YOAK - BACSU - GREMLIN Contacts

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YOAK - UPF0700 transmembrane protein YoaK

UniProt:	O34343	Sequences: MTAAAYRNTLLSLLCLTAGIVDVIGYLSLGHVFTANMTGNIVLLGLAIGKSIQVTVFNSLTALIGFICGVIIATLMVGKAENTLWPSAVTKALALEAFILFVFACLSFYRAFVPVHILIILMSISMGIQTTAAKKLGIAGISSTVLTGTLASLLEDISGRLFFKKQKKTFLRDTVLRALAIILYCVGAIIVALAEPDFYHFIIWVPIVLIFGIMMTAKLKLSGEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	225 (199)
Sequences:	2339 (1828)
Seq/√Len:	129.6

BACSU - YOAK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_I	124_I	3.635	1.00
41_I	185_C	3.508	1.00
97_A	214_M	3.353	1.00
130_T	144_T	3.335	1.00
67_I	154_L	3.218	1.00
71_I	158_S	3.183	1.00
16_L	190_I	2.941	1.00
12_S	183_L	2.873	1.00
104_A	204_W	2.840	1.00
44_L	56_V	2.623	1.00
129_Q	143_S	2.596	1.00
97_A	211_F	2.537	1.00
65_G	120_I	2.428	1.00
47_A	52_I	2.281	1.00
71_I	157_I	2.252	1.00
24_I	202_I	2.194	1.00
67_I	150_L	2.119	1.00
153_L	174_T	2.110	1.00
101_F	207_I	2.066	1.00
153_L	178_A	1.977	1.00
198_F	205_V	1.970	1.00
107_S	111_A	1.916	1.00
65_G	69_G	1.821	1.00
37_M	150_L	1.804	1.00
145_V	148_G	1.799	1.00
142_S	145_V	1.768	1.00
23_V	191_V	1.696	1.00
96_E	100_L	1.682	1.00
61_T	120_I	1.670	1.00
130_T	148_G	1.660	1.00
60_L	64_I	1.652	1.00
22_D	42_V	1.649	1.00
27_L	195_E	1.628	1.00
100_L	122_M	1.617	1.00
11_L	15_C	1.611	1.00
144_T	148_G	1.610	1.00
69_G	127_G	1.588	1.00
50_K	196_P	1.559	1.00
41_I	146_L	1.556	1.00
93_L	96_E	1.513	1.00
97_A	207_I	1.506	1.00
25_G	34_T	1.484	1.00
96_E	129_Q	1.480	1.00
36_N	151_A	1.480	1.00
36_N	142_S	1.452	1.00
37_M	40_N	1.434	1.00
33_F	43_L	1.386	1.00
201_F	204_W	1.380	1.00
34_T	126_M	1.369	1.00
130_T	145_V	1.367	1.00
150_L	181_I	1.365	1.00
20_I	191_V	1.355	1.00
45_G	188_A	1.323	1.00
171_L	175_V	1.320	1.00
142_S	152_S	1.295	1.00
202_I	205_V	1.293	1.00
148_G	180_A	1.262	1.00
209_L	212_G	1.255	1.00
37_M	62_A	1.245	1.00
91_K	95_L	1.232	1.00
182_I	186_V	1.229	1.00
67_I	153_L	1.219	1.00
130_T	142_S	1.217	1.00
37_M	146_L	1.214	0.99
39_G	66_F	1.201	0.99
149_T	181_I	1.200	0.99
186_V	190_I	1.182	0.99
17_T	210_I	1.182	0.99
22_D	33_F	1.180	0.99
35_A	38_T	1.170	0.99
35_A	126_M	1.170	0.99
96_E	210_I	1.158	0.99
47_A	56_V	1.153	0.99
106_L	114_P	1.150	0.99
73_A	131_T	1.147	0.99
73_A	132_A	1.147	0.99
203_I	206_P	1.145	0.99
28_S	195_E	1.145	0.99
34_T	129_Q	1.141	0.99
58_N	123_S	1.132	0.99
94_A	98_F	1.120	0.99
45_G	189_I	1.108	0.99
36_N	130_T	1.107	0.99
36_N	143_S	1.105	0.99
94_A	211_F	1.100	0.99
99_I	103_F	1.100	0.99
106_L	208_V	1.099	0.99
64_I	83_T	1.088	0.99
194_A	205_V	1.087	0.99
145_V	152_S	1.073	0.99
146_L	149_T	1.070	0.99
44_L	185_C	1.067	0.99
25_G	122_M	1.064	0.99
69_G	124_I	1.058	0.99
15_C	43_L	1.050	0.99
35_A	144_T	1.046	0.98
12_S	179_L	1.008	0.98
89_V	96_E	1.001	0.98
63_L	185_C	1.000	0.98
202_I	206_P	0.997	0.98
129_Q	132_A	0.996	0.98
70_V	131_T	0.992	0.98
20_I	194_A	0.979	0.98
73_A	128_I	0.972	0.98
101_F	204_W	0.970	0.98
33_F	40_N	0.970	0.98
21_V	206_P	0.966	0.97
96_E	154_L	0.964	0.97
70_V	155_E	0.962	0.97
10_L	213_I	0.939	0.97
146_L	181_I	0.939	0.97
145_V	151_A	0.939	0.97
106_L	186_V	0.935	0.97
15_C	180_A	0.930	0.97
21_V	147_T	0.928	0.97
73_A	127_G	0.928	0.97
35_A	130_T	0.926	0.97
17_T	209_L	0.925	0.97
182_I	194_A	0.910	0.96
143_S	151_A	0.907	0.96
156_D	177_R	0.907	0.96
69_G	123_S	0.895	0.96
68_C	124_I	0.895	0.96
36_N	145_V	0.889	0.96
71_I	161_L	0.887	0.96
139_A	176_L	0.887	0.96
22_D	145_V	0.885	0.96
16_L	186_V	0.884	0.96
78_G	162_F	0.884	0.96
134_K	142_S	0.882	0.96
37_M	126_M	0.882	0.96
35_A	119_I	0.881	0.96
36_N	43_L	0.873	0.95
34_T	62_A	0.871	0.95
68_C	164_K	0.868	0.95
113_V	117_I	0.864	0.95
111_A	208_V	0.860	0.95
116_H	120_I	0.853	0.95
21_V	100_L	0.852	0.95
98_F	215_M	0.837	0.94
22_D	89_V	0.834	0.94
10_L	141_I	0.830	0.94
13_L	209_L	0.825	0.94
36_N	66_F	0.822	0.94
102_V	197_D	0.818	0.93
149_T	177_R	0.818	0.93
142_S	151_A	0.816	0.93
64_I	68_C	0.814	0.93
38_T	42_V	0.808	0.93
54_V	102_V	0.807	0.93
35_A	213_I	0.805	0.93
27_L	34_T	0.804	0.93
52_I	55_T	0.801	0.93
175_V	179_L	0.801	0.93
76_M	91_K	0.798	0.93
33_F	134_K	0.796	0.93
26_Y	146_L	0.796	0.93
18_A	145_V	0.792	0.92
102_V	106_L	0.773	0.91
17_T	21_V	0.773	0.91
130_T	154_L	0.765	0.91
22_D	148_G	0.760	0.91
103_F	125_S	0.755	0.90
68_C	208_V	0.754	0.90
131_T	142_S	0.754	0.90
47_A	55_T	0.754	0.90
22_D	152_S	0.753	0.90
11_L	180_A	0.749	0.90
41_I	150_L	0.746	0.90
136_L	176_L	0.744	0.90
17_T	206_P	0.744	0.90
22_D	142_S	0.743	0.90
131_T	144_T	0.735	0.89
133_A	180_A	0.734	0.89
81_E	87_S	0.730	0.89
11_L	141_I	0.730	0.89
130_T	151_A	0.721	0.88
126_M	130_T	0.718	0.88
112_F	115_V	0.717	0.88
164_K	171_L	0.716	0.88
26_Y	135_K	0.714	0.88
194_A	197_D	0.712	0.88
134_K	156_D	0.703	0.87
103_F	203_I	0.699	0.87
21_V	122_M	0.698	0.87
9_T	211_F	0.695	0.86
104_A	207_I	0.694	0.86
27_L	46_L	0.693	0.86
42_V	127_G	0.693	0.86
160_R	164_K	0.691	0.86
127_G	144_T	0.690	0.86
145_V	180_A	0.686	0.86
102_V	190_I	0.684	0.86
42_V	181_I	0.683	0.85
54_V	57_F	0.680	0.85
74_T	159_G	0.679	0.85
68_C	71_I	0.676	0.85
64_I	67_I	0.676	0.85
147_T	150_L	0.669	0.84
156_D	173_D	0.665	0.84
190_I	194_A	0.664	0.84
131_T	151_A	0.664	0.84
15_C	33_F	0.661	0.84
148_G	184_Y	0.655	0.83
160_R	174_T	0.655	0.83
133_A	151_A	0.647	0.82
102_V	171_L	0.647	0.82
139_A	152_S	0.644	0.82
104_A	201_F	0.642	0.82
48_I	190_I	0.640	0.82
9_T	137_G	0.639	0.81
117_I	197_D	0.638	0.81
51_S	56_V	0.638	0.81
26_Y	58_N	0.632	0.81
38_T	43_L	0.632	0.81
137_G	176_L	0.630	0.81
134_K	145_V	0.629	0.80
68_C	178_A	0.625	0.80
194_A	198_F	0.625	0.80
47_A	54_V	0.624	0.80
129_Q	136_L	0.622	0.80
154_L	178_A	0.622	0.80
127_G	143_S	0.620	0.80
138_I	151_A	0.620	0.80
29_L	118_L	0.619	0.79
126_M	144_T	0.619	0.79
57_F	157_I	0.619	0.79
51_S	196_P	0.618	0.79
190_I	212_G	0.618	0.79
143_S	155_E	0.613	0.79
198_F	202_I	0.611	0.79
147_T	209_L	0.610	0.78
133_A	177_R	0.606	0.78
11_L	148_G	0.605	0.78
55_T	59_S	0.604	0.78
65_G	123_S	0.604	0.78
148_G	152_S	0.603	0.78
143_S	191_V	0.599	0.77
90_T	214_M	0.596	0.77
17_T	20_I	0.594	0.77
134_K	152_S	0.590	0.76
18_A	36_N	0.590	0.76
151_A	181_I	0.588	0.76
24_I	203_I	0.588	0.76
25_G	42_V	0.584	0.75
102_V	212_G	0.582	0.75
134_K	184_Y	0.580	0.75
45_G	49_G	0.580	0.75
159_G	173_D	0.579	0.75
29_L	146_L	0.579	0.75
60_L	107_S	0.577	0.75
199_Y	205_V	0.576	0.74
186_V	194_A	0.575	0.74
16_L	183_L	0.574	0.74
151_A	155_E	0.574	0.74
55_T	98_F	0.572	0.74
207_I	214_M	0.571	0.74
71_I	154_L	0.568	0.73
13_L	213_I	0.567	0.73
44_L	63_L	0.566	0.73
104_A	203_I	0.565	0.73
99_I	125_S	0.557	0.72
80_A	88_A	0.556	0.72
54_V	186_V	0.556	0.72
124_I	210_I	0.556	0.72
35_A	147_T	0.555	0.72
38_T	181_I	0.551	0.71
137_G	140_G	0.551	0.71
70_V	74_T	0.550	0.71
172_R	215_M	0.549	0.71
21_V	203_I	0.548	0.71
11_L	183_L	0.547	0.71
21_V	126_M	0.547	0.71
178_A	182_I	0.541	0.70
78_G	173_D	0.538	0.69
83_T	212_G	0.537	0.69
21_V	176_L	0.533	0.69
92_A	123_S	0.533	0.69
130_T	152_S	0.532	0.68
9_T	84_L	0.528	0.68
152_S	155_E	0.526	0.68
38_T	142_S	0.526	0.68
40_N	123_S	0.524	0.67
42_V	83_T	0.524	0.67
13_L	193_L	0.523	0.67
40_N	63_L	0.523	0.67
61_T	116_H	0.522	0.67
12_S	16_L	0.520	0.67
103_F	121_L	0.515	0.66
34_T	103_F	0.514	0.66
70_V	154_L	0.513	0.66
30_G	59_S	0.508	0.65
102_V	113_V	0.507	0.65
17_T	213_I	0.506	0.65
28_S	93_L	0.504	0.64
49_G	193_L	0.502	0.64
60_L	128_I	0.501	0.64
48_I	165_K	0.500	0.64

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
4ldsA	2	0.7956	90.3	0.893	Contact Map
4j05A	3	0.8044	90.1	0.893	Contact Map
1pw4A	1	0.8489	87.9	0.898	Contact Map
4zw9A	1	0.88	85.8	0.901	Contact Map
2cfqA	1	0.8444	84.5	0.903	Contact Map
3wdoA	1	0.8178	82.2	0.905	Contact Map
3o7qA	1	0.8267	82	0.905	Contact Map
4pypA	1	0.8489	79.1	0.908	Contact Map
4tphA	2	0.8178	75.2	0.911	Contact Map
4xnjA	1	0.8533	74	0.912	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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