YWRA - BACSU - GREMLIN Contacts

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YWRA - Uncharacterized transporter YwrA

UniProt:	O05215	Sequences: MISIYLFMAFFIANLLGYGGGPASIPLMFEEVVNRYSWLSNDQFSNMLALANALPGPIATKIAAYVGYSAGGWPGFLIALIATVVPSALALIVLLRIIQRFRQSPVIKGMTLSVQPVIAVMMLILTWQIGADGIKAIGWVQSIVITGISLLAMTKFKMHPAFLIIAAFLYGGLVIPYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	178 (167)
Sequences:	6558 (4548)
Seq/√Len:	352.0

BACSU - YWRA YWRB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_F	41_N	4.620	1.00
7_F	82_A	4.178	1.00
30_E	34_N	3.806	1.00
40_S	43_Q	3.688	1.00
43_Q	69_S	3.595	1.00
64_A	80_L	2.917	1.00
12_I	31_E	2.583	1.00
31_E	35_R	2.488	1.00
5_Y	36_Y	2.469	1.00
68_Y	76_F	2.226	1.00
8_M	12_I	2.137	1.00
30_E	35_R	2.096	1.00
29_F	34_N	2.078	1.00
159_H	162_F	2.067	1.00
78_I	82_A	2.031	1.00
150_L	154_T	2.022	1.00
39_L	66_V	1.985	1.00
6_L	71_G	1.880	1.00
7_F	85_V	1.856	1.00
47_M	65_Y	1.843	1.00
151_L	155_K	1.837	1.00
151_L	156_F	1.834	1.00
31_E	36_Y	1.775	1.00
9_A	31_E	1.765	1.00
120_V	124_I	1.754	1.00
153_M	163_L	1.733	1.00
130_G	134_I	1.701	1.00
152_A	156_F	1.665	1.00
170_Y	174_V	1.626	1.00
4_I	8_M	1.625	1.00
6_L	79_A	1.559	1.00
16_L	27_L	1.548	1.00
143_I	147_G	1.483	1.00
9_A	36_Y	1.469	1.00
11_F	15_L	1.456	1.00
166_A	170_Y	1.441	1.00
32_V	38_W	1.395	1.00
167_A	171_G	1.394	1.00
136_A	142_S	1.375	1.00
10_F	32_V	1.353	1.00
108_K	112_L	1.352	1.00
140_V	144_V	1.338	1.00
134_I	143_I	1.302	1.00
7_F	78_I	1.301	1.00
21_G	24_S	1.299	1.00
141_Q	144_V	1.299	1.00
146_T	150_L	1.296	1.00
29_F	128_Q	1.286	1.00
67_G	75_G	1.278	1.00
41_N	132_D	1.271	1.00
144_V	148_I	1.270	1.00
165_I	168_F	1.251	1.00
125_L	129_I	1.250	1.00
65_Y	69_S	1.240	1.00
158_M	162_F	1.231	1.00
33_V	44_F	1.223	1.00
140_V	143_I	1.190	1.00
10_F	79_A	1.181	1.00
149_S	167_A	1.171	1.00
127_W	131_A	1.167	1.00
13_A	28_M	1.148	1.00
24_S	59_A	1.147	1.00
42_D	46_N	1.129	1.00
130_G	133_G	1.112	1.00
161_A	165_I	1.109	1.00
73_W	77_L	1.107	1.00
162_F	166_A	1.101	1.00
64_A	76_F	1.085	1.00
6_L	10_F	1.070	1.00
91_L	94_L	1.064	1.00
12_I	16_L	1.049	1.00
102_R	108_K	1.036	1.00
77_L	81_I	1.032	1.00
124_I	128_Q	1.030	1.00
163_L	167_A	1.030	1.00
149_S	163_L	1.030	1.00
142_S	146_T	1.017	1.00
168_F	171_G	1.016	1.00
6_L	78_I	1.013	1.00
105_P	109_G	1.005	1.00
14_N	87_S	1.004	1.00
9_A	38_W	1.001	1.00
43_Q	46_N	0.997	1.00
44_F	48_L	0.988	1.00
17_G	44_F	0.982	1.00
168_F	172_G	0.963	1.00
72_G	75_G	0.960	1.00
17_G	24_S	0.958	1.00
32_V	66_V	0.953	1.00
75_G	79_A	0.950	1.00
128_Q	132_D	0.946	1.00
165_I	169_L	0.943	1.00
34_N	37_S	0.930	1.00
141_Q	170_Y	0.929	1.00
75_G	82_A	0.928	1.00
28_M	32_V	0.918	1.00
70_A	74_P	0.916	1.00
74_P	77_L	0.913	1.00
159_H	163_L	0.910	1.00
54_L	64_A	0.906	1.00
13_A	87_S	0.902	1.00
111_T	114_V	0.902	1.00
32_V	39_L	0.895	1.00
106_V	110_M	0.889	1.00
13_A	24_S	0.887	1.00
169_L	173_L	0.886	1.00
23_A	125_L	0.877	1.00
89_L	93_V	0.877	1.00
71_G	75_G	0.865	1.00
8_M	11_F	0.863	1.00
6_L	70_A	0.854	1.00
85_V	89_L	0.846	1.00
91_L	95_L	0.846	1.00
81_I	85_V	0.842	1.00
5_Y	9_A	0.838	1.00
109_G	113_S	0.838	1.00
15_L	90_A	0.837	1.00
63_A	83_T	0.836	1.00
47_M	62_I	0.834	1.00
122_M	125_L	0.832	1.00
158_M	163_L	0.824	1.00
74_P	78_I	0.819	1.00
51_A	54_L	0.818	1.00
148_I	152_A	0.816	1.00
101_F	107_I	0.816	1.00
11_F	85_V	0.814	1.00
134_I	146_T	0.811	1.00
50_L	54_L	0.806	1.00
141_Q	174_V	0.805	1.00
116_P	124_I	0.804	1.00
110_M	114_V	0.795	1.00
107_I	110_M	0.794	1.00
51_A	62_I	0.790	1.00
66_V	70_A	0.787	1.00
97_I	101_F	0.785	1.00
60_T	80_L	0.784	1.00
101_F	104_S	0.777	1.00
28_M	63_A	0.774	1.00
113_S	117_V	0.773	1.00
48_L	62_I	0.771	1.00
9_A	12_I	0.768	1.00
44_F	62_I	0.766	1.00
136_A	165_I	0.757	1.00
96_R	99_Q	0.756	1.00
9_A	13_A	0.752	1.00
149_S	156_F	0.745	1.00
105_P	108_K	0.745	1.00
58_I	62_I	0.744	1.00
54_L	60_T	0.733	1.00
7_F	11_F	0.724	0.99
126_T	130_G	0.720	0.99
136_A	140_V	0.700	0.99
28_M	59_A	0.697	0.99
25_I	44_F	0.693	0.99
146_T	153_M	0.693	0.99
140_V	155_K	0.691	0.99
99_Q	102_R	0.688	0.99
60_T	84_V	0.685	0.99
27_L	121_M	0.684	0.99
18_Y	24_S	0.683	0.99
13_A	54_L	0.675	0.99
54_L	80_L	0.674	0.99
14_N	27_L	0.673	0.99
39_L	43_Q	0.673	0.99
131_A	136_A	0.672	0.99
79_A	82_A	0.672	0.99
88_A	91_L	0.671	0.99
46_N	49_A	0.671	0.99
95_L	99_Q	0.667	0.99
151_L	172_G	0.663	0.99
147_G	155_K	0.661	0.99
21_G	59_A	0.661	0.99
100_R	104_S	0.658	0.99
17_G	23_A	0.655	0.99
141_Q	145_I	0.655	0.99
42_D	132_D	0.652	0.99
32_V	36_Y	0.646	0.99
94_L	97_I	0.640	0.99
151_L	154_T	0.639	0.99
87_S	116_P	0.637	0.99
41_N	45_S	0.633	0.99
22_P	118_I	0.628	0.98
24_S	83_T	0.628	0.98
146_T	149_S	0.626	0.98
45_S	133_G	0.626	0.98
5_Y	8_M	0.625	0.98
116_P	120_V	0.623	0.98
122_M	129_I	0.621	0.98
71_G	74_P	0.618	0.98
92_I	96_R	0.616	0.98
80_L	84_V	0.612	0.98
11_F	14_N	0.610	0.98
10_F	14_N	0.609	0.98
33_V	38_W	0.607	0.98
160_P	164_I	0.603	0.98
152_A	158_M	0.602	0.98
143_I	155_K	0.599	0.98
88_A	92_I	0.598	0.98
18_Y	118_I	0.596	0.98
59_A	83_T	0.596	0.98
98_I	107_I	0.589	0.98
4_I	7_F	0.586	0.98
22_P	54_L	0.586	0.98
22_P	58_I	0.584	0.98
141_Q	148_I	0.584	0.98
34_N	41_N	0.583	0.98
51_A	58_I	0.579	0.97
131_A	135_K	0.577	0.97
90_A	94_L	0.576	0.97
49_A	86_P	0.574	0.97
122_M	126_T	0.569	0.97
29_F	33_V	0.567	0.97
78_I	81_I	0.564	0.97
24_S	121_M	0.564	0.97
87_S	91_L	0.562	0.97
164_I	167_A	0.554	0.97
124_I	127_W	0.552	0.97
13_A	26_P	0.551	0.97
45_S	129_I	0.548	0.96
112_L	116_P	0.544	0.96
145_I	148_I	0.540	0.96
144_V	147_G	0.538	0.96
6_L	75_G	0.536	0.96
126_T	129_I	0.535	0.96
28_M	44_F	0.534	0.96
10_F	82_A	0.533	0.96
13_A	16_L	0.533	0.96
14_N	83_T	0.532	0.96
152_A	163_L	0.530	0.96
133_G	136_A	0.529	0.96
14_N	125_L	0.528	0.96
11_F	48_L	0.526	0.96
104_S	107_I	0.525	0.96
44_F	57_P	0.525	0.96
25_I	62_I	0.523	0.95
76_F	79_A	0.521	0.95
22_P	122_M	0.520	0.95
94_L	101_F	0.518	0.95
100_R	157_K	0.517	0.95
39_L	47_M	0.513	0.95
161_A	164_I	0.511	0.95
164_I	171_G	0.510	0.95
147_G	150_L	0.510	0.95
18_Y	57_P	0.507	0.95
103_Q	106_V	0.507	0.95
99_Q	103_Q	0.504	0.94
18_Y	114_V	0.502	0.94
22_P	26_P	0.501	0.94
38_W	118_I	0.500	0.94
60_T	64_A	0.500	0.94

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
2mnsA	1	0.1124	9.2	0.942	Contact Map
2h3oA	1	0.2472	8.3	0.943	Contact Map
3qnqA	2	0.7753	3.5	0.953	Contact Map
3izxA	3	0.4663	3.4	0.953	Contact Map
2l8sA	1	0.1461	2.4	0.956	Contact Map
4wrtB	1	0.3034	2.4	0.956	Contact Map
4wsbB	1	0.3146	1.9	0.959	Contact Map
4fibA	1	0.2191	1.9	0.959	Contact Map
1afoA	2	0.2247	1.8	0.959	Contact Map
2micA	2	0.2303	1.7	0.96	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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