YFIB - ECOLI - GREMLIN Contacts

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YFIB - Putative lipoprotein YfiB

UniProt:	P07021	Sequences: MIKHLVAPLVFTSLILTGCQSPQGKFTPEQVAAMQSYGFTESAGDWSLGLSDAILFAKNDYKLLPESQQQIQTMAAKLASTGLTHARMDGHTDNYGEDSYNEGLSLKRANVVADAWAMGGQIPRSNLTTQGLGKKYPIASNKTAQGRAENRRVAVVITTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11152
Length:	160 (142)
Sequences:	9077 (6884)
Seq/√Len:	577.7

ECOLI - YFIB PAL YIAD OMPA MBHA MOTB
BACSU - YTXE MOTB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_N	100_Y	3.500	1.00
57_A	64_L	3.344	1.00
89_D	132_L	3.309	1.00
141_N	146_G	3.057	1.00
105_S	131_G	2.931	1.00
132_L	136_Y	2.696	1.00
95_Y	147_R	2.694	1.00
103_G	107_K	2.667	1.00
72_Q	119_G	2.640	1.00
58_K	95_Y	2.636	1.00
139_A	146_G	2.625	1.00
106_L	110_N	2.566	1.00
71_I	115_A	2.388	1.00
91_H	136_Y	2.345	1.00
72_Q	115_A	2.271	1.00
61_Y	107_K	2.211	1.00
102_E	106_L	2.181	1.00
113_A	129_T	2.155	1.00
140_S	146_G	1.955	1.00
139_A	149_E	1.865	1.00
88_M	153_V	1.774	1.00
98_D	134_K	1.763	1.00
89_D	156_V	1.759	1.00
143_T	146_G	1.670	1.00
110_N	113_A	1.622	1.00
98_D	135_K	1.588	1.00
102_E	135_K	1.515	1.00
141_N	147_R	1.512	1.00
115_A	119_G	1.502	1.00
94_N	147_R	1.426	1.00
63_L	115_A	1.388	1.00
65_P	68_Q	1.381	1.00
117_A	127_L	1.372	1.00
113_A	117_A	1.348	1.00
113_A	127_L	1.337	1.00
88_M	113_A	1.325	1.00
87_R	128_T	1.291	1.00
100_Y	103_G	1.287	1.00
123_P	126_N	1.285	1.00
63_L	67_S	1.284	1.00
110_N	114_D	1.247	1.00
87_R	130_Q	1.223	1.00
57_A	60_D	1.219	1.00
142_K	146_G	1.214	1.00
100_Y	134_K	1.196	1.00
86_A	127_L	1.178	1.00
70_Q	73_T	1.175	1.00
110_N	129_T	1.157	1.00
91_H	137_P	1.123	1.00
58_K	93_D	1.115	1.00
122_I	127_L	1.075	1.00
89_D	136_Y	1.067	1.00
89_D	130_Q	1.046	1.00
75_A	116_W	1.044	1.00
91_H	154_A	1.044	1.00
122_I	126_N	1.037	1.00
76_A	79_A	1.031	1.00
85_H	128_T	1.023	1.00
93_D	101_N	1.021	1.00
68_Q	115_A	1.020	1.00
117_A	124_R	1.017	1.00
94_N	141_N	1.007	1.00
25_K	29_E	1.005	1.00
115_A	118_M	1.001	1.00
58_K	100_Y	0.988	1.00
76_A	80_S	0.982	1.00
64_L	67_S	0.959	1.00
69_Q	73_T	0.953	1.00
19_C	22_P	0.951	1.00
113_A	124_R	0.950	1.00
97_E	100_Y	0.942	1.00
137_P	150_N	0.939	1.00
24_G	27_T	0.935	1.00
79_A	122_I	0.928	1.00
75_A	120_G	0.926	1.00
11_F	15_I	0.923	1.00
114_D	118_M	0.914	1.00
9_L	13_S	0.913	1.00
55_L	67_S	0.912	1.00
49_G	154_A	0.907	1.00
63_L	111_V	0.904	1.00
81_T	84_T	0.903	1.00
58_K	96_G	0.898	1.00
25_K	28_P	0.885	1.00
94_N	142_K	0.883	1.00
69_Q	72_Q	0.880	1.00
96_G	99_S	0.873	1.00
75_A	119_G	0.871	1.00
42_S	45_D	0.869	1.00
28_P	31_V	0.866	1.00
94_N	134_K	0.863	1.00
23_Q	26_F	0.862	1.00
143_T	147_R	0.856	1.00
106_L	129_T	0.853	1.00
67_S	70_Q	0.836	1.00
61_Y	104_L	0.835	1.00
146_G	149_E	0.834	1.00
56_F	153_V	0.828	1.00
140_S	143_T	0.825	1.00
109_A	131_G	0.814	1.00
77_K	81_T	0.806	1.00
12_T	15_I	0.805	1.00
61_Y	111_V	0.805	1.00
17_T	20_Q	0.802	1.00
23_Q	27_T	0.801	1.00
44_G	47_S	0.796	1.00
100_Y	107_K	0.787	1.00
112_V	153_V	0.781	1.00
27_T	30_Q	0.780	1.00
68_Q	72_Q	0.778	1.00
114_D	117_A	0.772	1.00
94_N	146_G	0.770	1.00
138_I	149_E	0.769	1.00
91_H	152_R	0.769	1.00
103_G	106_L	0.764	1.00
106_L	131_G	0.763	1.00
74_M	155_V	0.761	1.00
145_Q	149_E	0.759	1.00
63_L	68_Q	0.755	1.00
96_G	101_N	0.750	1.00
47_S	154_A	0.750	1.00
12_T	16_L	0.748	1.00
56_F	90_G	0.748	1.00
107_K	110_N	0.746	1.00
11_F	14_L	0.743	1.00
75_A	122_I	0.742	1.00
137_P	147_R	0.741	1.00
79_A	123_P	0.738	1.00
89_D	154_A	0.730	1.00
45_D	49_G	0.728	1.00
47_S	156_V	0.720	1.00
13_S	17_T	0.714	1.00
56_F	112_V	0.714	1.00
87_R	156_V	0.710	1.00
25_K	30_Q	0.709	1.00
94_N	150_N	0.702	1.00
43_A	46_W	0.701	1.00
71_I	116_W	0.697	1.00
97_E	134_K	0.695	1.00
71_I	112_V	0.694	1.00
27_T	31_V	0.694	1.00
72_Q	76_A	0.694	1.00
142_K	147_R	0.693	1.00
61_Y	103_G	0.692	1.00
26_F	30_Q	0.688	1.00
95_Y	144_A	0.687	1.00
94_N	137_P	0.684	1.00
88_M	109_A	0.684	1.00
24_G	28_P	0.683	1.00
86_A	155_V	0.682	1.00
90_G	153_V	0.672	1.00
22_P	27_T	0.670	1.00
143_T	150_N	0.670	1.00
99_S	103_G	0.670	1.00
78_L	86_A	0.662	1.00
144_A	147_R	0.656	1.00
22_P	25_K	0.650	1.00
26_F	29_E	0.648	1.00
91_H	135_K	0.647	1.00
139_A	150_N	0.634	1.00
58_K	101_N	0.631	1.00
95_Y	100_Y	0.625	1.00
111_V	114_D	0.620	1.00
106_L	130_Q	0.618	1.00
75_A	79_A	0.616	1.00
26_F	31_V	0.615	1.00
10_V	14_L	0.611	1.00
49_G	52_D	0.610	1.00
22_P	26_F	0.605	1.00
45_D	48_L	0.604	1.00
98_D	133_G	0.602	1.00
73_T	77_K	0.588	1.00
64_L	148_A	0.580	1.00
139_A	147_R	0.580	1.00
73_T	76_A	0.579	1.00
25_K	31_V	0.578	1.00
74_M	78_L	0.577	1.00
137_P	141_N	0.574	1.00
7_A	10_V	0.573	1.00
77_K	84_T	0.570	1.00
15_I	18_G	0.569	1.00
66_E	69_Q	0.561	0.99
20_Q	25_K	0.557	0.99
46_W	50_L	0.557	0.99
11_F	17_T	0.553	0.99
88_M	155_V	0.553	0.99
18_G	21_S	0.547	0.99
75_A	115_A	0.547	0.99
91_H	132_L	0.546	0.99
88_M	127_L	0.545	0.99
57_A	62_K	0.543	0.99
55_L	148_A	0.541	0.99
95_Y	134_K	0.539	0.99
8_P	11_F	0.535	0.99
7_A	11_F	0.534	0.99
109_A	129_T	0.533	0.99
103_G	134_K	0.531	0.99
55_L	138_I	0.531	0.99
24_G	30_Q	0.528	0.99
18_G	22_P	0.527	0.99
42_S	46_W	0.525	0.99
24_G	29_E	0.524	0.99
17_T	22_P	0.522	0.99
116_W	122_I	0.520	0.99
43_A	47_S	0.519	0.99
16_L	19_C	0.513	0.99
8_P	12_T	0.510	0.99
102_E	134_K	0.508	0.99
96_G	100_Y	0.506	0.99
23_Q	30_Q	0.504	0.99
100_Y	104_L	0.504	0.99
15_I	19_C	0.502	0.99
144_A	148_A	0.500	0.99

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
3ldtA	2	0.8688	100	0.229	Contact Map
2l26A	1	0.9812	100	0.271	Contact Map
2k1sA	1	0.8812	100	0.272	Contact Map
2hqsH	1	0.675	100	0.277	Contact Map
1r1mA	1	0.7438	100	0.277	Contact Map
3s06A	3	0.8625	100	0.289	Contact Map
2aizP	1	0.8375	100	0.295	Contact Map
3oonA	2	0.7	100	0.296	Contact Map
3s0yA	4	0.9563	100	0.297	Contact Map
2kgwA	1	0.8063	100	0.297	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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