YSMB - BACSU - GREMLIN Contacts

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YSMB - Uncharacterized HTH-type transcriptional regulator YsmB

UniProt:	P97247	Sequences: MTSKPLEHVADIEKSLRHIAAIIKQKGREILNQYAITPPQFVGLQWLYELGDMTIGELSGKMYLACSTTTDLIDRMQKNELVERVKDPADRRVVRIHLLPEGERIIQEVITKRQEYLRDMFESFTDEEIAIFEKSLMKLQHEMKRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (131)
Sequences:	24429 (17908)
Seq/√Len:	1564.6

ECOLI - SLYA MARR MPRA
BACSU - YSMB YCGE YKOM YFIV YXAD YUSO OHRR YWAE YYBA MHQR YETL YDGG YWHA YPOP YDCH YDGJ YWOH YHJH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_V	97_H	3.139	1.00
128_E	138_K	2.875	1.00
83_E	97_H	2.623	1.00
54_T	93_V	2.539	1.00
87_D	95_R	2.490	1.00
52_D	97_H	2.470	1.00
125_T	128_E	2.380	1.00
131_I	134_K	2.199	1.00
131_I	135_S	2.078	1.00
86_K	94_V	2.049	1.00
48_Y	106_I	2.019	1.00
40_Q	79_N	1.991	1.00
124_F	135_S	1.927	1.00
54_T	57_E	1.895	1.00
87_D	93_V	1.883	1.00
48_Y	98_L	1.823	1.00
128_E	131_I	1.757	1.00
77_Q	84_R	1.652	1.00
15_S	137_M	1.637	1.00
80_E	101_E	1.627	1.00
55_I	73_I	1.607	1.00
132_F	135_S	1.601	1.00
101_E	105_I	1.573	1.00
40_Q	75_R	1.563	1.00
128_E	134_K	1.558	1.00
50_L	61_K	1.515	1.00
73_I	96_I	1.513	1.00
43_G	72_L	1.501	1.00
37_T	40_Q	1.453	1.00
74_D	78_K	1.443	1.00
101_E	104_R	1.426	1.00
48_Y	103_E	1.402	1.00
105_I	108_E	1.400	1.00
135_S	138_K	1.396	1.00
46_W	61_K	1.293	1.00
57_E	60_G	1.279	1.00
34_Y	112_K	1.273	1.00
15_S	140_Q	1.268	1.00
65_A	68_T	1.245	1.00
15_S	133_E	1.243	1.00
56_G	66_C	1.223	1.00
134_K	138_K	1.220	1.00
19_I	140_Q	1.214	1.00
74_D	91_R	1.209	1.00
43_G	69_T	1.205	1.00
84_R	94_V	1.195	1.00
55_I	94_V	1.179	1.00
104_R	108_E	1.155	1.00
56_G	60_G	1.150	1.00
30_I	112_K	1.144	1.00
34_Y	108_E	1.143	1.00
64_L	68_T	1.130	1.00
18_H	140_Q	1.095	1.00
129_I	133_E	1.059	1.00
55_I	69_T	1.055	1.00
52_D	95_R	1.050	1.00
133_E	137_M	1.046	1.00
127_E	131_I	1.030	1.00
28_R	32_N	1.029	1.00
112_K	115_E	1.024	1.00
33_Q	112_K	1.024	1.00
67_S	70_T	1.023	1.00
128_E	135_S	1.015	1.00
55_I	96_I	1.003	1.00
53_M	57_E	0.998	1.00
57_E	61_K	0.995	1.00
98_L	102_G	0.990	1.00
55_I	66_C	0.989	1.00
81_L	105_I	0.988	1.00
74_D	77_Q	0.983	1.00
70_T	74_D	0.976	1.00
51_G	103_E	0.975	1.00
83_E	99_L	0.971	1.00
68_T	71_D	0.963	1.00
100_P	103_E	0.956	1.00
30_I	115_E	0.950	1.00
39_P	72_L	0.940	1.00
79_N	101_E	0.938	1.00
117_L	120_M	0.933	1.00
64_L	69_T	0.932	1.00
53_M	61_K	0.927	1.00
50_L	53_M	0.924	1.00
65_A	71_D	0.916	1.00
85_V	95_R	0.915	1.00
86_K	91_R	0.913	1.00
100_P	104_R	0.910	1.00
22_I	140_Q	0.910	1.00
34_Y	109_V	0.907	1.00
124_F	139_L	0.904	1.00
30_I	119_D	0.896	1.00
47_L	82_V	0.896	1.00
79_N	105_I	0.893	1.00
19_I	136_L	0.880	1.00
103_E	107_Q	0.878	1.00
73_I	82_V	0.875	1.00
41_F	109_V	0.868	1.00
48_Y	107_Q	0.864	1.00
17_R	20_A	0.858	1.00
90_D	93_V	0.856	1.00
35_A	79_N	0.853	1.00
87_D	90_D	0.838	1.00
81_L	101_E	0.836	1.00
20_A	24_K	0.835	1.00
126_D	130_A	0.834	1.00
77_Q	83_E	0.828	1.00
108_E	112_K	0.822	1.00
48_Y	110_I	0.817	1.00
17_R	21_A	0.816	1.00
113_R	117_L	0.814	1.00
115_E	118_R	0.811	1.00
131_I	138_K	0.805	1.00
71_D	75_R	0.799	1.00
111_T	115_E	0.798	1.00
28_R	38_P	0.794	1.00
50_L	57_E	0.792	1.00
52_D	85_V	0.792	1.00
26_K	116_Y	0.786	1.00
12_I	133_E	0.781	1.00
46_W	62_M	0.767	1.00
125_T	129_I	0.765	1.00
71_D	74_D	0.762	1.00
119_D	122_E	0.748	1.00
42_V	62_M	0.747	1.00
130_A	133_E	0.746	1.00
121_F	129_I	0.745	1.00
130_A	134_K	0.744	1.00
43_G	62_M	0.737	1.00
77_Q	82_V	0.737	1.00
127_E	130_A	0.734	1.00
43_G	58_L	0.729	1.00
44_L	106_I	0.729	1.00
88_P	95_R	0.729	1.00
16_L	20_A	0.728	1.00
74_D	84_R	0.723	1.00
46_W	53_M	0.722	1.00
46_W	50_L	0.722	1.00
104_R	107_Q	0.719	1.00
55_I	70_T	0.716	1.00
39_P	68_T	0.714	1.00
75_R	78_K	0.712	1.00
30_I	116_Y	0.708	1.00
73_I	77_Q	0.706	1.00
59_S	66_C	0.704	1.00
30_I	33_Q	0.703	1.00
46_W	58_L	0.702	1.00
111_T	114_Q	0.698	1.00
21_A	25_Q	0.694	1.00
116_Y	119_D	0.694	1.00
51_G	97_H	0.682	1.00
98_L	103_E	0.677	1.00
24_K	28_R	0.669	1.00
59_S	69_T	0.668	1.00
75_R	79_N	0.668	1.00
47_L	53_M	0.666	1.00
115_E	119_D	0.665	1.00
137_M	141_H	0.663	1.00
26_K	119_D	0.659	1.00
19_I	139_L	0.659	1.00
124_F	129_I	0.656	1.00
41_F	113_R	0.654	1.00
69_T	73_I	0.649	1.00
114_Q	118_R	0.630	1.00
47_L	98_L	0.625	1.00
24_K	27_G	0.624	1.00
108_E	111_T	0.623	1.00
45_Q	49_E	0.609	1.00
26_K	29_E	0.606	1.00
134_K	137_M	0.587	1.00
76_M	81_L	0.584	1.00
15_S	18_H	0.583	1.00
44_L	48_Y	0.579	1.00
42_V	46_W	0.575	1.00
29_E	32_N	0.568	1.00
40_Q	72_L	0.567	1.00
99_L	102_G	0.560	1.00
41_F	106_I	0.559	1.00
135_S	139_L	0.555	1.00
45_Q	110_I	0.551	1.00
80_E	83_E	0.550	1.00
27_G	30_I	0.547	1.00
11_D	14_K	0.544	1.00
16_L	19_I	0.538	1.00
16_L	136_L	0.537	1.00
110_I	114_Q	0.535	1.00
121_F	125_T	0.530	1.00
23_I	26_K	0.529	1.00
27_G	113_R	0.526	1.00
106_I	110_I	0.524	1.00
107_Q	111_T	0.519	1.00
125_T	138_K	0.519	1.00
85_V	88_P	0.517	1.00
54_T	87_D	0.513	1.00
39_P	64_L	0.510	1.00
56_G	59_S	0.509	1.00
124_F	138_K	0.508	1.00
18_H	22_I	0.500	1.00

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
3cjnA	2	0.9589	99.9	0.235	Contact Map
3cdhA	4	0.9178	99.9	0.238	Contact Map
1z91A	2	0.9315	99.9	0.251	Contact Map
3deuA	2	0.8973	99.9	0.253	Contact Map
3jw4A	2	0.8904	99.9	0.253	Contact Map
3bj6A	2	0.9932	99.9	0.255	Contact Map
4rguA	4	0.9658	99.9	0.256	Contact Map
4yifA	2	0.9589	99.9	0.257	Contact Map
3e6mA	2	0.9863	99.9	0.258	Contact Map
3zplA	2	1	99.9	0.262	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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