NARI - ECOLI - GREMLIN Contacts

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NARI - Respiratory nitrate reductase 1 gamma chain

UniProt:	P11350	Sequences: MQFLNMFFFDIYPYIAGAVFLIGSWLRYDYGQYTWRAASSQMLDRKGMNLASNLFHIGILGIFVGHFFGMLTPHWMYEAWLPIEVKQKMAMFAGGASGVLCLIGGVLLLKRRLFSPRVRATTTGADILILSLLVIQCALGLLTIPFSAQHMDGSEMMKLVGWAQSVVTFHGGASQHLDGVAFIFRLHLVLGMTLFLLFPFSRLIHIWSVPVEYLTRKYQLVRARH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10640
Length:	225 (218)
Sequences:	1075 (652)
Seq/√Len:	44.1

ECOLI - NARI NARV
BACSU - NARI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_A	107_L	5.210	1.00
98_G	141_L	3.174	1.00
19_V	196_L	3.158	1.00
7_F	15_I	2.938	1.00
19_V	200_F	2.880	1.00
128_L	197_L	2.741	1.00
136_Q	191_G	2.702	1.00
91_M	148_A	2.673	1.00
194_L	203_L	2.639	1.00
182_F	186_L	2.577	1.00
20_F	24_S	2.552	1.00
119_R	127_I	2.457	1.00
75_W	79_A	2.402	1.00
12_Y	193_T	2.388	1.00
113_L	119_R	2.371	1.00
77_Y	83_I	2.350	1.00
82_P	85_V	2.347	1.00
58_G	104_G	2.274	1.00
59_I	101_C	2.195	1.00
74_H	154_S	2.193	1.00
18_A	22_I	2.182	1.00
125_A	197_L	2.138	1.00
54_L	103_I	2.126	1.00
132_L	197_L	2.027	0.99
62_I	101_C	1.942	0.99
8_F	189_V	1.877	0.99
61_G	97_S	1.841	0.99
136_Q	190_L	1.817	0.98
24_S	207_W	1.810	0.98
188_L	192_M	1.795	0.98
62_I	98_G	1.741	0.98
105_G	134_V	1.710	0.98
54_L	100_L	1.709	0.98
17_G	166_V	1.696	0.98
113_L	127_I	1.681	0.97
35_W	208_S	1.680	0.97
92_F	96_A	1.630	0.97
85_V	89_M	1.616	0.97
102_L	134_V	1.596	0.97
60_L	64_V	1.589	0.96
198_F	206_I	1.588	0.96
142_L	146_F	1.573	0.96
89_M	93_A	1.543	0.96
124_G	128_L	1.542	0.96
19_V	22_I	1.528	0.96
109_L	127_I	1.521	0.95
5_N	178_D	1.516	0.95
22_I	25_W	1.506	0.95
44_D	115_S	1.499	0.95
212_E	215_T	1.497	0.95
76_M	80_W	1.474	0.95
84_E	88_K	1.452	0.94
41_Q	45_R	1.432	0.94
88_K	92_F	1.417	0.93
96_A	100_L	1.399	0.93
110_K	114_F	1.394	0.93
106_V	110_K	1.376	0.92
61_G	93_A	1.361	0.92
76_M	79_A	1.344	0.91
81_L	85_V	1.341	0.91
74_H	77_Y	1.316	0.90
102_L	138_A	1.310	0.90
132_L	135_I	1.309	0.90
44_D	48_M	1.305	0.90
197_L	201_S	1.304	0.90
43_L	129_I	1.295	0.90
109_L	113_L	1.272	0.89
101_C	137_C	1.272	0.89
155_E	160_V	1.271	0.89
163_A	167_V	1.268	0.89
16_A	192_M	1.268	0.89
115_S	118_V	1.265	0.89
77_Y	80_W	1.255	0.88
74_H	83_I	1.253	0.88
43_L	117_R	1.253	0.88
66_H	111_R	1.245	0.88
11_I	171_G	1.238	0.87
155_E	158_K	1.237	0.87
99_V	103_I	1.232	0.87
106_V	134_V	1.231	0.87
189_V	193_T	1.207	0.86
16_A	196_L	1.193	0.85
24_S	198_F	1.191	0.85
5_N	185_R	1.189	0.85
74_H	157_M	1.186	0.85
46_K	210_P	1.170	0.84
132_L	136_Q	1.169	0.84
109_L	132_L	1.165	0.84
79_A	82_P	1.156	0.84
155_E	181_A	1.155	0.84
38_A	123_T	1.155	0.84
47_G	110_K	1.142	0.83
40_S	43_L	1.141	0.83
86_K	156_M	1.134	0.82
7_F	85_V	1.119	0.82
20_F	198_F	1.108	0.81
90_A	95_G	1.108	0.81
212_E	217_K	1.098	0.80
14_Y	171_G	1.089	0.80
26_L	31_G	1.083	0.79
47_G	51_A	1.080	0.79
88_K	151_M	1.078	0.79
132_L	190_L	1.074	0.79
105_G	109_L	1.064	0.78
139_L	186_L	1.058	0.78
24_S	204_I	1.058	0.78
68_F	92_F	1.057	0.78
202_R	213_Y	1.052	0.77
74_H	160_V	1.049	0.77
66_H	187_H	1.048	0.77
20_F	207_W	1.038	0.76
129_I	197_L	1.027	0.76
77_Y	154_S	1.021	0.75
112_R	205_H	1.006	0.74
143_T	159_L	0.991	0.73
31_G	218_Y	0.987	0.73
122_T	130_L	0.976	0.72
44_D	118_V	0.965	0.71
28_Y	83_I	0.964	0.71
64_V	68_F	0.951	0.70
173_A	176_H	0.948	0.70
111_R	187_H	0.945	0.69
122_T	127_I	0.941	0.69
139_L	190_L	0.934	0.68
84_E	151_M	0.933	0.68
109_L	134_V	0.931	0.68
26_L	57_I	0.931	0.68
131_S	135_I	0.931	0.68
169_F	172_G	0.928	0.68
193_T	211_V	0.924	0.68
59_I	64_V	0.912	0.67
50_L	54_L	0.904	0.66
134_V	138_A	0.896	0.65
119_R	122_T	0.893	0.65
127_I	131_S	0.892	0.65
38_A	217_K	0.887	0.64
75_W	160_V	0.887	0.64
114_F	186_L	0.884	0.64
83_I	160_V	0.879	0.64
153_G	184_F	0.871	0.63
61_G	100_L	0.867	0.63
65_G	69_G	0.864	0.62
76_M	160_V	0.863	0.62
63_F	135_I	0.863	0.62
56_H	205_H	0.855	0.61
86_K	163_A	0.854	0.61
11_I	169_F	0.852	0.61
32_Q	35_W	0.849	0.61
113_L	116_P	0.847	0.61
135_I	190_L	0.842	0.60
6_M	11_I	0.838	0.60
75_W	78_E	0.837	0.60
158_K	161_G	0.835	0.60
22_I	26_L	0.832	0.59
85_V	179_G	0.828	0.59
142_L	183_I	0.827	0.59
217_K	223_A	0.821	0.58
11_I	22_I	0.818	0.58
10_D	173_A	0.812	0.57
107_L	110_K	0.807	0.57
48_M	51_A	0.794	0.56
57_I	61_G	0.792	0.56
103_I	124_G	0.788	0.55
7_F	11_I	0.784	0.55
20_F	206_I	0.781	0.55
64_V	67_F	0.775	0.54
172_G	176_H	0.773	0.54
18_A	169_F	0.771	0.54
204_I	208_S	0.770	0.53
15_I	18_A	0.766	0.53
134_V	209_V	0.764	0.53
21_L	207_W	0.760	0.53
53_N	130_L	0.759	0.52
56_H	112_R	0.758	0.52
18_A	63_F	0.754	0.52
102_L	137_C	0.750	0.52
140_G	187_H	0.749	0.51
170_H	178_D	0.747	0.51
117_R	121_T	0.746	0.51
159_L	180_V	0.737	0.50
61_G	75_W	0.735	0.50
148_A	153_G	0.734	0.50
61_G	64_V	0.733	0.50
109_L	194_L	0.733	0.50
11_I	18_A	0.721	0.49
72_T	86_K	0.720	0.49
83_I	152_D	0.717	0.48
31_G	217_K	0.716	0.48
165_S	176_H	0.712	0.48
8_F	177_L	0.712	0.48
105_G	138_A	0.710	0.48
15_I	107_L	0.708	0.48
165_S	170_H	0.708	0.48
115_S	212_E	0.707	0.47
67_F	171_G	0.706	0.47
94_G	162_W	0.704	0.47
116_P	120_A	0.700	0.47
154_S	157_M	0.698	0.47
40_S	202_R	0.696	0.46
155_E	184_F	0.696	0.46
35_W	204_I	0.692	0.46
39_S	43_L	0.690	0.46
114_F	118_V	0.689	0.46
21_L	25_W	0.689	0.46
215_T	223_A	0.689	0.46
124_G	131_S	0.686	0.45
79_A	83_I	0.685	0.45
105_G	133_L	0.684	0.45
60_L	63_F	0.683	0.45
122_T	196_L	0.669	0.44
33_Y	218_Y	0.667	0.44
49_N	212_E	0.666	0.44
51_A	54_L	0.665	0.43
48_M	53_N	0.661	0.43
125_A	201_S	0.660	0.43
24_S	206_I	0.658	0.43
83_I	157_M	0.654	0.42
51_A	93_A	0.653	0.42
177_L	180_V	0.651	0.42
214_L	217_K	0.647	0.42
40_S	94_G	0.646	0.42
71_L	163_A	0.644	0.41
209_V	212_E	0.643	0.41
71_L	167_V	0.641	0.41
59_I	206_I	0.637	0.41
75_W	80_W	0.637	0.41
52_S	90_A	0.636	0.41
147_S	166_V	0.635	0.41
97_S	218_Y	0.634	0.41
28_Y	35_W	0.628	0.40
25_W	173_A	0.627	0.40
17_G	81_L	0.627	0.40
28_Y	31_G	0.624	0.40
108_L	112_R	0.624	0.40
25_W	169_F	0.623	0.40
194_L	214_L	0.620	0.39
90_A	144_I	0.618	0.39
34_T	129_I	0.613	0.39
165_S	172_G	0.608	0.38
32_Q	43_L	0.606	0.38
66_H	73_P	0.604	0.38
114_F	146_F	0.602	0.38
48_M	184_F	0.600	0.37
5_N	195_F	0.599	0.37
96_A	214_L	0.598	0.37
69_G	104_G	0.596	0.37
45_R	218_Y	0.595	0.37
74_H	137_C	0.592	0.37
112_R	122_T	0.592	0.37
156_M	221_V	0.591	0.37
48_M	108_L	0.587	0.36
111_R	205_H	0.585	0.36
12_Y	16_A	0.584	0.36
213_Y	216_R	0.584	0.36
103_I	106_V	0.580	0.36
158_K	179_G	0.579	0.36
81_L	89_M	0.578	0.35
57_I	60_L	0.577	0.35
100_L	104_G	0.577	0.35
18_A	99_V	0.577	0.35
61_G	223_A	0.576	0.35
29_D	33_Y	0.576	0.35
37_A	43_L	0.576	0.35
67_F	71_L	0.573	0.35
83_I	154_S	0.573	0.35
21_L	168_T	0.566	0.34
34_T	219_Q	0.565	0.34
187_H	205_H	0.565	0.34
5_N	139_L	0.564	0.34
10_D	165_S	0.564	0.34
26_L	29_D	0.564	0.34
63_F	166_V	0.562	0.34
126_D	202_R	0.561	0.34
87_Q	221_V	0.561	0.34
38_A	42_M	0.561	0.34
117_R	120_A	0.561	0.34
139_L	166_V	0.561	0.34
106_V	146_F	0.555	0.33
84_E	152_D	0.555	0.33
43_L	121_T	0.552	0.33
92_F	95_G	0.552	0.33
125_A	166_V	0.552	0.33
123_T	131_S	0.552	0.33
68_F	201_S	0.550	0.33
125_A	128_L	0.547	0.33
55_F	65_G	0.547	0.33
22_I	208_S	0.547	0.33
66_H	126_D	0.545	0.33
84_E	105_G	0.545	0.33
72_T	164_Q	0.542	0.32
59_I	192_M	0.539	0.32
63_F	96_A	0.538	0.32
53_N	57_I	0.536	0.32
95_G	152_D	0.536	0.32
12_Y	196_L	0.534	0.32
98_G	102_L	0.533	0.32
123_T	127_I	0.533	0.32
180_V	188_L	0.532	0.31
109_L	125_A	0.531	0.31
59_I	63_F	0.529	0.31
95_G	103_I	0.529	0.31
37_A	141_L	0.528	0.31
18_A	178_D	0.527	0.31
153_G	181_A	0.527	0.31
147_S	150_H	0.526	0.31
12_Y	189_V	0.524	0.31
117_R	207_W	0.524	0.31
43_L	207_W	0.519	0.30
179_G	185_R	0.516	0.30
155_E	221_V	0.515	0.30
66_H	140_G	0.514	0.30
127_I	220_L	0.512	0.30
129_I	194_L	0.511	0.30
33_Y	39_S	0.511	0.30
23_G	126_D	0.511	0.30
69_G	94_G	0.510	0.30
28_Y	218_Y	0.510	0.30
10_D	24_S	0.505	0.29
21_L	182_F	0.505	0.29
145_P	186_L	0.505	0.29
85_V	93_A	0.504	0.29
127_I	201_S	0.501	0.29
38_A	177_L	0.501	0.29
61_G	84_E	0.500	0.29
37_A	45_R	0.500	0.29
68_F	72_T	0.500	0.29
26_L	33_Y	0.500	0.29

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
1q16C	2	0.9911	100	0.323	Contact Map
2l2tA	2	0.1822	33.1	0.953	Contact Map
2wswA	3	0.8978	15.3	0.96	Contact Map
2ks1B	1	0.1822	11.7	0.962	Contact Map
2kluA	1	0.2311	10.3	0.963	Contact Map
4c7rA	3	0.9022	8.2	0.964	Contact Map
2m20A	2	0.2533	8.2	0.964	Contact Map
2l9uA	2	0.1778	4.9	0.968	Contact Map
2a65A	2	0.5022	4.1	0.969	Contact Map
1iijA	1	0.1422	3.3	0.97	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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