PTFA - BACSU - GREMLIN Contacts

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PTFA - Fructose-specific phosphotransferase enzyme IIA component

UniProt:	P26379	Sequences: MISVIISGHGDFPIALKESSGMIFGEENNLIAVPFFKGEGIQTLQEKYHQALKDIPEEHEVLFLVDIFGGTPYNAAASFIAEDQRMDMAAGVNLPILLEVLSLREHLALKDLLNNLKAMSQQSFQVCSEHLEKVKTANQDTREDEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (130)
Sequences:	2273 (1692)
Seq/√Len:	148.4

ECOLI - YADI PTNAB
BACSU - PTFA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_G	26_E	3.598	1.00
11_D	14_I	2.956	1.00
16_L	92_V	2.895	1.00
31_I	54_D	2.853	1.00
108_A	111_D	2.750	1.00
39_E	47_K	2.708	1.00
14_I	34_P	2.600	1.00
99_E	119_M	2.376	1.00
12_F	16_L	2.363	1.00
15_A	18_E	2.357	1.00
8_G	92_V	2.272	1.00
100_V	116_L	2.177	1.00
31_I	51_A	1.995	1.00
17_K	32_A	1.863	1.00
17_K	30_L	1.823	1.00
6_I	92_V	1.788	1.00
64_L	100_V	1.751	1.00
6_I	17_K	1.732	1.00
17_K	21_G	1.693	1.00
63_F	86_M	1.666	1.00
45_Q	78_S	1.661	1.00
11_D	15_A	1.633	1.00
35_F	44_L	1.622	1.00
46_E	50_Q	1.618	1.00
8_G	13_P	1.595	1.00
87_D	126_V	1.594	1.00
24_F	102_S	1.563	1.00
19_S	94_L	1.537	1.00
65_V	73_Y	1.531	1.00
48_Y	76_A	1.531	1.00
3_S	31_I	1.463	1.00
20_S	101_L	1.398	1.00
96_I	124_F	1.396	1.00
13_P	34_P	1.390	1.00
3_S	55_I	1.384	1.00
45_Q	75_A	1.382	1.00
89_A	117_K	1.356	1.00
7_S	48_Y	1.352	1.00
30_L	101_L	1.348	1.00
64_L	97_L	1.337	1.00
29_N	57_E	1.308	1.00
43_T	46_E	1.298	1.00
49_H	53_K	1.290	1.00
49_H	82_E	1.289	1.00
87_D	110_K	1.288	1.00
68_F	125_Q	1.275	1.00
118_A	122_Q	1.230	1.00
33_V	51_A	1.181	1.00
76_A	88_M	1.150	1.00
8_G	16_L	1.140	1.00
80_I	88_M	1.139	1.00
114_N	129_E	1.133	0.99
93_N	124_F	1.125	0.99
20_S	97_L	1.114	0.99
63_F	76_A	1.106	0.99
21_G	27_E	1.104	0.99
11_D	34_P	1.098	0.99
8_G	12_F	1.064	0.99
4_V	96_I	1.056	0.99
50_Q	54_D	1.055	0.99
5_I	63_F	1.053	0.99
64_L	96_I	1.045	0.99
73_Y	127_C	1.038	0.99
68_F	90_A	1.038	0.99
10_G	19_S	1.020	0.99
62_L	100_V	1.010	0.99
5_I	51_A	0.998	0.99
36_F	39_E	0.980	0.99
120_S	123_S	0.973	0.98
120_S	124_F	0.969	0.98
77_A	127_C	0.968	0.98
3_S	51_A	0.968	0.98
62_L	109_L	0.946	0.98
2_I	104_R	0.942	0.98
117_K	129_E	0.938	0.98
3_S	61_V	0.924	0.98
10_G	22_M	0.921	0.98
117_K	121_Q	0.905	0.98
8_G	34_P	0.901	0.97
99_E	103_L	0.900	0.97
96_I	120_S	0.892	0.97
64_L	92_V	0.881	0.97
4_V	100_V	0.873	0.97
2_I	60_E	0.863	0.97
6_I	97_L	0.861	0.97
23_I	94_L	0.852	0.96
45_Q	49_H	0.842	0.96
11_D	18_E	0.839	0.96
90_A	125_Q	0.829	0.96
5_I	55_I	0.828	0.96
113_L	126_V	0.827	0.96
43_T	47_K	0.817	0.95
33_V	40_G	0.811	0.95
47_K	50_Q	0.810	0.95
5_I	48_Y	0.806	0.95
19_S	70_G	0.802	0.95
5_I	33_V	0.798	0.95
2_I	109_L	0.797	0.95
72_P	76_A	0.795	0.95
3_S	29_N	0.790	0.95
126_V	129_E	0.788	0.94
109_L	113_L	0.783	0.94
83_D	86_M	0.780	0.94
79_F	82_E	0.779	0.94
41_I	71_T	0.777	0.94
18_E	21_G	0.772	0.94
92_V	97_L	0.772	0.94
106_H	111_D	0.766	0.94
50_Q	53_K	0.759	0.93
14_I	32_A	0.756	0.93
58_E	61_V	0.754	0.93
45_Q	82_E	0.753	0.93
55_I	61_V	0.752	0.93
4_V	101_L	0.751	0.93
55_I	58_E	0.741	0.92
22_M	37_K	0.736	0.92
36_F	71_T	0.734	0.92
44_L	71_T	0.730	0.92
27_E	104_R	0.727	0.92
64_L	93_N	0.726	0.92
14_I	18_E	0.725	0.92
78_S	82_E	0.719	0.91
71_T	74_N	0.716	0.91
35_F	73_Y	0.712	0.91
20_S	30_L	0.712	0.91
96_I	123_S	0.710	0.91
23_I	102_S	0.709	0.91
40_G	43_T	0.689	0.89
107_L	115_N	0.688	0.89
75_A	78_S	0.683	0.89
49_H	83_D	0.681	0.89
29_N	104_R	0.678	0.89
51_A	54_D	0.677	0.89
24_F	98_L	0.675	0.89
49_H	79_F	0.674	0.88
12_F	19_S	0.671	0.88
60_E	85_R	0.667	0.88
88_M	127_C	0.664	0.88
3_S	60_E	0.662	0.88
46_E	49_H	0.659	0.87
121_Q	124_F	0.655	0.87
99_E	115_N	0.635	0.85
33_V	48_Y	0.634	0.85
19_S	23_I	0.633	0.85
118_A	121_Q	0.633	0.85
125_Q	130_H	0.609	0.83
47_K	51_A	0.607	0.83
48_Y	75_A	0.605	0.82
68_F	88_M	0.598	0.82
59_H	108_A	0.598	0.82
117_K	126_V	0.594	0.81
115_N	118_A	0.591	0.81
35_F	72_P	0.589	0.81
87_D	113_L	0.588	0.81
7_S	35_F	0.587	0.81
22_M	74_N	0.583	0.80
116_L	119_M	0.581	0.80
41_I	44_L	0.581	0.80
11_D	36_F	0.573	0.79
12_F	15_A	0.572	0.79
60_E	109_L	0.570	0.79
68_F	127_C	0.560	0.77
119_M	122_Q	0.560	0.77
12_F	94_L	0.559	0.77
8_G	14_I	0.556	0.77
89_A	120_S	0.550	0.76
128_S	131_L	0.550	0.76
87_D	128_S	0.550	0.76
117_K	124_F	0.549	0.76
111_D	115_N	0.548	0.76
5_I	61_V	0.548	0.76
101_L	104_R	0.547	0.76
35_F	71_T	0.544	0.75
62_L	89_A	0.542	0.75
54_D	114_N	0.539	0.75
3_S	58_E	0.538	0.75
48_Y	79_F	0.533	0.74
114_N	118_A	0.533	0.74
35_F	75_A	0.532	0.74
21_G	25_G	0.529	0.73
56_P	61_V	0.528	0.73
68_F	130_H	0.526	0.73
93_N	120_S	0.523	0.72
56_P	60_E	0.522	0.72
119_M	123_S	0.521	0.72
15_A	19_S	0.520	0.72
15_A	20_S	0.519	0.72
6_I	30_L	0.518	0.72
20_S	24_F	0.511	0.71
48_Y	63_F	0.508	0.70
34_P	44_L	0.504	0.70
68_F	73_Y	0.503	0.70
11_D	19_S	0.503	0.70
27_E	30_L	0.502	0.69
2_I	112_L	0.500	0.69

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
3iprA	2	0.9178	100	0.205	Contact Map
3mtqA	2	0.911	100	0.213	Contact Map
3lfhA	2	0.9658	100	0.217	Contact Map
1pdoA	2	0.8767	100	0.225	Contact Map
3bedA	4	0.8836	100	0.228	Contact Map
4tkzA	2	0.8699	100	0.231	Contact Map
3gx1A	2	0.8219	100	0.34	Contact Map
3gdwA	2	0.8904	100	0.36	Contact Map
3ct6A	2	0.8493	99.9	0.375	Contact Map
3b48A	2	0.8425	99.9	0.4	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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