YMFJ - BACSU - GREMLIN Contacts

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YMFJ - Uncharacterized protein YmfJ

UniProt:	O31768	Sequences: MSVLENWDSWKNFLGDRLNYAQDKGMSQDTITDLATEIGSYLANEVESKNEQEKVLADLWSVASKDEQHAIANMMVKLVENNSTH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	85 (80)
Sequences:	273 (191)
Seq/√Len:	21.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_A	74_M	4.589	1.00
65_K	68_Q	2.661	0.99
67_E	77_K	2.355	0.97
57_A	61_S	2.275	0.96
22_Q	80_E	2.066	0.93
10_W	75_M	1.894	0.90
21_A	26_M	1.812	0.88
35_A	76_V	1.778	0.87
15_G	79_V	1.746	0.86
17_R	20_Y	1.698	0.84
63_A	71_I	1.676	0.83
69_H	74_M	1.675	0.83
4_L	53_E	1.632	0.82
47_E	54_K	1.632	0.82
34_L	38_I	1.586	0.80
48_S	54_K	1.572	0.79
36_T	40_S	1.490	0.75
63_A	74_M	1.482	0.75
62_V	77_K	1.414	0.71
3_V	13_F	1.365	0.68
18_L	79_V	1.355	0.68
3_V	75_M	1.353	0.68
46_V	49_K	1.287	0.64
10_W	39_G	1.281	0.63
15_G	18_L	1.239	0.61
54_K	57_A	1.223	0.60
18_L	24_K	1.214	0.59
52_Q	58_D	1.214	0.59
10_W	46_V	1.209	0.59
58_D	61_S	1.198	0.58
41_Y	53_E	1.186	0.57
59_L	74_M	1.167	0.56
62_V	78_L	1.165	0.56
2_S	23_D	1.121	0.53
4_L	17_R	1.117	0.53
7_W	52_Q	1.111	0.52
36_T	65_K	1.110	0.52
29_D	68_Q	1.086	0.51
64_S	67_E	1.084	0.50
6_N	16_D	1.078	0.50
19_N	81_N	1.073	0.50
36_T	68_Q	1.069	0.49
10_W	13_F	1.061	0.49
42_L	56_L	1.060	0.49
33_D	68_Q	1.040	0.48
12_N	61_S	0.999	0.45
55_V	67_E	0.993	0.44
16_D	20_Y	0.982	0.44
55_V	71_I	0.972	0.43
69_H	73_N	0.970	0.43
21_A	31_I	0.967	0.43
4_L	56_L	0.951	0.42
44_N	63_A	0.948	0.41
9_S	48_S	0.944	0.41
22_Q	48_S	0.915	0.39
27_S	30_T	0.899	0.38
41_Y	68_Q	0.891	0.38
5_E	70_A	0.869	0.36
23_D	28_Q	0.868	0.36
64_S	77_K	0.865	0.36
57_A	64_S	0.851	0.35
7_W	17_R	0.841	0.35
13_F	75_M	0.837	0.34
16_D	63_A	0.825	0.34
63_A	66_D	0.819	0.33
36_T	69_H	0.814	0.33
58_D	63_A	0.810	0.33
2_S	5_E	0.795	0.32
59_L	81_N	0.790	0.32
30_T	37_E	0.754	0.30
5_E	51_E	0.750	0.29
30_T	69_H	0.747	0.29
11_K	79_V	0.731	0.28
18_L	55_V	0.726	0.28
3_V	54_K	0.720	0.28
55_V	58_D	0.709	0.27
19_N	59_L	0.708	0.27
48_S	57_A	0.704	0.27
12_N	16_D	0.703	0.27
34_L	37_E	0.699	0.27
54_K	61_S	0.690	0.26
37_E	43_A	0.667	0.25
30_T	38_I	0.661	0.25
37_E	40_S	0.659	0.25
59_L	63_A	0.657	0.24
49_K	56_L	0.657	0.24
32_T	73_N	0.652	0.24
31_I	69_H	0.651	0.24
53_E	67_E	0.635	0.23
27_S	31_I	0.633	0.23
34_L	61_S	0.625	0.23
7_W	58_D	0.620	0.23
13_F	46_V	0.616	0.23
76_V	79_V	0.599	0.22
6_N	53_E	0.590	0.21
4_L	49_K	0.581	0.21
38_I	43_A	0.567	0.20
24_K	66_D	0.565	0.20
7_W	63_A	0.564	0.20
7_W	62_V	0.564	0.20
5_E	81_N	0.558	0.20
68_Q	79_V	0.556	0.20
9_S	57_A	0.556	0.20
29_D	73_N	0.555	0.20
47_E	68_Q	0.552	0.20
38_I	81_N	0.542	0.19
41_Y	45_E	0.542	0.19
8_D	22_Q	0.539	0.19
44_N	80_E	0.536	0.19
7_W	32_T	0.536	0.19
24_K	45_E	0.536	0.19
10_W	31_I	0.534	0.19
11_K	59_L	0.532	0.19
31_I	34_L	0.532	0.19
14_L	77_K	0.527	0.19
19_N	45_E	0.523	0.18
7_W	75_M	0.513	0.18
8_D	44_N	0.510	0.18
9_S	12_N	0.504	0.18
38_I	66_D	0.500	0.18

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
3d0wA	2	0.9647	100	0.112	Contact Map
3q23A	1	0.9412	19.4	0.921	Contact Map
3ivpA	2	1	18.6	0.922	Contact Map
3equA	1	0.9059	18	0.922	Contact Map
3viuA	1	0.7059	15.8	0.924	Contact Map
2ragA	2	0.6235	14.2	0.926	Contact Map
1ej5A	1	0.8824	14	0.926	Contact Map
2q01A	3	0.8824	13.1	0.927	Contact Map
1x9nA	1	1	12.6	0.927	Contact Map
1o2dA	1	0.6588	11.9	0.928	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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