PSDC - PFAM28P - GREMLIN Contacts

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PSDC - Phophatidylserine decarboxylase

PFAM:	PF12588	Sequences: HPVVQEFKDLIESDPVLRMLFTQMFEQVPRKPPYNKDPTGKPQVRDYDHMLRLLNHILTTAPEFTDNANETGLVGFPINAILDWPMGTPAGFAAFLDPKVNAQLKKILNAWGEFLSSPDSRYVLNDSPTGWFSPAALKAM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (134)
Sequences:	1159 (820)
Seq/√Len:	70.8
META:	0.677

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_E	106_K	4.451	1.00
27_Q	90_A	3.703	1.00
21_F	94_A	3.530	1.00
4_V	54_L	3.169	1.00
54_L	107_I	2.616	1.00
5_Q	9_D	2.612	1.00
54_L	78_I	2.440	1.00
44_V	53_L	2.332	1.00
85_P	95_F	2.309	1.00
23_Q	27_Q	2.072	1.00
61_A	123_V	2.030	1.00
10_L	103_Q	1.979	1.00
10_L	17_L	1.925	1.00
11_I	17_L	1.911	1.00
114_F	122_Y	1.874	1.00
3_V	103_Q	1.843	1.00
112_G	116_S	1.820	1.00
14_D	99_K	1.788	1.00
103_Q	106_K	1.758	1.00
3_V	110_A	1.744	1.00
5_Q	8_K	1.732	1.00
25_F	47_Y	1.724	1.00
11_I	51_L	1.700	1.00
7_F	103_Q	1.678	1.00
3_V	6_E	1.669	1.00
134_P	138_K	1.613	0.99
46_D	49_H	1.595	0.99
121_R	132_F	1.554	0.99
28_V	34_Y	1.553	0.99
94_A	100_V	1.498	0.99
11_I	47_Y	1.421	0.98
110_A	113_E	1.415	0.98
21_F	100_V	1.406	0.98
32_P	35_N	1.336	0.98
105_K	109_N	1.329	0.98
20_L	94_A	1.296	0.97
63_E	129_T	1.292	0.97
50_M	54_L	1.276	0.97
25_F	85_P	1.269	0.97
22_T	26_E	1.258	0.97
82_L	104_L	1.245	0.96
2_P	6_E	1.226	0.96
76_F	79_N	1.219	0.96
73_L	76_F	1.199	0.96
16_V	97_D	1.194	0.95
45_R	49_H	1.191	0.95
38_P	43_Q	1.171	0.95
50_M	81_I	1.149	0.94
9_D	13_S	1.141	0.94
74_V	80_A	1.136	0.94
125_N	129_T	1.132	0.94
72_G	76_F	1.125	0.94
3_V	106_K	1.120	0.94
3_V	7_F	1.117	0.93
4_V	7_F	1.114	0.93
31_K	35_N	1.113	0.93
79_N	83_D	1.060	0.92
119_D	122_Y	1.057	0.91
54_L	104_L	1.046	0.91
23_Q	90_A	1.040	0.91
10_L	102_A	1.031	0.90
73_L	79_N	1.026	0.90
102_A	105_K	1.017	0.90
7_F	100_V	1.013	0.90
124_L	132_F	1.011	0.90
118_P	121_R	1.000	0.89
58_L	78_I	0.983	0.88
30_R	35_N	0.982	0.88
76_F	86_M	0.975	0.88
20_L	90_A	0.970	0.88
53_L	81_I	0.967	0.87
80_A	83_D	0.966	0.87
128_P	135_A	0.966	0.87
17_L	100_V	0.964	0.87
61_A	122_Y	0.963	0.87
125_N	130_G	0.957	0.87
6_E	103_Q	0.956	0.87
16_V	20_L	0.955	0.87
84_W	87_G	0.946	0.86
109_N	112_G	0.943	0.86
79_N	86_M	0.942	0.86
19_M	93_A	0.939	0.86
15_P	19_M	0.936	0.86
8_K	47_Y	0.929	0.85
72_G	83_D	0.905	0.84
6_E	9_D	0.902	0.83
12_E	47_Y	0.899	0.83
29_P	34_Y	0.883	0.82
75_G	95_F	0.882	0.82
4_V	55_N	0.872	0.81
8_K	48_D	0.867	0.81
57_I	81_I	0.862	0.81
30_R	33_P	0.846	0.79
51_L	104_L	0.841	0.79
129_T	133_S	0.840	0.79
37_D	85_P	0.832	0.78
31_K	34_Y	0.825	0.78
64_F	135_A	0.825	0.78
70_E	139_A	0.818	0.77
18_R	22_T	0.813	0.77
128_P	139_A	0.798	0.75
34_Y	37_D	0.782	0.74
72_G	75_G	0.778	0.73
115_L	120_S	0.770	0.73
28_V	35_N	0.766	0.72
58_L	110_A	0.763	0.72
82_L	85_P	0.762	0.72
24_M	88_T	0.761	0.72
8_K	51_L	0.757	0.71
88_T	111_W	0.745	0.70
73_L	83_D	0.738	0.69
126_D	132_F	0.734	0.69
49_H	52_R	0.732	0.69
20_L	93_A	0.731	0.69
34_Y	38_P	0.730	0.68
125_N	128_P	0.730	0.68
63_E	122_Y	0.729	0.68
11_I	50_M	0.729	0.68
135_A	138_K	0.727	0.68
126_D	137_L	0.727	0.68
23_Q	26_E	0.727	0.68
8_K	12_E	0.722	0.68
25_F	50_M	0.715	0.67
80_A	87_G	0.712	0.67
126_D	138_K	0.711	0.66
53_L	56_H	0.710	0.66
79_N	85_P	0.707	0.66
126_D	134_P	0.692	0.64
133_S	137_L	0.687	0.64
20_L	108_L	0.683	0.63
45_R	127_S	0.683	0.63
71_T	74_V	0.675	0.62
99_K	102_A	0.675	0.62
88_T	101_N	0.674	0.62
111_W	115_L	0.673	0.62
76_F	87_G	0.672	0.62
75_G	79_N	0.664	0.61
30_R	76_F	0.660	0.61
127_S	133_S	0.658	0.60
54_L	70_E	0.657	0.60
53_L	84_W	0.653	0.60
27_Q	89_P	0.648	0.59
15_P	64_F	0.646	0.59
56_H	60_T	0.644	0.59
71_T	136_A	0.639	0.58
35_N	89_P	0.638	0.58
64_F	139_A	0.633	0.57
54_L	82_L	0.632	0.57
18_R	96_L	0.629	0.57
28_V	42_P	0.629	0.57
104_L	107_I	0.628	0.57
69_N	75_G	0.624	0.56
12_E	48_D	0.623	0.56
29_P	94_A	0.621	0.56
54_L	81_I	0.621	0.56
60_T	63_E	0.619	0.56
16_V	96_L	0.612	0.55
64_F	71_T	0.605	0.54
73_L	78_I	0.604	0.54
117_S	120_S	0.603	0.54
132_F	137_L	0.602	0.54
34_Y	98_P	0.598	0.53
18_R	25_F	0.597	0.53
133_S	138_K	0.591	0.52
114_F	126_D	0.587	0.52
71_T	76_F	0.587	0.52
11_I	21_F	0.584	0.52
71_T	75_G	0.582	0.51
78_I	83_D	0.580	0.51
69_N	108_L	0.579	0.51
13_S	126_D	0.579	0.51
9_D	113_E	0.570	0.50
87_G	92_F	0.570	0.50
2_P	5_Q	0.565	0.49
49_H	53_L	0.562	0.49
17_L	94_A	0.558	0.48
24_M	123_V	0.548	0.47
7_F	106_K	0.542	0.46
74_V	82_L	0.539	0.46
58_L	73_L	0.539	0.46
74_V	87_G	0.532	0.45
120_S	131_W	0.529	0.45
46_D	61_A	0.529	0.45
79_N	84_W	0.528	0.45
55_N	58_L	0.527	0.45
78_I	100_V	0.525	0.44
48_D	70_E	0.525	0.44
7_F	24_M	0.525	0.44
24_M	94_A	0.524	0.44
20_L	23_Q	0.522	0.44
70_E	135_A	0.521	0.44
126_D	130_G	0.521	0.44
98_P	118_P	0.520	0.44
38_P	84_W	0.513	0.43
64_F	70_E	0.512	0.43
7_F	16_V	0.509	0.42
64_F	136_A	0.509	0.42
117_S	123_V	0.503	0.42
28_V	43_Q	0.503	0.42
79_N	95_F	0.503	0.42
3_V	58_L	0.500	0.41

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
2cg9A	2	0.3929	72.1	0.914	Contact Map
2ioqA	2	0.3643	71.4	0.915	Contact Map
2cgeA	6	0.3929	71	0.915	Contact Map
2o1uA	2	0.4	69.7	0.916	Contact Map
1sf8A	5	0.3643	63.4	0.919	Contact Map
4ipeA	2	0.3857	62.4	0.92	Contact Map
4ivgA	4	0	58.4	0.922	Contact Map
3hjcA	5	0.3929	36.2	0.931	Contact Map
2qsfX	1	0.6643	32.7	0.933	Contact Map
4flbA	2	0.7071	31.7	0.933	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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