PDAB - BACSU - GREMLIN Contacts

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PDAB - Probable polysaccharide deacetylase PdaB

UniProt:	P50865	Sequences: MNHFYVWHIKRVKQLIIILIAAFAAASFFYIQRAVPLPVFSTDTGPKAIYKGETDSKDISLTFDISWGDERAEPILNTLKANGIKNATFFLSASWAERHPDTVARIVKDGHQIGSMGYAYKNYANLESSEIKKDMNRAQTAFEKLGVKDIQLLRPPTGQFNKNVLKVAKQYNYTVVHYSVNSQDWTNPGVEKIIDNVTKQVSGGDIILLHASDSAKQTEEALPDIIHQLKEKGLKNVTVGDLIANSDAKSAEVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (197)
Sequences:	6432 (4985)
Seq/√Len:	355.2

BACSU - PDAB PDAC YLXY YHEN PDAA YXKH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_K	109_D	4.081	1.00
82_N	227_H	3.857	1.00
105_R	109_D	3.121	1.00
112_Q	240_G	2.915	1.00
143_E	149_D	2.821	1.00
139_Q	173_Y	2.630	1.00
82_N	230_K	2.565	1.00
91_L	103_V	2.531	1.00
223_P	227_H	2.523	1.00
198_T	228_Q	2.474	1.00
133_K	137_R	2.413	1.00
77_N	105_R	2.368	1.00
81_A	223_P	2.212	1.00
194_I	224_D	2.142	1.00
183_Q	186_T	2.103	1.00
127_E	130_E	2.054	1.00
194_I	198_T	2.042	1.00
118_Y	137_R	2.026	1.00
158_G	178_Y	2.024	1.00
122_N	159_Q	1.991	1.00
228_Q	232_K	1.954	1.00
228_Q	231_E	1.904	1.00
58_D	235_K	1.886	1.00
73_E	105_R	1.873	1.00
128_S	163_N	1.847	1.00
91_L	106_I	1.830	1.00
201_V	229_L	1.828	1.00
84_I	226_I	1.810	1.00
107_V	148_K	1.806	1.00
82_N	223_P	1.800	1.00
97_E	141_A	1.692	1.00
93_A	118_Y	1.680	1.00
104_A	108_K	1.605	1.00
195_D	199_K	1.588	1.00
118_Y	141_A	1.585	1.00
136_N	171_Y	1.583	1.00
216_K	220_E	1.580	1.00
119_A	134_D	1.552	1.00
96_A	103_V	1.545	1.00
189_G	217_Q	1.528	1.00
155_P	177_H	1.519	1.00
124_A	159_Q	1.421	1.00
79_L	87_A	1.406	1.00
76_L	106_I	1.403	1.00
73_E	102_T	1.377	1.00
58_D	237_V	1.367	1.00
115_S	139_Q	1.348	1.00
90_F	152_L	1.334	1.00
82_N	226_I	1.325	1.00
141_A	145_L	1.324	1.00
59_I	229_L	1.323	1.00
116_M	120_Y	1.319	1.00
85_K	111_H	1.292	1.00
197_V	225_I	1.285	1.00
136_N	140_T	1.281	1.00
227_H	231_E	1.273	1.00
191_E	224_D	1.266	1.00
84_I	236_N	1.261	1.00
132_K	136_N	1.255	1.00
140_T	144_K	1.253	1.00
78_T	223_P	1.250	1.00
75_I	219_E	1.246	1.00
226_I	236_N	1.246	1.00
179_S	205_D	1.245	1.00
166_K	170_Q	1.243	1.00
57_K	234_L	1.238	1.00
77_N	81_A	1.238	1.00
78_T	82_N	1.236	1.00
126_L	130_E	1.234	1.00
224_D	228_Q	1.232	1.00
141_A	144_K	1.218	1.00
56_S	235_K	1.218	1.00
189_G	192_K	1.215	1.00
60_S	237_V	1.209	1.00
132_K	171_Y	1.205	1.00
132_K	170_Q	1.204	1.00
135_M	168_A	1.199	1.00
131_I	167_V	1.195	1.00
226_I	230_K	1.181	1.00
131_I	164_V	1.172	1.00
191_E	195_D	1.170	1.00
78_T	219_E	1.165	1.00
75_I	222_L	1.162	1.00
190_V	194_I	1.155	1.00
63_F	222_L	1.153	1.00
96_A	141_A	1.153	1.00
182_S	209_L	1.146	1.00
72_A	211_A	1.139	1.00
190_V	224_D	1.111	1.00
128_S	167_V	1.107	1.00
139_Q	149_D	1.099	1.00
122_N	157_T	1.090	1.00
77_N	109_D	1.090	1.00
237_V	241_D	1.089	1.00
176_V	239_V	1.085	1.00
121_K	134_D	1.083	1.00
74_P	220_E	1.050	1.00
105_R	108_K	1.039	1.00
122_N	125_N	1.025	1.00
74_P	78_T	1.022	1.00
222_L	226_I	1.021	1.00
167_V	170_Q	1.020	1.00
212_S	215_A	1.015	1.00
59_I	236_N	1.014	1.00
115_S	138_A	1.011	1.00
59_I	201_V	1.010	1.00
96_A	145_L	1.008	1.00
227_H	230_K	1.008	1.00
136_N	139_Q	1.008	1.00
107_V	146_G	0.988	1.00
128_S	132_K	0.985	1.00
132_K	167_V	0.981	1.00
168_A	175_V	0.977	1.00
113_I	146_G	0.977	1.00
137_R	140_T	0.970	1.00
181_N	185_W	0.970	1.00
103_V	145_L	0.961	1.00
135_M	153_L	0.953	1.00
142_F	146_G	0.947	1.00
78_T	226_I	0.941	1.00
65_I	211_A	0.940	1.00
130_E	133_K	0.935	1.00
138_A	141_A	0.934	1.00
117_G	121_K	0.925	1.00
67_W	211_A	0.923	1.00
123_Y	153_L	0.899	1.00
101_D	104_A	0.893	1.00
190_V	220_E	0.891	1.00
74_P	77_N	0.889	1.00
224_D	227_H	0.885	1.00
107_V	113_I	0.883	1.00
117_G	123_Y	0.876	1.00
118_Y	138_A	0.870	1.00
59_I	207_I	0.867	1.00
76_L	105_R	0.866	1.00
73_E	77_N	0.864	1.00
160_F	165_L	0.859	1.00
103_V	106_I	0.858	1.00
84_I	230_K	0.854	1.00
128_S	170_Q	0.847	1.00
71_R	74_P	0.842	1.00
80_K	105_R	0.842	1.00
62_T	206_I	0.839	1.00
153_L	168_A	0.835	1.00
180_V	205_D	0.834	1.00
209_L	225_I	0.833	1.00
140_T	143_E	0.831	1.00
92_S	117_G	0.827	1.00
88_T	112_Q	0.826	1.00
78_T	222_L	0.826	1.00
194_I	221_A	0.818	1.00
161_N	164_V	0.816	1.00
80_K	85_K	0.814	1.00
63_F	79_L	0.813	1.00
167_V	171_Y	0.805	1.00
83_G	230_K	0.800	1.00
182_S	196_N	0.791	1.00
162_K	166_K	0.791	1.00
76_L	111_H	0.790	1.00
112_Q	152_L	0.786	1.00
90_F	176_V	0.784	1.00
192_K	196_N	0.780	1.00
202_S	205_D	0.777	1.00
198_T	232_K	0.774	1.00
128_S	166_K	0.774	1.00
142_F	150_I	0.768	1.00
129_S	133_K	0.764	1.00
221_A	225_I	0.764	1.00
195_D	198_T	0.753	1.00
215_A	219_E	0.753	1.00
217_Q	220_E	0.745	1.00
194_I	228_Q	0.745	1.00
93_A	138_A	0.733	1.00
60_S	239_V	0.726	0.99
238_T	241_D	0.725	0.99
134_D	138_A	0.723	0.99
116_M	210_H	0.722	0.99
90_F	114_G	0.721	0.99
139_Q	150_I	0.719	0.99
63_F	75_I	0.716	0.99
237_V	242_L	0.706	0.99
181_N	186_T	0.701	0.99
96_A	100_P	0.699	0.99
119_A	137_R	0.697	0.99
76_L	109_D	0.695	0.99
106_I	113_I	0.690	0.99
62_T	154_R	0.688	0.99
160_F	164_V	0.687	0.99
197_V	207_I	0.685	0.99
188_P	217_Q	0.683	0.99
182_S	197_V	0.682	0.99
91_L	96_A	0.681	0.99
194_I	197_V	0.680	0.99
104_A	107_V	0.679	0.99
92_S	95_W	0.677	0.99
115_S	135_M	0.674	0.99
163_N	167_V	0.669	0.99
85_K	238_T	0.666	0.99
155_P	175_V	0.665	0.99
92_S	138_A	0.664	0.99
139_Q	143_E	0.661	0.99
206_I	239_V	0.659	0.99
103_V	146_G	0.659	0.99
165_L	175_V	0.653	0.99
76_L	80_K	0.646	0.99
44_T	47_K	0.645	0.99
96_A	142_F	0.641	0.99
145_L	148_K	0.640	0.99
152_L	240_G	0.637	0.99
163_N	166_K	0.636	0.99
193_I	221_A	0.636	0.99
78_T	81_A	0.636	0.99
80_K	111_H	0.634	0.99
67_W	72_A	0.634	0.99
61_L	79_L	0.634	0.99
65_I	92_S	0.632	0.99
124_A	161_N	0.630	0.99
138_A	142_F	0.630	0.99
65_I	116_M	0.630	0.99
97_E	118_Y	0.629	0.99
120_Y	156_P	0.626	0.99
71_R	219_E	0.624	0.98
64_D	120_Y	0.624	0.98
130_E	134_D	0.623	0.98
49_I	52_G	0.621	0.98
121_K	126_L	0.612	0.98
123_Y	131_I	0.609	0.98
162_K	165_L	0.607	0.98
72_A	76_L	0.606	0.98
152_L	239_V	0.604	0.98
104_A	145_L	0.604	0.98
190_V	217_Q	0.604	0.98
160_F	175_V	0.602	0.98
196_N	200_Q	0.602	0.98
94_S	98_R	0.601	0.98
123_Y	134_D	0.599	0.98
63_F	87_A	0.596	0.98
92_S	211_A	0.590	0.98
64_D	154_R	0.584	0.98
103_V	113_I	0.580	0.98
112_Q	238_T	0.577	0.97
180_V	207_I	0.577	0.97
85_K	241_D	0.576	0.97
90_F	239_V	0.576	0.97
85_K	236_N	0.575	0.97
180_V	197_V	0.574	0.97
90_F	154_R	0.573	0.97
158_G	177_H	0.572	0.97
97_E	100_P	0.569	0.97
54_T	58_D	0.568	0.97
126_L	131_I	0.563	0.97
193_I	197_V	0.558	0.97
100_P	145_L	0.557	0.97
93_A	141_A	0.556	0.97
123_Y	126_L	0.553	0.97
142_F	145_L	0.551	0.97
191_E	194_I	0.550	0.97
179_S	202_S	0.548	0.97
64_D	116_M	0.547	0.97
60_S	242_L	0.547	0.97
70_E	73_E	0.543	0.96
168_A	173_Y	0.543	0.96
72_A	106_I	0.542	0.96
120_Y	210_H	0.541	0.96
57_K	233_G	0.538	0.96
121_K	130_E	0.538	0.96
117_G	134_D	0.536	0.96
88_T	239_V	0.535	0.96
64_D	210_H	0.534	0.96
197_V	229_L	0.533	0.96
73_E	109_D	0.533	0.96
44_T	48_A	0.531	0.96
66_S	92_S	0.530	0.96
103_V	142_F	0.530	0.96
131_I	163_N	0.525	0.96
115_S	173_Y	0.523	0.96
68_G	71_R	0.523	0.96
194_I	225_I	0.522	0.95
45_G	48_A	0.522	0.95
52_G	58_D	0.521	0.95
66_S	211_A	0.516	0.95
97_E	144_K	0.516	0.95
74_P	223_P	0.512	0.95
72_A	102_T	0.510	0.95
126_L	134_D	0.509	0.95
60_S	238_T	0.507	0.95
100_P	104_A	0.506	0.95
164_V	168_A	0.505	0.95
47_K	50_Y	0.503	0.94
150_I	173_Y	0.503	0.94
140_T	149_D	0.502	0.94
60_S	88_T	0.502	0.94
188_P	192_K	0.502	0.94
116_M	208_L	0.500	0.94
45_G	49_I	0.500	0.94
94_S	119_A	0.500	0.94

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
4m1bA	1	0.7874	100	0.148	Contact Map
2iw0A	1	0.815	100	0.236	Contact Map
2y8uA	1	0.811	100	0.248	Contact Map
2vyoA	1	0.7835	100	0.257	Contact Map
2w3zA	1	0.752	100	0.258	Contact Map
4l1gA	1	0.8307	100	0.261	Contact Map
2cc0A	2	0.7598	100	0.265	Contact Map
2j13A	1	0.7874	100	0.271	Contact Map
1ny1A	1	0.8858	100	0.272	Contact Map
2c1iA	1	0.9331	100	0.273	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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