MSRA - HALSA - GREMLIN Contacts

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MSRA - Peptide methionine sulfoxide reductase MsrA

UniProt:	Q9HQG0	Sequences: MGTETATLGGGCFWCTEAAMEELAGVTDVTSGYAGGDTADPSYRDVCSGTTGHAEVVQVEYDTAELAYEDVLEVFFTVHDPTTVDREGPDVGSQYRSIVLPHDDQQHERATAFVDELAAADAFDGSIVTEIEPLETFYPAAEKHQNYFEKNPDAAYCTVNVAPKVSKVREQFGARTE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (158)
Sequences:	5921 (3708)
Seq/√Len:	295.0

ECOLI - MSRA
BACSU - MSRA
HALSA - MSRA
SULSO - MSRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_H	111_T	3.330	1.00
6_A	68_Y	3.258	1.00
7_T	102_H	3.249	1.00
5_T	58_Q	3.044	1.00
76_F	113_F	2.755	1.00
34_A	56_V	2.306	1.00
101_P	107_H	2.249	1.00
30_T	137_F	2.062	1.00
114_V	131_I	2.050	1.00
38_T	45_D	1.938	1.00
101_P	133_P	1.911	1.00
76_F	114_V	1.886	1.00
8_L	71_V	1.857	1.00
30_T	139_P	1.856	1.00
9_G	56_V	1.818	1.00
23_L	74_V	1.817	1.00
34_A	134_L	1.813	1.00
84_V	128_V	1.805	1.00
49_G	94_Q	1.800	1.00
54_A	96_R	1.785	1.00
10_G	16_T	1.784	1.00
69_E	109_R	1.761	1.00
24_A	65_E	1.758	1.00
7_T	58_Q	1.754	1.00
4_E	103_D	1.719	1.00
42_S	45_D	1.706	1.00
67_A	70_D	1.670	1.00
3_T	27_T	1.662	1.00
21_E	146_N	1.639	1.00
30_T	58_Q	1.626	1.00
31_S	145_Q	1.623	1.00
4_E	106_Q	1.583	1.00
23_L	66_L	1.575	1.00
99_V	110_A	1.556	1.00
16_T	78_V	1.553	1.00
35_G	98_I	1.527	1.00
104_D	107_H	1.522	1.00
3_T	63_T	1.500	1.00
21_E	149_E	1.499	1.00
54_A	132_E	1.481	1.00
69_E	112_A	1.470	1.00
86_R	91_V	1.465	1.00
108_E	112_A	1.447	1.00
54_A	98_I	1.433	1.00
5_T	60_E	1.430	1.00
83_T	86_R	1.414	1.00
36_G	53_H	1.382	1.00
7_T	56_V	1.351	1.00
79_H	97_S	1.345	1.00
30_T	60_E	1.329	1.00
28_D	60_E	1.324	1.00
73_E	113_F	1.286	1.00
7_T	34_A	1.277	1.00
13_F	33_Y	1.257	1.00
72_L	109_R	1.256	1.00
4_E	61_Y	1.243	1.00
4_E	63_T	1.230	1.00
21_E	29_V	1.211	1.00
9_G	98_I	1.192	1.00
62_D	65_E	1.184	1.00
142_E	150_K	1.172	1.00
52_G	93_S	1.165	1.00
112_A	116_E	1.125	1.00
10_G	78_V	1.121	1.00
17_E	21_E	1.121	1.00
102_H	106_Q	1.113	1.00
98_I	132_E	1.109	1.00
47_C	94_Q	1.102	1.00
69_E	116_E	1.100	1.00
34_A	135_E	1.094	1.00
70_D	73_E	1.075	1.00
98_I	130_E	1.072	1.00
97_S	129_T	1.069	1.00
146_N	149_E	1.068	1.00
41_P	138_Y	1.047	1.00
79_H	129_T	1.034	1.00
3_T	60_E	1.030	1.00
100_L	130_E	1.015	1.00
105_Q	108_E	1.012	1.00
155_A	158_T	1.009	1.00
102_H	134_L	1.007	1.00
123_F	126_S	1.001	1.00
26_V	66_L	0.995	1.00
96_R	130_E	0.989	1.00
93_S	96_R	0.986	1.00
101_P	131_I	0.985	1.00
118_A	127_I	0.977	1.00
19_A	78_V	0.972	1.00
117_L	127_I	0.966	1.00
158_T	162_A	0.958	1.00
8_L	72_L	0.958	1.00
111_T	115_D	0.957	1.00
7_T	134_L	0.957	1.00
158_T	161_V	0.953	1.00
61_Y	106_Q	0.951	1.00
5_T	102_H	0.947	1.00
44_R	143_K	0.942	1.00
18_A	21_E	0.940	1.00
8_L	68_Y	0.939	1.00
39_A	136_T	0.938	1.00
33_Y	141_A	0.899	1.00
54_A	100_L	0.892	1.00
107_H	133_P	0.882	1.00
20_M	59_V	0.877	1.00
38_T	41_P	0.877	1.00
111_T	114_V	0.869	1.00
114_V	127_I	0.868	1.00
155_A	159_V	0.866	1.00
104_D	108_E	0.864	1.00
18_A	160_N	0.859	1.00
108_E	111_T	0.858	1.00
39_A	138_Y	0.856	1.00
72_L	99_V	0.846	1.00
18_A	148_F	0.843	1.00
68_Y	110_A	0.838	1.00
113_F	117_L	0.837	1.00
15_C	148_F	0.834	1.00
160_N	163_P	0.832	1.00
110_A	131_I	0.825	1.00
8_L	20_M	0.823	1.00
46_V	51_T	0.820	1.00
17_E	29_V	0.820	1.00
153_D	158_T	0.819	1.00
73_E	116_E	0.808	1.00
112_A	115_D	0.799	0.99
132_E	135_E	0.797	0.99
66_L	70_D	0.790	0.99
27_T	30_T	0.786	0.99
114_V	118_A	0.784	0.99
105_Q	109_R	0.776	0.99
23_L	26_V	0.774	0.99
72_L	113_F	0.769	0.99
38_T	51_T	0.764	0.99
22_E	149_E	0.762	0.99
69_E	113_F	0.760	0.99
40_D	138_Y	0.760	0.99
152_P	155_A	0.755	0.99
89_P	159_V	0.751	0.99
37_D	52_G	0.749	0.99
4_E	105_Q	0.749	0.99
16_T	19_A	0.744	0.99
89_P	163_P	0.743	0.99
117_L	122_A	0.742	0.99
34_A	136_T	0.742	0.99
83_T	91_V	0.738	0.99
118_A	126_S	0.735	0.99
85_D	91_V	0.735	0.99
111_T	131_I	0.733	0.99
85_D	93_S	0.729	0.99
69_E	73_E	0.723	0.99
9_G	54_A	0.721	0.99
18_A	22_E	0.718	0.99
82_T	123_F	0.717	0.99
83_T	128_V	0.713	0.99
74_V	77_T	0.712	0.99
19_A	74_V	0.711	0.99
157_C	161_V	0.706	0.99
148_F	162_A	0.704	0.99
45_D	50_T	0.704	0.99
89_P	160_N	0.698	0.99
113_F	116_E	0.698	0.99
13_F	141_A	0.695	0.99
121_D	124_D	0.695	0.99
38_T	53_H	0.688	0.98
139_P	142_E	0.683	0.98
27_T	60_E	0.678	0.98
46_V	94_Q	0.678	0.98
32_G	137_F	0.676	0.98
8_L	59_V	0.675	0.98
146_N	150_K	0.666	0.98
72_L	76_F	0.664	0.98
26_V	59_V	0.664	0.98
74_V	78_V	0.663	0.98
49_G	93_S	0.659	0.98
58_Q	102_H	0.648	0.98
31_S	146_N	0.648	0.98
35_G	53_H	0.648	0.98
31_S	57_V	0.644	0.98
45_D	51_T	0.641	0.98
143_K	151_N	0.627	0.97
48_S	51_T	0.627	0.97
34_A	98_I	0.625	0.97
68_Y	106_Q	0.624	0.97
18_A	149_E	0.623	0.97
118_A	122_A	0.612	0.97
101_P	110_A	0.611	0.97
75_F	97_S	0.603	0.97
51_T	93_S	0.603	0.97
104_D	133_P	0.600	0.96
29_V	57_V	0.598	0.96
27_T	65_E	0.598	0.96
103_D	106_Q	0.598	0.96
159_V	162_A	0.597	0.96
148_F	152_P	0.593	0.96
75_F	79_H	0.588	0.96
118_A	121_D	0.582	0.96
18_A	23_L	0.581	0.96
34_A	100_L	0.579	0.96
54_A	93_S	0.577	0.96
35_G	100_L	0.577	0.96
109_R	112_A	0.576	0.96
109_R	113_F	0.576	0.96
16_T	57_V	0.572	0.95
115_D	118_A	0.568	0.95
16_T	31_S	0.568	0.95
15_C	19_A	0.563	0.95
33_Y	47_C	0.559	0.95
41_P	45_D	0.557	0.95
147_Y	151_N	0.553	0.94
101_P	134_L	0.552	0.94
28_D	139_P	0.549	0.94
158_T	163_P	0.548	0.94
80_D	86_R	0.547	0.94
54_A	97_S	0.547	0.94
38_T	42_S	0.546	0.94
15_C	31_S	0.539	0.94
8_L	99_V	0.538	0.94
48_S	93_S	0.534	0.93
82_T	128_V	0.533	0.93
33_Y	140_A	0.531	0.93
80_D	125_G	0.530	0.93
26_V	29_V	0.528	0.93
15_C	158_T	0.527	0.93
19_A	160_N	0.526	0.93
99_V	114_V	0.525	0.93
58_Q	139_P	0.523	0.93
148_F	157_C	0.522	0.93
24_A	66_L	0.522	0.93
16_T	75_F	0.521	0.93
30_T	145_Q	0.520	0.92
43_Y	141_A	0.519	0.92
87_E	92_G	0.518	0.92
155_A	162_A	0.513	0.92
84_V	93_S	0.513	0.92
9_G	100_L	0.509	0.92
123_F	127_I	0.506	0.91
100_L	132_E	0.500	0.91

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
3bqhA	1	0.9153	100	0.046	Contact Map
1ff3A	5	0.9492	100	0.058	Contact Map
1fvgA	1	0.8814	100	0.058	Contact Map
3e0mA	4	0.9661	100	0.06	Contact Map
2j89A	1	0.9605	100	0.064	Contact Map
4d7lA	3	0.9548	100	0.068	Contact Map
1nwaA	1	0.904	100	0.077	Contact Map
3pimA	2	0.887	100	0.082	Contact Map
4gwbA	2	0.9266	100	0.087	Contact Map
4lwlA	1	0.9322	100	0.157	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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