YTXH - BACSU - GREMLIN Contacts

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YTXH - Uncharacterized protein YtxH

UniProt:	P40780	Sequences: MSKDGINSKDFLIGTLIGGIIGATTALFLAPKSGKELRDDLGSQAVALRDKTDKMTADAKEKGTQYVSIAKDKTSNITQLVADQSGQIMNKVKDLRDRSKSDKTDSSTAMQDMREEAMQAADETKDQVLQTKEDVKDELKDAQKQAEQLNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	151 (116)
Sequences:	1632 (1470)
Seq/√Len:	136.4

BACSU - YTXH

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	33_S	2.495	1.00
107_S	111_Q	2.462	1.00
103_K	107_S	2.437	1.00
78_T	82_A	2.134	1.00
126_D	129_L	2.043	1.00
74_T	78_T	2.014	1.00
34_G	38_R	1.985	1.00
62_K	65_Q	1.938	1.00
49_R	53_D	1.922	1.00
84_Q	87_Q	1.871	1.00
57_A	60_K	1.814	1.00
38_R	42_G	1.794	1.00
35_K	38_R	1.789	1.00
34_G	37_L	1.729	1.00
75_S	78_T	1.713	1.00
39_D	43_S	1.684	1.00
115_E	118_M	1.632	1.00
118_M	122_D	1.626	1.00
51_K	54_K	1.605	1.00
56_T	60_K	1.566	1.00
125_K	129_L	1.560	1.00
131_T	134_D	1.555	1.00
34_G	41_L	1.548	1.00
35_K	39_D	1.513	1.00
30_A	33_S	1.490	1.00
85_S	125_K	1.488	1.00
86_G	89_M	1.487	1.00
85_S	89_M	1.470	1.00
68_S	72_D	1.470	1.00
41_L	44_Q	1.462	1.00
73_K	76_N	1.457	1.00
96_R	100_K	1.443	1.00
114_R	118_M	1.439	1.00
63_G	103_K	1.438	1.00
46_V	57_A	1.433	1.00
36_E	40_D	1.354	1.00
120_A	124_T	1.353	1.00
33_S	36_E	1.330	1.00
125_K	136_K	1.256	1.00
133_E	137_D	1.241	1.00
98_R	101_S	1.232	1.00
52_T	59_A	1.230	1.00
110_M	114_R	1.211	1.00
30_A	34_G	1.200	1.00
45_A	85_S	1.196	1.00
118_M	129_L	1.189	1.00
119_Q	130_Q	1.169	0.99
125_K	132_K	1.140	0.99
137_D	140_K	1.137	0.99
136_K	140_K	1.137	0.99
95_L	98_R	1.135	0.99
92_V	132_K	1.124	0.99
79_Q	82_A	1.117	0.99
41_L	81_V	1.111	0.99
136_K	139_L	1.105	0.99
40_D	44_Q	1.098	0.99
61_E	72_D	1.087	0.99
39_D	50_D	1.085	0.99
89_M	92_V	1.047	0.99
37_L	48_L	1.022	0.99
112_D	123_E	1.020	0.98
85_S	88_I	1.005	0.98
34_G	74_T	1.001	0.98
44_Q	47_A	0.992	0.98
97_D	101_S	0.990	0.98
50_D	61_E	0.990	0.98
46_V	50_D	0.977	0.98
51_K	55_M	0.961	0.98
31_P	40_D	0.955	0.98
34_G	40_D	0.955	0.98
89_M	93_K	0.948	0.98
104_T	107_S	0.943	0.97
112_D	116_E	0.937	0.97
113_M	117_A	0.934	0.97
38_R	49_R	0.931	0.97
88_I	128_V	0.928	0.97
46_V	49_R	0.918	0.97
52_T	55_M	0.889	0.96
29_L	34_G	0.884	0.96
113_M	116_E	0.874	0.96
96_R	99_S	0.868	0.96
133_E	136_K	0.866	0.96
31_P	36_E	0.862	0.96
116_E	134_D	0.860	0.96
31_P	35_K	0.856	0.96
93_K	97_D	0.855	0.96
124_T	128_V	0.852	0.95
36_E	47_A	0.844	0.95
131_T	142_A	0.843	0.95
43_S	47_A	0.839	0.95
40_D	43_S	0.838	0.95
62_K	66_Y	0.834	0.95
63_G	70_A	0.833	0.95
31_P	34_G	0.832	0.95
126_D	130_Q	0.828	0.95
75_S	79_Q	0.826	0.95
64_T	68_S	0.824	0.95
121_A	124_T	0.823	0.94
47_A	55_M	0.821	0.94
132_K	136_K	0.820	0.94
79_Q	119_Q	0.811	0.94
119_Q	122_D	0.810	0.94
58_D	69_I	0.805	0.94
56_T	96_R	0.798	0.94
79_Q	83_D	0.795	0.93
48_L	88_I	0.787	0.93
111_Q	115_E	0.786	0.93
68_S	71_K	0.786	0.93
90_N	94_D	0.783	0.93
63_G	67_V	0.775	0.93
74_T	114_R	0.766	0.92
50_D	72_D	0.766	0.92
87_Q	98_R	0.763	0.92
31_P	42_G	0.761	0.92
121_A	128_V	0.758	0.92
62_K	102_D	0.751	0.91
74_T	96_R	0.740	0.91
29_L	38_R	0.732	0.90
110_M	113_M	0.725	0.90
31_P	37_L	0.725	0.90
121_A	125_K	0.718	0.89
31_P	39_D	0.718	0.89
105_D	116_E	0.718	0.89
33_S	41_L	0.710	0.89
96_R	136_K	0.700	0.88
89_M	100_K	0.696	0.88
42_G	46_V	0.696	0.88
127_Q	131_T	0.694	0.88
33_S	37_L	0.694	0.88
52_T	56_T	0.693	0.88
137_D	141_D	0.681	0.87
117_A	120_A	0.681	0.87
138_E	141_D	0.681	0.87
53_D	57_A	0.677	0.86
108_T	111_Q	0.666	0.86
123_E	134_D	0.665	0.85
44_Q	84_Q	0.650	0.84
38_R	41_L	0.648	0.84
45_A	48_L	0.638	0.83
35_K	46_V	0.634	0.83
78_T	81_V	0.633	0.83
81_V	84_Q	0.633	0.83
103_K	106_S	0.625	0.82
45_A	49_R	0.622	0.81
52_T	92_V	0.609	0.80
32_K	42_G	0.609	0.80
121_A	134_D	0.607	0.80
81_V	121_A	0.605	0.80
91_K	95_L	0.601	0.79
54_K	65_Q	0.599	0.79
65_Q	105_D	0.599	0.79
130_Q	140_K	0.595	0.79
121_A	143_Q	0.589	0.78
68_S	97_D	0.587	0.78
114_R	121_A	0.577	0.76
87_Q	127_Q	0.573	0.76
67_V	70_A	0.570	0.76
61_E	65_Q	0.569	0.75
135_V	138_E	0.555	0.74
83_D	94_D	0.554	0.74
102_D	131_T	0.554	0.74
47_A	58_D	0.551	0.73
123_E	130_Q	0.537	0.71
56_T	67_V	0.534	0.71
72_D	83_D	0.534	0.71
61_E	101_S	0.531	0.70
134_D	138_E	0.523	0.69
130_Q	134_D	0.523	0.69
64_T	67_V	0.520	0.69
86_G	97_D	0.515	0.68
131_T	139_L	0.505	0.67
108_T	112_D	0.504	0.66
138_E	142_A	0.503	0.66
130_Q	133_E	0.500	0.66

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
2a01A	1	0.9669	89.9	0.771	Contact Map
2l7bA	1	0.9536	89.7	0.772	Contact Map
3s84A	2	0.8742	87	0.782	Contact Map
1eq1A	1	0.8543	76.6	0.806	Contact Map
2lemA	1	0.8212	71.5	0.814	Contact Map
3r2pA	2	0.8079	70.4	0.815	Contact Map
1nfnA	1	0.7086	59.6	0.827	Contact Map
2d4yA	1	0.7219	52.7	0.834	Contact Map
4ut1A	1	0.6821	41.5	0.845	Contact Map
2j69A	1	0.8675	35.7	0.851	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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