DUF3037 - PFAM28P - GREMLIN Contacts

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DUF3037 - Protein of unknown function (DUF3037)

PFAM:	PF11236	Sequences: YAVLRVVPRVERGEFVNVGVILFCPERGFLGARIELDEARLRALDPDLDLEAVRAHLAAIERICAGGPAAGPIAALPLRERFRWLVAPRSTVIQTSPVHTGLCDDPAAELERLFERLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (118)
Sequences:	9395 (6323)
Seq/√Len:	582.1
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_E	54_R	3.853	1.00
33_R	111_E	3.472	1.00
112_R	116_R	2.620	1.00
31_G	107_A	2.506	1.00
6_V	18_V	2.490	1.00
77_P	80_E	2.299	1.00
14_E	17_N	2.209	1.00
58_A	61_E	2.120	1.00
20_V	110_L	2.113	1.00
109_E	112_R	2.112	1.00
61_E	65_A	2.015	1.00
103_C	109_E	2.004	1.00
105_D	108_A	1.868	1.00
5_R	15_F	1.828	1.00
54_R	58_A	1.826	1.00
16_V	44_L	1.750	1.00
34_I	61_E	1.748	1.00
33_R	114_F	1.716	1.00
67_G	74_A	1.622	1.00
29_F	106_P	1.598	1.00
24_C	27_R	1.597	1.00
31_G	65_A	1.579	1.00
38_E	42_R	1.550	1.00
27_R	106_P	1.475	1.00
107_A	111_E	1.473	1.00
39_A	42_R	1.448	1.00
114_F	118_V	1.433	1.00
42_R	50_L	1.421	1.00
2_A	86_V	1.413	1.00
79_R	83_R	1.408	1.00
22_L	110_L	1.349	1.00
7_V	94_Q	1.330	1.00
86_V	98_V	1.318	1.00
72_P	75_A	1.290	1.00
68_P	75_A	1.246	1.00
28_G	78_L	1.242	1.00
25_P	79_R	1.231	1.00
48_L	53_V	1.225	1.00
49_D	52_A	1.213	1.00
20_V	113_L	1.212	1.00
88_P	97_P	1.207	1.00
32_A	61_E	1.206	1.00
31_G	61_E	1.190	1.00
18_V	57_L	1.186	1.00
59_A	63_I	1.183	1.00
6_V	41_L	1.179	1.00
6_V	53_V	1.175	1.00
76_L	80_E	1.165	1.00
62_R	67_G	1.156	1.00
70_A	74_A	1.151	1.00
39_A	43_A	1.141	1.00
111_E	115_E	1.134	1.00
16_V	41_L	1.112	1.00
22_L	109_E	1.095	1.00
50_L	54_R	1.094	1.00
13_G	99_H	1.090	1.00
60_I	95_T	1.077	1.00
14_E	40_R	1.077	1.00
31_G	110_L	1.071	1.00
56_H	59_A	1.052	1.00
52_A	55_A	1.032	1.00
71_G	74_A	1.021	1.00
35_E	114_F	1.007	1.00
86_V	89_R	1.002	1.00
10_V	94_Q	0.996	1.00
58_A	62_R	0.995	1.00
51_E	54_R	0.994	1.00
24_C	29_F	0.978	1.00
23_F	79_R	0.974	1.00
113_L	117_L	0.967	1.00
53_V	57_L	0.957	1.00
3_V	20_V	0.942	1.00
9_R	12_R	0.939	1.00
80_E	83_R	0.937	1.00
5_R	94_Q	0.936	1.00
16_V	40_R	0.930	1.00
63_I	66_G	0.923	1.00
85_L	89_R	0.917	1.00
22_L	106_P	0.905	1.00
25_P	77_P	0.881	1.00
62_R	69_A	0.881	1.00
38_E	50_L	0.875	1.00
29_F	107_A	0.864	1.00
52_A	56_H	0.858	1.00
32_A	64_C	0.856	1.00
40_R	44_L	0.856	1.00
89_R	95_T	0.853	1.00
41_L	48_L	0.853	1.00
83_R	87_A	0.842	1.00
108_A	112_R	0.838	1.00
103_C	106_P	0.824	1.00
32_A	60_I	0.823	1.00
62_R	65_A	0.821	1.00
84_W	87_A	0.820	1.00
5_R	17_N	0.812	1.00
4_L	95_T	0.809	1.00
101_G	109_E	0.807	1.00
73_I	76_L	0.805	1.00
23_F	78_L	0.801	1.00
38_E	51_E	0.775	1.00
55_A	58_A	0.762	1.00
70_A	73_I	0.761	1.00
104_D	109_E	0.746	1.00
103_C	108_A	0.736	1.00
108_A	111_E	0.734	1.00
22_L	29_F	0.726	1.00
23_F	83_R	0.723	1.00
72_P	76_L	0.718	1.00
55_A	59_A	0.718	1.00
40_R	43_A	0.712	1.00
5_R	13_G	0.712	1.00
23_F	30_L	0.709	1.00
88_P	91_T	0.705	1.00
41_L	53_V	0.703	1.00
9_R	45_D	0.698	1.00
42_R	48_L	0.692	1.00
3_V	17_N	0.687	1.00
82_F	98_V	0.682	1.00
67_G	70_A	0.679	1.00
13_G	97_P	0.677	1.00
42_R	45_D	0.672	1.00
109_E	113_L	0.671	1.00
29_F	110_L	0.670	1.00
33_R	110_L	0.669	1.00
45_D	48_L	0.664	1.00
18_V	48_L	0.657	1.00
36_L	54_R	0.651	1.00
25_P	28_G	0.637	1.00
1_Y	117_L	0.635	1.00
55_A	62_R	0.632	1.00
2_A	6_V	0.627	1.00
51_E	55_A	0.625	1.00
4_L	60_I	0.620	1.00
57_L	61_E	0.617	1.00
59_A	62_R	0.616	1.00
26_E	79_R	0.615	1.00
110_L	114_F	0.611	1.00
25_P	80_E	0.600	1.00
2_A	96_S	0.599	1.00
107_A	115_E	0.597	1.00
100_T	103_C	0.587	1.00
21_I	32_A	0.579	1.00
104_D	108_A	0.579	1.00
68_P	71_G	0.578	1.00
56_H	63_I	0.575	1.00
4_L	21_I	0.574	1.00
112_R	115_E	0.574	1.00
12_R	15_F	0.571	1.00
10_V	13_G	0.566	1.00
83_R	86_V	0.565	0.99
50_L	53_V	0.562	0.99
21_I	95_T	0.560	0.99
2_A	82_F	0.557	0.99
80_E	84_W	0.557	0.99
19_G	34_I	0.557	0.99
62_R	70_A	0.556	0.99
7_V	13_G	0.555	0.99
21_I	30_L	0.554	0.99
106_P	109_E	0.553	0.99
8_P	44_L	0.553	0.99
52_A	92_V	0.552	0.99
109_E	114_F	0.541	0.99
67_G	71_G	0.532	0.99
1_Y	99_H	0.530	0.99
68_P	72_P	0.529	0.99
4_L	34_I	0.522	0.99
3_V	117_L	0.521	0.99
15_F	44_L	0.520	0.99
67_G	75_A	0.519	0.99
6_V	48_L	0.519	0.99
109_E	116_R	0.517	0.99
19_G	114_F	0.516	0.99
12_R	90_S	0.515	0.99
49_D	53_V	0.514	0.99
114_F	117_L	0.508	0.99
49_D	56_H	0.501	0.99
42_R	46_P	0.500	0.99

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
2lj8A	1	0.6271	7.2	0.907	Contact Map
4mfuA	2	0.5254	6.9	0.908	Contact Map
1cnuA	1	0.6017	6.7	0.909	Contact Map
4uzzB	1	0.5	6.3	0.91	Contact Map
4lizA	1	0.6356	5.1	0.914	Contact Map
2xfaA	1	0.6271	4.7	0.915	Contact Map
4bex1	2	0.7119	4.6	0.916	Contact Map
2i2qA	1	0.5085	4.6	0.916	Contact Map
3silA	1	0.3475	4.4	0.917	Contact Map
4c5pA	1	0.4915	4.3	0.917	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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