YDBS - BACSU - GREMLIN Contacts

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YDBS - UPF0699 transmembrane protein YdbS

UniProt:	P96615	Sequences: MREQPKNQISPDGLKVWRLQEIIISAVCLLIVIAVAVLSYYFHWPYWISGVLGAVWLLGSIVTVFIIPKVRHKVWRYEVHEHEIDIQSGIFVVTRVIVPMVRVQHVDTSQGPLLKKYNLATVKISTAATVHSIPALEMEEADRLRDSISRLARVTDDDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	159 (141)
Sequences:	4423 (3726)
Seq/√Len:	313.8

BACSU - YDBS YDBT
HALSA - Q9HQ30 Q9HQ31

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_Q	138_M	3.316	1.00
140_E	143_R	3.260	1.00
108_T	120_A	3.040	1.00
87_Q	95_R	2.827	1.00
120_A	141_A	2.688	1.00
137_E	140_E	2.615	1.00
13_G	17_W	2.519	1.00
13_G	16_V	2.507	1.00
104_Q	127_A	2.202	1.00
114_L	135_A	2.179	1.00
80_H	83_E	2.002	1.00
143_R	147_S	1.996	1.00
105_H	125_S	1.982	1.00
85_D	95_R	1.950	1.00
14_L	17_W	1.947	1.00
120_A	138_M	1.917	1.00
12_D	15_K	1.916	1.00
110_Q	120_A	1.794	1.00
138_M	142_D	1.777	1.00
66_I	70_V	1.772	1.00
103_V	124_I	1.737	1.00
80_H	85_D	1.683	1.00
78_E	85_D	1.675	1.00
110_Q	115_K	1.673	1.00
118_N	138_M	1.661	1.00
111_G	114_L	1.652	1.00
79_V	100_M	1.642	1.00
67_I	71_R	1.642	1.00
136_L	141_A	1.538	1.00
17_W	20_Q	1.483	1.00
76_R	87_Q	1.467	1.00
109_S	123_K	1.463	1.00
70_V	90_I	1.454	1.00
121_T	132_S	1.423	1.00
75_W	86_I	1.397	1.00
17_W	21_E	1.397	1.00
28_C	32_V	1.383	1.00
69_K	73_K	1.369	1.00
75_W	134_P	1.363	1.00
114_L	121_T	1.344	1.00
108_T	145_R	1.337	1.00
37_V	40_Y	1.312	1.00
84_I	124_I	1.308	1.00
51_V	55_V	1.285	1.00
74_V	93_V	1.247	1.00
147_S	151_L	1.241	1.00
23_I	27_V	1.238	1.00
88_S	96_V	1.232	1.00
121_T	134_P	1.226	1.00
12_D	17_W	1.215	1.00
52_L	56_W	1.213	1.00
16_V	19_L	1.209	1.00
35_V	39_S	1.205	1.00
83_E	97_I	1.202	1.00
67_I	90_I	1.193	1.00
28_C	31_I	1.189	1.00
55_V	59_G	1.172	1.00
70_V	74_V	1.162	1.00
86_I	131_H	1.156	1.00
142_D	146_D	1.151	1.00
13_G	19_L	1.130	1.00
62_V	66_I	1.113	1.00
113_L	116_K	1.102	1.00
74_V	90_I	1.087	1.00
33_I	37_V	1.079	1.00
13_G	18_R	1.065	1.00
47_W	51_V	1.049	1.00
98_V	126_T	1.042	1.00
145_R	150_R	1.035	1.00
108_T	142_D	1.026	1.00
67_I	70_V	1.021	1.00
84_I	133_I	1.020	1.00
16_V	20_Q	1.011	1.00
107_D	123_K	1.007	1.00
139_E	143_R	1.006	1.00
112_P	116_K	1.002	1.00
18_R	69_K	0.996	1.00
107_D	125_S	0.992	1.00
114_L	119_L	0.983	1.00
79_V	147_S	0.979	1.00
25_S	28_C	0.977	1.00
96_V	105_H	0.968	1.00
99_P	102_R	0.952	1.00
14_L	69_K	0.940	1.00
34_A	38_L	0.936	1.00
87_Q	93_V	0.924	1.00
14_L	21_E	0.918	1.00
13_G	20_Q	0.913	1.00
18_R	65_F	0.906	1.00
21_E	24_I	0.891	1.00
119_L	135_A	0.890	1.00
98_V	131_H	0.883	1.00
15_K	18_R	0.882	1.00
140_E	147_S	0.879	1.00
85_D	97_I	0.878	1.00
12_D	16_V	0.871	1.00
72_H	88_S	0.870	1.00
32_V	39_S	0.869	1.00
125_S	129_T	0.863	1.00
146_D	150_R	0.861	1.00
77_Y	86_I	0.858	1.00
55_V	58_L	0.858	1.00
106_V	145_R	0.857	1.00
106_V	141_A	0.855	1.00
20_Q	23_I	0.852	1.00
100_M	151_L	0.846	1.00
103_V	148_I	0.844	1.00
122_V	141_A	0.842	1.00
24_I	27_V	0.837	1.00
21_E	37_V	0.833	1.00
29_L	32_V	0.824	1.00
65_F	69_K	0.816	1.00
38_L	41_Y	0.806	1.00
75_W	115_K	0.794	1.00
58_L	62_V	0.791	1.00
16_V	23_I	0.783	1.00
12_D	23_I	0.782	1.00
16_V	119_L	0.764	0.99
119_L	136_L	0.760	0.99
88_S	94_T	0.760	0.99
70_V	91_F	0.749	0.99
108_T	141_A	0.748	0.99
50_G	54_A	0.747	0.99
71_R	88_S	0.743	0.99
14_L	18_R	0.742	0.99
102_R	127_A	0.734	0.99
15_K	23_I	0.732	0.99
83_E	102_R	0.727	0.99
14_L	19_L	0.721	0.99
38_L	42_F	0.719	0.99
46_Y	49_S	0.716	0.99
16_V	21_E	0.712	0.99
139_E	142_D	0.708	0.99
100_M	148_I	0.707	0.99
109_S	121_T	0.705	0.99
104_Q	125_S	0.704	0.99
125_S	130_V	0.700	0.99
71_R	98_V	0.689	0.99
18_R	21_E	0.687	0.99
82_H	100_M	0.687	0.99
45_P	48_I	0.686	0.99
25_S	32_V	0.681	0.99
49_S	53_G	0.681	0.99
105_H	129_T	0.680	0.99
148_I	151_L	0.673	0.99
25_S	61_I	0.671	0.99
103_V	129_T	0.661	0.98
142_D	145_R	0.649	0.98
55_V	62_V	0.646	0.98
26_A	29_L	0.639	0.98
126_T	136_L	0.630	0.98
144_L	148_I	0.630	0.98
63_T	66_I	0.613	0.97
89_G	148_I	0.611	0.97
80_H	100_M	0.611	0.97
46_Y	52_L	0.607	0.97
64_V	68_P	0.603	0.97
133_I	136_L	0.593	0.97
36_A	40_Y	0.590	0.97
63_T	67_I	0.589	0.97
100_M	104_Q	0.588	0.97
78_E	108_T	0.588	0.97
103_V	152_A	0.587	0.97
108_T	122_V	0.585	0.97
103_V	131_H	0.585	0.97
17_W	23_I	0.584	0.97
128_A	131_H	0.583	0.97
100_M	131_H	0.580	0.96
27_V	30_L	0.579	0.96
37_V	41_Y	0.576	0.96
104_Q	110_Q	0.576	0.96
79_V	144_L	0.576	0.96
25_S	29_L	0.576	0.96
33_I	36_A	0.574	0.96
81_E	100_M	0.573	0.96
82_H	99_P	0.573	0.96
105_H	124_I	0.571	0.96
45_P	53_G	0.570	0.96
145_R	149_S	0.570	0.96
127_A	141_A	0.568	0.96
49_S	61_I	0.568	0.96
53_G	57_L	0.566	0.96
12_D	19_L	0.564	0.96
73_K	76_R	0.561	0.96
104_Q	126_T	0.560	0.96
106_V	148_I	0.555	0.95
125_S	131_H	0.552	0.95
34_A	41_Y	0.549	0.95
94_T	129_T	0.542	0.95
31_I	35_V	0.540	0.95
35_V	40_Y	0.537	0.95
126_T	144_L	0.535	0.94
77_Y	90_I	0.533	0.94
84_I	101_V	0.533	0.94
77_Y	119_L	0.532	0.94
110_Q	124_I	0.530	0.94
79_V	84_I	0.529	0.94
99_P	111_G	0.528	0.94
97_I	100_M	0.528	0.94
75_W	88_S	0.528	0.94
86_I	96_V	0.526	0.94
127_A	133_I	0.523	0.94
71_R	90_I	0.522	0.94
13_G	135_A	0.516	0.93
54_A	58_L	0.514	0.93
83_E	100_M	0.513	0.93
47_W	52_L	0.506	0.93
75_W	85_D	0.505	0.93
68_P	71_R	0.501	0.92
77_Y	136_L	0.501	0.92
96_V	129_T	0.500	0.92
34_A	42_F	0.500	0.92

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
4i0uA	4	0.4717	5.1	0.925	Contact Map
4ev6A	3	0.4654	4.1	0.928	Contact Map
3hsaA	3	0.6792	3.8	0.929	Contact Map
4khbD	1	0.6101	3.1	0.932	Contact Map
4ix7A	1	0.5094	3	0.933	Contact Map
4wxaA	1	0.2327	2.7	0.934	Contact Map
4e6zA	1	0.3145	2.5	0.936	Contact Map
2zqeA	1	0.2013	2.2	0.938	Contact Map
4y93A	1	0.6604	2.1	0.938	Contact Map
3encA	2	0.2327	2.1	0.938	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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