RE_NgoPII - PFAM28P - GREMLIN Contacts

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RE_NgoPII - NgoPII restriction endonuclease

PFAM:	PF09521	Sequences: TNILKAIINIVNNPITELKSYYSGRNRANNMGEALEEYIKDAFAGTFNETDEQKRLEKYSEVFSYLGNQNNPPDIIIKNGDAIEVKKIESKNSALALNSSYPKAKLYSDSPMITKACRNCENWTEKDIIYAVGVVKKNKLKSLWFVYGDCYAADKEIYERIKNTIKDGINSIPDVEFSETKELGRVNKVDPLGITYLRIRGMWGIENPLKVFDYIYEYDENKDFNLFAIINKEKYNSFPNEDREKLENLSNKNLSIKDVKIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	262 (262)
Sequences:	513 (412)
Seq/√Len:	25.5
META:	0.865

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_I	42_A	4.864	1.00
28_A	31_M	4.369	1.00
235_Y	247_E	4.125	1.00
196_Y	204_G	4.124	1.00
184_G	199_I	3.456	1.00
115_K	119_N	3.436	1.00
112_M	162_K	3.419	1.00
151_Y	211_V	3.409	1.00
229_I	259_V	3.379	1.00
232_K	236_N	3.050	1.00
58_K	61_E	2.942	1.00
75_I	83_I	2.644	0.99
131_A	145_F	2.606	0.99
185_R	196_Y	2.554	0.99
105_K	125_E	2.527	0.99
150_C	231_N	2.512	0.99
76_I	120_C	2.470	0.99
57_E	260_K	2.401	0.98
243_R	247_E	2.294	0.98
96_A	204_G	2.281	0.98
187_N	196_Y	2.200	0.97
49_E	54_K	2.198	0.97
185_R	204_G	2.193	0.97
178_S	185_R	2.177	0.97
215_I	259_V	2.121	0.97
110_S	162_K	2.051	0.96
249_L	254_L	2.038	0.96
111_P	181_K	2.032	0.96
178_S	187_N	2.007	0.95
155_K	159_E	2.006	0.95
44_A	62_V	1.974	0.95
89_E	137_K	1.974	0.95
187_N	204_G	1.954	0.95
129_I	147_Y	1.914	0.94
107_Y	155_K	1.888	0.93
22_Y	34_A	1.871	0.93
236_N	243_R	1.837	0.92
101_Y	110_S	1.801	0.92
1_T	62_V	1.799	0.92
65_Y	71_N	1.794	0.92
153_A	191_P	1.785	0.91
81_D	234_K	1.779	0.91
132_V	146_V	1.778	0.91
75_I	85_V	1.741	0.90
46_T	49_E	1.738	0.90
89_E	136_K	1.729	0.90
76_I	157_I	1.726	0.90
1_T	77_I	1.698	0.89
5_K	242_D	1.689	0.89
24_G	30_N	1.679	0.88
37_E	55_R	1.675	0.88
68_N	71_N	1.667	0.88
7_I	226_L	1.641	0.87
65_Y	116_A	1.618	0.87
214_Y	262_K	1.615	0.86
1_T	5_K	1.612	0.86
7_I	224_F	1.595	0.86
240_N	243_R	1.557	0.84
235_Y	243_R	1.556	0.84
150_C	261_I	1.536	0.84
89_E	135_V	1.527	0.83
64_S	126_K	1.527	0.83
39_I	131_A	1.517	0.83
164_T	171_S	1.481	0.81
132_V	212_F	1.480	0.81
95_L	132_V	1.478	0.81
227_F	231_N	1.466	0.80
150_C	230_I	1.445	0.80
68_N	176_E	1.435	0.79
68_N	193_G	1.396	0.77
219_D	222_K	1.393	0.77
188_K	193_G	1.348	0.74
149_D	231_N	1.338	0.74
68_N	188_K	1.333	0.74
83_I	147_Y	1.311	0.72
94_A	206_E	1.295	0.71
33_E	70_N	1.285	0.71
95_L	244_E	1.281	0.71
66_L	75_I	1.280	0.71
151_Y	194_I	1.276	0.70
176_E	188_K	1.272	0.70
104_A	155_K	1.266	0.70
110_S	214_Y	1.264	0.70
94_A	204_G	1.261	0.69
127_D	234_K	1.252	0.69
144_W	150_C	1.245	0.68
8_I	12_N	1.238	0.68
54_K	57_E	1.236	0.68
76_I	114_T	1.235	0.68
180_T	197_L	1.220	0.67
234_K	237_S	1.212	0.66
76_I	79_N	1.201	0.66
144_W	209_L	1.197	0.65
96_A	205_I	1.184	0.64
232_K	258_D	1.169	0.63
69_Q	128_I	1.168	0.63
22_Y	25_R	1.140	0.61
101_Y	159_E	1.140	0.61
144_W	227_F	1.139	0.61
13_N	38_Y	1.133	0.61
112_M	184_G	1.121	0.60
8_I	38_Y	1.102	0.59
240_N	244_E	1.101	0.59
15_I	22_Y	1.096	0.58
164_T	175_V	1.096	0.58
70_N	120_C	1.094	0.58
150_C	155_K	1.092	0.58
125_E	154_D	1.087	0.58
116_A	154_D	1.085	0.57
83_I	129_I	1.082	0.57
76_I	128_I	1.077	0.57
216_Y	227_F	1.065	0.56
5_K	8_I	1.059	0.56
109_D	155_K	1.051	0.55
55_R	59_Y	1.047	0.55
181_K	199_I	1.037	0.54
218_Y	225_N	1.030	0.54
65_Y	68_N	1.029	0.53
88_I	207_N	1.023	0.53
101_Y	112_M	1.023	0.53
194_I	211_V	1.016	0.52
4_L	246_L	1.010	0.52
129_I	144_W	0.997	0.51
168_G	172_I	0.993	0.51
4_L	59_Y	0.993	0.51
47_F	118_R	0.992	0.51
239_P	243_R	0.984	0.50
128_I	152_A	0.982	0.50
60_S	66_L	0.975	0.50
76_I	126_K	0.952	0.48
94_A	118_R	0.952	0.48
104_A	107_Y	0.951	0.48
196_Y	206_E	0.932	0.46
72_P	113_I	0.919	0.45
144_W	166_K	0.916	0.45
37_E	40_K	0.916	0.45
18_L	34_A	0.912	0.45
76_I	138_N	0.910	0.45
166_K	170_N	0.909	0.45
136_K	139_K	0.904	0.44
75_I	162_K	0.904	0.44
61_E	78_K	0.888	0.43
33_E	188_K	0.888	0.43
58_K	62_V	0.887	0.43
246_L	249_L	0.885	0.43
147_Y	238_F	0.885	0.43
164_T	228_A	0.882	0.43
180_T	185_R	0.881	0.43
11_V	38_Y	0.879	0.43
115_K	118_R	0.877	0.42
7_I	63_F	0.875	0.42
3_I	145_F	0.873	0.42
29_N	180_T	0.861	0.41
194_I	205_I	0.855	0.41
88_I	151_Y	0.852	0.41
33_E	69_Q	0.846	0.40
5_K	150_C	0.845	0.40
110_S	150_C	0.845	0.40
31_M	89_E	0.840	0.40
150_C	242_D	0.839	0.40
115_K	156_E	0.836	0.39
165_I	169_I	0.832	0.39
56_L	214_Y	0.829	0.39
161_I	168_G	0.828	0.39
246_L	254_L	0.825	0.39
42_A	47_F	0.816	0.38
160_R	168_G	0.814	0.38
178_S	199_I	0.810	0.38
59_Y	254_L	0.808	0.38
35_L	140_L	0.804	0.37
46_T	52_E	0.801	0.37
13_N	16_T	0.798	0.37
68_N	205_I	0.798	0.37
81_D	127_D	0.791	0.36
139_K	246_L	0.789	0.36
22_Y	41_D	0.788	0.36
16_T	21_Y	0.781	0.36
43_F	83_I	0.779	0.36
144_W	149_D	0.776	0.35
35_L	41_D	0.769	0.35
24_G	34_A	0.767	0.35
94_A	196_Y	0.766	0.35
171_S	233_E	0.765	0.35
164_T	186_V	0.765	0.35
240_N	252_K	0.764	0.35
165_I	172_I	0.763	0.35
43_F	147_Y	0.753	0.34
28_A	33_E	0.753	0.34
182_E	202_M	0.751	0.34
26_N	77_I	0.750	0.34
77_I	83_I	0.748	0.34
92_N	199_I	0.747	0.33
60_S	115_K	0.740	0.33
94_A	116_A	0.739	0.33
66_L	179_E	0.739	0.33
112_M	214_Y	0.738	0.33
106_L	128_I	0.734	0.33
198_R	202_M	0.731	0.32
95_L	143_L	0.726	0.32
165_I	207_N	0.722	0.32
116_A	229_I	0.720	0.32
239_P	257_K	0.719	0.32
30_N	34_A	0.716	0.31
220_E	226_L	0.716	0.31
16_T	20_S	0.715	0.31
144_W	154_D	0.712	0.31
57_E	61_E	0.712	0.31
56_L	60_S	0.710	0.31
160_R	205_I	0.707	0.31
41_D	59_Y	0.707	0.31
18_L	33_E	0.706	0.31
113_I	118_R	0.706	0.31
162_K	170_N	0.706	0.31
65_Y	106_L	0.706	0.31
233_E	252_K	0.703	0.31
70_N	161_I	0.696	0.30
189_V	193_G	0.695	0.30
24_G	144_W	0.694	0.30
166_K	209_L	0.687	0.30
109_D	145_F	0.687	0.30
44_A	59_Y	0.687	0.30
110_S	199_I	0.683	0.29
15_I	21_Y	0.681	0.29
95_L	216_Y	0.680	0.29
10_I	226_L	0.678	0.29
150_C	227_F	0.678	0.29
46_T	51_D	0.678	0.29
80_G	185_R	0.676	0.29
44_A	77_I	0.676	0.29
11_V	254_L	0.674	0.29
248_N	251_N	0.674	0.29
168_G	175_V	0.673	0.29
152_A	240_N	0.671	0.29
32_G	36_E	0.671	0.29
12_N	146_V	0.671	0.29
105_K	261_I	0.670	0.29
193_G	205_I	0.669	0.29
230_I	233_E	0.668	0.29
230_I	238_F	0.667	0.28
4_L	243_R	0.666	0.28
3_I	93_S	0.664	0.28
162_K	177_F	0.662	0.28
85_V	89_E	0.654	0.28
79_N	93_S	0.652	0.28
11_V	14_P	0.652	0.28
31_M	34_A	0.651	0.28
151_Y	205_I	0.649	0.27
145_F	238_F	0.647	0.27
59_Y	83_I	0.645	0.27
246_L	256_I	0.645	0.27
100_S	182_E	0.644	0.27
176_E	193_G	0.643	0.27
19_K	23_S	0.643	0.27
149_D	230_I	0.642	0.27
183_L	201_G	0.642	0.27
66_L	151_Y	0.640	0.27
112_M	181_K	0.640	0.27
176_E	189_V	0.639	0.27
124_T	248_N	0.638	0.27
40_K	89_E	0.638	0.27
18_L	85_V	0.637	0.27
18_L	30_N	0.637	0.27
38_Y	220_E	0.636	0.27
152_A	183_L	0.636	0.27
12_N	248_N	0.632	0.26
6_A	43_F	0.631	0.26
85_V	145_F	0.629	0.26
150_C	226_L	0.629	0.26
45_G	124_T	0.629	0.26
77_I	170_N	0.628	0.26
146_V	259_V	0.627	0.26
226_L	231_N	0.627	0.26
239_P	247_E	0.626	0.26
212_F	230_I	0.626	0.26
124_T	253_N	0.626	0.26
19_K	22_Y	0.625	0.26
41_D	55_R	0.625	0.26
86_K	100_S	0.625	0.26
22_Y	30_N	0.624	0.26
8_I	254_L	0.624	0.26
181_K	253_N	0.624	0.26
14_P	38_Y	0.623	0.26
162_K	168_G	0.620	0.26
245_K	249_L	0.619	0.26
50_T	53_Q	0.619	0.26
178_S	189_V	0.617	0.26
40_K	55_R	0.617	0.26
1_T	44_A	0.617	0.26
7_I	188_K	0.617	0.26
128_I	131_A	0.617	0.26
128_I	147_Y	0.616	0.26
166_K	184_G	0.614	0.25
13_N	47_F	0.614	0.25
146_V	199_I	0.612	0.25
76_I	121_E	0.604	0.25
68_N	96_A	0.603	0.25
38_Y	79_N	0.603	0.25
134_V	207_N	0.602	0.25
88_I	188_K	0.602	0.25
80_G	186_V	0.602	0.25
159_E	212_F	0.599	0.25
21_Y	25_R	0.594	0.24
61_E	157_I	0.593	0.24
6_A	10_I	0.590	0.24
159_E	213_D	0.587	0.24
163_N	252_K	0.587	0.24
9_N	259_V	0.586	0.24
33_E	252_K	0.585	0.24
178_S	196_Y	0.585	0.24
126_K	201_G	0.583	0.24
178_S	181_K	0.582	0.24
104_A	154_D	0.582	0.24
96_A	191_P	0.580	0.24
181_K	196_Y	0.580	0.24
103_K	194_I	0.580	0.24
127_D	147_Y	0.580	0.24
228_A	247_E	0.579	0.24
87_K	182_E	0.577	0.23
86_K	198_R	0.575	0.23
136_K	141_K	0.575	0.23
154_D	217_E	0.567	0.23
76_I	254_L	0.566	0.23
186_V	197_L	0.566	0.23
169_I	184_G	0.564	0.23
136_K	175_V	0.563	0.23
40_K	95_L	0.562	0.23
4_L	8_I	0.562	0.23
26_N	34_A	0.560	0.23
100_S	202_M	0.560	0.23
18_L	106_L	0.559	0.22
138_N	258_D	0.558	0.22
110_S	238_F	0.557	0.22
243_R	254_L	0.556	0.22
230_I	236_N	0.556	0.22
145_F	226_L	0.554	0.22
89_E	196_Y	0.554	0.22
7_I	11_V	0.553	0.22
168_G	193_G	0.553	0.22
162_K	214_Y	0.553	0.22
142_S	209_L	0.552	0.22
42_A	226_L	0.546	0.22
184_G	246_L	0.546	0.22
46_T	59_Y	0.545	0.22
101_Y	147_Y	0.544	0.22
35_L	195_T	0.544	0.22
102_P	190_D	0.544	0.22
12_N	58_K	0.543	0.22
62_V	77_I	0.542	0.22
122_N	179_E	0.541	0.22
5_K	44_A	0.539	0.21
135_V	154_D	0.539	0.21
94_A	169_I	0.536	0.21
20_S	48_N	0.535	0.21
231_N	261_I	0.534	0.21
112_M	168_G	0.534	0.21
88_I	211_V	0.534	0.21
10_I	227_F	0.531	0.21
142_S	212_F	0.531	0.21
29_N	69_Q	0.531	0.21
95_L	206_E	0.530	0.21
168_G	186_V	0.528	0.21
61_E	257_K	0.527	0.21
222_K	255_S	0.527	0.21
33_E	37_E	0.525	0.21
83_I	167_D	0.523	0.21
45_G	245_K	0.523	0.21
240_N	260_K	0.522	0.21
8_I	246_L	0.518	0.20
37_E	59_Y	0.518	0.20
239_P	242_D	0.517	0.20
154_D	221_N	0.516	0.20
79_N	167_D	0.515	0.20
177_F	186_V	0.514	0.20
166_K	210_K	0.513	0.20
182_E	198_R	0.512	0.20
255_S	260_K	0.512	0.20
51_D	54_K	0.512	0.20
138_N	145_F	0.511	0.20
14_P	22_Y	0.510	0.20
118_R	228_A	0.509	0.20
126_K	165_I	0.508	0.20
160_R	206_E	0.508	0.20
17_E	138_N	0.506	0.20
38_Y	59_Y	0.505	0.20
100_S	198_R	0.505	0.20
3_I	215_I	0.503	0.20
209_L	261_I	0.503	0.20
169_I	177_F	0.503	0.20
71_N	172_I	0.502	0.20
113_I	117_C	0.501	0.20
40_K	59_Y	0.500	0.20
47_F	62_V	0.500	0.20
114_T	157_I	0.500	0.20

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
4k0mC	1	0.3053	11.6	0.975	Contact Map
4r8aA	1	0.4008	4.7	0.979	Contact Map
2f5tX	2	0.2366	4.7	0.979	Contact Map
4oavB	2	0.2137	4.2	0.98	Contact Map
4lsbA	2	0.2672	3.5	0.981	Contact Map
2z3qA	1	0.416	3	0.981	Contact Map
2mh8A	1	0.2137	2.7	0.982	Contact Map
2gpvG	1	0.0458	2.3	0.982	Contact Map
2bsqE	2	0.2252	2.2	0.982	Contact Map
1na6A	2	0.5916	2.1	0.983	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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