NARJ - BACSU - GREMLIN Contacts

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NARJ - Probable nitrate reductase molybdenum cofactor assembly chaperone NarJ

UniProt:	P42178	Sequences: MNTTDRQITFSALSCLLSYPDEEWRAELPDWKALIQEIGNRQIREKLLHFFETSASYSPEALIEHYVYTFDFGKKTNMYVTYFNSGEQRERGIELLHLKNTYEQSGFLPTEKELPDYLPLMLEFAAAAEIEAARSVFEKYLSNVRELASRLEKNDSIYAELLHVLLAALENIGVRESVEGAVQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	184 (167)
Sequences:	989 (739)
Seq/√Len:	57.2

ECOLI - NARJ NARW
BACSU - NARJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_K	55_A	3.955	1.00
50_F	161_L	3.755	1.00
32_K	52_E	3.243	1.00
59_P	63_I	2.942	1.00
117_Y	120_L	2.883	1.00
100_N	104_Q	2.772	1.00
152_E	163_H	2.738	1.00
53_T	65_H	2.716	1.00
49_H	160_E	2.616	1.00
69_T	156_S	2.607	1.00
29_P	55_A	2.484	1.00
50_F	160_E	2.345	1.00
53_T	157_I	2.344	1.00
103_E	108_L	2.330	1.00
100_N	103_E	2.310	1.00
22_E	26_A	2.263	1.00
50_F	54_S	2.229	1.00
12_A	31_W	2.219	1.00
13_L	165_L	1.978	1.00
148_A	166_L	1.916	1.00
54_S	62_L	1.906	1.00
145_R	148_A	1.888	1.00
85_S	94_E	1.865	1.00
58_S	61_A	1.807	0.99
22_E	63_I	1.758	0.99
72_F	82_Y	1.739	0.99
27_E	30_D	1.736	0.99
78_M	119_P	1.728	0.99
24_W	54_S	1.642	0.99
109_P	120_L	1.589	0.98
147_L	162_L	1.574	0.98
35_I	38_I	1.562	0.98
36_Q	48_L	1.557	0.98
67_V	71_D	1.527	0.98
11_S	127_A	1.485	0.98
76_T	150_R	1.453	0.97
125_A	133_A	1.439	0.97
12_A	164_V	1.438	0.97
10_F	128_A	1.423	0.97
148_A	162_L	1.422	0.97
13_L	161_L	1.417	0.97
47_L	161_L	1.394	0.96
10_F	168_A	1.379	0.96
28_L	51_F	1.366	0.96
81_T	98_L	1.364	0.96
118_L	144_V	1.364	0.96
121_M	136_V	1.356	0.96
89_R	92_G	1.333	0.95
87_E	150_R	1.330	0.95
60_E	64_E	1.306	0.95
99_K	103_E	1.303	0.95
109_P	124_F	1.297	0.95
74_K	82_Y	1.283	0.94
29_P	33_A	1.249	0.94
101_T	136_V	1.235	0.93
171_N	174_V	1.228	0.93
28_L	55_A	1.215	0.93
65_H	158_Y	1.214	0.93
81_T	94_E	1.192	0.92
40_N	45_E	1.188	0.92
98_L	129_E	1.152	0.90
102_Y	124_F	1.140	0.90
8_I	34_L	1.135	0.90
57_Y	65_H	1.134	0.90
98_L	101_T	1.132	0.90
128_A	132_A	1.128	0.89
99_K	109_P	1.127	0.89
35_I	44_R	1.123	0.89
57_Y	61_A	1.108	0.89
10_F	134_R	1.102	0.88
132_A	135_S	1.092	0.88
85_S	90_E	1.079	0.87
73_G	76_T	1.064	0.87
135_S	139_K	1.058	0.86
152_E	159_A	1.041	0.85
46_K	49_H	1.040	0.85
34_L	37_E	1.035	0.85
23_E	26_A	1.032	0.85
18_S	117_Y	1.023	0.84
11_S	15_C	1.021	0.84
61_A	64_E	1.017	0.84
46_K	160_E	1.012	0.84
148_A	163_H	1.011	0.84
105_S	124_F	1.004	0.83
151_L	156_S	0.995	0.83
64_E	68_Y	0.993	0.82
93_I	97_H	0.987	0.82
149_S	153_K	0.987	0.82
11_S	14_S	0.981	0.82
74_K	94_E	0.968	0.81
103_E	109_P	0.958	0.80
45_E	49_H	0.955	0.80
86_G	94_E	0.947	0.79
15_C	27_E	0.936	0.79
33_A	36_Q	0.924	0.78
90_E	95_L	0.915	0.77
134_R	138_E	0.904	0.76
76_T	154_N	0.900	0.76
32_K	48_L	0.892	0.75
23_E	27_E	0.892	0.75
142_S	146_E	0.886	0.75
13_L	164_V	0.883	0.74
95_L	142_S	0.877	0.74
80_V	87_E	0.876	0.74
10_F	125_A	0.873	0.74
88_Q	146_E	0.864	0.73
93_I	121_M	0.862	0.73
83_F	143_N	0.860	0.72
107_F	128_A	0.859	0.72
61_A	65_H	0.859	0.72
82_Y	121_M	0.857	0.72
118_L	141_L	0.856	0.72
83_F	95_L	0.854	0.72
45_E	175_R	0.842	0.71
67_V	117_Y	0.834	0.70
33_A	37_E	0.833	0.70
83_F	87_E	0.829	0.70
93_I	96_L	0.826	0.69
26_A	29_P	0.825	0.69
16_L	83_F	0.822	0.69
9_T	38_I	0.822	0.69
93_I	140_Y	0.818	0.69
43_I	167_A	0.814	0.68
73_G	154_N	0.804	0.67
82_Y	169_L	0.802	0.67
101_T	104_Q	0.798	0.67
60_E	76_T	0.798	0.67
81_T	95_L	0.790	0.66
85_S	98_L	0.790	0.66
68_Y	171_N	0.788	0.66
45_E	52_E	0.787	0.66
78_M	147_L	0.785	0.65
21_D	25_R	0.778	0.65
107_F	127_A	0.769	0.64
31_W	34_L	0.767	0.64
105_S	127_A	0.756	0.62
57_Y	62_L	0.747	0.62
63_I	120_L	0.740	0.61
69_T	157_I	0.739	0.61
23_E	29_P	0.733	0.60
85_S	89_R	0.730	0.60
44_R	48_L	0.730	0.60
145_R	166_L	0.727	0.59
50_F	107_F	0.718	0.59
53_T	57_Y	0.715	0.58
84_N	98_L	0.711	0.58
141_L	169_L	0.709	0.58
10_F	107_F	0.706	0.57
72_F	142_S	0.703	0.57
40_N	147_L	0.703	0.57
72_F	85_S	0.701	0.57
28_L	110_T	0.677	0.54
77_N	150_R	0.674	0.54
82_Y	156_S	0.674	0.54
95_L	114_L	0.674	0.54
77_N	94_E	0.672	0.54
147_L	156_S	0.671	0.53
82_Y	85_S	0.670	0.53
83_F	88_Q	0.669	0.53
82_Y	88_Q	0.665	0.53
17_L	71_D	0.665	0.53
93_I	107_F	0.663	0.53
47_L	51_F	0.663	0.53
95_L	143_N	0.661	0.52
96_L	101_T	0.656	0.52
42_Q	131_E	0.653	0.51
113_E	147_L	0.651	0.51
36_Q	46_K	0.651	0.51
80_V	121_M	0.649	0.51
12_A	64_E	0.644	0.50
38_I	126_A	0.630	0.49
22_E	59_P	0.626	0.49
141_L	166_L	0.625	0.48
95_L	168_A	0.625	0.48
148_A	171_N	0.624	0.48
92_G	156_S	0.621	0.48
73_G	143_N	0.613	0.47
60_E	95_L	0.612	0.47
86_G	91_R	0.612	0.47
24_W	31_W	0.608	0.47
88_Q	140_Y	0.605	0.46
18_S	112_K	0.604	0.46
25_R	59_P	0.601	0.46
15_C	140_Y	0.598	0.45
21_D	127_A	0.597	0.45
30_D	33_A	0.595	0.45
74_K	89_R	0.594	0.45
16_L	74_K	0.594	0.45
147_L	168_A	0.592	0.45
26_A	131_E	0.591	0.45
27_E	31_W	0.586	0.44
86_G	89_R	0.586	0.44
166_L	169_L	0.585	0.44
97_H	139_K	0.584	0.44
14_S	27_E	0.584	0.44
11_S	126_A	0.583	0.44
117_Y	129_E	0.583	0.44
172_I	175_R	0.578	0.43
10_F	81_T	0.578	0.43
94_E	123_E	0.573	0.43
75_K	79_Y	0.571	0.43
43_I	168_A	0.569	0.42
80_V	143_N	0.569	0.42
24_W	72_F	0.568	0.42
84_N	140_Y	0.567	0.42
82_Y	143_N	0.566	0.42
82_Y	91_R	0.566	0.42
100_N	135_S	0.566	0.42
36_Q	56_S	0.564	0.42
45_E	131_E	0.564	0.42
43_I	131_E	0.564	0.42
75_K	88_Q	0.560	0.41
71_D	111_E	0.553	0.41
31_W	51_F	0.551	0.40
95_L	102_Y	0.550	0.40
130_I	163_H	0.549	0.40
118_L	122_L	0.548	0.40
81_T	85_S	0.542	0.39
48_L	52_E	0.539	0.39
25_R	29_P	0.538	0.39
87_E	162_L	0.537	0.39
91_R	98_L	0.534	0.39
142_S	149_S	0.533	0.39
120_L	152_E	0.532	0.38
78_M	123_E	0.531	0.38
8_I	13_L	0.531	0.38
84_N	143_N	0.530	0.38
32_K	39_G	0.530	0.38
59_P	138_E	0.529	0.38
81_T	121_M	0.525	0.38
14_S	66_Y	0.524	0.38
37_E	131_E	0.524	0.38
101_T	112_K	0.521	0.37
78_M	81_T	0.521	0.37
89_R	123_E	0.519	0.37
10_F	105_S	0.518	0.37
64_E	165_L	0.515	0.37
49_H	129_E	0.515	0.37
42_Q	48_L	0.514	0.37
23_E	33_A	0.513	0.36
11_S	167_A	0.510	0.36
14_S	133_A	0.509	0.36
18_S	147_L	0.509	0.36
123_E	159_A	0.509	0.36
72_F	81_T	0.508	0.36
77_N	103_E	0.506	0.36
119_P	123_E	0.503	0.35
120_L	162_L	0.503	0.35
79_Y	117_Y	0.500	0.35
24_W	63_I	0.500	0.35

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
2o9xA	2	0.837	99.9	0.564	Contact Map
1n1cA	2	0.9402	99.9	0.577	Contact Map
1s9uA	1	0.9674	99.9	0.603	Contact Map
2xolA	2	0.788	98.3	0.826	Contact Map
3htkC	1	0.4022	39.4	0.938	Contact Map
4fddA	1	0.8913	25.4	0.943	Contact Map
3w3wA	1	0.9185	18.5	0.947	Contact Map
1u6gC	1	0.5761	15.3	0.949	Contact Map
1vsy5	1	0.7337	14.8	0.949	Contact Map
4g3aA	1	0.587	13.9	0.95	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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