YRRD - BACSU - GREMLIN Contacts

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YRRD - Uncharacterized protein YrrD

UniProt:	O34402	Sequences: MSLRRKAKPKPVQQKVVDHTLRTCHEVEGFPVYSERTSSYLGTISDICFSLKGDCLGFILAQKRFLHHHHALLRACDISSIFDDRILASVSSEQLLPLPKSCFTYEQMKMKLVKSQEGDILGMLEDVYFCLDRGIIVAYELSDGFFSDLAGSKRQIQRADSLVEVRKDEIVLNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	174 (150)
Sequences:	268 (223)
Seq/√Len:	18.2

BACSU - YRRD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_L	88_A	5.826	1.00
74_R	77_D	4.303	1.00
128_Y	140_E	3.974	1.00
44_I	58_F	2.571	0.97
93_E	96_L	2.260	0.94
115_S	155_Q	2.184	0.92
75_A	134_G	2.059	0.90
108_M	114_K	2.026	0.89
44_I	104_T	1.994	0.88
82_F	85_R	1.989	0.88
55_C	89_S	1.945	0.87
138_A	155_Q	1.943	0.87
108_M	165_V	1.884	0.85
48_C	58_F	1.859	0.85
148_D	167_K	1.757	0.81
63_K	108_M	1.748	0.81
138_A	152_S	1.713	0.79
142_S	152_S	1.707	0.79
164_E	169_E	1.651	0.77
149_L	172_L	1.640	0.76
124_L	129_F	1.573	0.73
50_S	56_L	1.573	0.73
90_V	98_L	1.557	0.72
25_H	109_K	1.518	0.70
32_V	128_Y	1.505	0.70
142_S	153_K	1.478	0.68
23_T	26_E	1.472	0.68
85_R	115_S	1.451	0.67
82_F	115_S	1.436	0.66
58_F	86_I	1.435	0.66
38_S	110_M	1.415	0.65
30_F	82_F	1.398	0.64
103_F	141_L	1.396	0.64
44_I	172_L	1.394	0.63
139_Y	170_I	1.387	0.63
28_E	109_K	1.379	0.63
50_S	76_C	1.371	0.62
60_L	108_M	1.355	0.61
23_T	28_E	1.345	0.61
129_F	171_V	1.344	0.61
60_L	142_S	1.324	0.59
46_D	140_E	1.321	0.59
139_Y	168_D	1.303	0.58
73_L	95_L	1.266	0.56
31_P	82_F	1.257	0.55
88_A	109_K	1.256	0.55
144_G	148_D	1.256	0.55
47_I	58_F	1.254	0.55
58_F	73_L	1.252	0.55
58_F	100_K	1.252	0.55
77_D	113_V	1.239	0.54
127_V	148_D	1.218	0.53
65_F	132_D	1.215	0.53
78_I	151_G	1.212	0.52
52_K	92_S	1.206	0.52
126_D	139_Y	1.205	0.52
28_E	137_V	1.204	0.52
113_V	141_L	1.191	0.51
31_P	65_F	1.186	0.51
63_K	86_I	1.185	0.51
40_Y	74_R	1.169	0.50
40_Y	146_F	1.168	0.50
123_M	142_S	1.162	0.49
23_T	123_M	1.152	0.49
166_R	172_L	1.146	0.48
73_L	79_S	1.137	0.48
45_S	132_D	1.135	0.48
49_F	166_R	1.130	0.47
71_A	167_K	1.119	0.47
84_D	143_D	1.108	0.46
73_L	169_E	1.107	0.46
57_G	156_I	1.096	0.45
145_F	169_E	1.084	0.45
126_D	148_D	1.079	0.44
46_D	127_V	1.070	0.44
47_I	127_V	1.068	0.44
30_F	42_G	1.067	0.44
45_S	71_A	1.067	0.44
32_V	74_R	1.058	0.43
39_S	91_S	1.056	0.43
39_S	61_A	1.051	0.43
158_R	172_L	1.044	0.42
112_L	127_V	1.034	0.42
149_L	152_S	1.019	0.41
135_I	163_V	1.008	0.40
141_L	149_L	1.001	0.40
138_A	153_K	0.997	0.39
44_I	63_K	0.989	0.39
111_K	169_E	0.960	0.37
59_I	114_K	0.959	0.37
86_I	124_L	0.957	0.37
148_D	152_S	0.953	0.37
102_C	105_Y	0.951	0.37
24_C	126_D	0.951	0.37
40_Y	170_I	0.933	0.36
115_S	166_R	0.912	0.34
130_C	157_Q	0.910	0.34
32_V	150_A	0.900	0.34
59_I	119_D	0.895	0.34
35_E	83_D	0.894	0.33
151_G	155_Q	0.879	0.33
23_T	65_F	0.870	0.32
46_D	144_G	0.870	0.32
117_E	120_I	0.861	0.32
46_D	153_K	0.858	0.31
38_S	82_F	0.839	0.30
78_I	101_S	0.834	0.30
127_V	143_D	0.833	0.30
47_I	164_E	0.831	0.30
64_R	69_H	0.822	0.30
32_V	77_D	0.821	0.30
129_F	162_L	0.821	0.30
25_H	28_E	0.820	0.29
32_V	64_R	0.817	0.29
58_F	90_V	0.810	0.29
30_F	79_S	0.810	0.29
47_I	151_G	0.808	0.29
22_R	74_R	0.803	0.29
117_E	146_F	0.796	0.28
138_A	147_S	0.787	0.28
99_P	114_K	0.780	0.27
81_I	170_I	0.779	0.27
77_D	84_D	0.778	0.27
156_I	161_S	0.774	0.27
37_T	139_Y	0.770	0.27
111_K	165_V	0.769	0.27
44_I	136_I	0.769	0.27
107_Q	113_V	0.762	0.27
82_F	166_R	0.757	0.26
30_F	107_Q	0.752	0.26
113_V	164_E	0.751	0.26
26_E	80_S	0.748	0.26
49_F	153_K	0.744	0.26
87_L	137_V	0.743	0.26
135_I	157_Q	0.738	0.25
58_F	87_L	0.734	0.25
23_T	132_D	0.733	0.25
120_I	123_M	0.718	0.25
165_V	170_I	0.712	0.24
64_R	67_H	0.711	0.24
86_I	156_I	0.704	0.24
135_I	151_G	0.704	0.24
81_I	106_E	0.700	0.24
58_F	63_K	0.693	0.23
47_I	86_I	0.692	0.23
47_I	146_F	0.684	0.23
121_L	152_S	0.683	0.23
110_M	136_I	0.682	0.23
50_S	65_F	0.674	0.23
124_L	146_F	0.673	0.23
121_L	153_K	0.673	0.23
150_A	156_I	0.672	0.22
64_R	73_L	0.671	0.22
21_L	131_L	0.664	0.22
129_F	139_Y	0.661	0.22
57_G	142_S	0.657	0.22
51_L	89_S	0.655	0.22
49_F	159_A	0.653	0.22
121_L	166_R	0.652	0.22
81_I	117_E	0.652	0.22
142_S	169_E	0.651	0.22
62_Q	70_H	0.651	0.22
88_A	103_F	0.647	0.21
31_P	91_S	0.644	0.21
61_A	115_S	0.644	0.21
146_F	158_R	0.643	0.21
121_L	155_Q	0.641	0.21
51_L	56_L	0.640	0.21
43_T	168_D	0.638	0.21
38_S	138_A	0.635	0.21
118_G	122_G	0.632	0.21
60_L	141_L	0.628	0.21
125_E	171_V	0.626	0.21
26_E	156_I	0.624	0.20
82_F	87_L	0.624	0.20
54_D	119_D	0.624	0.20
113_V	165_V	0.619	0.20
128_Y	137_V	0.616	0.20
49_F	87_L	0.614	0.20
48_C	97_P	0.607	0.20
149_L	153_K	0.605	0.20
22_R	30_F	0.605	0.20
45_S	170_I	0.604	0.20
44_I	100_K	0.603	0.20
48_C	130_C	0.602	0.20
153_K	159_A	0.599	0.19
82_F	113_V	0.598	0.19
67_H	139_Y	0.596	0.19
46_D	108_M	0.596	0.19
25_H	125_E	0.594	0.19
131_L	171_V	0.593	0.19
21_L	67_H	0.592	0.19
128_Y	154_R	0.585	0.19
64_R	68_H	0.583	0.19
57_G	136_I	0.583	0.19
39_S	172_L	0.577	0.19
60_L	80_S	0.573	0.18
95_L	132_D	0.570	0.18
52_K	55_C	0.570	0.18
32_V	125_E	0.567	0.18
33_Y	44_I	0.566	0.18
37_T	70_H	0.566	0.18
30_F	148_D	0.564	0.18
27_V	129_F	0.559	0.18
31_P	85_R	0.557	0.18
113_V	145_F	0.547	0.18
143_D	155_Q	0.544	0.17
138_A	144_G	0.543	0.17
37_T	126_D	0.542	0.17
127_V	140_E	0.541	0.17
121_L	127_V	0.537	0.17
127_V	170_I	0.533	0.17
75_A	156_I	0.530	0.17
121_L	139_Y	0.529	0.17
128_Y	138_A	0.529	0.17
27_V	131_L	0.525	0.17
145_F	148_D	0.521	0.17
113_V	170_I	0.521	0.17
27_V	163_V	0.519	0.17
126_D	152_S	0.518	0.17
26_E	157_Q	0.516	0.16
95_L	116_Q	0.513	0.16
37_T	71_A	0.510	0.16
76_C	104_T	0.503	0.16
27_V	100_K	0.500	0.16

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
1pm3A	2	0.3908	99.2	0.769	Contact Map
3htrA	2	0.4483	98.2	0.835	Contact Map
1eysH	1	0.7586	96.5	0.878	Contact Map
2wjnH	1	0.7529	95.9	0.883	Contact Map
1rzhH	1	0.7241	95.6	0.886	Contact Map
3h9nA	3	0.8851	73	0.924	Contact Map
2f1lA	2	0.8506	68	0.927	Contact Map
1vrdA	3	0.3103	62.9	0.929	Contact Map
2dyiA	1	0.4943	56.1	0.932	Contact Map
1jcnA	6	0.7299	46.6	0.936	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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