LYSM - SULSO - GREMLIN Contacts

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LYSM - HTH-type transcriptional regulator LysM

UniProt:	Q980W9	Sequences: MGNANIDESDLKILEILKKNARTPYTLIAKELKVSEAAIRKRIEKLIRQGIIKRFTIEYELENEIRAIVMVQSTPQIPTPEISKKIAKIPGVEVVYETTGDYDILVIVRGTNITSINRTIDEIRSIQGVVGTNSTIILRTWF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	142 (133)
Sequences:	13503 (8671)
Seq/√Len:	751.8

ECOLI - ASNC LRP YBAO
BACSU - YWRC AZLB YUGG LRPC LRPB LRPA YEZC
HALSA - Q9HP41 Q9HNI1 Q9HQ13 Q9HQ33 Q9HQB6 Q9HQG1 Q9HNW8 Q9HP70
SULSO - LYSM Q7LXS6 Q97W90 Q7LX67 Q97XP7 Q980P3 Q97X78 Q97VN7 Q97VH3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_I	31_E	2.928	1.00
47_I	55_F	2.918	1.00
94_V	107_I	2.644	1.00
101_D	133_N	2.619	1.00
72_Q	131_G	2.428	1.00
25_Y	43_I	2.371	1.00
111_T	115_S	2.288	1.00
10_D	42_R	2.178	1.00
16_I	23_T	2.072	1.00
45_K	49_Q	2.007	1.00
53_K	60_E	1.996	1.00
74_T	130_V	1.960	1.00
89_I	122_E	1.884	1.00
78_P	81_E	1.834	1.00
53_K	58_E	1.820	1.00
89_I	119_T	1.794	1.00
68_I	96_Y	1.773	1.00
44_E	48_R	1.755	1.00
9_S	34_V	1.736	1.00
93_E	109_R	1.724	1.00
66_R	107_I	1.698	1.00
34_V	38_A	1.682	1.00
16_I	19_K	1.678	1.00
26_T	30_K	1.632	1.00
23_T	31_E	1.582	1.00
27_L	30_K	1.579	1.00
115_S	118_R	1.578	1.00
112_N	115_S	1.534	1.00
13_I	28_I	1.510	1.00
91_G	115_S	1.485	1.00
25_Y	40_R	1.481	1.00
85_K	126_I	1.474	1.00
34_V	39_I	1.460	1.00
70_M	135_T	1.457	1.00
85_K	88_K	1.453	1.00
117_N	139_R	1.452	1.00
83_S	87_A	1.436	1.00
82_I	86_I	1.434	1.00
35_S	38_A	1.417	1.00
26_T	36_E	1.404	1.00
32_L	39_I	1.404	1.00
22_R	55_F	1.392	1.00
118_R	121_D	1.350	1.00
80_P	84_K	1.338	1.00
71_V	106_V	1.325	1.00
72_Q	101_D	1.304	1.00
83_S	139_R	1.298	1.00
23_T	28_I	1.258	1.00
17_L	43_I	1.254	1.00
27_L	31_E	1.252	1.00
70_M	102_Y	1.252	1.00
8_E	12_K	1.251	1.00
19_K	31_E	1.248	1.00
9_S	12_K	1.224	1.00
63_N	111_T	1.204	1.00
91_G	122_E	1.200	1.00
73_S	82_I	1.190	1.00
72_Q	130_V	1.181	1.00
24_P	27_L	1.179	1.00
44_E	47_I	1.176	1.00
7_D	42_R	1.168	1.00
20_N	31_E	1.158	1.00
69_V	108_V	1.142	1.00
65_I	113_I	1.141	1.00
70_M	133_N	1.119	1.00
9_S	32_L	1.067	1.00
98_T	105_L	1.049	1.00
16_I	28_I	1.049	1.00
54_R	58_E	1.048	1.00
66_R	109_R	1.041	1.00
25_Y	29_A	1.027	1.00
15_E	19_K	1.015	1.00
83_S	104_I	1.009	1.00
95_V	106_V	0.993	1.00
92_V	108_V	0.993	1.00
12_K	15_E	0.987	1.00
12_K	16_I	0.977	1.00
23_T	27_L	0.972	1.00
110_G	115_S	0.970	1.00
29_A	39_I	0.969	1.00
64_E	112_N	0.966	1.00
81_E	85_K	0.964	1.00
25_Y	36_E	0.961	1.00
36_E	40_R	0.956	1.00
84_K	88_K	0.955	1.00
96_Y	107_I	0.954	1.00
21_A	55_F	0.949	1.00
68_I	105_L	0.946	1.00
110_G	119_T	0.939	1.00
108_V	119_T	0.924	1.00
84_K	87_A	0.913	1.00
29_A	34_V	0.907	1.00
22_R	47_I	0.904	1.00
40_R	44_E	0.902	1.00
6_I	11_L	0.899	1.00
110_G	116_I	0.898	1.00
68_I	107_I	0.869	1.00
46_L	51_I	0.866	1.00
28_I	43_I	0.836	1.00
26_T	40_R	0.834	1.00
12_K	32_L	0.833	1.00
92_V	95_V	0.826	1.00
10_D	45_K	0.805	1.00
11_L	15_E	0.803	1.00
92_V	106_V	0.802	1.00
68_I	137_I	0.793	1.00
118_R	122_E	0.780	1.00
79_T	104_I	0.777	1.00
120_I	134_S	0.773	1.00
28_I	39_I	0.773	1.00
86_I	95_V	0.768	1.00
82_I	104_I	0.767	1.00
85_K	89_I	0.761	1.00
80_P	83_S	0.759	1.00
96_Y	137_I	0.757	1.00
81_E	84_K	0.756	1.00
101_D	131_G	0.744	1.00
21_A	27_L	0.743	1.00
114_T	117_N	0.733	1.00
6_I	51_I	0.731	1.00
71_V	82_I	0.731	1.00
37_A	41_K	0.726	1.00
74_T	78_P	0.722	1.00
70_M	105_L	0.714	1.00
7_D	10_D	0.711	1.00
21_A	57_I	0.708	1.00
13_I	23_T	0.700	1.00
20_N	23_T	0.690	1.00
99_T	136_I	0.687	1.00
74_T	128_G	0.685	1.00
13_I	39_I	0.666	1.00
70_M	101_D	0.654	1.00
91_G	119_T	0.651	1.00
124_R	132_T	0.649	1.00
115_S	119_T	0.644	1.00
71_V	129_V	0.642	1.00
72_Q	102_Y	0.638	1.00
21_A	54_R	0.637	1.00
16_I	20_N	0.635	1.00
97_E	104_I	0.635	1.00
8_E	11_L	0.634	1.00
67_A	116_I	0.632	1.00
41_K	44_E	0.631	1.00
13_I	16_I	0.631	1.00
13_I	42_R	0.631	1.00
75_P	78_P	0.626	1.00
13_I	46_L	0.621	1.00
42_R	46_L	0.616	1.00
66_R	137_I	0.613	1.00
102_Y	133_N	0.612	1.00
120_I	132_T	0.611	1.00
86_I	106_V	0.604	1.00
113_I	136_I	0.598	1.00
41_K	45_K	0.597	1.00
63_N	109_R	0.587	1.00
25_Y	39_I	0.584	1.00
10_D	46_L	0.574	1.00
18_K	56_T	0.572	1.00
67_A	134_S	0.571	1.00
80_P	125_S	0.568	1.00
14_L	46_L	0.563	1.00
91_G	111_T	0.563	1.00
114_T	139_R	0.563	1.00
37_A	40_R	0.560	1.00
52_I	55_F	0.559	1.00
114_T	118_R	0.557	1.00
50_G	53_K	0.555	1.00
89_I	126_I	0.552	1.00
81_E	128_G	0.550	1.00
113_I	138_L	0.549	1.00
9_S	38_A	0.547	1.00
85_K	128_G	0.546	1.00
29_A	36_E	0.544	1.00
72_Q	133_N	0.544	1.00
32_L	38_A	0.542	1.00
69_V	132_T	0.542	1.00
11_L	18_K	0.537	1.00
89_I	92_V	0.532	1.00
132_T	138_L	0.532	1.00
69_V	106_V	0.531	1.00
13_I	43_I	0.529	1.00
78_P	128_G	0.525	1.00
66_R	96_Y	0.523	1.00
67_A	136_I	0.522	1.00
98_T	137_I	0.521	1.00
101_D	135_T	0.514	1.00
85_K	127_Q	0.514	1.00
97_E	103_D	0.514	1.00
93_E	107_I	0.513	1.00
70_M	98_T	0.511	1.00
81_E	127_Q	0.509	1.00
119_T	122_E	0.509	1.00
24_P	29_A	0.509	1.00
64_E	109_R	0.508	1.00
20_N	27_L	0.508	1.00
115_S	122_E	0.507	1.00
120_I	138_L	0.505	1.00
26_T	29_A	0.501	1.00
124_R	131_G	0.501	1.00
87_A	95_V	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
4ch7A	1	0.9648	100	0.179	Contact Map
4un1B	1	0.9789	100	0.213	Contact Map
4un1A	1	0.9507	100	0.222	Contact Map
2ia0A	2	0.9437	99.9	0.223	Contact Map
2p5vA	5	1	99.9	0.23	Contact Map
2e1cA	1	0.9648	99.9	0.235	Contact Map
4pcqA	2	0.993	99.9	0.235	Contact Map
2cg4A	6	0.9789	99.9	0.236	Contact Map
2pn6A	5	0.9577	99.9	0.279	Contact Map
3i4pA	5	0.9577	99.9	0.279	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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