HPR - BACSU - GREMLIN Contacts

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HPR - HTH-type transcriptional regulator Hpr

UniProt:	P11065	Sequences: MNRVEPPYDVKEALVFTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEMMCMIRHIYGDDFMEIFETSLTNIDNDFESVNGKLKKKAKDSAADEPAEELEPVNS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	203 (181)
Sequences:	100 (58)
Seq/√Len:	4.3

BACSU - HPR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_K	117_L	4.440	0.91
16_F	132_S	4.241	0.89
161_M	171_I	2.952	0.63
18_Q	117_L	2.926	0.62
16_F	20_M	2.582	0.52
11_K	177_S	2.453	0.48
30_S	126_N	2.440	0.48
111_T	114_F	2.394	0.46
129_F	146_A	2.359	0.45
135_L	150_C	2.301	0.43
67_A	164_F	2.286	0.43
104_V	158_D	2.276	0.43
89_Y	132_S	2.221	0.41
128_V	177_S	2.215	0.41
122_D	148_M	2.149	0.39
37_Q	131_G	2.146	0.39
13_A	146_A	2.105	0.38
91_R	97_N	2.079	0.37
113_V	136_Y	2.046	0.36
30_S	146_A	2.024	0.35
89_Y	137_H	1.898	0.32
31_I	145_V	1.875	0.31
27_L	71_V	1.844	0.31
36_Q	74_V	1.832	0.30
150_C	154_H	1.826	0.30
60_G	92_F	1.816	0.30
46_I	165_E	1.783	0.29
29_K	36_Q	1.781	0.29
62_S	167_S	1.717	0.28
67_A	151_M	1.716	0.28
67_A	142_F	1.709	0.27
59_N	105_Q	1.700	0.27
160_F	164_F	1.670	0.26
62_S	123_P	1.639	0.26
131_G	172_D	1.603	0.25
58_L	165_E	1.596	0.25
139_F	153_R	1.533	0.23
133_Q	142_F	1.520	0.23
29_K	74_V	1.520	0.23
121_F	165_E	1.488	0.22
19_K	91_R	1.469	0.22
126_N	151_M	1.468	0.22
12_E	150_C	1.450	0.22
114_F	119_E	1.436	0.21
89_Y	166_T	1.436	0.21
12_E	135_L	1.409	0.21
134_P	161_M	1.403	0.21
67_A	81_S	1.397	0.21
20_M	43_D	1.396	0.21
69_F	86_E	1.384	0.20
177_S	182_L	1.383	0.20
19_K	106_L	1.381	0.20
117_L	145_V	1.370	0.20
87_R	155_I	1.331	0.19
145_V	148_M	1.290	0.19
117_L	129_F	1.288	0.18
20_M	132_S	1.283	0.18
40_K	61_A	1.270	0.18
56_Y	114_F	1.258	0.18
169_T	183_K	1.248	0.18
65_E	126_N	1.241	0.18
124_T	162_E	1.240	0.18
13_A	125_R	1.227	0.17
46_I	68_K	1.217	0.17
65_E	185_K	1.192	0.17
33_K	46_I	1.190	0.17
21_A	36_Q	1.181	0.17
14_L	18_Q	1.180	0.17
96_L	123_P	1.164	0.16
13_A	154_H	1.159	0.16
116_S	136_Y	1.143	0.16
41_P	139_F	1.100	0.15
16_F	123_P	1.100	0.15
55_A	122_D	1.079	0.15
65_E	144_E	1.078	0.15
11_K	147_E	1.073	0.15
127_A	133_Q	1.070	0.15
12_E	154_H	1.061	0.15
42_Y	117_L	1.053	0.15
14_L	141_K	1.050	0.15
137_H	174_D	1.050	0.15
104_V	109_E	1.046	0.15
51_I	83_K	1.040	0.14
65_E	105_Q	1.038	0.14
108_E	111_T	1.030	0.14
20_M	116_S	1.029	0.14
67_A	160_F	1.002	0.14
106_L	145_V	0.999	0.14
13_A	129_F	0.998	0.14
141_K	182_L	0.988	0.14
57_Q	154_H	0.980	0.14
131_G	153_R	0.973	0.13
70_G	82_K	0.966	0.13
132_S	153_R	0.951	0.13
109_E	185_K	0.951	0.13
66_I	150_C	0.941	0.13
7_P	179_N	0.936	0.13
42_Y	91_R	0.929	0.13
15_V	108_E	0.928	0.13
124_T	130_K	0.927	0.13
127_A	165_E	0.925	0.13
19_K	149_M	0.923	0.13
171_I	181_K	0.919	0.13
124_T	173_N	0.917	0.13
65_E	114_F	0.911	0.13
7_P	178_V	0.901	0.12
54_I	159_D	0.898	0.12
148_M	168_L	0.894	0.12
81_S	140_G	0.893	0.12
11_K	180_G	0.891	0.12
173_N	183_K	0.886	0.12
62_S	106_L	0.885	0.12
61_A	90_L	0.882	0.12
121_F	177_S	0.879	0.12
13_A	18_Q	0.876	0.12
113_V	116_S	0.875	0.12
27_L	68_K	0.869	0.12
87_R	144_E	0.863	0.12
55_A	141_K	0.856	0.12
119_E	124_T	0.852	0.12
140_G	153_R	0.851	0.12
131_G	139_F	0.850	0.12
112_E	183_K	0.849	0.12
68_K	71_V	0.844	0.12
159_D	178_V	0.844	0.12
6_P	152_I	0.842	0.12
65_E	125_R	0.839	0.12
57_Q	114_F	0.837	0.12
42_Y	167_S	0.831	0.12
121_F	175_F	0.829	0.12
39_L	63_I	0.827	0.12
111_T	179_N	0.825	0.12
23_L	151_M	0.821	0.11
121_F	167_S	0.820	0.11
136_Y	171_I	0.814	0.11
43_D	116_S	0.812	0.11
158_D	170_N	0.810	0.11
108_E	153_R	0.804	0.11
112_E	116_S	0.801	0.11
62_S	86_E	0.797	0.11
19_K	129_F	0.796	0.11
43_D	113_V	0.795	0.11
10_V	177_S	0.791	0.11
65_E	150_C	0.791	0.11
116_S	166_T	0.790	0.11
7_P	155_I	0.785	0.11
19_K	146_A	0.783	0.11
69_F	163_I	0.783	0.11
117_L	148_M	0.779	0.11
133_Q	173_N	0.770	0.11
10_V	149_M	0.768	0.11
176_E	179_N	0.766	0.11
118_L	123_P	0.764	0.11
95_R	185_K	0.752	0.11
86_E	167_S	0.749	0.11
148_M	184_K	0.749	0.11
62_S	135_L	0.747	0.11
122_D	145_V	0.746	0.11
119_E	180_G	0.743	0.11
19_K	66_I	0.743	0.11
145_V	184_K	0.743	0.11
178_V	185_K	0.742	0.11
95_R	111_T	0.741	0.11
62_S	93_S	0.735	0.10
112_E	172_D	0.732	0.10
5_E	137_H	0.726	0.10
12_E	20_M	0.722	0.10
149_M	164_F	0.722	0.10
42_Y	59_N	0.719	0.10
77_A	104_V	0.718	0.10
45_N	54_I	0.717	0.10
33_K	58_L	0.717	0.10
114_F	169_T	0.717	0.10
12_E	17_T	0.717	0.10
19_K	168_L	0.710	0.10
167_S	175_F	0.710	0.10
5_E	43_D	0.709	0.10
14_L	31_I	0.708	0.10
169_T	179_N	0.683	0.10
78_F	90_L	0.680	0.10
88_G	122_D	0.679	0.10
120_E	168_L	0.676	0.10
86_E	112_E	0.673	0.10
15_V	153_R	0.669	0.10
60_G	93_S	0.667	0.10
150_C	180_G	0.666	0.10
30_S	115_W	0.662	0.10
124_T	171_I	0.659	0.10
106_L	173_N	0.659	0.10
124_T	183_K	0.657	0.10
89_Y	178_V	0.657	0.10
16_F	115_W	0.654	0.10
66_I	155_I	0.651	0.10
57_Q	83_K	0.651	0.10
37_Q	132_S	0.651	0.10
20_M	130_K	0.651	0.10
174_D	185_K	0.645	0.09
13_A	168_L	0.644	0.09
55_A	104_V	0.642	0.09
43_D	167_S	0.640	0.09
151_M	168_L	0.639	0.09
115_W	138_L	0.637	0.09
42_Y	120_E	0.634	0.09
109_E	112_E	0.633	0.09
41_P	131_G	0.624	0.09
129_F	135_L	0.623	0.09
17_T	99_K	0.618	0.09
162_E	172_D	0.612	0.09
114_F	184_K	0.611	0.09
37_Q	108_E	0.609	0.09
122_D	130_K	0.609	0.09
121_F	128_V	0.609	0.09
105_Q	178_V	0.607	0.09
46_I	71_V	0.606	0.09
54_I	87_R	0.601	0.09
116_S	119_E	0.600	0.09
113_V	148_M	0.596	0.09
78_F	93_S	0.595	0.09
90_L	142_F	0.593	0.09
129_F	177_S	0.587	0.09
89_Y	171_I	0.584	0.09
124_T	169_T	0.581	0.09
26_A	83_K	0.579	0.09
45_N	81_S	0.578	0.09
179_N	183_K	0.578	0.09
59_N	96_L	0.577	0.09
60_G	142_F	0.577	0.09
14_L	109_E	0.575	0.09
44_L	93_S	0.574	0.09
5_E	168_L	0.571	0.09
89_Y	174_D	0.571	0.09
13_A	135_L	0.569	0.09
77_A	140_G	0.567	0.09
53_W	92_F	0.567	0.09
126_N	135_L	0.561	0.09
116_S	137_H	0.560	0.09
81_S	92_F	0.557	0.09
40_K	88_G	0.552	0.09
66_I	141_K	0.550	0.09
6_P	173_N	0.549	0.09
8_Y	152_I	0.548	0.09
55_A	95_R	0.544	0.08
31_I	91_R	0.544	0.08
129_F	182_L	0.538	0.08
116_S	169_T	0.536	0.08
19_K	109_E	0.535	0.08
91_R	109_E	0.533	0.08
10_V	153_R	0.531	0.08
65_E	136_Y	0.529	0.08
117_L	154_H	0.528	0.08
69_F	167_S	0.523	0.08
142_F	164_F	0.522	0.08
21_A	74_V	0.521	0.08
54_I	163_I	0.521	0.08
162_E	173_N	0.521	0.08
35_W	52_L	0.520	0.08
36_Q	53_W	0.519	0.08
155_I	169_T	0.517	0.08
113_V	145_V	0.511	0.08
91_R	116_S	0.509	0.08
105_Q	181_K	0.508	0.08
65_E	160_F	0.507	0.08
22_Q	163_I	0.506	0.08
78_F	156_Y	0.503	0.08
53_W	134_P	0.502	0.08
59_N	122_D	0.502	0.08
6_P	137_H	0.501	0.08
47_N	98_D	0.500	0.08
47_N	102_T	0.500	0.08
47_N	75_S	0.500	0.08
98_D	102_T	0.500	0.08
75_S	102_T	0.500	0.08

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
2fxaA	4	0.8966	100	0.701	Contact Map
2rdpA	2	0.6897	99.2	0.876	Contact Map
2a61A	2	0.6995	99.2	0.877	Contact Map
1s3jA	2	0.7094	99.1	0.879	Contact Map
1z91A	2	0.6749	99.1	0.879	Contact Map
3broA	2	0.6798	99.1	0.88	Contact Map
3g3zA	2	0.6995	99.1	0.88	Contact Map
3cjnA	2	0.7192	99.1	0.88	Contact Map
4rguA	4	0.7094	99.1	0.881	Contact Map
3e6mA	2	0.7389	99.1	0.881	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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