Cad - PFAM28P - GREMLIN Contacts

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Cad - Cadmium resistance transporter

PFAM:	PF03596	Sequences: FAATNIDDIVVLTLFFAQANGRFRRRHIVAGQYLGFAALVAVSLLGALGALLIPEEWIIGLLGLLPIALGIKALLRGRRDDDEEADEELSSSGASSLVLTVAAVTIANCGGDNIGVYVPLFATSSLAELLVILAVFLVLVAVWCLAAYWLARHPAIARVLERYGHWLVPFVLIGLGLYILVESGTFSLLLSF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	192 (184)
Sequences:	2043 (1593)
Seq/√Len:	117.4
META:	0.671

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_I	118_V	4.586	1.00
15_F	104_V	4.580	1.00
37_A	137_L	4.178	1.00
33_Y	141_A	4.144	1.00
29_V	144_C	3.691	1.00
175_L	179_I	3.518	1.00
54_P	57_W	3.262	1.00
54_P	58_I	3.258	1.00
38_A	106_I	3.176	1.00
36_F	140_V	2.869	1.00
40_V	137_L	2.645	1.00
33_Y	140_V	2.574	1.00
51_L	54_P	2.485	1.00
124_S	132_I	2.438	1.00
71_I	75_L	2.244	1.00
72_K	76_R	2.217	1.00
113_N	117_Y	2.215	1.00
47_A	50_A	2.135	1.00
111_G	115_G	2.036	1.00
149_W	153_H	2.016	1.00
166_W	170_F	2.004	1.00
180_L	186_F	1.930	1.00
139_L	142_V	1.893	1.00
13_T	147_A	1.802	1.00
112_D	136_F	1.748	1.00
4_T	7_D	1.655	1.00
5_N	8_D	1.640	1.00
36_F	39_L	1.628	1.00
125_S	128_E	1.625	1.00
67_I	173_I	1.614	1.00
64_L	68_A	1.600	1.00
175_L	178_Y	1.592	1.00
5_N	9_I	1.565	1.00
40_V	133_L	1.562	1.00
39_L	110_G	1.561	1.00
177_L	181_V	1.535	1.00
129_L	132_I	1.416	1.00
126_L	130_L	1.412	1.00
49_G	52_L	1.384	1.00
39_L	106_I	1.383	1.00
174_G	178_Y	1.362	1.00
8_D	143_W	1.355	1.00
77_G	80_D	1.341	1.00
46_G	118_V	1.331	1.00
16_F	29_V	1.326	1.00
26_R	30_A	1.316	1.00
62_L	143_W	1.285	1.00
180_L	185_T	1.277	0.99
8_D	108_N	1.267	0.99
32_Q	36_F	1.261	0.99
115_G	119_P	1.258	0.99
60_G	183_S	1.255	0.99
108_N	143_W	1.248	0.99
11_V	15_F	1.248	0.99
9_I	150_L	1.241	0.99
70_G	173_I	1.240	0.99
27_H	97_L	1.234	0.99
5_N	108_N	1.230	0.99
55_E	58_I	1.227	0.99
23_F	27_H	1.201	0.99
134_A	138_V	1.200	0.99
43_S	115_G	1.190	0.99
78_R	81_D	1.183	0.99
8_D	16_F	1.180	0.99
148_Y	152_R	1.174	0.99
154_P	158_R	1.173	0.99
68_A	72_K	1.168	0.99
125_S	129_L	1.167	0.99
14_L	18_Q	1.154	0.99
35_G	105_T	1.140	0.99
113_N	118_V	1.139	0.99
106_I	114_I	1.124	0.99
8_D	36_F	1.124	0.99
87_E	90_S	1.119	0.99
9_I	147_A	1.103	0.99
174_G	177_L	1.095	0.98
105_T	113_N	1.084	0.98
80_D	86_D	1.082	0.98
8_D	113_N	1.080	0.98
156_I	172_L	1.076	0.98
8_D	105_T	1.072	0.98
5_N	36_F	1.071	0.98
44_L	133_L	1.050	0.98
5_N	32_Q	1.039	0.98
79_R	87_E	1.033	0.98
2_A	6_I	1.028	0.98
108_N	112_D	1.027	0.98
63_G	176_G	1.026	0.98
9_I	13_T	1.017	0.97
8_D	117_Y	0.999	0.97
5_N	117_Y	0.985	0.97
63_G	70_G	0.981	0.97
157_A	172_L	0.978	0.97
15_F	18_Q	0.976	0.97
99_L	103_A	0.970	0.97
5_N	139_L	0.968	0.97
48_L	52_L	0.956	0.96
8_D	32_Q	0.946	0.96
15_F	101_V	0.942	0.96
36_F	137_L	0.938	0.96
110_G	113_N	0.936	0.96
131_V	135_V	0.916	0.95
139_L	143_W	0.913	0.95
141_A	144_C	0.904	0.95
67_I	71_I	0.902	0.95
50_A	172_L	0.895	0.95
169_P	172_L	0.893	0.95
75_L	84_E	0.885	0.94
40_V	140_V	0.882	0.94
54_P	59_I	0.874	0.94
36_F	108_N	0.872	0.94
77_G	82_D	0.869	0.94
34_L	99_L	0.849	0.93
158_R	161_E	0.849	0.93
10_V	13_T	0.838	0.93
48_L	114_I	0.837	0.93
42_V	106_I	0.837	0.93
100_T	103_A	0.836	0.92
115_G	154_P	0.834	0.92
8_D	15_F	0.832	0.92
84_E	89_L	0.828	0.92
133_L	137_L	0.821	0.92
45_L	161_E	0.819	0.92
13_T	151_A	0.819	0.92
85_A	88_E	0.805	0.91
33_Y	168_V	0.802	0.91
123_T	183_S	0.802	0.91
84_E	88_E	0.801	0.91
77_G	81_D	0.800	0.91
115_G	118_V	0.799	0.91
37_A	103_A	0.798	0.91
24_R	27_H	0.798	0.91
171_V	175_L	0.793	0.90
84_E	87_E	0.791	0.90
127_A	130_L	0.789	0.90
75_L	78_R	0.783	0.90
42_V	46_G	0.774	0.89
69_L	111_G	0.766	0.89
82_D	85_A	0.761	0.88
32_Q	113_N	0.754	0.88
14_L	17_A	0.751	0.88
177_L	180_L	0.749	0.88
44_L	121_F	0.740	0.87
50_A	122_A	0.738	0.87
65_L	73_A	0.734	0.87
97_L	100_T	0.732	0.86
46_G	50_A	0.730	0.86
30_A	98_V	0.729	0.86
44_L	129_L	0.729	0.86
50_A	54_P	0.727	0.86
98_V	170_F	0.726	0.86
105_T	110_G	0.724	0.86
36_F	117_Y	0.721	0.86
49_G	55_E	0.717	0.85
60_G	185_T	0.714	0.85
120_L	132_I	0.709	0.85
67_I	158_R	0.707	0.85
35_G	110_G	0.701	0.84
170_F	174_G	0.698	0.84
47_A	129_L	0.696	0.84
17_A	28_I	0.695	0.84
104_V	142_V	0.689	0.83
122_A	157_A	0.689	0.83
70_G	121_F	0.683	0.82
79_R	82_D	0.678	0.82
105_T	117_Y	0.676	0.82
23_F	26_R	0.673	0.82
42_V	45_L	0.673	0.82
93_G	97_L	0.673	0.82
10_V	135_V	0.672	0.81
157_A	160_L	0.672	0.81
29_V	141_A	0.671	0.81
3_A	18_Q	0.668	0.81
161_E	164_G	0.665	0.81
32_Q	139_L	0.658	0.80
67_I	175_L	0.654	0.80
36_F	143_W	0.653	0.80
131_V	137_L	0.653	0.80
56_E	184_G	0.652	0.79
8_D	169_P	0.649	0.79
124_S	155_A	0.649	0.79
81_D	87_E	0.649	0.79
145_L	163_Y	0.644	0.79
176_G	179_I	0.642	0.78
35_G	136_F	0.640	0.78
86_D	89_L	0.635	0.78
43_S	110_G	0.632	0.77
102_A	147_A	0.626	0.77
68_A	174_G	0.625	0.77
136_F	139_L	0.624	0.76
151_A	157_A	0.620	0.76
47_A	51_L	0.615	0.75
65_L	124_S	0.615	0.75
32_Q	175_L	0.610	0.75
14_L	156_I	0.608	0.75
121_F	173_I	0.606	0.74
116_V	182_E	0.604	0.74
25_R	65_L	0.601	0.74
67_I	98_V	0.599	0.73
122_A	172_L	0.599	0.73
4_T	8_D	0.595	0.73
51_L	58_I	0.593	0.73
51_L	57_W	0.592	0.73
9_I	29_V	0.592	0.73
155_A	159_V	0.590	0.72
47_A	57_W	0.589	0.72
53_I	57_W	0.587	0.72
11_V	108_N	0.585	0.72
60_G	120_L	0.584	0.72
111_G	169_P	0.584	0.72
137_L	149_W	0.583	0.71
42_V	78_R	0.583	0.71
130_L	134_A	0.577	0.71
67_I	177_L	0.574	0.70
3_A	36_F	0.574	0.70
17_A	151_A	0.572	0.70
32_Q	112_D	0.572	0.70
53_I	78_R	0.571	0.70
82_D	90_S	0.569	0.70
178_Y	182_E	0.566	0.69
125_S	132_I	0.565	0.69
31_G	143_W	0.563	0.69
36_F	40_V	0.563	0.69
135_V	142_V	0.561	0.69
34_L	167_L	0.560	0.68
34_L	40_V	0.560	0.68
103_A	108_N	0.558	0.68
40_V	121_F	0.557	0.68
160_L	172_L	0.554	0.68
117_Y	175_L	0.550	0.67
53_I	61_L	0.547	0.67
5_N	11_V	0.547	0.67
123_T	132_I	0.546	0.67
67_I	180_L	0.545	0.66
26_R	98_V	0.543	0.66
51_L	59_I	0.540	0.66
138_V	142_V	0.539	0.66
152_R	161_E	0.539	0.66
144_C	168_V	0.538	0.65
115_G	129_L	0.537	0.65
6_I	174_G	0.537	0.65
17_A	157_A	0.537	0.65
57_W	116_V	0.533	0.65
85_A	131_V	0.532	0.65
117_Y	144_C	0.530	0.64
124_S	128_E	0.528	0.64
113_N	139_L	0.528	0.64
62_L	163_Y	0.527	0.64
91_S	181_V	0.526	0.64
168_V	172_L	0.524	0.63
11_V	112_D	0.524	0.63
48_L	54_P	0.524	0.63
153_H	157_A	0.522	0.63
136_F	168_V	0.520	0.63
27_H	61_L	0.520	0.63
179_I	183_S	0.520	0.63
81_D	90_S	0.518	0.62
23_F	28_I	0.518	0.62
48_L	141_A	0.518	0.62
95_S	98_V	0.515	0.62
74_L	173_I	0.515	0.62
28_I	157_A	0.513	0.62
155_A	158_R	0.513	0.62
13_T	160_L	0.512	0.62
70_G	168_V	0.511	0.61
101_V	140_V	0.510	0.61
68_A	134_A	0.509	0.61
163_Y	170_F	0.508	0.61
84_E	95_S	0.507	0.61
75_L	79_R	0.506	0.61
34_L	84_E	0.504	0.60
33_Y	36_F	0.503	0.60
25_R	148_Y	0.502	0.60
46_G	157_A	0.502	0.60
63_G	160_L	0.501	0.60
81_D	95_S	0.500	0.60

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
2gfpA	2	0.9479	32.6	0.937	Contact Map
4ikvA	1	0.5573	21.9	0.943	Contact Map
1pw4A	1	0.5625	20.8	0.943	Contact Map
3o7qA	1	0.9635	20.2	0.944	Contact Map
2wswA	3	0.401	15.1	0.947	Contact Map
3wdoA	1	0.5052	12.7	0.949	Contact Map
4xnjA	1	0.9688	10.9	0.95	Contact Map
2cfqA	1	0.9271	10.3	0.951	Contact Map
4ldsA	2	0.4531	6.4	0.955	Contact Map
4tphA	2	0.474	6.3	0.955	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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