PDXT - HALSA - GREMLIN Contacts

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PDXT - Glutamine amidotransferase subunit PdxT

UniProt:	Q9HMD2	Sequences: MTLTAGVVAVQGDVSEHAAAIRRAADAHGQPADVREIRTAGVVPECDVLLLPGGESTAISRLLDREGIDAEIRSHVAAGKPLLATCAGLIVSSTDANDDRVETLDVLDVTVDRNAFGRQVDSFEAPLDVDGLADPFPAVFIRAPVIDEVGADATVLASWDGRPVAIRDGPVVATSFHPELTADVRLHELAFFDRTPSAQAGDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	203 (186)
Sequences:	1652 (1099)
Seq/√Len:	80.5

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
75_H	80_K	3.558	1.00
167_R	193_D	3.217	1.00
166_I	173_A	3.192	1.00
4_T	33_D	2.845	1.00
89_L	173_A	2.754	1.00
146_I	166_I	2.707	1.00
76_V	82_L	2.603	1.00
154_T	167_R	2.448	1.00
188_E	192_F	2.353	1.00
95_D	110_T	2.324	1.00
21_I	50_L	2.318	1.00
107_L	166_I	2.253	1.00
108_D	168_D	2.230	1.00
165_A	174_T	2.161	1.00
7_V	18_A	2.151	1.00
145_V	162_R	2.146	1.00
74_S	78_A	2.114	1.00
112_D	147_D	2.038	1.00
126_P	137_P	2.036	1.00
95_D	148_E	2.012	1.00
21_I	32_A	1.991	1.00
83_L	174_T	1.990	1.00
18_A	34_V	1.958	1.00
18_A	36_E	1.935	1.00
107_L	171_V	1.923	1.00
9_A	36_E	1.885	1.00
4_T	35_R	1.816	1.00
172_V	193_D	1.804	1.00
165_A	186_L	1.801	1.00
139_V	181_T	1.763	1.00
89_L	146_I	1.756	1.00
5_A	48_V	1.744	1.00
51_L	91_V	1.681	1.00
109_V	173_A	1.677	1.00
94_T	108_D	1.642	1.00
158_S	161_G	1.638	1.00
34_V	50_L	1.629	1.00
184_V	188_E	1.607	1.00
69_D	104_L	1.594	1.00
19_A	22_R	1.574	1.00
97_N	147_D	1.570	1.00
60_S	102_E	1.567	1.00
89_L	175_S	1.549	0.99
130_D	154_T	1.525	0.99
126_P	135_P	1.515	0.99
23_R	184_V	1.512	0.99
6_G	46_C	1.489	0.99
69_D	73_R	1.462	0.99
106_V	171_V	1.456	0.99
96_A	103_T	1.454	0.99
110_T	148_E	1.434	0.99
107_L	173_A	1.433	0.99
115_A	145_V	1.411	0.99
116_F	175_S	1.398	0.99
127_L	138_A	1.376	0.99
94_T	106_V	1.372	0.99
60_S	103_T	1.352	0.99
145_V	175_S	1.344	0.99
108_D	150_G	1.342	0.99
60_S	64_D	1.340	0.99
76_V	106_V	1.336	0.98
89_L	111_V	1.327	0.98
136_F	185_R	1.297	0.98
149_V	163_P	1.255	0.98
72_I	75_H	1.233	0.97
25_A	32_A	1.231	0.97
18_A	22_R	1.219	0.97
63_L	91_V	1.202	0.97
97_N	112_D	1.200	0.97
155_V	163_P	1.197	0.97
73_R	77_A	1.188	0.97
35_R	45_E	1.182	0.97
129_V	186_L	1.166	0.96
93_S	111_V	1.162	0.96
64_D	69_D	1.156	0.96
40_A	67_G	1.141	0.96
84_A	174_T	1.136	0.96
149_V	155_V	1.120	0.95
124_E	137_P	1.119	0.95
167_R	189_L	1.110	0.95
20_A	184_V	1.110	0.95
5_A	191_F	1.100	0.95
14_V	38_R	1.089	0.95
15_S	19_A	1.065	0.94
4_T	45_E	1.064	0.94
46_C	81_P	1.042	0.93
20_A	24_A	1.041	0.93
59_I	91_V	1.040	0.93
83_L	186_L	1.033	0.93
158_S	163_P	1.030	0.93
172_V	190_A	1.028	0.93
39_T	42_V	1.016	0.93
37_I	46_C	1.013	0.92
22_R	34_V	1.011	0.92
46_C	75_H	1.003	0.92
35_R	46_C	1.001	0.92
32_A	50_L	0.988	0.91
156_L	165_A	0.978	0.91
129_V	136_F	0.970	0.91
60_S	101_V	0.970	0.91
135_P	185_R	0.966	0.90
124_E	139_V	0.963	0.90
150_G	153_A	0.959	0.90
24_A	32_A	0.953	0.90
68_I	71_E	0.949	0.90
63_L	104_L	0.949	0.90
83_L	172_V	0.945	0.90
24_A	191_F	0.937	0.89
83_L	190_A	0.932	0.89
58_A	62_L	0.930	0.89
131_G	154_T	0.930	0.89
124_E	181_T	0.914	0.88
43_V	46_C	0.912	0.88
64_D	102_E	0.908	0.88
70_A	74_S	0.908	0.88
116_F	163_P	0.901	0.87
192_F	195_T	0.898	0.87
76_V	171_V	0.893	0.87
8_V	49_L	0.887	0.86
40_A	71_E	0.873	0.85
37_I	68_I	0.869	0.85
153_A	156_L	0.864	0.85
21_I	187_H	0.862	0.85
43_V	72_I	0.858	0.84
20_A	187_H	0.857	0.84
127_L	157_A	0.852	0.84
43_V	75_H	0.847	0.84
82_L	106_V	0.845	0.84
129_V	165_A	0.842	0.83
9_A	14_V	0.838	0.83
155_V	158_S	0.831	0.82
20_A	23_R	0.829	0.82
5_A	194_R	0.826	0.82
92_S	171_V	0.820	0.82
22_R	33_D	0.820	0.82
129_V	157_A	0.803	0.80
61_R	65_R	0.796	0.80
14_V	36_E	0.790	0.79
139_V	180_L	0.789	0.79
107_L	168_D	0.789	0.79
129_V	132_L	0.775	0.78
136_F	186_L	0.773	0.78
50_L	84_A	0.765	0.77
10_V	62_L	0.765	0.77
189_L	193_D	0.760	0.76
46_C	80_K	0.760	0.76
96_A	99_D	0.756	0.76
60_S	100_R	0.752	0.76
102_E	105_D	0.748	0.75
36_E	42_V	0.747	0.75
96_A	100_R	0.745	0.75
48_V	80_K	0.743	0.75
118_R	186_L	0.741	0.75
81_P	170_P	0.735	0.74
172_V	189_L	0.731	0.74
14_V	24_A	0.729	0.73
72_I	106_V	0.728	0.73
130_D	158_S	0.726	0.73
138_A	157_A	0.724	0.73
136_F	183_D	0.720	0.73
15_S	18_A	0.717	0.72
146_I	175_S	0.711	0.72
109_V	146_I	0.706	0.71
6_G	43_V	0.703	0.71
42_V	68_I	0.701	0.71
128_D	135_P	0.699	0.70
124_E	127_L	0.695	0.70
116_F	138_A	0.694	0.70
42_V	45_E	0.693	0.70
159_W	174_T	0.689	0.69
132_L	136_F	0.688	0.69
112_D	145_V	0.687	0.69
163_P	166_I	0.678	0.68
110_T	147_D	0.677	0.68
162_R	175_S	0.674	0.68
132_L	135_P	0.668	0.67
101_V	105_D	0.667	0.67
49_L	82_L	0.664	0.66
24_A	184_V	0.662	0.66
165_A	172_V	0.661	0.66
154_T	193_D	0.657	0.66
93_S	109_V	0.656	0.65
130_D	133_A	0.654	0.65
132_L	186_L	0.648	0.64
37_I	49_L	0.646	0.64
76_V	104_L	0.646	0.64
115_A	162_R	0.645	0.64
14_V	18_A	0.642	0.64
13_D	180_L	0.642	0.64
116_F	165_A	0.640	0.64
43_V	68_I	0.638	0.63
57_T	123_F	0.635	0.63
163_P	175_S	0.634	0.63
62_L	65_R	0.632	0.63
60_S	69_D	0.629	0.62
24_A	118_R	0.628	0.62
69_D	102_E	0.627	0.62
112_D	115_A	0.625	0.62
116_F	120_V	0.624	0.62
134_D	185_R	0.620	0.61
94_T	109_V	0.619	0.61
62_L	66_E	0.618	0.61
14_V	61_R	0.618	0.61
94_T	171_V	0.618	0.61
4_T	195_T	0.616	0.61
125_A	138_A	0.615	0.60
131_G	189_L	0.615	0.60
59_I	72_I	0.614	0.60
13_D	145_V	0.613	0.60
159_W	162_R	0.611	0.60
21_I	34_V	0.609	0.60
19_A	23_R	0.608	0.60
40_A	68_I	0.608	0.60
115_A	173_A	0.601	0.59
72_I	80_K	0.595	0.58
90_I	146_I	0.594	0.58
128_D	134_D	0.594	0.58
73_R	106_V	0.591	0.57
13_D	58_A	0.591	0.57
60_S	99_D	0.589	0.57
95_D	151_A	0.587	0.57
49_L	72_I	0.585	0.57
159_W	165_A	0.585	0.57
152_D	168_D	0.583	0.56
10_V	63_L	0.578	0.56
92_S	106_V	0.578	0.56
116_F	127_L	0.577	0.56
89_L	145_V	0.573	0.55
78_A	151_A	0.569	0.55
76_V	92_S	0.568	0.55
42_V	66_E	0.567	0.54
38_R	115_A	0.565	0.54
181_T	189_L	0.564	0.54
132_L	137_P	0.563	0.54
124_E	138_A	0.561	0.54
97_N	110_T	0.561	0.54
34_V	42_V	0.561	0.54
169_G	192_F	0.560	0.53
84_A	107_L	0.557	0.53
136_F	181_T	0.555	0.53
152_D	155_V	0.555	0.53
48_V	190_A	0.554	0.53
7_V	34_V	0.554	0.53
170_P	193_D	0.552	0.52
62_L	93_S	0.551	0.52
76_V	170_P	0.550	0.52
93_S	96_A	0.549	0.52
76_V	81_P	0.548	0.52
99_D	103_T	0.548	0.52
116_F	124_E	0.547	0.52
63_L	76_V	0.543	0.51
94_T	168_D	0.540	0.51
44_P	71_E	0.538	0.51
6_G	124_E	0.537	0.50
35_R	42_V	0.535	0.50
9_A	105_D	0.535	0.50
126_P	136_F	0.532	0.50
190_A	194_R	0.529	0.49
62_L	115_A	0.529	0.49
136_F	139_V	0.525	0.49
61_R	64_D	0.524	0.49
4_T	94_T	0.522	0.49
22_R	50_L	0.522	0.49
147_D	162_R	0.521	0.48
121_D	159_W	0.519	0.48
48_V	191_F	0.517	0.48
73_R	191_F	0.515	0.48
127_L	164_V	0.514	0.47
63_L	69_D	0.513	0.47
168_D	186_L	0.512	0.47
13_D	83_L	0.509	0.47
41_G	44_P	0.508	0.47
128_D	158_S	0.506	0.46
32_A	191_F	0.505	0.46
7_V	21_I	0.504	0.46
39_T	46_C	0.504	0.46
39_T	45_E	0.502	0.46
24_A	78_A	0.501	0.46
74_S	77_A	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
2nv0A	1	0.9458	100	0.63	Contact Map
1q7rA	1	0.9704	100	0.632	Contact Map
2abwA	1	0.9852	100	0.637	Contact Map
2issD	1	0.9064	100	0.638	Contact Map
2ywdA	1	0.9212	100	0.649	Contact Map
2ywjA	1	0.9015	100	0.659	Contact Map
3en0A	2	0.9212	100	0.665	Contact Map
1jvnA	1	0.9557	100	0.695	Contact Map
1ka9H	1	0.9064	99.9	0.703	Contact Map
2vdjA	2	0.9409	99.9	0.723	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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