DUF2125 - PFAM28P - GREMLIN Contacts

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DUF2125 - Uncharacterized protein conserved in bacteria (DUF2125)

PFAM:	PF09898	Sequences: WFYAAGQAEAGLDAWRAREAAAGRVVSCASLSVGGFPFRFEVTCDDPSLADPSGGLAWSAPELLAVAQVYDPTHLIAEFPGPQTLADPGGGPSLTADWSQASLRASLRGLERASLVLDDLTLDRAAGALPAPLASADHLELHLRPAPGSPADNPAIDLALRLDGLSAPPLGPLAALPFDADLGATIDALLLGLTDFGPKPWPRRAAALREWRAAGGRLEIRRLRLQWGDLILVASGTLALDADGRPDGALTLTVAGLEALLDALVAAGLLPPNAAAAAAAGLGLLAKPGGLEGALTLPLTFQDGRVFLGPIPLGPAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	317 (312)
Sequences:	2926 (2401)
Seq/√Len:	135.9
META:	0.807

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_A	46_D	4.981	1.00
58_W	83_Q	4.385	1.00
15_W	19_E	3.217	1.00
137_D	164_G	3.209	1.00
117_L	120_L	3.117	1.00
144_R	157_D	2.943	1.00
19_E	22_A	2.761	1.00
301_F	306_V	2.760	1.00
114_S	142_H	2.733	1.00
105_A	109_G	2.716	1.00
7_Q	11_G	2.713	1.00
211_W	216_G	2.610	1.00
162_L	165_L	2.598	1.00
28_C	44_C	2.452	1.00
236_G	250_L	2.442	1.00
13_D	31_L	2.416	1.00
99_S	119_D	2.413	1.00
102_S	106_S	2.395	1.00
7_Q	10_A	2.387	1.00
26_V	49_L	2.376	1.00
43_T	62_E	2.350	1.00
17_A	20_A	2.243	1.00
262_D	279_A	2.241	1.00
271_P	274_A	2.213	1.00
13_D	17_A	2.202	1.00
28_C	31_L	2.196	1.00
4_A	40_F	2.157	1.00
47_P	60_A	2.122	1.00
241_D	245_R	2.065	1.00
306_V	314_G	2.057	1.00
103_L	107_L	2.055	1.00
240_L	246_P	2.035	1.00
9_E	13_D	2.013	1.00
119_D	137_D	1.949	1.00
299_L	308_L	1.905	1.00
209_R	212_R	1.899	1.00
305_R	312_P	1.878	1.00
43_T	64_L	1.845	1.00
281_G	284_L	1.833	1.00
253_T	296_T	1.829	1.00
103_L	106_S	1.819	1.00
265_V	275_A	1.803	1.00
308_L	313_L	1.791	1.00
19_E	24_R	1.777	1.00
3_Y	7_Q	1.745	1.00
76_I	142_H	1.744	1.00
67_A	75_L	1.740	1.00
300_T	307_F	1.723	1.00
301_F	316_A	1.708	1.00
30_S	45_D	1.701	1.00
217_R	239_A	1.694	1.00
9_E	31_L	1.669	1.00
219_E	237_T	1.667	1.00
6_G	9_E	1.655	1.00
41_E	66_V	1.646	1.00
33_V	42_V	1.641	1.00
16_R	26_V	1.628	1.00
44_C	47_P	1.610	1.00
5_A	33_V	1.602	1.00
278_A	281_G	1.593	1.00
226_Q	231_I	1.589	1.00
8_A	33_V	1.587	1.00
306_V	316_A	1.573	1.00
3_Y	6_G	1.565	1.00
16_R	28_C	1.539	1.00
307_F	313_L	1.518	1.00
68_Q	76_I	1.509	1.00
11_G	14_A	1.487	1.00
5_A	9_E	1.478	1.00
211_W	215_G	1.461	1.00
9_E	33_V	1.448	1.00
102_S	107_L	1.432	1.00
106_S	110_L	1.421	1.00
71_D	74_H	1.409	1.00
107_L	110_L	1.405	1.00
64_L	78_E	1.397	1.00
281_G	285_L	1.393	1.00
48_S	59_S	1.390	1.00
27_S	48_S	1.384	1.00
8_A	11_G	1.384	1.00
31_L	44_C	1.379	1.00
65_A	77_A	1.355	1.00
286_A	289_G	1.352	1.00
105_A	110_L	1.349	1.00
92_P	96_A	1.341	1.00
74_H	108_R	1.334	1.00
241_D	247_D	1.330	1.00
208_L	211_W	1.328	1.00
104_R	107_L	1.321	1.00
289_G	293_G	1.319	1.00
213_A	216_G	1.316	1.00
50_A	57_A	1.307	1.00
118_D	138_H	1.306	1.00
68_Q	74_H	1.300	1.00
2_F	5_A	1.287	1.00
104_R	108_R	1.282	1.00
39_R	74_H	1.279	1.00
146_A	157_D	1.273	1.00
143_L	156_I	1.265	1.00
39_R	76_I	1.242	1.00
36_F	40_F	1.240	1.00
39_R	66_V	1.220	1.00
253_T	294_A	1.218	1.00
256_G	259_A	1.215	1.00
45_D	62_E	1.209	1.00
305_R	315_P	1.208	1.00
245_R	304_G	1.206	1.00
20_A	23_G	1.202	1.00
46_D	61_P	1.195	1.00
237_T	249_A	1.193	1.00
51_D	54_G	1.188	1.00
158_L	193_L	1.180	0.99
297_L	308_L	1.177	0.99
307_F	312_P	1.174	0.99
74_H	142_H	1.173	0.99
40_F	69_V	1.159	0.99
224_R	233_V	1.153	0.99
63_L	79_F	1.147	0.99
168_P	173_L	1.140	0.99
25_V	50_A	1.135	0.99
87_D	90_G	1.129	0.99
60_A	83_Q	1.123	0.99
70_Y	76_I	1.118	0.99
124_R	127_G	1.115	0.99
66_V	76_I	1.114	0.99
8_A	40_F	1.104	0.99
76_I	106_S	1.099	0.99
12_L	42_V	1.097	0.99
290_G	293_G	1.088	0.99
106_S	109_G	1.088	0.99
146_A	150_P	1.088	0.99
262_D	266_A	1.086	0.99
47_P	63_L	1.084	0.99
281_G	286_A	1.079	0.99
112_R	116_V	1.078	0.99
302_Q	307_F	1.075	0.99
261_L	279_A	1.073	0.99
197_G	202_P	1.057	0.99
146_A	149_S	1.056	0.99
171_G	175_A	1.054	0.99
19_E	23_G	1.049	0.99
24_R	52_P	1.042	0.99
39_R	68_Q	1.039	0.99
103_L	110_L	1.035	0.99
249_A	302_Q	1.026	0.99
28_C	82_P	1.026	0.99
217_R	237_T	1.025	0.99
6_G	10_A	1.023	0.99
183_G	186_I	1.023	0.99
34_G	43_T	1.022	0.98
230_L	259_A	1.021	0.98
188_A	191_L	1.020	0.98
285_L	288_P	1.017	0.98
126_A	129_L	1.012	0.98
67_A	70_Y	1.004	0.98
307_F	310_P	1.002	0.98
34_G	41_E	0.996	0.98
254_V	257_L	0.991	0.98
103_L	109_G	0.991	0.98
138_H	163_D	0.986	0.98
41_E	69_V	0.984	0.98
251_T	298_P	0.983	0.98
230_L	260_L	0.978	0.98
224_R	231_I	0.978	0.98
66_V	78_E	0.978	0.98
41_E	64_L	0.976	0.98
137_D	163_D	0.968	0.98
24_R	49_L	0.958	0.98
168_P	171_G	0.957	0.98
288_P	291_L	0.956	0.98
190_L	222_R	0.953	0.98
38_F	76_I	0.947	0.98
142_H	159_A	0.946	0.98
38_F	68_Q	0.945	0.97
50_A	56_L	0.944	0.97
140_E	144_R	0.943	0.97
136_A	139_L	0.940	0.97
113_A	117_L	0.938	0.97
212_R	216_G	0.938	0.97
5_A	40_F	0.932	0.97
275_A	279_A	0.928	0.97
116_V	138_H	0.927	0.97
209_R	244_G	0.927	0.97
170_L	177_P	0.924	0.97
120_L	136_A	0.920	0.97
238_L	250_L	0.917	0.97
170_L	173_L	0.910	0.97
112_R	142_H	0.910	0.97
195_D	218_L	0.905	0.97
2_F	6_G	0.903	0.97
48_S	57_A	0.897	0.97
13_D	16_R	0.896	0.97
143_L	158_L	0.892	0.96
238_L	248_G	0.885	0.96
116_V	142_H	0.885	0.96
102_S	108_R	0.876	0.96
20_A	24_R	0.875	0.96
39_R	70_Y	0.871	0.96
87_D	93_S	0.870	0.96
76_I	159_A	0.863	0.96
82_P	98_W	0.863	0.96
200_P	203_R	0.861	0.96
169_P	173_L	0.860	0.96
38_F	78_E	0.859	0.96
231_I	255_A	0.858	0.96
87_D	91_G	0.858	0.96
275_A	281_G	0.857	0.96
44_C	98_W	0.857	0.96
252_L	299_L	0.848	0.95
167_A	170_L	0.848	0.95
20_A	27_S	0.847	0.95
265_V	270_L	0.846	0.95
257_L	282_L	0.845	0.95
199_K	204_R	0.843	0.95
40_F	67_A	0.842	0.95
270_L	273_N	0.841	0.95
265_V	272_P	0.841	0.95
245_R	301_F	0.838	0.95
15_W	26_V	0.836	0.95
72_P	75_L	0.836	0.95
269_L	275_A	0.829	0.95
191_L	195_D	0.828	0.95
306_V	315_P	0.827	0.95
41_E	68_Q	0.826	0.95
171_G	176_L	0.824	0.94
286_A	290_G	0.824	0.94
266_A	269_L	0.823	0.94
68_Q	71_D	0.822	0.94
76_I	144_R	0.820	0.94
79_F	83_Q	0.820	0.94
295_L	298_P	0.819	0.94
295_L	311_I	0.818	0.94
41_E	78_E	0.818	0.94
14_A	17_A	0.814	0.94
26_V	51_D	0.811	0.94
19_E	26_V	0.811	0.94
78_E	102_S	0.810	0.94
105_A	108_R	0.808	0.94
212_R	244_G	0.805	0.94
243_D	303_D	0.799	0.94
3_Y	10_A	0.798	0.93
70_Y	142_H	0.797	0.93
8_A	42_V	0.796	0.93
104_R	109_G	0.794	0.93
103_L	108_R	0.791	0.93
62_E	80_P	0.788	0.93
244_G	247_D	0.786	0.93
89_G	92_P	0.784	0.93
79_F	82_P	0.784	0.93
61_P	80_P	0.783	0.93
142_H	157_D	0.774	0.92
242_A	247_D	0.774	0.92
4_A	72_P	0.772	0.92
38_F	66_V	0.771	0.92
169_P	172_P	0.766	0.92
60_A	80_P	0.765	0.92
64_L	80_P	0.764	0.92
270_L	274_A	0.763	0.92
192_G	221_R	0.762	0.92
235_S	251_T	0.761	0.92
39_R	142_H	0.760	0.92
273_N	277_A	0.759	0.92
257_L	295_L	0.758	0.92
103_L	311_I	0.758	0.92
283_G	289_G	0.754	0.91
192_G	195_D	0.754	0.91
241_D	246_P	0.753	0.91
84_T	95_T	0.753	0.91
274_A	277_A	0.751	0.91
279_A	282_L	0.750	0.91
4_A	7_Q	0.750	0.91
301_F	304_G	0.749	0.91
249_A	300_T	0.747	0.91
139_L	162_L	0.745	0.91
306_V	313_L	0.741	0.91
44_C	82_P	0.737	0.90
211_W	240_L	0.736	0.90
212_R	241_D	0.734	0.90
172_P	177_P	0.734	0.90
144_R	159_A	0.730	0.90
69_V	72_P	0.729	0.90
286_A	291_L	0.726	0.90
116_V	140_E	0.726	0.90
68_Q	102_S	0.725	0.90
70_Y	74_H	0.724	0.90
176_L	179_D	0.723	0.90
113_A	116_V	0.722	0.90
229_D	259_A	0.718	0.89
88_P	91_G	0.716	0.89
65_A	75_L	0.716	0.89
76_I	102_S	0.713	0.89
273_N	276_A	0.711	0.89
169_P	177_P	0.709	0.89
275_A	278_A	0.709	0.89
204_R	207_A	0.707	0.89
272_P	283_G	0.704	0.88
14_A	18_R	0.704	0.88
239_A	247_D	0.702	0.88
194_T	221_R	0.699	0.88
59_S	86_A	0.699	0.88
172_P	179_D	0.699	0.88
228_G	263_A	0.696	0.88
36_F	41_E	0.695	0.88
16_R	31_L	0.693	0.88
207_A	212_R	0.692	0.88
237_T	301_F	0.691	0.87
188_A	192_G	0.690	0.87
52_P	55_G	0.690	0.87
96_A	122_L	0.688	0.87
16_R	20_A	0.681	0.87
271_P	275_A	0.680	0.87
117_L	122_L	0.679	0.87
190_L	195_D	0.676	0.86
183_G	189_L	0.671	0.86
173_L	179_D	0.671	0.86
76_I	104_R	0.669	0.86
112_R	120_L	0.668	0.86
66_V	74_H	0.668	0.86
175_A	178_F	0.668	0.86
278_A	284_L	0.667	0.86
311_I	314_G	0.661	0.85
247_D	301_F	0.661	0.85
197_G	201_W	0.659	0.85
58_W	67_A	0.659	0.85
13_D	139_L	0.658	0.85
96_A	99_S	0.654	0.84
78_E	142_H	0.651	0.84
67_A	72_P	0.651	0.84
81_G	306_V	0.650	0.84
196_F	217_R	0.645	0.84
302_Q	305_R	0.645	0.84
89_G	98_W	0.643	0.83
291_L	294_A	0.642	0.83
259_A	263_A	0.640	0.83
85_L	95_T	0.640	0.83
32_S	43_T	0.639	0.83
310_P	313_L	0.639	0.83
11_G	18_R	0.637	0.83
78_E	104_R	0.637	0.83
222_R	233_V	0.637	0.83
173_L	178_F	0.636	0.83
302_Q	306_V	0.634	0.83
282_L	285_L	0.634	0.83
41_E	159_A	0.633	0.82
274_A	280_A	0.632	0.82
274_A	278_A	0.628	0.82
111_E	117_L	0.628	0.82
116_V	119_D	0.628	0.82
234_A	250_L	0.628	0.82
68_Q	78_E	0.627	0.82
39_R	106_S	0.626	0.82
249_A	298_P	0.622	0.81
6_G	48_S	0.621	0.81
181_D	186_I	0.621	0.81
267_A	304_G	0.620	0.81
61_P	218_L	0.618	0.81
147_P	155_A	0.616	0.81
305_R	314_G	0.611	0.80
102_S	110_L	0.610	0.80
307_F	315_P	0.610	0.80
20_A	28_C	0.610	0.80
209_R	213_A	0.610	0.80
270_L	278_A	0.609	0.80
270_L	275_A	0.608	0.80
175_A	181_D	0.607	0.80
59_S	84_T	0.606	0.80
183_G	228_G	0.605	0.80
279_A	288_P	0.602	0.79
234_A	306_V	0.601	0.79
47_P	83_Q	0.601	0.79
136_A	165_L	0.598	0.79
10_A	13_D	0.598	0.79
173_L	177_P	0.596	0.79
258_E	283_G	0.594	0.78
60_A	79_F	0.590	0.78
81_G	97_D	0.589	0.78
212_R	240_L	0.589	0.78
12_L	16_R	0.587	0.78
62_E	66_V	0.587	0.78
60_A	82_P	0.584	0.77
282_L	286_A	0.583	0.77
275_A	280_A	0.582	0.77
28_C	98_W	0.580	0.77
77_A	134_A	0.577	0.76
140_E	161_R	0.576	0.76
312_P	315_P	0.576	0.76
248_G	301_F	0.576	0.76
259_A	262_D	0.575	0.76
288_P	292_E	0.573	0.76
208_L	240_L	0.570	0.75
61_P	82_P	0.570	0.75
277_A	284_L	0.569	0.75
252_L	272_P	0.568	0.75
38_F	41_E	0.567	0.75
70_Y	244_G	0.567	0.75
41_E	70_Y	0.566	0.75
52_P	63_L	0.565	0.75
128_A	131_A	0.565	0.75
255_A	294_A	0.565	0.75
234_A	251_T	0.565	0.75
241_D	244_G	0.565	0.75
141_L	156_I	0.564	0.75
160_L	224_R	0.562	0.74
198_P	214_A	0.560	0.74
38_F	74_H	0.558	0.74
278_A	306_V	0.557	0.74
46_D	49_L	0.557	0.74
127_G	131_A	0.556	0.74
123_D	171_G	0.555	0.74
183_G	192_G	0.552	0.73
295_L	308_L	0.552	0.73
38_F	62_E	0.551	0.73
99_S	118_D	0.551	0.73
251_T	296_T	0.550	0.73
102_S	109_G	0.550	0.73
111_E	115_L	0.549	0.73
177_P	181_D	0.548	0.73
222_R	227_W	0.547	0.72
211_W	241_D	0.546	0.72
24_R	28_C	0.543	0.72
260_L	264_L	0.542	0.72
211_W	268_G	0.542	0.72
111_E	116_V	0.541	0.72
186_I	191_L	0.541	0.72
1_W	37_P	0.541	0.72
134_A	165_L	0.538	0.71
300_T	306_V	0.536	0.71
36_F	83_Q	0.536	0.71
168_P	172_P	0.536	0.71
212_R	239_A	0.535	0.71
74_H	116_V	0.534	0.71
177_P	180_A	0.533	0.71
113_A	127_G	0.533	0.71
276_A	284_L	0.533	0.71
284_L	287_K	0.531	0.70
237_T	302_Q	0.529	0.70
304_G	316_A	0.526	0.70
119_D	126_A	0.526	0.70
258_E	279_A	0.524	0.69
239_A	249_A	0.522	0.69
212_R	247_D	0.522	0.69
74_H	112_R	0.521	0.69
93_S	96_A	0.521	0.69
28_C	72_P	0.521	0.69
314_G	317_P	0.520	0.69
66_V	70_Y	0.520	0.69
57_A	86_A	0.520	0.69
24_R	36_F	0.518	0.68
70_Y	85_L	0.516	0.68
216_G	240_L	0.516	0.68
46_D	59_S	0.516	0.68
162_L	241_D	0.513	0.68
38_F	156_I	0.513	0.68
250_L	294_A	0.513	0.68
261_L	278_A	0.513	0.68
90_G	132_P	0.510	0.67
277_A	281_G	0.506	0.67
12_L	164_G	0.505	0.66
38_F	142_H	0.505	0.66
62_E	81_G	0.505	0.66
189_L	192_G	0.505	0.66
25_V	81_G	0.504	0.66
15_W	18_R	0.504	0.66
208_L	213_A	0.503	0.66
215_G	239_A	0.502	0.66
21_A	52_P	0.502	0.66
66_V	142_H	0.501	0.66
7_Q	137_D	0.500	0.66

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
4ypjA	1	0.4448	7.9	0.955	Contact Map
3gm8A	1	0.4196	7.3	0.956	Contact Map
3whjA	2	0.2461	6.3	0.957	Contact Map
4b0yA	1	0.1577	5.2	0.958	Contact Map
2kgsA	1	0.2965	4.2	0.96	Contact Map
2q1fA	1	0.3375	4.2	0.96	Contact Map
2nqcA	1	0.1356	4.2	0.96	Contact Map
3jx8A	4	0.6656	3.4	0.962	Contact Map
2vrsA	3	0.2145	3.3	0.962	Contact Map
3ul4A	1	0.4259	3.3	0.962	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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