Spore_YhcN_YlaJ - PFAM28P - GREMLIN Contacts

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Spore_YhcN_YlaJ - Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)

PFAM:	PF09580	Sequences: ILLLLTGCGNNNNANDNNNNNNNTNNSGNTTNVNNNNNGPYNDNNNNDTNDNNNRGFGYVRYQNNNNDNNNNNNNNYNNNNREELADKIADRVAKLPGVDDAAVLVTDNNALVAVDLDDKNTDELKDKVKKAVKSVDPRYNVYVSTDPDLFDRIRNYANDIRNGRPVEGFFDEINEMIRRIF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	182 (176)
Sequences:	928 (827)
Seq/√Len:	62.4
META:	0.392

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_V	129_V	3.708	1.00
130_K	134_K	3.000	1.00
116_D	147_D	2.961	1.00
115_V	146_T	2.876	1.00
93_V	129_V	2.753	1.00
94_A	102_A	2.603	1.00
114_A	154_I	2.599	1.00
100_D	116_D	2.577	1.00
93_V	96_L	2.521	1.00
165_R	168_E	2.393	1.00
160_D	165_R	2.288	1.00
90_A	104_V	2.266	1.00
177_M	181_I	2.115	1.00
86_A	90_A	2.114	1.00
173_E	180_R	2.062	1.00
28_G	32_N	1.967	1.00
174_I	178_I	1.915	1.00
93_V	99_V	1.898	1.00
111_A	137_D	1.892	1.00
114_A	145_S	1.876	1.00
89_I	133_V	1.841	1.00
98_G	125_L	1.839	1.00
169_G	173_E	1.835	1.00
126_K	146_T	1.815	1.00
85_L	137_D	1.792	1.00
105_L	154_I	1.788	1.00
93_V	132_A	1.734	0.99
116_D	151_F	1.675	0.99
2_L	5_L	1.674	0.99
98_G	128_K	1.658	0.99
96_L	99_V	1.652	0.99
63_Q	66_N	1.644	0.99
39_G	42_N	1.618	0.99
132_A	135_S	1.592	0.99
97_P	138_P	1.585	0.99
133_V	142_V	1.581	0.99
110_N	141_N	1.560	0.99
145_S	150_L	1.546	0.99
3_L	7_G	1.522	0.98
98_G	111_A	1.442	0.98
62_Y	66_N	1.430	0.98
59_Y	63_Q	1.427	0.98
169_G	180_R	1.422	0.98
153_R	173_E	1.419	0.98
41_Y	44_N	1.418	0.98
153_R	176_E	1.383	0.97
82_R	108_D	1.375	0.97
59_Y	64_N	1.362	0.97
100_D	163_N	1.354	0.97
125_L	129_V	1.334	0.96
33_V	36_N	1.320	0.96
144_V	151_F	1.285	0.96
85_L	89_I	1.277	0.95
145_S	157_Y	1.267	0.95
49_T	53_N	1.261	0.95
13_N	16_D	1.240	0.95
85_L	143_Y	1.235	0.95
10_N	14_A	1.221	0.94
112_L	157_Y	1.205	0.94
60_V	66_N	1.202	0.94
46_N	52_N	1.193	0.94
59_Y	62_Y	1.189	0.93
85_L	106_V	1.180	0.93
58_G	61_R	1.179	0.93
14_A	17_N	1.168	0.93
86_A	105_L	1.168	0.93
40_P	44_N	1.166	0.93
110_N	143_Y	1.165	0.93
30_T	34_N	1.164	0.93
38_N	44_N	1.149	0.92
13_N	17_N	1.135	0.92
26_N	29_N	1.130	0.92
115_V	126_K	1.128	0.91
28_G	33_V	1.122	0.91
96_L	132_A	1.116	0.91
48_D	51_D	1.112	0.91
138_P	181_I	1.105	0.91
45_N	50_N	1.103	0.91
30_T	33_V	1.097	0.90
112_L	150_L	1.097	0.90
173_E	177_M	1.095	0.90
107_T	112_L	1.093	0.90
166_P	170_F	1.089	0.90
82_R	85_L	1.089	0.90
27_S	48_D	1.074	0.89
92_R	132_A	1.066	0.89
112_L	174_I	1.054	0.88
157_Y	160_D	1.053	0.88
154_I	174_I	1.053	0.88
108_D	135_S	1.051	0.88
107_T	169_G	1.049	0.88
98_G	117_L	1.045	0.88
174_I	177_M	1.039	0.88
160_D	169_G	1.036	0.88
170_F	181_I	1.027	0.87
129_V	137_D	1.026	0.87
112_L	145_S	1.009	0.86
7_G	38_N	1.005	0.86
122_T	146_T	0.998	0.85
46_N	51_D	0.991	0.85
104_V	174_I	0.985	0.85
37_N	43_D	0.985	0.85
103_A	151_F	0.966	0.84
65_N	70_N	0.959	0.83
109_N	140_Y	0.953	0.83
29_N	33_V	0.949	0.82
28_G	31_T	0.945	0.82
43_D	47_N	0.945	0.82
10_N	13_N	0.941	0.82
105_L	179_R	0.938	0.82
161_I	164_G	0.933	0.81
112_L	130_K	0.931	0.81
5_L	8_C	0.916	0.80
111_A	145_S	0.906	0.79
166_P	169_G	0.901	0.79
61_R	64_N	0.899	0.79
47_N	50_N	0.896	0.79
158_A	162_R	0.888	0.78
111_A	146_T	0.879	0.77
11_N	14_A	0.879	0.77
48_D	163_N	0.874	0.77
93_V	104_V	0.874	0.77
81_N	140_Y	0.873	0.77
17_N	20_N	0.861	0.76
27_S	32_N	0.860	0.76
90_A	94_A	0.857	0.76
114_A	150_L	0.857	0.76
145_S	151_F	0.851	0.75
82_R	107_T	0.844	0.74
126_K	150_L	0.842	0.74
62_Y	65_N	0.825	0.73
86_A	106_V	0.819	0.72
147_D	150_L	0.818	0.72
6_T	9_G	0.806	0.71
47_N	69_N	0.804	0.71
160_D	164_G	0.802	0.71
45_N	49_T	0.799	0.70
31_T	35_N	0.797	0.70
143_Y	157_Y	0.796	0.70
148_P	157_Y	0.790	0.69
57_F	61_R	0.782	0.69
29_N	32_N	0.782	0.69
40_P	47_N	0.778	0.68
37_N	40_P	0.777	0.68
40_P	48_D	0.775	0.68
175_N	179_R	0.752	0.66
113_V	149_D	0.750	0.65
33_V	41_Y	0.749	0.65
92_R	95_K	0.748	0.65
112_L	171_F	0.747	0.65
146_T	173_E	0.743	0.65
31_T	50_N	0.743	0.65
32_N	37_N	0.743	0.65
32_N	48_D	0.743	0.65
85_L	171_F	0.741	0.64
87_D	91_D	0.740	0.64
40_P	46_N	0.738	0.64
106_V	111_A	0.728	0.63
67_N	71_N	0.724	0.63
110_N	114_A	0.720	0.62
3_L	6_T	0.720	0.62
36_N	43_D	0.716	0.62
16_D	19_N	0.709	0.61
42_N	45_N	0.706	0.61
27_S	31_T	0.701	0.60
59_Y	68_D	0.697	0.60
82_R	112_L	0.697	0.60
73_N	120_K	0.693	0.59
4_L	7_G	0.692	0.59
82_R	143_Y	0.691	0.59
91_D	112_L	0.686	0.59
112_L	143_Y	0.684	0.58
168_E	173_E	0.673	0.57
99_V	125_L	0.670	0.57
18_N	25_N	0.670	0.57
90_A	103_A	0.666	0.56
65_N	73_N	0.664	0.56
39_G	44_N	0.658	0.55
47_N	80_N	0.656	0.55
7_G	10_N	0.656	0.55
9_G	15_N	0.648	0.54
45_N	52_N	0.643	0.54
6_T	76_N	0.641	0.53
39_G	48_D	0.640	0.53
48_D	159_N	0.639	0.53
96_L	129_V	0.638	0.53
122_T	129_V	0.635	0.53
111_A	173_E	0.632	0.52
32_N	42_N	0.630	0.52
175_N	178_I	0.628	0.52
126_K	147_D	0.623	0.51
118_D	138_P	0.620	0.51
12_N	17_N	0.617	0.51
171_F	175_N	0.617	0.51
48_D	53_N	0.616	0.51
31_T	34_N	0.609	0.50
44_N	51_D	0.606	0.49
15_N	18_N	0.606	0.49
56_G	61_R	0.604	0.49
44_N	47_N	0.603	0.49
4_L	13_N	0.602	0.49
38_N	41_Y	0.602	0.49
131_K	168_E	0.602	0.49
33_V	38_N	0.600	0.49
6_T	114_A	0.597	0.48
25_N	28_G	0.596	0.48
37_N	46_N	0.596	0.48
112_L	147_D	0.593	0.48
60_V	64_N	0.592	0.48
166_P	180_R	0.589	0.48
89_I	142_V	0.589	0.48
16_D	20_N	0.587	0.47
25_N	30_T	0.584	0.47
105_L	170_F	0.583	0.47
126_K	131_K	0.581	0.47
130_K	147_D	0.578	0.46
130_K	174_I	0.578	0.46
3_L	144_V	0.577	0.46
145_S	158_A	0.575	0.46
83_E	105_L	0.572	0.46
103_A	106_V	0.570	0.45
115_V	160_D	0.568	0.45
34_N	37_N	0.567	0.45
143_Y	150_L	0.566	0.45
129_V	140_Y	0.565	0.45
66_N	73_N	0.565	0.45
101_D	146_T	0.565	0.45
61_R	65_N	0.564	0.45
119_D	152_D	0.563	0.45
45_N	48_D	0.563	0.45
34_N	40_P	0.559	0.44
103_A	112_L	0.558	0.44
38_N	45_N	0.557	0.44
122_T	126_K	0.556	0.44
9_G	12_N	0.555	0.44
34_N	91_D	0.554	0.44
40_P	53_N	0.550	0.43
57_F	60_V	0.549	0.43
60_V	65_N	0.547	0.43
40_P	50_N	0.545	0.43
128_K	131_K	0.543	0.42
78_N	83_E	0.541	0.42
4_L	56_G	0.541	0.42
47_N	52_N	0.541	0.42
63_Q	68_D	0.540	0.42
30_T	40_P	0.537	0.42
97_P	135_S	0.536	0.42
73_N	78_N	0.536	0.42
46_N	49_T	0.525	0.40
103_A	145_S	0.524	0.40
126_K	134_K	0.524	0.40
5_L	98_G	0.522	0.40
130_K	140_Y	0.521	0.40
107_T	180_R	0.521	0.40
108_D	113_V	0.521	0.40
68_D	73_N	0.518	0.40
41_Y	46_N	0.518	0.40
31_T	38_N	0.516	0.39
29_N	35_N	0.514	0.39
41_Y	49_T	0.514	0.39
154_I	181_I	0.510	0.39
30_T	37_N	0.506	0.38
100_D	118_D	0.505	0.38
123_D	126_K	0.500	0.38

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
4q2lA	1	0.3516	77.1	0.875	Contact Map
2ru9A	1	0.3846	74.6	0.877	Contact Map
2g9oA	1	0.4176	39.5	0.902	Contact Map
3j09A	2	0.489	33.7	0.905	Contact Map
1q8lA	1	0.4615	33.7	0.905	Contact Map
1y3jA	1	0.4231	31	0.907	Contact Map
1kviA	1	0.4341	30.6	0.907	Contact Map
1opzA	1	0.4176	26.5	0.91	Contact Map
4oycA	1	0.4121	26.4	0.91	Contact Map
1fvqA	1	0.3956	26.3	0.91	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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