DEF1 - BACSU - GREMLIN Contacts

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DEF1 - Peptide deformylase 1

UniProt:	P94462	Sequences: MAVKKVVTHPAEVLETPAETVTVFDKKLKKLLDDMYDTMLEMDGVGLAAPQIGILKRAAVVEIGDDRGRIDLVNPEILEKSGEQTGIEGCLSFPNVYGDVTRADYVKVRAFNRQGKPFILEARGFLARAVQHEMDHLDGVLFTSKISKYYTEDELADMEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (149)
Sequences:	6110 (3852)
Seq/√Len:	315.6

ECOLI - DEF
BACSU - DEF1 DEF2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_R	138_D	3.466	1.00
110_A	118_F	2.843	1.00
109_R	117_P	2.471	1.00
59_A	134_M	2.466	1.00
112_N	116_K	2.427	1.00
36_Y	69_R	2.324	1.00
76_E	109_R	2.319	1.00
107_K	119_I	2.232	1.00
15_E	144_S	2.202	1.00
109_R	119_I	2.191	1.00
122_A	130_V	1.953	1.00
32_L	71_D	1.908	1.00
86_G	128_R	1.886	1.00
111_F	117_P	1.847	1.00
50_P	55_L	1.847	1.00
33_D	113_R	1.813	1.00
24_F	28_L	1.802	1.00
40_L	62_E	1.778	1.00
7_V	13_V	1.707	1.00
78_L	109_R	1.698	1.00
85_T	101_T	1.664	1.00
105_Y	121_E	1.658	1.00
103_A	131_Q	1.651	1.00
107_K	121_E	1.634	1.00
18_A	55_L	1.610	1.00
18_A	50_P	1.608	1.00
6_V	42_M	1.579	1.00
71_D	113_R	1.576	1.00
32_L	113_R	1.551	1.00
85_T	99_D	1.539	1.00
87_I	99_D	1.537	1.00
45_V	125_F	1.535	1.00
112_N	118_F	1.511	1.00
7_V	11_A	1.508	1.00
105_Y	123_R	1.503	1.00
80_K	103_A	1.468	1.00
31_L	54_I	1.467	1.00
4_K	52_I	1.446	1.00
81_S	105_Y	1.444	1.00
40_L	69_R	1.440	1.00
79_E	107_K	1.431	1.00
7_V	53_G	1.424	1.00
122_A	126_L	1.414	1.00
63_I	129_A	1.385	1.00
59_A	72_L	1.366	1.00
134_M	138_D	1.353	1.00
29_K	114_Q	1.341	1.00
29_K	113_R	1.326	1.00
17_P	20_T	1.316	1.00
104_D	124_G	1.309	1.00
24_F	111_F	1.309	1.00
32_L	58_A	1.291	1.00
20_T	57_R	1.284	1.00
4_K	34_D	1.280	1.00
32_L	73_V	1.274	1.00
70_I	120_L	1.260	1.00
30_K	34_D	1.258	1.00
8_T	94_P	1.257	1.00
31_L	58_A	1.252	1.00
72_L	110_A	1.246	1.00
16_T	55_L	1.214	1.00
26_K	29_K	1.206	1.00
25_D	28_L	1.174	1.00
72_L	130_V	1.170	1.00
31_L	52_I	1.170	1.00
20_T	76_E	1.150	1.00
98_G	142_F	1.148	1.00
34_D	38_T	1.146	1.00
19_E	55_L	1.138	1.00
140_V	145_K	1.135	1.00
36_Y	71_D	1.133	1.00
62_E	69_R	1.132	1.00
17_P	138_D	1.130	1.00
120_L	130_V	1.116	1.00
84_Q	103_A	1.080	1.00
32_L	36_Y	1.074	1.00
36_Y	40_L	1.069	1.00
13_V	55_L	1.053	1.00
58_A	73_V	1.027	1.00
36_Y	60_V	1.021	1.00
93_F	141_L	1.017	1.00
21_V	58_A	1.009	1.00
27_K	56_K	1.005	1.00
61_V	70_I	1.005	1.00
3_V	38_T	1.004	1.00
64_G	67_R	1.001	1.00
78_L	107_K	0.997	1.00
64_G	68_G	0.962	1.00
110_A	120_L	0.943	1.00
45_V	129_A	0.937	1.00
9_H	93_F	0.931	1.00
84_Q	101_T	0.926	1.00
72_L	118_F	0.925	1.00
125_F	129_A	0.920	1.00
13_V	53_G	0.916	1.00
147_S	150_Y	0.911	1.00
84_Q	104_D	0.907	1.00
18_A	57_R	0.907	1.00
101_T	147_S	0.902	1.00
78_L	119_I	0.897	1.00
79_E	82_G	0.879	1.00
135_D	145_K	0.878	1.00
126_L	130_V	0.870	1.00
75_P	137_L	0.869	1.00
9_H	143_T	0.868	1.00
135_D	140_V	0.866	1.00
38_T	52_I	0.863	1.00
77_I	80_K	0.860	1.00
111_F	115_G	0.846	1.00
97_Y	142_F	0.833	1.00
65_D	68_G	0.825	1.00
61_V	129_A	0.822	1.00
140_V	144_S	0.819	1.00
130_V	134_M	0.817	1.00
24_F	29_K	0.814	1.00
22_T	74_N	0.808	1.00
77_I	134_M	0.802	1.00
11_A	53_G	0.795	1.00
108_V	120_L	0.786	1.00
87_I	97_Y	0.786	1.00
70_I	126_L	0.784	1.00
83_E	101_T	0.782	1.00
4_K	54_I	0.781	1.00
28_L	58_A	0.777	1.00
9_H	141_L	0.769	0.99
33_D	37_D	0.765	0.99
106_V	122_A	0.760	0.99
120_L	126_L	0.759	0.99
3_V	34_D	0.747	0.99
96_V	142_F	0.746	0.99
17_P	57_R	0.739	0.99
108_V	130_V	0.734	0.99
72_L	108_V	0.733	0.99
4_K	30_K	0.731	0.99
29_K	32_L	0.730	0.99
19_E	22_T	0.729	0.99
98_G	146_I	0.729	0.99
3_V	41_E	0.726	0.99
45_V	63_I	0.725	0.99
63_I	125_F	0.724	0.99
28_L	56_K	0.723	0.99
63_I	126_L	0.720	0.99
9_H	15_E	0.717	0.99
147_S	151_T	0.712	0.99
104_D	123_R	0.708	0.99
3_V	37_D	0.706	0.99
34_D	37_D	0.698	0.99
89_G	97_Y	0.695	0.99
24_F	115_G	0.695	0.99
100_V	142_F	0.693	0.99
39_M	46_G	0.688	0.99
19_E	56_K	0.686	0.99
5_K	8_T	0.684	0.99
16_T	19_E	0.684	0.99
83_E	104_D	0.684	0.99
44_G	91_L	0.680	0.99
108_V	122_A	0.675	0.99
57_R	76_E	0.673	0.99
26_K	30_K	0.672	0.99
93_F	143_T	0.672	0.99
90_C	136_H	0.667	0.99
59_A	130_V	0.655	0.98
72_L	120_L	0.652	0.98
39_M	60_V	0.643	0.98
32_L	60_V	0.639	0.98
59_A	110_A	0.635	0.98
31_L	35_M	0.635	0.98
61_V	130_V	0.633	0.98
39_M	44_G	0.628	0.98
24_F	73_V	0.626	0.98
47_L	60_V	0.620	0.98
36_Y	39_M	0.620	0.98
23_V	26_K	0.619	0.98
30_K	33_D	0.619	0.98
116_K	119_I	0.616	0.98
28_L	31_L	0.614	0.97
77_I	103_A	0.613	0.97
39_M	42_M	0.607	0.97
73_V	111_F	0.604	0.97
77_I	106_V	0.602	0.97
35_M	47_L	0.596	0.97
61_V	126_L	0.596	0.97
38_T	41_E	0.588	0.97
9_H	96_V	0.587	0.97
84_Q	128_R	0.585	0.97
106_V	130_V	0.581	0.97
39_M	62_E	0.581	0.97
49_A	58_A	0.578	0.96
79_E	105_Y	0.577	0.96
22_T	25_D	0.577	0.96
51_Q	136_H	0.577	0.96
35_M	58_A	0.573	0.96
48_A	90_C	0.572	0.96
86_G	99_D	0.563	0.96
4_K	38_T	0.558	0.96
48_A	91_L	0.557	0.96
77_I	131_Q	0.556	0.96
15_E	141_L	0.548	0.95
60_V	71_D	0.546	0.95
61_V	72_L	0.540	0.95
146_I	150_Y	0.538	0.95
146_I	149_Y	0.538	0.95
15_E	143_T	0.530	0.94
12_E	16_T	0.529	0.94
81_S	84_Q	0.526	0.94
51_Q	90_C	0.526	0.94
35_M	91_L	0.524	0.94
142_F	146_I	0.524	0.94
18_A	59_A	0.524	0.94
61_V	110_A	0.522	0.94
39_M	45_V	0.522	0.94
108_V	134_M	0.521	0.94
78_L	81_S	0.521	0.94
33_D	71_D	0.521	0.94
9_H	151_T	0.520	0.94
46_G	133_E	0.518	0.94
17_P	140_V	0.518	0.94
13_V	16_T	0.515	0.93
9_H	146_I	0.514	0.93
110_A	122_A	0.510	0.93
78_L	117_P	0.509	0.93
31_L	34_D	0.507	0.93
13_V	18_A	0.506	0.93
98_G	147_S	0.500	0.92

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
3u04A	2	1	100	0.013	Contact Map
3e3uA	1	0.9938	100	0.027	Contact Map
1n5nA	1	0.9938	100	0.032	Contact Map
4e9aA	1	0.9812	100	0.034	Contact Map
1rl4A	1	0.9313	100	0.035	Contact Map
2w3tA	1	0.9938	100	0.039	Contact Map
3qu1A	2	0.9938	100	0.039	Contact Map
1xeoA	1	0.9938	100	0.04	Contact Map
4dr8A	1	0.9875	100	0.042	Contact Map
1y6hA	3	0.9938	100	0.044	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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