LrgA - PFAM28P - GREMLIN Contacts

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LrgA - LrgA family

PFAM:	PF03788	Sequences: QLLGELLVRLLGLPIPGPVIGMLLLFLLLLLRGVKLEWVEEAADFLLAHLSLLFVPAGVGVMLHLDLLAAEGLPILVALVVSTVLVLAVTGLVM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (92)
Sequences:	8566 (6060)
Seq/√Len:	631.8
META:	0.734

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_E	74_P	3.069	1.00
8_V	20_I	2.807	1.00
35_K	38_W	2.594	1.00
40_E	44_D	2.487	1.00
5_E	9_R	2.433	1.00
74_P	78_A	2.201	1.00
65_L	69_A	2.189	1.00
4_G	17_G	2.043	1.00
88_A	92_L	1.997	1.00
26_F	30_L	1.951	1.00
66_D	69_A	1.919	1.00
86_V	90_T	1.914	1.00
7_L	24_L	1.908	1.00
44_D	48_A	1.887	1.00
72_G	76_L	1.851	1.00
6_L	10_L	1.781	1.00
66_D	70_A	1.725	1.00
77_V	81_V	1.664	1.00
78_A	82_S	1.586	1.00
32_R	35_K	1.567	1.00
27_L	31_L	1.564	1.00
36_L	40_E	1.558	1.00
33_G	36_L	1.525	1.00
67_L	71_E	1.501	1.00
89_V	93_V	1.460	1.00
39_V	43_A	1.453	1.00
51_S	58_G	1.429	1.00
6_L	9_R	1.381	1.00
62_M	65_L	1.321	1.00
5_E	8_V	1.290	1.00
64_H	67_L	1.289	1.00
41_E	44_D	1.276	1.00
28_L	34_V	1.236	1.00
5_E	17_G	1.193	1.00
8_V	17_G	1.184	1.00
7_L	11_L	1.172	1.00
68_L	75_I	1.135	1.00
24_L	28_L	1.134	1.00
42_A	45_F	1.119	1.00
38_W	41_E	1.103	1.00
31_L	34_V	1.094	1.00
8_V	11_L	1.073	1.00
28_L	33_G	1.067	1.00
71_E	75_I	1.058	1.00
63_L	66_D	1.054	1.00
25_L	39_V	1.041	1.00
49_H	53_L	1.001	1.00
51_S	55_V	0.994	1.00
16_P	57_A	0.973	1.00
41_E	48_A	0.971	1.00
37_E	40_E	0.966	1.00
17_G	20_I	0.944	1.00
15_I	20_I	0.931	1.00
49_H	52_L	0.927	1.00
3_L	24_L	0.894	1.00
70_A	74_P	0.894	1.00
8_V	12_G	0.886	1.00
4_G	8_V	0.885	1.00
34_V	38_W	0.884	1.00
81_V	85_L	0.881	1.00
7_L	20_I	0.863	1.00
44_D	47_L	0.856	1.00
8_V	13_L	0.840	1.00
59_V	62_M	0.833	1.00
11_L	20_I	0.829	1.00
86_V	89_V	0.824	1.00
8_V	15_I	0.821	1.00
81_V	84_V	0.811	1.00
36_L	39_V	0.808	1.00
48_A	51_S	0.802	1.00
23_L	27_L	0.795	1.00
89_V	92_L	0.786	1.00
39_V	47_L	0.783	1.00
28_L	32_R	0.775	1.00
18_P	79_L	0.769	1.00
50_L	54_F	0.769	1.00
79_L	83_T	0.767	1.00
3_L	28_L	0.764	1.00
88_A	91_G	0.757	1.00
43_A	47_L	0.757	1.00
61_V	64_H	0.753	1.00
79_L	86_V	0.739	1.00
57_A	60_G	0.735	1.00
64_H	68_L	0.725	1.00
38_W	42_A	0.715	1.00
20_I	24_L	0.712	1.00
9_R	12_G	0.710	1.00
27_L	30_L	0.709	1.00
67_L	70_A	0.709	1.00
22_M	75_I	0.705	1.00
2_L	6_L	0.676	1.00
36_L	43_A	0.673	1.00
87_L	91_G	0.655	1.00
56_P	60_G	0.650	1.00
28_L	31_L	0.635	1.00
28_L	35_K	0.632	1.00
30_L	33_G	0.631	1.00
45_F	48_A	0.630	1.00
80_V	84_V	0.624	1.00
25_L	43_A	0.622	1.00
78_A	87_L	0.621	1.00
76_L	79_L	0.616	1.00
73_L	76_L	0.613	1.00
32_R	36_L	0.609	1.00
25_L	34_V	0.606	1.00
82_S	86_V	0.601	1.00
18_P	53_L	0.593	1.00
41_E	45_F	0.583	1.00
84_V	88_A	0.580	1.00
22_M	87_L	0.579	1.00
45_F	49_H	0.573	1.00
58_G	63_L	0.566	1.00
63_L	71_E	0.563	1.00
34_V	39_V	0.562	1.00
35_K	40_E	0.559	1.00
55_V	64_H	0.558	1.00
72_G	78_A	0.552	1.00
26_F	29_L	0.550	1.00
2_L	5_E	0.550	1.00
58_G	65_L	0.549	1.00
23_L	26_F	0.547	1.00
5_E	18_P	0.547	1.00
22_M	84_V	0.545	1.00
22_M	26_F	0.544	1.00
83_T	86_V	0.543	1.00
85_L	88_A	0.543	1.00
76_L	80_V	0.542	0.99
43_A	46_L	0.534	0.99
10_L	13_L	0.526	0.99
77_V	80_V	0.524	0.99
42_A	46_L	0.522	0.99
68_L	72_G	0.519	0.99
69_A	72_G	0.507	0.99
54_F	58_G	0.506	0.99
15_I	19_V	0.504	0.99
58_G	75_I	0.504	0.99
4_G	20_I	0.500	0.99
28_L	36_L	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
4cz8A	2	0.9574	19.9	0.87	Contact Map
4czbA	2	0.9574	16.6	0.875	Contact Map
4b4aA	1	0.3404	5.3	0.9	Contact Map
4bwzA	2	0.9255	3.9	0.906	Contact Map
4httA	1	0.3404	3.8	0.907	Contact Map
1a87A	1	0.5426	3.1	0.91	Contact Map
4gh4D	3	0.2553	2.5	0.915	Contact Map
2nq2A	2	0.3511	2.3	0.917	Contact Map
4hsuA	1	0.3404	2	0.92	Contact Map
2nwlA	3	0.8723	1.7	0.923	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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