TnpB_IS66 - PFAM28P - GREMLIN Contacts

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TnpB_IS66 - IS66 Orf2 like protein

PFAM:	PF05717	Sequences: KRIYLATGPTDMRKGFDGLAALVREVLGLDPFSGHLFVFRNRRRDRIKILYWDGDGFWLWYKRLEKGRFRWPRDAGDGVVELTAAQLALLLEGIDLRRVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	100 (98)
Sequences:	32255 (15558)
Seq/√Len:	1571.6
META:	0.96

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_K	18_G	3.359	1.00
40_R	71_W	2.521	1.00
17_D	63_R	2.435	1.00
51_Y	60_W	2.359	1.00
83_T	86_Q	2.351	1.00
46_R	61_Y	2.331	1.00
14_K	22_L	2.322	1.00
16_F	61_Y	2.289	1.00
40_R	44_R	2.260	1.00
21_A	25_E	2.198	1.00
36_L	49_I	2.030	1.00
84_A	88_A	1.990	1.00
29_L	79_V	1.933	1.00
51_Y	58_W	1.921	1.00
64_L	69_F	1.879	1.00
4_Y	35_H	1.683	1.00
41_N	45_D	1.681	1.00
10_T	22_L	1.532	1.00
9_P	42_R	1.514	1.00
23_V	37_F	1.479	1.00
38_V	49_I	1.472	1.00
48_K	61_Y	1.453	1.00
70_R	95_D	1.448	1.00
88_A	92_E	1.433	1.00
55_D	62_K	1.432	1.00
29_L	35_H	1.402	1.00
43_R	46_R	1.397	1.00
46_R	63_R	1.390	1.00
56_G	62_K	1.367	1.00
85_A	92_E	1.363	1.00
12_M	41_N	1.342	1.00
12_M	46_R	1.322	1.00
22_L	26_V	1.277	1.00
53_D	62_K	1.261	1.00
10_T	19_L	1.260	1.00
16_F	57_F	1.253	1.00
58_W	62_K	1.253	1.00
24_R	30_D	1.252	1.00
85_A	89_L	1.228	1.00
6_A	10_T	1.225	1.00
20_A	57_F	1.182	1.00
89_L	94_I	1.157	1.00
50_L	59_L	1.110	1.00
50_L	57_F	1.086	1.00
74_D	77_D	1.085	1.00
6_A	27_L	1.083	1.00
24_R	32_F	1.069	1.00
52_W	65_E	1.065	1.00
31_P	57_F	1.057	1.00
3_I	36_L	1.048	1.00
23_V	27_L	1.034	1.00
21_A	24_R	1.032	1.00
20_A	50_L	1.027	1.00
49_I	60_W	1.004	1.00
2_R	35_H	1.001	1.00
40_R	47_I	0.956	1.00
20_A	31_P	0.945	1.00
29_L	33_S	0.932	1.00
52_W	57_F	0.910	1.00
6_A	22_L	0.898	1.00
3_I	38_V	0.895	1.00
16_F	59_L	0.893	1.00
12_M	48_K	0.886	1.00
87_L	91_L	0.886	1.00
30_D	33_S	0.883	1.00
70_R	97_R	0.867	1.00
23_V	50_L	0.856	1.00
2_R	29_L	0.850	1.00
8_G	26_V	0.847	1.00
36_L	51_Y	0.843	1.00
4_Y	29_L	0.828	1.00
49_I	87_L	0.828	1.00
95_D	98_R	0.823	1.00
29_L	37_F	0.814	1.00
23_V	26_V	0.812	1.00
85_A	88_A	0.805	1.00
2_R	81_E	0.798	1.00
11_D	14_K	0.784	1.00
15_G	61_Y	0.780	1.00
44_R	68_R	0.763	1.00
70_R	96_L	0.754	1.00
95_D	99_V	0.746	1.00
32_F	57_F	0.745	1.00
20_A	24_R	0.742	1.00
23_V	39_F	0.727	1.00
38_V	87_L	0.721	1.00
26_V	35_H	0.716	1.00
9_P	41_N	0.708	1.00
75_A	78_G	0.706	1.00
53_D	56_G	0.706	1.00
5_L	40_R	0.705	1.00
52_W	55_D	0.704	1.00
44_R	71_W	0.698	1.00
7_T	80_V	0.688	1.00
92_E	99_V	0.685	1.00
15_G	59_L	0.672	1.00
83_T	88_A	0.665	1.00
44_R	73_R	0.659	1.00
33_S	37_F	0.655	1.00
27_L	79_V	0.647	1.00
89_L	92_E	0.642	1.00
6_A	26_V	0.641	1.00
86_Q	89_L	0.641	1.00
12_M	15_G	0.635	1.00
40_R	90_L	0.627	1.00
26_V	29_L	0.625	1.00
5_L	38_V	0.622	1.00
32_F	52_W	0.620	1.00
17_D	24_R	0.604	1.00
24_R	31_P	0.603	1.00
8_G	78_G	0.603	1.00
9_P	44_R	0.602	1.00
23_V	29_L	0.600	1.00
12_M	59_L	0.598	1.00
10_T	14_K	0.593	1.00
27_L	31_P	0.583	1.00
47_I	69_F	0.581	1.00
14_K	21_A	0.575	1.00
14_K	25_E	0.574	1.00
82_L	90_L	0.573	1.00
58_W	91_L	0.573	1.00
55_D	58_W	0.572	1.00
18_G	22_L	0.570	1.00
92_E	96_L	0.565	1.00
16_F	20_A	0.561	1.00
36_L	60_W	0.561	1.00
74_D	78_G	0.557	1.00
12_M	61_Y	0.553	1.00
80_V	97_R	0.549	1.00
62_K	65_E	0.544	1.00
86_Q	94_I	0.544	1.00
20_A	23_V	0.542	1.00
17_D	46_R	0.539	1.00
4_Y	7_T	0.539	1.00
53_D	58_W	0.533	1.00
70_R	86_Q	0.530	1.00
15_G	18_G	0.530	1.00
28_G	78_G	0.526	1.00
80_V	83_T	0.524	1.00
84_A	92_E	0.520	1.00
5_L	82_L	0.519	1.00
96_L	99_V	0.518	1.00
80_V	84_A	0.516	1.00
19_L	48_K	0.506	1.00
43_R	68_R	0.505	1.00
70_R	98_R	0.501	1.00
54_G	92_E	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
3wapA	2	0.63	34.8	0.883	Contact Map
3wamA	2	0.63	31.8	0.885	Contact Map
3vtwA	1	0.63	23.6	0.892	Contact Map
3vtvA	1	0.63	21.7	0.894	Contact Map
3h9dA	2	0.64	21	0.894	Contact Map
3w1yA	2	0.62	20.2	0.895	Contact Map
3ruiB	1	0.64	18.7	0.897	Contact Map
3m95A	1	0.63	17.1	0.899	Contact Map
2zjdA	1	0.66	13.9	0.903	Contact Map
2r2qA	1	0.66	12.6	0.904	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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