YgbA_NO - PFAM28P - GREMLIN Contacts

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YgbA_NO - Nitrous oxide-stimulated promoter

PFAM:	PF11756	Sequences: KRLEREKKTVEAMIRIYCRDHHGTKGGGLCPECAELLDYALKRLDKCPFGEEKPTCAKCPVHCYKPEMREKIREVMRYSGPRMLLRHPILALRHLLDGRRKKPKLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	106 (100)
Sequences:	4292 (3156)
Seq/√Len:	315.6
META:	0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_D	78_Y	3.483	1.00
49_F	61_V	3.045	1.00
68_M	71_K	2.588	1.00
65_K	68_M	2.290	1.00
11_E	37_L	2.279	1.00
36_L	72_I	2.214	1.00
34_A	38_D	2.181	1.00
36_L	75_V	2.127	1.00
70_E	73_R	2.011	1.00
71_K	74_E	1.990	1.00
7_K	45_D	1.965	1.00
11_E	15_R	1.888	1.00
30_C	33_C	1.854	1.00
32_E	71_K	1.833	1.00
7_K	41_L	1.788	1.00
42_K	46_K	1.781	1.00
89_I	93_R	1.742	1.00
37_L	41_L	1.685	1.00
10_V	72_I	1.664	1.00
55_T	98_G	1.627	1.00
12_A	90_L	1.597	1.00
35_E	68_M	1.521	1.00
22_H	33_C	1.504	1.00
2_R	97_D	1.465	1.00
12_A	16_I	1.459	1.00
91_A	95_L	1.457	1.00
18_C	22_H	1.445	1.00
5_R	97_D	1.409	1.00
14_I	37_L	1.383	1.00
22_H	30_C	1.318	1.00
18_C	30_C	1.316	1.00
87_H	90_L	1.256	1.00
18_C	33_C	1.222	1.00
17_Y	21_H	1.212	1.00
39_Y	43_R	1.206	1.00
70_E	74_E	1.200	1.00
55_T	58_K	1.164	1.00
4_E	8_K	1.162	1.00
11_E	41_L	1.152	1.00
16_I	86_R	1.143	1.00
78_Y	82_R	1.112	1.00
62_H	69_R	1.102	1.00
8_K	12_A	1.091	1.00
3_L	50_G	1.088	1.00
14_I	75_V	1.076	1.00
3_L	7_K	1.073	1.00
14_I	36_L	1.063	1.00
14_I	72_I	1.061	1.00
10_V	40_A	1.051	1.00
48_P	61_V	1.045	1.00
4_E	7_K	1.029	1.00
50_G	54_P	1.021	1.00
44_L	50_G	1.010	1.00
5_R	93_R	1.003	1.00
12_A	15_R	0.978	1.00
29_L	37_L	0.969	1.00
57_A	98_G	0.958	1.00
10_V	14_I	0.945	1.00
83_M	87_H	0.938	1.00
95_L	99_R	0.924	1.00
42_K	45_D	0.913	1.00
9_T	90_L	0.909	1.00
19_R	86_R	0.909	1.00
32_E	35_E	0.902	1.00
20_D	82_R	0.900	1.00
35_E	71_K	0.888	1.00
44_L	64_Y	0.882	1.00
21_H	74_E	0.874	1.00
49_F	60_P	0.869	1.00
16_I	20_D	0.862	1.00
20_D	86_R	0.861	1.00
31_P	34_A	0.859	1.00
92_L	96_L	0.856	1.00
34_A	37_L	0.852	1.00
67_E	71_K	0.834	1.00
15_R	19_R	0.816	1.00
56_C	59_C	0.813	1.00
66_P	69_R	0.810	1.00
16_I	78_Y	0.807	1.00
93_R	96_L	0.806	1.00
15_R	37_L	0.805	1.00
58_K	98_G	0.801	1.00
83_M	91_A	0.788	1.00
96_L	99_R	0.781	1.00
94_H	98_G	0.779	1.00
13_M	88_P	0.779	1.00
13_M	83_M	0.771	0.99
15_R	29_L	0.766	0.99
3_L	44_L	0.749	0.99
56_C	63_C	0.738	0.99
54_P	60_P	0.737	0.99
41_L	45_D	0.737	0.99
99_R	102_K	0.697	0.99
47_C	59_C	0.693	0.99
54_P	102_K	0.682	0.99
59_C	63_C	0.673	0.99
38_D	42_K	0.670	0.99
31_P	35_E	0.667	0.99
47_C	56_C	0.662	0.98
93_R	97_D	0.660	0.98
44_L	49_F	0.660	0.98
87_H	91_A	0.659	0.98
6_E	53_K	0.658	0.98
3_L	9_T	0.650	0.98
36_L	71_K	0.649	0.98
58_K	101_K	0.649	0.98
54_P	61_V	0.646	0.98
2_R	5_R	0.643	0.98
13_M	81_P	0.636	0.98
24_T	27_G	0.634	0.98
55_T	97_D	0.631	0.98
29_L	33_C	0.630	0.98
68_M	75_V	0.620	0.98
8_K	90_L	0.614	0.97
38_D	41_L	0.612	0.97
21_H	78_Y	0.604	0.97
62_H	72_I	0.597	0.97
92_L	95_L	0.593	0.97
16_I	79_S	0.593	0.97
8_K	11_E	0.587	0.97
40_A	72_I	0.586	0.97
98_G	101_K	0.585	0.97
66_P	70_E	0.584	0.97
57_A	97_D	0.582	0.97
55_T	62_H	0.579	0.96
76_M	80_G	0.577	0.96
74_E	78_Y	0.573	0.96
47_C	63_C	0.572	0.96
22_H	78_Y	0.569	0.96
12_A	87_H	0.567	0.96
90_L	93_R	0.566	0.96
67_E	70_E	0.564	0.96
57_A	69_R	0.557	0.96
10_V	36_L	0.552	0.95
58_K	102_K	0.552	0.95
97_D	100_R	0.544	0.95
98_G	102_K	0.543	0.95
54_P	97_D	0.538	0.95
6_E	13_M	0.536	0.95
97_D	101_K	0.534	0.94
5_R	90_L	0.533	0.94
46_K	98_G	0.531	0.94
84_L	95_L	0.522	0.94
16_I	91_A	0.520	0.94
49_F	53_K	0.519	0.94
9_T	55_T	0.511	0.93
79_S	86_R	0.507	0.93
84_L	92_L	0.506	0.93
82_R	86_R	0.503	0.93
28_G	35_E	0.500	0.92

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
1oywA	1	0.7642	5.1	0.94	Contact Map
3avrA	1	0.8679	2.5	0.948	Contact Map
4uf0A	2	0.8679	1.9	0.952	Contact Map
2ykgA	1	0.9623	1.6	0.953	Contact Map
4f7uE	1	0.2264	1.6	0.954	Contact Map
2cupA	1	0.566	1.5	0.954	Contact Map
2hl7A	1	0.2453	1.5	0.954	Contact Map
2plxB	1	0.2453	1.4	0.955	Contact Map
4bujB	1	0.783	1.4	0.955	Contact Map
1t6uA	6	0.4245	1.4	0.955	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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