YTCD - BACSU - GREMLIN Contacts

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YTCD - Uncharacterized HTH-type transcriptional regulator YtcD

UniProt:	O34533	Sequences: MEKKKYNISVEATLEVIGGKWKCVILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDMLCAWGANHINRVYGDTFSVLEESVLNDKLKQES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	126 (101)
Sequences:	9617 (5637)
Seq/√Len:	560.9

ECOLI - YTFH
BACSU - YTCD YYBR HXLR YDEP YKVN YODB YVAP YDZF
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
65_N	79_E	2.918	1.00
86_S	100_N	2.881	1.00
40_K	48_Q	2.850	1.00
49_K	53_Q	2.706	1.00
71_Q	75_K	2.602	1.00
67_I	79_E	2.551	1.00
29_L	64_I	2.323	1.00
28_H	42_L	2.208	1.00
65_N	81_S	2.169	1.00
69_Y	77_E	1.966	1.00
83_Y	101_H	1.894	1.00
69_Y	75_K	1.825	1.00
29_L	39_L	1.770	1.00
30_T	88_E	1.768	1.00
93_M	96_A	1.757	1.00
25_I	54_Q	1.755	1.00
90_I	93_M	1.703	1.00
80_L	84_G	1.692	1.00
89_G	93_M	1.692	1.00
56_R	59_E	1.611	1.00
33_K	79_E	1.581	1.00
34_K	42_L	1.554	1.00
33_K	77_E	1.463	1.00
13_T	94_L	1.455	1.00
85_R	88_E	1.426	1.00
66_R	76_V	1.413	1.00
22_K	57_E	1.377	1.00
50_M	53_Q	1.359	1.00
19_G	57_E	1.318	1.00
82_E	85_R	1.305	1.00
63_V	84_G	1.274	1.00
22_K	54_Q	1.273	1.00
48_Q	52_T	1.248	1.00
13_T	98_G	1.241	1.00
86_S	97_W	1.237	1.00
16_V	61_D	1.228	1.00
95_C	99_A	1.193	1.00
68_V	76_V	1.180	1.00
83_Y	104_R	1.173	1.00
37_S	41_R	1.163	1.00
83_Y	86_S	1.159	1.00
52_T	56_R	1.142	1.00
12_A	102_I	1.139	1.00
34_K	38_E	1.135	1.00
59_E	64_I	1.130	1.00
26_L	80_L	1.122	1.00
69_Y	73_P	1.117	1.00
67_I	77_E	1.099	1.00
35_R	77_E	1.099	1.00
19_G	54_Q	1.085	1.00
23_C	91_L	1.073	1.00
68_V	73_P	1.062	1.00
36_T	52_T	1.058	1.00
86_S	101_H	1.049	1.00
63_V	87_L	1.048	1.00
29_L	34_K	1.045	1.00
22_K	58_L	1.020	1.00
16_V	63_V	1.017	1.00
19_G	22_K	1.014	1.00
70_N	73_P	0.992	1.00
68_V	74_P	0.983	1.00
69_Y	72_V	0.978	1.00
79_E	85_R	0.969	1.00
25_I	43_M	0.963	1.00
38_E	41_R	0.922	1.00
69_Y	74_P	0.920	1.00
87_L	97_W	0.907	1.00
47_T	50_M	0.898	1.00
50_M	54_Q	0.895	1.00
88_E	92_D	0.884	1.00
36_T	48_Q	0.871	1.00
46_I	51_L	0.859	1.00
96_A	100_N	0.852	1.00
37_S	40_K	0.846	1.00
9_S	99_A	0.831	1.00
27_C	95_C	0.820	1.00
28_H	39_L	0.819	1.00
31_H	34_K	0.811	1.00
11_E	15_E	0.808	1.00
89_G	96_A	0.804	1.00
34_K	39_L	0.788	1.00
62_G	83_Y	0.784	1.00
27_C	30_T	0.771	1.00
90_I	94_L	0.762	1.00
43_M	46_I	0.752	1.00
68_V	72_V	0.746	1.00
25_I	46_I	0.740	1.00
22_K	61_D	0.722	1.00
6_Y	11_E	0.720	1.00
12_A	101_H	0.709	1.00
53_Q	57_E	0.700	1.00
92_D	96_A	0.699	1.00
57_E	61_D	0.694	1.00
68_V	71_Q	0.684	1.00
12_A	105_V	0.669	1.00
40_K	51_L	0.666	1.00
99_A	102_I	0.661	1.00
28_H	31_H	0.660	1.00
14_L	94_L	0.658	1.00
6_Y	15_E	0.656	1.00
26_L	87_L	0.652	1.00
10_V	27_C	0.644	1.00
101_H	104_R	0.640	1.00
29_L	33_K	0.638	1.00
71_Q	74_P	0.635	1.00
46_I	76_V	0.628	1.00
24_V	28_H	0.612	1.00
58_L	63_V	0.612	1.00
92_D	95_C	0.612	1.00
6_Y	12_A	0.609	1.00
32_G	85_R	0.606	1.00
21_W	46_I	0.602	1.00
59_E	68_V	0.601	1.00
72_V	76_V	0.596	1.00
98_G	102_I	0.593	1.00
71_Q	77_E	0.589	1.00
90_I	98_G	0.586	1.00
24_V	43_M	0.582	1.00
103_N	106_Y	0.579	1.00
83_Y	105_V	0.577	1.00
21_W	51_L	0.577	1.00
71_Q	76_V	0.576	0.99
14_L	23_C	0.571	0.99
38_E	42_L	0.568	0.99
35_R	69_Y	0.566	0.99
10_V	102_I	0.565	0.99
83_Y	102_I	0.564	0.99
30_T	80_L	0.563	0.99
59_E	66_R	0.558	0.99
30_T	34_K	0.558	0.99
28_H	34_K	0.553	0.99
30_T	92_D	0.552	0.99
73_P	77_E	0.546	0.99
29_L	59_E	0.544	0.99
37_S	48_Q	0.544	0.99
87_L	90_I	0.536	0.99
96_A	99_A	0.532	0.99
89_G	92_D	0.531	0.99
86_S	89_G	0.531	0.99
26_L	63_V	0.521	0.99
100_N	103_N	0.521	0.99
11_E	23_C	0.521	0.99
14_L	87_L	0.521	0.99
97_W	101_H	0.520	0.99
73_P	76_V	0.518	0.99
17_I	94_L	0.516	0.99
11_E	44_P	0.515	0.99
79_E	82_E	0.515	0.99
11_E	24_V	0.507	0.99
33_K	39_L	0.504	0.99
80_L	85_R	0.503	0.99
56_R	66_R	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	0.9365	99.8	0.44	Contact Map
4a5nA	2	0.8333	99.7	0.503	Contact Map
1yyvA	2	0.8413	99.7	0.506	Contact Map
2hztA	2	0.754	99.7	0.52	Contact Map
1z7uA	2	0.8571	99.7	0.52	Contact Map
2fswA	2	0.8095	99.7	0.535	Contact Map
2f2eA	4	0.9762	99.6	0.548	Contact Map
4hw0A	2	0.7778	99.6	0.554	Contact Map
3df8A	2	0.7937	99.5	0.578	Contact Map
4hqeA	2	0.8413	99.3	0.624	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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