DUF934 - PFAM28P - GREMLIN Contacts

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DUF934 - Bacterial protein of unknown function (DUF934)

PFAM:	PF06073	Sequences: GVRLAPDDDPEALAPDLDRLALIALDFPKFTDGRGYSQARLLRERYGYKGELRAVGDVLRDQLFFMRRCGFDAFELRDDQDAEAALAALADFSVVYQPAADGPLPLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	107 (105)
Sequences:	8649 (5050)
Seq/√Len:	492.8
META:	0.894

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_E	73_A	3.655	1.00
25_L	35_G	3.000	1.00
5_A	26_D	2.730	1.00
24_A	55_V	2.563	1.00
40_R	44_E	2.509	1.00
41_L	45_R	2.297	1.00
51_E	72_D	2.148	1.00
5_A	8_D	1.886	1.00
3_R	24_A	1.883	1.00
27_F	35_G	1.867	1.00
60_R	84_A	1.695	1.00
64_F	95_V	1.663	1.00
10_P	38_Q	1.658	1.00
6_P	28_P	1.635	1.00
63_L	74_F	1.598	1.00
88_A	91_D	1.580	1.00
16_D	20_L	1.552	1.00
3_R	55_V	1.523	1.00
27_F	54_A	1.522	1.00
3_R	26_D	1.521	1.00
63_L	85_A	1.467	1.00
36_Y	58_V	1.444	1.00
25_L	38_Q	1.443	1.00
53_R	73_A	1.442	1.00
9_D	12_A	1.422	1.00
68_R	101_D	1.420	1.00
59_L	62_Q	1.395	1.00
66_M	74_F	1.395	1.00
66_M	71_F	1.391	1.00
11_E	46_Y	1.359	1.00
76_L	80_Q	1.333	1.00
26_D	55_V	1.331	1.00
60_R	91_D	1.292	1.00
57_D	77_R	1.290	1.00
14_A	46_Y	1.259	1.00
1_G	22_L	1.249	1.00
60_R	88_A	1.238	1.00
44_E	100_A	1.227	1.00
15_P	18_D	1.211	1.00
82_A	86_L	1.193	1.00
64_F	92_F	1.185	1.00
6_P	38_Q	1.158	1.00
35_G	38_Q	1.155	1.00
36_Y	59_L	1.141	1.00
36_Y	62_Q	1.115	1.00
77_R	80_Q	1.099	1.00
76_L	85_A	1.088	1.00
14_A	17_L	1.081	1.00
2_V	20_L	1.077	1.00
8_D	12_A	1.077	1.00
58_V	66_M	1.074	1.00
84_A	87_A	1.055	1.00
67_R	89_L	1.051	1.00
43_R	72_D	1.048	1.00
83_E	86_L	1.043	1.00
8_D	38_Q	1.042	1.00
22_L	53_R	1.032	1.00
16_D	19_R	1.024	1.00
54_A	71_F	1.012	1.00
30_F	59_L	1.007	1.00
68_R	97_Q	1.003	1.00
27_F	66_M	1.002	1.00
68_R	99_A	0.990	1.00
22_L	73_A	0.988	1.00
52_L	71_F	0.988	1.00
4_L	8_D	0.984	1.00
39_A	52_L	0.970	1.00
4_L	10_P	0.966	1.00
64_F	91_D	0.964	1.00
63_L	76_L	0.961	1.00
59_L	77_R	0.954	1.00
85_A	89_L	0.948	1.00
86_L	90_A	0.901	1.00
81_D	84_A	0.896	1.00
18_D	21_A	0.895	1.00
30_F	62_Q	0.895	1.00
78_D	81_D	0.877	1.00
94_V	102_G	0.874	1.00
83_E	87_A	0.870	1.00
60_R	80_Q	0.866	1.00
25_L	39_A	0.861	1.00
81_D	85_A	0.859	1.00
7_D	38_Q	0.820	1.00
40_R	69_C	0.813	1.00
9_D	38_Q	0.810	1.00
6_P	35_G	0.807	1.00
17_L	20_L	0.807	1.00
35_G	71_F	0.797	1.00
84_A	88_A	0.793	1.00
58_V	74_F	0.785	1.00
2_V	13_L	0.781	1.00
95_V	103_P	0.772	1.00
98_P	102_G	0.764	1.00
24_A	75_E	0.764	1.00
62_Q	66_M	0.762	1.00
55_V	75_E	0.759	1.00
95_V	102_G	0.752	1.00
41_L	46_Y	0.752	1.00
80_Q	85_A	0.752	1.00
23_I	42_L	0.726	1.00
86_L	89_L	0.715	1.00
98_P	103_P	0.711	1.00
79_D	83_E	0.711	1.00
27_F	71_F	0.709	1.00
79_D	85_A	0.699	1.00
64_F	67_R	0.691	1.00
23_I	52_L	0.690	1.00
39_A	71_F	0.685	1.00
30_F	57_D	0.679	1.00
68_R	95_V	0.673	1.00
36_Y	57_D	0.667	1.00
63_L	67_R	0.658	1.00
38_Q	41_L	0.657	1.00
67_R	74_F	0.657	1.00
85_A	88_A	0.654	1.00
13_L	46_Y	0.653	1.00
63_L	81_D	0.641	1.00
63_L	89_L	0.636	1.00
80_Q	84_A	0.636	1.00
44_E	69_C	0.632	1.00
31_T	59_L	0.630	1.00
30_F	66_M	0.624	1.00
60_R	63_L	0.621	1.00
53_R	75_E	0.619	1.00
95_V	99_A	0.608	0.99
76_L	82_A	0.603	0.99
98_P	105_P	0.602	0.99
95_V	101_D	0.588	0.99
14_A	18_D	0.585	0.99
3_R	6_P	0.581	0.99
97_Q	101_D	0.576	0.99
20_L	23_I	0.575	0.99
13_L	20_L	0.574	0.99
102_G	105_P	0.566	0.99
94_V	98_P	0.565	0.99
10_P	46_Y	0.563	0.99
64_F	68_R	0.560	0.99
32_D	59_L	0.560	0.99
63_L	66_M	0.558	0.99
15_P	19_R	0.557	0.99
18_D	49_K	0.551	0.99
63_L	68_R	0.551	0.99
100_A	103_P	0.546	0.99
60_R	87_A	0.543	0.99
17_L	48_Y	0.539	0.99
37_S	61_D	0.537	0.99
43_R	47_G	0.536	0.99
64_F	89_L	0.531	0.99
28_P	35_G	0.531	0.99
37_S	65_F	0.523	0.98
87_A	91_D	0.517	0.98
94_V	97_Q	0.515	0.98
12_A	15_P	0.515	0.98
63_L	84_A	0.515	0.98
59_L	65_F	0.505	0.98
58_V	76_L	0.502	0.98
37_S	41_L	0.502	0.98
67_R	102_G	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
3inpA	6	0.8972	79.2	0.877	Contact Map
3ctlA	4	0.9065	77.8	0.879	Contact Map
4nu7A	5	0.9346	76.7	0.88	Contact Map
1h1yA	2	0.9065	76.5	0.88	Contact Map
1tqxA	2	0.9065	75.2	0.882	Contact Map
3ceuA	1	0.9439	72.2	0.884	Contact Map
1tqjA	4	0.8505	70	0.886	Contact Map
1rpxA	4	0.9159	66.5	0.889	Contact Map
4r9xA	2	0.8224	64.4	0.89	Contact Map
4ldaA	3	0.9252	63.7	0.891	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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