SECE - BACSU - GREMLIN Contacts

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SECE - Protein translocase subunit SecE

UniProt:	Q06799	Sequences: MRIMKFFKDVGKEMKKVSWPKGKELTRYTITVISTVIFFVIFFALLDTGISQLIRLIVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	59 (55)
Sequences:	170 (111)
Seq/√Len:	14.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_S	21_K	3.056	0.98
16_K	40_V	2.241	0.89
15_K	56_L	2.183	0.88
26_T	30_I	2.149	0.87
14_M	18_S	2.100	0.86
10_V	14_M	2.078	0.85
23_K	26_T	1.792	0.75
17_V	45_L	1.715	0.72
51_S	55_R	1.708	0.71
45_L	48_T	1.609	0.67
14_M	27_R	1.556	0.64
34_S	37_I	1.528	0.62
52_Q	55_R	1.504	0.61
8_K	41_I	1.399	0.55
54_I	58_V	1.356	0.53
10_V	18_S	1.312	0.51
33_I	52_Q	1.283	0.49
21_K	39_F	1.255	0.47
54_I	57_I	1.254	0.47
31_T	51_S	1.175	0.43
38_F	52_Q	1.155	0.42
4_M	11_G	1.152	0.42
31_T	53_L	1.152	0.42
9_D	31_T	1.142	0.41
44_A	51_S	1.131	0.41
4_M	54_I	1.105	0.39
26_T	34_S	1.103	0.39
23_K	28_Y	1.058	0.37
30_I	34_S	1.055	0.36
39_F	46_L	1.032	0.35
8_K	17_V	1.030	0.35
5_K	18_S	1.008	0.34
55_R	58_V	0.996	0.33
15_K	53_L	0.970	0.32
12_K	15_K	0.953	0.31
10_V	25_L	0.938	0.31
5_K	46_L	0.879	0.28
5_K	8_K	0.876	0.28
16_K	21_K	0.873	0.28
11_G	14_M	0.866	0.27
48_T	55_R	0.866	0.27
31_T	42_F	0.857	0.27
41_I	44_A	0.806	0.25
37_I	56_L	0.799	0.24
38_F	56_L	0.791	0.24
16_K	31_T	0.783	0.24
7_F	43_F	0.767	0.23
5_K	42_F	0.767	0.23
8_K	46_L	0.756	0.23
8_K	55_R	0.755	0.23
22_G	50_I	0.737	0.22
30_I	40_V	0.735	0.22
39_F	54_I	0.734	0.22
4_M	9_D	0.727	0.22
4_M	21_K	0.718	0.21
4_M	39_F	0.695	0.20
23_K	45_L	0.693	0.20
9_D	51_S	0.684	0.20
15_K	22_G	0.675	0.20
30_I	33_I	0.644	0.19
27_R	38_F	0.640	0.18
11_G	58_V	0.631	0.18
8_K	44_A	0.626	0.18
35_T	49_G	0.621	0.18
35_T	55_R	0.613	0.18
15_K	21_K	0.597	0.17
22_G	39_F	0.597	0.17
7_F	34_S	0.596	0.17
17_V	27_R	0.572	0.16
41_I	53_L	0.569	0.16
13_E	49_G	0.539	0.15
35_T	48_T	0.537	0.15
7_F	11_G	0.535	0.15
13_E	50_I	0.526	0.15
21_K	27_R	0.523	0.15
27_R	50_I	0.522	0.15
35_T	51_S	0.516	0.15
27_R	41_I	0.516	0.15
16_K	30_I	0.506	0.14
21_K	26_T	0.501	0.14
21_K	34_S	0.500	0.14
8_K	22_G	0.500	0.14

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
3j01B	1	1	99.6	0.393	Contact Map
3dl8C	1	0.5593	99.6	0.394	Contact Map
3dinD	1	0.8644	99.6	0.395	Contact Map
2zjsE	1	0.7797	99.6	0.411	Contact Map
3bo0B	1	1	99.3	0.507	Contact Map
3nymA	2	0.3898	37.7	0.878	Contact Map
1rh5B	1	0.9492	27.7	0.885	Contact Map
2ww9B	1	0.9322	18.8	0.894	Contact Map
4w252	1	1	16.7	0.897	Contact Map
3mp7B	1	0.8305	8.1	0.91	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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