Q9HMM5 - HALSA - GREMLIN Contacts

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Q9HMM5 - Nitrogen fixation protein

UniProt:	Q9HMM5	Sequences: MSMGSDMYRQQILDHYRNPRNQGELPEPSFTHEGYNPSCGDELEFDVALDDDGETIAHVAFRGDGCAISQASASMLSEELPGMTLAEVDALDRDDILDMLGVEVTPMRIKCAVLSEKVVQDGAEIYTGDGDEADRTTTEDDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	142 (120)
Sequences:	2627 (1319)
Seq/√Len:	120.4

ECOLI - ISCU
BACSU - SUFU
HALSA - Q9HMM5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_D	57_A	4.886	1.00
20_R	78_E	3.565	1.00
75_M	99_M	3.350	1.00
21_N	81_P	2.928	1.00
84_T	87_E	2.744	1.00
83_M	87_E	2.656	1.00
25_L	60_A	2.530	1.00
58_H	81_P	2.447	1.00
33_E	44_E	2.309	1.00
24_E	62_R	2.252	1.00
21_N	77_S	2.227	1.00
14_D	20_R	2.173	1.00
59_V	80_L	2.116	1.00
48_A	58_H	2.028	1.00
56_I	88_V	1.909	1.00
23_G	60_A	1.827	1.00
55_T	84_T	1.810	1.00
48_A	57_A	1.784	1.00
80_L	119_V	1.779	1.00
29_S	48_A	1.687	1.00
24_E	46_D	1.652	1.00
46_D	60_A	1.624	1.00
49_L	85_L	1.611	1.00
34_G	118_V	1.609	1.00
15_H	74_S	1.587	1.00
27_E	48_A	1.576	1.00
73_A	115_S	1.547	1.00
74_S	77_S	1.493	1.00
15_H	20_R	1.484	1.00
61_F	77_S	1.483	1.00
85_L	123_A	1.476	1.00
76_L	119_V	1.447	1.00
87_E	90_A	1.414	1.00
20_R	74_S	1.405	1.00
33_E	42_E	1.347	1.00
30_F	122_G	1.320	1.00
21_N	74_S	1.272	1.00
12_I	68_I	1.265	1.00
31_T	46_D	1.246	0.99
59_V	77_S	1.244	0.99
89_D	120_Q	1.216	0.99
25_L	46_D	1.191	0.99
75_M	96_I	1.170	0.99
75_M	79_E	1.161	0.99
32_H	45_F	1.150	0.99
120_Q	124_E	1.120	0.99
97_L	109_I	1.112	0.99
42_E	64_D	1.111	0.99
9_R	13_L	1.098	0.99
22_Q	70_Q	1.097	0.99
76_L	116_E	1.095	0.99
89_D	124_E	1.076	0.98
85_L	89_D	1.070	0.98
89_D	127_T	1.057	0.98
32_H	118_V	1.036	0.98
22_Q	63_G	1.029	0.98
124_E	127_T	0.996	0.97
119_V	123_A	0.976	0.97
15_H	78_E	0.962	0.97
47_V	59_V	0.955	0.97
68_I	112_A	0.942	0.96
95_D	98_D	0.940	0.96
125_I	129_D	0.938	0.96
36_N	106_P	0.922	0.96
25_L	29_S	0.909	0.95
72_S	116_E	0.901	0.95
21_N	78_E	0.899	0.95
43_L	63_G	0.878	0.95
50_D	53_G	0.876	0.94
109_I	113_V	0.862	0.94
9_R	101_G	0.854	0.94
24_E	60_A	0.851	0.94
11_Q	98_D	0.836	0.93
45_F	76_L	0.824	0.92
56_I	119_V	0.822	0.92
101_G	104_V	0.822	0.92
80_L	88_V	0.820	0.92
20_R	77_S	0.819	0.92
29_S	49_L	0.817	0.92
34_G	67_A	0.817	0.92
113_V	117_K	0.816	0.92
61_F	69_S	0.812	0.92
68_I	72_S	0.810	0.92
35_Y	42_E	0.808	0.92
31_T	44_E	0.802	0.91
50_D	55_T	0.801	0.91
8_Y	40_G	0.797	0.91
86_A	89_D	0.795	0.91
77_S	81_P	0.783	0.90
79_E	91_L	0.781	0.90
13_L	17_R	0.779	0.90
22_Q	62_R	0.774	0.90
79_E	83_M	0.769	0.90
39_C	114_L	0.764	0.89
39_C	110_K	0.750	0.88
100_L	103_E	0.746	0.88
72_S	115_S	0.745	0.88
104_V	120_Q	0.730	0.87
15_H	19_P	0.728	0.87
86_A	127_T	0.726	0.87
71_A	99_M	0.723	0.87
19_P	74_S	0.710	0.86
124_E	128_G	0.701	0.85
121_D	124_E	0.699	0.85
25_L	48_A	0.698	0.85
30_F	125_I	0.696	0.84
100_L	104_V	0.685	0.83
88_V	119_V	0.683	0.83
11_Q	14_D	0.678	0.83
97_L	113_V	0.669	0.82
28_P	84_T	0.663	0.81
76_L	80_L	0.663	0.81
125_I	128_G	0.660	0.81
68_I	108_R	0.658	0.81
23_G	58_H	0.655	0.81
36_N	63_G	0.651	0.80
79_E	96_I	0.650	0.80
56_I	80_L	0.649	0.80
38_S	96_I	0.648	0.80
67_A	109_I	0.648	0.80
34_G	121_D	0.643	0.79
51_D	86_A	0.642	0.79
103_E	106_P	0.635	0.79
109_I	114_L	0.633	0.78
63_G	69_S	0.632	0.78
36_N	68_I	0.632	0.78
46_D	62_R	0.631	0.78
9_R	17_R	0.630	0.78
110_K	114_L	0.627	0.78
69_S	108_R	0.623	0.77
23_G	62_R	0.621	0.77
65_G	69_S	0.616	0.76
89_D	123_A	0.614	0.76
9_R	109_I	0.612	0.76
49_L	122_G	0.611	0.76
25_L	61_F	0.599	0.74
35_Y	121_D	0.598	0.74
51_D	55_T	0.598	0.74
12_I	71_A	0.598	0.74
22_Q	61_F	0.589	0.73
40_G	65_G	0.585	0.73
14_D	18_N	0.583	0.72
59_V	74_S	0.581	0.72
44_E	62_R	0.579	0.72
24_E	31_T	0.578	0.72
106_P	110_K	0.574	0.71
101_G	122_G	0.572	0.71
30_F	47_V	0.571	0.71
63_G	108_R	0.564	0.70
76_L	91_L	0.562	0.70
79_E	99_M	0.551	0.68
37_P	40_G	0.548	0.68
68_I	110_K	0.547	0.68
101_G	112_A	0.545	0.67
36_N	116_E	0.545	0.67
84_T	123_A	0.545	0.67
76_L	115_S	0.543	0.67
11_Q	16_Y	0.539	0.67
26_P	128_G	0.539	0.67
17_R	67_A	0.536	0.66
19_P	22_Q	0.528	0.65
83_M	91_L	0.528	0.65
42_E	109_I	0.526	0.65
11_Q	109_I	0.526	0.65
11_Q	99_M	0.523	0.64
101_G	117_K	0.522	0.64
15_H	21_N	0.521	0.64
48_A	55_T	0.519	0.64
49_L	57_A	0.517	0.63
98_D	103_E	0.516	0.63
39_C	66_C	0.512	0.63
101_G	105_T	0.512	0.63
9_R	117_K	0.509	0.62
56_I	59_V	0.509	0.62
63_G	68_I	0.508	0.62
9_R	105_T	0.506	0.62
12_I	98_D	0.504	0.61
86_A	92_D	0.504	0.61
15_H	77_S	0.502	0.61
107_M	115_S	0.500	0.61

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
1su0B	1	0.838	100	0.169	Contact Map
1xjsA	1	0.8944	100	0.17	Contact Map
2qq4A	5	0.8592	100	0.186	Contact Map
2z7eA	5	0.9366	100	0.188	Contact Map
3lvlA	1	0.8592	100	0.194	Contact Map
4eb5C	1	0.9085	100	0.213	Contact Map
3g0mA	1	0.838	97.1	0.848	Contact Map
2e5aA	1	0.7183	71.2	0.914	Contact Map
3a7rA	1	0.7746	52	0.924	Contact Map
4lw4C	1	0.8451	51.4	0.924	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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