PTMA - BACSU - GREMLIN Contacts

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PTMA - Mannitol-specific phosphotransferase enzyme IIA component

UniProt:	C0H3V2	Sequences: MQVLAKENIKLNQTVSSKEEAIKLAGQTLIDNGYVTEDYISKMFEREETSSTFMGNFIAIPHGTEEAKSEVLHSGISIIQIPEGVEYGEGNTAKVVFGIAGKNNEHLDILSNIAIICSEEENIERLISAKSEEDLIAIFNEVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	143 (135)
Sequences:	6860 (5282)
Seq/√Len:	454.6

ECOLI - HRSA PTMA PTSN ULAC PTFA SGCA PTKA PTFAH PTM3C PTFX2 PTFX1 FRVR
BACSU - PTMA PTN3B PTF3A MANR MTLR LICR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_K	127_I	3.339	1.00
6_K	133_E	2.561	1.00
131_S	134_D	2.262	1.00
23_K	40_I	2.253	1.00
26_G	40_I	2.150	1.00
27_Q	31_D	2.117	1.00
38_D	70_E	2.057	1.00
36_T	72_L	2.034	1.00
81_I	96_V	1.993	1.00
25_A	98_G	1.956	1.00
124_E	128_S	1.948	1.00
10_K	28_T	1.940	1.00
15_V	24_L	1.929	1.00
43_M	98_G	1.845	1.00
14_T	82_P	1.841	1.00
17_S	20_E	1.838	1.00
34_Y	73_H	1.787	1.00
8_N	32_N	1.772	1.00
12_N	82_P	1.733	1.00
30_I	35_V	1.698	1.00
84_G	94_K	1.674	1.00
13_Q	79_I	1.661	1.00
34_Y	75_G	1.659	1.00
15_V	21_A	1.653	1.00
12_N	80_Q	1.618	1.00
7_E	32_N	1.612	1.00
41_S	45_E	1.589	1.00
75_G	100_A	1.579	1.00
25_A	79_I	1.557	1.00
71_V	100_A	1.536	1.00
39_Y	100_A	1.483	1.00
19_E	48_E	1.478	1.00
86_E	92_T	1.437	1.00
74_S	102_K	1.435	1.00
129_A	135_L	1.429	1.00
16_S	20_E	1.416	1.00
45_E	48_E	1.415	1.00
130_K	134_D	1.408	1.00
23_K	44_F	1.399	1.00
6_K	136_I	1.380	1.00
57_F	94_K	1.373	1.00
42_K	45_E	1.357	1.00
21_A	96_V	1.353	1.00
42_K	63_G	1.350	1.00
81_I	84_G	1.295	1.00
10_K	24_L	1.284	1.00
28_T	32_N	1.278	1.00
11_L	80_Q	1.278	1.00
28_T	31_D	1.249	1.00
56_N	123_I	1.246	1.00
133_E	137_A	1.244	1.00
19_E	44_F	1.237	1.00
22_I	43_M	1.236	1.00
47_E	54_M	1.235	1.00
26_G	43_M	1.187	1.00
36_T	70_E	1.184	1.00
129_A	134_D	1.170	1.00
93_A	96_V	1.153	1.00
87_Y	96_V	1.151	1.00
69_S	103_N	1.142	1.00
78_I	135_L	1.129	1.00
123_I	127_I	1.122	1.00
45_E	49_T	1.118	1.00
5_A	8_N	1.116	1.00
13_Q	24_L	1.070	1.00
40_I	44_F	1.062	1.00
6_K	132_E	1.047	1.00
35_V	39_Y	1.036	1.00
19_E	23_K	1.015	1.00
125_R	138_I	1.014	1.00
47_E	52_T	1.013	1.00
10_K	13_Q	1.010	1.00
95_V	127_I	0.996	1.00
15_V	81_I	0.990	1.00
24_L	28_T	0.990	1.00
111_S	115_I	0.977	1.00
65_E	70_E	0.977	1.00
84_G	92_T	0.962	1.00
26_G	98_G	0.960	1.00
86_E	90_G	0.958	1.00
74_S	101_G	0.955	1.00
30_I	37_E	0.947	1.00
11_L	135_L	0.941	1.00
14_T	83_E	0.934	1.00
116_I	122_N	0.932	1.00
132_E	136_I	0.931	1.00
9_I	132_E	0.920	1.00
33_G	72_L	0.914	1.00
129_A	138_I	0.914	1.00
114_A	118_S	0.912	1.00
80_Q	135_L	0.908	1.00
27_Q	30_I	0.903	1.00
28_T	77_S	0.899	1.00
76_I	109_I	0.898	1.00
20_E	23_K	0.897	1.00
29_L	77_S	0.892	1.00
9_I	135_L	0.891	1.00
81_I	94_K	0.889	1.00
119_E	122_N	0.888	1.00
134_D	137_A	0.881	1.00
44_F	48_E	0.872	1.00
18_K	88_G	0.861	1.00
78_I	95_V	0.859	1.00
29_L	100_A	0.856	1.00
30_I	40_I	0.846	1.00
125_R	128_S	0.843	1.00
136_I	140_N	0.841	1.00
23_K	41_S	0.836	1.00
20_E	24_L	0.824	1.00
122_N	138_I	0.819	1.00
21_A	81_I	0.812	1.00
80_Q	95_V	0.809	1.00
37_E	41_S	0.809	1.00
22_I	40_I	0.807	1.00
74_S	105_E	0.791	1.00
16_S	83_E	0.789	1.00
24_L	27_Q	0.788	1.00
11_L	132_E	0.787	1.00
111_S	114_A	0.784	1.00
24_L	79_I	0.784	1.00
39_Y	43_M	0.781	1.00
42_K	70_E	0.763	1.00
60_I	110_L	0.758	1.00
79_I	98_G	0.758	1.00
38_D	42_K	0.751	1.00
27_Q	40_I	0.750	1.00
137_A	140_N	0.743	1.00
42_K	65_E	0.736	1.00
18_K	47_E	0.724	1.00
81_I	85_V	0.711	1.00
78_I	97_F	0.707	1.00
8_N	34_Y	0.704	1.00
25_A	77_S	0.702	1.00
58_I	117_C	0.696	1.00
5_A	73_H	0.692	1.00
113_I	117_C	0.691	1.00
23_K	27_Q	0.690	1.00
21_A	85_V	0.689	1.00
55_G	58_I	0.686	1.00
101_G	109_I	0.681	1.00
15_V	79_I	0.680	1.00
5_A	32_N	0.680	1.00
106_H	110_L	0.676	1.00
125_R	134_D	0.670	1.00
116_I	139_F	0.663	1.00
83_E	94_K	0.662	1.00
46_R	61_P	0.661	1.00
13_Q	82_P	0.660	1.00
57_F	127_I	0.657	1.00
77_S	98_G	0.655	1.00
88_G	91_N	0.655	1.00
22_I	44_F	0.647	1.00
114_A	117_C	0.642	1.00
53_F	91_N	0.637	0.99
29_L	75_G	0.631	0.99
12_N	130_K	0.630	0.99
46_R	50_S	0.630	0.99
29_L	35_V	0.617	0.99
120_E	124_E	0.615	0.99
58_I	123_I	0.608	0.99
9_I	136_I	0.602	0.99
59_A	93_A	0.602	0.99
14_T	24_L	0.598	0.99
39_Y	98_G	0.595	0.99
38_D	41_S	0.584	0.99
5_A	34_Y	0.582	0.99
76_I	97_F	0.582	0.99
26_G	30_I	0.580	0.99
77_S	100_A	0.577	0.99
10_K	132_E	0.572	0.99
29_L	39_Y	0.569	0.99
101_G	106_H	0.566	0.99
46_R	52_T	0.565	0.99
132_E	135_L	0.564	0.99
53_F	89_E	0.562	0.99
5_A	136_I	0.560	0.99
97_F	113_I	0.560	0.99
47_E	51_S	0.558	0.99
71_V	75_G	0.551	0.98
112_N	116_I	0.549	0.98
125_R	129_A	0.539	0.98
56_N	91_N	0.538	0.98
121_E	125_R	0.534	0.98
38_D	69_S	0.534	0.98
65_E	71_V	0.533	0.98
107_L	111_S	0.530	0.98
115_I	119_E	0.530	0.98
18_K	22_I	0.527	0.98
23_K	37_E	0.523	0.98
39_Y	63_G	0.521	0.98
4_L	78_I	0.521	0.98
39_Y	75_G	0.519	0.98
108_D	111_S	0.517	0.98
108_D	115_I	0.516	0.98
124_E	127_I	0.516	0.98
53_F	87_Y	0.510	0.98
25_A	96_V	0.510	0.98
10_K	79_I	0.510	0.98
106_H	114_A	0.503	0.97
80_Q	130_K	0.501	0.97
80_Q	126_L	0.501	0.97
126_L	135_L	0.500	0.97

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
1a3aA	2	1	100	0.158	Contact Map
1a6jA	4	0.979	100	0.168	Contact Map
2oqtA	2	0.979	100	0.172	Contact Map
3bjvA	2	0.979	100	0.177	Contact Map
2oq3A	1	0.972	100	0.185	Contact Map
2a0jA	1	0.958	100	0.191	Contact Map
4m62S	1	0.979	100	0.194	Contact Map
3oxpA	2	0.979	100	0.194	Contact Map
3urrA	2	0.979	100	0.198	Contact Map
3t43A	2	0.8741	100	0.248	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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