PYRR - BACSU - GREMLIN Contacts

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PYRR - Bifunctional protein PyrR

UniProt:	P39765	Sequences: MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	181 (170)
Sequences:	1969 (1219)
Seq/√Len:	93.5

BACSU - PYRR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_E	61_P	3.898	1.00
18_T	53_R	3.279	1.00
100_K	129_S	3.185	1.00
35_I	94_V	3.131	1.00
108_L	147_A	3.114	1.00
131_Q	149_Y	3.066	1.00
9_D	12_A	3.048	1.00
53_R	56_Q	2.578	1.00
72_Y	123_D	2.483	1.00
21_A	50_L	2.410	1.00
51_A	64_V	2.296	1.00
118_M	130_I	2.261	1.00
140_H	156_T	2.189	1.00
49_R	173_D	2.184	1.00
165_Q	172_N	2.153	1.00
13_I	166_L	2.149	1.00
42_R	170_D	2.139	1.00
7_I	177_I	2.124	1.00
98_D	128_S	2.064	1.00
165_Q	174_L	2.052	1.00
36_L	51_A	2.006	1.00
28_N	131_Q	1.995	1.00
52_E	56_Q	1.988	1.00
146_R	153_N	1.925	1.00
6_V	174_L	1.919	1.00
33_N	99_Q	1.862	1.00
22_H	57_I	1.808	1.00
35_I	101_V	1.772	1.00
11_Q	14_R	1.739	1.00
27_R	131_Q	1.732	1.00
65_G	92_I	1.691	1.00
49_R	168_E	1.682	1.00
44_I	66_E	1.675	1.00
10_E	167_D	1.623	1.00
48_K	52_E	1.617	1.00
66_E	91_D	1.610	1.00
19_R	26_E	1.604	1.00
17_L	53_R	1.595	1.00
41_T	45_Y	1.513	1.00
45_Y	169_V	1.486	1.00
20_I	133_A	1.473	1.00
109_Y	158_K	1.465	1.00
65_G	90_A	1.434	0.99
67_I	118_M	1.396	0.99
13_I	135_L	1.353	0.99
36_L	54_I	1.349	0.99
8_L	175_V	1.347	0.99
19_R	23_E	1.314	0.99
96_I	121_L	1.308	0.99
20_I	149_Y	1.296	0.99
167_D	173_D	1.294	0.99
35_I	99_Q	1.267	0.99
20_I	24_M	1.262	0.99
60_N	63_T	1.252	0.99
165_Q	176_A	1.249	0.99
40_K	66_E	1.243	0.99
37_V	121_L	1.238	0.98
41_T	169_V	1.229	0.98
31_M	34_C	1.224	0.98
100_K	131_Q	1.224	0.98
41_T	166_L	1.219	0.98
36_L	104_V	1.191	0.98
92_I	124_V	1.189	0.98
168_E	171_Q	1.184	0.98
168_E	173_D	1.156	0.98
172_N	176_A	1.145	0.97
33_N	128_S	1.141	0.97
100_K	128_S	1.139	0.97
5_A	177_I	1.127	0.97
108_L	134_V	1.109	0.97
111_G	141_R	1.099	0.97
71_L	76_L	1.092	0.97
47_A	64_V	1.088	0.97
154_I	162_V	1.086	0.97
90_A	124_V	1.074	0.96
52_E	55_E	1.044	0.96
25_I	31_M	1.043	0.96
48_K	66_E	1.024	0.95
109_Y	138_R	1.023	0.95
65_G	94_V	1.014	0.95
34_C	102_I	1.007	0.95
6_V	176_A	1.000	0.94
7_I	154_I	0.985	0.94
140_H	155_P	0.974	0.94
23_E	27_R	0.973	0.94
46_L	166_L	0.971	0.94
90_A	93_P	0.966	0.93
39_I	114_V	0.966	0.93
78_K	98_D	0.961	0.93
119_D	123_D	0.961	0.93
39_I	69_I	0.957	0.93
104_V	133_A	0.954	0.93
51_A	55_E	0.953	0.93
71_L	87_V	0.946	0.93
103_L	125_G	0.932	0.92
24_M	133_A	0.931	0.92
150_I	153_N	0.928	0.92
128_S	142_E	0.928	0.92
17_L	46_L	0.926	0.92
110_T	122_V	0.921	0.92
116_A	119_D	0.909	0.91
14_R	53_R	0.909	0.91
30_G	58_E	0.900	0.91
152_K	155_P	0.898	0.91
52_E	61_P	0.882	0.90
146_R	157_S	0.878	0.90
28_N	149_Y	0.875	0.89
27_R	149_Y	0.865	0.89
96_I	125_G	0.856	0.88
114_V	132_L	0.852	0.88
65_G	93_P	0.840	0.88
155_P	160_E	0.824	0.86
162_V	176_A	0.823	0.86
79_K	163_M	0.822	0.86
8_L	177_I	0.821	0.86
79_K	82_N	0.814	0.86
45_Y	168_E	0.809	0.85
136_V	152_K	0.807	0.85
69_I	79_K	0.804	0.85
70_T	76_L	0.804	0.85
22_H	26_E	0.803	0.85
108_L	146_R	0.803	0.85
63_T	99_Q	0.796	0.85
50_L	104_V	0.793	0.84
44_I	67_I	0.780	0.83
87_V	90_A	0.778	0.83
110_T	142_E	0.775	0.83
32_N	60_N	0.774	0.83
54_I	58_E	0.773	0.83
22_H	54_I	0.770	0.83
22_H	153_N	0.765	0.82
127_P	130_I	0.757	0.81
8_L	13_I	0.756	0.81
152_K	157_S	0.754	0.81
96_I	103_L	0.747	0.81
37_V	65_G	0.742	0.80
12_A	16_A	0.733	0.79
21_A	54_I	0.733	0.79
131_Q	148_D	0.732	0.79
37_V	110_T	0.727	0.79
22_H	146_R	0.725	0.79
21_A	53_R	0.719	0.78
13_I	16_A	0.719	0.78
24_M	102_I	0.716	0.78
8_L	16_A	0.714	0.78
56_Q	59_G	0.709	0.77
10_E	14_R	0.708	0.77
40_K	68_D	0.701	0.76
115_R	119_D	0.696	0.76
26_E	160_E	0.695	0.76
140_H	160_E	0.694	0.76
23_E	29_K	0.693	0.75
14_R	173_D	0.692	0.75
41_T	44_I	0.690	0.75
167_D	172_N	0.686	0.75
77_S	80_T	0.679	0.74
146_R	155_P	0.678	0.74
65_G	127_P	0.676	0.74
77_S	87_V	0.675	0.74
24_M	34_C	0.675	0.74
91_D	94_V	0.673	0.73
18_T	57_I	0.669	0.73
6_V	10_E	0.669	0.73
29_K	58_E	0.667	0.73
166_L	169_V	0.660	0.72
40_K	70_T	0.659	0.72
59_G	168_E	0.656	0.71
51_A	62_V	0.655	0.71
45_Y	76_L	0.654	0.71
24_M	36_L	0.653	0.71
167_D	171_Q	0.653	0.71
8_L	154_I	0.653	0.71
36_L	50_L	0.652	0.71
76_L	79_K	0.651	0.71
37_V	92_I	0.650	0.71
61_P	128_S	0.649	0.71
122_V	130_I	0.648	0.70
48_K	64_V	0.646	0.70
65_G	124_V	0.643	0.70
96_I	101_V	0.642	0.70
139_G	155_P	0.639	0.69
6_V	9_D	0.630	0.68
30_G	33_N	0.625	0.68
11_Q	56_Q	0.620	0.67
37_V	122_V	0.619	0.67
136_V	175_V	0.614	0.66
103_L	121_L	0.611	0.66
156_T	160_E	0.610	0.66
26_E	152_K	0.609	0.66
42_R	166_L	0.605	0.65
15_R	26_E	0.596	0.64
71_L	90_A	0.595	0.64
88_K	91_D	0.594	0.64
28_N	102_I	0.591	0.63
5_A	154_I	0.589	0.63
46_L	165_Q	0.588	0.63
5_A	87_V	0.576	0.61
63_T	94_V	0.576	0.61
16_A	30_G	0.574	0.61
57_I	113_T	0.573	0.61
157_S	160_E	0.573	0.61
116_A	132_L	0.572	0.61
134_V	150_I	0.570	0.61
71_L	123_D	0.569	0.61
7_I	13_I	0.569	0.61
153_N	157_S	0.568	0.60
40_K	88_K	0.565	0.60
73_R	132_L	0.560	0.59
137_D	153_N	0.557	0.59
72_Y	122_V	0.556	0.59
42_R	169_V	0.556	0.59
37_V	72_Y	0.556	0.59
137_D	162_V	0.554	0.58
78_K	81_S	0.554	0.58
40_K	82_N	0.553	0.58
40_K	119_D	0.553	0.58
16_A	20_I	0.552	0.58
33_N	100_K	0.552	0.58
121_L	130_I	0.549	0.58
90_A	94_V	0.548	0.58
15_R	155_P	0.546	0.57
112_R	132_L	0.545	0.57
31_M	60_N	0.545	0.57
71_L	80_T	0.542	0.57
139_G	153_N	0.537	0.56
73_R	116_A	0.536	0.56
48_K	91_D	0.535	0.56
68_D	73_R	0.535	0.56
112_R	115_R	0.533	0.56
103_L	117_G	0.532	0.55
112_R	141_R	0.530	0.55
147_A	150_I	0.529	0.55
36_L	64_V	0.529	0.55
32_N	168_E	0.527	0.55
132_L	147_A	0.526	0.55
23_E	155_P	0.526	0.55
15_R	19_R	0.523	0.54
142_E	158_K	0.522	0.54
23_E	28_N	0.522	0.54
128_S	143_L	0.518	0.54
26_E	155_P	0.517	0.53
103_L	130_I	0.517	0.53
60_N	174_L	0.515	0.53
140_H	153_N	0.512	0.53
122_V	154_I	0.510	0.52
23_E	153_N	0.509	0.52
8_L	12_A	0.509	0.52
73_R	115_R	0.508	0.52
35_I	96_I	0.508	0.52
11_Q	171_Q	0.506	0.52
18_T	113_T	0.505	0.52
24_M	149_Y	0.504	0.52
125_G	141_R	0.502	0.51
6_V	172_N	0.501	0.51
81_S	97_T	0.500	0.51

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
1w30A	3	0.9337	100	0.54	Contact Map
1ufrA	2	0.9227	100	0.546	Contact Map
4p82A	2	0.9945	100	0.552	Contact Map
4lyyA	3	0.895	99.9	0.67	Contact Map
1pzmA	2	0.884	99.9	0.681	Contact Map
2xbuA	2	0.895	99.8	0.681	Contact Map
2jbhA	4	0.9392	99.8	0.682	Contact Map
4rhxA	3	0.9171	99.8	0.685	Contact Map
4raoA	4	0.9116	99.8	0.686	Contact Map
1tc1A	2	0.9503	99.8	0.686	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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