LRPA - BACSU - GREMLIN Contacts

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LRPA - HTH-type transcriptional regulator LrpA

UniProt:	P96652	Sequences: MIDEIDKKILDELSKNSRLTMKKLGEKVHLTAPATASRVVKLIDNGIIKGCSIEVNQVKLGFSIHAFLNIYIEKIHHQPYLAFIETQDNYVINNYKVSGDGCYLLECKFPSNEVLDQFLNDLNKHANYKVSIVIGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	136 (132)
Sequences:	13266 (8615)
Seq/√Len:	749.9

ECOLI - YBAO LRP ASNC
BACSU - LRPA LRPC LRPB AZLB YWRC YEZC YUGG
HALSA - Q9HQ13 Q9HQ33 Q9HNI1 Q9HQB6 Q9HP41 Q9HQG1 Q9HNW8 Q9HP70 Q9HQ80
SULSO - Q7LX67 Q7LXS6 Q97W90 Q97XP7 LYSM Q97X78 Q980P3 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
43_I	51_C	2.921	1.00
12_E	27_K	2.870	1.00
100_D	129_K	2.624	1.00
93_N	106_E	2.564	1.00
71_Y	127_N	2.369	1.00
110_P	114_V	2.300	1.00
21_M	39_V	2.295	1.00
58_V	113_E	2.146	1.00
6_D	38_R	2.030	1.00
49_K	56_N	1.988	1.00
12_E	19_L	1.976	1.00
41_K	45_N	1.953	1.00
73_E	126_A	1.869	1.00
67_F	95_Y	1.787	1.00
65_H	106_E	1.766	1.00
19_L	27_K	1.759	1.00
49_K	54_E	1.749	1.00
87_Q	118_F	1.739	1.00
40_V	44_D	1.709	1.00
30_L	34_A	1.670	1.00
12_E	15_K	1.669	1.00
5_I	30_L	1.659	1.00
92_I	108_K	1.657	1.00
117_Q	121_D	1.628	1.00
22_K	26_E	1.569	1.00
23_K	26_E	1.567	1.00
114_V	117_Q	1.561	1.00
9_I	24_L	1.525	1.00
69_N	131_S	1.499	1.00
111_S	114_V	1.488	1.00
30_L	35_T	1.461	1.00
83_F	86_T	1.457	1.00
80_Y	84_I	1.436	1.00
18_R	51_C	1.410	1.00
22_K	32_A	1.408	1.00
31_T	34_A	1.405	1.00
21_M	36_A	1.365	1.00
70_I	105_L	1.363	1.00
28_V	35_T	1.331	1.00
81_L	85_E	1.327	1.00
78_Q	82_A	1.325	1.00
89_N	114_V	1.293	1.00
69_N	101_G	1.276	1.00
71_Y	100_D	1.275	1.00
15_K	27_K	1.269	1.00
64_I	112_N	1.268	1.00
13_L	39_V	1.264	1.00
68_L	107_C	1.257	1.00
72_I	80_Y	1.251	1.00
69_N	129_K	1.241	1.00
23_K	27_K	1.227	1.00
19_L	24_L	1.226	1.00
4_E	8_K	1.221	1.00
62_F	110_P	1.209	1.00
76_H	79_P	1.188	1.00
5_I	8_K	1.186	1.00
20_T	23_K	1.152	1.00
16_N	27_K	1.135	1.00
40_V	43_I	1.129	1.00
3_D	38_R	1.126	1.00
5_I	28_V	1.091	1.00
19_L	23_K	1.090	1.00
71_Y	126_A	1.075	1.00
12_E	24_L	1.073	1.00
17_S	51_C	1.072	1.00
87_Q	121_D	1.064	1.00
65_H	108_K	1.059	1.00
63_S	111_S	1.047	1.00
56_N	59_K	1.043	1.00
21_M	25_G	1.028	1.00
50_G	54_E	1.028	1.00
8_K	11_D	1.026	1.00
11_D	15_K	1.026	1.00
94_N	105_L	0.994	1.00
25_G	35_T	0.991	1.00
67_F	104_L	0.985	1.00
109_F	118_F	0.982	1.00
8_K	12_E	0.980	1.00
79_P	83_F	0.971	1.00
97_V	104_L	0.971	1.00
32_A	36_A	0.969	1.00
91_V	107_C	0.962	1.00
109_F	114_V	0.959	1.00
67_F	106_E	0.952	1.00
18_R	43_I	0.947	1.00
116_D	120_N	0.940	1.00
21_M	32_A	0.934	1.00
16_N	19_L	0.931	1.00
95_Y	106_E	0.916	1.00
81_L	103_Y	0.910	1.00
82_A	85_E	0.907	1.00
109_F	115_L	0.892	1.00
67_F	133_V	0.885	1.00
96_K	120_N	0.882	1.00
107_C	118_F	0.880	1.00
2_I	7_K	0.879	1.00
82_A	86_T	0.878	1.00
42_L	47_I	0.876	1.00
25_G	30_L	0.861	1.00
36_A	40_V	0.857	1.00
24_L	39_V	0.856	1.00
17_S	53_I	0.855	1.00
57_Q	108_K	0.842	1.00
8_K	28_V	0.835	1.00
22_K	36_A	0.834	1.00
84_I	94_N	0.822	1.00
7_K	11_D	0.803	1.00
91_V	94_N	0.800	1.00
70_I	125_H	0.789	1.00
91_V	105_L	0.786	1.00
100_D	127_N	0.786	1.00
98_S	132_I	0.767	1.00
73_E	124_K	0.761	1.00
6_D	41_K	0.761	1.00
70_I	80_Y	0.752	1.00
119_L	134_I	0.752	1.00
79_P	82_A	0.746	1.00
73_E	76_H	0.742	1.00
95_Y	133_V	0.739	1.00
33_P	37_S	0.737	1.00
80_Y	103_Y	0.733	1.00
83_F	87_Q	0.728	1.00
69_N	104_L	0.723	1.00
78_Q	81_L	0.717	1.00
112_N	132_I	0.711	1.00
47_I	59_K	0.711	1.00
24_L	35_T	0.709	1.00
65_H	133_V	0.706	1.00
96_K	103_Y	0.695	1.00
71_Y	101_G	0.692	1.00
62_F	89_N	0.689	1.00
101_G	129_K	0.676	1.00
68_L	105_L	0.667	1.00
12_E	16_N	0.665	1.00
62_F	108_K	0.664	1.00
4_E	7_K	0.663	1.00
9_I	35_T	0.663	1.00
69_N	100_D	0.656	1.00
114_V	118_F	0.653	1.00
89_N	118_F	0.653	1.00
17_S	50_G	0.649	1.00
119_L	128_Y	0.643	1.00
9_I	12_E	0.642	1.00
9_I	38_R	0.640	1.00
9_I	19_L	0.640	1.00
25_G	32_A	0.639	1.00
37_S	41_K	0.635	1.00
83_F	124_K	0.635	1.00
113_E	116_D	0.632	1.00
56_N	60_L	0.630	1.00
66_A	115_L	0.626	1.00
112_N	134_I	0.624	1.00
6_D	42_L	0.614	1.00
21_M	35_T	0.614	1.00
33_P	36_A	0.613	1.00
46_G	49_K	0.613	1.00
70_I	128_Y	0.612	1.00
78_Q	120_N	0.602	1.00
37_S	40_V	0.601	1.00
97_V	133_V	0.594	1.00
38_R	42_L	0.592	1.00
9_I	42_L	0.591	1.00
84_I	105_L	0.589	1.00
97_V	101_G	0.584	1.00
3_D	6_D	0.581	1.00
55_V	60_L	0.580	1.00
128_Y	134_I	0.577	1.00
20_T	25_G	0.574	1.00
16_N	23_K	0.571	1.00
87_Q	91_V	0.567	1.00
15_K	19_L	0.565	1.00
48_I	51_C	0.565	1.00
14_S	52_S	0.563	1.00
10_L	42_L	0.561	1.00
84_I	122_L	0.560	1.00
69_N	97_V	0.556	1.00
65_H	95_Y	0.554	1.00
71_Y	129_K	0.553	1.00
68_L	128_Y	0.552	1.00
113_E	117_Q	0.550	1.00
77_H	121_D	0.546	1.00
66_A	109_F	0.546	1.00
2_I	47_I	0.538	1.00
89_N	110_P	0.536	1.00
87_Q	122_L	0.536	1.00
96_K	102_C	0.532	1.00
100_D	131_S	0.532	1.00
96_K	116_D	0.529	1.00
41_K	44_D	0.524	1.00
9_I	39_V	0.521	1.00
66_A	130_V	0.515	1.00
66_A	132_I	0.510	1.00
117_Q	120_N	0.508	1.00
107_C	115_L	0.506	1.00
75_I	96_K	0.503	1.00
116_D	119_L	0.503	1.00
97_V	131_S	0.500	1.00
7_K	14_S	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	0.9412	100	0.139	Contact Map
4un1B	1	0.9926	100	0.192	Contact Map
4un1A	1	0.9779	100	0.207	Contact Map
4pcqA	2	0.9926	100	0.208	Contact Map
2e1cA	1	0.9926	100	0.21	Contact Map
2ia0A	2	0.9632	100	0.215	Contact Map
2p5vA	5	0.9926	99.9	0.22	Contact Map
2cg4A	6	0.9926	99.9	0.233	Contact Map
3i4pA	5	0.9779	99.9	0.235	Contact Map
2pn6A	5	0.9853	99.9	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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