DctA-YdbH - PFAM28P - GREMLIN Contacts

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DctA-YdbH - Dicarboxylate transport

PFAM:	PF11739	Sequences: TIASINPGIPLTDGTIRFQGSYPLLPGGRLRIERASWPFLGGRLSLEPLRLDLGAEERRLTLRLDGLDLAELLALLGLEGLSATGTLDGRLPLVFDGGGVRIEGGRLAARGPGGLRYDGEAALAALAASNPQLDLAFDALENFRYDSLSATLDGDLDGELVLRLRLDGKNPDVLAGRPIRLNLNLEGNLPQLLRSLRLGYDLSEEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	206 (198)
Sequences:	2968 (2185)
Seq/√Len:	155.3
META:	0.827

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_D	110_R	4.258	1.00
142_N	172_D	4.156	1.00
13_D	38_P	3.258	1.00
36_S	43_R	2.871	1.00
41_G	71_E	2.800	1.00
73_L	83_A	2.706	1.00
104_G	153_D	2.669	1.00
47_E	63_R	2.668	1.00
71_E	74_A	2.596	1.00
134_D	138_D	2.564	1.00
96_D	99_G	2.438	1.00
63_R	90_R	2.373	1.00
138_D	141_E	2.271	1.00
84_T	145_Y	2.239	1.00
167_D	180_R	2.232	1.00
66_G	110_R	2.144	1.00
174_L	177_R	2.126	1.00
82_S	116_R	2.109	1.00
68_D	71_E	2.071	1.00
64_L	67_L	2.045	1.00
41_G	68_D	1.989	1.00
170_N	176_G	1.958	1.00
43_R	65_D	1.942	1.00
81_L	117_Y	1.938	1.00
66_G	88_D	1.922	1.00
146_D	167_D	1.915	1.00
68_D	86_T	1.835	1.00
45_S	65_D	1.798	1.00
106_R	149_S	1.730	1.00
94_V	103_E	1.719	1.00
14_G	37_W	1.709	1.00
136_A	181_L	1.589	1.00
57_E	96_D	1.583	1.00
113_G	145_Y	1.582	1.00
59_R	94_V	1.579	1.00
95_F	100_V	1.572	1.00
59_R	103_E	1.565	1.00
146_D	169_K	1.562	1.00
104_G	151_T	1.535	1.00
37_W	44_L	1.466	1.00
165_R	180_R	1.458	1.00
11_L	37_W	1.454	1.00
108_A	149_S	1.452	1.00
17_R	33_E	1.445	1.00
69_L	87_L	1.439	1.00
92_P	153_D	1.432	1.00
5_I	14_G	1.413	1.00
57_E	94_V	1.412	1.00
61_T	90_R	1.412	1.00
49_L	60_L	1.406	1.00
143_F	166_L	1.399	1.00
200_Y	203_S	1.393	1.00
4_S	10_P	1.370	1.00
38_P	43_R	1.370	1.00
188_N	191_Q	1.367	1.00
163_R	184_N	1.364	1.00
179_I	183_L	1.357	1.00
153_D	163_R	1.357	1.00
31_R	50_R	1.345	1.00
32_I	49_L	1.331	1.00
91_L	105_G	1.329	1.00
147_S	167_D	1.328	1.00
107_L	150_A	1.303	1.00
111_G	115_L	1.302	1.00
70_A	74_A	1.297	1.00
159_E	186_E	1.294	1.00
106_R	151_T	1.278	1.00
7_P	10_P	1.247	1.00
161_V	186_E	1.244	1.00
139_A	173_V	1.239	1.00
86_T	110_R	1.236	1.00
151_T	163_R	1.233	1.00
6_N	10_P	1.233	1.00
60_L	93_L	1.224	1.00
47_E	90_R	1.213	1.00
4_S	12_T	1.208	1.00
111_G	114_G	1.207	1.00
66_G	86_T	1.203	1.00
188_N	196_L	1.186	1.00
89_G	107_L	1.179	1.00
39_F	44_L	1.160	1.00
170_N	174_L	1.150	1.00
164_L	185_L	1.146	1.00
78_L	81_L	1.136	1.00
46_L	49_L	1.109	1.00
90_R	106_R	1.097	0.99
174_L	179_I	1.087	0.99
83_A	109_A	1.081	0.99
52_D	55_A	1.080	0.99
62_L	93_L	1.078	0.99
17_R	34_R	1.050	0.99
197_R	200_Y	1.030	0.99
139_A	179_I	1.024	0.99
19_Q	31_R	1.012	0.99
130_N	133_L	1.006	0.99
154_G	190_P	1.005	0.99
85_G	145_Y	1.003	0.99
135_L	173_V	0.999	0.99
29_R	52_D	0.998	0.99
197_R	201_D	0.985	0.99
64_L	107_L	0.984	0.99
109_A	148_L	0.983	0.99
105_G	184_N	0.981	0.99
114_G	144_R	0.978	0.99
187_G	192_L	0.977	0.99
68_D	72_L	0.974	0.99
144_R	171_P	0.971	0.99
119_G	123_L	0.968	0.99
19_Q	25_L	0.965	0.99
3_A	13_D	0.963	0.99
120_E	141_E	0.947	0.98
2_I	14_G	0.941	0.98
36_S	45_S	0.940	0.98
73_L	76_L	0.933	0.98
31_R	48_P	0.926	0.98
196_L	199_G	0.926	0.98
14_G	38_P	0.918	0.98
135_L	179_I	0.908	0.98
191_Q	197_R	0.900	0.98
118_D	141_E	0.898	0.98
45_S	63_R	0.886	0.98
173_V	176_G	0.884	0.98
150_A	164_L	0.882	0.97
170_N	173_V	0.880	0.97
119_G	122_A	0.879	0.97
133_L	136_A	0.879	0.97
55_A	58_R	0.872	0.97
109_A	145_Y	0.871	0.97
103_E	153_D	0.867	0.97
29_R	50_R	0.858	0.97
135_L	139_A	0.856	0.97
135_L	138_D	0.855	0.97
182_N	186_E	0.854	0.97
177_R	188_N	0.843	0.97
16_I	35_A	0.841	0.97
58_R	95_F	0.837	0.97
188_N	195_S	0.834	0.96
119_G	137_F	0.832	0.96
115_L	144_R	0.829	0.96
117_Y	154_G	0.828	0.96
137_F	143_F	0.822	0.96
35_A	46_L	0.820	0.96
15_T	36_S	0.818	0.96
115_L	145_Y	0.816	0.96
183_L	203_S	0.803	0.96
177_R	180_R	0.803	0.96
87_L	110_R	0.799	0.95
196_L	203_S	0.799	0.95
158_G	190_P	0.795	0.95
112_P	115_L	0.795	0.95
187_G	190_P	0.794	0.95
187_G	200_Y	0.792	0.95
154_G	160_L	0.790	0.95
131_P	134_D	0.783	0.95
9_I	12_T	0.780	0.95
80_G	95_F	0.776	0.95
132_Q	135_L	0.772	0.95
37_W	154_G	0.772	0.95
198_L	202_L	0.770	0.94
127_A	130_N	0.766	0.94
143_F	170_N	0.766	0.94
109_A	113_G	0.765	0.94
40_L	75_L	0.762	0.94
174_L	187_G	0.760	0.94
176_G	180_R	0.757	0.94
121_A	124_A	0.754	0.94
143_F	174_L	0.752	0.94
191_Q	194_R	0.751	0.94
185_L	193_L	0.748	0.94
89_G	150_A	0.747	0.94
76_L	187_G	0.747	0.94
14_G	154_G	0.743	0.93
167_D	178_P	0.740	0.93
174_L	180_R	0.740	0.93
40_L	67_L	0.740	0.93
154_G	158_G	0.737	0.93
3_A	12_T	0.733	0.93
177_R	187_G	0.728	0.93
159_E	188_N	0.722	0.92
136_A	158_G	0.721	0.92
116_R	142_N	0.720	0.92
76_L	150_A	0.717	0.92
2_I	5_I	0.716	0.92
88_D	108_A	0.715	0.92
196_L	200_Y	0.714	0.92
188_N	192_L	0.714	0.92
171_P	177_R	0.707	0.92
66_G	147_S	0.703	0.91
169_K	176_G	0.703	0.91
51_L	62_L	0.697	0.91
69_L	83_A	0.697	0.91
144_R	170_N	0.694	0.91
19_Q	33_E	0.690	0.91
94_V	101_R	0.688	0.90
199_G	203_S	0.688	0.90
194_R	202_L	0.685	0.90
16_I	34_R	0.683	0.90
32_I	35_A	0.679	0.90
152_L	162_L	0.677	0.90
191_Q	200_Y	0.674	0.90
170_N	175_A	0.666	0.89
136_A	179_I	0.663	0.89
92_P	182_N	0.661	0.89
186_E	197_R	0.656	0.88
10_P	40_L	0.656	0.88
173_V	177_R	0.654	0.88
133_L	166_L	0.651	0.88
4_S	7_P	0.643	0.87
79_E	181_L	0.641	0.87
119_G	124_A	0.634	0.87
56_E	97_G	0.631	0.86
25_L	29_R	0.628	0.86
61_T	94_V	0.628	0.86
187_G	197_R	0.627	0.86
65_D	90_R	0.618	0.85
173_V	179_I	0.618	0.85
63_R	82_S	0.615	0.85
28_G	52_D	0.612	0.85
91_L	102_I	0.608	0.84
91_L	161_V	0.608	0.84
142_N	171_P	0.604	0.84
169_K	174_L	0.604	0.84
164_L	183_L	0.600	0.83
51_L	58_R	0.598	0.83
177_R	186_E	0.598	0.83
89_G	109_A	0.594	0.83
14_G	18_F	0.594	0.83
194_R	197_R	0.591	0.82
136_A	143_F	0.587	0.82
187_G	198_L	0.587	0.82
125_A	129_S	0.585	0.82
70_A	98_G	0.585	0.82
189_L	202_L	0.582	0.82
14_G	39_F	0.582	0.82
47_E	61_T	0.580	0.81
144_R	169_K	0.577	0.81
67_L	196_L	0.575	0.81
11_L	14_G	0.573	0.81
119_G	141_E	0.573	0.81
190_P	193_L	0.572	0.80
87_L	183_L	0.571	0.80
116_R	120_E	0.570	0.80
140_L	148_L	0.570	0.80
134_D	184_N	0.569	0.80
179_I	187_G	0.569	0.80
189_L	193_L	0.569	0.80
183_L	188_N	0.569	0.80
10_P	131_P	0.565	0.80
41_G	86_T	0.565	0.80
169_K	175_A	0.565	0.80
180_R	183_L	0.563	0.79
122_A	137_F	0.561	0.79
42_G	67_L	0.560	0.79
101_R	156_L	0.557	0.79
16_I	32_I	0.556	0.79
15_T	34_R	0.556	0.79
150_A	158_G	0.552	0.78
157_D	190_P	0.551	0.78
138_D	173_V	0.550	0.78
70_A	82_S	0.550	0.78
189_L	196_L	0.545	0.77
91_L	152_L	0.544	0.77
177_R	202_L	0.543	0.77
10_P	15_T	0.543	0.77
74_A	82_S	0.540	0.77
104_G	108_A	0.536	0.76
197_R	203_S	0.533	0.76
194_R	201_D	0.525	0.75
190_P	197_R	0.524	0.74
24_L	60_L	0.523	0.74
198_L	201_D	0.522	0.74
109_A	147_S	0.521	0.74
15_T	56_E	0.520	0.74
187_G	191_Q	0.520	0.74
139_A	143_F	0.519	0.74
50_R	59_R	0.518	0.74
29_R	59_R	0.517	0.73
182_N	193_L	0.517	0.73
74_A	79_E	0.516	0.73
41_G	105_G	0.515	0.73
26_P	29_R	0.515	0.73
77_G	122_A	0.513	0.73
165_R	182_N	0.513	0.73
16_I	107_L	0.512	0.73
150_A	157_D	0.512	0.73
117_Y	137_F	0.511	0.73
155_D	159_E	0.507	0.72
102_I	182_N	0.506	0.72
171_P	176_G	0.506	0.72
37_W	62_L	0.503	0.71
39_F	67_L	0.502	0.71
56_E	162_L	0.502	0.71
13_D	104_G	0.501	0.71
55_A	96_D	0.501	0.71
136_A	140_L	0.501	0.71
102_I	181_L	0.500	0.71
143_F	181_L	0.500	0.71

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
2xmxA	1	0.4175	10.6	0.94	Contact Map
4jtmA	2	0.3204	8.2	0.943	Contact Map
1yycA	1	0.5583	2.9	0.954	Contact Map
2ekfA	1	0.2087	2.8	0.954	Contact Map
2oplA	2	0.7087	2.7	0.955	Contact Map
1hekA	1	0.1408	2.5	0.956	Contact Map
2ru9A	1	0.1893	2.5	0.956	Contact Map
3vz9B	1	0.3495	2.4	0.956	Contact Map
2ywqA	1	0.3641	2.1	0.958	Contact Map
2qifA	2	0.2961	2	0.958	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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