YHCF - BACSU - GREMLIN Contacts

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YHCF - Uncharacterized HTH-type transcriptional regulator YhcF

UniProt:	P54590	Sequences: MDNQFQSSKPIYLQIADQIFYRLVRKELLPGDKLPSVREMAIQTKVNPNTIQRTYSEMERLGIVETRRGQGTFIAEKAEIVDELKDKLTREVLEGFVKQMKELGLTKEEMLEGIKTFTEGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	121 (107)
Sequences:	8247 (6196)
Seq/√Len:	599.0

ECOLI - MNGR YIHL PHNF YEGW FRLR YDCR YIDP PDHR EXUR YJIR UXUR NANR GLCC FADR LLDR YIEP DGOR YDFH
BACSU - YHCF YTRA YVOA YYDK YISV GMUR YURK YMFC YDFD TRER YBGA GABR YDEL YHDI YCBG YDEF YCXD
SULSO - Q97XX0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_L	32_D	3.970	1.00
22_R	27_E	3.030	1.00
67_R	70_Q	2.895	1.00
20_F	61_L	2.726	1.00
37_V	48_P	2.710	1.00
9_K	17_D	2.491	1.00
16_A	57_E	2.460	1.00
66_T	72_T	2.289	1.00
65_E	75_A	2.207	1.00
34_L	64_V	2.019	1.00
20_F	63_I	1.922	1.00
18_Q	22_R	1.905	1.00
16_A	61_L	1.901	1.00
57_E	60_R	1.854	1.00
92_V	95_G	1.802	1.00
16_A	20_F	1.796	1.00
30_P	76_E	1.768	1.00
33_K	73_F	1.762	1.00
52_Q	56_S	1.757	1.00
39_E	43_Q	1.753	1.00
64_V	72_T	1.660	1.00
31_G	65_E	1.600	1.00
28_L	74_I	1.599	1.00
59_E	64_V	1.569	1.00
21_Y	25_R	1.536	1.00
106_T	109_E	1.500	1.00
15_I	46_V	1.495	1.00
70_Q	73_F	1.488	1.00
13_L	17_D	1.481	1.00
22_R	28_L	1.407	1.00
31_G	76_E	1.385	1.00
87_K	91_E	1.348	1.00
92_V	99_Q	1.341	1.00
49_N	52_Q	1.280	1.00
23_L	74_I	1.276	1.00
18_Q	44_T	1.210	1.00
107_K	111_L	1.200	1.00
59_E	66_T	1.194	1.00
56_S	60_R	1.189	1.00
9_K	13_L	1.171	1.00
93_L	96_F	1.145	1.00
93_L	110_M	1.143	1.00
23_L	63_I	1.142	1.00
20_F	24_V	1.140	1.00
56_S	59_E	1.119	1.00
30_P	77_K	1.109	1.00
39_E	42_I	1.088	1.00
15_I	54_T	1.087	1.00
44_T	55_Y	1.036	1.00
96_F	100_M	1.014	1.00
12_Y	53_R	0.975	1.00
95_G	99_Q	0.972	1.00
46_V	51_I	0.953	1.00
53_R	57_E	0.948	1.00
105_L	109_E	0.943	1.00
57_E	61_L	0.938	1.00
97_V	110_M	0.938	1.00
36_S	39_E	0.938	1.00
38_R	41_A	0.926	1.00
12_Y	57_E	0.915	1.00
92_V	96_F	0.913	1.00
18_Q	21_Y	0.913	1.00
88_L	92_V	0.912	1.00
65_E	76_E	0.901	1.00
19_I	23_L	0.886	1.00
79_E	82_D	0.877	1.00
101_K	107_K	0.873	1.00
91_E	95_G	0.873	1.00
67_R	73_F	0.849	1.00
47_N	52_Q	0.849	1.00
11_I	47_N	0.845	1.00
19_I	34_L	0.827	1.00
55_Y	64_V	0.825	1.00
85_K	90_R	0.818	1.00
28_L	34_L	0.817	1.00
49_N	66_T	0.811	1.00
40_M	51_I	0.809	1.00
15_I	51_I	0.807	1.00
94_E	107_K	0.794	1.00
37_V	52_Q	0.794	1.00
47_N	50_T	0.794	1.00
50_T	53_R	0.788	1.00
16_A	63_I	0.776	1.00
17_D	21_Y	0.773	1.00
40_M	55_Y	0.772	1.00
55_Y	72_T	0.767	1.00
14_Q	18_Q	0.765	1.00
38_R	55_Y	0.761	1.00
52_Q	66_T	0.741	1.00
69_G	72_T	0.741	1.00
80_I	83_E	0.739	1.00
89_T	92_V	0.737	1.00
36_S	68_R	0.737	1.00
98_K	102_E	0.737	1.00
65_E	73_F	0.723	1.00
95_G	98_K	0.718	1.00
15_I	44_T	0.713	1.00
7_S	14_Q	0.709	1.00
59_E	72_T	0.707	1.00
49_N	53_R	0.703	1.00
37_V	69_G	0.701	1.00
89_T	97_V	0.699	1.00
26_K	29_L	0.697	1.00
19_I	28_L	0.692	1.00
85_K	89_T	0.680	1.00
33_K	36_S	0.677	1.00
87_K	90_R	0.665	1.00
53_R	56_S	0.658	1.00
28_L	43_Q	0.650	1.00
99_Q	102_E	0.648	1.00
37_V	72_T	0.644	1.00
108_E	111_L	0.633	1.00
10_P	14_Q	0.632	1.00
89_T	100_M	0.626	1.00
36_S	69_G	0.619	1.00
97_V	101_K	0.616	1.00
90_R	94_E	0.615	1.00
13_L	16_A	0.609	1.00
89_T	96_F	0.609	1.00
33_K	71_G	0.602	1.00
88_L	91_E	0.600	1.00
11_I	14_Q	0.600	1.00
89_T	105_L	0.594	1.00
20_F	58_M	0.592	1.00
91_E	94_E	0.588	1.00
101_K	111_L	0.575	1.00
53_R	99_Q	0.575	1.00
52_Q	55_Y	0.574	1.00
64_V	74_I	0.572	1.00
86_D	90_R	0.569	1.00
19_I	40_M	0.567	1.00
24_V	63_I	0.567	1.00
37_V	66_T	0.565	1.00
11_I	46_V	0.561	1.00
24_V	27_E	0.558	1.00
17_D	20_F	0.551	0.99
30_P	75_A	0.550	0.99
94_E	98_K	0.549	0.99
55_Y	59_E	0.548	0.99
22_R	25_R	0.543	0.99
35_P	40_M	0.537	0.99
12_Y	50_T	0.534	0.99
78_A	83_E	0.534	0.99
31_G	67_R	0.532	0.99
28_L	32_D	0.526	0.99
94_E	101_K	0.526	0.99
37_V	55_Y	0.526	0.99
105_L	110_M	0.525	0.99
11_I	50_T	0.518	0.99
51_I	54_T	0.513	0.99
85_K	103_L	0.513	0.99
100_M	105_L	0.509	0.99
21_Y	24_V	0.508	0.99
37_V	56_S	0.508	0.99
80_I	88_L	0.506	0.99
98_K	104_G	0.504	0.99
38_R	42_I	0.502	0.99
91_E	107_K	0.501	0.99
96_F	101_K	0.501	0.99
68_R	73_F	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
3neuA	2	0.9835	99.9	0.301	Contact Map
4r1hA	2	0.9587	99.9	0.319	Contact Map
4u0wA	2	1	99.9	0.319	Contact Map
3ic7A	2	0.9174	99.9	0.324	Contact Map
3by6A	2	1	99.9	0.324	Contact Map
2ra5A	2	0.2397	99.9	0.341	Contact Map
2ek5A	4	0.9339	99.9	0.342	Contact Map
3tqnA	2	0.8843	99.9	0.36	Contact Map
3bwgA	2	0.9091	99.9	0.378	Contact Map
3edpA	2	0.8926	99.9	0.381	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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