XKDS - BACSU - GREMLIN Contacts

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XKDS - Phage-like element PBSX protein XkdS

UniProt:	P54338	Sequences: MALTPEVEFEDIEVESEVIETSQTYKIDFENGRITNELITGLEAIRQFVYIALQTERYAYSIYSHNVGNELQDVLTDHETTDAYKKMEIPRLIEEALVYDDRISAVTDFEIEKQGDAFHVSFVVETDEGTLEIEEVIGEDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	141 (121)
Sequences:	355 (319)
Seq/√Len:	29.0

BACSU - XKDS YQBS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_T	125_E	4.758	1.00
88_E	91_R	4.242	1.00
45_I	49_V	3.342	1.00
109_F	122_F	3.225	1.00
45_I	126_T	2.998	1.00
47_Q	100_D	2.610	0.99
43_E	46_R	2.349	0.99
52_A	96_A	2.337	0.99
51_I	67_V	2.221	0.98
53_L	129_G	2.074	0.97
51_I	63_Y	2.067	0.97
22_S	45_I	2.064	0.97
89_I	92_L	1.995	0.97
51_I	55_T	1.919	0.96
59_A	64_S	1.737	0.93
24_T	47_Q	1.719	0.92
88_E	95_E	1.685	0.92
93_I	109_F	1.673	0.91
48_F	100_D	1.656	0.91
90_P	111_I	1.642	0.91
11_D	14_V	1.612	0.90
59_A	72_Q	1.610	0.90
49_V	103_I	1.558	0.88
27_I	51_I	1.496	0.86
21_T	102_R	1.487	0.86
49_V	124_V	1.476	0.85
27_I	47_Q	1.432	0.83
74_V	92_L	1.429	0.83
82_D	113_K	1.425	0.83
24_T	102_R	1.386	0.81
57_R	70_E	1.377	0.81
26_K	43_E	1.291	0.76
56_E	69_N	1.278	0.76
69_N	93_I	1.278	0.76
24_T	100_D	1.272	0.75
22_S	100_D	1.268	0.75
20_E	102_R	1.196	0.71
45_I	103_I	1.179	0.69
27_I	34_I	1.179	0.69
96_A	129_G	1.177	0.69
86_K	111_I	1.176	0.69
19_I	127_D	1.154	0.68
71_L	89_I	1.139	0.67
62_I	99_Y	1.125	0.66
89_I	118_F	1.122	0.66
112_E	119_H	1.114	0.65
45_I	120_V	1.098	0.64
101_D	124_V	1.089	0.63
27_I	32_G	1.058	0.61
108_D	122_F	1.043	0.60
108_D	121_S	1.040	0.60
104_S	127_D	1.005	0.57
124_V	131_L	1.004	0.57
21_T	24_T	0.994	0.56
27_I	100_D	0.990	0.56
41_G	129_G	0.976	0.55
22_S	34_I	0.972	0.54
22_S	102_R	0.969	0.54
108_D	123_V	0.962	0.54
41_G	115_G	0.960	0.53
12_I	15_E	0.935	0.51
84_Y	93_I	0.930	0.51
40_T	102_R	0.927	0.51
105_A	125_E	0.916	0.50
48_F	99_Y	0.902	0.49
86_K	118_F	0.901	0.49
28_D	75_L	0.893	0.48
40_T	47_Q	0.893	0.48
69_N	96_A	0.874	0.47
14_V	112_E	0.871	0.46
71_L	74_V	0.867	0.46
24_T	27_I	0.860	0.46
56_E	72_Q	0.857	0.45
37_E	96_A	0.851	0.45
45_I	53_L	0.846	0.45
46_R	124_V	0.844	0.44
69_N	75_L	0.843	0.44
73_D	134_E	0.838	0.44
111_I	118_F	0.835	0.44
94_E	105_A	0.834	0.44
93_I	98_V	0.834	0.44
28_D	31_N	0.824	0.43
18_V	104_S	0.824	0.43
48_F	101_D	0.822	0.43
86_K	113_K	0.821	0.43
16_S	41_G	0.820	0.43
51_I	91_R	0.814	0.42
62_I	101_D	0.813	0.42
40_T	100_D	0.805	0.41
20_E	127_D	0.801	0.41
23_Q	38_L	0.800	0.41
49_V	113_K	0.798	0.41
16_S	107_T	0.792	0.40
34_I	100_D	0.789	0.40
58_Y	70_E	0.782	0.40
114_Q	117_A	0.780	0.40
70_E	99_Y	0.777	0.39
93_I	120_V	0.775	0.39
47_Q	102_R	0.772	0.39
42_L	46_R	0.767	0.39
56_E	92_L	0.762	0.38
26_K	37_E	0.753	0.38
76_T	92_L	0.752	0.37
91_R	95_E	0.747	0.37
89_I	105_A	0.744	0.37
17_E	110_E	0.741	0.37
34_I	48_F	0.741	0.37
70_E	92_L	0.730	0.36
53_L	83_A	0.730	0.36
23_Q	26_K	0.727	0.36
86_K	116_D	0.715	0.35
28_D	33_R	0.713	0.35
22_S	126_T	0.710	0.34
60_Y	90_P	0.710	0.34
41_G	86_K	0.702	0.34
103_I	113_K	0.701	0.34
130_T	133_I	0.701	0.34
50_Y	54_Q	0.697	0.34
114_Q	119_H	0.695	0.33
70_E	103_I	0.694	0.33
47_Q	96_A	0.694	0.33
52_A	69_N	0.692	0.33
38_L	69_N	0.687	0.33
61_S	99_Y	0.687	0.33
61_S	73_D	0.684	0.33
76_T	85_K	0.682	0.32
57_R	65_H	0.682	0.32
22_S	40_T	0.678	0.32
34_I	83_A	0.673	0.32
28_D	57_R	0.670	0.32
94_E	109_F	0.668	0.32
57_R	68_G	0.668	0.32
55_T	67_V	0.667	0.31
69_N	92_L	0.666	0.31
123_V	132_E	0.664	0.31
31_N	125_E	0.662	0.31
27_I	82_D	0.660	0.31
42_L	49_V	0.652	0.30
62_I	84_Y	0.647	0.30
24_T	40_T	0.646	0.30
37_E	102_R	0.646	0.30
14_V	17_E	0.643	0.30
81_T	131_L	0.642	0.30
44_A	64_S	0.642	0.30
112_E	121_S	0.639	0.30
24_T	101_D	0.636	0.29
22_S	48_F	0.632	0.29
56_E	84_Y	0.628	0.29
21_T	49_V	0.623	0.29
24_T	48_F	0.619	0.28
15_E	18_V	0.608	0.28
103_I	106_V	0.603	0.27
66_N	70_E	0.599	0.27
124_V	130_T	0.596	0.27
13_E	125_E	0.586	0.26
48_F	98_V	0.585	0.26
87_M	118_F	0.579	0.26
58_Y	65_H	0.564	0.25
52_A	99_Y	0.563	0.25
29_F	90_P	0.561	0.25
74_V	84_Y	0.555	0.24
70_E	91_R	0.554	0.24
108_D	119_H	0.551	0.24
42_L	87_M	0.549	0.24
33_R	58_Y	0.549	0.24
16_S	112_E	0.546	0.24
74_V	88_E	0.545	0.24
73_D	92_L	0.543	0.24
93_I	122_F	0.539	0.24
60_Y	118_F	0.537	0.23
67_V	88_E	0.535	0.23
49_V	81_T	0.535	0.23
85_K	119_H	0.533	0.23
51_I	116_D	0.527	0.23
28_D	101_D	0.526	0.23
90_P	94_E	0.524	0.23
81_T	126_T	0.511	0.22
55_T	133_I	0.508	0.22
21_T	100_D	0.505	0.22
71_L	96_A	0.503	0.22
32_G	123_V	0.501	0.21
115_G	121_S	0.500	0.21

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
4hrzA	2	0.8085	99	0.756	Contact Map
2ia7A	1	0.7163	98.8	0.773	Contact Map
2e7gA	1	0.4965	36	0.933	Contact Map
1josA	1	0.4113	16.9	0.943	Contact Map
3w61A	2	0.3972	14.6	0.944	Contact Map
2zztA	2	0.4043	13.8	0.945	Contact Map
2dyjA	1	0.3972	12.1	0.946	Contact Map
3bypA	2	0.4043	11.7	0.947	Contact Map
2kzfA	1	0.4468	11.2	0.947	Contact Map
1v4eA	3	0.6596	7.8	0.951	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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