DUF4096 - PFAM28P - GREMLIN Contacts

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DUF4096 - Putative transposase of IS4/5 family (DUF4096)

PFAM:	PF13340	Sequences: LTDEQWALIEPLLPPPKPRPGRPRKVDLREVLNAILYVLRTGCPWRDLPEDFGPWSTVYRRFRRWRRDGVWERIH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (74)
Sequences:	55458 (23515)
Seq/√Len:	2733.6
META:	0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_Y	63_R	3.666	1.00
41_T	47_D	3.391	1.00
37_Y	43_C	2.825	1.00
41_T	44_P	2.680	1.00
28_L	61_R	2.235	1.00
46_R	55_W	2.232	1.00
56_S	60_R	2.223	1.00
63_R	67_R	2.205	1.00
44_P	47_D	2.061	1.00
40_R	44_P	1.843	1.00
24_R	28_L	1.795	1.00
3_D	29_R	1.659	1.00
48_L	58_V	1.551	1.00
60_R	64_R	1.520	1.00
55_W	59_Y	1.516	1.00
2_T	5_Q	1.470	1.00
56_S	59_Y	1.439	1.00
62_F	66_R	1.426	1.00
38_V	43_C	1.373	1.00
40_R	47_D	1.371	1.00
53_G	58_V	1.350	1.00
54_P	57_T	1.340	1.00
63_R	66_R	1.331	1.00
29_R	33_N	1.299	1.00
34_A	58_V	1.295	1.00
16_P	19_R	1.252	1.00
27_D	30_E	1.223	1.00
64_R	68_D	1.210	1.00
22_R	25_K	1.199	1.00
7_A	10_E	1.192	1.00
1_L	5_Q	1.170	1.00
13_L	28_L	1.135	1.00
32_L	71_W	1.044	1.00
61_R	64_R	1.034	1.00
34_A	53_G	1.032	1.00
57_T	60_R	1.019	1.00
69_G	72_E	0.972	1.00
60_R	63_R	0.971	1.00
9_I	32_L	0.944	1.00
32_L	36_L	0.938	1.00
46_R	56_S	0.937	1.00
26_V	57_T	0.931	1.00
31_V	35_I	0.926	1.00
10_E	14_P	0.921	1.00
26_V	31_V	0.904	1.00
6_W	29_R	0.891	1.00
17_K	20_P	0.865	1.00
3_D	7_A	0.856	1.00
70_V	73_R	0.847	1.00
61_R	65_W	0.843	1.00
8_L	11_P	0.837	1.00
16_P	20_P	0.822	1.00
62_F	71_W	0.811	1.00
37_Y	49_P	0.799	1.00
33_N	52_F	0.797	1.00
26_V	54_P	0.793	1.00
38_V	48_L	0.793	1.00
16_P	28_L	0.779	1.00
54_P	60_R	0.767	1.00
4_E	8_L	0.748	1.00
70_V	74_I	0.744	1.00
7_A	11_P	0.732	1.00
30_E	33_N	0.728	1.00
55_W	63_R	0.723	1.00
34_A	52_F	0.722	1.00
30_E	53_G	0.716	1.00
38_V	41_T	0.704	1.00
66_R	71_W	0.694	1.00
16_P	23_P	0.690	1.00
32_L	74_I	0.690	1.00
9_I	74_I	0.684	1.00
31_V	57_T	0.683	1.00
56_S	63_R	0.677	1.00
1_L	32_L	0.675	1.00
31_V	61_R	0.668	1.00
4_E	7_A	0.658	1.00
5_Q	9_I	0.648	1.00
57_T	61_R	0.646	1.00
20_P	23_P	0.638	1.00
15_P	18_P	0.632	1.00
3_D	6_W	0.626	1.00
50_E	53_G	0.623	1.00
28_L	65_W	0.605	1.00
28_L	31_V	0.594	1.00
47_D	50_E	0.585	1.00
24_R	61_R	0.576	1.00
49_P	52_F	0.575	1.00
18_P	24_R	0.571	1.00
5_Q	8_L	0.570	1.00
20_P	24_R	0.567	1.00
69_G	73_R	0.566	1.00
13_L	70_V	0.563	1.00
10_E	28_L	0.560	1.00
12_L	73_R	0.553	1.00
16_P	24_R	0.549	1.00
8_L	12_L	0.547	1.00
25_K	30_E	0.546	1.00
34_A	48_L	0.536	1.00
66_R	72_E	0.535	1.00
14_P	70_V	0.519	1.00
29_R	34_A	0.517	1.00
25_K	31_V	0.515	1.00
65_W	68_D	0.515	1.00
35_I	62_F	0.507	1.00
37_Y	52_F	0.507	1.00
16_P	22_R	0.505	1.00
14_P	17_K	0.504	1.00
33_N	51_D	0.503	1.00
43_C	48_L	0.503	1.00
55_W	58_V	0.503	1.00
26_V	53_G	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
4bqqA	2	0.52	34.3	0.834	Contact Map
4ch7A	1	0.5733	33.2	0.836	Contact Map
2optA	2	0.6933	31.5	0.838	Contact Map
2fe3A	2	0.9067	24.2	0.847	Contact Map
1jkoC	1	0.6	24.2	0.847	Contact Map
1ji8A	1	0.6933	15.4	0.86	Contact Map
3mwmA	2	0.6933	13.6	0.863	Contact Map
2m8eA	1	0.7467	13.4	0.863	Contact Map
3or1C	1	0.6933	12.7	0.865	Contact Map
2g7gA	2	0.64	12.6	0.865	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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