NA37 - PFAM28P - GREMLIN Contacts

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NA37 - 37-kD nucleoid-associated bacterial protein

PFAM:	PF04245	Sequences: IIHKVGNKSDEEVLSELELLDDELVELLLKYFLKPFKSKEGKYGRFSEHSEDLVYNYLSEIFEDPDNDFVEFSKNIAKHLYEQSNHPNLIKGGELYVAYFEDCGVDAIGIFKSENKETFLKNLEIEEEKGININKLDKCLIINLEKETNPDEGYYVSFIDKRNKGEDASYWFDDFLGCKPREDSKEQTKNLLKACKDFVKEELLEKAEQIDLLNRSVDYFKENDEFDEEIFLEEVAEEVFEDEPEAKDFFQEEEDYELPDEFPISKKKALKKQKRVIKLDINLSINFDAYDRIIYDDGTDSLIIKGIPKNLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	312 (302)
Sequences:	4260 (3181)
Seq/√Len:	183.1
META:	0.666

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
247_K	251_Q	5.131	1.00
1_I	70_V	4.436	1.00
54_V	76_I	4.014	1.00
247_K	250_F	3.774	1.00
95_L	110_I	3.718	1.00
236_A	239_V	3.606	1.00
99_Y	106_D	3.159	1.00
70_V	74_K	3.080	1.00
49_H	52_D	2.752	1.00
231_F	235_V	2.751	1.00
77_A	95_L	2.745	1.00
237_E	240_F	2.625	1.00
121_K	128_E	2.539	1.00
68_D	71_E	2.511	1.00
240_F	243_E	2.449	1.00
230_I	235_V	2.427	1.00
59_S	146_K	2.368	1.00
248_D	251_Q	2.359	1.00
49_H	53_L	2.330	1.00
73_S	97_V	2.307	1.00
63_E	146_K	2.304	1.00
156_V	178_C	2.273	1.00
249_F	253_E	2.242	1.00
61_I	99_Y	2.185	1.00
140_L	143_N	2.171	1.00
218_D	222_E	2.143	1.00
223_N	234_E	2.084	1.00
236_A	240_F	2.066	1.00
281_I	286_N	2.007	1.00
61_I	72_F	1.974	1.00
80_L	175_F	1.974	1.00
101_E	106_D	1.970	1.00
250_F	253_E	1.940	1.00
75_N	78_K	1.928	1.00
105_V	143_N	1.855	1.00
72_F	75_N	1.840	1.00
283_L	286_N	1.837	1.00
277_I	285_I	1.822	1.00
48_E	51_E	1.802	1.00
100_F	109_G	1.801	1.00
243_E	246_A	1.754	1.00
74_K	78_K	1.741	1.00
249_F	252_E	1.702	1.00
282_N	286_N	1.680	1.00
248_D	252_E	1.660	1.00
76_I	95_L	1.611	1.00
281_I	285_I	1.606	1.00
64_D	68_D	1.589	1.00
280_D	285_I	1.586	1.00
277_I	280_D	1.561	1.00
204_L	209_Q	1.560	1.00
57_Y	75_N	1.533	1.00
275_R	286_N	1.528	1.00
125_I	130_G	1.515	1.00
275_R	280_D	1.509	1.00
275_R	281_I	1.482	1.00
281_I	284_S	1.482	1.00
57_Y	72_F	1.473	1.00
237_E	243_E	1.454	1.00
277_I	281_I	1.443	1.00
28_L	32_F	1.442	1.00
279_L	282_N	1.438	1.00
279_L	287_F	1.419	1.00
228_E	232_L	1.410	1.00
273_Q	279_L	1.406	1.00
196_K	213_L	1.401	1.00
239_V	243_E	1.399	1.00
48_E	52_D	1.387	1.00
226_F	231_F	1.384	1.00
158_F	172_F	1.375	1.00
9_S	12_E	1.374	1.00
226_F	230_I	1.366	1.00
58_L	108_I	1.358	1.00
238_E	242_D	1.355	1.00
16_E	74_K	1.346	1.00
112_K	138_K	1.343	1.00
47_S	179_K	1.343	1.00
282_N	285_I	1.327	1.00
240_F	244_P	1.322	1.00
275_R	279_L	1.309	1.00
191_L	195_C	1.307	1.00
83_Q	174_D	1.307	1.00
139_C	142_I	1.302	1.00
139_C	143_N	1.290	1.00
295_Y	299_T	1.290	1.00
65_P	69_F	1.264	1.00
277_I	287_F	1.260	1.00
60_E	72_F	1.254	1.00
279_L	284_S	1.251	1.00
279_L	283_L	1.243	1.00
283_L	288_D	1.241	1.00
45_R	48_E	1.238	1.00
238_E	243_E	1.226	1.00
56_N	60_E	1.226	1.00
10_D	13_V	1.220	1.00
283_L	287_F	1.213	1.00
78_K	82_E	1.213	1.00
12_E	15_S	1.202	1.00
60_E	75_N	1.194	1.00
275_R	282_N	1.189	1.00
304_I	307_I	1.183	1.00
239_V	242_D	1.181	1.00
273_Q	280_D	1.181	1.00
273_Q	281_I	1.180	1.00
145_E	181_R	1.177	1.00
282_N	287_F	1.174	1.00
242_D	245_E	1.165	1.00
271_K	274_K	1.164	1.00
17_L	20_L	1.158	1.00
280_D	283_L	1.154	1.00
192_L	217_V	1.148	1.00
279_L	285_I	1.147	1.00
280_D	286_N	1.147	1.00
158_F	178_C	1.146	1.00
279_L	286_N	1.145	1.00
71_E	75_N	1.137	1.00
275_R	287_F	1.133	1.00
219_Y	223_N	1.123	1.00
275_R	284_S	1.120	1.00
270_L	279_L	1.113	1.00
223_N	230_I	1.110	1.00
275_R	283_L	1.106	1.00
270_L	273_Q	1.099	1.00
280_D	284_S	1.097	1.00
59_S	63_E	1.094	1.00
1_I	69_F	1.093	1.00
106_D	143_N	1.092	1.00
76_I	97_V	1.087	1.00
236_A	243_E	1.087	1.00
96_Y	113_S	1.086	1.00
195_C	199_V	1.083	1.00
284_S	287_F	1.082	1.00
76_I	110_I	1.078	1.00
61_I	108_I	1.073	1.00
169_S	172_F	1.071	1.00
194_A	197_D	1.071	1.00
61_I	64_D	1.071	1.00
284_S	288_D	1.065	1.00
17_L	21_D	1.062	1.00
281_I	296_D	1.055	1.00
294_I	297_D	1.055	1.00
216_S	219_Y	1.052	1.00
278_K	283_L	1.029	1.00
282_N	288_D	1.029	1.00
242_D	246_A	1.025	1.00
239_V	244_P	1.025	1.00
277_I	286_N	1.024	1.00
273_Q	285_I	1.022	1.00
68_D	72_F	1.019	0.99
57_Y	79_H	1.015	0.99
213_L	216_S	1.015	0.99
133_I	136_L	1.015	0.99
27_L	31_Y	1.014	0.99
187_Q	190_N	1.014	0.99
79_H	83_Q	1.009	0.99
48_E	53_L	1.004	0.99
171_W	175_F	1.001	0.99
55_Y	59_S	1.001	0.99
226_F	235_V	0.999	0.99
189_K	193_K	0.991	0.99
295_Y	300_D	0.991	0.99
65_P	68_D	0.990	0.99
277_I	282_N	0.987	0.99
183_D	186_E	0.980	0.99
275_R	278_K	0.978	0.99
9_S	15_S	0.972	0.99
60_E	65_P	0.971	0.99
280_D	287_F	0.970	0.99
237_E	242_D	0.969	0.99
235_V	240_F	0.965	0.99
241_E	244_P	0.965	0.99
72_F	76_I	0.961	0.99
182_E	187_Q	0.961	0.99
79_H	82_E	0.952	0.99
76_I	175_F	0.945	0.99
279_L	289_A	0.944	0.99
46_F	156_V	0.943	0.99
28_L	96_Y	0.941	0.99
224_D	230_I	0.935	0.99
231_F	261_E	0.928	0.99
158_F	162_R	0.924	0.99
90_I	171_W	0.920	0.99
98_A	109_G	0.918	0.99
145_E	152_E	0.917	0.99
28_L	35_P	0.916	0.99
103_C	142_I	0.907	0.99
10_D	15_S	0.905	0.99
277_I	283_L	0.903	0.99
262_F	265_S	0.903	0.99
254_E	257_E	0.902	0.99
97_V	110_I	0.901	0.99
269_A	275_R	0.898	0.99
285_I	302_L	0.896	0.99
152_E	155_Y	0.895	0.99
50_S	53_L	0.895	0.99
168_A	172_F	0.894	0.99
270_L	287_F	0.889	0.99
211_D	215_R	0.889	0.99
164_K	167_D	0.889	0.99
191_L	239_V	0.882	0.99
253_E	256_Y	0.879	0.99
7_N	14_L	0.873	0.98
59_S	147_E	0.872	0.98
71_E	74_K	0.871	0.98
229_E	261_E	0.870	0.98
184_S	265_S	0.868	0.98
114_E	138_K	0.864	0.98
51_E	57_Y	0.863	0.98
272_K	286_N	0.863	0.98
296_D	299_T	0.862	0.98
251_Q	254_E	0.861	0.98
9_S	13_V	0.859	0.98
113_S	133_I	0.856	0.98
64_D	99_Y	0.853	0.98
273_Q	284_S	0.853	0.98
281_I	287_F	0.846	0.98
270_L	280_D	0.843	0.98
58_L	141_I	0.841	0.98
236_A	241_E	0.831	0.98
281_I	288_D	0.829	0.98
269_A	272_K	0.826	0.98
18_E	70_V	0.820	0.98
208_E	211_D	0.818	0.98
235_V	243_E	0.812	0.97
228_E	235_V	0.811	0.97
160_D	168_A	0.810	0.97
225_E	263_P	0.808	0.97
207_A	210_I	0.800	0.97
274_K	277_I	0.800	0.97
73_S	77_A	0.800	0.97
138_K	160_D	0.800	0.97
46_F	49_H	0.792	0.97
247_K	252_E	0.790	0.97
278_K	284_S	0.787	0.97
272_K	283_L	0.784	0.97
274_K	284_S	0.783	0.97
202_E	205_E	0.781	0.97
26_E	30_K	0.780	0.97
278_K	286_N	0.777	0.97
70_V	73_S	0.777	0.97
154_Y	160_D	0.775	0.97
57_Y	60_E	0.772	0.97
14_L	77_A	0.769	0.97
269_A	287_F	0.765	0.96
103_C	107_A	0.763	0.96
199_V	212_L	0.762	0.96
81_Y	85_N	0.761	0.96
32_F	109_G	0.760	0.96
138_K	175_F	0.759	0.96
172_F	178_C	0.759	0.96
274_K	280_D	0.759	0.96
59_S	154_Y	0.759	0.96
6_G	12_E	0.753	0.96
93_G	112_K	0.753	0.96
23_E	26_E	0.751	0.96
293_I	298_G	0.749	0.96
239_V	246_A	0.749	0.96
247_K	253_E	0.749	0.96
224_D	231_F	0.748	0.96
162_R	166_E	0.743	0.96
207_A	211_D	0.740	0.96
194_A	256_Y	0.739	0.96
210_I	214_N	0.735	0.96
214_N	218_D	0.733	0.95
293_I	303_I	0.732	0.95
80_L	84_S	0.731	0.95
169_S	173_D	0.728	0.95
94_E	113_S	0.728	0.95
137_D	140_L	0.728	0.95
278_K	281_I	0.727	0.95
275_R	285_I	0.726	0.95
191_L	228_E	0.724	0.95
190_N	193_K	0.721	0.95
269_A	283_L	0.716	0.95
272_K	281_I	0.714	0.95
286_N	289_A	0.713	0.95
126_E	129_K	0.712	0.95
215_R	218_D	0.710	0.95
47_S	53_L	0.709	0.95
43_Y	157_S	0.708	0.95
276_V	281_I	0.708	0.95
269_A	284_S	0.702	0.94
261_E	265_S	0.702	0.94
192_L	220_F	0.702	0.94
272_K	284_S	0.701	0.94
286_N	290_Y	0.700	0.94
142_I	157_S	0.692	0.94
227_D	230_I	0.692	0.94
91_K	171_W	0.689	0.94
8_K	82_E	0.689	0.94
273_Q	278_K	0.687	0.94
116_K	119_F	0.687	0.94
114_E	137_D	0.686	0.94
133_I	137_D	0.684	0.93
295_Y	302_L	0.684	0.93
232_L	258_L	0.684	0.93
270_L	284_S	0.683	0.93
5_V	14_L	0.681	0.93
299_T	303_I	0.680	0.93
8_K	13_V	0.679	0.93
269_A	281_I	0.678	0.93
84_S	87_P	0.678	0.93
193_K	197_D	0.673	0.93
267_K	273_Q	0.671	0.93
274_K	286_N	0.670	0.93
233_E	247_K	0.669	0.93
191_L	194_A	0.667	0.93
272_K	287_F	0.666	0.93
25_V	29_L	0.665	0.92
231_F	240_F	0.664	0.92
94_E	121_K	0.661	0.92
9_S	14_L	0.659	0.92
80_L	95_L	0.657	0.92
184_S	263_P	0.656	0.92
195_C	212_L	0.654	0.92
4_K	38_S	0.654	0.92
69_F	73_S	0.653	0.92
195_C	250_F	0.651	0.92
147_E	152_E	0.649	0.92
269_A	273_Q	0.648	0.92
278_K	288_D	0.648	0.92
11_E	14_L	0.646	0.91
12_E	81_Y	0.645	0.91
299_T	302_L	0.644	0.91
47_S	50_S	0.642	0.91
129_K	132_N	0.641	0.91
187_Q	259_P	0.641	0.91
283_L	290_Y	0.641	0.91
83_Q	86_H	0.640	0.91
237_E	241_E	0.639	0.91
227_D	261_E	0.637	0.91
283_L	289_A	0.637	0.91
230_I	233_E	0.636	0.91
211_D	214_N	0.635	0.91
45_R	49_H	0.633	0.91
237_E	247_K	0.633	0.91
270_L	281_I	0.628	0.90
273_Q	286_N	0.627	0.90
197_D	201_E	0.627	0.90
143_N	153_G	0.627	0.90
229_E	232_L	0.625	0.90
236_A	244_P	0.623	0.90
182_E	186_E	0.622	0.90
3_H	73_S	0.618	0.89
30_K	34_K	0.615	0.89
292_R	306_G	0.614	0.89
298_G	302_L	0.609	0.89
276_V	287_F	0.606	0.89
16_E	19_L	0.605	0.88
190_N	258_L	0.604	0.88
293_I	296_D	0.603	0.88
182_E	257_E	0.596	0.88
273_Q	288_D	0.595	0.88
94_E	116_K	0.593	0.87
157_S	160_D	0.592	0.87
11_E	15_S	0.591	0.87
138_K	170_Y	0.591	0.87
206_K	209_Q	0.591	0.87
219_Y	224_D	0.590	0.87
58_L	61_I	0.590	0.87
87_P	90_I	0.589	0.87
46_F	53_L	0.589	0.87
139_C	144_L	0.589	0.87
136_L	159_I	0.588	0.87
96_Y	136_L	0.587	0.87
268_K	285_I	0.584	0.87
273_Q	283_L	0.583	0.87
293_I	301_S	0.582	0.87
300_D	304_I	0.579	0.86
223_N	227_D	0.577	0.86
240_F	246_A	0.576	0.86
269_A	274_K	0.576	0.86
227_D	231_F	0.575	0.86
231_F	234_E	0.574	0.86
117_E	132_N	0.573	0.86
21_D	24_L	0.573	0.86
112_K	160_D	0.571	0.85
197_D	256_Y	0.571	0.85
54_V	110_I	0.569	0.85
302_L	307_I	0.569	0.85
144_L	155_Y	0.568	0.85
276_V	286_N	0.568	0.85
142_I	145_E	0.568	0.85
167_D	172_F	0.567	0.85
62_F	144_L	0.565	0.85
278_K	287_F	0.564	0.85
20_L	23_E	0.564	0.85
276_V	283_L	0.563	0.85
7_N	90_I	0.562	0.85
297_D	302_L	0.562	0.85
45_R	181_R	0.562	0.85
256_Y	260_D	0.561	0.84
186_E	190_N	0.561	0.84
301_S	306_G	0.561	0.84
69_F	177_G	0.561	0.84
155_Y	160_D	0.560	0.84
1_I	5_V	0.559	0.84
281_I	289_A	0.558	0.84
297_D	300_D	0.558	0.84
276_V	280_D	0.557	0.84
276_V	284_S	0.557	0.84
4_K	13_V	0.555	0.84
57_Y	78_K	0.555	0.84
234_E	237_E	0.554	0.84
75_N	82_E	0.553	0.84
85_N	174_D	0.551	0.83
91_K	178_C	0.550	0.83
223_N	226_F	0.548	0.83
298_G	305_K	0.546	0.83
236_A	242_D	0.546	0.83
220_F	223_N	0.545	0.83
220_F	230_I	0.544	0.83
293_I	297_D	0.544	0.83
214_N	217_V	0.539	0.82
109_G	178_C	0.539	0.82
187_Q	262_F	0.539	0.82
270_L	275_R	0.537	0.82
60_E	66_D	0.537	0.82
269_A	285_I	0.535	0.82
246_A	250_F	0.533	0.81
300_D	306_G	0.532	0.81
128_E	132_N	0.532	0.81
140_L	176_L	0.530	0.81
125_I	128_E	0.529	0.81
116_K	130_G	0.527	0.81
235_V	246_A	0.527	0.81
54_V	57_Y	0.525	0.80
5_V	77_A	0.525	0.80
277_I	284_S	0.524	0.80
269_A	282_N	0.522	0.80
298_G	303_I	0.522	0.80
294_I	305_K	0.521	0.80
269_A	279_L	0.521	0.80
143_N	146_K	0.521	0.80
300_D	307_I	0.521	0.80
300_D	305_K	0.520	0.80
47_S	52_D	0.520	0.80
65_P	99_Y	0.519	0.80
217_V	223_N	0.518	0.80
79_H	177_G	0.517	0.79
8_K	11_E	0.517	0.79
270_L	286_N	0.512	0.79
134_N	161_K	0.511	0.79
273_Q	287_F	0.509	0.78
296_D	301_S	0.508	0.78
299_T	307_I	0.507	0.78
159_I	163_N	0.505	0.78
191_L	220_F	0.503	0.78
58_L	142_I	0.502	0.77
197_D	254_E	0.502	0.77
279_L	306_G	0.502	0.77
285_I	297_D	0.501	0.77
156_V	160_D	0.500	0.77

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
1h6qA	1	0.3077	4.6	0.961	Contact Map
1ucrA	2	0.2276	4.4	0.961	Contact Map
1yz1A	1	0.3013	3.9	0.962	Contact Map
1txjA	1	0.3077	3.7	0.963	Contact Map
1bazA	4	0.0513	2.1	0.967	Contact Map
3k7cA	2	0.3237	1.9	0.968	Contact Map
2a4hA	1	0.1987	1.9	0.968	Contact Map
2fu4A	2	0.2404	1.8	0.968	Contact Map
4x86A	1	0.1635	1.8	0.968	Contact Map
3b34A	1	0.2404	1.8	0.968	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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