AntA - PFAM28P - GREMLIN Contacts

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AntA - AntA/AntB antirepressor

PFAM:	PF08346	Sequences: VSARELHEFLEVKTDFSDWIKDRIEEYGFVENEDFISFLKKNSGGGRPSKDYALTLDMAKELAMVERN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (68)
Sequences:	4011 (3282)
Seq/√Len:	398.0
META:	0.818

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_D	18_D	3.877	1.00
16_F	52_Y	2.667	1.00
14_T	22_D	2.663	1.00
29_F	58_M	2.393	1.00
26_E	67_R	2.375	1.00
30_V	33_E	2.002	1.00
3_A	16_F	1.827	1.00
2_S	5_E	1.782	1.00
23_R	66_E	1.689	1.00
27_Y	65_V	1.688	1.00
20_I	24_I	1.623	1.00
39_L	43_S	1.615	1.00
3_A	54_L	1.559	1.00
39_L	42_N	1.522	1.00
14_T	18_D	1.403	1.00
44_G	47_R	1.379	1.00
44_G	48_P	1.370	1.00
27_Y	61_E	1.350	1.00
27_Y	58_M	1.324	1.00
36_I	53_A	1.323	1.00
58_M	62_L	1.287	1.00
2_S	53_A	1.168	1.00
54_L	58_M	1.165	1.00
42_N	46_G	1.135	1.00
3_A	52_Y	1.133	1.00
15_D	21_K	1.122	1.00
9_F	63_A	1.087	1.00
41_K	44_G	1.084	1.00
23_R	26_E	1.079	1.00
20_I	52_Y	1.074	1.00
43_S	46_G	1.052	1.00
43_S	48_P	1.052	1.00
40_K	43_S	1.024	1.00
42_N	45_G	1.022	1.00
17_S	21_K	1.009	1.00
37_S	50_K	1.004	1.00
2_S	51_D	0.993	1.00
37_S	42_N	0.993	1.00
5_E	9_F	0.972	1.00
17_S	22_D	0.963	1.00
37_S	47_R	0.963	1.00
24_I	58_M	0.950	1.00
32_N	36_I	0.931	1.00
54_L	62_L	0.929	1.00
43_S	47_R	0.925	1.00
57_D	61_E	0.918	1.00
18_D	22_D	0.903	1.00
7_H	12_V	0.886	1.00
46_G	49_S	0.858	1.00
20_I	54_L	0.855	1.00
61_E	65_V	0.838	1.00
42_N	47_R	0.831	1.00
57_D	60_K	0.829	1.00
40_K	44_G	0.825	1.00
45_G	49_S	0.821	1.00
14_T	17_S	0.796	1.00
41_K	48_P	0.790	1.00
12_V	66_E	0.777	1.00
4_R	16_F	0.761	1.00
6_L	54_L	0.758	1.00
41_K	45_G	0.750	1.00
12_V	15_D	0.749	1.00
56_L	60_K	0.745	1.00
38_F	47_R	0.732	1.00
6_L	63_A	0.727	1.00
39_L	44_G	0.722	1.00
37_S	45_G	0.706	1.00
59_A	63_A	0.699	1.00
22_D	25_E	0.682	0.99
53_A	63_A	0.682	0.99
40_K	45_G	0.679	0.99
38_F	53_A	0.669	0.99
5_E	8_E	0.667	0.99
24_I	27_Y	0.658	0.99
23_R	62_L	0.636	0.99
37_S	48_P	0.634	0.99
53_A	56_L	0.631	0.99
38_F	41_K	0.631	0.99
37_S	44_G	0.625	0.99
4_R	51_D	0.616	0.99
23_R	27_Y	0.607	0.99
18_D	21_K	0.606	0.99
41_K	47_R	0.603	0.99
20_I	25_E	0.602	0.99
15_D	22_D	0.600	0.99
24_I	29_F	0.597	0.99
38_F	42_N	0.592	0.99
62_L	65_V	0.591	0.99
17_S	50_K	0.591	0.99
65_V	68_N	0.589	0.98
55_T	58_M	0.574	0.98
39_L	46_G	0.570	0.98
28_G	61_E	0.559	0.98
31_E	37_S	0.554	0.98
18_D	40_K	0.548	0.98
6_L	10_L	0.532	0.97
18_D	39_L	0.524	0.97
3_A	20_I	0.514	0.96
5_E	56_L	0.510	0.96
37_S	40_K	0.503	0.96
33_E	36_I	0.501	0.96
60_K	64_M	0.500	0.96

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
3bbnI	1	0.9559	23.3	0.853	Contact Map
5aj3I	1	0.9412	14.7	0.865	Contact Map
4tp8I	1	0.9412	14.6	0.866	Contact Map
2qlzA	2	0.8676	13.6	0.868	Contact Map
4rb5I	1	0.9412	12.3	0.87	Contact Map
2btoA	4	0.6765	9.5	0.876	Contact Map
3zeyK	1	0.8824	7.3	0.883	Contact Map
4w23Q	1	0.8676	7	0.884	Contact Map
4bpeI	1	0.8676	6.8	0.884	Contact Map
3hrzD	1	0.4412	6.6	0.885	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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