YBFM - BACSU - GREMLIN Contacts

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YBFM - Uncharacterized membrane protein YbfM

UniProt:	O31453	Sequences: MELVQQLIADYGYLAIFLMLVLGIVGLPIPDEVMMTVVGYFTHTDVLNYELSILISFVGALLGMLISYMIGRKAGRPFIDKYGKWVGLKEKRMMKVEKWMKKYGPYSLILGYFIPGVRHVTCYFSGIGKMDLKTYVAFAAIGAFLWCFVFITIGRVIGIIHV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	162 (153)
Sequences:	6162 (4043)
Seq/√Len:	326.9

ECOLI - YABI YGHB DEDA YQJA YOHD YDJZ YDJX
BACSU - YBFM YKOX YNGC YHJE YQED YTXB
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_L	132_L	3.238	1.00
48_N	51_L	3.166	1.00
57_F	144_F	2.713	1.00
42_T	155_R	2.675	1.00
21_V	66_I	2.416	1.00
65_L	136_V	2.409	1.00
89_K	92_R	2.365	1.00
61_L	140_A	2.358	1.00
103_Y	106_Y	2.342	1.00
105_P	134_T	2.238	1.00
109_I	141_I	2.225	1.00
8_I	12_G	2.186	1.00
53_I	148_F	2.156	1.00
56_S	147_C	2.148	1.00
131_D	134_T	2.101	1.00
105_P	138_F	1.955	1.00
55_I	59_G	1.948	1.00
97_E	101_K	1.900	1.00
49_Y	152_T	1.890	1.00
20_L	59_G	1.808	1.00
13_Y	48_N	1.780	1.00
152_T	156_V	1.772	1.00
21_V	62_L	1.740	1.00
53_I	151_I	1.682	1.00
49_Y	53_I	1.607	1.00
35_M	151_I	1.596	1.00
76_R	97_E	1.591	1.00
132_L	136_V	1.581	1.00
23_G	31_D	1.559	1.00
38_V	52_S	1.558	1.00
17_F	59_G	1.531	1.00
72_R	129_K	1.524	1.00
49_Y	151_I	1.517	1.00
90_E	94_M	1.506	1.00
13_Y	51_L	1.465	1.00
17_F	58_V	1.460	1.00
80_D	90_E	1.451	1.00
17_F	55_I	1.451	1.00
64_M	112_Y	1.432	1.00
71_G	127_I	1.412	1.00
16_I	56_S	1.408	1.00
13_Y	55_I	1.400	1.00
69_M	132_L	1.365	1.00
133_K	137_A	1.359	1.00
94_M	98_K	1.358	1.00
61_L	143_A	1.354	1.00
113_F	145_L	1.350	1.00
69_M	73_K	1.336	1.00
52_S	151_I	1.330	1.00
42_T	49_Y	1.330	1.00
50_E	152_T	1.290	1.00
11_Y	15_A	1.282	1.00
106_Y	110_L	1.265	1.00
51_L	55_I	1.261	1.00
6_Q	9_A	1.260	1.00
73_K	77_P	1.237	1.00
111_G	121_T	1.224	1.00
26_G	67_S	1.218	1.00
100_M	125_S	1.210	1.00
91_K	95_K	1.201	1.00
54_L	58_V	1.184	1.00
109_I	145_L	1.179	1.00
17_F	62_L	1.158	1.00
50_E	54_L	1.149	1.00
97_E	128_G	1.147	1.00
67_S	123_Y	1.141	1.00
76_R	80_D	1.141	1.00
53_I	152_T	1.138	1.00
35_M	56_S	1.089	1.00
139_A	143_A	1.086	1.00
82_Y	85_W	1.083	1.00
94_M	97_E	1.075	1.00
47_L	52_S	1.074	1.00
133_K	136_V	1.064	1.00
69_M	72_R	1.064	1.00
39_G	154_G	1.061	1.00
57_F	61_L	1.059	1.00
60_A	143_A	1.057	1.00
137_A	141_I	1.053	1.00
24_I	27_L	1.042	1.00
98_K	102_K	1.004	1.00
61_L	136_V	0.997	1.00
65_L	69_M	0.995	1.00
35_M	39_G	0.987	1.00
79_I	88_L	0.966	1.00
37_V	40_Y	0.956	1.00
7_L	12_G	0.949	1.00
37_V	41_F	0.943	1.00
145_L	148_F	0.928	1.00
53_I	57_F	0.928	1.00
68_Y	132_L	0.926	1.00
43_H	155_R	0.926	1.00
83_G	88_L	0.924	1.00
54_L	57_F	0.913	1.00
56_S	151_I	0.911	1.00
32_E	118_R	0.903	1.00
40_Y	43_H	0.902	1.00
79_I	93_M	0.900	1.00
64_M	139_A	0.899	1.00
24_I	28_P	0.898	1.00
6_Q	10_D	0.897	1.00
11_Y	14_L	0.897	1.00
13_Y	47_L	0.896	1.00
108_L	130_M	0.890	1.00
99_W	107_S	0.887	1.00
39_G	151_I	0.886	1.00
148_F	152_T	0.872	1.00
57_F	147_C	0.866	1.00
43_H	159_I	0.862	1.00
96_V	128_G	0.854	1.00
51_L	54_L	0.844	1.00
70_I	74_A	0.844	1.00
16_I	52_S	0.843	1.00
84_K	88_L	0.836	1.00
8_I	15_A	0.831	1.00
16_I	38_V	0.827	1.00
9_A	12_G	0.825	1.00
98_K	101_K	0.823	1.00
104_G	130_M	0.822	1.00
50_E	53_I	0.792	1.00
125_S	130_M	0.782	1.00
136_V	140_A	0.777	1.00
114_I	117_V	0.776	1.00
8_I	11_Y	0.771	1.00
122_C	139_A	0.771	1.00
92_R	95_K	0.764	1.00
74_A	77_P	0.762	1.00
83_G	90_E	0.760	1.00
64_M	132_L	0.757	0.99
58_V	62_L	0.756	0.99
65_L	139_A	0.755	0.99
107_S	110_L	0.754	0.99
61_L	139_A	0.751	0.99
12_G	15_A	0.747	0.99
39_G	52_S	0.732	0.99
77_P	81_K	0.727	0.99
24_I	112_Y	0.725	0.99
82_Y	90_E	0.721	0.99
149_V	152_T	0.719	0.99
20_L	147_C	0.719	0.99
76_R	79_I	0.719	0.99
74_A	78_F	0.715	0.99
137_A	140_A	0.711	0.99
100_M	107_S	0.701	0.99
42_T	52_S	0.698	0.99
106_Y	138_F	0.697	0.99
97_E	129_K	0.696	0.99
10_D	14_L	0.693	0.99
42_T	151_I	0.686	0.99
23_G	112_Y	0.685	0.99
155_R	159_I	0.682	0.99
107_S	121_T	0.678	0.99
67_S	119_H	0.677	0.99
75_G	79_I	0.677	0.99
144_F	148_F	0.677	0.99
95_K	98_K	0.675	0.99
147_C	151_I	0.659	0.99
77_P	80_D	0.657	0.99
81_K	85_W	0.656	0.99
92_R	96_V	0.649	0.98
115_P	119_H	0.645	0.98
31_D	139_A	0.643	0.98
66_I	69_M	0.641	0.98
100_M	121_T	0.640	0.98
156_V	159_I	0.640	0.98
81_K	84_K	0.637	0.98
78_F	82_Y	0.629	0.98
17_F	21_V	0.625	0.98
19_M	34_M	0.618	0.98
109_I	113_F	0.618	0.98
22_L	26_G	0.618	0.98
78_F	81_K	0.616	0.98
46_V	50_E	0.615	0.98
119_H	150_F	0.614	0.98
60_A	112_Y	0.613	0.98
31_D	135_Y	0.607	0.98
105_P	130_M	0.605	0.98
134_T	137_A	0.603	0.97
135_Y	142_G	0.602	0.97
24_I	122_C	0.602	0.97
68_Y	126_G	0.596	0.97
32_E	112_Y	0.596	0.97
153_I	156_V	0.595	0.97
153_I	157_I	0.590	0.97
81_K	88_L	0.590	0.97
41_F	46_V	0.588	0.97
38_V	151_I	0.585	0.97
43_H	158_G	0.585	0.97
135_Y	139_A	0.582	0.97
22_L	27_L	0.579	0.97
149_V	153_I	0.577	0.97
36_T	40_Y	0.577	0.97
32_E	142_G	0.576	0.97
9_A	46_V	0.575	0.97
126_G	129_K	0.573	0.97
31_D	115_P	0.570	0.96
85_W	88_L	0.569	0.96
28_P	116_G	0.563	0.96
134_T	138_F	0.562	0.96
75_G	78_F	0.557	0.96
95_K	99_W	0.554	0.96
27_L	67_S	0.554	0.96
91_K	94_M	0.552	0.96
12_G	47_L	0.551	0.96
62_L	66_I	0.548	0.96
29_I	119_H	0.548	0.96
80_D	85_W	0.544	0.95
20_L	119_H	0.544	0.95
49_Y	148_F	0.542	0.95
16_I	55_I	0.541	0.95
7_L	10_D	0.539	0.95
23_G	119_H	0.538	0.95
43_H	46_V	0.537	0.95
106_Y	124_F	0.534	0.95
111_G	115_P	0.534	0.95
60_A	146_W	0.527	0.95
68_Y	125_S	0.527	0.95
112_Y	118_R	0.525	0.94
99_W	102_K	0.524	0.94
14_L	17_F	0.523	0.94
140_A	144_F	0.521	0.94
96_V	120_V	0.521	0.94
38_V	47_L	0.514	0.94
112_Y	139_A	0.512	0.94
24_I	119_H	0.512	0.94
93_M	100_M	0.509	0.94
80_D	91_K	0.505	0.93
152_T	155_R	0.504	0.93
79_I	82_Y	0.502	0.93
7_L	11_Y	0.500	0.93

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
2lbgA	1	0.1667	5.6	0.941	Contact Map
1tpxA	1	0.4691	5.5	0.941	Contact Map
4ma7A	1	0.5	5.5	0.942	Contact Map
3spcA	3	0.3827	4.8	0.943	Contact Map
4eneA	2	0.5802	4.5	0.944	Contact Map
3syaA	3	0.4136	4.2	0.945	Contact Map
4w6vA	1	0.4691	3.7	0.946	Contact Map
4xtlA	1	0.9074	3.3	0.948	Contact Map
2qksA	4	0.3827	3.3	0.948	Contact Map
2kncA	1	0.3272	3.1	0.948	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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