PADC - BACSU - GREMLIN Contacts

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PADC - Phenolic acid decarboxylase PadC

UniProt:	O07006	Sequences: MENFIGSHMIYTYENGWEYEIYIKNDHTIDYRIHSGMVAGRWVRDQEVNIVKLTEGVYKVSWTEPTGTDVSLNFMPNEKRMHGIIFFPKWVHEHPEITVCYQNDHIDLMKESREKYETYPKYVVPEFAEITFLKNEGVDNEEVISKAPYEGMTDDIRAGRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	161 (142)
Sequences:	184 (69)
Seq/√Len:	5.8

BACSU - PADC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_I	29_I	5.148	0.99
7_S	135_N	4.804	0.98
14_E	129_E	4.467	0.96
49_N	125_P	3.265	0.83
29_I	48_V	2.458	0.61
94_H	97_I	2.393	0.58
21_I	70_V	2.096	0.48
75_M	125_P	2.094	0.48
12_T	15_N	2.023	0.46
9_M	21_I	2.011	0.45
70_V	85_I	1.865	0.40
122_Y	135_N	1.828	0.39
89_K	93_E	1.820	0.39
44_R	101_Y	1.784	0.37
115_K	119_Y	1.778	0.37
106_I	110_K	1.761	0.37
79_K	106_I	1.744	0.36
33_I	99_V	1.705	0.35
45_D	123_V	1.691	0.34
106_I	131_T	1.689	0.34
81_M	128_A	1.625	0.32
10_I	79_K	1.622	0.32
12_T	131_T	1.580	0.31
26_D	107_D	1.577	0.31
39_A	104_D	1.567	0.31
61_S	73_N	1.522	0.29
10_I	14_E	1.509	0.29
29_I	141_E	1.508	0.29
118_T	121_K	1.498	0.29
23_I	60_V	1.485	0.28
55_E	107_D	1.483	0.28
7_S	133_L	1.464	0.28
48_V	140_N	1.442	0.27
89_K	115_K	1.430	0.27
70_V	83_G	1.428	0.27
26_D	77_N	1.420	0.26
114_E	117_E	1.418	0.26
22_Y	113_R	1.382	0.25
53_L	124_V	1.381	0.25
122_Y	125_P	1.381	0.25
112_S	116_Y	1.380	0.25
47_E	96_E	1.374	0.25
110_K	139_D	1.363	0.25
18_E	72_L	1.362	0.25
57_V	123_V	1.329	0.24
97_I	116_Y	1.321	0.24
83_G	127_F	1.307	0.24
63_T	69_D	1.302	0.23
56_G	74_F	1.287	0.23
100_C	105_H	1.256	0.22
12_T	16_G	1.248	0.22
33_I	98_T	1.211	0.21
53_L	72_L	1.188	0.21
25_N	80_R	1.177	0.20
137_G	144_I	1.155	0.20
10_I	133_L	1.154	0.20
57_V	71_S	1.144	0.20
95_P	107_D	1.143	0.20
6_G	32_R	1.126	0.19
23_I	35_S	1.123	0.19
75_M	136_E	1.117	0.19
44_R	141_E	1.106	0.19
54_T	75_M	1.092	0.19
99_V	105_H	1.083	0.18
21_I	72_L	1.075	0.18
96_E	125_P	1.074	0.18
110_K	145_S	1.055	0.18
65_P	109_M	1.044	0.18
84_I	98_T	1.043	0.18
97_I	112_S	1.040	0.17
33_I	72_L	1.024	0.17
3_N	74_F	1.023	0.17
60_V	70_V	1.009	0.17
118_T	124_V	0.991	0.17
53_L	73_N	0.987	0.16
3_N	80_R	0.983	0.16
7_S	25_N	0.982	0.16
75_M	124_V	0.975	0.16
107_D	145_S	0.973	0.16
71_S	100_C	0.969	0.16
115_K	125_P	0.968	0.16
9_M	74_F	0.964	0.16
9_M	79_K	0.949	0.16
9_M	81_M	0.944	0.16
63_T	122_Y	0.930	0.15
93_E	128_A	0.919	0.15
20_E	67_G	0.918	0.15
48_V	121_K	0.905	0.15
29_I	44_R	0.902	0.15
70_V	133_L	0.896	0.15
15_N	126_E	0.895	0.15
65_P	102_Q	0.871	0.14
35_S	100_C	0.854	0.14
19_Y	33_I	0.853	0.14
54_T	91_V	0.845	0.14
50_I	144_I	0.844	0.14
102_Q	109_M	0.841	0.14
79_K	133_L	0.841	0.14
48_V	60_V	0.834	0.14
8_H	136_E	0.832	0.14
24_K	122_Y	0.831	0.14
4_F	9_M	0.829	0.14
80_R	110_K	0.827	0.14
37_M	112_S	0.790	0.13
140_N	143_V	0.782	0.13
4_F	111_E	0.782	0.13
93_E	129_E	0.780	0.13
91_V	98_T	0.779	0.13
9_M	130_I	0.779	0.13
95_P	140_N	0.774	0.13
27_H	129_E	0.772	0.13
22_Y	82_H	0.770	0.13
132_F	140_N	0.768	0.13
89_K	120_P	0.767	0.13
8_H	121_K	0.757	0.12
3_N	56_G	0.754	0.12
137_G	140_N	0.753	0.12
40_G	81_M	0.750	0.12
42_W	70_V	0.746	0.12
26_D	80_R	0.742	0.12
69_D	121_K	0.740	0.12
91_V	97_I	0.738	0.12
73_N	124_V	0.734	0.12
63_T	114_E	0.734	0.12
56_G	93_E	0.730	0.12
35_S	105_H	0.714	0.12
97_I	117_E	0.710	0.12
75_M	97_I	0.707	0.12
11_Y	40_G	0.707	0.12
63_T	121_K	0.707	0.12
20_E	34_H	0.703	0.12
93_E	107_D	0.702	0.12
89_K	114_E	0.698	0.12
38_V	65_P	0.697	0.12
53_L	78_E	0.696	0.12
40_G	92_H	0.693	0.12
9_M	56_G	0.692	0.12
38_V	109_M	0.669	0.11
46_Q	66_T	0.661	0.11
49_N	70_V	0.658	0.11
44_R	133_L	0.656	0.11
15_N	104_D	0.656	0.11
20_E	116_Y	0.651	0.11
7_S	77_N	0.647	0.11
72_L	81_M	0.646	0.11
70_V	119_Y	0.639	0.11
92_H	110_K	0.631	0.11
31_Y	36_G	0.625	0.11
107_D	111_E	0.624	0.11
56_G	108_L	0.621	0.11
49_N	56_G	0.619	0.11
92_H	100_C	0.618	0.11
44_R	58_Y	0.618	0.11
114_E	119_Y	0.618	0.11
54_T	145_S	0.614	0.10
101_Y	108_L	0.613	0.10
8_H	11_Y	0.610	0.10
18_E	118_T	0.608	0.10
8_H	132_F	0.607	0.10
96_E	129_E	0.606	0.10
7_S	61_S	0.602	0.10
33_I	74_F	0.599	0.10
132_F	136_E	0.595	0.10
94_H	115_K	0.591	0.10
15_N	101_Y	0.586	0.10
52_K	142_E	0.584	0.10
60_V	93_E	0.583	0.10
49_N	55_E	0.582	0.10
7_S	106_I	0.582	0.10
30_D	42_W	0.579	0.10
76_P	130_I	0.577	0.10
28_T	72_L	0.577	0.10
6_G	117_E	0.576	0.10
38_V	99_V	0.576	0.10
105_H	108_L	0.575	0.10
4_F	108_L	0.574	0.10
50_I	63_T	0.573	0.10
104_D	144_I	0.569	0.10
60_V	142_E	0.568	0.10
4_F	49_N	0.564	0.10
32_R	103_N	0.562	0.10
4_F	106_I	0.559	0.10
95_P	117_E	0.558	0.10
42_W	83_G	0.558	0.10
47_E	136_E	0.557	0.10
3_N	53_L	0.557	0.10
94_H	137_G	0.556	0.10
7_S	52_K	0.556	0.10
45_D	135_N	0.555	0.10
29_I	142_E	0.551	0.10
116_Y	125_P	0.551	0.10
78_E	110_K	0.551	0.10
66_T	87_F	0.547	0.10
24_K	42_W	0.540	0.10
5_I	97_I	0.539	0.10
6_G	22_Y	0.538	0.10
6_G	126_E	0.537	0.09
26_D	120_P	0.534	0.09
86_F	126_E	0.532	0.09
120_P	131_T	0.531	0.09
8_H	33_I	0.528	0.09
19_Y	34_H	0.525	0.09
59_K	127_F	0.525	0.09
25_N	122_Y	0.525	0.09
60_V	140_N	0.523	0.09
53_L	118_T	0.520	0.09
9_M	125_P	0.516	0.09
10_I	57_V	0.515	0.09
56_G	77_N	0.514	0.09
29_I	68_T	0.514	0.09
39_A	84_I	0.510	0.09
102_Q	143_V	0.508	0.09
84_I	123_V	0.500	0.09

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
4uu3A	2	0.9938	100	0.146	Contact Map
2w2aA	2	1	100	0.192	Contact Map
2p8gA	2	1	100	0.198	Contact Map
4q51A	2	0.8137	97.4	0.906	Contact Map
1ckmA	3	0.6708	33.6	0.96	Contact Map
3rtxA	2	0.3478	23.1	0.963	Contact Map
4k0mC	1	0.5155	6.4	0.971	Contact Map
3q12A	2	0.4969	5.8	0.972	Contact Map
1vw4P	1	0.0497	5.2	0.972	Contact Map
2kxtA	1	0.5963	5.2	0.972	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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