NIRD - ECOLI - GREMLIN Contacts

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NIRD - Nitrite reductase (NADH) small subunit

UniProt:	P0A9I8	Sequences: MSQWKDICKIDDILPETGVCALLGDEQVAIFRPYHSDQVFAISNIDPFFESSVLSRGLIAEHQGELWVASPLKKQRFRLSDGLCMEDEQFSVKHYEARVKDGVVQLRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10655
Length:	108 (103)
Sequences:	1043 (652)
Seq/√Len:	64.2

ECOLI - NIRD
BACSU - NASE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_L	92_V	3.604	1.00
65_E	78_R	3.487	1.00
43_S	93_K	3.256	1.00
6_D	103_V	3.031	1.00
98_R	105_Q	2.982	1.00
61_E	64_G	2.672	1.00
76_R	86_E	2.283	1.00
62_H	76_R	2.265	1.00
49_F	72_L	2.197	1.00
67_W	76_R	2.186	1.00
27_Q	52_S	2.048	1.00
9_K	12_D	2.008	1.00
45_I	52_S	1.996	1.00
48_F	77_F	1.993	1.00
42_I	92_V	1.967	1.00
39_V	97_A	1.906	1.00
39_V	99_V	1.860	1.00
49_F	73_K	1.805	1.00
78_R	81_D	1.804	1.00
44_N	55_S	1.684	0.99
100_K	105_Q	1.633	0.99
45_I	50_E	1.630	0.99
62_H	86_E	1.611	0.99
6_D	105_Q	1.580	0.99
13_I	17_T	1.542	0.99
65_E	83_L	1.530	0.99
65_E	80_S	1.516	0.99
99_V	104_V	1.514	0.99
31_F	68_V	1.475	0.98
9_K	103_V	1.456	0.98
26_E	43_S	1.437	0.98
48_F	90_F	1.374	0.97
38_Q	80_S	1.371	0.97
69_A	76_R	1.342	0.97
32_R	37_D	1.306	0.96
4_W	98_R	1.298	0.96
27_Q	44_N	1.275	0.96
62_H	67_W	1.205	0.94
7_I	21_A	1.187	0.94
10_I	39_V	1.186	0.94
13_I	32_R	1.183	0.94
48_F	87_D	1.166	0.93
83_L	91_S	1.156	0.93
18_G	31_F	1.106	0.91
14_L	58_L	1.047	0.89
42_I	54_L	1.033	0.88
21_A	28_V	0.994	0.86
7_I	106_L	0.983	0.86
33_P	36_S	0.962	0.84
20_C	55_S	0.950	0.83
7_I	23_L	0.949	0.83
10_I	99_V	0.936	0.83
36_S	59_I	0.932	0.82
48_F	75_Q	0.932	0.82
7_I	30_I	0.921	0.82
60_A	67_W	0.900	0.80
45_I	49_F	0.894	0.80
99_V	102_G	0.866	0.77
46_D	70_S	0.865	0.77
6_D	9_K	0.856	0.77
21_A	39_V	0.849	0.76
43_S	95_Y	0.842	0.75
8_C	46_D	0.836	0.75
10_I	32_R	0.831	0.74
8_C	30_I	0.823	0.74
53_V	72_L	0.816	0.73
8_C	13_I	0.798	0.71
33_P	40_F	0.798	0.71
14_L	17_T	0.771	0.69
30_I	97_A	0.754	0.67
69_A	77_F	0.743	0.66
61_E	78_R	0.735	0.65
35_H	38_Q	0.732	0.65
17_T	55_S	0.729	0.64
19_V	44_N	0.728	0.64
33_P	66_L	0.725	0.64
63_Q	80_S	0.723	0.64
52_S	67_W	0.721	0.64
11_D	102_G	0.714	0.63
23_L	106_L	0.713	0.63
10_I	15_P	0.705	0.62
39_V	43_S	0.703	0.62
60_A	66_L	0.702	0.62
13_I	64_G	0.693	0.61
16_E	33_P	0.690	0.60
10_I	37_D	0.687	0.60
33_P	42_I	0.682	0.59
33_P	59_I	0.676	0.59
28_V	37_D	0.675	0.58
20_C	27_Q	0.675	0.58
37_D	94_H	0.674	0.58
26_E	95_Y	0.668	0.58
61_E	67_W	0.665	0.57
8_C	104_V	0.654	0.56
20_C	28_V	0.649	0.56
23_L	28_V	0.647	0.55
68_V	92_V	0.639	0.54
24_G	35_H	0.638	0.54
16_E	35_H	0.630	0.53
16_E	58_L	0.627	0.53
16_E	59_I	0.625	0.53
10_I	13_I	0.621	0.52
67_W	86_E	0.614	0.51
50_E	96_E	0.614	0.51
49_F	75_Q	0.611	0.51
17_T	32_R	0.610	0.51
14_L	19_V	0.609	0.51
77_F	84_C	0.609	0.51
21_A	30_I	0.608	0.51
30_I	64_G	0.602	0.50
15_P	51_S	0.600	0.50
6_D	96_E	0.588	0.48
8_C	75_Q	0.583	0.48
16_E	19_V	0.580	0.48
9_K	102_G	0.579	0.47
17_T	20_C	0.577	0.47
77_F	87_D	0.576	0.47
16_E	72_L	0.575	0.47
35_H	61_E	0.575	0.47
32_R	106_L	0.573	0.47
33_P	81_D	0.569	0.46
88_E	101_D	0.566	0.46
13_I	39_V	0.565	0.46
30_I	75_Q	0.562	0.45
8_C	22_L	0.557	0.45
4_W	105_Q	0.556	0.45
18_G	79_L	0.554	0.45
67_W	73_K	0.554	0.45
52_S	61_E	0.553	0.44
64_G	87_D	0.552	0.44
70_S	75_Q	0.552	0.44
27_Q	56_R	0.548	0.44
61_E	66_L	0.548	0.44
18_G	68_V	0.547	0.44
5_K	105_Q	0.546	0.44
13_I	72_L	0.545	0.44
15_P	89_Q	0.541	0.43
12_D	26_E	0.539	0.43
46_D	78_R	0.538	0.43
87_D	90_F	0.537	0.43
65_E	86_E	0.529	0.42
10_I	102_G	0.523	0.41
30_I	95_Y	0.522	0.41
33_P	52_S	0.517	0.40
35_H	58_L	0.513	0.40
58_L	61_E	0.512	0.40
48_F	84_C	0.511	0.40
89_Q	92_V	0.506	0.39
35_H	66_L	0.505	0.39
26_E	93_K	0.505	0.39
16_E	44_N	0.504	0.39
14_L	32_R	0.504	0.39
19_V	22_L	0.500	0.38
8_C	25_D	0.500	0.38

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
2jzaA	1	0.9907	99.9	0.532	Contact Map
2jo6A	1	0.9907	99.9	0.534	Contact Map
3c0dA	1	0.9815	99.9	0.54	Contact Map
4aivA	1	0.9722	99.8	0.572	Contact Map
2de6D	1	0.9074	99.8	0.59	Contact Map
2i7fA	1	0.9167	99.8	0.593	Contact Map
3gceA	1	0.9259	99.8	0.596	Contact Map
1fqtA	2	0.9259	99.8	0.597	Contact Map
3d89A	1	0.963	99.8	0.606	Contact Map
1vm9A	1	0.9259	99.7	0.61	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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