LYTT - BACSU - GREMLIN Contacts

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LYTT - Sensory transduction protein LytT

UniProt:	P94514	Sequences: MLRVLIVDDEMLARDELAYLLKRTNDEMEINEAENIESAFDQMMDQKPDLLFLDVDLSGENGFDIAKRLKKMKHPPAIVFATAYDQYALKAFEVDALDYLTKPFDEERIQQTLKKYKKVNRDIVETEQNSHAGQHKLALSVGESIVIVDTKDIIYAGTEDGHVNVKTFDHSYTVSDTLVVIEKKLPDSDFIRVHRSFVVNTEYIKEIQPWFNSTYNLIMKDGSKIPVSRTYAKELKKLLHI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (203)
Sequences:	61631 (46610)
Seq/√Len:	3271.4

ECOLI - YPDB YEHT YEDW PHOP CUSR RSTA DCUR QSEB KDPE BASR PHOB OMPR ARCA CREB RCSC UVRY YHJB BAER CPXR TORS BARA TORR RSSB EVGA YJJQ ARCB CHEB UHPA DPIA YGEK NARP FIMZ RCSB NARL BGLJ CSGD GLRR ZRAR NTRC RCSA ATOC RCSD EVGS
BACSU - LYTT NATR YESN CHEB CITT YXDJ YVCP PHOP BCER MALR YVRH YFIK YCLJ YVFU YYCF LIAR GLNL SP0A CSSR CMPA YKOG YCBL RESD DESR YHCZ YRKP YDFI YXJL DEGU DCTR YBDJ CHEV CCDB
HALSA - CHEB Q9HNM3 Q9HR09 O51970 BAT Q9HRE5 Q9HP91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	32_E	4.044	1.00
14_R	34_E	3.665	1.00
18_A	32_E	3.418	1.00
7_V	39_A	2.765	1.00
40_F	68_R	2.762	1.00
36_I	60_E	2.622	1.00
31_N	48_P	2.597	1.00
60_E	68_R	2.466	1.00
37_E	59_G	2.448	1.00
33_A	42_Q	2.342	1.00
35_N	59_G	2.268	1.00
3_R	31_N	2.253	1.00
20_L	106_E	2.230	1.00
31_N	42_Q	2.198	1.00
88_A	108_R	2.144	1.00
80_F	96_A	2.108	1.00
18_A	22_K	2.061	1.00
3_R	29_E	2.053	1.00
44_M	72_M	2.039	1.00
56_D	84_Y	2.024	1.00
66_A	78_I	1.982	1.00
24_T	110_Q	1.946	1.00
31_N	46_Q	1.944	1.00
98_D	112_T	1.863	1.00
53_L	65_I	1.811	1.00
5_L	33_A	1.799	1.00
136_K	149_D	1.791	1.00
34_E	38_S	1.751	1.00
51_L	76_P	1.693	1.00
35_N	38_S	1.692	1.00
36_I	65_I	1.691	1.00
61_N	64_D	1.687	1.00
42_Q	46_Q	1.632	1.00
97_L	119_V	1.617	1.00
80_F	91_A	1.592	1.00
66_A	80_F	1.573	1.00
40_F	65_I	1.551	1.00
60_E	64_D	1.530	1.00
164_N	168_F	1.506	1.00
195_R	198_V	1.505	1.00
37_E	60_E	1.477	1.00
55_V	80_F	1.465	1.00
43_M	69_L	1.458	1.00
8_D	14_R	1.444	1.00
200_N	203_Y	1.438	1.00
68_R	71_K	1.437	1.00
64_D	67_K	1.434	1.00
176_D	198_V	1.409	1.00
84_Y	87_Y	1.406	1.00
68_R	72_M	1.403	1.00
53_L	66_A	1.393	1.00
180_V	184_K	1.391	1.00
145_I	152_D	1.375	1.00
55_V	63_F	1.367	1.00
70_K	97_L	1.359	1.00
138_A	147_I	1.340	1.00
42_Q	45_D	1.340	1.00
7_V	57_L	1.339	1.00
42_Q	48_P	1.335	1.00
21_L	113_L	1.316	1.00
40_F	60_E	1.312	1.00
9_D	54_D	1.302	1.00
11_M	34_E	1.292	1.00
3_R	46_Q	1.281	1.00
50_L	113_L	1.274	1.00
67_K	94_V	1.267	1.00
33_A	39_A	1.258	1.00
5_L	39_A	1.245	1.00
133_G	138_A	1.238	1.00
63_F	90_K	1.238	1.00
41_D	45_D	1.237	1.00
93_E	114_K	1.232	1.00
110_Q	114_K	1.229	1.00
79_V	116_Y	1.221	1.00
147_I	152_D	1.191	1.00
39_A	65_I	1.178	1.00
141_V	164_N	1.163	1.00
5_L	48_P	1.154	1.00
38_S	41_D	1.154	1.00
40_F	44_M	1.144	1.00
67_K	90_K	1.142	1.00
6_I	17_L	1.126	1.00
37_E	41_D	1.124	1.00
165_V	184_K	1.123	1.00
24_T	114_K	1.111	1.00
88_A	101_T	1.109	1.00
169_D	172_Y	1.107	1.00
63_F	91_A	1.095	1.00
140_S	143_E	1.089	1.00
97_L	116_Y	1.069	1.00
38_S	42_Q	1.065	1.00
77_A	119_V	1.056	1.00
73_K	76_P	1.048	1.00
51_L	78_I	1.032	1.00
7_V	51_L	1.023	1.00
11_M	15_D	1.018	1.00
170_H	174_V	1.018	1.00
131_H	138_A	1.017	1.00
52_F	109_I	1.016	1.00
90_K	94_V	1.016	1.00
51_L	69_L	1.013	1.00
199_V	202_E	1.013	1.00
12_L	16_E	1.013	1.00
39_A	43_M	1.008	1.00
158_T	161_G	0.995	1.00
44_M	73_K	0.994	1.00
17_L	81_A	0.989	1.00
43_M	73_K	0.983	1.00
66_A	94_V	0.982	1.00
3_R	28_M	0.979	1.00
55_V	61_N	0.970	1.00
93_E	111_Q	0.968	1.00
90_K	93_E	0.968	1.00
17_L	109_I	0.960	1.00
57_L	65_I	0.950	1.00
15_D	32_E	0.949	1.00
79_V	112_T	0.948	1.00
98_D	115_K	0.948	1.00
10_E	13_A	0.948	1.00
108_R	112_T	0.943	1.00
33_A	38_S	0.937	1.00
77_A	123_I	0.929	1.00
89_L	93_E	0.928	1.00
81_A	104_F	0.909	1.00
161_G	164_N	0.908	1.00
5_L	42_Q	0.906	1.00
175_S	180_V	0.905	1.00
15_D	18_A	0.905	1.00
165_V	174_V	0.893	1.00
64_D	68_R	0.891	1.00
85_D	101_T	0.889	1.00
139_L	160_D	0.888	1.00
89_L	107_E	0.885	1.00
63_F	94_V	0.884	1.00
53_L	78_I	0.884	1.00
165_V	169_D	0.884	1.00
56_D	83_A	0.883	1.00
52_F	81_A	0.877	1.00
106_E	110_Q	0.875	1.00
50_L	117_K	0.872	1.00
18_A	30_I	0.871	1.00
55_V	84_Y	0.866	1.00
139_L	167_T	0.866	1.00
7_V	33_A	0.863	1.00
19_Y	23_R	0.859	1.00
16_E	20_L	0.859	1.00
28_M	114_K	0.855	1.00
3_R	48_P	0.852	1.00
116_Y	119_V	0.846	1.00
65_I	69_L	0.842	1.00
87_Y	90_K	0.834	1.00
41_D	44_M	0.830	1.00
5_L	31_N	0.820	1.00
144_S	161_G	0.820	1.00
111_Q	115_K	0.816	1.00
202_E	206_E	0.811	1.00
11_M	14_R	0.809	1.00
36_I	40_F	0.806	1.00
77_A	120_N	0.797	1.00
66_A	96_A	0.794	1.00
69_L	78_I	0.793	1.00
53_L	80_F	0.792	1.00
196_S	200_N	0.788	1.00
8_D	57_L	0.786	1.00
6_I	14_R	0.785	1.00
92_F	112_T	0.784	1.00
115_K	118_K	0.784	1.00
7_V	65_I	0.777	1.00
75_P	123_I	0.777	1.00
82_T	88_A	0.774	1.00
104_F	109_I	0.770	1.00
4_V	28_M	0.769	1.00
5_L	43_M	0.769	1.00
130_S	142_G	0.765	1.00
147_I	150_T	0.763	1.00
43_M	76_P	0.763	1.00
15_D	19_Y	0.762	1.00
91_A	96_A	0.753	1.00
107_E	111_Q	0.753	1.00
179_V	183_K	0.746	1.00
157_G	161_G	0.741	1.00
108_R	111_Q	0.734	1.00
14_R	18_A	0.734	1.00
4_V	50_L	0.731	1.00
180_V	183_K	0.728	1.00
13_A	104_F	0.722	1.00
77_A	97_L	0.722	1.00
69_L	74_H	0.717	1.00
60_E	65_I	0.717	1.00
159_E	207_I	0.716	1.00
158_T	186_P	0.713	1.00
43_M	48_P	0.713	1.00
88_A	105_D	0.713	1.00
148_V	209_P	0.711	1.00
52_F	113_L	0.710	1.00
136_K	148_V	0.708	1.00
36_I	59_G	0.706	1.00
112_T	116_Y	0.705	1.00
67_K	71_K	0.703	1.00
83_A	103_P	0.698	1.00
43_M	51_L	0.693	1.00
142_G	172_Y	0.692	1.00
120_N	124_V	0.691	1.00
55_V	87_Y	0.690	1.00
6_I	18_A	0.688	1.00
144_S	160_D	0.684	1.00
22_K	25_N	0.682	1.00
28_M	110_Q	0.680	1.00
93_E	108_R	0.679	1.00
105_D	108_R	0.678	1.00
6_I	30_I	0.677	1.00
3_R	49_D	0.671	1.00
6_I	32_E	0.670	1.00
52_F	79_V	0.667	1.00
148_V	151_K	0.664	1.00
140_S	145_I	0.662	1.00
77_A	116_Y	0.662	1.00
131_H	140_S	0.661	1.00
161_G	165_V	0.661	1.00
165_V	168_F	0.659	1.00
141_V	168_F	0.656	1.00
149_D	152_D	0.653	1.00
55_V	91_A	0.652	1.00
33_A	36_I	0.649	1.00
165_V	181_I	0.647	1.00
40_F	43_M	0.646	1.00
93_E	98_D	0.646	1.00
7_V	53_L	0.646	1.00
44_M	68_R	0.639	1.00
184_K	187_D	0.635	1.00
25_N	28_M	0.632	1.00
114_K	118_K	0.632	1.00
162_H	166_K	0.631	1.00
43_M	65_I	0.629	1.00
188_S	191_I	0.627	1.00
162_H	165_V	0.625	1.00
4_V	21_L	0.624	1.00
199_V	203_Y	0.623	1.00
13_A	16_E	0.621	1.00
117_K	120_N	0.618	1.00
20_L	110_Q	0.618	1.00
139_L	146_V	0.609	1.00
79_V	98_D	0.608	1.00
69_L	76_P	0.597	1.00
7_V	36_I	0.597	1.00
182_E	186_P	0.596	1.00
20_L	24_T	0.588	1.00
137_L	148_V	0.586	1.00
29_E	46_Q	0.585	1.00
75_P	122_D	0.583	1.00
70_K	76_P	0.579	1.00
193_V	196_S	0.579	1.00
172_Y	175_S	0.578	1.00
133_G	136_K	0.578	1.00
160_D	164_N	0.576	1.00
89_L	92_F	0.576	1.00
43_M	74_H	0.574	1.00
194_H	197_F	0.569	1.00
114_K	117_K	0.569	1.00
53_L	57_L	0.567	1.00
182_E	187_D	0.565	1.00
55_V	94_V	0.563	1.00
117_K	121_R	0.561	1.00
66_A	70_K	0.561	1.00
111_Q	114_K	0.558	1.00
204_I	208_Q	0.557	1.00
113_L	116_Y	0.553	1.00
80_F	94_V	0.552	1.00
176_D	180_V	0.552	1.00
139_L	164_N	0.551	1.00
115_K	119_V	0.548	1.00
195_R	199_V	0.545	1.00
167_T	170_H	0.545	1.00
113_L	117_K	0.544	1.00
203_Y	206_E	0.544	1.00
182_E	192_R	0.541	1.00
50_L	77_A	0.540	1.00
50_L	116_Y	0.540	1.00
16_E	19_Y	0.538	1.00
120_N	123_I	0.537	1.00
164_N	167_T	0.536	1.00
92_F	96_A	0.536	1.00
159_E	162_H	0.532	1.00
107_E	110_Q	0.532	1.00
47_K	74_H	0.529	1.00
56_D	86_Q	0.528	1.00
4_V	52_F	0.528	1.00
47_K	73_K	0.526	1.00
169_D	174_V	0.526	1.00
17_L	104_F	0.525	1.00
88_A	92_F	0.525	1.00
156_A	207_I	0.524	1.00
163_V	166_K	0.523	1.00
145_I	148_V	0.520	1.00
134_Q	167_T	0.518	1.00
179_V	194_H	0.516	1.00
12_L	15_D	0.515	1.00
63_F	87_Y	0.512	1.00
172_Y	180_V	0.510	1.00
28_M	117_K	0.508	1.00
5_L	51_L	0.507	1.00
146_V	153_I	0.506	1.00
119_V	123_I	0.503	1.00
188_S	192_R	0.500	1.00

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
4cbvA	2	0.971	100	0.269	Contact Map
3r0jA	2	0.9046	100	0.365	Contact Map
1kgsA	1	0.9004	100	0.373	Contact Map
1ys7A	2	0.9295	100	0.376	Contact Map
4g97A	1	0.5311	100	0.379	Contact Map
3n0rA	1	0.4979	100	0.382	Contact Map
2oqrA	2	0.9253	100	0.383	Contact Map
3breA	4	0.971	100	0.393	Contact Map
4kfcA	2	0.9087	100	0.395	Contact Map
3q9sA	1	0.8631	99.9	0.398	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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