PTJB - BACSU - GREMLIN Contacts

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PTJB - Lichenan-specific phosphotransferase enzyme IIB component

UniProt:	P46318	Sequences: MNILLVCAAGMSTSLLVSKMEKSAQEQGKDYTIWAVSGDSVQNHIDKADVLLLGPQVRYMLPQLKKLGESKGVPVDVINTVHYGTCNGAEVLKSAEQLGHVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	102 (96)
Sequences:	1191 (844)
Seq/√Len:	86.2

ECOLI - PTQB
BACSU - PTJB PTEB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_L	65_K	3.503	1.00
27_Q	93_K	3.437	1.00
79_N	94_S	2.352	1.00
2_N	32_T	2.295	1.00
82_H	87_N	2.065	1.00
89_A	93_K	2.041	1.00
41_V	64_L	1.988	1.00
18_S	21_E	1.968	1.00
42_Q	67_L	1.911	1.00
50_V	98_L	1.847	1.00
16_L	91_V	1.842	1.00
17_V	33_I	1.806	1.00
79_N	82_H	1.772	1.00
18_S	22_K	1.772	1.00
29_K	96_E	1.755	1.00
82_H	90_E	1.671	1.00
4_L	48_A	1.604	1.00
65_K	69_E	1.569	1.00
4_L	36_V	1.544	1.00
23_S	27_Q	1.521	1.00
20_M	33_I	1.488	0.99
22_K	26_E	1.464	0.99
27_Q	89_A	1.415	0.99
62_P	65_K	1.414	0.99
94_S	97_Q	1.409	0.99
31_Y	96_E	1.363	0.99
22_K	25_Q	1.344	0.99
23_S	26_E	1.331	0.99
76_D	98_L	1.296	0.99
15_L	18_S	1.289	0.98
87_N	90_E	1.282	0.98
11_M	14_S	1.227	0.98
93_K	97_Q	1.202	0.98
60_M	63_Q	1.177	0.97
6_V	41_V	1.170	0.97
52_L	76_D	1.170	0.97
23_S	89_A	1.166	0.97
66_K	69_E	1.161	0.97
23_S	88_G	1.147	0.97
21_E	25_Q	1.125	0.96
15_L	86_C	1.124	0.96
82_H	94_S	1.119	0.96
82_H	91_V	1.108	0.96
76_D	94_S	1.101	0.96
46_D	71_K	1.091	0.96
38_G	60_M	1.090	0.96
90_E	93_K	1.088	0.96
5_L	13_T	1.086	0.96
4_L	34_W	1.062	0.95
27_Q	96_E	1.040	0.94
64_L	75_V	1.037	0.94
24_A	33_I	1.036	0.94
45_I	68_G	1.036	0.94
61_L	76_D	1.031	0.94
92_L	96_E	1.011	0.94
44_H	47_K	0.996	0.93
34_W	48_A	0.989	0.93
29_K	92_L	0.985	0.93
3_I	31_Y	0.977	0.92
63_Q	66_K	0.967	0.92
69_E	72_G	0.962	0.92
51_L	73_V	0.961	0.92
26_E	89_A	0.958	0.92
9_A	37_S	0.956	0.91
68_G	71_K	0.952	0.91
61_L	75_V	0.951	0.91
6_V	36_V	0.938	0.91
24_A	31_Y	0.935	0.91
51_L	68_G	0.932	0.90
21_E	32_T	0.924	0.90
41_V	48_A	0.923	0.90
53_L	57_V	0.914	0.90
3_I	95_A	0.913	0.90
20_M	95_A	0.904	0.89
64_L	68_G	0.891	0.88
16_L	78_I	0.868	0.87
23_S	92_L	0.867	0.87
61_L	77_V	0.858	0.86
13_T	54_G	0.856	0.86
2_N	34_W	0.846	0.86
51_L	64_L	0.834	0.85
50_V	95_A	0.804	0.83
6_V	51_L	0.803	0.83
85_T	90_E	0.764	0.79
34_W	44_H	0.750	0.78
53_L	61_L	0.740	0.77
53_L	77_V	0.733	0.76
36_V	48_A	0.731	0.76
95_A	98_L	0.727	0.76
78_I	91_V	0.714	0.75
19_K	22_K	0.709	0.74
2_N	48_A	0.707	0.74
41_V	51_L	0.692	0.72
88_G	91_V	0.681	0.71
24_A	92_L	0.672	0.70
15_L	19_K	0.671	0.70
38_G	64_L	0.667	0.69
18_S	25_Q	0.661	0.69
7_C	10_G	0.636	0.66
81_V	87_N	0.632	0.65
52_L	94_S	0.626	0.65
8_A	37_S	0.616	0.63
12_S	83_Y	0.615	0.63
36_V	44_H	0.610	0.63
93_K	96_E	0.607	0.62
39_D	60_M	0.604	0.62
4_L	68_G	0.595	0.61
17_V	20_M	0.594	0.61
68_G	72_G	0.592	0.60
11_M	15_L	0.588	0.60
40_S	43_N	0.585	0.59
43_N	47_K	0.579	0.59
62_P	66_K	0.578	0.58
36_V	40_S	0.575	0.58
57_V	60_M	0.575	0.58
13_T	20_M	0.574	0.58
86_C	91_V	0.574	0.58
76_D	79_N	0.568	0.57
6_V	64_L	0.567	0.57
6_V	57_V	0.560	0.56
2_N	47_K	0.560	0.56
38_G	44_H	0.556	0.56
6_V	40_S	0.556	0.56
8_A	38_G	0.555	0.55
25_Q	30_D	0.553	0.55
69_E	75_V	0.549	0.55
38_G	57_V	0.548	0.54
5_L	20_M	0.539	0.53
20_M	91_V	0.535	0.53
53_L	92_L	0.535	0.53
7_C	35_A	0.532	0.52
69_E	74_P	0.530	0.52
39_D	57_V	0.527	0.52
81_V	85_T	0.525	0.51
24_A	29_K	0.523	0.51
45_I	69_E	0.518	0.50
7_C	13_T	0.516	0.50
43_N	46_D	0.513	0.50
4_L	51_L	0.512	0.50
12_S	84_G	0.509	0.49
8_A	56_Q	0.506	0.49
31_Y	59_Y	0.504	0.49
71_K	75_V	0.501	0.48
17_V	23_S	0.500	0.48

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
3nbmA	1	0.9706	99.9	0.334	Contact Map
4mgeA	3	1	99.9	0.343	Contact Map
2l2qA	1	1	99.9	0.377	Contact Map
1e2bA	1	0.9804	99.9	0.399	Contact Map
2kyrA	1	0.9314	99.9	0.429	Contact Map
4tn5A	2	0.9314	99.9	0.432	Contact Map
2r4qA	1	0.9118	99.9	0.436	Contact Map
2m1zA	1	0.9314	99.9	0.442	Contact Map
1tvmA	1	0.8824	99.6	0.587	Contact Map
3czcA	1	0.8824	99.3	0.647	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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