LSPA - BACSU - GREMLIN Contacts

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LSPA - Lipoprotein signal peptidase

UniProt:	Q45479	Sequences: MLYYMIALLIIAADQLTKWLVVKNMELGQSIPIIDQVFYITSHRNTGAAWGILAGQMWFFYLITTAVIIGIVYYIQRYTKGQRLLGVALGLMLGGAIGNFIDRAVRQEVVDFIHVIIVNYNYPIFNIADSSLCVGVMLLFIQMLLDSGKKKKEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	154 (142)
Sequences:	4395 (3249)
Seq/√Len:	272.6

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
10_I	131_S	4.022	1.00
17_T	112_F	3.715	1.00
11_I	101_I	2.787	1.00
10_I	94_G	2.735	1.00
44_R	108_E	2.636	1.00
22_V	110_V	2.555	1.00
38_F	113_I	2.339	1.00
20_L	24_N	2.266	1.00
21_V	25_M	2.117	1.00
25_M	31_I	2.074	1.00
50_W	123_P	2.064	1.00
17_T	127_I	2.036	1.00
39_Y	114_H	2.028	1.00
130_S	134_V	1.985	1.00
15_Q	101_I	1.917	1.00
22_V	44_R	1.883	1.00
88_A	138_L	1.814	1.00
39_Y	116_I	1.787	1.00
7_A	93_L	1.778	1.00
133_C	137_M	1.751	1.00
127_I	130_S	1.725	1.00
43_H	124_I	1.696	1.00
30_S	39_Y	1.681	1.00
32_P	35_D	1.673	1.00
46_T	54_A	1.614	1.00
92_M	135_G	1.612	1.00
16_L	20_L	1.608	1.00
71_I	93_L	1.579	1.00
68_I	93_L	1.576	1.00
46_T	108_E	1.529	1.00
106_R	110_V	1.522	1.00
73_Y	77_R	1.509	1.00
127_I	131_S	1.500	1.00
19_W	23_K	1.486	1.00
122_Y	133_C	1.438	1.00
90_G	94_G	1.403	1.00
21_V	42_S	1.381	1.00
68_I	96_A	1.364	1.00
25_M	42_S	1.355	1.00
69_I	73_Y	1.353	1.00
7_A	90_G	1.348	1.00
34_I	37_V	1.345	1.00
21_V	40_I	1.336	1.00
13_A	127_I	1.276	1.00
41_T	124_I	1.268	1.00
30_S	41_T	1.235	1.00
12_A	16_L	1.220	1.00
88_A	135_G	1.201	1.00
64_T	100_F	1.199	1.00
84_L	88_A	1.166	1.00
33_I	40_I	1.160	1.00
130_S	133_C	1.156	1.00
84_L	138_L	1.139	1.00
17_T	113_I	1.139	1.00
32_P	39_Y	1.133	1.00
11_I	97_I	1.132	1.00
41_T	114_H	1.128	1.00
40_I	113_I	1.127	1.00
134_V	138_L	1.119	1.00
88_A	139_L	1.105	1.00
38_F	115_V	1.084	1.00
71_I	89_L	1.080	1.00
6_I	10_I	1.079	1.00
61_Y	100_F	1.077	1.00
88_A	142_Q	1.070	1.00
94_G	131_S	1.068	1.00
66_A	70_G	1.057	1.00
26_E	42_S	1.051	1.00
65_T	69_I	1.048	1.00
114_H	117_I	1.045	1.00
114_H	124_I	1.040	1.00
136_V	140_F	1.038	1.00
113_I	130_S	1.036	1.00
141_I	145_L	1.033	1.00
30_S	114_H	1.031	1.00
62_L	66_A	1.010	1.00
57_M	61_Y	0.999	1.00
26_E	29_Q	0.988	1.00
46_T	51_G	0.982	1.00
42_S	110_V	0.975	1.00
83_R	87_V	0.972	1.00
101_I	105_V	0.966	1.00
33_I	38_F	0.965	1.00
70_G	74_Y	0.944	1.00
61_Y	104_A	0.938	1.00
10_I	90_G	0.931	1.00
22_V	106_R	0.914	1.00
53_L	60_F	0.912	1.00
64_T	68_I	0.910	1.00
48_A	60_F	0.905	1.00
70_G	73_Y	0.892	1.00
53_L	56_Q	0.890	1.00
42_S	108_E	0.889	1.00
51_G	54_A	0.882	1.00
56_Q	59_F	0.879	1.00
25_M	29_Q	0.874	1.00
73_Y	76_Q	0.872	1.00
91_L	131_S	0.866	1.00
137_M	141_I	0.862	1.00
72_V	76_Q	0.851	1.00
10_I	91_L	0.848	1.00
14_D	18_K	0.839	1.00
84_L	142_Q	0.836	1.00
82_Q	85_L	0.831	0.99
35_D	39_Y	0.831	0.99
17_T	20_L	0.815	0.99
11_I	15_Q	0.814	0.99
6_I	90_G	0.808	0.99
85_L	142_Q	0.806	0.99
50_W	122_Y	0.805	0.99
67_V	96_A	0.804	0.99
7_A	97_I	0.803	0.99
75_I	86_G	0.802	0.99
17_T	21_V	0.790	0.99
112_F	127_I	0.785	0.99
142_Q	146_D	0.772	0.99
85_L	89_L	0.771	0.99
133_C	140_F	0.770	0.99
7_A	94_G	0.770	0.99
115_V	125_F	0.769	0.99
32_P	36_Q	0.768	0.99
75_I	90_G	0.762	0.99
48_A	52_I	0.758	0.99
68_I	100_F	0.756	0.99
21_V	27_L	0.756	0.99
64_T	103_R	0.739	0.99
91_L	135_G	0.732	0.99
92_M	132_L	0.727	0.99
6_I	87_V	0.725	0.99
92_M	139_L	0.725	0.99
21_V	24_N	0.723	0.99
44_R	110_V	0.721	0.99
3_Y	75_I	0.708	0.98
43_H	51_G	0.706	0.98
142_Q	145_L	0.702	0.98
137_M	140_F	0.698	0.98
98_G	101_I	0.697	0.98
15_Q	105_V	0.693	0.98
76_Q	79_T	0.692	0.98
78_Y	82_Q	0.687	0.98
5_M	9_L	0.680	0.98
96_A	132_L	0.677	0.98
4_Y	76_Q	0.677	0.98
116_I	119_N	0.676	0.98
15_Q	19_W	0.672	0.98
125_F	130_S	0.667	0.98
79_T	82_Q	0.666	0.98
75_I	89_L	0.660	0.97
10_I	127_I	0.655	0.97
32_P	116_I	0.652	0.97
49_A	123_P	0.647	0.97
86_G	90_G	0.646	0.97
3_Y	90_G	0.645	0.97
100_F	104_A	0.644	0.97
82_Q	142_Q	0.640	0.97
37_V	116_I	0.640	0.97
78_Y	81_G	0.638	0.97
53_L	59_F	0.638	0.97
36_Q	39_Y	0.637	0.97
58_W	61_Y	0.636	0.97
51_G	123_P	0.636	0.97
63_I	67_V	0.636	0.97
22_V	42_S	0.634	0.97
57_M	60_F	0.622	0.96
92_M	96_A	0.617	0.96
11_I	94_G	0.606	0.96
13_A	17_T	0.605	0.96
65_T	100_F	0.604	0.96
61_Y	64_T	0.603	0.96
44_R	106_R	0.600	0.96
140_F	143_M	0.596	0.95
7_A	11_I	0.595	0.95
22_V	108_E	0.593	0.95
3_Y	86_G	0.588	0.95
114_H	118_V	0.583	0.95
134_V	137_M	0.581	0.95
27_L	44_R	0.581	0.95
72_V	93_L	0.576	0.94
91_L	138_L	0.575	0.94
71_I	96_A	0.573	0.94
15_Q	106_R	0.569	0.94
31_I	40_I	0.567	0.94
21_V	30_S	0.566	0.94
37_V	113_I	0.554	0.93
13_A	16_L	0.552	0.93
116_I	124_I	0.551	0.93
66_A	69_I	0.551	0.93
91_L	134_V	0.551	0.93
16_L	19_W	0.549	0.93
46_T	53_L	0.548	0.93
10_I	130_S	0.545	0.93
136_V	143_M	0.544	0.93
102_D	110_V	0.544	0.93
85_L	146_D	0.540	0.92
67_V	132_L	0.539	0.92
21_V	112_F	0.537	0.92
61_Y	107_Q	0.537	0.92
25_M	28_G	0.535	0.92
113_I	123_P	0.535	0.92
113_I	124_I	0.533	0.92
26_E	30_S	0.532	0.92
20_L	25_M	0.528	0.92
118_V	122_Y	0.521	0.91
4_Y	8_L	0.521	0.91
97_I	101_I	0.519	0.91
8_L	12_A	0.512	0.90
122_Y	125_F	0.511	0.90
117_I	122_Y	0.510	0.90
56_Q	64_T	0.509	0.90
58_W	62_L	0.507	0.90
27_L	30_S	0.507	0.90
74_Y	89_L	0.501	0.89
59_F	62_L	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
4x5mA	2	0.5909	10.5	0.941	Contact Map
4qncA	2	0.526	8	0.944	Contact Map
3qe7A	2	0.9416	5	0.949	Contact Map
2m20A	2	0.2338	4	0.952	Contact Map
2kv5A	1	0.2143	3.8	0.952	Contact Map
4px7A	1	0.8571	3.6	0.953	Contact Map
2kluA	1	0.2143	3.5	0.953	Contact Map
3j01B	1	0.3831	3	0.955	Contact Map
4lz6A	1	0.5649	2.6	0.956	Contact Map
2cfqA	1	0.8571	2.5	0.956	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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