NRFF - ECOLI - GREMLIN Contacts

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NRFF - Formate-dependent nitrite reductase complex subunit NrfF

UniProt:	P32711	Sequences: MNKGLLTLLLLFTCFAHAQVVDTWQFANPQQQQQALNIASQLRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKNEVEIIGWMTERYGDFVRYNPPLTGQTLVLWALPVVLLLLMALILWRVRAKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11949
Length:	127 (119)
Sequences:	1365 (964)
Seq/√Len:	88.3

ECOLI - NRFF CCMH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_Q	77_E	3.673	1.00
90_D	97_P	3.567	1.00
98_L	107_A	2.829	1.00
70_M	75_K	2.732	1.00
100_G	103_L	2.710	1.00
31_Q	71_V	2.705	1.00
82_G	86_E	2.673	1.00
45_P	59_V	2.577	1.00
75_K	79_E	2.485	1.00
90_D	99_T	2.390	1.00
50_Q	56_N	2.155	1.00
78_V	82_G	2.151	1.00
98_L	103_L	2.132	1.00
46_Q	59_V	2.119	1.00
118_L	122_R	2.013	1.00
98_L	102_T	1.992	1.00
35_A	39_A	1.961	1.00
50_Q	54_E	1.803	1.00
115_L	119_I	1.776	1.00
76_N	79_E	1.772	1.00
41_Q	95_N	1.757	1.00
66_Q	69_S	1.669	1.00
63_M	84_M	1.641	1.00
32_Q	68_Y	1.638	1.00
41_Q	81_I	1.636	1.00
97_P	102_T	1.610	1.00
28_N	31_Q	1.608	1.00
67_V	80_I	1.567	1.00
49_N	91_F	1.528	1.00
66_Q	83_W	1.520	1.00
37_N	77_E	1.499	1.00
24_W	35_A	1.437	0.99
27_A	72_A	1.419	0.99
48_Q	91_F	1.406	0.99
66_Q	70_M	1.400	0.99
69_S	73_E	1.359	0.99
103_L	107_A	1.338	0.99
40_S	51_N	1.322	0.99
83_W	88_Y	1.316	0.99
70_M	73_E	1.315	0.99
85_T	90_D	1.280	0.99
7_T	11_L	1.263	0.98
81_I	93_R	1.227	0.98
26_F	35_A	1.227	0.98
111_V	115_L	1.212	0.98
80_I	84_M	1.138	0.97
29_P	32_Q	1.127	0.97
26_F	68_Y	1.124	0.97
119_I	122_R	1.100	0.96
114_L	118_L	1.079	0.96
24_W	68_Y	1.069	0.96
39_A	52_L	1.053	0.95
22_D	26_F	1.052	0.95
37_N	40_S	1.028	0.94
31_Q	34_Q	1.006	0.94
49_N	94_Y	1.000	0.94
46_Q	58_P	0.997	0.94
37_N	41_Q	0.992	0.93
8_L	11_L	0.975	0.93
9_L	12_F	0.958	0.92
35_A	68_Y	0.942	0.91
13_T	18_A	0.940	0.91
95_N	98_L	0.933	0.91
21_V	25_Q	0.931	0.91
107_A	111_V	0.929	0.91
75_K	80_I	0.920	0.90
110_V	114_L	0.905	0.90
31_Q	72_A	0.904	0.90
93_R	97_P	0.881	0.88
80_I	92_V	0.871	0.88
122_R	125_A	0.868	0.88
60_A	88_Y	0.867	0.88
71_V	84_M	0.856	0.87
45_P	60_A	0.853	0.87
35_A	71_V	0.852	0.87
67_V	92_V	0.844	0.86
42_L	67_V	0.832	0.85
7_T	10_L	0.819	0.85
38_I	84_M	0.817	0.84
39_A	53_L	0.811	0.84
34_Q	71_V	0.800	0.83
51_N	94_Y	0.800	0.83
15_F	114_L	0.798	0.83
66_Q	84_M	0.796	0.83
10_L	13_T	0.793	0.83
31_Q	35_A	0.788	0.82
106_W	116_M	0.773	0.81
64_R	116_M	0.772	0.81
42_L	81_I	0.769	0.81
119_I	123_V	0.767	0.80
30_Q	33_Q	0.763	0.80
26_F	39_A	0.763	0.80
50_Q	64_R	0.760	0.80
13_T	17_H	0.753	0.79
11_L	14_C	0.752	0.79
35_A	53_L	0.741	0.78
51_N	85_T	0.740	0.78
42_L	49_N	0.726	0.77
36_L	53_L	0.716	0.76
27_A	31_Q	0.714	0.75
72_A	120_L	0.705	0.75
53_L	65_H	0.699	0.74
50_Q	93_R	0.698	0.74
81_I	84_M	0.687	0.73
14_C	17_H	0.680	0.72
83_W	87_R	0.672	0.71
8_L	13_T	0.655	0.69
18_A	121_W	0.653	0.69
19_Q	88_Y	0.634	0.67
109_P	112_L	0.633	0.66
14_C	76_N	0.629	0.66
39_A	63_M	0.628	0.66
54_E	116_M	0.624	0.65
32_Q	36_L	0.623	0.65
8_L	15_F	0.621	0.65
58_P	112_L	0.620	0.65
12_F	16_A	0.618	0.65
13_T	16_A	0.617	0.64
47_C	64_R	0.616	0.64
24_W	53_L	0.616	0.64
39_A	42_L	0.609	0.63
42_L	84_M	0.607	0.63
49_N	60_A	0.602	0.63
25_Q	35_A	0.601	0.62
22_D	51_N	0.599	0.62
59_V	94_Y	0.598	0.62
38_I	92_V	0.597	0.62
23_T	65_H	0.593	0.61
90_D	102_T	0.592	0.61
53_L	91_F	0.590	0.61
56_N	61_V	0.590	0.61
31_Q	39_A	0.588	0.61
60_A	74_G	0.588	0.61
111_V	122_R	0.587	0.61
41_Q	88_Y	0.584	0.60
59_V	91_F	0.583	0.60
113_L	116_M	0.579	0.60
7_T	119_I	0.578	0.59
76_N	122_R	0.578	0.59
88_Y	113_L	0.578	0.59
45_P	108_L	0.569	0.58
26_F	94_Y	0.569	0.58
61_V	65_H	0.562	0.57
14_C	19_Q	0.559	0.57
70_M	80_I	0.556	0.57
115_L	118_L	0.556	0.57
40_S	53_L	0.555	0.56
15_F	124_R	0.553	0.56
52_L	63_M	0.552	0.56
63_M	93_R	0.552	0.56
83_W	93_R	0.552	0.56
107_A	110_V	0.550	0.56
53_L	71_V	0.549	0.56
34_Q	68_Y	0.548	0.55
35_A	64_R	0.548	0.55
117_A	121_W	0.546	0.55
25_Q	36_L	0.544	0.55
48_Q	54_E	0.536	0.54
84_M	92_V	0.535	0.54
42_L	92_V	0.535	0.54
62_S	105_L	0.535	0.54
59_V	63_M	0.531	0.53
59_V	62_S	0.531	0.53
42_L	94_Y	0.530	0.53
35_A	61_V	0.523	0.52
67_V	70_M	0.521	0.52
52_L	84_M	0.519	0.52
29_P	33_Q	0.517	0.51
29_P	68_Y	0.512	0.51
56_N	64_R	0.512	0.51
50_Q	101_Q	0.509	0.50
57_A	93_R	0.504	0.49
35_A	46_Q	0.504	0.49
48_Q	62_S	0.503	0.49
85_T	93_R	0.503	0.49
36_L	39_A	0.502	0.49
7_T	15_F	0.502	0.49
99_T	108_L	0.500	0.49

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
2hl7A	1	0.6457	100	0.322	Contact Map
2kw0A	1	0.6378	100	0.327	Contact Map
4pj0V	1	0.5512	61.3	0.919	Contact Map
4xxlA	1	0.4803	56.2	0.921	Contact Map
1fftB	1	0.6142	42.2	0.927	Contact Map
1odfA	1	0.9921	36.3	0.93	Contact Map
3wfdC	1	0.9134	34	0.931	Contact Map
2yevB	1	0.3701	31.4	0.932	Contact Map
2blfB	1	0.5748	30.1	0.933	Contact Map
1c2nA	1	0.6929	29.9	0.933	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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