HtaA - PFAM28P - GREMLIN Contacts

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HtaA - Htaa

PFAM:	PF04213	Sequences: VTGGTLDWGVKESFRSYVTGPIAKGSITLSGGATRAGGGAFRFPAGSGTYDPDTGTGTVAFGGSVRFTGHGGALDLTLSDPRVEVSGGTGTLTADVTSKDMEGGAPVTGDRVPLATLDLSGATVAGGTVTLTGAPATLTAAGAAAFGGFYPAGTALDPVTLSVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	164 (162)
Sequences:	1595 (1283)
Seq/√Len:	100.8
META:	0.438

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_A	156_L	3.933	1.00
66_R	75_D	3.706	1.00
136_A	159_V	3.378	1.00
30_S	64_S	3.338	1.00
117_L	134_A	3.164	1.00
80_D	111_R	3.086	1.00
91_T	113_P	2.906	1.00
70_H	74_L	2.651	1.00
9_G	15_R	2.628	1.00
83_V	117_L	2.506	1.00
117_L	136_A	2.455	1.00
94_A	114_L	2.307	1.00
95_D	111_R	2.287	1.00
6_L	61_F	2.274	1.00
12_E	16_S	2.263	1.00
113_P	141_A	2.133	1.00
51_D	54_T	2.045	1.00
82_R	111_R	2.021	1.00
9_G	157_D	2.007	1.00
139_T	142_G	2.003	1.00
93_T	111_R	1.878	1.00
115_A	136_A	1.808	1.00
69_G	72_G	1.775	1.00
10_V	67_F	1.773	1.00
84_E	93_T	1.760	1.00
7_D	42_R	1.753	1.00
22_I	69_G	1.753	1.00
131_L	161_L	1.746	1.00
151_P	154_T	1.739	1.00
50_Y	54_T	1.725	1.00
69_G	74_L	1.722	1.00
99_K	106_P	1.716	1.00
93_T	113_P	1.700	1.00
12_E	157_D	1.680	1.00
15_R	157_D	1.668	1.00
23_A	69_G	1.575	1.00
27_I	41_F	1.569	1.00
81_P	94_A	1.514	1.00
118_D	135_P	1.506	1.00
19_T	35_R	1.491	1.00
4_G	46_G	1.487	1.00
83_V	161_L	1.477	1.00
68_T	72_G	1.474	1.00
15_R	67_F	1.427	1.00
97_T	108_T	1.402	1.00
81_P	111_R	1.383	1.00
50_Y	57_G	1.374	0.99
13_S	17_Y	1.310	0.99
11_K	154_T	1.310	0.99
57_G	85_V	1.300	0.99
68_T	75_D	1.298	0.99
35_R	38_G	1.284	0.99
140_A	152_A	1.278	0.99
78_L	94_A	1.268	0.99
20_G	23_A	1.266	0.99
4_G	44_P	1.248	0.99
76_L	98_S	1.214	0.99
117_L	159_V	1.193	0.99
130_T	160_T	1.187	0.98
47_S	60_A	1.154	0.98
28_T	66_R	1.151	0.98
64_S	79_S	1.132	0.98
32_G	64_S	1.124	0.98
35_R	39_G	1.107	0.98
138_L	143_A	1.105	0.98
82_R	93_T	1.103	0.98
24_K	69_G	1.096	0.97
70_H	73_A	1.073	0.97
146_F	150_Y	1.069	0.97
46_G	62_G	1.065	0.97
18_V	67_F	1.059	0.97
136_A	156_L	1.052	0.97
91_T	116_T	1.036	0.96
36_A	40_A	1.022	0.96
131_L	134_A	1.022	0.96
14_F	67_F	1.021	0.96
58_T	84_E	1.007	0.96
60_A	82_R	1.006	0.96
11_K	17_Y	1.006	0.96
31_G	64_S	1.001	0.96
78_L	81_P	0.994	0.95
139_T	143_A	0.991	0.95
113_P	116_T	0.983	0.95
61_F	81_P	0.963	0.95
64_S	77_T	0.962	0.94
41_F	67_F	0.944	0.94
10_V	15_R	0.942	0.94
43_F	46_G	0.939	0.94
90_G	117_L	0.938	0.94
35_R	41_F	0.937	0.94
118_D	121_G	0.926	0.93
118_D	122_A	0.919	0.93
137_T	155_A	0.919	0.93
14_F	74_L	0.912	0.93
24_K	71_G	0.906	0.93
80_D	95_D	0.905	0.92
33_A	43_F	0.899	0.92
80_D	110_D	0.888	0.92
140_A	143_A	0.873	0.91
138_L	146_F	0.870	0.91
17_Y	70_H	0.870	0.91
100_D	107_V	0.864	0.91
59_V	161_L	0.863	0.91
116_T	137_T	0.841	0.89
109_G	112_V	0.836	0.89
130_T	162_S	0.835	0.89
138_L	142_G	0.820	0.88
143_A	146_F	0.819	0.88
44_P	62_G	0.809	0.88
112_V	141_A	0.809	0.88
90_G	119_L	0.793	0.87
96_V	145_A	0.792	0.86
143_A	153_G	0.790	0.86
21_P	24_K	0.789	0.86
38_G	94_A	0.784	0.86
62_G	81_P	0.783	0.86
58_T	82_R	0.776	0.85
95_D	112_V	0.768	0.85
119_L	135_P	0.766	0.85
29_L	35_R	0.755	0.84
51_D	55_G	0.752	0.83
18_V	25_G	0.752	0.83
27_I	67_F	0.752	0.83
12_E	162_S	0.746	0.83
63_G	80_D	0.742	0.83
17_Y	74_L	0.740	0.83
117_L	122_A	0.737	0.82
37_G	40_A	0.719	0.81
122_A	134_A	0.717	0.80
143_A	148_G	0.717	0.80
14_F	76_L	0.717	0.80
137_T	140_A	0.716	0.80
138_L	156_L	0.712	0.80
141_A	144_A	0.705	0.79
73_A	100_D	0.704	0.79
48_G	145_A	0.702	0.79
43_F	65_V	0.701	0.79
49_T	60_A	0.694	0.78
143_A	151_P	0.694	0.78
129_V	163_V	0.689	0.78
140_A	144_A	0.685	0.77
34_T	42_R	0.683	0.77
134_A	159_V	0.680	0.77
31_G	120_S	0.678	0.77
59_V	163_V	0.677	0.77
25_G	69_G	0.674	0.76
3_G	7_D	0.672	0.76
121_G	124_V	0.666	0.75
2_T	53_D	0.662	0.75
97_T	106_P	0.661	0.75
98_S	109_G	0.660	0.75
81_P	92_L	0.659	0.75
11_K	150_Y	0.656	0.74
85_V	119_L	0.647	0.73
27_I	35_R	0.640	0.72
72_G	103_G	0.640	0.72
57_G	72_G	0.639	0.72
38_G	42_R	0.633	0.72
128_T	162_S	0.631	0.71
80_D	93_T	0.630	0.71
118_D	137_T	0.630	0.71
89_T	125_A	0.627	0.71
43_F	81_P	0.627	0.71
81_P	85_V	0.624	0.71
27_I	149_F	0.624	0.71
35_R	40_A	0.623	0.70
135_P	158_P	0.621	0.70
84_E	91_T	0.619	0.70
2_T	128_T	0.618	0.70
119_L	122_A	0.611	0.69
149_F	156_L	0.610	0.69
44_P	63_G	0.610	0.69
9_G	12_E	0.605	0.68
15_R	27_I	0.605	0.68
91_T	114_L	0.601	0.68
99_K	104_G	0.600	0.68
11_K	157_D	0.594	0.67
80_D	92_L	0.589	0.66
113_P	139_T	0.589	0.66
101_M	105_A	0.586	0.66
88_G	119_L	0.583	0.65
18_V	27_I	0.581	0.65
98_S	147_G	0.580	0.65
2_T	49_T	0.576	0.64
33_A	65_V	0.574	0.64
29_L	41_F	0.570	0.64
15_R	41_F	0.570	0.64
3_G	46_G	0.569	0.64
125_A	128_T	0.568	0.63
13_S	150_Y	0.568	0.63
78_L	114_L	0.567	0.63
12_E	37_G	0.566	0.63
20_G	69_G	0.566	0.63
6_L	45_A	0.563	0.63
28_T	124_V	0.562	0.63
33_A	42_R	0.561	0.62
94_A	112_V	0.560	0.62
100_D	103_G	0.560	0.62
44_P	83_V	0.559	0.62
51_D	56_T	0.557	0.62
119_L	134_A	0.557	0.62
118_D	134_A	0.557	0.62
11_K	15_R	0.555	0.62
2_T	99_K	0.553	0.61
43_F	57_G	0.551	0.61
100_D	105_A	0.547	0.61
109_G	127_G	0.547	0.61
12_E	39_G	0.545	0.60
25_G	67_F	0.545	0.60
23_A	70_H	0.543	0.60
87_G	90_G	0.543	0.60
11_K	16_S	0.542	0.60
5_T	45_A	0.538	0.59
29_L	33_A	0.533	0.59
2_T	163_V	0.532	0.58
4_G	61_F	0.531	0.58
47_S	144_A	0.530	0.58
103_G	106_P	0.528	0.58
127_G	131_L	0.528	0.58
69_G	73_A	0.524	0.57
57_G	63_G	0.521	0.57
26_S	68_T	0.520	0.57
10_V	156_L	0.519	0.57
138_L	154_T	0.518	0.56
68_T	98_S	0.518	0.56
114_L	156_L	0.518	0.56
30_S	66_R	0.518	0.56
39_G	65_V	0.513	0.56
79_S	94_A	0.510	0.55
12_E	19_T	0.508	0.55
19_T	27_I	0.507	0.55
92_L	159_V	0.507	0.55
98_S	107_V	0.506	0.55
143_A	152_A	0.506	0.55
146_F	149_F	0.506	0.55
65_V	81_P	0.505	0.55
76_L	149_F	0.504	0.54
142_G	156_L	0.503	0.54
13_S	115_A	0.502	0.54
2_T	5_T	0.502	0.54
14_F	145_A	0.500	0.54
52_P	126_G	0.500	0.54
143_A	149_F	0.500	0.54

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
3us9A	1	0.4512	6.6	0.941	Contact Map
2pb9A	3	0.3293	6.1	0.941	Contact Map
4tshB	1	0.3354	4.5	0.945	Contact Map
3qv0A	3	0.3293	3	0.95	Contact Map
2q2kA	3	0.1341	2.6	0.951	Contact Map
2lt9A	1	0.4634	2.5	0.952	Contact Map
3szeA	1	0.811	2.5	0.952	Contact Map
2hyxA	2	0.7805	2.4	0.952	Contact Map
3ht4A	4	0.2439	2.3	0.953	Contact Map
1yqfA	3	0.3293	2.2	0.953	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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