MDTJ - ECOLI - GREMLIN Contacts

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MDTJ - Spermidine export protein MdtJ

UniProt:	P69212	Sequences: MYIYWILLGLAIATEITGTLSMKWASVSEGNGGFILMLVMISLSYIFLSFAVKKIALGVAYALWEGIGILFITLFSVLLFDESLSLMKIAGLTTLVAGIVLIKSGTRKARKPELEVNHGAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13927
Length:	121 (104)
Sequences:	4750 (3293)
Seq/√Len:	322.9

ECOLI - MDTJ SUGE MDTI EMRE
BACSU - YVAE EBRB YVDR YKKC YKKD YVDS EBRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_G	101_L	2.833	1.00
14_T	43_L	2.646	1.00
50_F	53_K	2.497	1.00
77_V	84_L	2.351	1.00
21_S	36_L	2.322	1.00
4_Y	54_K	2.287	1.00
7_L	50_F	2.284	1.00
17_T	40_M	2.060	1.00
75_F	79_L	2.003	1.00
73_T	92_L	1.899	1.00
12_I	67_I	1.866	1.00
94_T	98_G	1.744	1.00
55_I	60_A	1.720	1.00
52_V	60_A	1.708	1.00
46_I	50_F	1.629	1.00
18_G	40_M	1.578	1.00
93_T	97_A	1.532	1.00
32_G	36_L	1.523	1.00
86_L	90_A	1.511	1.00
41_I	45_Y	1.503	1.00
25_A	34_F	1.499	1.00
20_L	75_F	1.497	1.00
38_L	42_S	1.474	1.00
52_V	57_L	1.460	1.00
20_L	24_W	1.437	1.00
25_A	28_S	1.426	1.00
17_T	36_L	1.423	1.00
94_T	97_A	1.400	1.00
22_M	37_M	1.383	1.00
30_G	33_G	1.374	1.00
28_S	34_F	1.369	1.00
91_G	105_G	1.346	1.00
18_G	41_I	1.336	1.00
16_I	71_F	1.329	1.00
7_L	47_F	1.324	1.00
14_T	40_M	1.268	1.00
91_G	98_G	1.268	1.00
85_S	88_K	1.267	1.00
100_V	104_S	1.266	1.00
51_A	60_A	1.260	1.00
24_W	80_F	1.251	1.00
87_M	105_G	1.246	1.00
89_I	93_T	1.206	1.00
31_N	34_F	1.201	1.00
95_L	98_G	1.182	1.00
17_T	21_S	1.139	1.00
95_L	99_I	1.130	1.00
88_K	102_I	1.127	1.00
83_S	88_K	1.102	1.00
42_S	46_I	1.090	1.00
69_I	73_T	1.090	1.00
48_L	60_A	1.073	1.00
92_L	102_I	1.069	1.00
84_L	89_I	1.060	1.00
76_S	82_E	1.051	1.00
26_S	30_G	1.046	1.00
87_M	90_A	1.031	1.00
91_G	95_L	1.018	1.00
32_G	35_I	1.010	1.00
82_E	88_K	0.998	1.00
69_I	96_V	0.970	1.00
9_G	67_I	0.944	1.00
23_K	27_V	0.924	1.00
6_I	10_L	0.915	1.00
86_L	89_I	0.908	1.00
21_S	24_W	0.906	1.00
74_L	78_L	0.899	1.00
5_W	63_L	0.889	1.00
84_L	88_K	0.876	1.00
26_S	29_E	0.873	1.00
12_I	44_S	0.870	1.00
29_E	34_F	0.866	1.00
9_G	12_I	0.864	1.00
58_G	62_A	0.864	1.00
4_Y	55_I	0.859	1.00
70_L	92_L	0.859	1.00
57_L	72_I	0.857	1.00
31_N	35_I	0.851	1.00
35_I	39_V	0.836	1.00
62_A	65_E	0.832	1.00
10_L	47_F	0.831	1.00
91_G	94_T	0.828	1.00
56_A	59_V	0.825	1.00
11_A	47_F	0.816	1.00
21_S	40_M	0.810	1.00
75_F	80_F	0.809	1.00
59_V	88_K	0.807	1.00
97_A	101_L	0.805	1.00
63_L	67_I	0.798	1.00
66_G	99_I	0.765	1.00
29_E	53_K	0.764	1.00
87_M	91_G	0.763	0.99
34_F	37_M	0.758	0.99
16_I	75_F	0.756	0.99
76_S	80_F	0.738	0.99
21_S	37_M	0.737	0.99
19_T	72_I	0.719	0.99
83_S	86_L	0.719	0.99
13_A	71_F	0.716	0.99
39_V	43_L	0.705	0.99
21_S	25_A	0.702	0.99
101_L	105_G	0.696	0.99
41_I	65_E	0.686	0.99
8_L	51_A	0.682	0.99
78_L	81_D	0.680	0.99
7_L	51_A	0.678	0.99
25_A	30_G	0.676	0.99
50_F	54_K	0.675	0.99
70_L	96_V	0.674	0.99
51_A	54_K	0.674	0.99
28_S	33_G	0.673	0.99
20_L	76_S	0.670	0.99
96_V	100_V	0.665	0.99
20_L	80_F	0.663	0.99
19_T	41_I	0.663	0.99
15_E	44_S	0.660	0.99
22_M	64_W	0.651	0.98
77_V	89_I	0.647	0.98
94_T	101_L	0.647	0.98
29_E	33_G	0.645	0.98
82_E	85_S	0.643	0.98
25_A	29_E	0.643	0.98
90_A	94_T	0.643	0.98
4_Y	7_L	0.643	0.98
67_I	71_F	0.643	0.98
57_L	80_F	0.625	0.98
66_G	69_I	0.623	0.98
36_L	40_M	0.619	0.98
65_E	72_I	0.616	0.98
13_A	17_T	0.610	0.98
59_V	62_A	0.600	0.97
25_A	37_M	0.595	0.97
56_A	106_T	0.592	0.97
41_I	57_L	0.585	0.97
20_L	23_K	0.580	0.97
18_G	37_M	0.572	0.96
11_A	48_L	0.567	0.96
76_S	88_K	0.564	0.96
103_K	106_T	0.558	0.96
35_I	38_L	0.555	0.96
62_A	92_L	0.550	0.96
65_E	76_S	0.545	0.95
71_F	75_F	0.545	0.95
22_M	45_Y	0.543	0.95
62_A	102_I	0.533	0.95
39_V	42_S	0.529	0.95
21_S	38_L	0.526	0.94
25_A	33_G	0.525	0.94
8_L	60_A	0.523	0.94
73_T	102_I	0.521	0.94
77_V	83_S	0.511	0.93
23_K	26_S	0.506	0.93
9_G	13_A	0.505	0.93
29_E	83_S	0.504	0.93
77_V	88_K	0.501	0.93
28_S	31_N	0.500	0.93

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
3b5dA	2	0.843	99.9	0.402	Contact Map
2i68A	2	0.6446	99.9	0.408	Contact Map
4ikvA	1	0.9091	13	0.931	Contact Map
1pw4A	1	0.9917	7.6	0.938	Contact Map
4qtnA	3	0.9008	7.6	0.938	Contact Map
4xnjA	1	0.8926	6.5	0.94	Contact Map
2cfqA	1	0.9752	6	0.941	Contact Map
2r9rB	3	0.686	5.2	0.942	Contact Map
3j8eG	3	0.9669	4.9	0.943	Contact Map
4gx0A	3	0.7686	4.8	0.944	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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