XKDU - BACSU - GREMLIN Contacts

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XKDU - Phage-like element PBSX protein XkdU

UniProt:	P54340	Sequences: MSKQDDMRAYLPPFLTSLKEMAELLKAEAPEFDKQNDSIFDLTDQLFVPTATWGLSRWEKILNVPRESGDTDEIRRLRLISKMSNIPPITYRAIEQAVNRFLKNPSAQVRLLPGEYRFNVDINVDDLQHMNELIEAIENMKPAHLAYTLRGGLNETLRIKDTVILNHRRYRTASELKVGYSVTLNNNEVVLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (167)
Sequences:	377 (337)
Seq/√Len:	26.1

BACSU - XKDU YQCA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
165_L	173_A	4.734	1.00
156_T	165_L	4.542	1.00
156_T	173_A	4.526	1.00
49_P	80_I	4.030	1.00
112_L	115_E	4.006	1.00
118_F	141_K	3.595	1.00
45_Q	52_T	3.170	1.00
55_L	79_L	2.850	1.00
15_L	21_M	2.822	1.00
160_K	169_R	2.503	0.99
51_A	55_L	2.497	0.99
41_D	52_T	2.408	0.99
70_D	78_R	2.407	0.99
45_Q	53_W	2.336	0.98
62_L	83_M	2.254	0.98
67_E	70_D	2.216	0.98
41_D	45_Q	2.050	0.96
59_E	75_R	1.972	0.95
164_I	167_H	1.863	0.93
23_E	26_K	1.817	0.92
55_L	76_R	1.796	0.92
141_K	147_Y	1.693	0.90
137_I	147_Y	1.685	0.89
138_E	141_K	1.666	0.89
11_L	25_L	1.648	0.88
55_L	72_D	1.603	0.87
118_F	145_L	1.587	0.86
14_F	17_S	1.568	0.85
48_V	83_M	1.545	0.85
58_W	83_M	1.543	0.85
168_R	171_R	1.506	0.83
163_V	168_R	1.505	0.83
9_A	79_L	1.504	0.83
27_A	40_F	1.480	0.82
165_L	172_T	1.466	0.81
25_L	28_E	1.453	0.81
168_R	173_A	1.452	0.81
160_K	171_R	1.403	0.78
157_L	166_N	1.397	0.78
165_L	171_R	1.383	0.77
95_E	99_N	1.382	0.77
7_M	25_L	1.380	0.77
7_M	29_A	1.353	0.76
118_F	138_E	1.346	0.75
48_V	79_L	1.341	0.75
157_L	160_K	1.307	0.73
156_T	168_R	1.293	0.72
165_L	169_R	1.270	0.71
88_P	111_L	1.260	0.70
142_P	145_L	1.254	0.70
15_L	24_L	1.242	0.69
170_Y	174_S	1.204	0.67
163_V	171_R	1.199	0.66
41_D	53_W	1.181	0.65
48_V	62_L	1.155	0.63
46_L	144_H	1.146	0.63
169_R	174_S	1.138	0.62
111_L	145_L	1.122	0.61
10_Y	31_E	1.120	0.61
91_Y	111_L	1.119	0.61
74_I	78_R	1.103	0.60
82_K	139_N	1.078	0.58
126_D	149_L	1.058	0.57
133_L	149_L	1.047	0.56
119_N	150_R	1.042	0.55
159_I	172_T	1.038	0.55
50_T	76_R	1.036	0.55
160_K	173_A	1.034	0.55
51_A	76_R	1.028	0.54
8_R	22_A	1.025	0.54
90_T	116_Y	1.018	0.54
71_T	81_S	1.015	0.53
167_H	170_Y	1.015	0.53
6_D	33_D	1.014	0.53
28_E	32_F	1.005	0.53
169_R	173_A	0.998	0.52
95_E	108_Q	0.987	0.51
163_V	173_A	0.987	0.51
101_F	133_L	0.985	0.51
112_L	119_N	0.985	0.51
160_K	168_R	0.965	0.50
160_K	174_S	0.957	0.49
6_D	29_A	0.956	0.49
159_I	162_T	0.955	0.49
155_E	168_R	0.955	0.49
84_S	97_A	0.946	0.48
45_Q	58_W	0.946	0.48
53_W	144_H	0.941	0.48
155_E	158_R	0.937	0.48
171_R	174_S	0.935	0.47
158_R	174_S	0.926	0.47
159_I	163_V	0.903	0.45
53_W	82_K	0.891	0.44
45_Q	54_G	0.889	0.44
8_R	25_L	0.884	0.44
160_K	166_N	0.871	0.43
107_A	126_D	0.869	0.43
70_D	132_E	0.856	0.42
64_V	111_L	0.856	0.42
98_V	105_P	0.843	0.41
167_H	171_R	0.842	0.41
99_N	119_N	0.840	0.41
134_I	149_L	0.835	0.40
127_L	151_G	0.834	0.40
56_S	66_R	0.830	0.40
156_T	163_V	0.819	0.39
137_I	141_K	0.812	0.39
116_Y	145_L	0.812	0.39
163_V	167_H	0.811	0.38
85_N	139_N	0.808	0.38
17_S	22_A	0.808	0.38
90_T	104_N	0.807	0.38
170_Y	173_A	0.805	0.38
156_T	160_K	0.805	0.38
15_L	18_L	0.800	0.38
31_E	47_F	0.798	0.38
54_G	66_R	0.789	0.37
6_D	79_L	0.786	0.37
118_F	147_Y	0.785	0.37
156_T	159_I	0.783	0.37
102_L	124_V	0.781	0.36
166_N	169_R	0.780	0.36
29_A	33_D	0.774	0.36
163_V	170_Y	0.772	0.36
99_N	112_L	0.771	0.36
112_L	117_R	0.765	0.35
21_M	92_R	0.763	0.35
70_D	74_I	0.762	0.35
118_F	137_I	0.759	0.35
102_L	123_N	0.759	0.35
138_E	147_Y	0.756	0.35
109_V	120_V	0.756	0.35
45_Q	144_H	0.756	0.35
169_R	172_T	0.753	0.35
131_N	134_I	0.740	0.34
157_L	174_S	0.740	0.34
48_V	107_A	0.737	0.33
157_L	169_R	0.733	0.33
165_L	168_R	0.730	0.33
101_F	130_M	0.724	0.33
62_L	79_L	0.722	0.32
44_D	57_R	0.721	0.32
121_D	150_R	0.719	0.32
166_N	171_R	0.719	0.32
77_L	100_R	0.717	0.32
47_F	59_E	0.717	0.32
17_S	137_I	0.714	0.32
27_A	38_S	0.705	0.31
89_I	92_R	0.697	0.31
154_N	160_K	0.696	0.31
89_I	93_A	0.689	0.30
111_L	116_Y	0.687	0.30
162_T	166_N	0.685	0.30
120_V	155_E	0.685	0.30
133_L	140_M	0.685	0.30
64_V	67_E	0.680	0.30
28_E	105_P	0.678	0.30
89_I	98_V	0.677	0.30
6_D	9_A	0.677	0.30
31_E	54_G	0.675	0.29
165_L	170_Y	0.675	0.29
155_E	160_K	0.674	0.29
163_V	169_R	0.667	0.29
7_M	20_E	0.663	0.29
17_S	37_D	0.652	0.28
159_I	173_A	0.651	0.28
157_L	171_R	0.648	0.28
166_N	172_T	0.642	0.27
27_A	121_D	0.642	0.27
73_E	120_V	0.641	0.27
54_G	58_W	0.640	0.27
88_P	144_H	0.630	0.27
49_P	78_R	0.628	0.27
72_D	79_L	0.627	0.27
79_L	83_M	0.625	0.27
97_A	118_F	0.625	0.27
159_I	165_L	0.622	0.26
159_I	168_R	0.621	0.26
94_I	130_M	0.620	0.26
51_A	54_G	0.612	0.26
135_E	140_M	0.611	0.26
155_E	159_I	0.609	0.26
70_D	87_P	0.609	0.26
20_E	144_H	0.607	0.25
17_S	30_P	0.606	0.25
110_R	120_V	0.604	0.25
107_A	130_M	0.604	0.25
58_W	88_P	0.604	0.25
48_V	80_I	0.604	0.25
20_E	28_E	0.602	0.25
18_L	21_M	0.602	0.25
28_E	64_V	0.596	0.25
98_V	137_I	0.596	0.25
101_F	147_Y	0.595	0.25
8_R	15_L	0.594	0.25
160_K	165_L	0.592	0.25
121_D	154_N	0.587	0.24
73_E	76_R	0.584	0.24
151_G	173_A	0.584	0.24
110_R	115_E	0.583	0.24
44_D	114_G	0.580	0.24
7_M	18_L	0.580	0.24
158_R	167_H	0.579	0.24
74_I	132_E	0.575	0.24
64_V	95_E	0.574	0.24
120_V	133_L	0.571	0.24
88_P	98_V	0.567	0.23
47_F	75_R	0.565	0.23
27_A	159_I	0.562	0.23
63_N	94_I	0.562	0.23
162_T	168_R	0.560	0.23
81_S	132_E	0.558	0.23
89_I	144_H	0.557	0.23
87_P	98_V	0.557	0.23
94_I	106_S	0.557	0.23
119_N	148_T	0.553	0.23
151_G	156_T	0.550	0.22
43_T	47_F	0.548	0.22
114_G	167_H	0.548	0.22
165_L	174_S	0.544	0.22
81_S	154_N	0.542	0.22
19_K	22_A	0.540	0.22
111_L	144_H	0.538	0.22
40_F	73_E	0.538	0.22
41_D	58_W	0.537	0.22
109_V	136_A	0.537	0.22
68_S	137_I	0.534	0.22
84_S	100_R	0.532	0.21
155_E	165_L	0.532	0.21
32_F	158_R	0.531	0.21
166_N	174_S	0.528	0.21
91_Y	109_V	0.524	0.21
78_R	97_A	0.523	0.21
77_L	130_M	0.522	0.21
82_K	85_N	0.522	0.21
164_I	170_Y	0.521	0.21
46_L	94_I	0.520	0.21
56_S	76_R	0.519	0.21
133_L	136_A	0.519	0.21
53_W	109_V	0.516	0.21
145_L	151_G	0.513	0.21
90_T	111_L	0.510	0.20
48_V	51_A	0.508	0.20
157_L	168_R	0.508	0.20
40_F	117_R	0.507	0.20
98_V	102_L	0.506	0.20
71_T	74_I	0.506	0.20
61_I	68_S	0.506	0.20
155_E	173_A	0.505	0.20
45_Q	97_A	0.500	0.20

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
3vlfB	1	0.3646	22.3	0.944	Contact Map
5afrA	2	0	12.8	0.95	Contact Map
1a3wA	3	0.5156	12.3	0.951	Contact Map
4kctB	3	0.5469	11.2	0.952	Contact Map
3n4sA	2	0.2031	10.8	0.952	Contact Map
2oqoA	2	0.4323	10.6	0.952	Contact Map
4e17B	1	0.1458	10.2	0.952	Contact Map
3a24A	1	0.4219	8.4	0.954	Contact Map
3khdA	3	0.5781	8.3	0.954	Contact Map
4jpoC	1	0.375	7.7	0.955	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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