YOBD - BACSU - GREMLIN Contacts

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YOBD - Uncharacterized HTH-type transcriptional regulator YobD

UniProt:	O34647	Sequences: MYCQRLRQLRKAHKLTMEQLAEKIGIAKSSYGGYEAESKKPPLDKLVILARLYDVSVDYILGLTDDPDPKVERKNLKEFLEKPDIHWDGYKLTPEILDPIRKILKLVTANNN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	112 (106)
Sequences:	1239 (1124)
Seq/√Len:	109.2

ECOLI - DICA
BACSU - YOBD YQAE ANSR YONR RGHRB SLRR SINR RGHR XRE IMMR YQAF YGZD YAZB
HALSA - O51961 Q9HRZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_L	31_Y	3.600	1.00
18_E	22_E	3.200	1.00
18_E	28_K	3.047	1.00
51_R	63_L	2.606	1.00
15_L	52_L	2.429	1.00
2_Y	6_L	2.395	1.00
10_R	35_E	2.294	1.00
3_C	37_E	2.228	1.00
29_S	33_G	2.223	1.00
12_A	67_P	2.178	1.00
23_K	52_L	2.096	1.00
57_V	61_L	2.044	1.00
9_L	53_Y	2.038	1.00
27_A	30_S	1.997	1.00
40_K	43_L	1.947	1.00
26_I	31_Y	1.902	1.00
93_T	96_I	1.889	1.00
20_L	53_Y	1.809	1.00
103_I	106_L	1.760	1.00
33_G	38_S	1.705	1.00
29_S	32_G	1.676	1.00
99_P	106_L	1.642	1.00
30_S	33_G	1.601	1.00
33_G	39_K	1.595	1.00
58_D	63_L	1.472	1.00
64_T	67_P	1.466	1.00
28_K	32_G	1.440	1.00
5_R	59_Y	1.406	1.00
27_A	33_G	1.400	1.00
20_L	49_L	1.394	1.00
43_L	46_L	1.377	1.00
50_A	63_L	1.344	1.00
6_L	31_Y	1.300	0.99
26_I	30_S	1.288	0.99
102_K	106_L	1.277	0.99
33_G	36_A	1.270	0.99
99_P	103_I	1.206	0.99
46_L	61_L	1.182	0.99
103_I	107_V	1.177	0.99
17_M	28_K	1.175	0.99
100_I	104_L	1.165	0.99
17_M	21_A	1.140	0.98
24_I	49_L	1.096	0.98
34_Y	45_K	1.079	0.98
32_G	36_A	1.067	0.98
46_L	57_V	1.053	0.97
40_K	45_K	1.051	0.97
87_W	91_K	1.034	0.97
19_Q	22_E	1.015	0.97
5_R	62_G	1.015	0.97
86_H	89_G	1.007	0.97
15_L	19_Q	1.005	0.97
2_Y	43_L	1.003	0.97
42_P	45_K	0.985	0.96
99_P	107_V	0.983	0.96
15_L	23_K	0.964	0.96
19_Q	23_K	0.953	0.95
5_R	63_L	0.951	0.95
34_Y	39_K	0.933	0.95
28_K	36_A	0.927	0.95
92_L	97_L	0.924	0.95
4_Q	37_E	0.922	0.94
27_A	32_G	0.922	0.94
5_R	8_Q	0.912	0.94
32_G	41_P	0.908	0.94
5_R	65_D	0.892	0.93
96_I	99_P	0.887	0.93
89_G	93_T	0.882	0.93
28_K	31_Y	0.881	0.93
13_H	23_K	0.879	0.93
75_N	79_F	0.875	0.93
45_K	48_I	0.875	0.93
2_Y	46_L	0.855	0.92
89_G	97_L	0.851	0.92
89_G	92_L	0.832	0.91
6_L	20_L	0.826	0.91
34_Y	41_P	0.825	0.90
8_Q	12_A	0.814	0.90
41_P	58_D	0.813	0.90
21_A	31_Y	0.798	0.89
48_I	51_R	0.776	0.88
99_P	102_K	0.772	0.87
104_L	107_V	0.769	0.87
17_M	31_Y	0.760	0.86
101_R	104_L	0.759	0.86
93_T	99_P	0.756	0.86
92_L	104_L	0.741	0.85
46_L	58_D	0.734	0.85
98_D	102_K	0.733	0.84
86_H	92_L	0.725	0.84
2_Y	53_Y	0.725	0.84
9_L	55_V	0.724	0.84
96_I	103_I	0.708	0.82
28_K	38_S	0.706	0.82
16_T	19_Q	0.704	0.82
64_T	69_P	0.695	0.81
9_L	52_L	0.685	0.80
27_A	39_K	0.667	0.78
77_K	80_L	0.660	0.78
25_G	48_I	0.659	0.78
20_L	52_L	0.657	0.77
28_K	33_G	0.656	0.77
89_G	104_L	0.656	0.77
101_R	105_K	0.654	0.77
89_G	101_R	0.647	0.76
29_S	39_K	0.640	0.76
87_W	94_P	0.640	0.76
43_L	47_V	0.638	0.75
29_S	36_A	0.637	0.75
88_D	105_K	0.635	0.75
26_I	34_Y	0.628	0.74
66_D	69_P	0.626	0.74
100_I	103_I	0.623	0.74
25_G	29_S	0.620	0.73
26_I	49_L	0.611	0.72
41_P	46_L	0.608	0.72
85_I	101_R	0.601	0.71
101_R	107_V	0.600	0.71
17_M	33_G	0.592	0.70
24_I	52_L	0.591	0.70
36_A	39_K	0.587	0.69
100_I	107_V	0.584	0.69
36_A	40_K	0.584	0.69
79_F	83_P	0.582	0.68
28_K	42_P	0.582	0.68
75_N	80_L	0.576	0.68
79_F	89_G	0.574	0.67
32_G	49_L	0.573	0.67
31_Y	34_Y	0.572	0.67
32_G	42_P	0.568	0.67
55_V	59_Y	0.566	0.66
21_A	33_G	0.565	0.66
21_A	28_K	0.556	0.65
20_L	24_I	0.552	0.64
7_R	10_R	0.549	0.64
80_L	84_D	0.548	0.64
21_A	29_S	0.544	0.63
88_D	97_L	0.542	0.63
55_V	60_I	0.541	0.63
2_Y	60_I	0.538	0.62
39_K	42_P	0.537	0.62
22_E	25_G	0.537	0.62
7_R	35_E	0.531	0.61
47_V	63_L	0.530	0.61
34_Y	42_P	0.530	0.61
32_G	39_K	0.529	0.61
8_Q	22_E	0.525	0.61
54_D	68_D	0.515	0.59
16_T	29_S	0.514	0.59
29_S	38_S	0.513	0.59
26_I	29_S	0.513	0.59
94_P	98_D	0.510	0.58
43_L	61_L	0.509	0.58
97_L	101_R	0.508	0.58
27_A	38_S	0.507	0.58
44_D	48_I	0.506	0.58
100_I	105_K	0.505	0.58
82_K	90_Y	0.503	0.57
22_E	26_I	0.500	0.57

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
4ndwA	2	1	99.8	0.336	Contact Map
3r1fA	2	1	99.8	0.349	Contact Map
4o8bA	2	0.8661	99.8	0.361	Contact Map
3qwgA	2	0.7143	99.8	0.383	Contact Map
4jcyA	2	0.7857	99.8	0.385	Contact Map
1b0nA	2	0.9107	99.7	0.4	Contact Map
3op9A	4	0.9196	99.7	0.407	Contact Map
3ivpA	2	0.9196	99.7	0.407	Contact Map
2p5tA	2	0.3571	99.7	0.435	Contact Map
2ebyA	2	0.8661	99.7	0.439	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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