LSPA - ECOLI - GREMLIN Contacts

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LSPA - Lipoprotein signal peptidase

UniProt:	P00804	Sequences: MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPSLNLHYARNYGAAFSFLADSGGWQRWFFAGIAIGISVILAVMMYRSKATQKLNNIAYALIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLADTAICVGAALIVLEGFLPSRAKKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10548
Length:	164 (142)
Sequences:	4394 (3260)
Seq/√Len:	273.6

ECOLI - LSPA
BACSU - LSPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_V	143_A	3.814	1.00
26_S	124_M	3.709	1.00
19_V	106_G	2.725	1.00
20_L	113_F	2.721	1.00
52_R	120_F	2.591	1.00
126_D	133_H	2.544	1.00
31_L	122_V	2.512	1.00
46_L	125_I	2.208	1.00
29_L	33_N	2.178	1.00
30_I	34_F	2.102	1.00
34_F	40_V	2.068	1.00
58_F	135_A	2.019	1.00
26_S	139_L	1.977	1.00
24_L	113_F	1.964	1.00
142_T	146_V	1.935	1.00
31_L	52_R	1.896	1.00
47_N	126_D	1.768	1.00
145_C	149_A	1.749	1.00
16_V	105_I	1.741	1.00
100_A	150_L	1.718	1.00
41_P	44_P	1.707	1.00
51_A	136_T	1.704	1.00
139_L	142_T	1.665	1.00
47_N	128_Y	1.642	1.00
54_Y	62_A	1.598	1.00
25_G	29_L	1.571	1.00
39_T	47_N	1.534	1.00
104_I	147_G	1.526	1.00
83_L	105_I	1.521	1.00
80_S	105_I	1.512	1.00
134_F	145_C	1.510	1.00
85_V	89_R	1.477	1.00
139_L	143_A	1.467	1.00
54_Y	120_F	1.442	1.00
28_Y	32_Q	1.423	1.00
102_A	106_G	1.391	1.00
16_V	102_A	1.362	1.00
30_I	50_Y	1.361	1.00
34_F	50_Y	1.349	1.00
22_I	139_L	1.340	1.00
81_V	85_V	1.321	1.00
30_I	48_L	1.311	1.00
39_T	49_H	1.294	1.00
49_H	136_T	1.273	1.00
118_H	122_V	1.231	1.00
41_P	47_N	1.229	1.00
142_T	145_C	1.214	1.00
76_A	112_L	1.185	1.00
21_I	25_G	1.178	1.00
82_I	86_M	1.164	1.00
96_L	150_L	1.164	1.00
49_H	126_D	1.148	1.00
100_A	147_G	1.146	1.00
46_L	127_F	1.132	1.00
42_L	48_L	1.123	1.00
77_I	81_V	1.101	1.00
106_G	143_A	1.101	1.00
100_A	154_E	1.100	1.00
26_S	125_I	1.099	1.00
20_L	109_L	1.093	1.00
78_G	82_I	1.088	1.00
96_L	100_A	1.081	1.00
80_S	108_A	1.079	1.00
48_L	125_I	1.067	1.00
54_Y	59_S	1.066	1.00
95_K	99_I	1.064	1.00
100_A	151_I	1.059	1.00
15_L	19_V	1.043	1.00
35_A	50_Y	1.040	1.00
146_V	150_L	1.038	1.00
126_D	129_V	1.036	1.00
125_I	142_T	1.035	1.00
148_A	152_V	1.034	1.00
39_T	126_D	1.023	1.00
153_L	157_L	0.999	1.00
59_S	62_A	0.973	1.00
12_W	87_M	0.969	1.00
42_L	46_L	0.958	1.00
69_R	73_A	0.957	1.00
74_G	78_G	0.952	1.00
35_A	38_D	0.950	1.00
50_Y	122_V	0.945	1.00
56_A	72_F	0.943	1.00
82_I	85_V	0.925	1.00
113_F	117_W	0.919	1.00
73_A	112_L	0.915	1.00
34_F	38_D	0.911	1.00
87_M	101_Y	0.909	1.00
19_V	102_A	0.904	1.00
96_L	154_E	0.901	1.00
50_Y	120_F	0.893	1.00
68_Q	71_F	0.893	1.00
61_L	72_F	0.882	1.00
76_A	80_S	0.878	1.00
126_D	136_T	0.877	1.00
149_A	153_L	0.875	1.00
94_Q	97_N	0.870	1.00
124_M	139_L	0.867	1.00
103_L	143_A	0.866	1.00
84_A	88_Y	0.864	1.00
15_L	102_A	0.860	1.00
61_L	68_Q	0.854	1.00
23_D	27_K	0.849	1.00
19_V	103_L	0.840	1.00
73_A	116_L	0.839	1.00
83_L	101_Y	0.829	0.99
85_V	88_Y	0.826	0.99
16_V	106_G	0.826	0.99
26_S	30_I	0.823	0.99
26_S	29_L	0.819	0.99
127_F	137_F	0.813	0.99
87_M	98_N	0.804	0.99
30_I	36_L	0.801	0.99
145_C	152_V	0.796	0.99
128_Y	133_H	0.793	0.99
128_Y	132_W	0.793	0.99
44_P	47_N	0.792	0.99
12_W	102_A	0.785	0.99
97_N	154_E	0.784	0.99
20_L	24_L	0.780	0.99
12_W	98_N	0.780	0.99
16_V	109_L	0.779	0.99
103_L	147_G	0.772	0.99
80_S	112_L	0.771	0.99
58_F	134_F	0.765	0.99
104_I	151_I	0.765	0.99
56_A	60_F	0.764	0.99
97_N	101_Y	0.761	0.99
94_Q	154_E	0.757	0.99
154_E	158_P	0.755	0.99
154_E	157_L	0.752	0.99
79_I	108_A	0.747	0.99
76_A	115_R	0.740	0.99
90_S	94_Q	0.737	0.99
24_L	117_W	0.732	0.99
110_G	113_F	0.731	0.99
24_L	28_Y	0.725	0.99
19_V	139_L	0.722	0.99
15_L	99_I	0.718	0.99
51_A	59_S	0.718	0.99
129_V	133_H	0.715	0.98
73_A	119_G	0.714	0.98
137_F	142_T	0.710	0.98
47_N	133_H	0.710	0.98
41_P	128_Y	0.709	0.98
52_R	122_V	0.703	0.98
14_W	18_V	0.702	0.98
125_I	139_L	0.675	0.98
59_S	135_A	0.671	0.98
30_I	33_N	0.668	0.98
87_M	102_A	0.667	0.98
104_I	144_I	0.667	0.98
57_A	135_A	0.653	0.97
16_V	20_L	0.651	0.97
149_A	152_V	0.651	0.97
73_A	76_A	0.649	0.97
112_L	116_L	0.647	0.97
76_A	108_A	0.647	0.97
98_N	102_A	0.645	0.97
62_A	68_Q	0.642	0.97
104_I	108_A	0.640	0.97
63_D	68_Q	0.635	0.97
146_V	149_A	0.634	0.97
20_L	106_G	0.631	0.97
84_A	105_I	0.628	0.97
22_I	26_S	0.627	0.97
31_L	120_F	0.626	0.97
125_I	135_A	0.625	0.97
129_V	132_W	0.622	0.96
93_T	158_P	0.620	0.96
152_V	155_G	0.615	0.96
22_I	25_G	0.606	0.96
30_I	124_M	0.605	0.96
13_L	88_Y	0.602	0.96
108_A	144_I	0.600	0.96
132_W	135_A	0.597	0.95
128_Y	136_T	0.597	0.95
24_L	118_H	0.594	0.95
29_L	34_F	0.588	0.95
31_L	50_Y	0.584	0.95
70_W	74_G	0.582	0.95
125_I	136_T	0.582	0.95
11_R	14_W	0.580	0.95
80_S	109_L	0.577	0.95
25_G	28_Y	0.577	0.95
77_I	112_L	0.574	0.94
13_L	17_V	0.571	0.94
33_N	36_L	0.570	0.94
17_V	21_I	0.563	0.94
31_L	118_H	0.554	0.93
78_G	81_V	0.543	0.93
36_L	52_R	0.542	0.93
45_S	128_Y	0.542	0.93
69_R	119_G	0.541	0.93
97_N	158_P	0.538	0.92
11_R	90_S	0.538	0.92
44_P	128_Y	0.537	0.92
36_L	39_T	0.534	0.92
30_I	39_T	0.531	0.92
148_A	155_G	0.524	0.91
155_G	158_P	0.523	0.91
109_L	113_F	0.518	0.91
68_Q	72_F	0.518	0.91
24_L	114_D	0.514	0.91
133_H	136_T	0.514	0.91
19_V	142_T	0.512	0.90
103_L	150_L	0.510	0.90
71_F	74_G	0.507	0.90
103_L	146_V	0.507	0.90
134_F	137_F	0.507	0.90
56_A	69_R	0.503	0.90
70_W	73_A	0.502	0.89
129_V	134_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
3rlbA	1	0.9329	19	0.937	Contact Map
4x5mA	2	0.5488	14.3	0.94	Contact Map
4qncA	2	0.5	10.4	0.944	Contact Map
4tkrA	2	0.939	9.5	0.945	Contact Map
4rfsS	1	0.9146	8.4	0.946	Contact Map
2cfqA	1	0.9024	6.4	0.949	Contact Map
2qi9A	2	0.9817	6.3	0.949	Contact Map
4ev6A	3	0.4207	6.2	0.949	Contact Map
4i0uA	4	0.4085	4.9	0.952	Contact Map
4huqS	1	0.8963	4.5	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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