DUF4397 - PFAM28P - GREMLIN Contacts

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DUF4397 - Domain of unknown function (DUF4397)

PFAM:	PF14344	Sequences: ARVRVVHASPDAPAVDVYVNGTLVLSNVAFGTASGYLSVPAGTYTVAVRPAGTTPAGTPVLLSTTVTLAAGTAYTVVAVGTAGALTLLVLTDDLTAPAAGKARVRVVHASPDAPAVDVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (117)
Sequences:	20446 (16118)
Seq/√Len:	1490.1
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_R	73_A	3.084	1.00
20_N	44_Y	3.052	1.00
79_V	88_L	3.012	1.00
69_A	72_T	2.735	1.00
18_Y	23_L	2.670	1.00
72_T	91_T	2.612	1.00
2_R	38_S	2.345	1.00
25_L	28_V	2.095	1.00
23_L	26_S	2.088	1.00
43_T	67_T	2.079	1.00
29_A	32_T	2.036	1.00
69_A	74_Y	1.957	1.00
45_T	63_S	1.947	1.00
6_V	33_A	1.917	1.00
18_Y	49_R	1.872	1.00
75_T	92_D	1.821	1.00
9_S	85_L	1.733	1.00
73_A	94_L	1.708	1.00
14_A	29_A	1.638	1.00
57_G	60_V	1.600	1.00
50_P	53_T	1.588	1.00
93_D	103_R	1.573	1.00
49_R	53_T	1.514	1.00
45_T	65_T	1.506	1.00
19_V	46_V	1.505	1.00
76_V	89_V	1.497	1.00
77_V	90_L	1.471	1.00
25_L	34_S	1.441	1.00
47_A	63_S	1.434	1.00
19_V	24_V	1.417	1.00
43_T	65_T	1.408	1.00
9_S	80_G	1.376	1.00
77_V	109_A	1.358	1.00
76_V	87_L	1.326	1.00
79_V	86_T	1.312	1.00
9_S	12_A	1.305	1.00
14_A	27_N	1.301	1.00
36_Y	75_T	1.288	1.00
8_A	109_A	1.276	1.00
79_V	109_A	1.253	1.00
6_V	77_V	1.248	1.00
80_G	86_T	1.233	1.00
4_R	36_Y	1.182	1.00
88_L	107_V	1.175	1.00
98_A	101_K	1.165	1.00
19_V	44_Y	1.155	1.00
3_V	76_V	1.155	1.00
21_G	47_A	1.154	1.00
36_Y	92_D	1.134	1.00
5_V	17_V	1.127	1.00
7_H	12_A	1.124	1.00
40_P	44_Y	1.113	1.00
16_D	27_N	1.108	1.00
94_L	103_R	1.107	1.00
79_V	107_V	1.090	1.00
74_Y	89_V	1.053	1.00
18_Y	47_A	1.049	1.00
97_P	100_G	1.033	1.00
54_T	58_T	1.031	1.00
62_L	65_T	1.028	1.00
6_V	75_T	1.021	1.00
16_D	23_L	1.019	1.00
46_V	66_V	1.003	1.00
56_A	59_P	0.999	1.00
39_V	44_Y	0.996	1.00
90_L	107_V	0.994	1.00
110_S	113_A	0.989	1.00
4_R	33_A	0.987	1.00
106_V	118_V	0.971	1.00
97_P	103_R	0.968	1.00
11_D	81_T	0.967	1.00
25_L	37_L	0.942	1.00
81_T	84_A	0.931	1.00
98_A	103_R	0.924	1.00
41_A	70_A	0.921	1.00
48_V	78_A	0.911	1.00
92_D	105_R	0.903	1.00
49_R	54_T	0.896	1.00
28_V	32_T	0.877	1.00
74_Y	91_T	0.874	1.00
4_R	35_G	0.859	1.00
4_R	34_S	0.859	1.00
54_T	59_P	0.856	1.00
12_A	15_V	0.843	1.00
17_V	48_V	0.841	1.00
113_A	116_V	0.840	1.00
108_H	113_A	0.825	1.00
24_V	37_L	0.821	1.00
80_G	84_A	0.804	1.00
49_R	52_G	0.795	1.00
110_S	114_P	0.786	1.00
11_D	82_A	0.786	1.00
49_R	59_P	0.772	1.00
95_T	103_R	0.765	1.00
93_D	97_P	0.763	1.00
2_R	36_Y	0.757	1.00
8_A	77_V	0.752	1.00
62_L	87_L	0.750	1.00
47_A	62_L	0.749	1.00
54_T	57_G	0.747	1.00
4_R	75_T	0.743	1.00
67_T	70_A	0.738	1.00
80_G	85_L	0.738	1.00
78_A	85_L	0.726	1.00
26_S	51_A	0.726	1.00
41_A	44_Y	0.724	1.00
26_S	52_G	0.723	1.00
86_T	89_V	0.721	1.00
45_T	62_L	0.718	1.00
11_D	80_G	0.717	1.00
28_V	34_S	0.714	1.00
18_Y	57_G	0.707	1.00
49_R	60_V	0.704	1.00
96_A	101_K	0.704	1.00
36_Y	73_A	0.701	1.00
7_H	15_V	0.692	1.00
19_V	39_V	0.688	1.00
68_L	74_Y	0.681	1.00
46_V	68_L	0.680	1.00
7_H	78_A	0.669	1.00
80_G	83_G	0.661	1.00
112_D	115_A	0.656	1.00
90_L	105_R	0.656	1.00
56_A	60_V	0.654	1.00
77_V	107_V	0.652	1.00
93_D	96_A	0.650	1.00
7_H	30_F	0.649	1.00
103_R	106_V	0.639	1.00
87_L	90_L	0.638	1.00
53_T	57_G	0.637	1.00
21_G	24_V	0.633	1.00
39_V	68_L	0.632	1.00
63_S	66_V	0.627	1.00
7_H	13_P	0.621	1.00
96_A	103_R	0.620	1.00
13_P	82_A	0.618	1.00
89_V	92_D	0.616	1.00
73_A	92_D	0.616	1.00
86_T	90_L	0.615	1.00
34_S	37_L	0.600	1.00
16_D	51_A	0.595	1.00
9_S	78_A	0.592	1.00
81_T	111_P	0.589	1.00
90_L	109_A	0.583	1.00
43_T	69_A	0.577	1.00
64_T	87_L	0.576	1.00
47_A	54_T	0.570	1.00
44_Y	68_L	0.567	1.00
53_T	56_A	0.565	1.00
52_G	57_G	0.560	1.00
91_T	94_L	0.552	1.00
66_V	89_V	0.548	1.00
5_V	78_A	0.547	1.00
96_A	99_A	0.545	1.00
25_L	29_A	0.543	1.00
28_V	33_A	0.541	1.00
20_N	24_V	0.539	1.00
27_N	51_A	0.536	1.00
88_L	109_A	0.536	1.00
18_Y	54_T	0.535	1.00
18_Y	56_A	0.534	1.00
5_V	25_L	0.534	1.00
33_A	77_V	0.532	1.00
33_A	36_Y	0.521	1.00
49_R	57_G	0.516	1.00
23_L	27_N	0.513	1.00
20_N	47_A	0.513	1.00
1_A	68_L	0.512	1.00
8_A	79_V	0.511	1.00
17_V	28_V	0.510	1.00
66_V	76_V	0.510	1.00
108_H	114_P	0.509	1.00
102_A	106_V	0.509	1.00
5_V	28_V	0.501	1.00
97_P	101_K	0.500	1.00
12_A	82_A	0.500	1.00

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
2vzsA	1	0	51	0.839	Contact Map
4kmqA	1	0.5378	25.7	0.864	Contact Map
2vzpA	1	0.5378	19.9	0.87	Contact Map
4qb6A	1	0.5462	16.4	0.875	Contact Map
3v9fA	1	0.563	12.5	0.882	Contact Map
2w47A	1	0.605	12.1	0.883	Contact Map
3wnoA	2	0.9244	9.3	0.888	Contact Map
2wz8A	1	0.5546	8.3	0.891	Contact Map
1b77A	3	0.6303	8.1	0.891	Contact Map
4f7kA	1	0.8319	7.7	0.892	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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