NFI - HALSA - GREMLIN Contacts

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NFI - Endonuclease V

UniProt:	Q9HS81	Sequences: MRVVRPEFRPAPGLDTDAMASRQRDIAAVADFADDHGLTPERIGLDEPPGEQAALGGATTSGEAAPVVVGVDQAFRDDEVSVSAAVAIRDGAVIERAAGNAPLDVPYVPGLLAFREGSAVIDALSSLSVEPDLLVVDGSGRIHYRQAGLATHVGVLFDVPAVGVAKSLLCGTPAAALADPLPAGTRVAIEADDSMDAPDGAVVGYALQSRQYPTPETRHINPLYVSPGHRVSAGTAADLVEATCTQYKLPAPTRLADQYAADLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	264 (207)
Sequences:	856 (578)
Seq/√Len:	40.2

ECOLI - NFI
BACSU - NFI
HALSA - NFI
SULSO - NFI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_Q	201_A	3.813	1.00
173_P	224_Y	3.481	1.00
147_A	151_T	3.387	1.00
67_V	94_I	3.153	1.00
205_Y	237_A	3.139	1.00
180_P	185_T	3.139	1.00
71_V	120_V	3.110	1.00
135_V	253_T	2.762	1.00
257_D	261_A	2.724	1.00
209_S	223_L	2.624	1.00
96_R	259_Y	2.520	1.00
89_R	243_T	2.461	1.00
133_L	239_L	2.389	1.00
227_P	233_A	2.351	1.00
141_R	151_T	2.285	1.00
49_P	52_Q	2.239	1.00
124_L	157_F	2.195	0.99
182_P	211_Q	2.194	0.99
232_S	235_T	2.174	0.99
209_S	244_C	2.117	0.99
134_L	161_A	2.091	0.99
158_D	230_R	2.073	0.99
202_V	205_Y	2.014	0.99
162_V	240_V	2.007	0.99
95_E	128_S	1.976	0.99
44_G	47_E	1.912	0.99
83_S	88_I	1.901	0.98
124_L	134_L	1.899	0.98
75_F	103_L	1.887	0.98
168_L	206_A	1.883	0.98
139_S	142_I	1.872	0.98
52_Q	56_G	1.861	0.98
141_R	227_P	1.832	0.98
56_G	155_V	1.806	0.98
51_E	55_L	1.788	0.98
52_Q	55_L	1.697	0.97
173_P	176_A	1.669	0.96
42_R	111_L	1.661	0.96
85_A	88_I	1.649	0.96
117_G	153_V	1.608	0.96
74_A	260_A	1.587	0.95
207_L	241_E	1.583	0.95
205_Y	233_A	1.578	0.95
122_D	125_S	1.544	0.94
168_L	189_I	1.502	0.94
206_A	224_Y	1.488	0.93
182_P	185_T	1.487	0.93
136_V	153_V	1.485	0.93
153_V	157_F	1.447	0.92
186_R	205_Y	1.445	0.92
181_L	185_T	1.437	0.92
101_A	122_D	1.422	0.92
53_A	56_G	1.422	0.92
135_V	164_V	1.419	0.92
202_V	233_A	1.372	0.90
60_T	232_S	1.371	0.90
146_Q	198_P	1.369	0.90
101_A	119_A	1.357	0.90
46_D	111_L	1.350	0.89
189_I	206_A	1.343	0.89
105_V	257_D	1.323	0.88
181_L	219_H	1.313	0.88
74_A	261_A	1.307	0.88
165_A	255_L	1.295	0.87
73_Q	120_V	1.295	0.87
58_A	227_P	1.271	0.86
136_V	252_P	1.263	0.86
45_L	49_P	1.247	0.85
186_R	237_A	1.238	0.85
257_D	260_A	1.230	0.84
142_I	204_G	1.229	0.84
139_S	167_S	1.206	0.83
170_C	203_V	1.172	0.81
135_V	243_T	1.166	0.81
76_R	79_E	1.156	0.80
211_Q	220_I	1.154	0.80
135_V	240_V	1.149	0.80
162_V	239_L	1.134	0.79
50_G	53_A	1.130	0.79
173_P	187_V	1.126	0.79
134_L	159_V	1.101	0.77
142_I	189_I	1.089	0.76
48_P	51_E	1.075	0.75
176_A	187_V	1.075	0.75
41_E	44_G	1.068	0.75
175_A	181_L	1.065	0.75
41_E	49_P	1.065	0.75
41_E	45_L	1.064	0.75
73_Q	223_L	1.053	0.74
71_V	153_V	1.053	0.74
139_S	165_A	1.051	0.74
88_I	127_L	1.049	0.74
198_P	203_V	1.043	0.73
47_E	50_G	1.041	0.73
49_P	56_G	1.029	0.72
65_A	239_L	1.019	0.71
110_G	152_H	1.017	0.71
124_L	153_V	1.007	0.70
210_R	244_C	1.005	0.70
210_R	220_I	1.000	0.70
149_L	169_L	0.997	0.70
95_E	129_V	0.997	0.70
165_A	253_T	0.988	0.69
239_L	242_A	0.972	0.68
65_A	132_D	0.970	0.68
82_V	119_A	0.970	0.68
139_S	171_G	0.968	0.67
74_A	257_D	0.957	0.66
252_P	255_L	0.955	0.66
134_L	153_V	0.953	0.66
45_L	48_P	0.947	0.66
227_P	236_A	0.947	0.66
198_P	201_A	0.940	0.65
111_L	142_I	0.939	0.65
56_G	227_P	0.939	0.65
71_V	134_L	0.936	0.65
51_E	54_A	0.932	0.64
251_A	254_R	0.932	0.64
222_P	254_R	0.925	0.64
78_D	87_A	0.924	0.64
124_L	130_E	0.922	0.64
82_V	85_A	0.922	0.64
183_A	246_Q	0.920	0.63
76_R	83_S	0.910	0.62
239_L	252_P	0.906	0.62
188_A	205_Y	0.904	0.62
74_A	82_V	0.904	0.62
97_A	126_S	0.901	0.62
121_I	157_F	0.901	0.62
74_A	83_S	0.900	0.62
40_P	48_P	0.897	0.61
99_G	126_S	0.895	0.61
62_G	65_A	0.888	0.61
139_S	169_L	0.885	0.60
46_D	49_P	0.881	0.60
210_R	252_P	0.880	0.60
151_T	161_A	0.861	0.58
83_S	261_A	0.861	0.58
207_L	244_C	0.859	0.58
71_V	112_L	0.849	0.57
88_I	129_V	0.848	0.57
44_G	49_P	0.845	0.57
75_F	83_S	0.841	0.56
120_V	136_V	0.839	0.56
77_D	80_V	0.837	0.56
53_A	68_V	0.836	0.56
123_A	127_L	0.830	0.55
42_R	46_D	0.825	0.55
59_T	62_G	0.824	0.55
164_V	248_K	0.817	0.54
59_T	235_T	0.808	0.53
209_S	241_E	0.808	0.53
59_T	232_S	0.806	0.53
237_A	241_E	0.800	0.53
48_P	111_L	0.797	0.52
55_L	59_T	0.794	0.52
68_V	71_V	0.794	0.52
172_T	197_A	0.792	0.52
103_L	260_A	0.786	0.51
86_V	124_L	0.784	0.51
111_L	155_V	0.783	0.51
82_V	103_L	0.782	0.51
79_E	82_V	0.778	0.51
79_E	83_S	0.775	0.50
87_A	93_V	0.771	0.50
248_K	254_R	0.767	0.50
241_E	244_C	0.758	0.49
49_P	55_L	0.747	0.48
69_V	167_S	0.747	0.48
164_V	260_A	0.746	0.48
73_Q	117_G	0.727	0.46
70_G	115_R	0.712	0.45
120_V	153_V	0.712	0.45
44_G	54_A	0.712	0.45
205_Y	227_P	0.711	0.44
48_P	52_Q	0.709	0.44
137_D	166_K	0.708	0.44
224_Y	234_G	0.706	0.44
255_L	258_Q	0.704	0.44
62_G	234_G	0.696	0.43
68_V	92_A	0.692	0.43
126_S	156_L	0.691	0.43
94_I	247_Y	0.691	0.43
65_A	167_S	0.689	0.43
82_V	121_I	0.688	0.42
47_E	54_A	0.687	0.42
65_A	231_V	0.678	0.42
184_G	241_E	0.677	0.41
161_A	175_A	0.675	0.41
202_V	225_V	0.673	0.41
133_L	249_L	0.672	0.41
71_V	124_L	0.669	0.41
57_G	62_G	0.668	0.41
160_P	236_A	0.665	0.40
259_Y	262_D	0.665	0.40
84_A	87_A	0.665	0.40
223_L	240_V	0.661	0.40
60_T	235_T	0.660	0.40
165_A	203_V	0.659	0.40
180_P	187_V	0.659	0.40
48_P	56_G	0.655	0.39
117_G	252_P	0.655	0.39
57_G	61_S	0.654	0.39
207_L	237_A	0.653	0.39
98_A	259_Y	0.650	0.39
245_T	252_P	0.650	0.39
118_S	208_Q	0.646	0.39
42_R	45_L	0.646	0.39
67_V	132_D	0.640	0.38
39_T	221_N	0.639	0.38
155_V	229_H	0.638	0.38
164_V	209_S	0.638	0.38
113_A	260_A	0.637	0.38
180_P	241_E	0.636	0.38
168_L	205_Y	0.633	0.38
69_V	132_D	0.633	0.38
154_G	229_H	0.631	0.37
99_G	122_D	0.630	0.37
240_V	248_K	0.628	0.37
113_A	139_S	0.627	0.37
72_D	166_K	0.624	0.37
208_Q	220_I	0.619	0.36
133_L	162_V	0.619	0.36
66_P	129_V	0.618	0.36
135_V	157_F	0.617	0.36
46_D	50_G	0.615	0.36
61_S	232_S	0.614	0.36
86_V	93_V	0.612	0.36
49_P	53_A	0.604	0.35
113_A	261_A	0.598	0.35
141_R	147_A	0.595	0.34
131_P	184_G	0.592	0.34
56_G	61_S	0.590	0.34
75_F	261_A	0.590	0.34
113_A	199_D	0.589	0.34
51_E	225_V	0.589	0.34
123_A	210_R	0.589	0.34
74_A	258_Q	0.588	0.34
258_Q	262_D	0.588	0.34
222_P	248_K	0.588	0.34
227_P	230_R	0.586	0.34
73_Q	149_L	0.582	0.33
83_S	260_A	0.582	0.33
76_R	100_N	0.581	0.33
133_L	257_D	0.580	0.33
92_A	175_A	0.580	0.33
79_E	202_V	0.576	0.33
225_V	231_V	0.576	0.33
135_V	158_D	0.574	0.33
107_Y	112_L	0.573	0.33
101_A	232_S	0.572	0.32
208_Q	233_A	0.572	0.32
71_V	161_A	0.570	0.32
152_H	156_L	0.569	0.32
67_V	129_V	0.568	0.32
43_I	46_D	0.567	0.32
77_D	159_V	0.565	0.32
73_Q	80_V	0.564	0.32
99_G	123_A	0.563	0.32
127_L	131_P	0.560	0.32
85_A	260_A	0.557	0.31
95_E	126_S	0.557	0.31
83_S	119_A	0.556	0.31
105_V	261_A	0.555	0.31
153_V	159_V	0.553	0.31
170_C	198_P	0.553	0.31
184_G	220_I	0.552	0.31
164_V	261_A	0.551	0.31
81_S	85_A	0.551	0.31
103_L	119_A	0.550	0.31
122_D	126_S	0.549	0.31
167_S	210_R	0.547	0.30
107_Y	115_R	0.547	0.30
48_P	55_L	0.547	0.30
135_V	162_V	0.546	0.30
76_R	82_V	0.545	0.30
207_L	231_V	0.544	0.30
56_G	60_T	0.540	0.30
105_V	108_V	0.539	0.30
48_P	53_A	0.538	0.30
85_A	98_A	0.537	0.30
131_P	152_H	0.534	0.29
180_P	207_L	0.532	0.29
94_I	161_A	0.531	0.29
131_P	248_K	0.529	0.29
70_G	253_T	0.527	0.29
255_L	259_Y	0.524	0.29
71_V	77_D	0.523	0.29
110_G	114_F	0.522	0.29
154_G	251_A	0.522	0.29
112_L	165_A	0.521	0.29
120_V	124_L	0.520	0.28
123_A	249_L	0.519	0.28
74_A	253_T	0.519	0.28
113_A	152_H	0.517	0.28
117_G	159_V	0.517	0.28
73_Q	249_L	0.516	0.28
66_P	133_L	0.516	0.28
236_A	244_C	0.516	0.28
83_S	86_V	0.516	0.28
57_G	60_T	0.514	0.28
189_I	224_Y	0.509	0.28
234_G	238_D	0.508	0.28
160_P	257_D	0.506	0.27
79_E	112_L	0.504	0.27
183_A	238_D	0.504	0.27
44_G	55_L	0.502	0.27
45_L	52_Q	0.501	0.27
121_I	156_L	0.500	0.27
119_A	188_A	0.500	0.27

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
3ga2A	1	0.8371	100	0.283	Contact Map
4nspA	1	0.822	100	0.305	Contact Map
2w36A	1	0.8258	100	0.374	Contact Map
3gocA	2	0.822	100	0.406	Contact Map
2qh9A	2	0.6477	100	0.527	Contact Map
2nrrA	1	0.5189	96.7	0.923	Contact Map
2ygkA	2	0.8598	94.4	0.934	Contact Map
3c65A	1	0.5417	94	0.936	Contact Map
2nrtA	1	0.7386	91.6	0.94	Contact Map
1yvuA	1	0.8144	70.6	0.954	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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