DUF2279 - PFAM28P - GREMLIN Contacts

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DUF2279 - Predicted periplasmic lipoprotein (DUF2279)

PFAM:	PF10043	Sequences: NEGWFNDNTEWLGMDKLGHFYTSYFLSRLGYELLRWAGVSRKKALLYGALLGLAFQTAIEILDGFSKGWGFSWGDLAANTAGAGLAVLLYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (79)
Sequences:	6420 (4253)
Seq/√Len:	478.4
META:	0.953

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_W	77_A	2.862	1.00
53_L	80_T	2.347	1.00
40_S	43_K	2.250	1.00
20_F	81_A	2.157	1.00
26_L	56_Q	1.925	1.00
23_S	56_Q	1.866	1.00
57_T	76_L	1.856	1.00
81_A	84_G	1.850	1.00
21_Y	25_F	1.662	1.00
20_F	85_L	1.653	1.00
31_Y	48_G	1.646	1.00
77_A	81_A	1.641	1.00
41_R	45_L	1.574	1.00
61_I	65_F	1.523	1.00
76_L	79_N	1.394	1.00
71_F	76_L	1.382	1.00
25_F	28_R	1.372	1.00
31_Y	35_R	1.369	1.00
28_R	32_E	1.355	1.00
46_L	50_L	1.329	1.00
34_L	47_Y	1.300	1.00
27_S	83_A	1.281	1.00
54_A	58_A	1.272	1.00
74_G	77_A	1.257	1.00
47_Y	50_L	1.241	1.00
53_L	57_T	1.231	1.00
35_R	41_R	1.221	1.00
77_A	80_T	1.217	1.00
50_L	54_A	1.208	1.00
31_Y	41_R	1.184	1.00
58_A	62_L	1.180	1.00
48_G	52_G	1.173	1.00
25_F	29_L	1.131	1.00
43_K	47_Y	1.128	1.00
18_G	22_T	1.113	1.00
49_A	53_L	1.103	1.00
30_G	51_L	1.093	1.00
61_I	71_F	1.068	1.00
61_I	64_G	1.058	1.00
66_S	69_W	1.051	1.00
27_S	52_G	1.033	1.00
30_G	34_L	1.027	1.00
17_L	20_F	1.021	1.00
20_F	78_A	1.009	1.00
49_A	83_A	1.003	1.00
53_L	83_A	0.998	1.00
29_L	32_E	0.998	1.00
30_G	33_L	0.993	1.00
53_L	76_L	0.971	1.00
23_S	79_N	0.967	1.00
46_L	49_A	0.960	1.00
34_L	39_V	0.960	1.00
17_L	21_Y	0.951	1.00
26_L	30_G	0.948	1.00
33_L	37_A	0.944	1.00
62_L	66_S	0.920	1.00
31_Y	44_A	0.907	1.00
23_S	83_A	0.893	1.00
39_V	43_K	0.890	1.00
51_L	54_A	0.890	1.00
50_L	53_L	0.886	1.00
18_G	59_I	0.869	1.00
78_A	81_A	0.853	1.00
57_T	71_F	0.849	1.00
34_L	51_L	0.842	1.00
29_L	33_L	0.831	1.00
55_F	58_A	0.827	1.00
28_R	86_A	0.827	1.00
27_S	48_G	0.825	1.00
42_K	45_L	0.818	1.00
35_R	44_A	0.814	1.00
33_L	36_W	0.806	1.00
32_E	36_W	0.805	1.00
49_A	87_V	0.803	1.00
23_S	63_D	0.799	1.00
76_L	80_T	0.787	1.00
64_G	70_G	0.773	1.00
45_L	49_A	0.771	1.00
23_S	52_G	0.756	1.00
31_Y	86_A	0.754	1.00
27_S	49_A	0.753	1.00
31_Y	45_L	0.751	1.00
46_L	87_V	0.746	1.00
18_G	69_W	0.746	1.00
52_G	83_A	0.740	1.00
57_T	61_I	0.729	1.00
80_T	84_G	0.724	1.00
44_A	48_G	0.721	1.00
26_L	55_F	0.699	1.00
45_L	87_V	0.696	1.00
42_K	46_L	0.694	1.00
9_T	12_L	0.694	1.00
74_G	78_A	0.677	1.00
73_W	76_L	0.674	1.00
81_A	85_L	0.669	1.00
9_T	74_G	0.666	1.00
24_Y	86_A	0.657	1.00
32_E	35_R	0.652	1.00
13_G	74_G	0.648	1.00
22_T	25_F	0.635	1.00
59_I	69_W	0.618	0.99
40_S	44_A	0.617	0.99
57_T	79_N	0.607	0.99
56_Q	79_N	0.588	0.99
39_V	44_A	0.578	0.99
39_V	47_Y	0.575	0.99
28_R	31_Y	0.570	0.99
22_T	26_L	0.560	0.99
38_G	44_A	0.558	0.99
30_G	52_G	0.541	0.99
22_T	56_Q	0.539	0.99
34_L	37_A	0.529	0.98
59_I	63_D	0.528	0.98
15_D	19_H	0.509	0.98
43_K	46_L	0.505	0.98
64_G	71_F	0.501	0.98
80_T	83_A	0.500	0.98
47_Y	51_L	0.500	0.98

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
2pn2A	2	0.7143	2.3	0.923	Contact Map
2ls4A	1	0.2308	1.8	0.927	Contact Map
3j6dA	3	0.022	1.7	0.929	Contact Map
2kluA	1	0.2637	1.6	0.93	Contact Map
3alxA	4	0.2967	1.5	0.931	Contact Map
1vlaA	3	0.6923	1.5	0.931	Contact Map
4qtnA	3	0.6154	1.5	0.931	Contact Map
3c6fA	4	0.4615	1.4	0.932	Contact Map
4g1iA	1	0.0879	1.4	0.932	Contact Map
4mh4A	2	0.6923	1.3	0.933	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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