MCR_D - PFAM28P - GREMLIN Contacts

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MCR_D - Methyl-coenzyme M reductase operon protein D

PFAM:	PF02505	Sequences: QIEIFPERLLNPETTEKLLNELYEIEGIRRIVINGPRLPATVPYGPAKGLPNPHPDRKVIKVGGQEVELQVKVGRILLELEDEEVIEEIRAACEEVLPFGFEIQEGRFMKTKPTVTDYAKYGPDEADKRLLGLVDPKAKSSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	142 (140)
Sequences:	582 (267)
Seq/√Len:	22.5
META:	0.888

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_E	101_F	6.608	1.00
83_E	105_E	4.259	1.00
21_E	95_E	3.312	1.00
3_E	75_R	3.170	1.00
90_R	94_E	2.752	0.99
61_K	64_G	2.666	0.99
18_L	76_I	2.547	0.98
15_T	36_P	2.260	0.97
104_Q	108_F	2.194	0.96
26_E	116_T	2.072	0.94
123_P	126_A	2.009	0.93
87_E	90_R	1.947	0.92
25_I	92_A	1.904	0.91
126_A	129_R	1.795	0.89
34_N	75_R	1.793	0.89
15_T	33_I	1.727	0.87
88_E	91_A	1.714	0.86
4_I	78_L	1.706	0.86
62_V	95_E	1.687	0.85
34_N	71_V	1.667	0.85
69_L	73_V	1.656	0.84
3_E	34_N	1.606	0.82
37_R	70_Q	1.601	0.82
48_K	55_P	1.564	0.81
13_E	68_E	1.557	0.80
19_L	62_V	1.555	0.80
23_Y	31_I	1.552	0.80
59_V	68_E	1.522	0.79
92_A	96_V	1.503	0.78
6_P	10_L	1.481	0.77
16_E	20_N	1.471	0.76
27_G	85_V	1.466	0.76
42_V	45_G	1.466	0.76
54_H	58_K	1.453	0.75
54_H	57_R	1.446	0.75
42_V	46_P	1.437	0.75
41_T	51_P	1.356	0.70
136_P	139_K	1.336	0.69
64_G	67_V	1.329	0.68
118_Y	127_D	1.291	0.66
61_K	66_E	1.278	0.65
18_L	32_V	1.267	0.65
3_E	77_L	1.262	0.64
7_E	100_G	1.255	0.64
22_L	28_I	1.207	0.61
56_D	133_L	1.179	0.59
112_K	115_V	1.173	0.59
113_P	123_P	1.171	0.58
94_E	98_P	1.161	0.58
45_G	49_G	1.161	0.58
18_L	97_L	1.127	0.55
132_G	135_D	1.094	0.53
107_R	111_T	1.074	0.52
129_R	138_A	1.063	0.51
36_P	43_P	1.062	0.51
116_T	126_A	1.051	0.50
22_L	25_I	1.050	0.50
15_T	73_V	1.048	0.50
3_E	104_Q	1.040	0.49
89_I	107_R	1.038	0.49
17_K	85_V	1.037	0.49
1_Q	119_A	1.026	0.49
119_A	126_A	1.019	0.48
10_L	19_L	1.017	0.48
43_P	48_K	1.013	0.48
3_E	109_M	1.012	0.48
80_L	97_L	1.003	0.47
56_D	72_K	0.981	0.45
78_L	89_I	0.981	0.45
1_Q	27_G	0.980	0.45
44_Y	47_A	0.979	0.45
56_D	128_K	0.972	0.45
68_E	107_R	0.970	0.45
32_V	36_P	0.963	0.44
67_V	89_I	0.956	0.44
111_T	139_K	0.946	0.43
29_R	107_R	0.943	0.43
14_T	19_L	0.927	0.42
127_D	136_P	0.902	0.40
18_L	53_P	0.898	0.40
2_I	82_D	0.888	0.39
4_I	8_R	0.887	0.39
58_K	113_P	0.882	0.39
59_V	66_E	0.878	0.39
24_E	116_T	0.878	0.39
45_G	48_K	0.868	0.38
1_Q	12_P	0.867	0.38
9_L	130_L	0.866	0.38
27_G	81_E	0.863	0.38
11_N	67_V	0.863	0.38
5_F	102_E	0.862	0.38
111_T	127_D	0.860	0.37
16_E	77_L	0.856	0.37
78_L	88_E	0.855	0.37
26_E	76_I	0.854	0.37
1_Q	7_E	0.852	0.37
77_L	110_K	0.841	0.36
6_P	18_L	0.838	0.36
16_E	58_K	0.837	0.36
84_E	88_E	0.833	0.36
36_P	99_F	0.829	0.35
12_P	36_P	0.823	0.35
80_L	131_L	0.822	0.35
76_I	133_L	0.820	0.35
70_Q	134_V	0.820	0.35
22_L	55_P	0.814	0.34
96_V	116_T	0.812	0.34
10_L	14_T	0.808	0.34
41_T	46_P	0.807	0.34
36_P	78_L	0.794	0.33
80_L	140_S	0.792	0.33
6_P	115_V	0.792	0.33
115_V	131_L	0.777	0.32
53_P	80_L	0.771	0.32
24_E	63_G	0.764	0.31
117_D	120_K	0.762	0.31
44_Y	48_K	0.762	0.31
34_N	98_P	0.746	0.30
72_K	89_I	0.735	0.30
32_V	51_P	0.735	0.30
119_A	123_P	0.732	0.30
68_E	108_F	0.727	0.29
28_I	128_K	0.725	0.29
15_T	38_L	0.724	0.29
40_A	67_V	0.723	0.29
68_E	130_L	0.719	0.29
32_V	133_L	0.719	0.29
17_K	84_E	0.719	0.29
115_V	140_S	0.717	0.29
37_R	93_C	0.713	0.28
112_K	128_K	0.711	0.28
38_L	138_A	0.710	0.28
7_E	102_E	0.709	0.28
77_L	104_Q	0.705	0.28
80_L	92_A	0.701	0.28
34_N	72_K	0.693	0.27
5_F	97_L	0.691	0.27
91_A	95_E	0.684	0.27
57_R	60_I	0.683	0.27
51_P	61_K	0.680	0.27
33_I	52_N	0.679	0.27
134_V	139_K	0.670	0.26
11_N	72_K	0.669	0.26
37_R	55_P	0.668	0.26
4_I	45_G	0.663	0.26
1_Q	126_A	0.659	0.26
1_Q	137_K	0.657	0.25
37_R	76_I	0.657	0.25
47_A	108_F	0.651	0.25
42_V	47_A	0.648	0.25
26_E	87_E	0.647	0.25
32_V	77_L	0.642	0.25
71_V	89_I	0.638	0.24
119_A	137_K	0.637	0.24
28_I	85_V	0.636	0.24
18_L	38_L	0.634	0.24
29_R	66_E	0.634	0.24
68_E	78_L	0.630	0.24
32_V	47_A	0.630	0.24
6_P	76_I	0.629	0.24
2_I	26_E	0.626	0.24
36_P	85_V	0.621	0.24
87_E	92_A	0.620	0.24
103_I	138_A	0.613	0.23
40_A	77_L	0.609	0.23
124_D	128_K	0.609	0.23
6_P	116_T	0.608	0.23
40_A	65_Q	0.607	0.23
6_P	71_V	0.605	0.23
10_L	25_I	0.602	0.23
4_I	18_L	0.598	0.22
42_V	52_N	0.596	0.22
48_K	109_M	0.593	0.22
40_A	95_E	0.591	0.22
23_Y	62_V	0.588	0.22
20_N	67_V	0.586	0.22
20_N	103_I	0.585	0.22
3_E	29_R	0.582	0.22
23_Y	47_A	0.579	0.22
20_N	108_F	0.576	0.21
113_P	126_A	0.574	0.21
81_E	130_L	0.572	0.21
79_E	109_M	0.571	0.21
78_L	83_E	0.567	0.21
21_E	28_I	0.563	0.21
45_G	52_N	0.555	0.20
73_V	118_Y	0.549	0.20
54_H	60_I	0.547	0.20
33_I	65_Q	0.547	0.20
21_E	96_V	0.547	0.20
22_L	31_I	0.547	0.20
36_P	58_K	0.545	0.20
91_A	94_E	0.545	0.20
34_N	109_M	0.544	0.20
17_K	78_L	0.543	0.20
21_E	24_E	0.543	0.20
81_E	128_K	0.541	0.20
107_R	133_L	0.539	0.20
84_E	91_A	0.527	0.19
100_G	109_M	0.525	0.19
83_E	100_G	0.520	0.19
12_P	15_T	0.516	0.19
34_N	119_A	0.516	0.19
39_P	42_V	0.516	0.19
103_I	108_F	0.513	0.19
33_I	51_P	0.513	0.19
90_R	105_E	0.511	0.19
20_N	33_I	0.509	0.19
19_L	133_L	0.507	0.18
6_P	64_G	0.500	0.18

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
1vw4K	1	0.8803	32.5	0.947	Contact Map
5c1zA	2	0.5	27.1	0.949	Contact Map
1uelA	1	0.5	24	0.95	Contact Map
1oqyA	1	0.5211	17.9	0.953	Contact Map
4k95A	4	0.4577	17.3	0.954	Contact Map
2kjrA	1	0.5634	15.5	0.954	Contact Map
3bboO	1	0.4789	15.5	0.954	Contact Map
2mrpA	1	0.5	15	0.955	Contact Map
2kdbA	1	0.4648	14	0.955	Contact Map
2kanA	1	0.6268	14	0.955	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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