YWSB - BACSU - GREMLIN Contacts

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YWSB - Cell wall-binding protein YwsB

UniProt:	P96729	Sequences: MNKPTKLFSTLALAAGMTAAAAGGAGTIHAQQPETTVSIDDLYSYPIDSYLVSAEALNVRTKPSASSQKADTLHLGDSLKLISFSNADWAKVKYKNGKTGFVSTHYIVKAATTVKTKTKTKVYTSADGKSIKTLPADTSVSFLGWSKTNKGGFDFDWVFVDYGGTTGYMKTKDLHMTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	178 (139)
Sequences:	187 (178)
Seq/√Len:	15.1

BACSU - YWSB YFHK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_K	67_S	5.459	1.00
64_S	67_S	3.903	1.00
73_L	79_L	2.646	0.95
164_G	168_Y	2.497	0.94
52_V	57_L	2.421	0.93
79_L	107_I	2.139	0.87
59_V	73_L	2.058	0.85
152_G	156_D	2.022	0.84
79_L	92_V	1.988	0.83
60_R	89_W	1.924	0.80
154_D	157_W	1.838	0.77
163_G	166_T	1.829	0.77
90_A	107_I	1.816	0.76
59_V	92_V	1.816	0.76
34_E	38_S	1.814	0.76
101_F	105_H	1.793	0.75
157_W	161_D	1.706	0.72
155_F	166_T	1.673	0.70
156_D	159_F	1.660	0.69
153_F	156_D	1.645	0.69
163_G	167_G	1.632	0.68
89_W	100_G	1.629	0.68
159_F	164_G	1.572	0.65
61_T	68_Q	1.551	0.64
55_E	63_P	1.522	0.63
162_Y	166_T	1.517	0.62
138_T	141_S	1.516	0.62
145_W	156_D	1.510	0.62
147_K	157_W	1.502	0.61
106_Y	126_A	1.479	0.60
148_T	157_W	1.476	0.60
91_K	99_T	1.467	0.60
54_A	57_L	1.453	0.59
74_H	77_D	1.435	0.58
156_D	162_Y	1.429	0.57
147_K	154_D	1.408	0.56
164_G	167_G	1.395	0.56
162_Y	165_T	1.381	0.55
102_V	106_Y	1.375	0.54
145_W	154_D	1.364	0.54
146_S	154_D	1.332	0.52
155_F	163_G	1.310	0.51
156_D	166_T	1.304	0.50
145_W	149_N	1.298	0.50
51_L	111_A	1.287	0.50
161_D	166_T	1.286	0.49
57_L	106_Y	1.277	0.49
154_D	159_F	1.249	0.47
155_F	167_G	1.245	0.47
146_S	155_F	1.241	0.47
57_L	88_D	1.240	0.47
146_S	153_F	1.237	0.47
43_Y	118_T	1.215	0.45
64_S	86_N	1.196	0.44
157_W	166_T	1.190	0.44
145_W	148_T	1.189	0.44
29_H	32_Q	1.166	0.43
57_L	103_S	1.156	0.42
148_T	152_G	1.150	0.42
35_T	46_P	1.137	0.41
103_S	106_Y	1.134	0.41
152_G	159_F	1.131	0.41
70_A	90_A	1.129	0.41
155_F	159_F	1.128	0.41
120_T	132_K	1.117	0.40
62_K	90_A	1.116	0.40
120_T	124_T	1.107	0.40
156_D	163_G	1.104	0.39
137_D	141_S	1.097	0.39
154_D	167_G	1.083	0.38
81_L	90_A	1.082	0.38
85_S	92_V	1.075	0.38
162_Y	168_Y	1.044	0.36
49_S	78_S	1.040	0.36
157_W	163_G	1.036	0.36
146_S	156_D	1.027	0.35
146_S	149_N	1.015	0.35
155_F	161_D	1.005	0.34
114_V	124_T	1.004	0.34
61_T	99_T	0.986	0.33
152_G	162_Y	0.976	0.33
147_K	150_K	0.974	0.33
149_N	152_G	0.974	0.33
42_L	77_D	0.970	0.32
85_S	91_K	0.952	0.32
145_W	157_W	0.948	0.31
155_F	158_V	0.946	0.31
52_V	58_N	0.940	0.31
152_G	157_W	0.938	0.31
155_F	162_Y	0.917	0.30
159_F	163_G	0.906	0.29
70_A	100_G	0.905	0.29
28_I	33_P	0.896	0.29
146_S	157_W	0.885	0.28
37_V	43_Y	0.882	0.28
146_S	152_G	0.872	0.28
77_D	91_K	0.865	0.27
90_A	104_T	0.863	0.27
54_A	127_D	0.854	0.27
115_K	119_K	0.854	0.27
156_D	167_G	0.851	0.27
155_F	164_G	0.842	0.26
157_W	167_G	0.835	0.26
148_T	156_D	0.829	0.26
73_L	117_K	0.818	0.25
102_V	107_I	0.810	0.25
47_I	81_L	0.797	0.25
161_D	164_G	0.791	0.24
54_A	79_L	0.789	0.24
153_F	157_W	0.788	0.24
93_K	108_V	0.775	0.24
136_A	140_V	0.771	0.23
137_D	142_F	0.770	0.23
151_G	156_D	0.765	0.23
48_D	77_D	0.759	0.23
71_D	92_V	0.747	0.23
131_I	135_P	0.743	0.22
145_W	152_G	0.739	0.22
152_G	163_G	0.736	0.22
152_G	166_T	0.735	0.22
149_N	156_D	0.735	0.22
153_F	158_V	0.729	0.22
159_F	162_Y	0.728	0.22
62_K	65_A	0.728	0.22
162_Y	167_G	0.727	0.22
154_D	158_V	0.723	0.22
156_D	160_V	0.722	0.22
134_L	140_V	0.722	0.22
159_F	166_T	0.721	0.22
32_Q	58_N	0.708	0.21
131_I	140_V	0.697	0.21
91_K	101_F	0.690	0.20
86_N	92_V	0.689	0.20
149_N	155_F	0.688	0.20
37_V	45_Y	0.687	0.20
37_V	136_A	0.685	0.20
149_N	153_F	0.684	0.20
147_K	153_F	0.682	0.20
77_D	94_Y	0.672	0.20
65_A	68_Q	0.670	0.20
160_V	165_T	0.669	0.20
31_Q	81_L	0.666	0.19
84_F	116_T	0.661	0.19
36_T	101_F	0.649	0.19
60_R	100_G	0.643	0.19
92_V	97_G	0.642	0.19
50_Y	54_A	0.640	0.19
64_S	159_F	0.639	0.19
163_G	168_Y	0.638	0.19
145_W	150_K	0.637	0.18
135_P	139_S	0.633	0.18
147_K	151_G	0.633	0.18
149_N	159_F	0.630	0.18
133_T	144_G	0.627	0.18
81_L	107_I	0.620	0.18
69_K	98_K	0.619	0.18
40_D	81_L	0.618	0.18
133_T	136_A	0.615	0.18
54_A	92_V	0.615	0.18
73_L	77_D	0.615	0.18
73_L	115_K	0.613	0.18
134_L	137_D	0.611	0.18
58_N	68_Q	0.611	0.18
145_W	153_F	0.609	0.18
83_S	91_K	0.604	0.17
63_P	89_W	0.603	0.17
52_V	79_L	0.602	0.17
75_L	98_K	0.602	0.17
39_I	64_S	0.597	0.17
145_W	167_G	0.591	0.17
133_T	149_N	0.586	0.17
69_K	166_T	0.582	0.17
141_S	144_G	0.579	0.17
66_S	84_F	0.574	0.16
69_K	86_N	0.573	0.16
118_T	123_Y	0.571	0.16
72_T	163_G	0.570	0.16
99_T	127_D	0.569	0.16
73_L	101_F	0.567	0.16
71_D	77_D	0.562	0.16
59_V	79_L	0.559	0.16
86_N	90_A	0.558	0.16
112_T	129_K	0.556	0.16
98_K	121_K	0.554	0.16
146_S	162_Y	0.552	0.16
71_D	94_Y	0.552	0.16
56_A	72_T	0.550	0.16
98_K	101_F	0.547	0.16
114_V	123_Y	0.547	0.16
74_H	132_K	0.545	0.16
150_K	153_F	0.541	0.15
101_F	160_V	0.539	0.15
126_A	141_S	0.539	0.15
111_A	139_S	0.535	0.15
155_F	165_T	0.533	0.15
37_V	54_A	0.533	0.15
67_S	85_S	0.533	0.15
72_T	94_Y	0.531	0.15
31_Q	74_H	0.530	0.15
128_G	148_T	0.527	0.15
92_V	100_G	0.524	0.15
72_T	114_V	0.524	0.15
152_G	165_T	0.524	0.15
86_N	135_P	0.523	0.15
160_V	164_G	0.519	0.15
63_P	112_T	0.516	0.15
150_K	157_W	0.504	0.14
83_S	104_T	0.500	0.14

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
2kt8A	1	0.4213	99.4	0.636	Contact Map
2kq8A	1	0.3933	99.4	0.639	Contact Map
2krsA	1	0.4101	99.3	0.65	Contact Map
3npfA	2	0.7528	99.1	0.688	Contact Map
3h41A	1	0.9101	99	0.69	Contact Map
4krtA	1	0.5281	98.9	0.707	Contact Map
2hbwA	1	0.7247	98.6	0.736	Contact Map
3m1uA	2	0.9831	98.2	0.765	Contact Map
1v1cA	1	0.3539	92.8	0.86	Contact Map
1ng2A	2	0.7022	90.9	0.867	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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