YCAP - ECOLI - GREMLIN Contacts

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YCAP - UPF0702 transmembrane protein YcaP

UniProt:	P75839	Sequences: MKAFDLHRMAFDKVPFDFLGEVALRSLYTFVLVFLFLKMTGRRGVRQMSLFEVLIILTLGSAAGDVAFYDDVPMVPVLIVFITLALLYRLVMWLMAHSEKLEDLLEGKPVVIIEDGELAWSKLNNSNMTEFEFFMELRLRGVEQLGQVRLAILETNGQISVYFFEDDKVKPGLLILPSDCTQRYKVVPESADYACIRCSEIIHMKAGEKQLCPRCANPEWTKASRAKRVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13700
Length:	230 (219)
Sequences:	279 (219)
Seq/√Len:	14.8

ECOLI - YCAP
BACSU - YDFR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
194_A	223_A	4.356	1.00
194_A	201_I	3.118	0.98
34_F	141_G	3.034	0.98
118_L	133_F	2.929	0.97
8_R	15_P	2.900	0.97
28_Y	74_M	2.647	0.95
69_Y	72_V	2.630	0.95
162_Y	176_L	2.599	0.95
61_S	68_F	2.374	0.91
61_S	80_V	2.364	0.91
73_P	156_N	2.309	0.90
57_L	66_V	2.304	0.90
165_E	168_K	2.254	0.89
30_F	66_V	2.189	0.88
42_R	67_A	2.174	0.87
114_E	119_A	2.164	0.87
208_E	219_E	2.152	0.87
218_P	222_K	2.074	0.85
118_L	123_L	2.067	0.84
213_P	216_A	1.980	0.82
103_D	108_K	1.975	0.82
146_G	195_C	1.930	0.80
44_G	56_I	1.925	0.80
151_A	159_I	1.895	0.79
129_T	156_N	1.882	0.78
195_C	198_C	1.871	0.78
15_P	71_D	1.857	0.77
173_L	177_P	1.845	0.77
172_G	177_P	1.823	0.76
114_E	178_S	1.822	0.76
29_T	48_M	1.799	0.75
61_S	64_G	1.786	0.74
72_V	162_Y	1.776	0.74
88_Y	132_E	1.755	0.73
38_K	58_T	1.755	0.73
29_T	67_A	1.705	0.71
143_E	149_R	1.700	0.71
52_E	64_G	1.700	0.71
5_D	8_R	1.677	0.69
30_F	91_V	1.626	0.67
44_G	51_F	1.591	0.65
47_Q	60_G	1.584	0.65
28_Y	166_D	1.579	0.65
10_A	199_S	1.574	0.64
54_L	81_F	1.564	0.64
115_D	192_D	1.561	0.64
68_F	72_V	1.558	0.64
61_S	65_D	1.551	0.63
104_L	128_M	1.538	0.62
15_P	22_V	1.518	0.61
28_Y	78_L	1.503	0.61
94_L	101_L	1.499	0.60
34_F	66_V	1.479	0.59
10_A	48_M	1.478	0.59
37_L	65_D	1.420	0.56
44_G	65_D	1.413	0.56
92_M	132_E	1.408	0.55
205_K	211_L	1.399	0.55
200_E	216_A	1.397	0.55
24_L	79_I	1.390	0.55
60_G	80_V	1.344	0.52
105_L	176_L	1.332	0.51
146_G	198_C	1.319	0.51
60_G	65_D	1.317	0.50
6_L	9_M	1.302	0.50
68_F	80_V	1.301	0.50
20_G	100_K	1.300	0.49
37_L	60_G	1.294	0.49
208_E	211_L	1.293	0.49
201_I	223_A	1.283	0.49
44_G	156_N	1.275	0.48
60_G	160_S	1.266	0.48
211_L	218_P	1.259	0.47
44_G	61_S	1.252	0.47
40_T	73_P	1.247	0.47
43_R	161_V	1.245	0.46
57_L	107_G	1.240	0.46
90_L	114_E	1.235	0.46
11_F	16_F	1.226	0.45
206_A	216_A	1.222	0.45
35_L	135_M	1.194	0.44
120_W	170_K	1.177	0.43
25_R	43_R	1.170	0.42
122_K	211_L	1.152	0.41
21_E	146_G	1.141	0.41
103_D	155_T	1.123	0.40
211_L	219_E	1.114	0.39
29_T	42_R	1.104	0.39
89_R	129_T	1.093	0.38
90_L	117_E	1.077	0.37
121_S	124_N	1.066	0.37
106_E	194_A	1.064	0.37
49_S	69_Y	1.064	0.37
108_K	115_D	1.058	0.36
146_G	172_G	1.040	0.35
65_D	68_F	1.039	0.35
51_F	55_I	1.037	0.35
64_G	77_V	1.037	0.35
11_F	203_H	1.026	0.35
86_L	165_E	1.026	0.35
19_L	79_I	1.024	0.35
63_A	81_F	1.021	0.34
38_K	122_K	1.018	0.34
37_L	61_S	1.013	0.34
23_A	74_M	1.013	0.34
54_L	113_I	1.011	0.34
42_R	77_V	1.005	0.34
50_L	74_M	1.002	0.34
36_F	141_G	0.997	0.33
75_V	97_H	0.996	0.33
79_I	178_S	0.994	0.33
44_G	106_E	0.991	0.33
172_G	198_C	0.988	0.33
81_F	132_E	0.984	0.33
88_Y	160_S	0.978	0.32
43_R	130_E	0.971	0.32
48_M	67_A	0.971	0.32
173_L	195_C	0.949	0.31
44_G	52_E	0.947	0.31
12_D	70_D	0.945	0.31
28_Y	128_M	0.943	0.31
30_F	43_R	0.942	0.31
48_M	54_L	0.938	0.30
8_R	137_L	0.936	0.30
177_P	195_C	0.934	0.30
6_L	30_F	0.932	0.30
183_R	219_E	0.931	0.30
57_L	95_M	0.927	0.30
156_N	221_T	0.926	0.30
28_Y	66_V	0.926	0.30
65_D	132_E	0.919	0.30
12_D	152_I	0.918	0.29
56_I	65_D	0.905	0.29
82_I	139_L	0.904	0.29
11_F	17_D	0.904	0.29
125_N	190_S	0.901	0.29
117_E	200_E	0.897	0.29
86_L	213_P	0.894	0.28
55_I	113_I	0.893	0.28
64_G	80_V	0.891	0.28
60_G	64_G	0.891	0.28
59_L	146_G	0.889	0.28
13_K	142_V	0.885	0.28
209_K	218_P	0.885	0.28
37_L	44_G	0.880	0.28
70_D	148_V	0.874	0.27
43_R	53_V	0.873	0.27
113_I	219_E	0.871	0.27
21_E	25_R	0.866	0.27
177_P	198_C	0.856	0.27
52_E	145_L	0.854	0.27
125_N	166_D	0.846	0.26
97_H	124_N	0.838	0.26
115_D	189_E	0.836	0.26
68_F	73_P	0.835	0.26
60_G	72_V	0.833	0.26
179_D	224_S	0.833	0.26
64_G	68_F	0.831	0.26
112_I	123_L	0.831	0.26
51_F	132_E	0.830	0.26
112_I	118_L	0.823	0.25
190_S	218_P	0.821	0.25
10_A	32_L	0.816	0.25
132_E	149_R	0.815	0.25
87_L	156_N	0.815	0.25
213_P	218_P	0.814	0.25
165_E	201_I	0.814	0.25
58_T	84_L	0.812	0.25
113_I	149_R	0.808	0.25
31_V	35_L	0.807	0.25
25_R	30_F	0.805	0.25
132_E	160_S	0.805	0.25
56_I	132_E	0.805	0.25
82_I	167_D	0.800	0.24
142_V	185_K	0.799	0.24
91_V	213_P	0.798	0.24
30_F	59_L	0.796	0.24
74_M	141_G	0.793	0.24
210_Q	216_A	0.791	0.24
212_C	215_C	0.787	0.24
205_K	210_Q	0.787	0.24
120_W	125_N	0.787	0.24
91_V	139_L	0.781	0.24
5_D	11_F	0.776	0.23
52_E	88_Y	0.772	0.23
46_R	95_M	0.771	0.23
34_F	67_A	0.770	0.23
31_V	90_L	0.769	0.23
63_A	69_Y	0.768	0.23
43_R	49_S	0.759	0.23
115_D	167_D	0.758	0.23
32_L	113_I	0.751	0.22
85_A	96_A	0.749	0.22
21_E	142_V	0.747	0.22
42_R	92_M	0.744	0.22
112_I	126_S	0.739	0.22
57_L	159_I	0.739	0.22
88_Y	92_M	0.739	0.22
8_R	152_I	0.738	0.22
145_L	172_G	0.738	0.22
22_V	52_E	0.737	0.22
219_E	222_K	0.736	0.22
8_R	12_D	0.736	0.22
21_E	59_L	0.730	0.22
74_M	150_L	0.729	0.22
55_I	73_P	0.727	0.21
45_V	65_D	0.725	0.21
29_T	57_L	0.723	0.21
38_K	66_V	0.719	0.21
146_G	177_P	0.718	0.21
82_I	113_I	0.717	0.21
196_I	209_K	0.716	0.21
27_L	209_K	0.715	0.21
33_V	150_L	0.715	0.21
21_E	195_C	0.707	0.21
179_D	185_K	0.707	0.21
82_I	148_V	0.703	0.21
11_F	216_A	0.700	0.20
185_K	213_P	0.694	0.20
130_E	219_E	0.693	0.20
22_V	68_F	0.684	0.20
172_G	195_C	0.684	0.20
217_N	221_T	0.684	0.20
81_F	129_T	0.682	0.20
120_W	126_S	0.677	0.20
5_D	17_D	0.677	0.20
6_L	223_A	0.674	0.20
112_I	121_S	0.665	0.19
185_K	206_A	0.662	0.19
77_V	80_V	0.655	0.19
22_V	58_T	0.655	0.19
22_V	29_T	0.646	0.19
114_E	122_K	0.645	0.19
78_L	222_K	0.643	0.18
92_M	131_F	0.642	0.18
32_L	78_L	0.641	0.18
144_Q	147_Q	0.641	0.18
125_N	218_P	0.641	0.18
38_K	104_L	0.641	0.18
36_F	57_L	0.641	0.18
73_P	143_E	0.640	0.18
53_V	128_M	0.639	0.18
35_L	82_I	0.639	0.18
26_S	53_V	0.637	0.18
56_I	64_G	0.634	0.18
47_Q	56_I	0.634	0.18
58_T	61_S	0.633	0.18
6_L	17_D	0.633	0.18
63_A	66_V	0.630	0.18
173_L	198_C	0.626	0.18
35_L	115_D	0.626	0.18
113_I	131_F	0.625	0.18
189_E	204_M	0.623	0.18
210_Q	222_K	0.620	0.18
151_A	161_V	0.618	0.18
5_D	167_D	0.616	0.18
114_E	129_T	0.615	0.18
129_T	221_T	0.611	0.17
57_L	105_L	0.610	0.17
24_L	104_L	0.609	0.17
66_V	77_V	0.608	0.17
40_T	55_I	0.607	0.17
9_M	204_M	0.595	0.17
209_K	213_P	0.594	0.17
196_I	201_I	0.592	0.17
186_V	192_D	0.591	0.17
86_L	204_M	0.590	0.17
20_G	115_D	0.589	0.17
56_I	62_A	0.589	0.17
25_R	73_P	0.586	0.17
36_F	149_R	0.580	0.16
36_F	56_I	0.578	0.16
145_L	173_L	0.576	0.16
129_T	199_S	0.574	0.16
206_A	219_E	0.574	0.16
40_T	112_I	0.574	0.16
50_L	176_L	0.571	0.16
56_I	133_F	0.571	0.16
62_A	81_F	0.567	0.16
46_R	214_R	0.566	0.16
20_G	211_L	0.566	0.16
24_L	28_Y	0.566	0.16
101_L	105_L	0.566	0.16
49_S	64_G	0.564	0.16
35_L	39_M	0.563	0.16
202_I	206_A	0.562	0.16
42_R	48_M	0.562	0.16
75_V	146_G	0.560	0.16
98_S	188_P	0.560	0.16
9_M	206_A	0.559	0.16
185_K	211_L	0.555	0.16
21_E	198_C	0.555	0.16
171_P	202_I	0.551	0.16
66_V	135_M	0.550	0.16
49_S	106_E	0.549	0.15
64_G	173_L	0.549	0.15
210_Q	218_P	0.546	0.15
19_L	216_A	0.545	0.15
106_E	132_E	0.543	0.15
63_A	109_P	0.538	0.15
206_A	213_P	0.537	0.15
205_K	218_P	0.535	0.15
58_T	81_F	0.534	0.15
147_Q	169_V	0.533	0.15
98_S	170_K	0.532	0.15
51_F	88_Y	0.528	0.15
192_D	201_I	0.527	0.15
23_A	103_D	0.524	0.15
7_H	222_K	0.521	0.15
51_F	56_I	0.521	0.15
101_L	124_N	0.520	0.15
46_R	88_Y	0.518	0.15
105_L	112_I	0.518	0.15
190_S	205_K	0.517	0.15
37_L	45_V	0.516	0.15
63_A	132_E	0.515	0.15
72_V	142_V	0.515	0.15
11_F	158_Q	0.515	0.15
217_N	222_K	0.514	0.15
44_G	88_Y	0.508	0.14
209_K	221_T	0.507	0.14
6_L	78_L	0.507	0.14
198_C	215_C	0.505	0.14
203_H	211_L	0.505	0.14
49_S	52_E	0.503	0.14
21_E	35_L	0.501	0.14
22_V	38_K	0.500	0.14
113_I	130_E	0.500	0.14

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
3c6fA	4	0.4739	99.8	0.746	Contact Map
3eyyA	2	0.4609	71.3	0.947	Contact Map
2kdxA	1	0.4565	71.3	0.947	Contact Map
4aybP	1	0.1609	70.1	0.948	Contact Map
3h0gL	1	0.1783	66.9	0.949	Contact Map
3h7hA	1	0.2261	65.4	0.95	Contact Map
1twfL	1	0.1826	64.9	0.95	Contact Map
5aunA	1	0.4565	64.1	0.95	Contact Map
2ayjA	1	0.2348	60.6	0.951	Contact Map
4qiwP	1	0.1522	58.1	0.952	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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