YGFS - ECOLI - GREMLIN Contacts

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YGFS - Putative electron transport protein YgfS

UniProt:	Q46819	Sequences: MKSLIIVNPADCIGCRTCEVACVVAHPSEQELNADVFLPRLKVQRLDSISAPVMCHQCENAPCVGACPVGALTMGEQVVQTNSARCIGCQSCVSACPFGMITIQSLPGDTRQQIVKCDLCEQREEGPACVESCPTQALQLLTERELRRVRQQRIVASGENPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13069
Length:	162 (147)
Sequences:	4280 (2510)
Seq/√Len:	207.0

ECOLI - YGFS HYDN HYCB NRFC HYFA FDOH FDNH YSAA YNFG DMSB YDHX HYBA YDHY AEGA YGFT NAPG NARY NARH
BACSU - NARH
HALSA - DMSB
SULSO - Q97XX9 Q97V38 Q97V75

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_V	72_L	3.144	1.00
90_Q	103_I	2.723	1.00
66_A	95_A	2.584	1.00
72_L	81_T	2.504	1.00
25_A	122_Q	2.460	1.00
127_P	130_V	2.256	1.00
16_R	19_E	2.245	1.00
26_H	118_D	2.162	1.00
60_N	65_G	2.148	1.00
72_L	101_I	2.119	1.00
93_V	114_I	2.029	1.00
130_V	138_L	2.023	1.00
73_T	82_N	2.022	1.00
41_L	44_Q	2.011	1.00
15_C	18_C	1.967	1.00
61_A	74_M	1.935	1.00
5_I	119_L	1.882	1.00
90_Q	93_V	1.868	1.00
75_G	80_Q	1.843	1.00
21_A	132_S	1.838	1.00
73_T	80_Q	1.805	1.00
4_L	143_E	1.790	1.00
78_V	119_L	1.782	1.00
13_I	135_T	1.733	1.00
104_Q	115_V	1.732	1.00
139_Q	149_V	1.712	1.00
121_E	125_E	1.701	1.00
149_V	152_Q	1.686	1.00
66_A	91_S	1.684	1.00
123_R	131_E	1.641	1.00
86_C	92_C	1.622	1.00
67_C	92_C	1.550	1.00
101_I	114_I	1.540	1.00
12_C	18_C	1.529	1.00
12_C	15_C	1.503	1.00
103_I	114_I	1.482	1.00
67_C	86_C	1.478	1.00
82_N	85_R	1.467	1.00
64_V	74_M	1.444	1.00
8_N	11_D	1.437	1.00
149_V	153_R	1.408	1.00
81_T	114_I	1.403	1.00
69_V	87_I	1.391	1.00
145_E	148_R	1.376	1.00
7_V	52_P	1.345	1.00
7_V	138_L	1.320	1.00
80_Q	121_E	1.316	1.00
142_T	145_E	1.308	1.00
75_G	125_E	1.297	1.00
61_A	64_V	1.284	1.00
6_I	150_R	1.283	1.00
104_Q	111_R	1.280	1.00
71_A	85_R	1.278	1.00
143_E	147_R	1.278	1.00
75_G	78_V	1.273	1.00
86_C	89_C	1.263	1.00
34_A	115_V	1.263	1.00
89_C	92_C	1.259	1.00
74_M	79_V	1.252	1.00
25_A	128_A	1.246	1.00
12_C	133_C	1.245	1.00
90_Q	114_I	1.244	1.00
123_R	128_A	1.243	1.00
3_S	142_T	1.218	1.00
78_V	124_E	1.206	1.00
90_Q	105_S	1.198	1.00
69_V	72_L	1.197	1.00
32_L	35_D	1.176	1.00
148_R	151_Q	1.174	1.00
5_I	130_V	1.115	1.00
6_I	153_R	1.100	1.00
67_C	89_C	1.097	1.00
17_T	20_V	1.087	1.00
141_L	145_E	1.076	1.00
15_C	133_C	1.074	1.00
83_S	113_Q	1.068	1.00
26_H	122_Q	1.064	1.00
75_G	121_E	1.055	1.00
139_Q	153_R	1.054	1.00
41_L	45_R	1.039	1.00
91_S	94_S	1.028	1.00
38_L	41_L	1.023	1.00
139_Q	150_R	1.003	1.00
17_T	132_S	0.969	1.00
104_Q	112_Q	0.967	1.00
83_S	111_R	0.954	0.99
105_S	110_T	0.953	0.99
147_R	151_Q	0.952	0.99
147_R	152_Q	0.942	0.99
18_C	133_C	0.939	0.99
68_P	87_I	0.939	0.99
8_N	139_Q	0.936	0.99
39_P	43_V	0.935	0.99
54_M	138_L	0.918	0.99
7_V	54_M	0.917	0.99
119_L	140_L	0.914	0.99
25_A	123_R	0.913	0.99
37_F	41_L	0.912	0.99
148_R	152_Q	0.901	0.99
57_Q	79_V	0.900	0.99
150_R	153_R	0.889	0.99
62_P	95_A	0.872	0.99
13_I	134_P	0.868	0.99
11_D	137_A	0.863	0.99
14_G	50_S	0.850	0.99
124_E	140_L	0.845	0.99
57_Q	116_K	0.844	0.99
93_V	103_I	0.842	0.99
9_P	51_A	0.828	0.99
17_T	134_P	0.819	0.98
146_L	150_R	0.816	0.98
104_Q	110_T	0.814	0.98
32_L	36_V	0.807	0.98
3_S	140_L	0.804	0.98
42_K	45_R	0.796	0.98
103_I	112_Q	0.796	0.98
66_A	94_S	0.791	0.98
115_V	118_D	0.786	0.98
118_D	122_Q	0.778	0.98
52_P	138_L	0.773	0.98
74_M	78_V	0.772	0.98
116_K	120_C	0.767	0.98
53_V	56_H	0.762	0.97
4_L	146_L	0.755	0.97
26_H	128_A	0.753	0.97
146_L	149_V	0.741	0.97
40_R	47_D	0.730	0.97
119_L	124_E	0.718	0.96
5_I	54_M	0.716	0.96
136_Q	139_Q	0.711	0.96
37_F	40_R	0.704	0.96
18_C	22_C	0.697	0.96
122_Q	125_E	0.697	0.96
31_E	34_A	0.694	0.96
87_I	91_S	0.688	0.95
91_S	95_A	0.687	0.95
146_L	151_Q	0.687	0.95
55_C	58_C	0.674	0.95
76_E	121_E	0.672	0.95
14_G	18_C	0.666	0.95
33_N	36_V	0.665	0.95
80_Q	118_D	0.664	0.94
117_C	120_C	0.663	0.94
20_V	24_V	0.662	0.94
17_T	135_T	0.653	0.94
141_L	146_L	0.653	0.94
25_A	118_D	0.648	0.94
76_E	125_E	0.643	0.94
142_T	148_R	0.640	0.93
36_V	102_T	0.635	0.93
93_V	105_S	0.635	0.93
39_P	44_Q	0.632	0.93
30_Q	37_F	0.624	0.92
72_L	114_I	0.623	0.92
27_P	30_Q	0.622	0.92
40_R	43_V	0.621	0.92
95_A	100_M	0.619	0.92
143_E	146_L	0.617	0.92
10_A	91_S	0.616	0.92
38_L	46_L	0.616	0.92
5_I	52_P	0.615	0.92
14_G	17_T	0.613	0.92
21_A	25_A	0.610	0.92
105_S	111_R	0.601	0.91
42_K	47_D	0.595	0.91
57_Q	124_E	0.588	0.90
29_E	32_L	0.585	0.90
68_P	92_C	0.583	0.90
103_I	111_R	0.582	0.90
88_G	116_K	0.580	0.89
54_M	119_L	0.577	0.89
6_I	139_Q	0.577	0.89
58_C	97_P	0.576	0.89
59_E	62_P	0.573	0.89
97_P	116_K	0.573	0.89
71_A	74_M	0.571	0.89
146_L	153_R	0.571	0.89
102_T	115_V	0.565	0.88
5_I	56_H	0.563	0.88
76_E	80_Q	0.562	0.88
23_V	28_S	0.556	0.87
16_R	118_D	0.553	0.87
20_V	30_Q	0.551	0.87
9_P	52_P	0.551	0.87
8_N	153_R	0.549	0.87
28_S	34_A	0.548	0.87
52_P	56_H	0.548	0.87
73_T	85_R	0.548	0.87
64_V	79_V	0.547	0.87
127_P	138_L	0.546	0.87
10_A	153_R	0.542	0.86
24_V	30_Q	0.538	0.86
128_A	132_S	0.534	0.85
11_D	136_Q	0.533	0.85
81_T	100_M	0.532	0.85
78_V	121_E	0.527	0.85
69_V	73_T	0.525	0.84
4_L	150_R	0.523	0.84
41_L	46_L	0.522	0.84
69_V	89_C	0.521	0.84
35_D	138_L	0.519	0.84
13_I	17_T	0.515	0.83
119_L	143_E	0.514	0.83
17_T	24_V	0.512	0.83
102_T	105_S	0.512	0.83
75_G	124_E	0.512	0.83
30_Q	33_N	0.511	0.83
144_R	149_V	0.511	0.83
5_I	140_L	0.511	0.83
13_I	16_R	0.511	0.83
15_C	22_C	0.510	0.83
64_V	73_T	0.509	0.82
61_A	79_V	0.507	0.82
41_L	47_D	0.507	0.82
13_I	19_E	0.506	0.82
3_S	76_E	0.503	0.82
21_A	128_A	0.503	0.82
62_P	65_G	0.501	0.81
81_T	101_I	0.501	0.81
31_E	35_D	0.500	0.81

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
1h0hB	1	0.9691	100	0.309	Contact Map
1kqfB	3	0.9753	100	0.311	Contact Map
2ivfB	1	0.9753	100	0.312	Contact Map
1ti6B	2	0.9568	100	0.314	Contact Map
2vpzB	2	0.9691	100	0.358	Contact Map
1q16B	2	0.9753	100	0.447	Contact Map
4z3xE	2	0.9074	99.9	0.459	Contact Map
3mm5B	2	0.9321	99.8	0.604	Contact Map
2fgoA	1	0.4938	99.3	0.713	Contact Map
2zvsA	1	0.4815	99.3	0.714	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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