SECG - BACSU - GREMLIN Contacts

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SECG - Probable protein-export membrane protein SecG

UniProt:	O32233	Sequences: MHAVLITLLVIVSIALIIVVLLQSSKSAGLSGAISGGAEQLFGKQKARGLDLILHRITVVLAVLFFVLTIALAYIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	76 (73)
Sequences:	460 (271)
Seq/√Len:	31.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_L	49_G	2.866	1.00
24_S	51_D	2.659	1.00
67_V	71_A	2.621	1.00
9_L	69_T	2.494	0.99
63_V	67_V	2.388	0.99
12_V	64_L	2.354	0.99
60_V	64_L	2.338	0.99
51_D	55_H	2.173	0.99
12_V	68_L	1.899	0.97
53_I	57_I	1.878	0.96
45_Q	49_G	1.813	0.96
42_F	49_G	1.792	0.95
8_L	11_I	1.690	0.93
12_V	61_L	1.610	0.92
34_I	43_G	1.530	0.89
29_G	32_G	1.506	0.89
41_L	45_Q	1.468	0.87
7_T	11_I	1.444	0.87
3_A	70_I	1.420	0.86
31_S	34_I	1.322	0.81
30_L	34_I	1.316	0.81
38_A	43_G	1.302	0.80
16_L	62_A	1.264	0.78
9_L	72_L	1.213	0.75
52_L	56_R	1.204	0.75
40_Q	49_G	1.200	0.74
40_Q	45_Q	1.199	0.74
42_F	52_L	1.137	0.70
15_A	61_L	1.136	0.70
56_R	63_V	1.113	0.69
57_I	61_L	1.088	0.67
2_H	72_L	1.073	0.66
3_A	7_T	1.057	0.64
21_L	25_S	1.034	0.63
2_H	6_I	1.028	0.62
14_I	18_I	1.012	0.61
13_S	69_T	1.002	0.60
20_V	61_L	1.002	0.60
11_I	61_L	0.999	0.60
15_A	57_I	0.998	0.60
23_Q	58_T	0.993	0.60
53_I	66_F	0.980	0.59
46_K	67_V	0.979	0.58
28_A	32_G	0.978	0.58
27_S	43_G	0.953	0.56
56_R	60_V	0.950	0.56
9_L	13_S	0.947	0.56
19_V	57_I	0.913	0.53
26_K	33_A	0.901	0.52
8_L	12_V	0.889	0.51
42_F	56_R	0.856	0.48
22_L	55_H	0.842	0.47
21_L	65_F	0.833	0.47
40_Q	43_G	0.814	0.45
42_F	47_A	0.812	0.45
63_V	68_L	0.795	0.44
42_F	45_Q	0.791	0.43
24_S	50_L	0.771	0.42
19_V	54_L	0.769	0.41
5_L	63_V	0.763	0.41
18_I	25_S	0.748	0.40
17_I	42_F	0.737	0.39
13_S	43_G	0.734	0.39
2_H	7_T	0.729	0.38
68_L	72_L	0.728	0.38
48_R	61_L	0.710	0.37
11_I	59_V	0.702	0.36
64_L	68_L	0.688	0.35
10_V	35_S	0.680	0.35
3_A	6_I	0.659	0.33
21_L	30_L	0.658	0.33
59_V	63_V	0.654	0.33
16_L	20_V	0.652	0.33
20_V	57_I	0.651	0.33
45_Q	74_Y	0.650	0.32
10_V	26_K	0.644	0.32
9_L	66_F	0.636	0.31
53_I	62_A	0.636	0.31
11_I	62_A	0.631	0.31
34_I	39_E	0.629	0.31
62_A	70_I	0.628	0.31
53_I	60_V	0.626	0.31
57_I	70_I	0.625	0.31
18_I	22_L	0.619	0.30
53_I	59_V	0.618	0.30
29_G	34_I	0.613	0.30
35_S	56_R	0.610	0.30
31_S	54_L	0.606	0.29
31_S	44_K	0.601	0.29
15_A	19_V	0.599	0.29
16_L	50_L	0.598	0.29
47_A	52_L	0.591	0.28
6_I	51_D	0.589	0.28
41_L	73_A	0.584	0.28
23_Q	72_L	0.579	0.28
65_F	70_I	0.574	0.27
49_G	73_A	0.571	0.27
43_G	50_L	0.570	0.27
27_S	59_V	0.569	0.27
38_A	50_L	0.567	0.27
4_V	68_L	0.565	0.27
10_V	74_Y	0.558	0.26
13_S	72_L	0.558	0.26
11_I	65_F	0.545	0.25
5_L	68_L	0.544	0.25
34_I	54_L	0.529	0.24
35_S	74_Y	0.524	0.24
3_A	14_I	0.506	0.23
59_V	70_I	0.501	0.23
5_L	53_I	0.500	0.23

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
3dinE	1	0.8421	99.7	0.376	Contact Map
3dl8E	1	0.8421	99.7	0.378	Contact Map
2akhX	1	0.9605	99.7	0.384	Contact Map
3j45G	1	0.8421	99.6	0.444	Contact Map
2kz7C	1	0.5132	7.8	0.916	Contact Map
2bg9A	1	0.4211	6.1	0.92	Contact Map
2nwlA	3	0.8947	5.4	0.921	Contact Map
4av3A	2	0.8158	5.1	0.922	Contact Map
3giaA	1	1	5	0.923	Contact Map
1rz2A	1	0.0263	5	0.923	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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