DUF3708 - PFAM28P - GREMLIN Contacts

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DUF3708 - Phosphate ATP-binding cassette transporter

PFAM:	PF12501	Sequences: LLLLLALAAAAYFLGRRRALALAGGGGRRLHSLPGYYGAYVALWCALPALLLLALWLAFEPSIITSLVLASLPAEVLPLSAAELSLVLNDIRNLASGNIVLSAAAAAAAAAAYADLRALLAAVGVALAAAGAGAVLRIAPDFRARNRVERIVMGLLIACSAIAILM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	166 (164)
Sequences:	4568 (3810)
Seq/√Len:	297.5
META:	0.85

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_G	137_R	2.974	1.00
105_A	108_A	2.887	1.00
113_Y	117_R	2.769	1.00
112_A	116_L	2.750	1.00
8_A	46_A	2.509	1.00
80_S	83_E	2.485	1.00
113_Y	116_L	2.461	1.00
116_L	120_L	2.443	1.00
74_A	77_L	2.391	1.00
15_G	41_V	2.387	1.00
102_S	105_A	2.360	1.00
112_A	115_D	2.313	1.00
150_R	153_M	2.175	1.00
16_R	20_L	2.069	1.00
131_G	137_R	2.026	1.00
133_G	136_L	2.009	1.00
154_G	158_A	1.973	1.00
11_A	41_V	1.911	1.00
40_Y	44_W	1.885	1.00
19_A	30_L	1.761	1.00
120_L	124_G	1.739	1.00
106_A	109_A	1.735	1.00
114_A	118_A	1.697	1.00
106_A	110_A	1.670	1.00
55_L	59_F	1.657	1.00
26_G	29_R	1.651	1.00
114_A	117_R	1.644	1.00
79_L	83_E	1.601	1.00
143_R	146_N	1.585	1.00
115_D	120_L	1.560	1.00
31_H	143_R	1.553	1.00
107_A	110_A	1.522	1.00
65_T	88_L	1.522	1.00
117_R	121_A	1.505	1.00
25_G	28_R	1.473	1.00
103_A	106_A	1.461	1.00
63_I	67_L	1.454	1.00
102_S	106_A	1.449	1.00
131_G	134_A	1.436	1.00
118_A	122_A	1.436	1.00
65_T	92_R	1.390	1.00
115_D	118_A	1.375	1.00
47_L	151_I	1.372	1.00
74_A	78_P	1.361	1.00
113_Y	121_A	1.353	1.00
115_D	119_L	1.343	1.00
116_L	119_L	1.341	1.00
17_R	21_A	1.335	1.00
4_L	8_A	1.324	1.00
102_S	108_A	1.309	1.00
108_A	111_A	1.293	1.00
114_A	120_L	1.274	1.00
43_L	151_I	1.268	1.00
104_A	107_A	1.268	1.00
151_I	155_L	1.265	1.00
145_R	149_E	1.256	1.00
61_P	65_T	1.255	1.00
31_H	146_N	1.238	1.00
73_P	76_V	1.237	1.00
43_L	148_V	1.236	1.00
113_Y	124_G	1.225	1.00
35_G	39_A	1.221	1.00
40_Y	142_F	1.216	1.00
113_Y	119_L	1.211	1.00
161_A	165_L	1.195	1.00
6_A	10_A	1.190	1.00
101_L	105_A	1.183	1.00
12_Y	16_R	1.180	1.00
117_R	120_L	1.170	1.00
104_A	108_A	1.168	1.00
105_A	110_A	1.165	1.00
19_A	23_A	1.160	1.00
7_L	45_C	1.141	1.00
131_G	135_V	1.136	1.00
120_L	123_V	1.111	1.00
76_V	87_V	1.103	1.00
113_Y	120_L	1.102	1.00
19_A	22_L	1.095	1.00
52_L	156_L	1.070	1.00
160_S	163_A	1.058	1.00
121_A	125_V	1.051	1.00
119_L	124_G	1.033	1.00
69_L	84_L	1.018	1.00
161_A	164_I	1.017	1.00
86_L	89_N	1.017	1.00
119_L	122_A	1.014	1.00
87_V	91_I	1.013	1.00
130_A	133_G	1.008	1.00
23_A	33_L	1.002	1.00
11_A	45_C	0.996	1.00
56_W	60_E	0.991	1.00
24_G	27_G	0.986	1.00
7_L	11_A	0.986	1.00
40_Y	147_R	0.984	1.00
114_A	123_V	0.964	1.00
58_A	62_S	0.963	1.00
46_A	50_L	0.951	1.00
134_A	137_R	0.947	1.00
47_L	51_L	0.941	1.00
41_V	138_I	0.941	1.00
82_A	85_S	0.935	1.00
130_A	134_A	0.927	1.00
112_A	120_L	0.923	1.00
59_F	62_S	0.922	1.00
69_L	88_L	0.921	1.00
103_A	109_A	0.916	1.00
121_A	124_G	0.914	1.00
101_L	106_A	0.892	1.00
82_A	86_L	0.877	1.00
51_L	55_L	0.874	1.00
43_L	47_L	0.866	1.00
131_G	136_L	0.866	1.00
66_S	70_A	0.862	1.00
42_A	46_A	0.852	1.00
103_A	108_A	0.848	1.00
113_Y	122_A	0.846	1.00
101_L	108_A	0.842	1.00
45_C	49_A	0.841	1.00
22_L	138_I	0.840	1.00
93_N	99_I	0.838	1.00
107_A	111_A	0.837	1.00
160_S	164_I	0.834	1.00
111_A	115_D	0.820	1.00
103_A	107_A	0.820	1.00
130_A	135_V	0.816	1.00
157_I	161_A	0.815	1.00
117_R	123_V	0.811	1.00
68_V	71_S	0.800	1.00
145_R	148_V	0.793	0.99
113_Y	118_A	0.788	0.99
40_Y	159_C	0.785	0.99
90_D	93_N	0.783	0.99
158_A	162_I	0.779	0.99
20_L	24_G	0.769	0.99
102_S	107_A	0.767	0.99
105_A	109_A	0.767	0.99
154_G	157_I	0.767	0.99
18_R	21_A	0.764	0.99
89_N	93_N	0.764	0.99
111_A	114_A	0.759	0.99
87_V	90_D	0.757	0.99
92_R	96_S	0.750	0.99
101_L	109_A	0.750	0.99
110_A	113_Y	0.745	0.99
67_L	71_S	0.740	0.99
22_L	30_L	0.734	0.99
64_I	68_V	0.733	0.99
60_E	64_I	0.727	0.99
93_N	98_N	0.724	0.99
112_A	124_G	0.722	0.99
103_A	110_A	0.718	0.99
115_D	124_G	0.714	0.99
30_L	34_P	0.710	0.99
17_R	20_L	0.710	0.99
23_A	26_G	0.705	0.99
116_L	121_A	0.705	0.99
150_R	154_G	0.703	0.99
18_R	22_L	0.702	0.99
119_L	123_V	0.700	0.99
117_R	124_G	0.700	0.99
104_A	110_A	0.695	0.99
72_L	77_L	0.695	0.99
73_P	77_L	0.694	0.99
149_E	160_S	0.691	0.99
12_Y	35_G	0.688	0.99
62_S	66_S	0.685	0.98
151_I	154_G	0.685	0.98
24_G	29_R	0.685	0.98
152_V	156_L	0.682	0.98
127_L	136_L	0.675	0.98
10_A	13_F	0.675	0.98
22_L	140_P	0.673	0.98
9_A	13_F	0.670	0.98
33_L	36_Y	0.669	0.98
23_A	27_G	0.663	0.98
156_L	160_S	0.661	0.98
91_I	95_A	0.659	0.98
118_A	121_A	0.658	0.98
10_A	14_L	0.657	0.98
128_A	131_G	0.651	0.98
127_L	130_A	0.647	0.98
35_G	41_V	0.646	0.98
129_A	133_G	0.646	0.98
155_L	159_C	0.645	0.98
112_A	117_R	0.645	0.98
113_Y	125_V	0.641	0.98
122_A	125_V	0.638	0.98
159_C	164_I	0.634	0.98
101_L	110_A	0.630	0.97
145_R	159_C	0.625	0.97
113_Y	123_V	0.623	0.97
112_A	119_L	0.621	0.97
2_L	6_A	0.614	0.97
157_I	164_I	0.613	0.97
111_A	119_L	0.610	0.97
114_A	119_L	0.605	0.97
130_A	136_L	0.603	0.97
111_A	116_L	0.603	0.97
147_R	150_R	0.602	0.97
53_L	57_L	0.598	0.96
56_W	64_I	0.597	0.96
114_A	122_A	0.595	0.96
145_R	160_S	0.590	0.96
32_S	37_Y	0.590	0.96
114_A	125_V	0.589	0.96
114_A	121_A	0.587	0.96
77_L	80_S	0.585	0.96
15_G	138_I	0.581	0.96
25_G	29_R	0.581	0.96
80_S	84_L	0.578	0.96
149_E	163_A	0.574	0.96
116_L	124_G	0.573	0.96
149_E	164_I	0.571	0.95
132_A	136_L	0.566	0.95
31_H	37_Y	0.566	0.95
132_A	137_R	0.564	0.95
13_F	16_R	0.563	0.95
114_A	124_G	0.561	0.95
156_L	159_C	0.553	0.95
159_C	163_A	0.551	0.94
52_L	160_S	0.550	0.94
116_L	123_V	0.550	0.94
88_L	91_I	0.550	0.94
104_A	109_A	0.549	0.94
72_L	91_I	0.547	0.94
88_L	92_R	0.546	0.94
126_A	130_A	0.545	0.94
36_Y	148_V	0.536	0.94
83_E	90_D	0.535	0.94
67_L	70_A	0.532	0.93
22_L	25_G	0.530	0.93
51_L	58_A	0.529	0.93
127_L	135_V	0.528	0.93
73_P	91_I	0.521	0.93
147_R	153_M	0.521	0.93
50_L	54_A	0.519	0.93
101_L	111_A	0.517	0.92
125_V	128_A	0.515	0.92
25_G	30_L	0.513	0.92
5_L	9_A	0.511	0.92
19_A	90_D	0.510	0.92
120_L	125_V	0.509	0.92
130_A	137_R	0.508	0.92
128_A	134_A	0.507	0.92
68_V	88_L	0.505	0.92
124_G	128_A	0.500	0.91

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
2mofA	1	0.1566	19.7	0.927	Contact Map
2mfrA	1	0.1867	7.7	0.939	Contact Map
2ks1B	1	0.1446	6.8	0.941	Contact Map
2jwaA	2	0.1386	5.2	0.944	Contact Map
1iijA	1	0.1084	5.1	0.944	Contact Map
4us3A	1	0.3193	4.9	0.945	Contact Map
2m20A	2	0.247	4.8	0.945	Contact Map
2l2tA	2	0.1506	4.5	0.946	Contact Map
2k1kA	2	0.1084	4	0.947	Contact Map
2onkC	2	0.6325	3.5	0.948	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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