YXZK - BACSU - GREMLIN Contacts

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YXZK - Putative integral membrane protein YxzK

UniProt:	C0H3T7	Sequences: MKVIRIILQVLILYVFFMIGEAIQHLFHLPVSGSIVGLVLLLICLGLRIVPVSIIEDGAGFLLSFLPLLFIPAMTGVINYPSLISFNGLMLLITVVLSTIVTIIAAGFASQLLEKKAKKREEKEKCSKHVSRSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	134 (114)
Sequences:	1830 (1415)
Seq/√Len:	132.6

ECOLI - YOHJ
BACSU - YXZK LRGA CIDA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_F	44_C	4.557	1.00
43_I	47_L	2.789	1.00
108_F	111_Q	2.764	1.00
105_A	109_A	2.699	1.00
107_G	111_Q	2.467	1.00
39_V	43_I	2.368	1.00
104_I	108_F	2.362	1.00
24_Q	36_V	2.150	1.00
97_L	101_V	2.134	1.00
20_G	33_G	1.902	1.00
15_V	19_I	1.900	1.00
16_F	40_L	1.834	1.00
87_N	90_M	1.796	1.00
90_M	94_T	1.775	1.00
78_I	81_P	1.767	1.00
36_V	40_L	1.767	1.00
17_F	21_E	1.756	1.00
8_L	54_I	1.750	1.00
9_Q	58_G	1.746	1.00
21_E	25_H	1.702	1.00
19_I	44_C	1.693	1.00
84_I	91_L	1.638	1.00
17_F	34_S	1.588	1.00
34_S	69_L	1.572	1.00
22_A	26_L	1.543	1.00
109_A	112_L	1.507	1.00
51_P	54_I	1.490	1.00
108_F	112_L	1.488	1.00
38_L	74_M	1.462	1.00
32_S	73_A	1.459	1.00
52_V	55_I	1.428	1.00
112_L	116_K	1.389	1.00
93_I	97_L	1.371	1.00
40_L	44_C	1.369	1.00
77_V	80_Y	1.362	1.00
23_I	26_L	1.333	1.00
52_V	56_E	1.260	1.00
48_R	51_P	1.240	1.00
56_E	60_G	1.202	0.99
80_Y	83_L	1.187	0.99
23_I	40_L	1.184	0.99
82_S	85_S	1.165	0.99
116_K	119_K	1.144	0.99
110_S	114_E	1.120	0.99
24_Q	28_H	1.113	0.99
113_L	116_K	1.104	0.99
81_P	85_S	1.103	0.99
10_V	58_G	1.095	0.99
16_F	20_G	1.085	0.99
39_V	61_F	1.065	0.99
82_S	86_F	1.061	0.99
38_L	110_S	1.049	0.99
20_G	36_V	1.029	0.98
44_C	50_V	1.017	0.98
83_L	87_N	1.012	0.98
102_T	106_A	1.011	0.98
64_S	73_A	1.009	0.98
78_I	96_V	1.006	0.98
22_A	25_H	0.991	0.98
35_I	67_P	0.986	0.98
24_Q	33_G	0.986	0.98
95_V	102_T	0.982	0.98
106_A	110_S	0.982	0.98
8_L	11_L	0.975	0.98
24_Q	27_F	0.974	0.98
23_I	36_V	0.974	0.98
67_P	71_I	0.950	0.97
13_L	58_G	0.945	0.97
23_I	56_E	0.945	0.97
112_L	115_K	0.943	0.97
41_L	50_V	0.939	0.97
44_C	49_I	0.934	0.97
20_G	76_G	0.918	0.97
49_I	52_V	0.913	0.97
9_Q	16_F	0.893	0.96
21_E	33_G	0.888	0.96
38_L	55_I	0.885	0.96
23_I	28_H	0.857	0.95
42_L	46_G	0.853	0.95
87_N	91_L	0.843	0.95
100_I	104_I	0.840	0.95
19_I	40_L	0.839	0.95
99_T	102_T	0.820	0.94
35_I	63_L	0.816	0.94
10_V	20_G	0.801	0.93
70_F	73_A	0.797	0.93
50_V	55_I	0.794	0.93
56_E	76_G	0.786	0.93
14_Y	106_A	0.784	0.92
65_F	68_L	0.782	0.92
6_I	57_D	0.770	0.92
19_I	118_K	0.766	0.92
17_F	32_S	0.765	0.91
23_I	27_F	0.753	0.91
12_I	15_V	0.740	0.90
79_N	82_S	0.739	0.90
8_L	53_S	0.739	0.90
63_L	66_L	0.735	0.90
44_C	47_L	0.733	0.90
9_Q	61_F	0.733	0.90
20_G	40_L	0.732	0.90
39_V	42_L	0.730	0.89
14_Y	76_G	0.728	0.89
62_L	67_P	0.726	0.89
55_I	63_L	0.723	0.89
93_I	119_K	0.720	0.89
67_P	74_M	0.714	0.88
53_S	62_L	0.704	0.88
43_I	109_A	0.703	0.88
95_V	99_T	0.698	0.87
24_Q	29_L	0.691	0.87
10_V	98_S	0.683	0.86
74_M	81_P	0.677	0.86
111_Q	116_K	0.675	0.85
34_S	103_I	0.664	0.85
50_V	54_I	0.660	0.84
75_T	78_I	0.655	0.84
31_V	37_G	0.655	0.84
94_T	103_I	0.644	0.83
110_S	113_L	0.643	0.83
99_T	103_I	0.637	0.82
107_G	116_K	0.636	0.82
8_L	12_I	0.633	0.82
46_G	49_I	0.630	0.81
30_P	35_I	0.630	0.81
33_G	36_V	0.629	0.81
74_M	77_V	0.626	0.81
50_V	66_L	0.626	0.81
67_P	98_S	0.620	0.80
14_Y	20_G	0.620	0.80
52_V	87_N	0.619	0.80
22_A	96_V	0.608	0.79
28_H	39_V	0.605	0.79
61_F	66_L	0.603	0.78
7_I	11_L	0.602	0.78
25_H	84_I	0.599	0.78
48_R	52_V	0.589	0.77
52_V	59_A	0.588	0.77
34_S	42_L	0.588	0.77
66_L	102_T	0.585	0.76
74_M	80_Y	0.582	0.76
68_L	83_L	0.581	0.76
20_G	38_L	0.579	0.76
27_F	36_V	0.575	0.75
7_I	117_A	0.573	0.75
44_C	48_R	0.570	0.74
31_V	76_G	0.569	0.74
17_F	110_S	0.564	0.74
7_I	26_L	0.564	0.74
75_T	82_S	0.563	0.74
9_Q	57_D	0.557	0.73
41_L	55_I	0.555	0.73
94_T	104_I	0.554	0.72
35_I	75_T	0.553	0.72
56_E	102_T	0.552	0.72
18_M	100_I	0.549	0.72
13_L	98_S	0.539	0.70
73_A	84_I	0.539	0.70
51_P	97_L	0.538	0.70
86_F	97_L	0.538	0.70
59_A	100_I	0.535	0.70
58_G	80_Y	0.531	0.69
87_N	97_L	0.522	0.68
66_L	81_P	0.521	0.68
49_I	53_S	0.517	0.67
17_F	38_L	0.516	0.67
55_I	59_A	0.513	0.67
16_F	84_I	0.510	0.66
35_I	80_Y	0.508	0.66
66_L	70_F	0.508	0.66
24_Q	31_V	0.500	0.65

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
4cz8A	2	0.9701	67.9	0.895	Contact Map
4mt1A	3	0.8507	61	0.9	Contact Map
4czbA	2	0.9701	55.5	0.903	Contact Map
3w9iA	3	0.8881	51.8	0.905	Contact Map
2kluA	1	0.3806	44.5	0.909	Contact Map
3aqpA	1	0.8358	41.3	0.911	Contact Map
4j72A	2	0.291	30.3	0.917	Contact Map
3ne5A	3	0.9104	30.1	0.917	Contact Map
4dx5A	3	0.9552	23.5	0.922	Contact Map
4bwzA	2	0.9254	23.1	0.922	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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