MlaD - PFAM28P - GREMLIN Contacts

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MlaD - MlaD protein

PFAM:	PF02470	Sequences: DGYTVTAYFDNAGGLKPGAPVRIAGVKVGRVTSIELDPDGGRVRVTLRIDKDKDVPIPKDSRASIRTLGLLGEKYVELDPG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (78)
Sequences:	71733 (42937)
Seq/√Len:	4861.7
META:	0.822

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_P	27_K	3.326	1.00
7_A	47_L	3.005	1.00
6_T	44_R	2.975	1.00
32_T	48_R	2.836	1.00
8_Y	44_R	2.799	1.00
6_T	46_T	2.292	1.00
33_S	46_T	2.173	1.00
4_T	46_T	2.157	1.00
8_Y	42_R	1.939	1.00
22_R	75_Y	1.812	1.00
35_E	46_T	1.726	1.00
4_T	32_T	1.704	1.00
4_T	48_R	1.605	1.00
66_R	77_E	1.594	1.00
22_R	27_K	1.572	1.00
23_I	28_V	1.548	1.00
5_V	47_L	1.491	1.00
7_A	63_A	1.456	1.00
9_F	45_V	1.444	1.00
63_A	78_L	1.371	1.00
37_D	44_R	1.326	1.00
17_P	33_S	1.321	1.00
35_E	44_R	1.312	1.00
53_K	56_P	1.302	1.00
61_S	78_L	1.282	1.00
32_T	46_T	1.281	1.00
68_L	73_E	1.245	1.00
58_P	61_S	1.187	1.00
27_K	30_R	1.180	1.00
18_G	30_R	1.176	1.00
64_S	79_D	1.175	1.00
66_R	75_Y	1.123	1.00
67_T	71_L	1.115	1.00
21_V	47_L	1.075	1.00
39_D	42_R	1.061	1.00
2_G	48_R	1.039	1.00
19_A	73_E	1.033	1.00
37_D	42_R	1.021	1.00
64_S	77_E	1.003	1.00
8_Y	37_D	0.999	1.00
12_A	34_I	0.993	1.00
20_P	68_L	0.967	1.00
15_L	45_V	0.960	1.00
10_D	42_R	0.911	1.00
67_T	74_K	0.902	1.00
62_R	79_D	0.895	1.00
57_I	78_L	0.887	1.00
16_K	19_A	0.885	1.00
47_L	76_V	0.862	1.00
22_R	68_L	0.861	1.00
65_I	74_K	0.856	1.00
15_L	19_A	0.848	1.00
69_G	73_E	0.848	1.00
31_V	45_V	0.842	1.00
19_A	74_K	0.833	1.00
7_A	76_V	0.819	1.00
23_I	57_I	0.815	1.00
52_D	55_V	0.805	1.00
37_D	40_G	0.804	1.00
67_T	73_E	0.801	1.00
30_R	48_R	0.801	1.00
3_Y	49_I	0.801	1.00
17_P	34_I	0.798	1.00
21_V	49_I	0.796	1.00
19_A	31_V	0.771	1.00
49_I	57_I	0.765	1.00
68_L	75_Y	0.750	1.00
26_V	43_V	0.737	1.00
16_K	27_K	0.731	1.00
34_I	45_V	0.729	1.00
27_K	50_D	0.724	1.00
63_A	76_V	0.708	1.00
60_D	80_P	0.705	1.00
24_A	80_P	0.700	1.00
69_G	74_K	0.684	1.00
50_D	53_K	0.683	1.00
5_V	49_I	0.679	1.00
28_V	49_I	0.679	1.00
24_A	79_D	0.674	1.00
50_D	54_D	0.672	1.00
20_P	30_R	0.666	1.00
9_F	12_A	0.661	1.00
58_P	80_P	0.658	1.00
22_R	77_E	0.642	1.00
16_K	20_P	0.623	1.00
67_T	70_L	0.622	1.00
68_L	71_L	0.609	1.00
3_Y	7_A	0.605	1.00
3_Y	54_D	0.598	1.00
37_D	41_G	0.591	1.00
22_R	66_R	0.586	1.00
26_V	34_I	0.576	1.00
44_R	47_L	0.573	1.00
39_D	43_V	0.568	1.00
9_F	65_I	0.568	1.00
62_R	66_R	0.567	1.00
71_L	74_K	0.567	1.00
15_L	31_V	0.563	1.00
13_G	74_K	0.559	1.00
3_Y	56_P	0.559	1.00
70_L	74_K	0.558	1.00
31_V	76_V	0.555	1.00
2_G	53_K	0.548	1.00
17_P	20_P	0.548	1.00
32_T	47_L	0.543	1.00
26_V	36_L	0.539	1.00
17_P	32_T	0.532	1.00
57_I	61_S	0.532	1.00
8_Y	39_D	0.525	1.00
4_T	8_Y	0.521	1.00
9_F	76_V	0.518	1.00
41_G	58_P	0.514	1.00
24_A	36_L	0.514	1.00
14_G	22_R	0.512	1.00
25_G	29_G	0.511	1.00
38_P	41_G	0.506	1.00
52_D	60_D	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
3ttgA	1	0.8642	30.8	0.812	Contact Map
1wosA	1	0.9259	28.3	0.815	Contact Map
1yx2A	1	0.9259	27.9	0.816	Contact Map
1v5vA	2	0.963	27.3	0.817	Contact Map
3girA	1	0.9383	26.8	0.817	Contact Map
1wsrA	2	0.9259	23	0.823	Contact Map
1pj5A	3	0.9259	20.8	0.826	Contact Map
3tfiA	2	0.9012	16.5	0.834	Contact Map
2xyyA	9	0.8642	11.2	0.847	Contact Map
3wnoA	2	1	8.8	0.853	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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