DUF4180 - PFAM28P - GREMLIN Contacts

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DUF4180 - Domain of unknown function (DUF4180)

PFAM:	PF13788	Sequences: NGVKIAEVSSDGPLIRDEQDALDLLIGAAYETGADRIILPKENLTPDFFDLSTGLAGEILQKFVNYRVRLAIVGDFSKYVATSKSLRDFIYESNRGRQIFFVADLEEALERL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (108)
Sequences:	3653 (2834)
Seq/√Len:	272.7
META:	0.84

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_E	58_E	3.283	1.00
104_D	107_E	3.017	1.00
36_R	69_R	2.848	1.00
103_A	107_E	2.696	1.00
27_G	31_E	2.473	1.00
60_L	89_F	2.375	1.00
17_D	20_D	2.356	1.00
60_L	99_I	2.162	1.00
54_G	58_E	2.154	1.00
85_S	88_D	2.135	1.00
28_A	31_E	1.993	1.00
41_K	78_K	1.976	1.00
50_D	85_S	1.908	1.00
40_P	43_N	1.905	1.00
91_Y	95_R	1.849	1.00
23_D	27_G	1.799	1.00
87_R	91_Y	1.787	1.00
88_D	91_Y	1.776	1.00
61_Q	65_N	1.732	1.00
47_D	50_D	1.727	1.00
84_K	88_D	1.719	1.00
52_S	85_S	1.508	1.00
16_R	20_D	1.505	1.00
19_Q	22_L	1.460	1.00
4_K	33_G	1.443	1.00
105_L	109_L	1.425	1.00
26_I	29_A	1.410	1.00
106_E	109_L	1.407	1.00
7_E	105_L	1.358	1.00
48_F	56_A	1.340	1.00
39_L	70_L	1.331	1.00
89_F	93_S	1.318	1.00
100_F	111_R	1.299	1.00
49_F	79_Y	1.285	1.00
38_I	73_V	1.280	1.00
107_E	110_E	1.278	1.00
64_V	98_Q	1.270	1.00
76_F	90_I	1.246	1.00
83_S	86_L	1.238	1.00
97_R	100_F	1.224	1.00
55_L	59_I	1.215	1.00
41_K	46_P	1.179	1.00
19_Q	23_D	1.176	1.00
86_L	90_I	1.168	1.00
38_I	105_L	1.162	1.00
45_T	55_L	1.161	1.00
102_V	111_R	1.146	1.00
21_A	63_F	1.146	1.00
7_E	40_P	1.113	1.00
47_D	53_T	1.099	1.00
37_I	68_V	1.097	1.00
67_R	98_Q	1.092	1.00
28_A	32_T	1.090	1.00
25_L	29_A	1.082	1.00
106_E	110_E	1.058	1.00
63_F	70_L	1.051	1.00
40_P	105_L	1.050	1.00
36_R	108_A	1.046	1.00
72_I	99_I	1.038	1.00
18_E	54_G	1.036	1.00
29_A	35_D	1.014	1.00
90_I	101_F	1.011	1.00
26_I	68_V	1.003	1.00
3_V	36_R	0.969	1.00
5_I	109_L	0.952	1.00
12_G	43_N	0.890	1.00
5_I	38_I	0.888	1.00
36_R	71_A	0.885	1.00
29_A	68_V	0.881	1.00
10_S	13_P	0.877	1.00
41_K	79_Y	0.871	1.00
73_V	102_V	0.866	1.00
15_I	59_I	0.861	1.00
13_P	16_R	0.859	1.00
3_V	35_D	0.857	1.00
16_R	45_T	0.852	1.00
96_G	100_F	0.840	1.00
14_L	43_N	0.836	1.00
47_D	55_L	0.826	0.99
18_E	55_L	0.821	0.99
84_K	87_R	0.820	0.99
51_L	92_E	0.818	0.99
102_V	108_A	0.816	0.99
60_L	93_S	0.810	0.99
102_V	107_E	0.802	0.99
35_D	67_R	0.800	0.99
76_F	79_Y	0.769	0.99
44_L	72_I	0.753	0.99
25_L	68_V	0.749	0.99
35_D	68_V	0.730	0.99
25_L	63_F	0.727	0.99
10_S	14_L	0.718	0.99
75_D	78_K	0.717	0.99
26_I	30_Y	0.712	0.98
73_V	105_L	0.712	0.98
21_A	59_I	0.706	0.98
93_S	99_I	0.698	0.98
76_F	86_L	0.692	0.98
29_A	34_A	0.684	0.98
89_F	97_R	0.678	0.98
26_I	37_I	0.677	0.98
27_G	30_Y	0.669	0.98
71_A	100_F	0.667	0.98
89_F	92_E	0.664	0.98
28_A	34_A	0.662	0.98
61_Q	64_V	0.655	0.97
3_V	7_E	0.651	0.97
78_K	82_T	0.649	0.97
69_R	98_Q	0.645	0.97
50_D	54_G	0.637	0.97
11_D	42_E	0.637	0.97
63_F	68_V	0.623	0.96
100_F	108_A	0.618	0.96
61_Q	93_S	0.617	0.96
8_V	25_L	0.610	0.96
57_G	65_N	0.610	0.96
40_P	73_V	0.609	0.96
13_P	43_N	0.607	0.96
86_L	93_S	0.604	0.96
69_R	100_F	0.602	0.96
22_L	62_K	0.601	0.96
4_K	13_P	0.595	0.95
20_D	23_D	0.595	0.95
9_S	13_P	0.593	0.95
63_F	99_I	0.591	0.95
64_V	67_R	0.588	0.95
64_V	99_I	0.587	0.95
41_K	76_F	0.580	0.95
74_G	82_T	0.576	0.94
62_K	66_Y	0.575	0.94
103_A	110_E	0.573	0.94
94_N	101_F	0.573	0.94
75_D	79_Y	0.573	0.94
71_A	108_A	0.568	0.94
8_V	39_L	0.566	0.94
38_I	71_A	0.561	0.94
93_S	101_F	0.557	0.93
59_I	63_F	0.556	0.93
38_I	108_A	0.555	0.93
30_Y	68_V	0.554	0.93
26_I	31_E	0.550	0.93
15_I	44_L	0.544	0.93
38_I	45_T	0.543	0.93
18_E	22_L	0.535	0.92
13_P	44_L	0.534	0.92
23_D	66_Y	0.532	0.92
79_Y	82_T	0.532	0.92
26_I	32_T	0.529	0.92
4_K	7_E	0.528	0.92
65_N	86_L	0.527	0.91
60_L	70_L	0.525	0.91
23_D	26_I	0.525	0.91
44_L	49_F	0.523	0.91
55_L	60_L	0.521	0.91
90_I	94_N	0.514	0.90
30_Y	35_D	0.513	0.90
30_Y	33_G	0.509	0.90
25_L	37_I	0.506	0.90
56_A	59_I	0.504	0.90
82_T	101_F	0.501	0.89
64_V	96_G	0.501	0.89
22_L	27_G	0.500	0.89

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
3bl4A	2	0.9018	82.6	0.878	Contact Map
2q3lA	2	0.9196	80.3	0.881	Contact Map
2ookA	2	0.9196	76.7	0.885	Contact Map
4xs5A	1	0.8929	66.2	0.893	Contact Map
2ka5A	1	0.8929	55.5	0.9	Contact Map
1th8B	1	0.8929	45.7	0.906	Contact Map
4qtpA	2	0.8839	45.6	0.906	Contact Map
2vg3A	2	0.9554	45.5	0.906	Contact Map
1h4xA	1	0.8839	45.5	0.906	Contact Map
4q9mA	2	0.9643	44.9	0.906	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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