YTFH - ECOLI - GREMLIN Contacts

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YTFH - Uncharacterized HTH-type transcriptional regulator YtfH

UniProt:	P0ACN2	Sequences: MSQVSLSQQLKEGNLFAEQCPSREVLKHVTSRWGVLILVALREGTHRFSDLRRKIGGVSEKMLAQSLQALEQDGFLNRIAYPVVPPHVEYSLTPLGEQVSEKVAALADWIELNLPEVLAVRDERAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12508
Length:	126 (101)
Sequences:	9632 (5705)
Seq/√Len:	567.7

ECOLI - YTFH
BACSU - YDEP YYBR YTCD HXLR YKVN YODB 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
52_R	60_E	2.874	1.00
77_N	91_S	2.831	1.00
98_Q	112_L	2.706	1.00
61_K	65_Q	2.678	1.00
83_V	87_H	2.595	1.00
42_R	100_S	2.577	1.00
79_I	91_S	2.555	1.00
41_L	76_L	2.314	1.00
40_A	54_K	2.107	1.00
77_N	93_T	2.099	1.00
81_Y	89_E	1.913	1.00
95_L	113_N	1.849	1.00
81_Y	87_H	1.729	1.00
41_L	51_L	1.720	1.00
105_A	108_D	1.712	1.00
37_I	66_S	1.666	1.00
101_E	105_A	1.664	1.00
102_K	105_A	1.652	1.00
92_L	96_G	1.625	1.00
46_H	54_K	1.553	1.00
68_Q	71_E	1.533	1.00
45_T	91_S	1.513	1.00
25_V	106_L	1.444	1.00
45_T	89_E	1.430	1.00
94_P	97_E	1.411	1.00
34_G	69_A	1.408	1.00
62_M	65_Q	1.397	1.00
78_R	88_V	1.385	1.00
97_E	100_S	1.377	1.00
75_F	96_G	1.351	1.00
95_L	98_Q	1.296	1.00
31_S	69_A	1.274	1.00
34_G	66_S	1.208	1.00
98_Q	109_W	1.204	1.00
28_H	73_D	1.193	1.00
25_V	110_I	1.190	1.00
107_A	111_E	1.190	1.00
60_E	64_A	1.187	1.00
95_L	116_E	1.150	1.00
24_E	114_L	1.142	1.00
79_I	89_E	1.134	1.00
81_Y	85_P	1.128	1.00
41_L	46_H	1.120	1.00
38_L	92_L	1.120	1.00
71_E	76_L	1.116	1.00
46_H	50_D	1.112	1.00
80_A	85_P	1.086	1.00
49_S	53_R	1.082	1.00
80_A	88_V	1.064	1.00
31_S	66_S	1.062	1.00
28_H	75_F	1.057	1.00
64_A	68_Q	1.053	1.00
98_Q	113_N	1.039	1.00
82_P	85_P	1.031	1.00
35_V	103_V	1.021	1.00
31_S	34_G	1.014	1.00
75_F	99_V	1.014	1.00
47_R	89_E	1.013	1.00
91_S	97_E	1.013	1.00
34_G	70_L	1.008	1.00
37_I	55_I	1.007	1.00
48_F	64_A	1.005	1.00
80_A	86_P	1.004	1.00
81_Y	86_P	0.986	1.00
81_Y	84_V	0.940	1.00
100_S	104_A	0.932	1.00
62_M	66_S	0.931	1.00
50_D	53_R	0.917	1.00
99_V	109_W	0.896	1.00
101_E	108_D	0.891	1.00
58_V	63_L	0.865	1.00
48_F	60_E	0.854	1.00
43_E	46_H	0.854	1.00
108_D	112_L	0.846	1.00
23_R	27_K	0.843	1.00
59_S	62_M	0.843	1.00
74_G	95_L	0.837	1.00
42_R	92_L	0.832	1.00
49_S	52_R	0.829	1.00
42_R	104_A	0.821	1.00
80_A	84_V	0.818	1.00
21_P	111_E	0.809	1.00
39_V	107_A	0.805	1.00
34_G	73_D	0.800	1.00
40_A	51_L	0.771	1.00
46_H	51_L	0.767	1.00
102_K	106_L	0.748	1.00
69_A	73_D	0.745	1.00
24_E	113_N	0.742	1.00
18_E	23_R	0.739	1.00
37_I	58_V	0.720	1.00
39_V	42_R	0.714	1.00
55_I	58_V	0.698	1.00
104_A	108_D	0.695	1.00
65_Q	69_A	0.692	1.00
104_A	107_A	0.688	1.00
83_V	89_E	0.671	1.00
80_A	83_V	0.667	1.00
40_A	43_E	0.660	1.00
26_L	106_L	0.660	1.00
113_N	116_E	0.657	1.00
111_E	114_L	0.654	1.00
58_V	88_V	0.654	1.00
33_W	58_V	0.653	1.00
84_V	88_V	0.634	1.00
18_E	27_K	0.626	1.00
71_E	80_A	0.626	1.00
70_L	75_F	0.622	1.00
26_L	35_V	0.616	1.00
110_I	114_L	0.608	1.00
38_L	99_V	0.606	1.00
83_V	86_P	0.598	1.00
99_V	102_K	0.596	1.00
47_R	50_D	0.591	1.00
95_L	114_L	0.590	1.00
47_R	81_Y	0.582	1.00
108_D	111_E	0.579	1.00
41_L	45_T	0.575	1.00
71_E	78_R	0.574	1.00
43_E	54_K	0.573	1.00
41_L	71_E	0.573	1.00
45_T	51_L	0.571	0.99
36_L	55_I	0.569	0.99
112_L	115_P	0.567	0.99
16_F	22_S	0.562	0.99
85_P	88_V	0.562	0.99
22_S	114_L	0.561	0.99
24_E	27_K	0.557	0.99
109_W	113_N	0.555	0.99
16_F	19_Q	0.550	0.99
102_K	110_I	0.548	0.99
49_S	60_E	0.547	0.99
60_E	66_S	0.547	0.99
50_D	54_K	0.546	0.99
52_R	63_L	0.544	0.99
101_E	104_A	0.543	0.99
36_L	40_A	0.541	0.99
41_L	92_L	0.540	0.99
29_V	106_L	0.539	0.99
98_Q	101_E	0.537	0.99
44_G	97_E	0.536	0.99
38_L	75_F	0.535	0.99
48_F	52_R	0.530	0.99
40_A	46_H	0.525	0.99
45_T	79_I	0.515	0.99
83_V	88_V	0.515	0.99
92_L	97_E	0.514	0.99
23_R	36_L	0.508	0.99
29_V	99_V	0.506	0.99
101_E	112_L	0.504	0.99
64_A	78_R	0.504	0.99
17_A	56_G	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	0.8413	99.9	0.421	Contact Map
1yyvA	2	0.8889	99.8	0.481	Contact Map
4a5nA	2	0.8333	99.7	0.502	Contact Map
2fswA	2	0.8175	99.7	0.52	Contact Map
1z7uA	2	0.881	99.7	0.526	Contact Map
2hztA	2	0.754	99.7	0.532	Contact Map
2f2eA	4	0.8889	99.7	0.543	Contact Map
4hw0A	2	0.754	99.6	0.565	Contact Map
3df8A	2	0.8333	99.6	0.572	Contact Map
4hqeA	2	0.8413	99.4	0.613	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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