YMDE - ECOLI - GREMLIN Contacts

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YMDE - Putative uncharacterized protein YmdE

UniProt:	Q7DFV4	Sequences: MEDGVQAMRDYLAGLDIASPEHQVLMNVTAKSEVAPSIIKENLSLHLTHTVKWTESLDTFLNMPTPVAFLEISNKPYLGNMLNDFAGVDQQRVMHCRKAFSDAKVFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14357
Length:	107 (94)
Sequences:	5366 (4393)
Seq/√Len:	453.1

ECOLI - YMDE FABD
BACSU - FABD PKSD PKSE PKSC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_K	55_E	3.256	1.00
45_L	49_H	2.835	1.00
54_T	58_D	2.635	1.00
9_R	41_E	2.374	1.00
24_V	38_I	2.373	1.00
27_N	56_S	2.341	1.00
7_A	11_Y	2.288	1.00
2_E	48_T	2.271	1.00
12_L	17_I	2.183	1.00
5_V	44_S	2.014	1.00
4_G	47_L	1.998	1.00
25_L	32_S	1.944	1.00
57_L	82_L	1.918	1.00
61_L	86_A	1.791	1.00
5_V	9_R	1.655	1.00
86_A	93_V	1.609	1.00
28_V	49_H	1.589	1.00
2_E	44_S	1.577	1.00
9_R	44_S	1.529	1.00
33_E	38_I	1.483	1.00
27_N	46_H	1.477	1.00
54_T	85_F	1.464	1.00
41_E	45_L	1.458	1.00
34_V	37_S	1.406	1.00
25_L	59_T	1.392	1.00
7_A	10_D	1.378	1.00
93_V	96_C	1.366	1.00
59_T	63_M	1.354	1.00
37_S	40_K	1.342	1.00
31_K	59_T	1.283	1.00
33_E	37_S	1.283	1.00
9_R	13_A	1.281	1.00
25_L	63_M	1.247	1.00
5_V	41_E	1.242	1.00
25_L	56_S	1.206	1.00
92_R	95_H	1.193	1.00
57_L	85_F	1.189	1.00
19_S	35_A	1.184	1.00
29_T	45_L	1.164	1.00
59_T	62_N	1.163	1.00
53_W	82_L	1.126	1.00
61_L	69_F	1.123	1.00
8_M	47_L	1.123	1.00
20_P	35_A	1.111	1.00
10_D	13_A	1.080	1.00
61_L	87_G	1.060	1.00
19_S	36_P	1.059	1.00
60_F	66_P	1.053	1.00
4_G	8_M	1.034	1.00
23_Q	32_S	1.023	1.00
28_V	46_H	0.992	1.00
6_Q	44_S	0.949	1.00
6_Q	9_R	0.936	1.00
69_F	82_L	0.930	1.00
24_V	33_E	0.920	1.00
32_S	59_T	0.913	1.00
66_P	69_F	0.908	1.00
6_Q	10_D	0.902	1.00
31_K	37_S	0.896	1.00
26_M	29_T	0.896	1.00
11_Y	14_G	0.878	1.00
32_S	56_S	0.872	1.00
30_A	56_S	0.861	1.00
2_E	5_V	0.856	1.00
63_M	66_P	0.853	1.00
5_V	48_T	0.845	1.00
58_D	85_F	0.837	1.00
92_R	96_C	0.836	1.00
58_D	61_L	0.836	1.00
71_E	78_L	0.826	1.00
44_S	47_L	0.820	1.00
62_N	89_D	0.810	1.00
83_N	87_G	0.805	1.00
58_D	89_D	0.804	1.00
18_A	21_E	0.796	1.00
80_N	83_N	0.788	1.00
32_S	63_M	0.782	1.00
76_P	80_N	0.765	1.00
25_L	60_F	0.761	1.00
61_L	89_D	0.757	1.00
28_V	45_L	0.746	1.00
50_T	54_T	0.744	1.00
61_L	88_V	0.740	1.00
61_L	85_F	0.734	1.00
17_I	39_I	0.733	1.00
8_M	12_L	0.726	1.00
67_V	91_Q	0.707	1.00
20_P	38_I	0.700	1.00
58_D	62_N	0.700	1.00
56_S	59_T	0.686	1.00
19_S	39_I	0.681	1.00
56_S	60_F	0.680	1.00
82_L	85_F	0.679	1.00
13_A	41_E	0.678	1.00
87_G	90_Q	0.675	1.00
4_G	7_A	0.670	1.00
77_Y	81_M	0.670	1.00
3_D	6_Q	0.664	1.00
58_D	88_V	0.660	1.00
64_P	67_V	0.654	1.00
24_V	42_N	0.651	1.00
24_V	27_N	0.641	0.99
55_E	58_D	0.635	0.99
12_L	15_L	0.635	0.99
89_D	93_V	0.635	0.99
8_M	46_H	0.609	0.99
20_P	36_P	0.608	0.99
87_G	93_V	0.607	0.99
82_L	86_A	0.606	0.99
28_V	42_N	0.589	0.99
79_G	95_H	0.584	0.99
27_N	51_V	0.577	0.99
90_Q	93_V	0.576	0.99
35_A	38_I	0.571	0.99
37_S	45_L	0.570	0.99
66_P	75_K	0.568	0.99
29_T	37_S	0.566	0.99
88_V	92_R	0.564	0.99
57_L	69_F	0.561	0.99
13_A	17_I	0.558	0.99
10_D	14_G	0.554	0.99
82_L	93_V	0.545	0.98
50_T	55_E	0.543	0.98
90_Q	95_H	0.542	0.98
5_V	45_L	0.537	0.98
43_L	71_E	0.534	0.98
30_A	55_E	0.534	0.98
27_N	42_N	0.534	0.98
24_V	37_S	0.530	0.98
12_L	44_S	0.527	0.98
26_M	42_N	0.523	0.98
79_G	82_L	0.522	0.98
25_L	66_P	0.520	0.98
91_Q	94_M	0.520	0.98
61_L	91_Q	0.518	0.98
60_F	69_F	0.510	0.97
3_D	74_N	0.505	0.97
61_L	67_V	0.503	0.97
43_L	53_W	0.502	0.97
51_V	71_E	0.502	0.97
76_P	79_G	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
2qo3A	2	0.9907	99.9	0.242	Contact Map
4mz0A	2	0.9907	99.9	0.25	Contact Map
4rl1A	1	0.9626	99.9	0.254	Contact Map
2hg4A	2	0.9907	99.9	0.254	Contact Map
4qbuA	1	0.9907	99.9	0.28	Contact Map
3tzyA	1	0.9907	99.9	0.3	Contact Map
3sbmA	1	0.8131	99.9	0.301	Contact Map
4rr5A	1	0.9533	99.9	0.304	Contact Map
3ptwA	1	0.972	99.9	0.307	Contact Map
3g87A	1	0.8318	99.9	0.307	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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