PDXT - SULSO - GREMLIN Contacts

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PDXT - Glutamine amidotransferase subunit PdxT

UniProt:	Q9UWX4	Sequences: MKIGIIAYQGSFEEHFLQLKRAFDKLSLNGEIISIKIPKDLKGVDGVIIPGGESTTIGLVAKRLGLLDELKEKITSGLPVLGTCAGAIMLAKEVSDAKVGKTSQPLIGTMNISVIRNYYGRQKESFEAIVDLSKIGKDKAHVVFIRAPAIAKVWGKAQSLAELNGVTVFAEENNMLATTFHPELSDTTSIHEYFLHLVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (185)
Sequences:	1643 (1119)
Seq/√Len:	82.3

BACSU - PDXT
HALSA - PDXT
SULSO - PDXT

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_K	78_L	3.622	1.00
171_E	197_L	3.345	1.00
170_A	177_A	3.206	1.00
2_K	31_E	2.890	1.00
87_A	177_A	2.785	1.00
150_I	170_A	2.704	1.00
74_I	80_V	2.640	1.00
158_Q	171_E	2.472	1.00
192_E	196_H	2.342	1.00
93_E	113_S	2.330	1.00
19_L	48_I	2.317	1.00
110_M	170_A	2.284	1.00
111_N	172_E	2.222	1.00
169_F	178_T	2.170	1.00
5_I	16_F	2.128	1.00
149_A	166_V	2.113	1.00
72_E	76_S	2.033	1.00
129_I	141_H	2.016	1.00
19_L	30_G	2.004	1.00
81_L	178_T	2.001	1.00
93_E	152_K	1.997	1.00
115_I	151_A	1.990	1.00
16_F	34_S	1.941	1.00
110_M	175_M	1.939	1.00
7_A	34_S	1.936	1.00
16_F	32_I	1.916	1.00
176_L	197_L	1.817	1.00
2_K	33_I	1.802	1.00
143_V	185_S	1.795	1.00
169_F	190_I	1.794	1.00
87_A	150_I	1.772	1.00
3_I	46_G	1.747	1.00
49_I	89_M	1.716	1.00
92_K	111_N	1.692	1.00
112_I	177_A	1.688	1.00
32_I	48_I	1.632	1.00
188_T	192_E	1.611	1.00
95_S	151_A	1.586	1.00
17_L	20_K	1.573	1.00
67_L	107_I	1.572	1.00
58_G	105_P	1.559	1.00
94_V	106_L	1.548	1.00
133_S	158_Q	1.545	1.00
21_R	188_T	1.538	1.00
67_L	71_K	1.524	0.99
4_G	44_V	1.524	0.99
87_A	179_T	1.524	0.99
162_E	165_G	1.475	0.99
109_T	175_M	1.463	0.99
113_S	152_K	1.456	0.99
129_I	139_K	1.430	0.99
110_M	177_A	1.423	0.99
119_Y	179_T	1.420	0.99
118_Y	149_A	1.394	0.99
58_G	106_L	1.387	0.99
149_A	179_T	1.384	0.99
74_I	109_T	1.381	0.99
87_A	114_V	1.343	0.99
130_V	142_V	1.342	0.99
92_K	109_T	1.332	0.99
97_A	104_Q	1.327	0.99
58_G	62_K	1.324	0.99
140_A	189_S	1.282	0.98
33_I	43_G	1.268	0.98
3_I	195_L	1.253	0.98
159_S	167_T	1.248	0.98
70_L	73_K	1.238	0.98
153_V	167_T	1.231	0.98
61_A	89_M	1.219	0.97
16_F	20_K	1.217	0.97
111_N	154_W	1.198	0.97
91_A	114_V	1.183	0.97
38_P	65_G	1.180	0.97
95_S	115_I	1.164	0.97
132_L	190_I	1.163	0.97
71_K	75_T	1.134	0.96
62_K	67_L	1.124	0.96
171_E	193_Y	1.121	0.96
18_Q	188_T	1.120	0.96
127_E	141_H	1.117	0.96
82_G	178_T	1.108	0.96
2_K	43_G	1.100	0.95
153_V	159_S	1.097	0.95
12_F	36_K	1.082	0.95
81_L	190_I	1.041	0.94
28_L	195_L	1.025	0.93
44_V	79_P	1.024	0.93
162_E	167_T	1.023	0.93
134_K	158_Q	1.018	0.93
13_E	17_L	1.015	0.93
20_K	32_I	0.998	0.92
37_I	40_D	0.994	0.92
139_K	189_S	0.988	0.92
35_I	44_V	0.987	0.92
33_I	44_V	0.981	0.92
56_T	60_V	0.972	0.91
154_W	157_A	0.970	0.91
44_V	73_K	0.966	0.91
176_L	194_F	0.966	0.91
57_I	89_M	0.961	0.91
66_L	69_E	0.956	0.91
81_L	176_L	0.956	0.91
127_E	143_V	0.949	0.90
132_L	140_A	0.939	0.90
81_L	194_F	0.935	0.90
30_G	48_I	0.932	0.89
68_D	72_E	0.922	0.89
74_I	175_M	0.910	0.88
38_P	69_E	0.905	0.88
61_A	107_I	0.902	0.88
35_I	66_L	0.902	0.88
119_Y	167_T	0.901	0.88
19_L	191_H	0.897	0.87
130_V	161_A	0.885	0.87
127_E	185_S	0.884	0.87
3_I	198_V	0.884	0.87
6_I	47_V	0.871	0.86
41_L	44_V	0.871	0.86
80_V	109_T	0.865	0.86
20_K	31_E	0.864	0.85
62_K	105_P	0.862	0.85
132_L	135_I	0.861	0.85
41_L	70_L	0.858	0.85
160_L	169_F	0.855	0.85
135_I	139_K	0.855	0.85
132_L	169_F	0.854	0.85
90_L	175_M	0.853	0.85
18_Q	191_H	0.845	0.84
41_L	73_K	0.845	0.84
159_S	162_E	0.836	0.84
157_A	160_L	0.833	0.83
7_A	12_F	0.828	0.83
58_G	104_Q	0.824	0.83
18_Q	21_R	0.823	0.83
110_M	172_E	0.819	0.82
59_L	63_R	0.813	0.82
48_I	82_G	0.804	0.81
193_Y	197_L	0.795	0.80
140_A	190_I	0.793	0.80
40_D	43_G	0.793	0.80
132_L	161_A	0.787	0.80
176_L	193_Y	0.780	0.79
12_F	34_S	0.765	0.78
44_V	78_L	0.758	0.77
34_S	40_D	0.754	0.77
121_R	190_I	0.752	0.77
131_D	139_K	0.750	0.76
143_V	184_L	0.747	0.76
8_Y	60_V	0.743	0.76
70_L	109_T	0.740	0.75
46_G	78_L	0.730	0.74
133_S	162_E	0.729	0.74
79_P	174_N	0.728	0.74
166_V	179_T	0.723	0.74
169_F	176_L	0.722	0.74
133_S	136_G	0.721	0.73
113_S	151_A	0.719	0.73
140_A	187_T	0.717	0.73
94_V	97_A	0.715	0.73
28_L	188_T	0.712	0.73
112_I	150_I	0.712	0.73
105_P	108_G	0.711	0.72
4_G	41_L	0.710	0.72
13_E	16_F	0.705	0.72
58_G	103_S	0.699	0.71
150_I	179_T	0.695	0.71
167_T	170_A	0.695	0.71
135_I	140_A	0.694	0.71
158_Q	197_L	0.680	0.69
135_I	190_I	0.680	0.69
119_Y	142_V	0.679	0.69
163_L	178_T	0.679	0.69
127_E	130_V	0.675	0.69
104_Q	108_G	0.675	0.69
40_D	66_L	0.674	0.68
142_V	161_A	0.673	0.68
90_L	109_T	0.673	0.68
55_T	126_F	0.671	0.68
118_Y	166_V	0.670	0.68
58_G	67_L	0.656	0.66
41_L	66_L	0.652	0.66
60_V	63_R	0.650	0.66
67_L	105_P	0.649	0.65
167_T	179_T	0.646	0.65
18_Q	28_L	0.646	0.65
11_S	184_L	0.640	0.64
115_I	149_A	0.639	0.64
12_F	16_F	0.636	0.64
92_K	175_M	0.635	0.64
113_S	154_W	0.634	0.64
19_L	32_I	0.633	0.64
119_Y	169_F	0.633	0.64
47_V	70_L	0.633	0.64
35_I	47_V	0.628	0.63
93_E	155_G	0.625	0.63
11_S	56_T	0.625	0.63
47_V	80_V	0.623	0.62
12_F	59_L	0.623	0.62
88_I	150_I	0.620	0.62
156_K	159_S	0.619	0.62
74_I	107_I	0.618	0.62
194_F	198_V	0.617	0.62
91_A	112_I	0.614	0.61
60_V	64_L	0.611	0.61
115_I	118_Y	0.610	0.61
92_K	112_I	0.609	0.61
119_Y	123_K	0.608	0.60
70_L	78_L	0.608	0.60
156_K	172_E	0.606	0.60
136_G	139_K	0.606	0.60
46_G	195_L	0.605	0.60
57_I	70_L	0.598	0.59
11_S	149_A	0.598	0.59
119_Y	130_V	0.595	0.59
58_G	97_A	0.593	0.59
71_K	109_T	0.592	0.58
12_F	28_L	0.591	0.58
8_Y	61_A	0.588	0.58
17_L	21_R	0.588	0.58
163_L	169_F	0.585	0.58
128_A	142_V	0.582	0.57
134_K	193_Y	0.579	0.57
185_S	193_Y	0.578	0.57
38_P	66_L	0.577	0.56
118_Y	177_A	0.577	0.56
42_K	69_E	0.577	0.56
174_N	197_L	0.575	0.56
135_I	189_S	0.575	0.56
82_G	110_M	0.574	0.56
136_G	192_E	0.571	0.56
163_L	166_V	0.571	0.56
111_N	156_K	0.569	0.55
173_N	196_H	0.569	0.55
119_Y	127_E	0.567	0.55
74_I	90_L	0.566	0.55
140_A	185_S	0.565	0.55
124_E	163_L	0.564	0.55
30_G	195_L	0.564	0.55
39_K	42_K	0.562	0.55
60_V	118_Y	0.556	0.54
5_I	32_I	0.555	0.54
87_A	149_A	0.554	0.54
92_K	172_E	0.552	0.53
127_E	142_V	0.550	0.53
60_V	91_A	0.550	0.53
130_V	168_V	0.546	0.52
4_G	127_E	0.545	0.52
61_A	74_I	0.542	0.52
36_K	118_Y	0.541	0.52
140_A	143_V	0.539	0.52
135_I	141_H	0.537	0.51
41_L	69_E	0.535	0.51
46_G	194_F	0.532	0.51
40_D	64_L	0.532	0.51
2_K	45_D	0.530	0.50
72_E	75_T	0.530	0.50
71_K	195_L	0.529	0.50
5_I	19_L	0.528	0.50
74_I	79_P	0.528	0.50
11_S	81_L	0.524	0.50
74_I	174_N	0.524	0.50
7_A	108_G	0.523	0.49
97_A	106_L	0.523	0.49
37_I	123_K	0.522	0.49
129_I	140_A	0.521	0.49
97_A	103_S	0.519	0.49
152_K	179_T	0.515	0.48
128_A	140_A	0.514	0.48
96_D	104_Q	0.513	0.48
95_S	113_S	0.511	0.48
8_Y	41_L	0.509	0.48
118_Y	191_H	0.509	0.48
138_D	189_S	0.507	0.47
59_L	62_K	0.507	0.47
129_I	135_I	0.507	0.47
131_D	138_D	0.505	0.47
151_A	166_V	0.505	0.47
69_E	72_E	0.500	0.46

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
2issD	1	0.92	100	0.635	Contact Map
2nv0A	1	0.925	100	0.635	Contact Map
1q7rA	1	0.94	100	0.641	Contact Map
2abwA	1	0.97	100	0.642	Contact Map
3en0A	2	0.97	100	0.653	Contact Map
2ywdA	1	0.94	100	0.659	Contact Map
2ywjA	1	0.915	100	0.66	Contact Map
1jvnA	1	0.93	99.9	0.7	Contact Map
2vdjA	2	0.935	99.9	0.705	Contact Map
2h2wA	2	0.925	99.9	0.71	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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