DUF2155 - PFAM28P - GREMLIN Contacts

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DUF2155 - Uncharacterized protein conserved in bacteria (DUF2155)

PFAM:	PF09923	Sequences: AVLRGLDKITGRTSDFEVPVGETVRFGTLEITVRACRTRPPEEPPETAAFLQVDDLRPDEPVFSGWMFASSPALNALEHPVYDVWLLDC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (89)
Sequences:	5950 (3018)
Seq/√Len:	319.9
META:	0.921

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_E	70_S	2.936	1.00
34_R	52_Q	2.834	1.00
19_P	22_E	2.769	1.00
47_T	69_A	2.521	1.00
23_T	30_E	2.447	1.00
38_T	88_D	2.369	1.00
25_R	30_E	2.353	1.00
52_Q	64_S	2.328	1.00
18_V	24_V	2.247	1.00
32_T	54_D	2.207	1.00
34_R	50_F	2.142	1.00
63_F	75_N	2.029	1.00
49_A	86_L	2.009	1.00
51_L	67_M	1.937	1.00
4_R	15_D	1.912	1.00
5_G	26_F	1.898	1.00
23_T	32_T	1.796	1.00
30_E	56_L	1.756	1.00
55_D	79_H	1.753	1.00
2_V	17_E	1.746	1.00
48_A	68_F	1.677	1.00
5_G	16_F	1.653	1.00
50_F	64_S	1.637	1.00
30_E	54_D	1.571	1.00
29_L	53_V	1.361	1.00
20_V	33_V	1.261	1.00
16_F	24_V	1.245	1.00
37_R	48_A	1.204	1.00
71_S	74_L	1.196	1.00
2_V	5_G	1.166	1.00
18_V	33_V	1.162	1.00
28_T	55_D	1.157	1.00
42_E	45_P	1.151	1.00
53_V	77_L	1.140	1.00
3_L	51_L	1.138	1.00
32_T	52_Q	1.124	1.00
7_D	81_V	1.124	1.00
53_V	84_V	1.104	1.00
15_D	87_L	1.100	1.00
56_L	60_E	1.090	1.00
41_P	44_P	1.089	1.00
38_T	47_T	1.083	1.00
38_T	43_E	1.082	1.00
1_A	33_V	1.078	1.00
25_R	56_L	1.070	1.00
4_R	13_T	1.065	1.00
14_S	24_V	1.019	1.00
62_V	77_L	1.008	1.00
2_V	15_D	1.007	1.00
55_D	62_V	0.981	1.00
21_G	34_R	0.981	1.00
4_R	87_L	0.949	1.00
5_G	14_S	0.916	1.00
36_C	89_C	0.915	1.00
77_L	84_V	0.857	1.00
16_F	26_F	0.848	1.00
10_T	13_T	0.848	1.00
76_A	85_W	0.847	1.00
67_M	77_L	0.834	1.00
68_F	71_S	0.833	1.00
57_R	60_E	0.803	1.00
28_T	58_P	0.797	1.00
33_V	49_A	0.788	1.00
2_V	88_D	0.780	1.00
57_R	61_P	0.766	0.99
47_T	88_D	0.762	0.99
33_V	36_C	0.757	0.99
18_V	22_E	0.756	0.99
40_P	43_E	0.744	0.99
58_P	61_P	0.741	0.99
5_G	84_V	0.740	0.99
41_P	45_P	0.709	0.99
14_S	26_F	0.708	0.99
29_L	77_L	0.706	0.99
84_V	87_L	0.702	0.99
47_T	86_L	0.699	0.99
36_C	83_D	0.696	0.99
3_L	18_V	0.695	0.99
27_G	31_I	0.694	0.99
31_I	84_V	0.692	0.99
18_V	32_T	0.689	0.99
28_T	57_R	0.671	0.99
35_A	39_R	0.668	0.99
4_R	85_W	0.667	0.99
28_T	61_P	0.650	0.98
25_R	58_P	0.637	0.98
9_I	14_S	0.635	0.98
39_R	47_T	0.635	0.98
79_H	82_Y	0.633	0.98
39_R	72_P	0.616	0.98
37_R	85_W	0.609	0.97
56_L	59_D	0.604	0.97
25_R	28_T	0.603	0.97
5_G	29_L	0.603	0.97
38_T	46_E	0.597	0.97
39_R	43_E	0.597	0.97
50_F	75_N	0.595	0.97
53_V	67_M	0.585	0.97
80_P	83_D	0.581	0.97
7_D	10_T	0.579	0.97
3_L	16_F	0.577	0.97
26_F	31_I	0.576	0.96
18_V	88_D	0.571	0.96
53_V	62_V	0.570	0.96
3_L	84_V	0.567	0.96
60_E	64_S	0.566	0.96
50_F	85_W	0.561	0.96
17_E	60_E	0.560	0.96
39_R	48_A	0.557	0.96
75_N	78_E	0.554	0.96
73_A	78_E	0.550	0.95
54_D	61_P	0.549	0.95
73_A	76_A	0.545	0.95
65_G	75_N	0.543	0.95
6_L	78_E	0.542	0.95
75_N	85_W	0.540	0.95
6_L	11_G	0.538	0.95
53_V	71_S	0.537	0.95
29_L	55_D	0.536	0.95
78_E	85_W	0.528	0.94
46_E	71_S	0.528	0.94
9_I	81_V	0.526	0.94
4_R	19_P	0.523	0.94
50_F	77_L	0.523	0.94
54_D	59_D	0.523	0.94
67_M	86_L	0.517	0.94
9_I	26_F	0.515	0.94
39_R	45_P	0.513	0.93
52_Q	68_F	0.511	0.93
19_P	23_T	0.508	0.93
34_R	64_S	0.504	0.93
63_F	72_P	0.502	0.93
19_P	33_V	0.501	0.93
29_L	36_C	0.500	0.93

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
2y9yB	1	0.9101	16.2	0.896	Contact Map
4gt9A	3	0.7416	10.3	0.905	Contact Map
3hgbA	1	0.9551	6.6	0.913	Contact Map
3cfuA	1	0.7865	6.5	0.913	Contact Map
3pieA	1	0.3371	5.8	0.915	Contact Map
4ic6A	4	0.8764	5.2	0.917	Contact Map
3cddA	3	0.9438	5.1	0.917	Contact Map
2hzmA	1	0.9551	4.8	0.918	Contact Map
2x2uA	2	0.6629	4.7	0.918	Contact Map
1y96A	1	0.5506	4.4	0.919	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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