BioW - PFAM28P - GREMLIN Contacts

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BioW - 6-carboxyhexanoate--CoA ligase

PFAM:	PF03744	Sequences: YSVRMRASKGGRHISGAERIVPEEEIEEVVAELLERALSHSRGKPDFINITIEKIKEEPIRYIPALPVTTVEVSSPEEGRKAARKLLESAGISEEAIEKALELLASGGNMRGAMLLDADTGERLEPDKERGVRVSRMDITDEARAKLSLKLAGLNNERVREALVLASKVASAPGIVAELCWSDDPDYTTGYVASKKLGYVRIPHLKEKGSPRGGRVFFVRGGADLEELIDYLEKQPVLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	239 (239)
Sequences:	590 (513)
Seq/√Len:	33.2
META:	0.708

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_I	167_S	6.046	1.00
19_R	138_D	5.072	1.00
175_I	228_L	3.527	1.00
41_S	186_D	3.386	1.00
40_H	43_G	3.090	1.00
126_P	229_I	3.086	1.00
139_I	164_V	3.083	1.00
4_R	136_R	2.966	1.00
110_M	125_E	2.877	1.00
33_L	138_D	2.708	1.00
130_R	233_E	2.684	1.00
189_T	202_I	2.680	1.00
116_L	216_V	2.674	1.00
27_E	35_E	2.637	1.00
169_V	217_F	2.628	1.00
51_T	136_R	2.487	1.00
170_A	194_S	2.467	1.00
19_R	33_L	2.425	0.99
73_V	79_G	2.394	0.99
219_V	228_L	2.374	0.99
188_T	204_H	2.339	0.99
30_V	34_L	2.278	0.99
104_L	181_W	2.238	0.99
93_S	96_A	2.171	0.99
4_R	51_T	2.145	0.99
171_S	231_Y	2.127	0.99
188_T	203_P	2.094	0.98
37_A	48_I	2.091	0.98
114_M	216_V	1.992	0.98
110_M	127_D	1.806	0.96
111_R	123_R	1.789	0.96
3_V	52_I	1.778	0.96
147_L	151_L	1.771	0.96
28_E	32_E	1.771	0.96
97_I	101_L	1.748	0.95
103_L	114_M	1.742	0.95
125_E	128_K	1.712	0.95
187_Y	199_Y	1.702	0.94
194_S	198_G	1.677	0.94
115_L	219_V	1.672	0.94
164_V	239_I	1.656	0.94
134_V	217_F	1.651	0.93
20_I	55_I	1.625	0.93
17_A	36_R	1.606	0.93
111_R	125_E	1.585	0.92
231_Y	237_V	1.537	0.91
47_F	51_T	1.529	0.91
194_S	200_V	1.517	0.90
66_L	167_S	1.514	0.90
100_A	218_F	1.482	0.89
80_R	105_A	1.475	0.89
149_L	153_G	1.450	0.88
125_E	130_R	1.436	0.88
117_D	221_G	1.427	0.87
121_G	218_F	1.422	0.87
123_R	130_R	1.418	0.87
115_L	228_L	1.398	0.86
83_A	192_V	1.389	0.86
111_R	127_D	1.372	0.85
82_A	85_K	1.360	0.84
55_I	236_P	1.357	0.84
223_A	228_L	1.354	0.84
96_A	100_A	1.315	0.82
13_H	16_G	1.314	0.82
119_D	220_R	1.300	0.82
111_R	130_R	1.298	0.82
23_E	44_K	1.273	0.80
96_A	118_A	1.268	0.80
4_R	53_E	1.258	0.79
117_D	124_L	1.251	0.79
110_M	123_R	1.230	0.78
21_V	29_V	1.227	0.78
36_R	165_L	1.218	0.77
14_I	47_F	1.212	0.77
166_A	193_A	1.199	0.76
172_A	228_L	1.197	0.76
13_H	18_E	1.194	0.76
80_R	205_L	1.185	0.75
111_R	233_E	1.174	0.74
30_V	38_L	1.171	0.74
165_L	184_D	1.169	0.74
75_S	78_E	1.165	0.74
222_G	228_L	1.161	0.74
137_M	164_V	1.159	0.74
4_R	135_S	1.152	0.73
14_I	40_H	1.148	0.73
156_N	159_V	1.147	0.73
1_Y	4_R	1.146	0.73
68_V	154_L	1.134	0.72
166_A	170_A	1.123	0.71
6_R	14_I	1.121	0.71
6_R	46_D	1.117	0.71
174_G	181_W	1.116	0.71
137_M	165_L	1.109	0.70
53_E	136_R	1.108	0.70
121_G	219_V	1.095	0.69
83_A	181_W	1.094	0.69
175_I	193_A	1.087	0.69
181_W	205_L	1.087	0.69
230_D	234_K	1.085	0.68
26_I	38_L	1.075	0.68
167_S	171_S	1.060	0.67
107_G	125_E	1.040	0.65
84_R	98_E	1.030	0.64
224_D	228_L	1.030	0.64
21_V	33_L	1.028	0.64
56_K	59_P	1.027	0.64
179_L	218_F	1.021	0.64
79_G	189_T	1.015	0.63
107_G	127_D	1.003	0.62
22_P	89_S	1.002	0.62
185_P	209_G	0.999	0.62
134_V	169_V	0.996	0.62
119_D	221_G	0.990	0.61
73_V	204_H	0.990	0.61
167_S	205_L	0.985	0.61
8_S	11_G	0.979	0.60
79_G	192_V	0.978	0.60
55_I	145_A	0.977	0.60
137_M	217_F	0.974	0.60
53_E	205_L	0.956	0.59
224_D	227_E	0.954	0.58
127_D	130_R	0.953	0.58
114_M	125_E	0.947	0.58
140_T	143_A	0.946	0.58
35_E	39_S	0.938	0.57
144_R	160_R	0.932	0.57
79_G	205_L	0.926	0.56
14_I	43_G	0.919	0.55
44_K	54_K	0.916	0.55
15_S	18_E	0.913	0.55
80_R	83_A	0.908	0.55
163_L	182_S	0.907	0.54
55_I	61_R	0.903	0.54
68_V	161_E	0.900	0.54
65_A	106_S	0.895	0.53
115_L	175_I	0.886	0.53
83_A	90_A	0.886	0.53
8_S	47_F	0.881	0.52
42_R	92_I	0.879	0.52
36_R	48_I	0.878	0.52
80_R	181_W	0.869	0.51
207_E	210_S	0.866	0.51
139_I	147_L	0.866	0.51
100_A	121_G	0.865	0.51
6_R	237_V	0.853	0.50
85_K	104_L	0.849	0.50
53_E	67_P	0.846	0.49
87_L	203_P	0.843	0.49
161_E	165_L	0.842	0.49
219_V	223_A	0.838	0.49
107_G	218_F	0.835	0.48
87_L	192_V	0.826	0.48
88_E	94_E	0.820	0.47
1_Y	157_E	0.818	0.47
92_I	96_A	0.815	0.47
96_A	99_K	0.813	0.47
43_G	137_M	0.811	0.46
41_S	99_K	0.807	0.46
138_D	164_V	0.805	0.46
20_I	56_K	0.805	0.46
137_M	161_E	0.804	0.46
136_R	234_K	0.804	0.46
119_D	239_I	0.802	0.46
65_A	139_I	0.798	0.45
194_S	197_L	0.795	0.45
21_V	138_D	0.792	0.45
26_I	118_A	0.790	0.45
30_V	101_L	0.789	0.45
158_R	184_D	0.788	0.45
201_R	206_K	0.785	0.44
114_M	233_E	0.785	0.44
33_L	139_I	0.784	0.44
15_S	40_H	0.782	0.44
50_I	132_V	0.781	0.44
25_E	52_I	0.774	0.43
76_P	207_E	0.773	0.43
101_L	105_A	0.772	0.43
8_S	181_W	0.772	0.43
159_V	218_F	0.770	0.43
29_V	34_L	0.769	0.43
102_E	230_D	0.768	0.43
65_A	167_S	0.765	0.43
114_M	123_R	0.764	0.43
75_S	146_K	0.763	0.43
143_A	147_L	0.762	0.42
4_R	100_A	0.760	0.42
143_A	151_L	0.753	0.42
80_R	210_S	0.751	0.42
109_N	158_R	0.750	0.41
100_A	116_L	0.742	0.41
114_M	138_D	0.741	0.41
20_I	108_G	0.736	0.40
81_K	226_E	0.736	0.40
24_E	98_E	0.735	0.40
122_E	221_G	0.732	0.40
155_N	158_R	0.732	0.40
75_S	192_V	0.726	0.40
22_P	25_E	0.724	0.39
158_R	219_V	0.724	0.39
70_T	203_P	0.718	0.39
36_R	110_M	0.717	0.39
124_L	193_A	0.717	0.39
64_P	167_S	0.716	0.39
37_A	45_P	0.714	0.39
189_T	201_R	0.714	0.39
74_S	78_E	0.714	0.39
86_L	197_L	0.711	0.38
220_R	224_D	0.711	0.38
100_A	179_L	0.710	0.38
105_A	129_E	0.706	0.38
43_G	184_D	0.699	0.37
92_I	176_V	0.696	0.37
110_M	130_R	0.694	0.37
84_R	95_E	0.692	0.37
175_I	219_V	0.691	0.37
96_A	216_V	0.690	0.37
104_L	109_N	0.688	0.37
5_M	13_H	0.686	0.36
20_I	60_I	0.686	0.36
33_L	114_M	0.686	0.36
93_S	118_A	0.684	0.36
231_Y	235_Q	0.683	0.36
65_A	239_I	0.682	0.36
71_V	200_V	0.681	0.36
107_G	116_L	0.680	0.36
50_I	89_S	0.679	0.36
161_E	217_F	0.676	0.36
73_V	101_L	0.673	0.35
6_R	13_H	0.672	0.35
147_L	159_V	0.672	0.35
188_T	202_I	0.671	0.35
40_H	156_N	0.670	0.35
159_V	163_L	0.669	0.35
39_S	186_D	0.669	0.35
37_A	177_A	0.668	0.35
29_V	141_D	0.667	0.35
55_I	204_H	0.665	0.35
17_A	147_L	0.664	0.35
206_K	213_G	0.662	0.35
111_R	114_M	0.661	0.34
92_I	100_A	0.657	0.34
135_S	169_V	0.655	0.34
83_A	179_L	0.654	0.34
79_G	83_A	0.651	0.34
37_A	169_V	0.650	0.34
214_G	218_F	0.649	0.34
107_G	114_M	0.647	0.33
123_R	233_E	0.640	0.33
37_A	43_G	0.638	0.33
100_A	151_L	0.638	0.33
100_A	107_G	0.636	0.33
3_V	29_V	0.634	0.32
189_T	199_Y	0.633	0.32
22_P	141_D	0.628	0.32
68_V	163_L	0.624	0.32
222_G	227_E	0.618	0.31
136_R	236_P	0.616	0.31
26_I	239_I	0.615	0.31
5_M	43_G	0.614	0.31
75_S	142_E	0.613	0.31
90_A	194_S	0.612	0.31
115_L	229_I	0.611	0.31
4_R	139_I	0.611	0.31
107_G	110_M	0.609	0.31
225_L	234_K	0.608	0.31
27_E	52_I	0.604	0.30
109_N	115_L	0.604	0.30
202_I	205_L	0.603	0.30
193_A	198_G	0.603	0.30
36_R	158_R	0.598	0.30
35_E	236_P	0.597	0.30
115_L	217_F	0.597	0.30
199_Y	206_K	0.596	0.30
229_I	233_E	0.594	0.30
4_R	20_I	0.593	0.30
155_N	161_E	0.592	0.29
37_A	40_H	0.592	0.29
20_I	150_K	0.591	0.29
64_P	176_V	0.589	0.29
5_M	8_S	0.585	0.29
20_I	212_R	0.584	0.29
95_E	99_K	0.584	0.29
86_L	200_V	0.580	0.29
124_L	174_G	0.578	0.29
60_I	94_E	0.577	0.28
92_I	218_F	0.577	0.28
117_D	120_T	0.576	0.28
62_Y	145_A	0.575	0.28
206_K	209_G	0.573	0.28
52_I	188_T	0.572	0.28
122_E	219_V	0.572	0.28
121_G	228_L	0.571	0.28
181_W	189_T	0.570	0.28
174_G	231_Y	0.569	0.28
92_I	210_S	0.568	0.28
89_S	115_L	0.567	0.28
25_E	141_D	0.566	0.28
135_S	161_E	0.566	0.28
132_V	234_K	0.565	0.28
109_N	114_M	0.563	0.27
101_L	114_M	0.562	0.27
65_A	68_V	0.561	0.27
30_V	50_I	0.560	0.27
79_G	188_T	0.559	0.27
101_L	195_K	0.559	0.27
79_G	202_I	0.558	0.27
103_L	163_L	0.557	0.27
83_A	205_L	0.556	0.27
115_L	197_L	0.554	0.27
37_A	135_S	0.552	0.27
136_R	159_V	0.551	0.27
173_P	238_L	0.550	0.27
33_L	96_A	0.549	0.27
121_G	135_S	0.549	0.27
35_E	63_I	0.546	0.26
218_F	223_A	0.546	0.26
126_P	130_R	0.545	0.26
93_S	216_V	0.545	0.26
226_E	239_I	0.543	0.26
49_N	205_L	0.542	0.26
228_L	232_L	0.542	0.26
115_L	184_D	0.541	0.26
188_T	205_L	0.540	0.26
84_R	237_V	0.537	0.26
44_K	101_L	0.537	0.26
230_D	235_Q	0.536	0.26
218_F	228_L	0.536	0.26
134_V	204_H	0.536	0.26
34_L	52_I	0.536	0.26
67_P	198_G	0.535	0.26
9_K	12_R	0.534	0.26
87_L	166_A	0.531	0.25
23_E	34_L	0.529	0.25
221_G	225_L	0.528	0.25
21_V	26_I	0.528	0.25
67_P	208_K	0.526	0.25
95_E	209_G	0.526	0.25
5_M	40_H	0.525	0.25
82_A	202_I	0.524	0.25
36_R	127_D	0.523	0.25
77_E	134_V	0.519	0.25
179_L	216_V	0.519	0.25
64_P	67_P	0.518	0.25
187_Y	191_Y	0.518	0.25
78_E	82_A	0.513	0.24
208_K	230_D	0.512	0.24
132_V	212_R	0.510	0.24
55_I	102_E	0.510	0.24
104_L	212_R	0.509	0.24
121_G	179_L	0.507	0.24
182_S	201_R	0.507	0.24
27_E	38_L	0.506	0.24
34_L	186_D	0.505	0.24
20_I	51_T	0.505	0.24
6_R	15_S	0.503	0.24
120_T	151_L	0.503	0.24
23_E	236_P	0.500	0.24

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
3do6A	3	0.6569	18.6	0.969	Contact Map
2px0A	4	0.569	12.9	0.972	Contact Map
3dy5A	1	0.3891	10.8	0.973	Contact Map
4rptA	2	0.2176	9.4	0.973	Contact Map
3rh9A	2	0.9247	8.6	0.974	Contact Map
3bh1A	4	0.5565	8.5	0.974	Contact Map
2iruA	1	0.2008	8.2	0.974	Contact Map
4f3xA	4	0.8117	7.8	0.974	Contact Map
4h7nA	2	0.9163	7.8	0.974	Contact Map
2impA	4	0.8117	7.5	0.974	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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