DUF4395 - PFAM28P - GREMLIN Contacts

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DUF4395 - Domain of unknown function (DUF4395)

PFAM:	PF14340	Sequences: VDERAPRFNAGIVVVLLLVALVTGSPWLLALLALVFAIRALLGPRLSPLGLLYRRVVRPRLGPPPELEDAPPKRFAQGIGLVFLLAALVLFLLGATTLGWVLAGLLLVAAFLEAAFGFCLGCEIYLLLMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (129)
Sequences:	11666 (7146)
Seq/√Len:	629.1
META:	0.927

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_F	115_A	3.907	1.00
118_F	123_E	3.850	1.00
37_A	81_L	3.666	1.00
123_E	127_L	3.234	1.00
51_L	55_R	3.070	1.00
90_L	98_L	3.050	1.00
109_A	120_L	2.261	1.00
91_F	99_G	2.127	1.00
79_I	83_F	2.088	1.00
30_A	88_L	2.068	1.00
52_L	56_V	2.053	1.00
33_A	85_L	2.001	1.00
42_L	46_L	1.954	1.00
40_A	78_G	1.858	1.00
34_L	38_I	1.686	1.00
33_A	88_L	1.685	1.00
11_G	114_A	1.670	1.00
20_A	28_L	1.646	1.00
8_F	53_Y	1.638	1.00
83_F	102_L	1.634	1.00
78_G	82_V	1.576	1.00
79_I	124_I	1.559	1.00
17_L	107_L	1.497	1.00
101_V	105_L	1.464	1.00
84_L	106_L	1.463	1.00
51_L	54_R	1.435	1.00
16_L	28_L	1.426	1.00
69_D	72_P	1.397	1.00
33_A	84_L	1.376	1.00
105_L	109_A	1.370	1.00
90_L	102_L	1.365	1.00
90_L	95_A	1.347	1.00
4_R	63_P	1.303	1.00
14_V	111_F	1.301	1.00
97_T	101_V	1.293	1.00
37_A	85_L	1.290	1.00
111_F	116_F	1.284	1.00
100_W	104_G	1.279	1.00
86_A	102_L	1.275	1.00
87_A	103_A	1.268	1.00
29_L	87_A	1.253	1.00
20_A	23_T	1.251	1.00
12_I	49_L	1.249	1.00
97_T	100_W	1.243	1.00
95_A	98_L	1.227	1.00
93_L	96_T	1.225	1.00
125_Y	129_M	1.224	1.00
121_G	126_L	1.199	1.00
19_V	23_T	1.199	1.00
52_L	57_V	1.184	1.00
1_V	6_P	1.176	1.00
38_I	42_L	1.173	1.00
123_E	126_L	1.172	1.00
88_L	92_L	1.159	1.00
74_R	78_G	1.157	1.00
35_V	49_L	1.157	1.00
20_A	29_L	1.138	1.00
104_G	108_V	1.117	1.00
26_P	88_L	1.113	1.00
20_A	103_A	1.087	1.00
40_A	81_L	1.082	1.00
16_L	32_L	1.071	1.00
14_V	110_A	1.055	1.00
86_A	90_L	1.021	1.00
75_F	79_I	1.011	1.00
89_V	93_L	0.992	1.00
31_L	35_V	0.975	1.00
100_W	103_A	0.968	1.00
14_V	107_L	0.964	1.00
26_P	30_A	0.958	1.00
79_I	109_A	0.958	1.00
87_A	102_L	0.950	1.00
2_D	5_A	0.946	1.00
64_P	67_L	0.945	1.00
35_V	39_R	0.930	1.00
84_L	88_L	0.918	1.00
25_S	28_L	0.915	1.00
37_A	41_L	0.915	1.00
9_N	13_V	0.912	1.00
120_L	123_E	0.901	1.00
58_R	63_P	0.893	1.00
56_V	59_P	0.891	1.00
83_F	106_L	0.890	1.00
82_V	86_A	0.889	1.00
21_L	100_W	0.889	1.00
39_R	47_S	0.889	1.00
124_I	127_L	0.877	1.00
5_A	8_F	0.872	1.00
91_F	100_W	0.858	1.00
27_W	31_L	0.855	1.00
42_L	45_R	0.851	1.00
33_A	81_L	0.844	1.00
5_A	54_R	0.837	1.00
18_L	107_L	0.836	1.00
29_L	91_F	0.832	1.00
33_A	37_A	0.829	1.00
106_L	109_A	0.824	1.00
26_P	91_F	0.823	1.00
5_A	58_R	0.822	1.00
112_L	116_F	0.816	1.00
29_L	103_A	0.811	1.00
81_L	85_L	0.807	1.00
17_L	106_L	0.790	1.00
35_V	38_I	0.784	1.00
101_V	104_G	0.780	1.00
96_T	100_W	0.776	1.00
53_Y	58_R	0.774	1.00
4_R	65_P	0.768	1.00
3_E	66_E	0.761	1.00
76_A	80_G	0.756	1.00
36_F	81_L	0.755	1.00
35_V	47_S	0.746	1.00
38_I	46_L	0.739	1.00
29_L	84_L	0.735	1.00
47_S	50_G	0.735	1.00
83_F	105_L	0.727	1.00
12_I	16_L	0.722	1.00
14_V	115_A	0.714	1.00
21_L	24_G	0.702	1.00
15_V	19_V	0.699	1.00
16_L	20_A	0.694	1.00
17_L	103_A	0.693	1.00
8_F	12_I	0.684	1.00
9_N	49_L	0.676	1.00
44_P	70_A	0.674	1.00
3_E	67_L	0.673	1.00
110_A	113_E	0.672	1.00
113_E	116_F	0.669	1.00
11_G	15_V	0.668	1.00
117_G	123_E	0.662	1.00
88_L	91_F	0.661	1.00
26_P	92_L	0.657	1.00
78_G	81_L	0.655	1.00
91_F	96_T	0.645	1.00
119_C	122_C	0.645	1.00
108_V	111_F	0.641	1.00
112_L	118_F	0.639	1.00
44_P	50_G	0.638	1.00
75_F	121_G	0.638	1.00
3_E	6_P	0.635	1.00
20_A	91_F	0.631	1.00
17_L	32_L	0.630	1.00
18_L	22_V	0.625	1.00
126_L	129_M	0.624	1.00
8_F	11_G	0.617	1.00
32_L	36_F	0.615	1.00
11_G	14_V	0.613	1.00
36_F	80_G	0.608	1.00
30_A	92_L	0.604	1.00
20_A	24_G	0.604	1.00
104_G	107_L	0.603	1.00
109_A	118_F	0.603	1.00
58_R	67_L	0.601	1.00
21_L	107_L	0.599	1.00
13_V	17_L	0.599	1.00
77_Q	113_E	0.597	1.00
9_N	53_Y	0.597	1.00
72_P	76_A	0.597	1.00
10_A	13_V	0.596	1.00
38_I	41_L	0.595	1.00
79_I	121_G	0.592	1.00
87_A	106_L	0.589	1.00
83_F	124_I	0.589	1.00
1_V	73_K	0.588	1.00
80_G	83_F	0.579	1.00
72_P	75_F	0.578	1.00
79_I	82_V	0.573	1.00
45_R	51_L	0.572	1.00
41_L	78_G	0.566	1.00
22_V	25_S	0.564	1.00
112_L	120_L	0.561	1.00
113_E	117_G	0.559	1.00
3_E	68_E	0.557	1.00
4_R	8_F	0.556	1.00
41_L	81_L	0.555	1.00
70_A	74_R	0.552	1.00
12_I	15_V	0.549	1.00
106_L	110_A	0.549	1.00
13_V	49_L	0.544	1.00
45_R	48_P	0.541	0.99
36_F	39_R	0.541	0.99
120_L	124_I	0.539	0.99
14_V	18_L	0.537	0.99
1_V	4_R	0.535	0.99
110_A	114_A	0.531	0.99
25_S	31_L	0.529	0.99
54_R	58_R	0.527	0.99
73_K	76_A	0.523	0.99
29_L	88_L	0.523	0.99
124_I	128_L	0.514	0.99
99_G	102_L	0.509	0.99
60_R	63_P	0.504	0.99
103_A	106_L	0.501	0.99
75_F	125_Y	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
1zzaA	1	0.3231	11	0.909	Contact Map
2mpnA	2	0.4923	10.7	0.909	Contact Map
2b2hA	3	0.9462	8.9	0.912	Contact Map
1u7gA	3	0.9462	4	0.926	Contact Map
4od4A	1	0.8615	3.5	0.928	Contact Map
3ze3A	4	0.7	3.5	0.928	Contact Map
2jlnA	1	0.8154	3.1	0.93	Contact Map
3hd6A	3	0.9462	1.7	0.939	Contact Map
1jmoA	1	0.3615	1.5	0.94	Contact Map
3k3fA	3	0.8462	1.5	0.94	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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