YAAK - BACSU - GREMLIN Contacts

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YAAK - Nucleoid-associated protein YaaK

UniProt:	P24281	Sequences: MRGGMGNMQKMMKQMQKMQKDMAKAQEELAEKVVEGTAGGGMVTVKANGQKEILDVIIKEEVVDPEDIDMLQDLVLAATNEALKKVDEITNETMGQFTKGMNMPGLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	107 (100)
Sequences:	2325 (1466)
Seq/√Len:	146.6

ECOLI - YBAB
BACSU - YAAK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_V	68_I	2.635	1.00
34_V	89_I	2.309	1.00
21_D	24_K	2.115	1.00
33_V	46_K	2.095	1.00
24_K	28_E	2.062	1.00
35_E	44_T	2.050	1.00
51_K	87_D	2.048	1.00
17_K	21_D	2.000	1.00
47_A	53_I	1.934	1.00
93_T	96_Q	1.891	1.00
36_G	81_E	1.868	1.00
44_T	57_I	1.830	1.00
57_I	72_Q	1.778	1.00
35_E	46_K	1.769	1.00
48_N	54_L	1.769	1.00
81_E	85_K	1.763	1.00
27_E	30_A	1.735	1.00
30_A	50_Q	1.733	1.00
23_A	27_E	1.717	1.00
32_K	93_T	1.717	1.00
46_K	55_D	1.687	1.00
33_V	54_L	1.678	1.00
32_K	89_I	1.627	1.00
37_T	44_T	1.540	1.00
60_E	68_I	1.516	1.00
45_V	79_T	1.505	1.00
51_K	86_V	1.499	1.00
20_K	24_K	1.463	1.00
88_E	92_E	1.433	1.00
53_I	79_T	1.411	1.00
47_A	82_A	1.408	1.00
28_E	32_K	1.403	1.00
11_M	15_M	1.391	1.00
45_V	53_I	1.367	1.00
7_N	10_K	1.350	1.00
52_E	84_K	1.329	1.00
45_V	56_V	1.323	1.00
81_E	84_K	1.311	1.00
27_E	31_E	1.307	1.00
28_E	93_T	1.280	1.00
38_A	77_A	1.258	1.00
47_A	83_L	1.239	1.00
47_A	86_V	1.186	1.00
84_K	88_E	1.172	1.00
67_D	70_M	1.134	0.99
89_I	93_T	1.100	0.99
88_E	91_N	1.090	0.99
20_K	23_A	1.068	0.99
14_Q	17_K	1.066	0.99
68_I	72_Q	1.064	0.99
16_Q	20_K	1.055	0.99
89_I	92_E	1.036	0.99
39_G	77_A	1.025	0.99
55_D	72_Q	1.014	0.99
46_K	54_L	1.009	0.99
57_I	68_I	1.001	0.99
25_A	97_F	0.992	0.99
47_A	79_T	0.984	0.98
49_G	86_V	0.955	0.98
51_K	83_L	0.941	0.98
79_T	83_L	0.934	0.98
6_G	10_K	0.919	0.98
28_E	31_E	0.910	0.97
50_Q	87_D	0.895	0.97
53_I	56_V	0.880	0.97
58_I	75_V	0.880	0.97
85_K	88_E	0.877	0.97
56_V	76_L	0.873	0.97
17_K	20_K	0.872	0.97
48_N	52_E	0.869	0.97
10_K	13_K	0.863	0.97
80_N	83_L	0.852	0.96
25_A	93_T	0.852	0.96
83_L	87_D	0.847	0.96
52_E	80_N	0.823	0.95
39_G	74_L	0.816	0.95
36_G	78_A	0.813	0.95
12_M	15_M	0.809	0.95
34_V	49_G	0.806	0.95
24_K	27_E	0.795	0.95
10_K	14_Q	0.776	0.94
42_M	61_E	0.772	0.94
68_I	71_L	0.767	0.93
44_T	59_K	0.756	0.93
32_K	49_G	0.756	0.93
75_V	79_T	0.748	0.93
7_N	17_K	0.745	0.92
13_K	16_Q	0.745	0.92
70_M	73_D	0.729	0.92
86_V	90_T	0.729	0.92
40_G	77_A	0.722	0.91
62_V	71_L	0.719	0.91
9_Q	12_M	0.714	0.91
25_A	94_M	0.712	0.91
37_T	85_K	0.701	0.90
45_V	75_V	0.696	0.90
46_K	57_I	0.694	0.90
30_A	99_K	0.693	0.89
62_V	74_L	0.689	0.89
49_G	89_I	0.680	0.89
63_V	71_L	0.678	0.88
33_V	55_D	0.672	0.88
64_D	70_M	0.669	0.88
7_N	13_K	0.665	0.87
59_K	62_V	0.664	0.87
82_A	86_V	0.662	0.87
66_E	69_D	0.662	0.87
6_G	9_Q	0.651	0.86
99_K	102_N	0.645	0.86
35_E	85_K	0.644	0.86
29_L	86_V	0.638	0.85
91_N	95_G	0.630	0.85
29_L	90_T	0.629	0.84
42_M	59_K	0.626	0.84
37_T	41_G	0.609	0.82
34_V	47_A	0.609	0.82
11_M	14_Q	0.607	0.82
29_L	32_K	0.605	0.82
53_I	76_L	0.595	0.81
47_A	76_L	0.593	0.81
56_V	72_Q	0.591	0.81
18_M	22_M	0.590	0.80
58_I	68_I	0.588	0.80
34_V	86_V	0.586	0.80
76_L	80_N	0.580	0.79
65_P	68_I	0.573	0.79
45_V	76_L	0.572	0.78
92_E	96_Q	0.572	0.78
63_V	66_E	0.570	0.78
60_E	65_P	0.569	0.78
63_V	67_D	0.562	0.77
38_A	78_A	0.558	0.77
25_A	28_E	0.557	0.77
73_D	77_A	0.557	0.77
11_M	17_K	0.554	0.76
56_V	79_T	0.551	0.76
23_A	26_Q	0.551	0.76
25_A	96_Q	0.538	0.74
29_L	49_G	0.534	0.74
36_G	85_K	0.532	0.73
29_L	93_T	0.531	0.73
72_Q	76_L	0.529	0.73
37_T	81_E	0.529	0.73
8_M	15_M	0.528	0.73
36_G	43_V	0.523	0.72
15_M	42_M	0.523	0.72
25_A	90_T	0.518	0.71
37_T	40_G	0.515	0.71
36_G	56_V	0.501	0.69
85_K	89_I	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
1ybxA	2	0.8598	100	0.107	Contact Map
1j8bA	2	0.8598	100	0.185	Contact Map
3f42A	4	0.8692	100	0.256	Contact Map
4chgG	2	0.2056	18.4	0.923	Contact Map
4bjqA	2	0.5047	14.4	0.926	Contact Map
3efmA	1	0.6262	11.5	0.93	Contact Map
4xcoC	1	0.9346	10.3	0.931	Contact Map
2kzxA	1	0.729	10.1	0.931	Contact Map
3r07C	1	0.7383	9.8	0.932	Contact Map
3txsA	5	0.271	8.5	0.933	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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