YABP - BACSU - GREMLIN Contacts

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YABP - Spore protein YabP

UniProt:	P37558	Sequences: MNSYYDQKGSSSVPEQHDVTMKGRKHLDISGVKHVESFDNEEFLLETVMGMLSVRGQNLQMKNLDVEKGIVSIKGRVFDLVYLDEQQGDKAKGFFSKLFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	100 (90)
Sequences:	497 (368)
Seq/√Len:	38.8

BACSU - YABP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_T	52_L	4.475	1.00
21_M	27_L	4.157	1.00
52_L	80_L	3.821	1.00
34_H	60_Q	2.856	1.00
34_H	70_I	2.360	1.00
32_V	47_T	2.321	1.00
57_Q	76_R	2.277	1.00
35_V	45_L	2.268	1.00
40_N	43_F	1.881	0.98
22_K	26_H	1.779	0.97
36_E	51_M	1.754	0.97
63_N	72_S	1.730	0.97
60_Q	66_V	1.700	0.96
77_V	80_L	1.563	0.94
46_E	51_M	1.546	0.94
21_M	59_L	1.479	0.92
18_D	22_K	1.476	0.92
84_D	93_G	1.456	0.92
79_D	92_K	1.454	0.92
29_I	32_V	1.427	0.91
39_D	98_L	1.396	0.90
39_D	71_V	1.389	0.90
63_N	70_I	1.378	0.89
16_Q	97_K	1.372	0.89
58_N	76_R	1.269	0.85
35_V	60_Q	1.255	0.84
34_H	65_D	1.255	0.84
41_E	98_L	1.250	0.84
53_S	81_V	1.221	0.83
15_E	23_G	1.212	0.82
65_D	68_K	1.210	0.82
69_G	84_D	1.206	0.82
41_E	99_F	1.155	0.79
43_F	70_I	1.141	0.78
85_E	96_S	1.130	0.78
61_M	71_V	1.110	0.76
43_F	62_K	1.110	0.76
47_T	50_G	1.099	0.76
79_D	91_A	1.058	0.73
17_H	69_G	1.051	0.72
60_Q	74_K	1.043	0.72
62_K	94_F	1.038	0.71
39_D	52_L	1.031	0.71
17_H	72_S	1.021	0.70
61_M	66_V	1.012	0.69
54_V	86_Q	1.010	0.69
80_L	85_E	1.007	0.69
41_E	57_Q	1.003	0.69
37_S	44_L	0.990	0.68
21_M	95_F	0.968	0.66
55_R	91_A	0.968	0.66
21_M	80_L	0.963	0.65
30_S	70_I	0.901	0.60
27_L	35_V	0.896	0.60
23_G	86_Q	0.885	0.59
42_E	93_G	0.884	0.59
39_D	84_D	0.878	0.58
39_D	78_F	0.874	0.58
58_N	86_Q	0.860	0.57
45_L	62_K	0.825	0.54
55_R	100_K	0.815	0.53
17_H	49_M	0.809	0.52
26_H	94_F	0.800	0.51
35_V	66_V	0.799	0.51
45_L	98_L	0.795	0.51
14_P	52_L	0.792	0.51
51_M	95_F	0.769	0.48
69_G	97_K	0.766	0.48
40_N	51_M	0.765	0.48
22_K	97_K	0.760	0.48
15_E	67_E	0.755	0.47
41_E	64_L	0.753	0.47
15_E	80_L	0.743	0.46
44_L	51_M	0.737	0.46
74_K	96_S	0.737	0.46
30_S	99_F	0.736	0.46
67_E	74_K	0.734	0.45
18_D	43_F	0.734	0.45
16_Q	30_S	0.719	0.44
14_P	99_F	0.714	0.44
84_D	92_K	0.710	0.43
26_H	33_K	0.708	0.43
66_V	86_Q	0.701	0.42
37_S	100_K	0.697	0.42
96_S	100_K	0.695	0.42
21_M	26_H	0.694	0.42
29_I	85_E	0.694	0.42
57_Q	96_S	0.687	0.41
89_D	93_G	0.686	0.41
15_E	48_V	0.683	0.41
57_Q	91_A	0.680	0.41
89_D	92_K	0.678	0.40
45_L	71_V	0.651	0.38
63_N	99_F	0.648	0.38
41_E	68_K	0.645	0.38
14_P	19_V	0.640	0.37
40_N	60_Q	0.632	0.36
63_N	68_K	0.629	0.36
77_V	93_G	0.626	0.36
14_P	90_K	0.625	0.36
33_K	58_N	0.620	0.35
36_E	83_L	0.615	0.35
66_V	74_K	0.599	0.34
19_V	67_E	0.598	0.34
30_S	82_Y	0.593	0.33
21_M	52_L	0.585	0.33
35_V	91_A	0.581	0.32
69_G	98_L	0.578	0.32
39_D	81_V	0.575	0.32
49_M	77_V	0.567	0.31
34_H	51_M	0.564	0.31
18_D	23_G	0.564	0.31
16_Q	99_F	0.561	0.31
27_L	68_K	0.561	0.31
34_H	76_R	0.555	0.30
13_V	76_R	0.554	0.30
40_N	58_N	0.554	0.30
79_D	98_L	0.552	0.30
68_K	71_V	0.544	0.29
54_V	82_Y	0.543	0.29
45_L	54_V	0.540	0.29
73_I	76_R	0.538	0.29
29_I	40_N	0.534	0.29
19_V	96_S	0.525	0.28
42_E	53_S	0.522	0.28
23_G	91_A	0.522	0.28
62_K	74_K	0.522	0.28
14_P	21_M	0.522	0.28
20_T	28_D	0.519	0.28
15_E	100_K	0.518	0.28
41_E	44_L	0.515	0.27
49_M	98_L	0.510	0.27
90_K	98_L	0.501	0.26
16_Q	86_Q	0.501	0.26
43_F	65_D	0.500	0.26

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
2ks0A	2	0.66	99.7	0.453	Contact Map
3f2bA	1	0.43	27.1	0.906	Contact Map
2og2A	1	0	4.7	0.934	Contact Map
1ycyA	5	0.62	3.7	0.937	Contact Map
1yoxA	3	0.42	3.1	0.94	Contact Map
2yh5A	1	0.59	2.9	0.94	Contact Map
2bolA	2	0.76	2.6	0.942	Contact Map
2x55A	1	0.61	2.2	0.944	Contact Map
4fmrA	2	0.93	1.9	0.946	Contact Map
1xaxA	1	0.93	1.9	0.946	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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