PDAD - HALSA - GREMLIN Contacts

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PDAD - Pyruvoyl-dependent arginine decarboxylase

UniProt:	Q9HNQ0	Sequences: MPRIRIAWGSGVAPTEMAAYDAALADANVHNYNLIRVSSVIPADATVSPVDTAPDLGPAGNTLTVVEARGQTAGPGQASAGLAWAPRDGAPGLFYEAADETTPDDVADRVTTGITAGMDVRDWDGVEPSVRTETVTADAGEHAAAVVIAAYGDSDPVFDQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (148)
Sequences:	267 (192)
Seq/√Len:	15.7

HALSA - PDAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_A	144_A	5.997	1.00
29_V	148_I	3.875	1.00
32_Y	63_L	3.623	1.00
21_D	121_R	2.395	0.93
127_E	130_V	2.228	0.90
83_A	114_I	2.157	0.89
108_D	112_T	2.152	0.88
88_D	124_D	2.140	0.88
72_T	136_T	2.075	0.87
9_G	27_A	2.053	0.86
19_A	71_Q	2.052	0.86
107_A	111_T	2.044	0.86
11_G	87_R	2.039	0.86
85_A	125_G	2.027	0.85
72_T	137_A	1.830	0.79
36_R	69_R	1.824	0.78
118_M	125_G	1.766	0.76
11_G	22_A	1.756	0.76
32_Y	54_P	1.745	0.75
46_T	125_G	1.729	0.74
79_S	107_A	1.722	0.74
114_I	126_V	1.720	0.74
20_Y	67_E	1.716	0.74
80_A	145_A	1.703	0.73
85_A	118_M	1.702	0.73
6_I	18_A	1.691	0.73
4_I	149_A	1.678	0.72
111_T	115_T	1.536	0.65
127_E	137_A	1.509	0.64
81_G	131_R	1.500	0.63
16_E	44_D	1.471	0.62
28_N	50_V	1.452	0.61
116_A	119_D	1.445	0.60
75_P	140_G	1.440	0.60
9_G	48_S	1.409	0.58
79_S	99_D	1.394	0.57
26_D	29_V	1.385	0.57
20_Y	65_V	1.368	0.56
125_G	137_A	1.368	0.56
45_A	67_E	1.350	0.55
45_A	141_E	1.343	0.54
6_I	87_R	1.331	0.54
94_F	149_A	1.297	0.52
130_V	133_E	1.287	0.51
99_D	102_T	1.273	0.50
74_G	77_Q	1.272	0.50
108_D	111_T	1.253	0.49
103_P	134_T	1.222	0.47
130_V	135_V	1.213	0.47
47_V	50_V	1.197	0.46
112_T	116_A	1.185	0.45
122_D	130_V	1.176	0.45
81_G	132_T	1.172	0.45
22_A	121_R	1.163	0.44
111_T	130_V	1.141	0.43
41_I	94_F	1.127	0.42
83_A	110_V	1.123	0.42
63_L	82_L	1.120	0.42
4_I	47_V	1.112	0.41
112_T	115_T	1.111	0.41
21_D	31_N	1.104	0.41
127_E	131_R	1.100	0.41
27_A	37_V	1.098	0.40
71_Q	144_A	1.097	0.40
14_P	109_R	1.077	0.39
93_L	150_A	1.070	0.39
15_T	110_V	1.063	0.38
124_D	127_E	1.049	0.38
36_R	68_A	1.032	0.37
76_G	139_A	1.028	0.37
90_A	139_A	1.021	0.36
12_V	70_G	1.013	0.36
13_A	17_M	1.011	0.36
133_E	137_A	1.010	0.36
127_E	133_E	0.989	0.35
3_R	52_T	0.987	0.34
140_G	143_A	0.984	0.34
46_T	124_D	0.983	0.34
74_G	111_T	0.982	0.34
4_I	41_I	0.980	0.34
124_D	136_T	0.956	0.33
36_R	67_E	0.953	0.33
107_A	119_D	0.953	0.33
76_G	137_A	0.948	0.32
8_W	119_D	0.947	0.32
122_D	129_S	0.946	0.32
28_N	89_G	0.944	0.32
122_D	133_E	0.938	0.32
15_T	18_A	0.937	0.32
71_Q	138_D	0.937	0.32
32_Y	64_T	0.935	0.32
44_D	139_A	0.929	0.31
79_S	137_A	0.927	0.31
103_P	107_A	0.918	0.31
111_T	119_D	0.909	0.31
68_A	133_E	0.904	0.30
117_G	121_R	0.900	0.30
66_V	146_V	0.887	0.29
66_V	95_Y	0.884	0.29
26_D	100_E	0.883	0.29
31_N	121_R	0.882	0.29
30_H	45_A	0.872	0.29
97_A	114_I	0.863	0.28
69_R	144_A	0.855	0.28
13_A	22_A	0.850	0.28
95_Y	113_G	0.847	0.28
130_V	134_T	0.847	0.28
104_D	140_G	0.845	0.27
135_V	149_A	0.837	0.27
83_A	144_A	0.837	0.27
6_I	41_I	0.834	0.27
66_V	150_A	0.830	0.27
66_V	144_A	0.827	0.27
110_V	117_G	0.826	0.27
72_T	147_V	0.823	0.26
44_D	56_L	0.818	0.26
30_H	69_R	0.812	0.26
127_E	132_T	0.802	0.26
104_D	108_D	0.802	0.26
59_A	91_P	0.801	0.26
79_S	89_G	0.800	0.25
43_A	95_Y	0.795	0.25
34_L	146_V	0.789	0.25
35_I	45_A	0.784	0.25
18_A	109_R	0.780	0.25
105_D	109_R	0.771	0.24
74_G	100_E	0.770	0.24
82_L	99_D	0.764	0.24
127_E	136_T	0.747	0.23
78_A	139_A	0.747	0.23
65_V	117_G	0.746	0.23
95_Y	142_H	0.745	0.23
22_A	65_V	0.740	0.23
126_V	132_T	0.737	0.23
57_G	63_L	0.729	0.22
88_D	136_T	0.729	0.22
54_P	107_A	0.725	0.22
29_V	52_T	0.714	0.22
70_G	99_D	0.714	0.22
81_G	118_M	0.712	0.22
58_P	97_A	0.712	0.22
123_W	127_E	0.701	0.21
48_S	56_L	0.697	0.21
6_I	103_P	0.694	0.21
83_A	128_P	0.691	0.21
101_T	111_T	0.684	0.21
66_V	149_A	0.675	0.20
30_H	117_G	0.675	0.20
40_V	43_A	0.674	0.20
122_D	137_A	0.672	0.20
125_G	128_P	0.672	0.20
91_P	120_V	0.670	0.20
31_N	65_V	0.664	0.20
41_I	59_A	0.663	0.20
6_I	84_W	0.662	0.20
13_A	93_L	0.661	0.20
12_V	75_P	0.659	0.20
108_D	119_D	0.658	0.20
14_P	97_A	0.649	0.19
72_T	143_A	0.648	0.19
81_G	130_V	0.647	0.19
17_M	20_Y	0.644	0.19
102_T	106_V	0.643	0.19
85_A	114_I	0.642	0.19
80_A	88_D	0.641	0.19
45_A	121_R	0.639	0.19
67_E	98_A	0.637	0.19
90_A	106_V	0.636	0.19
21_D	25_A	0.628	0.19
11_G	132_T	0.625	0.19
3_R	49_P	0.623	0.19
29_V	65_V	0.617	0.18
79_S	82_L	0.616	0.18
49_P	140_G	0.616	0.18
19_A	35_I	0.614	0.18
22_A	29_V	0.613	0.18
30_H	151_Y	0.607	0.18
44_D	129_S	0.606	0.18
93_L	148_I	0.604	0.18
9_G	146_V	0.604	0.18
65_V	151_Y	0.599	0.18
37_V	72_T	0.598	0.18
61_N	148_I	0.594	0.18
144_A	149_A	0.592	0.17
141_E	145_A	0.586	0.17
16_E	71_Q	0.580	0.17
57_G	87_R	0.578	0.17
45_A	87_R	0.577	0.17
6_I	81_G	0.569	0.17
7_A	93_L	0.566	0.17
82_L	135_V	0.563	0.17
66_V	140_G	0.560	0.16
135_V	138_D	0.560	0.16
81_G	117_G	0.558	0.16
45_A	115_T	0.557	0.16
10_S	103_P	0.549	0.16
31_N	117_G	0.547	0.16
80_A	146_V	0.546	0.16
36_R	151_Y	0.545	0.16
40_V	63_L	0.542	0.16
68_A	143_A	0.540	0.16
68_A	81_G	0.538	0.16
17_M	85_A	0.536	0.16
15_T	114_I	0.536	0.16
58_P	106_V	0.532	0.16
28_N	32_Y	0.532	0.16
123_W	133_E	0.532	0.16
32_Y	122_D	0.531	0.16
86_P	90_A	0.528	0.15
81_G	110_V	0.523	0.15
122_D	126_V	0.523	0.15
126_V	133_E	0.522	0.15
90_A	123_W	0.521	0.15
63_L	91_P	0.521	0.15
31_N	106_V	0.521	0.15
143_A	147_V	0.521	0.15
46_T	119_D	0.515	0.15
29_V	87_R	0.514	0.15
12_V	135_V	0.512	0.15
21_D	53_A	0.511	0.15
21_D	93_L	0.508	0.15
20_Y	62_T	0.500	0.15

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
1n2mA	3	0.925	100	0.224	Contact Map
1n13B	3	0.6687	100	0.497	Contact Map
1n13A	3	0.2375	99.6	0.74	Contact Map
1pyaB	3	0.8875	54.2	0.938	Contact Map
2ozlB	2	0.675	29.1	0.947	Contact Map
3komA	2	0.675	23.2	0.95	Contact Map
3ju3A	4	0.65	21.6	0.951	Contact Map
3hq1A	2	0.5062	18	0.952	Contact Map
1umdB	2	0.6687	17.1	0.953	Contact Map
3uk1A	2	0.6687	14.6	0.954	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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