YNGA - BACSU - GREMLIN Contacts

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YNGA - Uncharacterized membrane protein YngA

UniProt:	O31821	Sequences: MTATRIFYEGRFVTLKEKIKTLGRFCTVGVGNTLIDFGVFFLLTACHVSYLPAQICSYTAGIVNSYVWNRNWTFCVKRKADGKEIVRFLMINIAASGITFLLLYLFQNCGCSLLVSKLAATIGGMMMNFIGNRIWVFGDSLKNIQDQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (123)
Sequences:	2759 (2107)
Seq/√Len:	190.0

BACSU - YNGA YWCD
HALSA - Q9HQ53 Q9HNK2
SULSO - Q97ZX3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_N	68_W	2.935	1.00
39_V	60_A	2.591	1.00
132_N	136_V	2.515	1.00
32_N	65_S	2.447	1.00
21_T	133_R	2.358	1.00
63_V	85_I	2.353	1.00
20_K	24_R	2.287	1.00
106_F	116_S	2.060	1.00
54_Q	117_K	2.040	1.00
35_I	64_N	1.999	1.00
40_F	57_S	1.920	1.00
66_Y	81_D	1.890	1.00
91_I	131_G	1.868	1.00
70_R	84_E	1.840	1.00
31_G	64_N	1.822	1.00
36_D	57_S	1.785	1.00
102_L	120_A	1.707	1.00
40_F	113_L	1.695	1.00
36_D	54_Q	1.695	1.00
54_Q	103_L	1.619	1.00
41_F	114_L	1.616	1.00
36_D	99_T	1.578	1.00
120_A	124_G	1.527	1.00
28_V	68_W	1.513	1.00
58_Y	62_I	1.512	1.00
24_R	72_W	1.502	1.00
21_T	129_F	1.489	1.00
69_N	73_T	1.455	1.00
43_L	56_C	1.453	1.00
55_I	96_S	1.438	1.00
44_T	113_L	1.406	1.00
87_R	135_W	1.353	1.00
55_I	100_F	1.326	1.00
130_I	134_I	1.325	1.00
58_Y	96_S	1.324	1.00
83_K	87_R	1.316	1.00
40_F	117_K	1.313	1.00
54_Q	100_F	1.300	1.00
70_R	137_F	1.289	1.00
66_Y	84_E	1.267	1.00
98_I	127_M	1.247	1.00
36_D	117_K	1.244	1.00
51_L	100_F	1.227	1.00
26_C	30_V	1.199	1.00
86_V	90_M	1.162	1.00
32_N	64_N	1.158	1.00
122_I	126_M	1.158	1.00
42_L	46_C	1.156	1.00
65_S	92_N	1.148	1.00
43_L	53_A	1.148	1.00
85_I	89_L	1.140	1.00
105_L	108_N	1.130	1.00
22_L	26_C	1.119	1.00
39_V	43_L	1.116	1.00
18_K	129_F	1.115	1.00
51_L	104_Y	1.099	1.00
18_K	21_T	1.086	1.00
37_F	117_K	1.081	1.00
25_F	128_N	1.079	1.00
76_V	84_E	1.078	1.00
93_I	97_G	1.069	1.00
98_I	124_G	1.053	1.00
59_T	89_L	1.046	1.00
62_I	92_N	1.045	1.00
90_M	94_A	1.022	1.00
88_F	96_S	1.021	1.00
106_F	111_C	1.007	1.00
102_L	106_F	1.007	1.00
95_A	127_M	1.004	1.00
126_M	130_I	1.001	1.00
111_C	116_S	1.000	0.99
92_N	132_N	0.997	0.99
65_S	69_N	0.989	0.99
59_T	63_V	0.969	0.99
50_Y	103_L	0.966	0.99
30_V	33_T	0.966	0.99
40_F	44_T	0.961	0.99
48_V	53_A	0.957	0.99
31_G	68_W	0.943	0.99
38_G	42_L	0.940	0.99
67_V	71_N	0.939	0.99
37_F	41_F	0.937	0.99
82_G	86_V	0.913	0.99
27_T	31_G	0.898	0.99
50_Y	107_Q	0.898	0.99
37_F	121_T	0.894	0.99
30_V	34_L	0.893	0.99
105_L	109_C	0.891	0.99
19_I	26_C	0.884	0.99
65_S	88_F	0.880	0.99
96_S	100_F	0.870	0.99
35_I	61_G	0.869	0.99
127_M	131_G	0.861	0.98
33_T	36_D	0.854	0.98
99_T	103_L	0.847	0.98
104_Y	107_Q	0.839	0.98
45_A	113_L	0.829	0.98
33_T	125_M	0.827	0.98
33_T	65_S	0.815	0.98
99_T	117_K	0.806	0.98
95_A	124_G	0.803	0.98
49_S	52_P	0.797	0.98
41_F	45_A	0.793	0.97
40_F	103_L	0.788	0.97
91_I	136_V	0.785	0.97
98_I	102_L	0.780	0.97
103_L	117_K	0.776	0.97
118_L	122_I	0.775	0.97
131_G	135_W	0.774	0.97
26_C	125_M	0.745	0.96
32_N	69_N	0.743	0.96
43_L	48_V	0.731	0.96
32_N	36_D	0.730	0.96
24_R	28_V	0.730	0.96
99_T	121_T	0.722	0.96
54_Q	65_S	0.719	0.95
80_A	83_K	0.712	0.95
99_T	124_G	0.706	0.95
97_G	101_L	0.704	0.95
79_K	83_K	0.704	0.95
20_K	75_C	0.703	0.95
25_F	132_N	0.702	0.95
81_D	84_E	0.698	0.95
100_F	103_L	0.691	0.94
70_R	76_V	0.690	0.94
36_D	61_G	0.687	0.94
55_I	59_T	0.684	0.94
32_N	68_W	0.681	0.94
131_G	136_V	0.675	0.94
66_Y	70_R	0.673	0.94
57_S	61_G	0.673	0.94
99_T	120_A	0.669	0.93
39_V	61_G	0.668	0.93
23_G	27_T	0.663	0.93
25_F	28_V	0.660	0.93
129_F	133_R	0.658	0.93
33_T	66_Y	0.656	0.93
51_L	54_Q	0.654	0.93
28_V	73_T	0.651	0.92
19_I	23_G	0.650	0.92
22_L	130_I	0.650	0.92
104_Y	108_N	0.648	0.92
58_Y	128_N	0.645	0.92
117_K	121_T	0.643	0.92
25_F	92_N	0.641	0.92
37_F	125_M	0.639	0.92
63_V	89_L	0.638	0.92
100_F	104_Y	0.637	0.92
103_L	120_A	0.636	0.92
63_V	67_V	0.636	0.92
36_D	40_F	0.634	0.91
92_N	95_A	0.626	0.91
61_G	92_N	0.620	0.90
74_F	88_F	0.620	0.90
96_S	103_L	0.618	0.90
102_L	124_G	0.618	0.90
25_F	125_M	0.614	0.90
32_N	121_T	0.610	0.90
106_F	109_C	0.606	0.89
23_G	26_C	0.605	0.89
61_G	64_N	0.593	0.88
81_D	85_I	0.583	0.88
20_K	23_G	0.576	0.87
44_T	55_I	0.565	0.86
43_L	46_C	0.563	0.86
19_I	22_L	0.553	0.85
40_F	95_A	0.550	0.84
127_M	137_F	0.547	0.84
96_S	121_T	0.547	0.84
73_T	129_F	0.546	0.84
25_F	124_G	0.544	0.84
32_N	62_I	0.543	0.84
96_S	124_G	0.539	0.83
61_G	65_S	0.533	0.83
52_P	86_V	0.522	0.81
62_I	85_I	0.522	0.81
88_F	92_N	0.519	0.81
25_F	117_K	0.516	0.81
74_F	133_R	0.509	0.80
40_F	45_A	0.507	0.79
40_F	96_S	0.504	0.79
37_F	114_L	0.503	0.79
107_Q	110_G	0.501	0.79
25_F	32_N	0.500	0.78

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
3w4tA	1	0.9122	30.3	0.914	Contact Map
1mhsA	2	0.973	29.1	0.915	Contact Map
4n7wA	2	0.8986	25.7	0.917	Contact Map
3zuxA	1	0.8716	20.3	0.921	Contact Map
3mktA	1	0.9527	14.8	0.926	Contact Map
4humA	1	0.9392	13.3	0.927	Contact Map
2kncA	1	0.3243	13	0.928	Contact Map
4av3A	2	0.6419	8.9	0.932	Contact Map
2l8sA	1	0.3041	8.9	0.933	Contact Map
4lz6A	1	0.9392	8.8	0.933	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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