DPM3 - PFAM28P - GREMLIN Contacts

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DPM3 - Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)

PFAM:	PF08285	Sequences: MTRAQQWLSLLLLLSALWLALLLGLLPLPLPKIQREIIPVLPLWALVSFGCYSLASLGYGVLTFNDCPEAAKELQKEIKEAKADLRKKGVD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (90)
Sequences:	589 (456)
Seq/√Len:	48.1
META:	0.367

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_C	58_G	3.842	1.00
70_A	73_E	3.810	1.00
80_E	84_D	2.825	1.00
53_S	57_L	2.645	1.00
3_R	7_W	2.503	1.00
54_L	58_G	2.467	1.00
77_E	80_E	2.194	1.00
47_V	51_C	1.986	0.99
44_W	51_C	1.898	0.99
57_L	64_F	1.858	0.99
53_S	56_S	1.841	0.99
58_G	61_V	1.803	0.99
49_F	53_S	1.788	0.99
44_W	48_S	1.708	0.98
79_K	83_A	1.669	0.98
44_W	58_G	1.654	0.98
67_C	70_A	1.627	0.98
72_K	76_K	1.614	0.98
47_V	58_G	1.542	0.97
73_E	77_E	1.523	0.96
47_V	54_L	1.489	0.96
51_C	54_L	1.445	0.95
78_I	82_K	1.425	0.95
53_S	67_C	1.425	0.95
13_L	16_A	1.400	0.94
78_I	81_A	1.381	0.94
51_C	61_V	1.371	0.94
59_Y	63_T	1.361	0.93
64_F	85_L	1.354	0.93
71_A	75_Q	1.350	0.93
2_T	5_Q	1.336	0.93
72_K	75_Q	1.305	0.92
16_A	20_A	1.300	0.92
49_F	57_L	1.232	0.89
76_K	79_K	1.200	0.88
9_S	12_L	1.180	0.87
4_A	7_W	1.179	0.87
70_A	85_L	1.143	0.86
54_L	74_L	1.111	0.84
70_A	84_D	1.068	0.81
83_A	86_R	1.063	0.81
17_L	31_P	1.062	0.81
67_C	71_A	1.035	0.79
84_D	87_K	1.031	0.79
81_A	84_D	1.001	0.77
60_G	90_V	0.972	0.75
9_S	13_L	0.948	0.73
86_R	90_V	0.936	0.72
16_A	83_A	0.930	0.72
65_N	85_L	0.925	0.71
18_W	39_P	0.917	0.70
84_D	88_K	0.914	0.70
83_A	87_K	0.899	0.69
74_L	77_E	0.892	0.68
2_T	7_W	0.859	0.65
3_R	60_G	0.848	0.64
43_L	47_V	0.840	0.64
66_D	73_E	0.832	0.63
32_K	36_E	0.831	0.63
46_L	50_G	0.810	0.61
34_Q	38_I	0.797	0.60
29_P	44_W	0.795	0.59
3_R	6_Q	0.782	0.58
4_A	60_G	0.779	0.58
57_L	60_G	0.777	0.58
24_G	35_R	0.771	0.57
43_L	46_L	0.770	0.57
52_Y	56_S	0.766	0.57
48_S	51_C	0.761	0.56
8_L	15_S	0.761	0.56
80_E	88_K	0.756	0.56
54_L	66_D	0.749	0.55
27_P	39_P	0.743	0.54
27_P	37_I	0.735	0.53
7_W	61_V	0.732	0.53
49_F	89_G	0.729	0.53
46_L	49_F	0.720	0.52
62_L	82_K	0.710	0.51
44_W	54_L	0.707	0.51
17_L	28_L	0.703	0.50
21_L	38_I	0.702	0.50
11_L	21_L	0.687	0.49
12_L	27_P	0.686	0.49
2_T	6_Q	0.682	0.48
3_R	10_L	0.677	0.48
8_L	13_L	0.676	0.47
6_Q	23_L	0.674	0.47
20_A	87_K	0.671	0.47
3_R	14_L	0.666	0.46
37_I	40_V	0.658	0.46
56_S	67_C	0.655	0.45
19_L	34_Q	0.653	0.45
33_I	78_I	0.652	0.45
64_F	67_C	0.644	0.44
19_L	38_I	0.638	0.44
42_P	81_A	0.637	0.44
50_G	89_G	0.631	0.43
56_S	60_G	0.629	0.43
39_P	44_W	0.629	0.43
75_Q	78_I	0.620	0.42
11_L	70_A	0.614	0.41
4_A	8_L	0.611	0.41
76_K	80_E	0.608	0.41
79_K	87_K	0.602	0.40
60_G	70_A	0.599	0.40
42_P	49_F	0.599	0.40
56_S	68_P	0.598	0.40
28_L	35_R	0.594	0.39
25_L	34_Q	0.589	0.39
22_L	39_P	0.587	0.39
20_A	76_K	0.580	0.38
44_W	47_V	0.577	0.38
21_L	62_L	0.576	0.38
24_G	76_K	0.574	0.38
57_L	61_V	0.569	0.37
2_T	73_E	0.569	0.37
42_P	82_K	0.566	0.37
18_W	22_L	0.564	0.37
60_G	64_F	0.538	0.34
40_V	43_L	0.537	0.34
85_L	90_V	0.536	0.34
56_S	61_V	0.532	0.34
44_W	75_Q	0.531	0.34
57_L	67_C	0.529	0.33
29_P	41_L	0.526	0.33
40_V	46_L	0.520	0.33
55_A	62_L	0.516	0.32
85_L	89_G	0.513	0.32
8_L	52_Y	0.512	0.32
62_L	69_E	0.512	0.32
72_K	79_K	0.511	0.32
70_A	77_E	0.503	0.31
10_L	68_P	0.502	0.31
12_L	22_L	0.502	0.31
12_L	46_L	0.500	0.31

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
3avxA	1	0.4066	63	0.856	Contact Map
4pc3C	1	0.4176	33.1	0.879	Contact Map
2cp9A	1	0.4615	32.8	0.88	Contact Map
1aipC	2	0.4286	29.1	0.883	Contact Map
4qinA	2	1	28.8	0.883	Contact Map
4c7rA	3	0.989	18.9	0.893	Contact Map
1xb2B	1	0.4286	17.7	0.894	Contact Map
4q4gX	1	0	17.5	0.894	Contact Map
3layA	5	0.6374	11.8	0.903	Contact Map
1xjtA	1	0.8571	11.6	0.903	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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