LRPC - BACSU - GREMLIN Contacts

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LRPC - HTH-type transcriptional regulator LrpC

UniProt:	P96582	Sequences: MKLDQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQYTLEVDQKKLGLPVSCIVEATVKNADYERFKSYIQTLPNIEFCYRIAGAACYMLKINAESLEAVEDFINKTSPYAQTVTHVIFSEIDTKNGRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	144 (135)
Sequences:	13482 (8853)
Seq/√Len:	761.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_E	28_K	2.895	1.00
44_E	52_Y	2.844	1.00
72_T	127_Q	2.605	1.00
100_A	129_V	2.567	1.00
93_F	106_K	2.390	1.00
110_E	114_A	2.267	1.00
22_M	40_V	2.219	1.00
59_K	113_E	2.081	1.00
7_D	39_R	2.057	1.00
42_Q	46_F	2.038	1.00
13_E	20_L	1.957	1.00
50_K	57_D	1.944	1.00
74_K	126_A	1.833	1.00
66_S	106_K	1.831	1.00
20_L	28_K	1.781	1.00
92_E	108_N	1.752	1.00
68_I	95_Y	1.743	1.00
50_K	55_E	1.739	1.00
6_I	31_L	1.737	1.00
41_R	45_S	1.670	1.00
70_E	131_H	1.648	1.00
88_L	118_F	1.626	1.00
23_R	27_R	1.620	1.00
13_E	16_K	1.612	1.00
31_L	35_S	1.595	1.00
114_A	117_D	1.504	1.00
24_E	27_R	1.497	1.00
111_S	114_A	1.483	1.00
31_L	36_V	1.476	1.00
88_L	121_K	1.475	1.00
23_R	33_P	1.452	1.00
32_S	35_S	1.447	1.00
84_Y	87_T	1.428	1.00
81_F	85_I	1.407	1.00
82_K	86_Q	1.387	1.00
10_I	25_L	1.378	1.00
19_R	52_Y	1.366	1.00
71_A	105_L	1.366	1.00
90_N	114_A	1.363	1.00
22_M	37_T	1.353	1.00
72_T	100_A	1.323	1.00
117_D	121_K	1.295	1.00
116_E	135_S	1.288	1.00
70_E	101_A	1.281	1.00
69_V	107_I	1.280	1.00
79_E	83_S	1.274	1.00
29_I	36_V	1.271	1.00
77_D	80_R	1.268	1.00
5_Q	9_N	1.263	1.00
72_T	126_A	1.260	1.00
65_V	112_L	1.260	1.00
20_L	25_L	1.225	1.00
24_E	28_K	1.220	1.00
63_L	110_E	1.211	1.00
73_V	81_F	1.207	1.00
6_I	9_N	1.203	1.00
14_L	40_V	1.199	1.00
82_K	135_S	1.174	1.00
16_K	28_K	1.169	1.00
41_R	44_E	1.163	1.00
17_D	28_K	1.163	1.00
20_L	24_E	1.146	1.00
70_E	129_V	1.138	1.00
21_S	24_E	1.097	1.00
13_E	25_L	1.088	1.00
51_Q	55_E	1.083	1.00
4_D	39_R	1.070	1.00
6_I	29_I	1.064	1.00
66_S	108_N	1.051	1.00
22_M	26_G	1.045	1.00
9_N	13_E	1.043	1.00
18_S	52_Y	1.014	1.00
26_G	36_V	1.010	1.00
9_N	12_E	1.003	1.00
109_A	114_A	1.002	1.00
17_D	20_L	0.999	1.00
80_R	84_Y	0.990	1.00
91_I	107_I	0.969	1.00
94_C	105_L	0.965	1.00
82_K	103_Y	0.964	1.00
12_E	16_K	0.961	1.00
83_S	86_Q	0.961	1.00
37_T	41_R	0.957	1.00
9_N	29_I	0.940	1.00
33_P	37_T	0.939	1.00
57_D	60_K	0.938	1.00
97_I	104_M	0.937	1.00
95_Y	106_K	0.936	1.00
68_I	104_M	0.931	1.00
19_R	44_E	0.921	1.00
3_L	8_L	0.917	1.00
68_I	106_K	0.912	1.00
109_A	115_V	0.895	1.00
109_A	118_F	0.891	1.00
26_G	31_L	0.875	1.00
22_M	33_P	0.867	1.00
23_R	37_T	0.855	1.00
74_K	77_D	0.852	1.00
58_Q	108_N	0.852	1.00
83_S	87_T	0.849	1.00
64_P	111_S	0.847	1.00
107_I	118_F	0.846	1.00
43_L	48_I	0.845	1.00
7_D	42_Q	0.845	1.00
95_Y	133_I	0.827	1.00
116_E	120_N	0.821	1.00
119_I	130_T	0.820	1.00
68_I	133_I	0.818	1.00
84_Y	88_L	0.817	1.00
18_S	54_L	0.814	1.00
91_I	94_C	0.812	1.00
8_L	12_E	0.804	1.00
95_Y	136_E	0.798	1.00
74_K	124_P	0.791	1.00
79_E	82_K	0.789	1.00
100_A	127_Q	0.773	1.00
70_E	104_M	0.765	1.00
85_I	94_C	0.760	1.00
4_D	7_D	0.758	1.00
98_A	132_V	0.756	1.00
91_I	105_L	0.754	1.00
101_A	129_V	0.754	1.00
10_I	39_R	0.752	1.00
34_P	38_E	0.747	1.00
25_L	40_V	0.732	1.00
90_N	121_K	0.732	1.00
82_K	137_I	0.731	1.00
112_L	132_V	0.730	1.00
71_A	81_F	0.727	1.00
72_T	101_A	0.723	1.00
10_I	36_V	0.709	1.00
66_S	133_I	0.709	1.00
80_R	83_S	0.706	1.00
78_Y	103_Y	0.705	1.00
13_E	17_D	0.699	1.00
25_L	36_V	0.696	1.00
3_L	48_I	0.694	1.00
63_L	90_N	0.693	1.00
90_N	118_F	0.693	1.00
70_E	100_A	0.685	1.00
69_V	105_L	0.680	1.00
71_A	125_Y	0.678	1.00
117_D	120_N	0.672	1.00
119_I	128_T	0.672	1.00
5_Q	8_L	0.669	1.00
48_I	60_K	0.667	1.00
80_R	124_P	0.660	1.00
118_F	122_T	0.648	1.00
81_F	103_Y	0.640	1.00
10_I	40_V	0.633	1.00
84_Y	124_P	0.632	1.00
38_E	42_Q	0.631	1.00
96_R	103_Y	0.629	1.00
63_L	108_N	0.628	1.00
39_R	43_L	0.622	1.00
85_I	105_L	0.621	1.00
113_E	116_E	0.619	1.00
26_G	33_P	0.616	1.00
34_P	37_T	0.615	1.00
11_I	43_L	0.615	1.00
114_A	118_F	0.609	1.00
16_K	20_L	0.608	1.00
90_N	110_E	0.605	1.00
10_I	13_E	0.604	1.00
38_E	41_R	0.604	1.00
18_S	51_Q	0.599	1.00
66_S	136_E	0.599	1.00
71_A	128_T	0.599	1.00
47_G	50_K	0.596	1.00
97_I	101_A	0.587	1.00
7_D	43_L	0.586	1.00
67_C	132_V	0.585	1.00
69_V	128_T	0.581	1.00
57_D	61_L	0.580	1.00
84_Y	123_S	0.579	1.00
67_C	115_V	0.579	1.00
96_R	120_N	0.570	1.00
112_L	134_F	0.569	1.00
22_M	36_V	0.568	1.00
10_I	20_L	0.565	1.00
56_V	61_L	0.563	1.00
72_T	129_V	0.560	1.00
10_I	43_L	0.554	1.00
97_I	133_I	0.547	1.00
49_I	52_Y	0.546	1.00
42_Q	45_S	0.544	1.00
113_E	117_D	0.542	1.00
70_E	97_I	0.527	1.00
66_S	95_Y	0.526	1.00
23_R	26_G	0.524	1.00
100_A	131_H	0.521	1.00
7_D	46_F	0.516	1.00
15_K	53_T	0.515	1.00
67_C	109_A	0.514	1.00
21_S	26_G	0.514	1.00
6_I	35_S	0.509	1.00
96_R	102_C	0.508	1.00
119_I	134_F	0.508	1.00
12_E	15_K	0.507	1.00
67_C	130_T	0.501	1.00
85_I	122_T	0.500	1.00
17_D	24_E	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	0.9514	100	0.152	Contact Map
4un1B	1	1	100	0.193	Contact Map
4pcqA	2	0.9861	100	0.218	Contact Map
2e1cA	1	0.9931	100	0.226	Contact Map
4un1A	1	0.9653	100	0.226	Contact Map
2p5vA	5	1	100	0.231	Contact Map
2ia0A	2	0.9653	100	0.233	Contact Map
2cfxA	5	0.9722	100	0.238	Contact Map
2cg4A	6	1	100	0.249	Contact Map
3i4pA	5	0.9792	100	0.253	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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