YDEP - BACSU - GREMLIN Contacts

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YDEP - Uncharacterized HTH-type transcriptional regulator YdeP

UniProt:	P96673	Sequences: MRNRKLGIDYSSDDFEGCPVETTLDIIGGKWKGILLYHLIDGKKRFNEFRKLYPKITQRMLTLQLRELERDGVIHREVYKQVPPKVEYSLTEFGRTLEPVILHMKDWGEKYKDRIDKLEAARKAEDKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	128 (102)
Sequences:	9779 (5848)
Seq/√Len:	579.0

ECOLI - YTFH
BACSU - YDEP YYBR YTCD YKVN YODB HXLR YDZF YVAP
HALSA - Q9HRG9 Q9HPZ4
SULSO - Q97UU6 Q97U48

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_R	58_Q	2.778	1.00
96_T	110_K	2.776	1.00
75_H	89_S	2.776	1.00
59_R	63_L	2.715	1.00
40_I	98_E	2.552	1.00
81_Q	85_K	2.500	1.00
77_E	89_S	2.478	1.00
39_L	74_I	2.360	1.00
75_H	91_T	2.267	1.00
38_H	52_L	2.040	1.00
79_Y	87_E	1.932	1.00
39_L	49_F	1.859	1.00
93_F	111_Y	1.794	1.00
103_H	106_D	1.759	1.00
79_Y	85_K	1.729	1.00
90_L	94_G	1.711	1.00
100_V	103_H	1.640	1.00
35_L	64_Q	1.638	1.00
99_P	103_H	1.636	1.00
66_R	69_E	1.592	1.00
43_K	89_S	1.579	1.00
44_K	52_L	1.553	1.00
43_K	87_E	1.460	1.00
95_R	98_E	1.441	1.00
32_K	67_E	1.433	1.00
60_M	63_L	1.405	1.00
92_E	95_R	1.355	1.00
76_R	86_V	1.350	1.00
32_K	64_Q	1.338	1.00
73_V	94_G	1.332	1.00
23_T	104_M	1.326	1.00
96_T	107_W	1.273	1.00
29_G	67_E	1.265	1.00
58_Q	62_T	1.231	1.00
26_I	71_D	1.221	1.00
105_K	109_E	1.205	1.00
78_V	83_P	1.192	1.00
93_F	96_T	1.176	1.00
23_T	108_G	1.170	1.00
79_Y	83_P	1.159	1.00
22_T	112_K	1.159	1.00
39_L	44_K	1.149	1.00
47_N	51_K	1.135	1.00
29_G	64_Q	1.128	1.00
36_L	90_L	1.116	1.00
93_F	114_R	1.106	1.00
69_E	74_I	1.102	1.00
44_K	48_E	1.079	1.00
77_E	87_E	1.072	1.00
46_F	62_T	1.066	1.00
80_K	83_P	1.059	1.00
62_T	66_R	1.054	1.00
73_V	97_L	1.050	1.00
78_V	86_V	1.028	1.00
32_K	68_L	1.024	1.00
26_I	73_V	1.000	1.00
96_T	111_Y	0.998	1.00
33_G	101_I	0.980	1.00
35_L	53_Y	0.977	1.00
78_V	84_P	0.967	1.00
60_M	64_Q	0.964	1.00
57_T	60_M	0.950	1.00
45_R	87_E	0.949	1.00
89_S	95_R	0.941	1.00
29_G	32_K	0.934	1.00
56_I	61_L	0.930	1.00
79_Y	84_P	0.928	1.00
79_Y	82_V	0.922	1.00
97_L	107_W	0.907	1.00
40_I	90_L	0.906	1.00
48_E	51_K	0.894	1.00
106_D	110_K	0.879	1.00
46_F	58_Q	0.872	1.00
41_D	44_K	0.870	1.00
98_E	102_L	0.867	1.00
99_P	106_D	0.847	1.00
32_K	71_D	0.834	1.00
72_G	93_F	0.823	1.00
44_K	49_F	0.806	1.00
38_H	49_F	0.799	1.00
47_N	50_R	0.799	1.00
21_E	25_D	0.795	1.00
67_E	71_D	0.793	1.00
40_I	102_L	0.781	1.00
37_Y	105_K	0.776	1.00
100_V	104_M	0.773	1.00
78_V	82_V	0.761	1.00
19_P	109_E	0.753	1.00
102_L	106_D	0.751	1.00
22_T	111_Y	0.728	1.00
31_W	56_I	0.721	1.00
63_L	67_E	0.710	1.00
16_E	21_E	0.692	1.00
78_V	81_Q	0.688	1.00
53_Y	56_I	0.686	1.00
35_L	56_I	0.686	1.00
37_Y	40_I	0.677	1.00
102_L	105_K	0.673	1.00
31_W	61_L	0.671	1.00
24_L	104_M	0.665	1.00
38_H	41_D	0.660	1.00
36_L	97_L	0.656	1.00
16_E	25_D	0.653	1.00
106_D	109_E	0.650	1.00
69_E	78_V	0.647	1.00
50_R	61_L	0.646	1.00
45_R	79_Y	0.637	1.00
24_L	33_G	0.637	1.00
111_Y	114_R	0.626	1.00
97_L	100_V	0.620	1.00
68_L	73_V	0.620	1.00
108_G	112_K	0.616	1.00
39_L	43_K	0.616	1.00
56_I	86_V	0.614	1.00
107_W	111_Y	0.614	1.00
41_D	52_L	0.609	1.00
109_E	112_K	0.609	1.00
83_P	86_V	0.605	1.00
43_K	49_F	0.601	1.00
24_L	97_L	0.586	1.00
81_Q	87_E	0.586	1.00
82_V	86_V	0.583	1.00
42_G	95_R	0.575	1.00
58_Q	64_Q	0.572	1.00
45_R	48_E	0.564	0.99
93_F	115_I	0.563	0.99
34_I	53_Y	0.563	0.99
81_Q	84_P	0.561	0.99
110_K	113_D	0.560	0.99
14_D	20_V	0.558	0.99
22_T	115_I	0.556	0.99
48_E	52_L	0.554	0.99
43_K	48_E	0.551	0.99
39_L	69_E	0.550	0.99
81_Q	86_V	0.544	0.99
96_T	99_P	0.544	0.99
20_V	112_K	0.543	0.99
16_E	22_T	0.542	0.99
100_V	108_G	0.539	0.99
77_E	80_K	0.537	0.99
69_E	76_R	0.536	0.99
20_V	37_Y	0.533	0.99
18_C	46_F	0.529	0.99
82_V	85_K	0.521	0.99
90_L	95_R	0.518	0.99
36_L	73_V	0.514	0.99
39_L	90_L	0.511	0.99
34_I	38_H	0.511	0.99
27_I	104_M	0.507	0.99
93_F	112_K	0.503	0.99
92_E	96_T	0.502	0.99
31_W	60_M	0.502	0.99
23_T	27_I	0.500	0.99

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
4gcvA	3	0.8594	99.9	0.428	Contact Map
4a5nA	2	0.8203	99.7	0.501	Contact Map
1yyvA	2	0.875	99.7	0.507	Contact Map
2fswA	2	0.8047	99.7	0.517	Contact Map
2hztA	2	0.7422	99.7	0.518	Contact Map
1z7uA	2	0.8672	99.7	0.524	Contact Map
2f2eA	4	0.9062	99.6	0.544	Contact Map
4hw0A	2	0.7656	99.6	0.562	Contact Map
3df8A	2	0.8203	99.6	0.566	Contact Map
4hqeA	2	0.8281	99.4	0.609	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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