YKVN - BACSU - GREMLIN Contacts

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YKVN - Uncharacterized HTH-type transcriptional regulator YkvN

UniProt:	O31679	Sequences: MKKFSCGFEVTKEVIGGKWKGLVLYFLMNGPKRTSELKRIIPNITQKMLIQTLRELEASGLVSRKMYNQVPPKVEYSSTELGESLKPILQELCQWGGYYAEQEYAEGEYEIVQPEQLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	118 (99)
Sequences:	10052 (6050)
Seq/√Len:	608.0

ECOLI - YTFH
BACSU - YKVN YODB YTCD YYBR YDEP HXLR 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
63_S	77_S	2.790	1.00
38_K	46_Q	2.776	1.00
84_S	98_Y	2.602	1.00
47_K	51_Q	2.575	1.00
28_M	86_K	2.541	1.00
65_K	77_S	2.413	1.00
69_Q	73_K	2.366	1.00
27_L	62_V	2.264	1.00
26_F	40_I	2.159	1.00
63_S	79_T	2.070	1.00
67_Y	75_E	1.931	1.00
81_L	99_Y	1.856	1.00
67_Y	73_K	1.722	1.00
23_V	52_T	1.715	1.00
27_L	37_L	1.657	1.00
87_P	91_E	1.655	1.00
91_E	94_Q	1.654	1.00
88_I	91_E	1.650	1.00
78_S	82_G	1.638	1.00
54_R	57_E	1.586	1.00
31_P	77_S	1.506	1.00
31_P	75_E	1.493	1.00
32_K	40_I	1.458	1.00
48_M	51_Q	1.425	1.00
20_K	55_E	1.391	1.00
83_E	86_K	1.359	1.00
11_T	92_L	1.325	1.00
84_S	95_W	1.298	1.00
61_L	82_G	1.298	1.00
20_K	52_T	1.297	1.00
64_R	74_V	1.294	1.00
80_E	83_E	1.277	1.00
81_L	84_S	1.258	1.00
17_G	55_E	1.241	1.00
93_C	97_G	1.170	1.00
57_E	62_V	1.144	1.00
14_V	59_S	1.142	1.00
46_Q	50_I	1.139	1.00
67_Y	71_P	1.135	1.00
81_L	102_Q	1.132	1.00
10_V	100_A	1.119	1.00
11_T	96_G	1.109	1.00
27_L	32_K	1.105	1.00
20_K	56_L	1.104	1.00
65_K	75_E	1.092	1.00
66_M	74_V	1.077	1.00
17_G	20_K	1.075	1.00
50_I	54_R	1.066	1.00
35_S	39_R	1.066	1.00
32_K	36_E	1.060	1.00
84_S	99_Y	1.054	1.00
17_G	52_T	1.050	1.00
33_R	75_E	1.043	1.00
61_L	85_L	1.041	1.00
21_G	89_L	1.022	1.00
77_S	83_E	1.017	1.00
24_L	78_S	0.989	1.00
68_N	71_P	0.987	1.00
66_M	72_P	0.984	1.00
34_T	50_I	0.980	1.00
23_V	41_I	0.979	1.00
67_Y	72_P	0.972	1.00
14_V	61_L	0.964	1.00
66_M	71_P	0.960	1.00
67_Y	70_V	0.939	1.00
36_E	39_R	0.922	1.00
86_K	90_Q	0.916	1.00
48_M	52_T	0.913	1.00
85_L	95_W	0.893	1.00
35_S	38_K	0.885	1.00
45_T	48_M	0.871	1.00
44_I	49_L	0.865	1.00
28_M	78_S	0.853	1.00
26_F	37_L	0.852	1.00
87_P	94_Q	0.851	1.00
29_N	32_K	0.846	1.00
34_T	46_Q	0.840	1.00
60_G	81_L	0.832	1.00
9_E	13_E	0.809	1.00
41_I	44_I	0.796	1.00
25_Y	93_C	0.789	1.00
94_Q	98_Y	0.777	1.00
55_E	59_S	0.768	1.00
90_Q	94_Q	0.765	1.00
7_G	97_G	0.747	1.00
10_V	103_E	0.745	1.00
20_K	59_S	0.743	1.00
32_K	37_L	0.723	1.00
88_I	92_L	0.721	1.00
96_G	100_A	0.712	1.00
26_F	29_N	0.709	1.00
66_M	69_Q	0.707	1.00
28_M	90_Q	0.704	1.00
66_M	70_V	0.696	1.00
51_Q	55_E	0.687	1.00
38_K	49_L	0.683	1.00
25_Y	28_M	0.682	1.00
19_W	44_I	0.680	1.00
10_V	99_Y	0.670	1.00
22_L	41_I	0.661	1.00
23_V	44_I	0.660	1.00
69_Q	72_P	0.655	1.00
97_G	100_A	0.653	1.00
22_L	26_F	0.630	1.00
12_K	21_G	0.627	1.00
99_Y	102_Q	0.622	1.00
90_Q	93_C	0.622	1.00
85_L	88_I	0.615	1.00
33_R	67_Y	0.614	1.00
94_Q	97_G	0.612	1.00
70_V	74_V	0.611	1.00
8_F	100_A	0.609	1.00
6_C	34_T	0.609	1.00
81_L	103_E	0.605	1.00
33_R	36_E	0.603	1.00
26_F	32_K	0.601	1.00
35_S	46_Q	0.596	1.00
30_G	83_E	0.589	1.00
57_E	64_R	0.583	1.00
12_K	92_L	0.578	1.00
69_Q	75_E	0.577	1.00
95_W	99_Y	0.574	1.00
24_L	85_L	0.573	1.00
87_P	90_Q	0.572	1.00
27_L	31_P	0.568	1.00
81_L	100_A	0.568	1.00
8_F	25_Y	0.567	1.00
9_E	21_G	0.567	1.00
29_N	40_I	0.562	1.00
11_T	61_L	0.558	1.00
44_I	74_V	0.555	1.00
80_E	84_S	0.554	1.00
88_I	96_G	0.547	0.99
84_S	87_P	0.540	0.99
36_E	40_I	0.540	0.99
99_Y	103_E	0.536	0.99
10_V	25_Y	0.525	0.99
12_K	85_L	0.524	0.99
19_W	49_L	0.524	0.99
34_T	38_K	0.523	0.99
27_L	57_E	0.521	0.99
57_E	66_M	0.517	0.99
18_K	51_Q	0.513	0.99
69_Q	74_V	0.512	0.99
83_E	87_P	0.508	0.99
56_L	61_L	0.503	0.99
60_G	102_Q	0.503	0.99
31_P	65_K	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	0.9492	99.9	0.417	Contact Map
4a5nA	2	0.8898	99.7	0.5	Contact Map
1yyvA	2	0.8983	99.7	0.504	Contact Map
2hztA	2	0.8051	99.7	0.519	Contact Map
1z7uA	2	0.9068	99.7	0.521	Contact Map
2fswA	2	0.8475	99.7	0.525	Contact Map
2f2eA	4	0.9831	99.6	0.538	Contact Map
4hw0A	2	0.8305	99.6	0.559	Contact Map
3df8A	2	0.8305	99.5	0.573	Contact Map
4hqeA	2	0.8983	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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