XKDN - BACSU - GREMLIN Contacts

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XKDN - Phage-like element PBSX protein XkdN

UniProt:	P54333	Sequences: MSEKNENVYDLSFFMPGKTIEAEEIKVPISKRFVDKKGNVIPFILKPITTERIDELEKENTTFKNVKGRGRVKDLDSQRFYARIAIESTIYPDFRSKDLREAYKTADPVEVAKRVLSVGGEYANWLNKAIEINGFEDDLEDLEEEAKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (137)
Sequences:	179 (153)
Seq/√Len:	13.1

BACSU - XKDN YQBN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_K	44_I	4.265	1.00
89_T	125_W	4.167	1.00
53_I	80_F	3.630	0.99
93_D	96_S	3.416	0.99
97_K	101_E	3.204	0.98
19_T	32_R	2.649	0.93
66_V	69_R	2.545	0.92
15_M	146_A	2.524	0.91
94_F	100_R	2.466	0.90
105_T	111_V	2.345	0.88
94_F	112_A	2.085	0.81
89_T	94_F	2.060	0.80
26_K	42_P	1.975	0.77
128_K	131_E	1.964	0.77
100_R	111_V	1.943	0.76
124_N	127_N	1.882	0.73
59_E	83_R	1.846	0.72
13_F	41_I	1.832	0.71
19_T	102_A	1.791	0.70
79_R	83_R	1.780	0.69
30_S	33_F	1.748	0.68
94_F	115_V	1.724	0.67
48_I	84_I	1.693	0.65
11_L	30_S	1.687	0.65
43_F	94_F	1.662	0.64
52_R	87_E	1.649	0.63
26_K	140_E	1.594	0.60
13_F	17_G	1.577	0.59
24_E	44_I	1.575	0.59
32_R	121_E	1.575	0.59
56_L	60_N	1.473	0.54
100_R	115_V	1.462	0.53
80_F	133_N	1.421	0.51
20_I	141_D	1.403	0.50
32_R	116_L	1.391	0.50
60_N	83_R	1.359	0.48
43_F	91_Y	1.356	0.48
88_S	133_N	1.351	0.48
51_E	114_R	1.338	0.47
80_F	84_I	1.335	0.47
75_L	122_Y	1.328	0.46
24_E	60_N	1.327	0.46
48_I	110_E	1.312	0.46
48_I	54_D	1.307	0.45
37_K	110_E	1.296	0.45
74_D	142_L	1.260	0.43
49_T	63_F	1.258	0.43
33_F	116_L	1.230	0.41
12_S	51_E	1.230	0.41
83_R	122_Y	1.224	0.41
140_E	144_E	1.217	0.41
46_K	87_E	1.208	0.40
45_L	88_S	1.174	0.39
62_T	140_E	1.144	0.37
32_R	117_S	1.122	0.36
46_K	137_D	1.080	0.34
107_D	129_A	1.032	0.32
76_D	137_D	1.011	0.31
16_P	114_R	1.010	0.31
45_L	79_R	1.001	0.30
84_I	108_P	0.999	0.30
25_I	45_L	0.984	0.30
43_F	116_L	0.968	0.29
56_L	114_R	0.968	0.29
97_K	106_A	0.960	0.29
95_R	108_P	0.955	0.28
57_E	96_S	0.954	0.28
16_P	103_Y	0.946	0.28
67_K	117_S	0.943	0.28
10_D	96_S	0.939	0.28
16_P	102_A	0.935	0.27
119_G	135_F	0.930	0.27
80_F	105_T	0.927	0.27
31_K	137_D	0.925	0.27
72_V	78_Q	0.915	0.27
130_I	134_G	0.914	0.27
116_L	125_W	0.903	0.26
110_E	132_I	0.901	0.26
109_V	119_G	0.881	0.25
10_D	112_A	0.875	0.25
89_T	115_V	0.871	0.25
13_F	30_S	0.863	0.25
17_G	126_L	0.857	0.24
113_K	122_Y	0.853	0.24
20_I	24_E	0.853	0.24
93_D	112_A	0.849	0.24
44_I	135_F	0.845	0.24
34_V	104_K	0.840	0.24
107_D	110_E	0.835	0.24
42_P	87_E	0.832	0.23
46_K	141_D	0.830	0.23
12_S	82_A	0.826	0.23
29_I	38_G	0.817	0.23
80_F	100_R	0.816	0.23
100_R	112_A	0.809	0.23
60_N	68_G	0.804	0.22
98_D	144_E	0.803	0.22
42_P	49_T	0.802	0.22
19_T	116_L	0.795	0.22
55_E	93_D	0.795	0.22
27_V	30_S	0.792	0.22
19_T	135_F	0.791	0.22
145_E	148_N	0.779	0.21
37_K	144_E	0.778	0.21
57_E	135_F	0.773	0.21
95_R	107_D	0.769	0.21
36_K	131_E	0.769	0.21
85_A	126_L	0.768	0.21
55_E	141_D	0.762	0.21
48_I	53_I	0.761	0.21
136_E	144_E	0.757	0.21
94_F	102_A	0.749	0.20
36_K	40_V	0.744	0.20
86_I	104_K	0.739	0.20
27_V	45_L	0.735	0.20
64_K	141_D	0.724	0.20
48_I	142_L	0.723	0.20
55_E	84_I	0.721	0.19
30_S	116_L	0.720	0.19
134_G	145_E	0.717	0.19
81_Y	141_D	0.715	0.19
99_L	103_Y	0.715	0.19
18_K	90_I	0.714	0.19
42_P	53_I	0.714	0.19
41_I	75_L	0.712	0.19
88_S	135_F	0.709	0.19
12_S	73_K	0.706	0.19
65_N	96_S	0.704	0.19
74_D	130_I	0.694	0.19
120_G	129_A	0.692	0.19
11_L	105_T	0.691	0.19
76_D	89_T	0.686	0.18
41_I	146_A	0.682	0.18
94_F	111_V	0.678	0.18
42_P	101_E	0.678	0.18
82_A	113_K	0.678	0.18
59_E	98_D	0.672	0.18
89_T	143_E	0.671	0.18
30_S	38_G	0.667	0.18
80_F	88_S	0.662	0.18
15_M	69_R	0.657	0.17
20_I	26_K	0.652	0.17
65_N	70_G	0.650	0.17
15_M	76_D	0.644	0.17
123_A	127_N	0.639	0.17
85_A	96_S	0.638	0.17
45_L	128_K	0.632	0.17
114_R	123_A	0.628	0.17
18_K	105_T	0.624	0.16
19_T	121_E	0.622	0.16
59_E	122_Y	0.618	0.16
109_V	128_K	0.611	0.16
65_N	69_R	0.611	0.16
83_R	109_V	0.606	0.16
54_D	113_K	0.606	0.16
89_T	135_F	0.602	0.16
80_F	94_F	0.602	0.16
53_I	89_T	0.601	0.16
25_I	127_N	0.600	0.16
15_M	77_S	0.599	0.16
138_D	143_E	0.597	0.16
33_F	85_A	0.596	0.16
124_N	136_E	0.594	0.16
98_D	122_Y	0.594	0.16
33_F	103_Y	0.594	0.16
16_P	19_T	0.587	0.15
42_P	46_K	0.586	0.15
82_A	123_A	0.585	0.15
11_L	111_V	0.577	0.15
21_E	44_I	0.573	0.15
40_V	43_F	0.571	0.15
84_I	88_S	0.566	0.15
18_K	143_E	0.560	0.15
50_T	53_I	0.555	0.15
54_D	137_D	0.554	0.15
15_M	75_L	0.552	0.15
103_Y	115_V	0.549	0.14
63_F	117_S	0.537	0.14
53_I	125_W	0.537	0.14
117_S	128_K	0.535	0.14
17_G	98_D	0.533	0.14
17_G	25_I	0.529	0.14
45_L	129_A	0.527	0.14
117_S	134_G	0.526	0.14
48_I	88_S	0.525	0.14
28_P	116_L	0.525	0.14
79_R	127_N	0.524	0.14
56_L	83_R	0.524	0.14
81_Y	97_K	0.521	0.14
57_E	119_G	0.521	0.14
102_A	143_E	0.518	0.14
14_F	121_E	0.516	0.14
39_N	66_V	0.516	0.14
21_E	84_I	0.516	0.14
26_K	71_R	0.514	0.14
60_N	119_G	0.511	0.13
23_E	90_I	0.511	0.13
28_P	82_A	0.511	0.13
98_D	141_D	0.511	0.13
122_Y	133_N	0.510	0.13
136_E	145_E	0.509	0.13
51_E	146_A	0.508	0.13
61_T	73_K	0.507	0.13
12_S	28_P	0.503	0.13
63_F	71_R	0.502	0.13
57_E	131_E	0.500	0.13

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
3kluA	1	0.8041	100	0.182	Contact Map
4dvyP	1	0.7838	6.2	0.957	Contact Map
4mafA	2	0.8649	6.1	0.957	Contact Map
3j8bE	1	0.473	5.2	0.959	Contact Map
2mb9A	1	0.6486	4.9	0.96	Contact Map
3pmkN	1	0.2027	4.6	0.96	Contact Map
2kdoA	1	0.7095	4.4	0.961	Contact Map
1g5zA	2	0.5473	4.2	0.961	Contact Map
1yjgA	2	0.5	4.2	0.961	Contact Map
1djxA	1	0.6351	4	0.961	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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