XKDM - BACSU - GREMLIN Contacts

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XKDM - Phage-like element PBSX protein XkdM

UniProt:	P54332	Sequences: MALKAQNTISGKEGRLFLDGEEMAHIKTFEANVEKNKSEVNIMGRRMTGHKTTGANGTGTATFYKVTSKFVLLMMDYVKKGSDPYFTLQAVLDDQSSGRGTERVTLYDVNFDSAKIASLDVDSEALEEEVPFTFEDFDVPEKLSDTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (138)
Sequences:	295 (229)
Seq/√Len:	19.5

BACSU - XKDM YQBM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_G	132_F	4.111	1.00
57_G	134_F	3.141	0.99
39_E	56_N	2.927	0.99
37_K	133_T	2.904	0.99
32_N	113_S	2.900	0.99
14_G	119_L	2.895	0.99
47_M	55_A	2.809	0.99
39_E	50_H	2.777	0.99
34_E	113_S	2.599	0.98
29_F	106_L	2.583	0.98
72_L	142_K	2.565	0.98
37_K	112_D	2.368	0.96
34_E	58_T	2.287	0.95
120_D	123_S	2.096	0.92
31_A	106_L	2.032	0.91
83_D	110_N	1.990	0.90
79_K	138_D	1.981	0.90
28_T	62_T	1.938	0.89
13_E	46_R	1.900	0.88
34_E	56_N	1.899	0.88
112_D	133_T	1.812	0.85
16_L	24_A	1.807	0.85
19_D	73_L	1.804	0.85
14_G	26_I	1.753	0.83
35_K	83_D	1.739	0.83
75_M	137_F	1.735	0.82
29_F	88_L	1.704	0.81
11_G	14_G	1.666	0.80
16_L	29_F	1.665	0.80
51_K	94_D	1.516	0.73
14_G	61_A	1.512	0.73
60_T	131_P	1.473	0.71
35_K	110_N	1.467	0.70
116_I	137_F	1.461	0.70
89_Q	140_P	1.445	0.69
28_T	120_D	1.440	0.69
38_S	129_E	1.431	0.68
79_K	136_D	1.411	0.67
94_D	100_G	1.400	0.66
30_E	118_S	1.369	0.65
65_K	102_E	1.365	0.64
107_Y	138_D	1.260	0.58
21_E	69_K	1.244	0.57
17_F	91_V	1.226	0.56
36_N	54_G	1.224	0.56
90_A	117_A	1.197	0.54
36_N	104_V	1.177	0.53
15_R	91_V	1.166	0.52
24_A	63_F	1.152	0.51
29_F	90_A	1.139	0.50
15_R	22_E	1.134	0.50
106_L	109_V	1.133	0.50
73_L	93_D	1.118	0.49
37_K	110_N	1.117	0.49
27_K	127_E	1.112	0.49
48_T	56_N	1.100	0.48
87_T	105_T	1.100	0.48
23_M	88_L	1.096	0.48
21_E	103_R	1.090	0.47
108_D	135_E	1.086	0.47
40_V	61_A	1.060	0.45
68_S	102_E	1.059	0.45
112_D	131_P	1.055	0.45
65_K	71_V	1.051	0.45
67_T	70_F	1.038	0.44
102_E	143_L	1.038	0.44
72_L	76_D	1.028	0.43
9_I	143_L	1.018	0.43
50_H	56_N	1.011	0.42
32_N	60_T	0.996	0.41
38_S	52_T	0.996	0.41
26_I	61_A	0.981	0.40
101_T	141_E	0.980	0.40
33_V	78_V	0.960	0.39
76_D	79_K	0.960	0.39
35_K	52_T	0.950	0.39
105_T	140_P	0.930	0.37
85_Y	110_N	0.924	0.37
42_I	45_R	0.901	0.36
19_D	76_D	0.901	0.36
110_N	133_T	0.891	0.35
11_G	123_S	0.881	0.34
28_T	118_S	0.878	0.34
113_S	130_V	0.875	0.34
14_G	43_M	0.871	0.34
78_V	136_D	0.858	0.33
75_M	79_K	0.857	0.33
47_M	136_D	0.857	0.33
93_D	101_T	0.831	0.32
49_G	135_E	0.824	0.31
27_K	64_Y	0.817	0.31
16_L	88_L	0.816	0.31
33_V	134_F	0.815	0.31
49_G	85_Y	0.803	0.30
5_A	51_K	0.802	0.30
34_E	60_T	0.800	0.30
28_T	108_D	0.798	0.30
36_N	53_T	0.789	0.29
51_K	100_G	0.786	0.29
79_K	137_F	0.781	0.29
38_S	60_T	0.771	0.28
26_I	118_S	0.766	0.28
92_L	101_T	0.761	0.28
49_G	137_F	0.758	0.28
92_L	143_L	0.758	0.28
45_R	49_G	0.749	0.27
37_K	83_D	0.743	0.27
24_A	136_D	0.741	0.27
76_D	80_K	0.734	0.27
59_G	109_V	0.726	0.26
7_N	102_E	0.723	0.26
50_H	108_D	0.720	0.26
59_G	131_P	0.713	0.25
46_R	55_A	0.712	0.25
30_E	119_L	0.706	0.25
15_R	119_L	0.689	0.24
11_G	128_E	0.688	0.24
26_I	109_V	0.688	0.24
61_A	119_L	0.682	0.24
95_Q	100_G	0.679	0.24
60_T	139_V	0.678	0.24
6_Q	96_S	0.678	0.24
92_L	102_E	0.676	0.24
77_Y	143_L	0.670	0.23
38_S	120_D	0.665	0.23
76_D	136_D	0.661	0.23
45_R	136_D	0.659	0.23
33_V	57_G	0.656	0.23
28_T	123_S	0.655	0.23
33_V	116_I	0.651	0.23
49_G	112_D	0.650	0.23
37_K	135_E	0.649	0.23
55_A	116_I	0.648	0.22
17_F	103_R	0.648	0.22
39_E	131_P	0.646	0.22
32_N	114_A	0.646	0.22
25_H	67_T	0.645	0.22
33_V	55_A	0.645	0.22
68_S	139_V	0.643	0.22
92_L	103_R	0.643	0.22
29_F	117_A	0.642	0.22
44_G	121_V	0.641	0.22
112_D	135_E	0.641	0.22
62_T	127_E	0.632	0.22
36_N	56_N	0.629	0.22
38_S	54_G	0.627	0.22
20_G	76_D	0.625	0.21
65_K	128_E	0.624	0.21
96_S	103_R	0.623	0.21
6_Q	76_D	0.620	0.21
89_Q	101_T	0.617	0.21
103_R	143_L	0.613	0.21
32_N	56_N	0.607	0.21
7_N	19_D	0.594	0.20
19_D	32_N	0.593	0.20
67_T	105_T	0.589	0.20
53_T	73_L	0.587	0.20
58_T	127_E	0.583	0.20
55_A	128_E	0.582	0.20
62_T	123_S	0.580	0.20
4_K	21_E	0.578	0.19
43_M	121_V	0.576	0.19
15_R	93_D	0.576	0.19
96_S	105_T	0.572	0.19
14_G	129_E	0.570	0.19
39_E	47_M	0.568	0.19
71_V	139_V	0.568	0.19
27_K	62_T	0.562	0.19
26_I	130_V	0.562	0.19
118_S	127_E	0.561	0.19
26_I	132_F	0.560	0.19
35_K	135_E	0.556	0.19
90_A	119_L	0.552	0.18
9_I	97_S	0.551	0.18
99_R	143_L	0.549	0.18
78_V	116_I	0.548	0.18
24_A	116_I	0.547	0.18
89_Q	105_T	0.546	0.18
28_T	32_N	0.543	0.18
47_M	57_G	0.542	0.18
54_G	128_E	0.539	0.18
63_F	67_T	0.538	0.18
7_N	99_R	0.534	0.18
76_D	125_A	0.534	0.18
26_I	88_L	0.534	0.18
39_E	129_E	0.531	0.18
21_E	131_P	0.528	0.18
39_E	59_G	0.527	0.18
4_K	76_D	0.522	0.17
18_L	23_M	0.518	0.17
8_T	41_N	0.517	0.17
68_S	141_E	0.516	0.17
5_A	82_S	0.514	0.17
74_M	139_V	0.513	0.17
107_Y	136_D	0.513	0.17
12_K	17_F	0.510	0.17
42_I	49_G	0.509	0.17
115_K	118_S	0.506	0.17
14_G	31_A	0.505	0.17
30_E	130_V	0.505	0.17
29_F	59_G	0.504	0.17
109_V	132_F	0.503	0.17
5_A	135_E	0.503	0.17
91_V	103_R	0.503	0.17
53_T	80_K	0.502	0.17
58_T	83_D	0.501	0.17
40_V	125_A	0.500	0.17

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
2gujA	1	0.9048	100	0.087	Contact Map
3j9qS	11	0.932	28.3	0.938	Contact Map
3v4hA	5	0.7823	18.4	0.943	Contact Map
3he1A	3	0.8231	17.7	0.944	Contact Map
4ksrA	3	0.8776	15.1	0.945	Contact Map
3wx6A	6	0.7483	14.5	0.946	Contact Map
2k4qA	1	0.8912	14.4	0.946	Contact Map
3eaaA	3	0.9184	11.6	0.948	Contact Map
4hkhA	1	0.8912	9.6	0.95	Contact Map
1y12A	3	0.9116	9.4	0.95	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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