	0.506	0.84
50_F	54_S	0.505	0.84
152_N	163_A	0.503	0.84
112_F	116_G	0.502	0.84
63_Y	66_K	0.501	0.83
130_A	137_K	0.500	0.83
108_I	111_E	0.500	0.83

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
4mndA	2	0.8601	100	0.409	Contact Map
4o6mA	2	0.8653	99.9	0.456	Contact Map
3tx3A	2	0.7668	14.3	0.942	Contact Map
1vryA	1	0.3161	6.4	0.951	Contact Map
3j08A	2	0.3264	5.7	0.952	Contact Map
1oedE	1	0.4767	4.5	0.954	Contact Map
1oedC	1	0.4767	4.3	0.954	Contact Map
1oedB	1	0.4611	3.9	0.955	Contact Map
1oedA	1	0.4611	3.1	0.957	Contact Map
3wu2J	1	0.2021	2.7	0.959	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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