YWRB - BACSU - GREMLIN Contacts

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YWRB - Uncharacterized transporter YwrB

UniProt:	O05216	Sequences: MKNHPYRDMTAAMVRTGILGFGGGPSVIPLIRHEAVNKYKWIDDDEFGEILAIANALPGPIATKMAAYLGFKLKGTLGAIVAILAHILPTCLAMVGLFAAVNVLSHSAIVAGMIGAVTPVIAVMLGIMAYEFGQKALKGFGWVTGILFFIIAFIGLQTLQINPGLVIIIFLAYGAFHFKLKDKITNKHSKDKGMSAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	197 (170)
Sequences:	6612 (4608)
Seq/√Len:	353.4

BACSU - YWRB YWRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_R	44_D	4.801	1.00
10_T	85_A	4.375	1.00
33_H	37_N	3.961	1.00
43_D	46_E	3.748	1.00
46_E	72_K	3.711	1.00
67_A	83_I	2.919	1.00
6_Y	81_V	2.833	1.00
15_R	34_E	2.692	1.00
8_D	39_Y	2.536	1.00
34_E	38_K	2.479	1.00
11_A	15_R	2.192	1.00
32_R	37_N	2.180	1.00
71_F	79_A	2.125	1.00
162_N	165_L	2.112	1.00
81_V	85_A	1.986	1.00
33_H	38_K	1.973	1.00
42_I	69_L	1.967	1.00
34_E	39_Y	1.839	1.00
10_T	88_L	1.834	1.00
154_I	159_L	1.822	1.00
50_I	68_Y	1.821	1.00
154_I	158_T	1.817	1.00
123_V	127_I	1.808	1.00
7_R	11_A	1.754	1.00
9_M	74_K	1.751	1.00
12_A	34_E	1.698	1.00
155_G	159_L	1.697	1.00
153_F	157_Q	1.697	1.00
133_G	137_L	1.689	1.00
9_M	82_A	1.685	1.00
19_L	30_L	1.556	1.00
170_F	174_G	1.535	1.00
156_L	166_V	1.527	1.00
14_V	18_I	1.519	1.00
146_I	150_I	1.425	1.00
44_D	135_K	1.403	1.00
169_I	173_Y	1.382	1.00
75_G	78_G	1.369	1.00
111_A	115_G	1.368	1.00
147_L	151_I	1.362	1.00
35_A	41_W	1.341	1.00
13_M	35_A	1.316	1.00
32_R	131_E	1.315	1.00
9_M	73_L	1.309	1.00
12_A	39_Y	1.299	1.00
143_V	147_L	1.294	1.00
68_Y	72_K	1.286	1.00
171_L	174_G	1.286	1.00
70_G	78_G	1.270	1.00
9_M	13_M	1.250	1.00
173_Y	177_H	1.245	1.00
45_D	49_E	1.239	1.00
16_T	31_I	1.231	1.00
144_T	147_L	1.225	1.00
128_M	132_F	1.222	1.00
13_M	82_A	1.195	1.00
149_F	153_F	1.179	1.00
144_T	177_H	1.178	1.00
24_G	27_V	1.170	1.00
36_V	47_F	1.159	1.00
168_I	171_L	1.146	1.00
27_V	62_A	1.133	1.00
6_Y	74_K	1.130	1.00
137_L	146_I	1.125	1.00
161_I	165_L	1.124	1.00
10_T	81_V	1.116	1.00
139_G	145_G	1.114	1.00
133_G	136_A	1.098	1.00
139_G	143_V	1.094	1.00
76_T	80_I	1.092	1.00
137_L	149_F	1.085	1.00
15_R	19_L	1.084	1.00
67_A	79_A	1.079	1.00
164_G	168_I	1.067	1.00
73_L	77_L	1.067	1.00
17_G	90_T	1.051	1.00
145_G	149_F	1.040	1.00
152_A	170_F	1.033	1.00
166_V	170_F	1.033	1.00
94_M	97_L	1.025	1.00
143_V	146_I	1.014	1.00
12_A	41_W	1.003	1.00
46_E	49_E	1.003	1.00
144_T	173_Y	0.995	1.00
78_G	82_A	0.995	1.00
109_I	113_M	0.989	1.00
80_I	84_L	0.987	1.00
127_I	131_E	0.984	1.00
152_A	166_V	0.983	1.00
31_I	35_A	0.983	1.00
35_A	69_L	0.978	1.00
20_G	47_F	0.976	1.00
171_L	175_A	0.972	1.00
105_S	111_A	0.970	1.00
92_L	96_G	0.959	1.00
6_Y	77_L	0.956	1.00
37_N	40_K	0.947	1.00
130_Y	134_Q	0.945	1.00
78_G	85_A	0.941	1.00
20_G	27_V	0.937	1.00
57_L	67_A	0.929	1.00
47_F	51_L	0.922	1.00
11_A	14_V	0.921	1.00
16_T	90_T	0.900	1.00
9_M	81_V	0.892	1.00
16_T	27_V	0.886	1.00
108_A	112_G	0.884	1.00
114_I	117_V	0.879	1.00
18_I	93_A	0.877	1.00
172_A	176_F	0.877	1.00
54_A	57_L	0.871	1.00
168_I	172_A	0.871	1.00
77_L	80_I	0.868	1.00
50_I	65_M	0.868	1.00
110_V	113_M	0.866	1.00
125_L	128_M	0.861	1.00
26_S	128_M	0.859	1.00
165_L	169_I	0.855	1.00
94_M	98_F	0.851	1.00
74_K	78_G	0.849	1.00
88_L	92_L	0.839	1.00
69_L	73_L	0.824	1.00
119_P	127_I	0.816	1.00
14_V	88_L	0.815	1.00
162_N	166_V	0.814	1.00
31_I	66_A	0.812	1.00
77_L	81_V	0.810	1.00
35_A	42_I	0.804	1.00
116_A	120_V	0.801	1.00
112_G	116_A	0.801	1.00
54_A	65_M	0.799	1.00
37_N	44_D	0.786	1.00
31_I	62_A	0.778	1.00
53_I	57_L	0.778	1.00
149_F	152_A	0.778	1.00
100_A	104_L	0.777	1.00
113_M	117_V	0.777	1.00
6_Y	10_T	0.777	1.00
63_T	83_I	0.776	1.00
8_D	12_A	0.776	1.00
161_I	166_V	0.774	1.00
51_L	65_M	0.769	1.00
66_A	86_H	0.767	1.00
129_A	133_G	0.767	1.00
104_L	110_V	0.759	1.00
35_A	73_L	0.755	1.00
47_F	65_M	0.747	1.00
12_A	16_T	0.741	1.00
24_G	64_K	0.741	1.00
84_L	88_L	0.740	1.00
28_I	47_F	0.734	1.00
61_I	65_M	0.730	1.00
12_A	15_R	0.722	0.99
139_G	168_I	0.710	0.99
149_F	156_L	0.698	0.99
57_L	63_T	0.689	0.99
99_A	102_N	0.683	0.99
119_P	123_V	0.682	0.99
16_T	57_L	0.679	0.99
42_I	46_E	0.677	0.99
164_G	171_L	0.672	0.99
30_L	124_M	0.670	0.99
132_F	136_A	0.668	0.99
21_F	27_V	0.668	0.99
63_T	87_I	0.661	0.99
25_P	64_K	0.660	0.99
61_I	64_K	0.659	0.99
13_M	17_G	0.658	0.99
151_I	155_G	0.656	0.99
173_Y	178_F	0.655	0.99
154_I	169_I	0.654	0.99
104_L	107_S	0.653	0.99
102_N	105_S	0.650	0.99
91_C	95_V	0.646	0.99
10_T	14_V	0.645	0.99
163_P	167_I	0.640	0.99
57_L	83_I	0.629	0.99
131_E	135_K	0.629	0.99
48_G	136_A	0.627	0.98
27_V	86_H	0.627	0.98
102_N	106_H	0.626	0.98
115_G	119_P	0.625	0.98
136_A	139_G	0.624	0.98
17_G	30_L	0.614	0.98
106_H	109_I	0.614	0.98
49_E	52_A	0.611	0.98
83_I	87_I	0.610	0.98
97_L	100_A	0.604	0.98
53_I	64_K	0.602	0.98
90_T	119_P	0.600	0.98
169_I	172_A	0.598	0.98
20_G	26_S	0.597	0.98
101_V	110_V	0.596	0.98
21_F	121_I	0.594	0.98
88_L	91_C	0.592	0.98
8_D	11_A	0.587	0.98
82_A	85_A	0.587	0.98
91_C	94_M	0.586	0.98
148_F	152_A	0.584	0.98
44_D	48_G	0.580	0.98
45_D	135_K	0.576	0.97
14_V	17_G	0.576	0.97
101_V	104_L	0.576	0.97
103_V	107_S	0.571	0.97
24_G	62_A	0.569	0.97
62_A	86_H	0.569	0.97
95_V	99_A	0.568	0.97
74_K	77_L	0.567	0.97
167_I	174_G	0.567	0.97
25_P	57_L	0.565	0.97
103_V	158_T	0.564	0.97
90_T	94_M	0.564	0.97
108_A	111_A	0.563	0.97
6_Y	9_M	0.563	0.97
16_T	29_P	0.561	0.97
25_P	121_I	0.561	0.97
9_M	78_G	0.561	0.97
168_I	178_F	0.560	0.97
17_G	86_H	0.553	0.97
52_A	89_P	0.552	0.97
25_P	61_I	0.552	0.97
155_G	161_I	0.545	0.96
63_T	67_A	0.542	0.96
151_I	173_Y	0.540	0.96
98_F	102_N	0.540	0.96
130_Y	133_G	0.539	0.96
129_A	132_F	0.538	0.96
131_E	134_Q	0.537	0.96
175_A	178_F	0.537	0.96
144_T	148_F	0.536	0.96
173_Y	176_F	0.535	0.96
147_L	150_I	0.532	0.96
146_I	158_T	0.532	0.96
52_A	167_I	0.532	0.96
31_I	47_F	0.530	0.96
42_I	72_K	0.526	0.96
163_P	172_A	0.526	0.96
154_I	175_A	0.525	0.96
24_G	128_M	0.523	0.95
81_V	84_L	0.522	0.95
42_I	50_I	0.522	0.95
16_T	19_L	0.521	0.95
24_G	61_I	0.518	0.95
54_A	61_I	0.517	0.95
25_P	125_L	0.517	0.95
47_F	60_P	0.516	0.95
41_W	121_I	0.509	0.95
174_G	178_F	0.508	0.95
66_A	83_I	0.507	0.95
31_I	86_H	0.507	0.95
25_P	28_I	0.506	0.95
25_P	29_P	0.504	0.94
164_G	167_I	0.501	0.94
109_I	175_A	0.500	0.94
152_A	159_L	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
4rp9A	2	0.9188	37.7	0.929	Contact Map
4pypA	1	0.8782	19.8	0.938	Contact Map
3qe7A	2	0.8629	19	0.939	Contact Map
2cfqA	1	0.9188	17.8	0.939	Contact Map
4q65A	1	0.9086	13.1	0.943	Contact Map
2xq2A	2	0.8731	12.3	0.944	Contact Map
4ikvA	1	0.9086	10.7	0.945	Contact Map
2h3oA	1	0.2234	10.7	0.945	Contact Map
2mnsA	1	0.1015	10.4	0.945	Contact Map
2kncA	1	0.2183	8.9	0.947	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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