YOCM - BACSU - GREMLIN Contacts

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YOCM - Uncharacterized protein YocM

UniProt:	O34321	Sequences: MDFEKMKQWMEFAQQMYGGDFWKQVFDEDQKTPFMTNGQSPFPFAQQDQRGKGDASFPSMDIVDTVAEVQFLIYLPGYRKQDVHILSYGDYLVVKGQRFSYFNEQDFRQKEGKYGSFEKKIPLSDHLHGKMNAIFKDGILYITIQKDEGQAKTIVIDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	158 (124)
Sequences:	1020 (866)
Seq/√Len:	77.8

BACSU - YOCM COTP
HALSA - Q9HP50 Q9HHW1 Q9HSS6
SULSO - Q97VL9 Q97W19

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_M	73_I	3.883	1.00
73_I	94_V	3.495	1.00
79_R	82_D	3.284	1.00
96_G	117_F	3.166	1.00
127_L	144_I	3.117	1.00
79_R	137_D	3.081	1.00
74_Y	139_I	2.711	1.00
111_E	119_K	2.589	1.00
87_S	123_L	2.457	1.00
75_L	135_F	2.248	1.00
58_P	117_F	2.208	1.00
37_N	40_S	2.193	1.00
61_D	112_G	2.162	1.00
64_D	146_K	2.128	1.00
132_N	157_D	2.100	1.00
84_H	153_T	2.071	1.00
39_Q	43_P	2.048	1.00
97_Q	116_S	2.026	1.00
65_T	68_E	1.906	1.00
83_V	135_F	1.858	1.00
69_V	146_K	1.854	1.00
84_H	95_K	1.786	1.00
35_M	39_Q	1.766	1.00
60_M	121_I	1.691	1.00
58_P	96_G	1.607	1.00
78_Y	96_G	1.552	0.99
71_F	121_I	1.495	0.99
107_F	110_K	1.471	0.99
75_L	83_V	1.471	0.99
92_L	131_M	1.402	0.99
95_K	118_E	1.374	0.99
39_Q	44_F	1.361	0.98
68_E	143_T	1.353	0.98
126_H	146_K	1.342	0.98
93_V	120_K	1.328	0.98
75_L	117_F	1.283	0.98
46_Q	157_D	1.283	0.98
36_T	39_Q	1.270	0.98
80_K	84_H	1.266	0.98
69_V	126_H	1.250	0.97
37_N	42_F	1.241	0.97
87_S	131_M	1.232	0.97
91_Y	120_K	1.174	0.96
72_L	141_Y	1.168	0.96
64_D	121_I	1.160	0.96
36_T	40_S	1.135	0.95
65_T	70_Q	1.092	0.94
112_G	124_S	1.069	0.94
111_E	115_G	1.064	0.93
44_F	47_Q	1.030	0.92
71_F	142_I	1.026	0.92
116_S	153_T	1.013	0.92
56_S	115_G	1.000	0.91
83_V	112_G	0.996	0.91
58_P	75_L	0.990	0.91
124_S	127_L	0.987	0.91
60_M	94_V	0.972	0.90
34_F	37_N	0.959	0.89
34_F	38_G	0.953	0.89
83_V	114_Y	0.922	0.87
129_G	152_K	0.914	0.87
41_P	49_Q	0.906	0.86
80_K	137_D	0.904	0.86
70_Q	73_I	0.902	0.86
42_F	103_N	0.901	0.86
62_I	131_M	0.893	0.86
43_P	47_Q	0.890	0.85
90_D	125_D	0.889	0.85
90_D	122_P	0.875	0.85
106_D	121_I	0.870	0.84
74_Y	114_Y	0.867	0.84
119_K	133_A	0.859	0.83
56_S	96_G	0.855	0.83
47_Q	88_Y	0.854	0.83
64_D	78_Y	0.853	0.83
60_M	87_S	0.851	0.83
85_I	154_I	0.849	0.83
78_Y	98_R	0.847	0.83
114_Y	135_F	0.845	0.82
120_K	125_D	0.845	0.82
44_F	66_V	0.835	0.82
92_L	154_I	0.831	0.81
107_F	142_I	0.830	0.81
137_D	141_Y	0.826	0.81
61_D	74_Y	0.825	0.81
75_L	96_G	0.811	0.80
74_Y	96_G	0.798	0.79
109_Q	135_F	0.798	0.79
38_G	41_P	0.798	0.79
117_F	131_M	0.792	0.78
34_F	127_L	0.791	0.78
58_P	78_Y	0.791	0.78
62_I	121_I	0.786	0.78
58_P	153_T	0.781	0.77
96_G	115_G	0.780	0.77
49_Q	154_I	0.778	0.77
142_I	148_E	0.763	0.75
112_G	117_F	0.754	0.75
88_Y	128_H	0.753	0.75
69_V	131_M	0.751	0.74
36_T	152_K	0.749	0.74
129_G	132_N	0.740	0.73
134_I	141_Y	0.730	0.72
74_Y	98_R	0.730	0.72
101_Y	104_E	0.728	0.72
49_Q	70_Q	0.718	0.71
144_I	151_A	0.713	0.70
86_L	151_A	0.713	0.70
100_S	154_I	0.704	0.69
89_G	93_V	0.702	0.69
56_S	98_R	0.700	0.69
61_D	78_Y	0.694	0.68
58_P	115_G	0.690	0.68
91_Y	101_Y	0.689	0.68
98_R	114_Y	0.685	0.67
61_D	110_K	0.683	0.67
108_R	144_I	0.679	0.67
39_Q	42_F	0.671	0.66
94_V	104_E	0.671	0.66
60_M	119_K	0.670	0.66
47_Q	132_N	0.665	0.65
72_L	152_K	0.657	0.64
71_F	92_L	0.654	0.64
56_S	135_F	0.650	0.63
61_D	75_L	0.650	0.63
67_A	150_Q	0.650	0.63
46_Q	156_I	0.644	0.63
99_F	142_I	0.641	0.62
70_Q	141_Y	0.640	0.62
91_Y	122_P	0.638	0.62
112_G	139_I	0.629	0.61
85_I	99_F	0.628	0.61
63_V	132_N	0.624	0.60
118_E	151_A	0.623	0.60
45_A	48_D	0.621	0.60
130_K	139_I	0.621	0.60
50_R	82_D	0.610	0.58
76_P	110_K	0.608	0.58
78_Y	82_D	0.607	0.58
80_K	122_P	0.602	0.57
71_F	110_K	0.599	0.57
108_R	113_K	0.599	0.57
74_Y	124_S	0.589	0.56
99_F	114_Y	0.588	0.56
122_P	154_I	0.586	0.55
61_D	70_Q	0.578	0.54
40_S	44_F	0.578	0.54
42_F	66_V	0.575	0.54
152_K	155_V	0.571	0.54
39_Q	47_Q	0.569	0.53
108_R	131_M	0.564	0.53
73_I	85_I	0.562	0.52
74_Y	125_D	0.561	0.52
81_Q	97_Q	0.558	0.52
103_N	124_S	0.551	0.51
75_L	92_L	0.548	0.51
61_D	72_L	0.547	0.50
41_P	46_Q	0.547	0.50
80_K	96_G	0.544	0.50
35_M	43_P	0.538	0.49
54_D	151_A	0.537	0.49
68_E	146_K	0.535	0.49
71_F	108_R	0.533	0.49
58_P	135_F	0.530	0.48
134_I	156_I	0.528	0.48
67_A	155_V	0.526	0.48
124_S	131_M	0.524	0.48
136_K	153_T	0.523	0.47
56_S	113_K	0.520	0.47
134_I	157_D	0.520	0.47
91_Y	154_I	0.520	0.47
45_A	94_V	0.520	0.47
128_H	147_D	0.519	0.47
57_F	121_I	0.519	0.47
85_I	136_K	0.517	0.47
129_G	139_I	0.517	0.47
109_Q	141_Y	0.517	0.47
112_G	115_G	0.516	0.47
76_P	139_I	0.516	0.47
45_A	143_T	0.507	0.45
110_K	137_D	0.507	0.45
78_Y	115_G	0.506	0.45
89_G	149_G	0.505	0.45
47_Q	156_I	0.503	0.45
103_N	107_F	0.503	0.45
66_V	136_K	0.500	0.44

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
3w1zA	7	0.8608	100	0.367	Contact Map
4eldA	4	0.6962	100	0.376	Contact Map
3aabA	2	0.7089	99.9	0.402	Contact Map
1gmeA	6	0.8987	99.9	0.414	Contact Map
3glaA	2	0.6139	99.9	0.427	Contact Map
2bolA	2	0.9367	99.9	0.43	Contact Map
4feiA	2	0.6392	99.9	0.444	Contact Map
4jutA	4	0.557	99.9	0.456	Contact Map
4ye0A	2	0.6076	99.9	0.467	Contact Map
2klrA	2	0.5063	99.9	0.473	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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